Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	ACHILLES_Lineage_Results_Top_Genes	CGC_CancerGermlineMut	CGC_CancerMolecularGenetics	CGC_CancerSomaticMut	CGC_CancerSyndrome	CGC_Chr	CGC_ChrBand	CGC_GeneID	CGC_Name	CGC_OtherGermlineMut	CGC_TissueType	COSMIC_n_overlapping_mutations	COSMIC_overlapping_mutation_descriptions	ClinVar_ASSEMBLY	ClinVar_HGMD_ID	ClinVar_SYM	ClinVar_TYPE	ClinVar_rs	Ensembl_so_accession	Ensembl_so_term	Familial_Cancer_Genes_Reference	Familial_Cancer_Genes_Synonym	annotation_transcript	bcgsc	broad	build	ccds_id	dbNSFP_1000Gp1_AC	dbNSFP_1000Gp1_AF	dbNSFP_1000Gp1_AFR_AC	dbNSFP_1000Gp1_AFR_AF	dbNSFP_1000Gp1_AMR_AC	dbNSFP_1000Gp1_AMR_AF	dbNSFP_1000Gp1_ASN_AC	dbNSFP_1000Gp1_ASN_AF	dbNSFP_1000Gp1_EUR_AC	dbNSFP_1000Gp1_EUR_AF	dbNSFP_Ancestral_allele	dbNSFP_CADD_phred	dbNSFP_CADD_raw	dbNSFP_CADD_raw_rankscore	dbNSFP_ESP6500_AA_AF	dbNSFP_ESP6500_EA_AF	dbNSFP_Ensembl_geneid	dbNSFP_Ensembl_transcriptid	dbNSFP_FATHMM_pred	dbNSFP_FATHMM_rankscore	dbNSFP_FATHMM_score	dbNSFP_GERP_NR	dbNSFP_GERP_RS	dbNSFP_GERP_RS_rankscore	dbNSFP_Interpro_domain	dbNSFP_LRT_Omega	dbNSFP_LRT_converted_rankscore	dbNSFP_LRT_pred	dbNSFP_LRT_score	dbNSFP_LR_pred	dbNSFP_LR_rankscore	dbNSFP_LR_score	dbNSFP_MutationAssessor_pred	dbNSFP_MutationAssessor_rankscore	dbNSFP_MutationAssessor_score	dbNSFP_MutationTaster_converted_rankscore	dbNSFP_MutationTaster_pred	dbNSFP_MutationTaster_score	dbNSFP_Polyphen2_HDIV_pred	dbNSFP_Polyphen2_HDIV_rankscore	dbNSFP_Polyphen2_HDIV_score	dbNSFP_Polyphen2_HVAR_pred	dbNSFP_Polyphen2_HVAR_rankscore	dbNSFP_Polyphen2_HVAR_score	dbNSFP_RadialSVM_pred	dbNSFP_RadialSVM_rankscore	dbNSFP_RadialSVM_score	dbNSFP_Reliability_index	dbNSFP_SIFT_converted_rankscore	dbNSFP_SIFT_pred	dbNSFP_SIFT_score	dbNSFP_SLR_test_statistic	dbNSFP_SiPhy_29way_logOdds	dbNSFP_SiPhy_29way_logOdds_rankscore	dbNSFP_SiPhy_29way_pi	dbNSFP_UniSNP_ids	dbNSFP_Uniprot_aapos	dbNSFP_Uniprot_acc	dbNSFP_Uniprot_id	dbNSFP_aaalt	dbNSFP_aapos	dbNSFP_aapos_FATHMM	dbNSFP_aapos_SIFT	dbNSFP_aaref	dbNSFP_cds_strand	dbNSFP_codonpos	dbNSFP_folddegenerate	dbNSFP_genename	dbNSFP_hg18_pos1coor	dbNSFP_phastCons100way_vertebrate	dbNSFP_phastCons100way_vertebrate_rankscore	dbNSFP_phastCons46way_placental	dbNSFP_phastCons46way_placental_rankscore	dbNSFP_phastCons46way_primate	dbNSFP_phastCons46way_primate_rankscore	dbNSFP_phyloP100way_vertebrate	dbNSFP_phyloP100way_vertebrate_rankscore	dbNSFP_phyloP46way_placental	dbNSFP_phyloP46way_placental_rankscore	dbNSFP_phyloP46way_primate	dbNSFP_phyloP46way_primate_rankscore	dbNSFP_refcodon	entrez_gene_id	external_id_capture	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	hgsc	igv_bad	ucsc	t_alt_count	t_ref_count	n_alt_count	n_ref_count	validation_judgement_rna	validation_power_rna	validation_tumor_alt_count_rna	validation_tumor_ref_count_rna	validation_normal_alt_count_rna	validation_normal_ref_count_rna	min_val_count_rna	validation_judgement_targeted	validation_power_targeted	validation_tumor_alt_count_targeted	validation_tumor_ref_count_targeted	validation_normal_alt_count_targeted	validation_normal_ref_count_targeted	min_val_count_targeted	validation_judgement_localAssembly	validation_power_localAssembly	t_alt_count_localAssembly	t_ref_count_localAssembly	n_alt_count_localAssembly	n_ref_count_localAssembly	min_val_count_localAssembly	validation_judgement_KRAS	validation_power_KRAS	t_alt_count_KRAS	t_ref_count_KRAS	n_alt_count_KRAS	n_ref_count_KRAS	min_val_count_KRAS	pon_loglike	pon_pass_loglike	localAssembly_detected	ExAC_AN	ExAC_AC	ExAC_LQ	passExAC	SCNA_NA	SCNA_NB	SCNA_q_hat	SCNA_tau	IS_SCNA	purity	ploidy	dna_fraction_in_tumor	CCF_hat	CCF_CI95_low	CCF_CI95_high	CCF_mode	CCF_mean	CCF_median	clonal	CCF_CI_low	CCF_CI_high
HPSE2	60495	broad.mit.edu	37	10	100503755	100503755	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr10:100503755delA	ENST00000370552.3	-	4	728	c.669delT	c.(667-669)tttfs	p.F223fs	HPSE2_ENST00000370549.1_Intron|HPSE2_ENST00000370546.1_Frame_Shift_Del_p.F223fs|HPSE2_ENST00000404542.1_Intron	NM_021828.4	NP_068600.4	Q8WWQ2	HPSE2_HUMAN	heparanase 2 (inactive)			40					CATTTAGAGCAAATATCAGGT	0.428000																								0							SO:0001589	frameshift_variant			ENST00000370552.3	1	0	hg19	CCDS7477.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	HPSE2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049789.1	1	0	0	63	337	0	71			0	0	0	71				0	0	0	0		1	0.985025	81	335	5	71	45								-20.000000	1	1	0	0		1	1	2	3	2.070880	0	0.380000	1.890000	0.384676	0.830000	6.500000e-01	1.000000	1.000000	0.843072	0.830000	0	0.740000	0.950000
SMAD4	4089	broad.mit.edu	37	18	48603039	48603066	+	Frame_Shift_Del	DEL	TGCAGCAGCAGGCGGCTACTGCACAAGC	TGCAGCAGCAGGCGGCTACTGCACAAGC	-			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08			TGCAGCAGCAGGCGGCTACTGCACAAGC	-	TGCAGCAGCAGGCGGCTACTGCACAAGC	TGCAGCAGCAGGCGGCTACTGCACAAGC		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr18:48603039_48603066delTGCAGCAGCAGGCGGCTACTGCACAAGC	ENST00000342988.3	+	11	1878_1905	c.1340_1367delTGCAGCAGCAGGCGGCTACTGCACAAGC	c.(1339-1368)atgcagcagcaggcggctactgcacaagctfs	p.MQQQAATAQA447fs	SMAD4_ENST00000588745.1_Frame_Shift_Del_p.MQQQAATAQA351fs|SMAD4_ENST00000398417.2_Frame_Shift_Del_p.MQQQAATAQA447fs	NM_005359.5	NP_005350.1	Q13485	SMAD4_HUMAN	SMAD family member 4	p.0?(36)|p.Q448fs*20(2)|p.?(2)|p.Q450fs*17(1)|p.R441fs*16(1)		454		all_cancers(7;0.203)|Colorectal(6;0.003)|all_epithelial(6;0.00336)			CATCGACAGATGCAGCAGCAGGCGGCTACTGCACAAGCTGCAGCAGCT	0.452000																								42	Whole gene deletion(36)|Deletion - Frameshift(4)|Unknown(2)	GRCh37	CD064636|CM021631	SMAD4	D|M		SO:0001589	frameshift_variant			ENST00000342988.3	0	1	hg19	CCDS11950.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	SMAD4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255993.3	1	0	0	14	162	0	48	0	1.152198e-01	0	7	0	48	2	1	1	72	586	0	549	2	1	0.024834	47	193	5	53	35								-6.296979	1	1	0	0		1	0	1	1	1.636180	1	0.380000	1.890000	0.238142	0.340000	1.900000e-01	0.530000	0.340000	0.354417	0.340000	0	0.260000	0.440000
PPRC1	23082	broad.mit.edu	37	10	103900075	103900075	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr10:103900075C>T	ENST00000278070.2	+	5	1849	c.1810C>T	c.(1810-1812)Cct>Tct	p.P604S	PPRC1_ENST00000413464.2_Missense_Mutation_p.P604S|PPRC1_ENST00000370012.1_5'Flank	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1			56		Colorectal(252;0.122)			TCTAGCTGGCCCTGTACCTGT	0.577000																								0							SO:0001583	missense			ENST00000278070.2	0	1	hg19	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	C	15.91	2.971154	0.53614	.	.	ENSG00000148840	ENST00000278070;ENST00000413464	T;T	0.33438	1.41;1.41	4.3	-1.15	0.09709	.	0.231155	0.22393	N	0.060651	T	0.12135	0.0295	N	0.19112	0.55	0.09310	N	0.999999	B;B;B	0.17667	0.013;0.023;0.013	B;B;B	0.12156	0.003;0.007;0.003	T	0.13229	-1.0517	10	0.19147	T	0.46	.	0.2406	0.00191	0.2904:0.289:0.1519:0.2687	.	604;484;604	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	S	604	ENSP00000278070:P604S;ENSP00000399743:P604S	ENSP00000278070:P604S	P	+	1	0	PPRC1	103890065	0.000000	0.05858	0.001000	0.08648	0.094000	0.18550	-0.480000	0.06559	-0.177000	0.10690	0.561000	0.74099	CCT		TCGA-FB-AAQ3-01A-11D-A40W-08	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050021.1	0	0	0	5	383	0	86		0	0	0	0	86	2		0	0	0	0	0	2	1	0.934895	5	376	0	86	2								-3.134258	1	1	0	0		1	1	2	3	2.070880	0	0.380000	1.890000	0.384676	0.070000	2.000000e-02	1.000000	0.070000	0.107694	0.070000	0	0.040000	0.120000
DOCK1	1793	broad.mit.edu	37	10	129216680	129216680	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr10:129216680G>A	ENST00000280333.6	+	45	4613	c.4504G>A	c.(4504-4506)Gac>Aac	p.D1502N		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1			72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)			GCTGACGAACGACAAGATCAA	0.587000																								0							SO:0001583	missense			ENST00000280333.6	1	1	hg19		.	.	.	.	.	.	.	.	.	.	G	20.5	3.999692	0.74818	2.27E-4	0.0	ENSG00000150760	ENST00000280333	T	0.16897	2.31	4.8	4.8	0.61643	.	0.060595	0.64402	D	0.000002	T	0.15782	0.0380	N	0.14661	0.345	0.80722	D	1	B;P;P	0.48834	0.36;0.567;0.916	B;B;P	0.46320	0.22;0.09;0.512	T	0.04811	-1.0925	10	0.51188	T	0.08	.	18.0621	0.89380	0.0:0.0:1.0:0.0	.	1502;1568;1502	B2RUU3;A8MU08;Q14185	.;.;DOCK1_HUMAN	N	1502	ENSP00000280333:D1502N	ENSP00000280333:D1502N	D	+	1	0	DOCK1	129106670	1.000000	0.71417	0.982000	0.44146	0.873000	0.50193	9.595000	0.98260	2.492000	0.84095	0.555000	0.69702	GAC		TCGA-FB-AAQ3-01A-11D-A40W-08	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	1	0	1	34	135	0	45	0	7.284487e-01	1	11	0	45	2		0	0	0	0	0	2	1	1.000000	34	134	0	45	2								-3.564564	1	1	121402	2	33	1	1	2	3	2.070880	0	0.380000	1.890000	0.384676	0.990000	7.700000e-01	1.000000	1.000000	0.968262	0.990000	1	0.910000	1.000000
OR52R1	119695	broad.mit.edu	37	11	4824947	4824947	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr11:4824947C>T	ENST00000356069.2	-	1	663	c.664G>A	c.(664-666)Gtg>Atg	p.V222M	MMP26_ENST00000477339.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.V301M|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1			29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)			AAAATCATCACGTATGACATA	0.473000																								0							SO:0001583	missense			ENST00000356069.2	0	1	hg19	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	C	5.145	0.212274	0.09757	2.27E-4	1.16E-4	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00265	8.39;8.39	5.57	-1.2	0.09554	GPCR, rhodopsin-like superfamily (1);	0.599214	0.14194	N	0.335121	T	0.00210	0.0006	L	0.54908	1.71	0.09310	N	1	B	0.33919	0.432	B	0.36134	0.218	T	0.26292	-1.0107	10	0.54805	T	0.06	.	11.3854	0.49782	0.0:0.482:0.0:0.518	.	222	Q8NGF1	O52R1_HUMAN	M	222;301	ENSP00000348368:V222M;ENSP00000369742:V301M	ENSP00000348368:V222M	V	-	1	0	OR52R1	4781523	0.000000	0.05858	0.813000	0.32504	0.024000	0.10985	-2.137000	0.01304	-0.109000	0.12044	-1.314000	0.01303	GTG		TCGA-FB-AAQ3-01A-11D-A40W-08	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	0	0	0	5	235	0	40		0	0	0	0	40	2		0	0	0	0	0	2	1	0.936814	5	233	0	39	2								-6.454115	1	1	121412	15	42	1	1	2	3	2.049603	0	0.380000	1.890000	0.381176	0.110000	4.000000e-02	0.250000	0.110000	0.129861	0.110000	0	0.070000	0.180000
OR5P2	120065	broad.mit.edu	37	11	7818171	7818171	+	Missense_Mutation	SNP	C	C	T	rs147652902		TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr11:7818171C>T	ENST00000329434.2	-	1	349	c.319G>A	c.(319-321)Gaa>Aaa	p.E107K	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	p.E107K(1)		22					AGGACGCATTCGACTGTTGCA	0.493000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000329434.2	1	1	hg19	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.724582	0.48833	4.75E-4	0.0	ENSG00000183303	ENST00000329434	T	0.00414	7.52	5.5	5.5	0.81552	GPCR, rhodopsin-like superfamily (1);	0.087192	0.49916	D	0.000131	T	0.01835	0.0058	M	0.92219	3.285	0.36026	D	0.8391	D	0.76494	0.999	D	0.73380	0.98	T	0.33085	-0.9882	10	0.87932	D	0	-34.5014	16.9428	0.86222	0.0:1.0:0.0:0.0	.	107	Q8WZ92	OR5P2_HUMAN	K	107	ENSP00000331823:E107K	ENSP00000331823:E107K	E	-	1	0	OR5P2	7774747	0.025000	0.19082	0.822000	0.32727	0.009000	0.06853	1.607000	0.36836	2.868000	0.98415	0.555000	0.69702	GAA		TCGA-FB-AAQ3-01A-11D-A40W-08	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	1	0	0	101	427	0	119		0	0	0	0	119	2		0	0	0	0	0	2	1	1.000000	100	424	0	118	2								-3.245289	1	1	120744	4	38	1	1	2	3	2.049603	0	0.380000	1.890000	0.381176	0.990000	8.300000e-01	1.000000	1.000000	0.969670	0.990000	1	0.910000	1.000000
MED13L	23389	broad.mit.edu	37	12	116413394	116413394	+	Missense_Mutation	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr12:116413394C>A	ENST00000281928.3	-	24	5720	c.5514G>T	c.(5512-5514)tgG>tgT	p.W1838C		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like			85	all_neural(191;0.117)|Medulloblastoma(191;0.163)				AAGCCAAAAGCCAGCGCTGGT	0.483000																								0							SO:0001583	missense			ENST00000281928.3	1	1	hg19	CCDS9177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.652595|4.652595	0.88056|0.88056	.|.	.|.	ENSG00000123066|ENSG00000123066	ENST00000552447|ENST00000281928	.|D	.|0.98400	.|-4.91	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99093|0.99093	0.9688|0.9688	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	D|D	0.99585|0.99585	1.0974|1.0974	5|10	.|0.87932	.|D	.|0	-8.283|-8.283	20.5632|20.5632	0.99335|0.99335	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1838	.|Q71F56	.|MD13L_HUMAN	S|C	31|1838	.|ENSP00000281928:W1838C	.|ENSP00000281928:W1838C	A|W	-|-	1|3	0|0	MED13L|MED13L	114897777|114897777	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.445000|7.445000	0.80570|0.80570	2.937000|2.937000	0.99478|0.99478	0.650000|0.650000	0.86243|0.86243	GCT|TGG		TCGA-FB-AAQ3-01A-11D-A40W-08	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3	1	0	1	30	210	0	45	0	4.604415e-02	0	3	0	45	2		0	0	0	0	0	2	1	1.000000	30	205	0	45	2								-14.059710	1	1	0	0		1	0	0	0	1.994408	0	0.380000	1.890000	0.363057	0.630000	4.400000e-01	0.860000	0.630000	0.651411	0.630000	0	0.530000	0.760000
FZD10	11211	broad.mit.edu	37	12	130648664	130648664	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr12:130648664G>A	ENST00000229030.4	+	1	1661	c.1177G>A	c.(1177-1179)Gcg>Acg	p.A393T	FZD10_ENST00000539839.1_Missense_Mutation_p.R360H|FZD10-AS1_ENST00000505807.2_RNA			Q9ULW2	FZD10_HUMAN	frizzled class receptor 10	p.A393S(1)		35	all_neural(191;0.101)|Medulloblastoma(191;0.163)				GGACGTCAACGCGCTCACCGG	0.657000																								1	Substitution - Missense(1)						SO:0001583	missense			ENST00000229030.4	1	1	hg19	CCDS9267.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.29|15.29	2.790730|2.790730	0.50102|0.50102	.|.	.|.	ENSG00000111432|ENSG00000111432	ENST00000229030|ENST00000539839	D|.	0.82526|.	-1.62|.	5.21|5.21	5.21|5.21	0.72293|0.72293	GPCR, family 2-like (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	D|D	0.82549|0.82549	0.5061|0.5061	M|M	0.83223|0.83223	2.63|2.63	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.72982|.	0.979|.	D|D	0.85526|0.85526	0.1206|0.1206	10|6	0.48119|0.87932	T|D	0.1|0	.|.	18.7539|18.7539	0.91825|0.91825	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	393|.	Q9ULW2|.	FZD10_HUMAN|.	T|H	393|360	ENSP00000229030:A393T|.	ENSP00000229030:A393T|ENSP00000438460:R360H	A|R	+|+	1|2	0|0	FZD10|FZD10	129214617|129214617	1.000000|1.000000	0.71417|0.71417	0.223000|0.223000	0.23860|0.23860	0.980000|0.980000	0.70556|0.70556	9.643000|9.643000	0.98464|0.98464	2.432000|2.432000	0.82394|0.82394	0.561000|0.561000	0.74099|0.74099	GCG|CGC		TCGA-FB-AAQ3-01A-11D-A40W-08	FZD10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		1	0	1	52	270	0	53	0	2.717949e-02	0	2	0	53	2		0	0	0	0	0	2	1	1.000000	52	261	0	51	2								-20.000000	1	1	121410	2	35	1	0	0	0	1.994408	0	0.380000	1.890000	0.363057	0.820000	6.300000e-01	1.000000	1.000000	0.830393	0.820000	0	0.720000	0.930000
KRAS	3845	broad.mit.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08			C	T	C	C		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)		GCCTACGCCACCAGCTCCAAC	0.348000	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		pancreatic, colorectal, lung, thyroid, AML, others				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)			Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		L, E, M, O	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)						SO:0001583	missense	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ENST00000256078.4	1	1	hg19	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		TCGA-FB-AAQ3-01A-11D-A40W-08	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	1	0	1	30	186	0	83	0	0	0	1	0	83	2	1	1	83	490	0	434	2	1	1.000000	30	185	0	81	2								-15.365490	1	1	121404	2	44	1	0	0	0	1.994408	0	0.380000	1.890000	0.363057	0.710000	4.900000e-01	0.950000	0.710000	0.721819	0.710000	0	0.590000	0.840000
WNT10B	7480	broad.mit.edu	37	12	49360058	49360058	+	Silent	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr12:49360058C>T	ENST00000301061.4	-	5	1338	c.990G>A	c.(988-990)agG>agA	p.R330R	WNT10B_ENST00000407467.1_3'UTR|WNT10B_ENST00000403957.1_3'UTR	NM_003394.3	NP_003385.2	O00744	WN10B_HUMAN	wingless-type MMTV integration site family, member 10B			23					AGGCCCGGCCCCTTGTCCCTG	0.642000																								0							SO:0001819	synonymous_variant			ENST00000301061.4	1	1	hg19	CCDS8775.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	WNT10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319864.1	1	0	1	37	154	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	37	147	0	49	2								-20.000000	1	1	0	0		1	0	0	0	1.994408	0	0.380000	1.890000	0.363057	0.980000	7.200000e-01	1.000000	1.000000	0.941949	0.980000	1	0.840000	1.000000
PPFIA2	8499	broad.mit.edu	37	12	81769706	81769706	+	Missense_Mutation	SNP	C	C	G			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr12:81769706C>G	ENST00000549396.1	-	10	1160	c.1000G>C	c.(1000-1002)Gaa>Caa	p.E334Q	PPFIA2_ENST00000550359.2_Missense_Mutation_p.E181Q|RP11-315E17.1_ENST00000546936.1_RNA|PPFIA2_ENST00000548586.1_Missense_Mutation_p.E334Q|PPFIA2_ENST00000443686.3_Missense_Mutation_p.E235Q|PPFIA2_ENST00000552948.1_Missense_Mutation_p.E334Q|PPFIA2_ENST00000545296.2_5'UTR|PPFIA2_ENST00000550584.2_Missense_Mutation_p.E334Q|PPFIA2_ENST00000333447.7_Missense_Mutation_p.E316Q|PPFIA2_ENST00000549325.1_Missense_Mutation_p.E316Q|PPFIA2_ENST00000407050.4_Missense_Mutation_p.E260Q	NM_001220476.1|NM_001282536.1|NM_003625.3	NP_001207405.1|NP_001269465.1|NP_003616.2	O75334	LIPA2_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 2			85					TCCATATCTTCCTTTTGTGCC	0.308000																								0							SO:0001583	missense			ENST00000549396.1	1	1	hg19	CCDS55857.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.7|27.7	4.853780|4.853780	0.91355|0.91355	.|.	.|.	ENSG00000139220|ENSG00000139220	ENST00000549396;ENST00000549325;ENST00000407050;ENST00000541501;ENST00000333447;ENST00000548586;ENST00000443686;ENST00000552948|ENST00000548790	T;T;T;T;T;T;T|.	0.78246|.	1.25;1.25;1.25;-1.16;1.25;1.25;1.25|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.76730|0.76730	0.4028|0.4028	M|M	0.73430|0.73430	2.235|2.235	0.80722|0.80722	D|D	1|1	D;P|.	0.61080|.	0.989;0.9|.	D;B|.	0.72982|.	0.979;0.38|.	T|T	0.76369|0.76369	-0.2984|-0.2984	10|5	0.52906|.	T|.	0.07|.	-17.607|-17.607	19.0352|19.0352	0.92974|0.92974	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	234;334|.	B7Z4H8;O75334|.	.;LIPA2_HUMAN|.	Q|S	334;316;260;345;316;334;235;334|151	ENSP00000450337:E334Q;ENSP00000450298:E316Q;ENSP00000385093:E260Q;ENSP00000327416:E316Q;ENSP00000449338:E334Q;ENSP00000388373:E235Q;ENSP00000447868:E334Q|.	ENSP00000327416:E316Q|.	E|R	-|-	1|3	0|2	PPFIA2|PPFIA2	80293837|80293837	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.765000|7.765000	0.85310|0.85310	2.567000|2.567000	0.86603|0.86603	0.650000|0.650000	0.86243|0.86243	GAA|AGG		TCGA-FB-AAQ3-01A-11D-A40W-08	PPFIA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408030.1	1	0	0	21	252	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	0.999998	21	248	0	49	2								-3.142700	1	1	0	0		1	0	0	0	1.994408	0	0.380000	1.890000	0.363057	0.390000	2.500000e-01	0.570000	0.390000	0.407228	0.390000	0	0.310000	0.490000
PLXNC1	10154	broad.mit.edu	37	12	94658986	94658986	+	Silent	SNP	G	G	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr12:94658986G>T	ENST00000258526.4	+	21	3831	c.3582G>T	c.(3580-3582)ccG>ccT	p.P1194P	PLXNC1_ENST00000545312.1_5'UTR|PLXNC1_ENST00000547057.1_Silent_p.P241P	NM_005761.2	NP_005752.1	O60486	PLXC1_HUMAN	plexin C1			64					GGCAGGTTCCGGAATTCAGTA	0.453000																								0							SO:0001819	synonymous_variant			ENST00000258526.4	1	1	hg19	CCDS9049.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	PLXNC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408126.2	1	0	1	131	691	0	186	0	2.570041e-02	0	2	0	186	2		0	0	0	0	0	2	1	1.000000	126	668	0	184	2								-2.921532	1	1	0	0		1	0	0	0	1.994408	0	0.380000	1.890000	0.363057	0.810000	6.800000e-01	0.940000	0.820000	0.818855	0.810000	0	0.740000	0.880000
EML1	2009	broad.mit.edu	37	14	100380996	100380996	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr14:100380996G>A	ENST00000262233.6	+	15	1853	c.1714G>A	c.(1714-1716)Gct>Act	p.A572T	EML1_ENST00000327921.9_Missense_Mutation_p.A560T|EML1_ENST00000334192.4_Missense_Mutation_p.A591T	NM_004434.2	NP_004425.2	O00423	EMAL1_HUMAN	echinoderm microtubule associated protein like 1			42		Melanoma(154;0.0879)|all_epithelial(191;0.216)			TCTCTGGGACGCTGTGGGTCA	0.453000																								0							SO:0001583	missense			ENST00000262233.6	1	1	hg19	CCDS32155.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.334759	0.81801	.	.	ENSG00000066629	ENST00000327921;ENST00000262233;ENST00000334192;ENST00000542138	T;T;T	0.39229	1.09;1.09;1.09	5.14	5.14	0.70334	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.050391	0.85682	D	0.000000	T	0.39200	0.1069	N	0.15975	0.35	0.58432	D	0.999998	D;B;D	0.61697	0.961;0.089;0.99	B;B;P	0.50970	0.371;0.006;0.655	T	0.32719	-0.9896	10	0.41790	T	0.15	-19.4889	18.6177	0.91308	0.0:0.0:1.0:0.0	.	560;572;591	F8W717;O00423;O00423-3	.;EMAL1_HUMAN;.	T	560;572;591;591	ENSP00000327384:A560T;ENSP00000262233:A572T;ENSP00000334314:A591T	ENSP00000262233:A572T	A	+	1	0	EML1	99450749	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	4.708000	0.61859	2.396000	0.81511	0.655000	0.94253	GCT		TCGA-FB-AAQ3-01A-11D-A40W-08	EML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413943.1	1	0	1	26	102	0	36	0	1.949304e-01	0	4	0	36	2		0	0	0	0	0	2	1	1.000000	25	100	0	36	2								-20.000000	1	1	0	0		1	1	2	3	2.051019	0	0.380000	1.890000	0.381176	0.990000	7.300000e-01	1.000000	1.000000	0.961380	0.990000	1	0.890000	1.000000
CIDEB	27141	broad.mit.edu	37	14	24779887	24779887	+	Translation_Start_Site	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr14:24779887G>A	ENST00000336557.5	-	0	714				CIDEB_ENST00000555817.1_5'Flank|LTB4R2_ENST00000533293.1_Missense_Mutation_p.R6H|LTB4R_ENST00000345363.3_5'Flank|CIDEB_ENST00000554411.1_5'Flank|LTB4R_ENST00000396789.4_5'Flank|LTB4R2_ENST00000528054.1_Missense_Mutation_p.R37H|CIDEB_ENST00000258807.5_De_novo_Start_OutOfFrame|LTB4R2_ENST00000543919.1_Missense_Mutation_p.R6H			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b			7					GTCTGCTACCGTCCCCCAGGG	0.662000																								0											ENST00000336557.5	0	1	hg19	CCDS32056.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.033641	0.54896	.	.	ENSG00000213906	ENST00000527924;ENST00000528054;ENST00000533293;ENST00000543919;ENST00000530080	T;T;T;T;T	0.78246	-1.16;1.2;-0.33;-0.33;-0.33	5.26	3.08	0.35506	.	1.634670	0.03830	U	0.268870	T	0.65533	0.2700	N	0.19112	0.55	0.25938	N	0.982902	B	0.28208	0.203	B	0.17098	0.017	T	0.56092	-0.8036	10	0.48119	T	0.1	.	8.2552	0.31751	0.2082:0.0:0.7918:0.0	.	37	Q9NPC1	LT4R2_HUMAN	H	6;37;6;6;6	ENSP00000436668:R6H;ENSP00000432146:R37H;ENSP00000433290:R6H;ENSP00000445772:R6H;ENSP00000434760:R6H	ENSP00000337731:R37H	R	+	2	0	LTB4R2	23849727	0.000000	0.05858	0.423000	0.26634	0.986000	0.74619	-0.139000	0.10358	1.232000	0.43678	0.561000	0.74099	CGT		TCGA-FB-AAQ3-01A-11D-A40W-08	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1	0	0	0	9	239	0	47	0	1.752988e-03	0	2	0	47	2		0	0	0	0	0	2	1	0.994252	9	237	0	47	2								-3.182267	1	1	0	0		1	1	2	3	2.051019	0	0.380000	1.890000	0.381176	0.190000	9.000000e-02	0.350000	0.190000	0.209551	0.190000	0	0.140000	0.270000
MKRN3	7681	broad.mit.edu	37	15	23811290	23811290	+	Missense_Mutation	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr15:23811290C>A	ENST00000314520.3	+	1	837	c.361C>A	c.(361-363)Ctt>Att	p.L121I	RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000564592.1_Intron|MKRN3_ENST00000568252.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3			61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)			TTCGCACGACCTTTCTGGTCG	0.602000																								0							SO:0001583	missense			ENST00000314520.3	0	1	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.208879	0.79240	.	.	ENSG00000179455	ENST00000314520	T	0.35236	1.32	3.94	2.05	0.26809	Zinc finger, CCCH-type (2);	0.280449	0.29451	N	0.012115	T	0.26484	0.0647	L	0.47016	1.485	0.47245	D	0.999361	B	0.26935	0.164	B	0.23852	0.049	T	0.09400	-1.0676	10	0.59425	D	0.04	.	4.7645	0.13125	0.2134:0.6766:0.0:0.1099	.	121	Q13064	MKRN3_HUMAN	I	121	ENSP00000313881:L121I	ENSP00000313881:L121I	L	+	1	0	MKRN3	21362383	0.221000	0.23642	0.010000	0.14722	0.327000	0.28475	1.320000	0.33666	0.631000	0.30412	0.563000	0.77884	CTT		TCGA-FB-AAQ3-01A-11D-A40W-08	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	0	0	0	7	281	0	65		0	0	0	0	65	2		0	0	0	0	0	2	1	0.979459	7	275	0	63	2								-3.664649	1	1	0	0		1	0	0	0	2.022469	0	0.380000	1.890000	0.375252	0.130000	5.000000e-02	0.250000	0.120000	0.143258	0.130000	0	0.080000	0.190000
APBA2	321	broad.mit.edu	37	15	29347038	29347038	+	Splice_Site	SNP	G	G	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr15:29347038G>T	ENST00000558402.1	+	5	1550	c.951G>T	c.(949-951)caG>caT	p.Q317H	APBA2_ENST00000411764.1_Splice_Site_p.Q317H|APBA2_ENST00000558259.1_Splice_Site_p.Q317H|APBA2_ENST00000558330.1_Splice_Site_p.Q317H|APBA2_ENST00000561069.1_Splice_Site_p.Q317H			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2			59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)			CCCACGAGCAGGTAGGACCCT	0.657000																								0							SO:0001630	splice_region_variant			ENST00000558402.1	0	0	hg19	CCDS10022.1	.	.	.	.	.	.	.	.	.	.	G	12.79	2.044513	0.36085	.	.	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.31247	1.5	5.24	5.24	0.73138	.	0.130714	0.51477	D	0.000095	T	0.37046	0.0989	M	0.65975	2.015	0.58432	D	0.999999	P;P;P	0.43662	0.814;0.668;0.814	B;B;B	0.40477	0.33;0.186;0.33	T	0.29731	-1.0002	10	0.46703	T	0.11	.	17.8166	0.88637	0.0:0.0:1.0:0.0	.	317;317;317	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	H	317	ENSP00000409312:Q317H	ENSP00000219865:Q317H	Q	+	3	2	APBA2	27134330	1.000000	0.71417	1.000000	0.80357	0.195000	0.23768	7.205000	0.77881	2.422000	0.82143	0.650000	0.86243	CAG		TCGA-FB-AAQ3-01A-11D-A40W-08	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	1	0	1	10	69	0	15	0	2.985016e-01	0	8	0	15	2		0	0	0	0	0	2	1	0.997151	9	68	0	15	2								-17.691170	1	1	0	0		1	0	0	0	2.022469	0	0.380000	1.890000	0.375252	0.670000	3.500000e-01	1.000000	1.000000	0.687263	0.670000	0	0.490000	0.880000
ZNF500	26048	broad.mit.edu	37	16	4815918	4815918	+	Missense_Mutation	SNP	T	T	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr16:4815918T>A	ENST00000219478.6	-	2	361	c.62A>T	c.(61-63)gAg>gTg	p.E21V	ZNF500_ENST00000545009.1_Missense_Mutation_p.E21V			O60304	ZN500_HUMAN	zinc finger protein 500			21					AATCAGGATCTCTTCCTGTTC	0.602000																								0							SO:0001583	missense			ENST00000219478.6	1	1	hg19	CCDS32383.1	.	.	.	.	.	.	.	.	.	.	T	13.84	2.357740	0.41801	.	.	ENSG00000103199	ENST00000545009;ENST00000219478	T;T	0.07688	3.25;3.17	4.32	3.22	0.36961	.	.	.	.	.	T	0.15176	0.0366	M	0.80982	2.52	0.24263	N	0.995279	P;P	0.52316	0.952;0.952	P;P	0.45998	0.5;0.5	T	0.15435	-1.0437	9	0.72032	D	0.01	.	6.5932	0.22658	0.0:0.1129:0.0:0.8871	.	21;21	B4DNN9;O60304	.;ZN500_HUMAN	V	21	ENSP00000445714:E21V;ENSP00000219478:E21V	ENSP00000219478:E21V	E	-	2	0	ZNF500	4755919	0.130000	0.22417	0.709000	0.30452	0.828000	0.46876	0.360000	0.20250	0.540000	0.28808	0.533000	0.62120	GAG		TCGA-FB-AAQ3-01A-11D-A40W-08	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	0	0	0	11	362	0	88	1	3.220021e-03	2	1	0	88	2		0	0	0	0	0	2	1	0.998212	10	357	0	87	2								-11.399370	1	1	0	0		1	1	2	3	2.070350	0	0.380000	1.890000	0.384676	0.160000	8.000000e-02	1.000000	0.160000	0.192896	0.160000	0	0.110000	0.220000
SYNRG	11276	broad.mit.edu	37	17	35960421	35960421	+	Missense_Mutation	SNP	C	C	G			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr17:35960421C>G	ENST00000339208.6	-	2	247	c.107G>C	c.(106-108)aGa>aCa	p.R36T	SYNRG_ENST00000346661.4_Missense_Mutation_p.R36T|SYNRG_ENST00000502449.2_Missense_Mutation_p.R36T|SYNRG_ENST00000585472.1_Missense_Mutation_p.R36T|SYNRG_ENST00000591288.1_Missense_Mutation_p.R36T|SYNRG_ENST00000394378.2_Missense_Mutation_p.R36T|SYNRG_ENST00000345615.4_Missense_Mutation_p.R36T	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma			36					TTGAGGGGGTCTTATCCCACC	0.308000																								0							SO:0001583	missense			ENST00000339208.6	1	1	hg19	CCDS11321.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.098767	0.56183	.	.	ENSG00000006114	ENST00000346661;ENST00000339208;ENST00000345615;ENST00000502449;ENST00000394378;ENST00000394379	T;T;T;T;T	0.46451	1.46;1.46;0.87;0.87;0.87	5.4	5.4	0.78164	.	0.171371	0.51477	D	0.000087	T	0.36635	0.0974	L	0.44542	1.39	0.38571	D	0.949948	P;B;B;P;B;B;P	0.41265	0.578;0.435;0.435;0.578;0.435;0.435;0.744	B;B;B;B;B;B;B	0.38842	0.283;0.157;0.157;0.157;0.157;0.283;0.21	T	0.23511	-1.0186	10	0.31617	T	0.26	-22.8269	15.0288	0.71691	0.0:1.0:0.0:0.0	.	36;36;36;36;36;36;36	A8MYE0;B7ZKZ2;Q9UMZ2-3;A8MWU4;Q9UMZ2-4;Q9UMZ2-5;Q9UMZ2	.;.;.;.;.;.;SYNRG_HUMAN	T	36	ENSP00000005279:R36T;ENSP00000343610:R36T;ENSP00000315722:R36T;ENSP00000424893:R36T;ENSP00000377903:R36T	ENSP00000343610:R36T	R	-	2	0	SYNRG	33034534	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.329000	0.65892	2.693000	0.91896	0.650000	0.86243	AGA		TCGA-FB-AAQ3-01A-11D-A40W-08	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	1	0	0	17	193	0	41		0	0	0	0	41	2		0	0	0	0	0	2	1	0.999969	16	192	0	41	2								-19.998520	1	0	0	0		1	1	2	3	2.446222	1	0.380000	1.890000	0.478992	0.510000	3.100000e-01	0.760000	0.510000	0.529015	0.510000	0	0.400000	0.640000
NWD1	284434	broad.mit.edu	37	19	16884049	16884049	+	Silent	SNP	C	C	T	rs144961672	by1000genomes	TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr19:16884049C>T	ENST00000552788.1	+	9	2523	c.2523C>T	c.(2521-2523)tgC>tgT	p.C841C	NWD1_ENST00000379808.3_Silent_p.C841C|NWD1_ENST00000524140.2_Silent_p.C841C|NWD1_ENST00000339803.6_Silent_p.C706C|NWD1_ENST00000523826.1_Silent_p.C635C|NWD1_ENST00000549814.1_Silent_p.C841C			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1			67					TCCAGTTGTGCGCACACCCTG	0.622000																								0							SO:0001819	synonymous_variant			ENST00000552788.1	0	1	hg19																																																																																					TCGA-FB-AAQ3-01A-11D-A40W-08	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	0	0	0	6	273	0	51		0	0	0	0	51	2		0	0	0	0	0	2	1	0.963849	6	270	0	51	2								-6.545265	1	1	121406	7	40	1	1	2	3	2.057370	0	0.380000	1.890000	0.382347	0.120000	4.000000e-02	0.260000	0.120000	0.139362	0.120000	0	0.070000	0.180000
PDE4C	5143	broad.mit.edu	37	19	18331319	18331319	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr19:18331319G>A	ENST00000355502.3	-	10	1473	c.602C>T	c.(601-603)aCg>aTg	p.T201M	PDE4C_ENST00000262805.12_Missense_Mutation_p.T169M|PDE4C_ENST00000597297.1_Intron|PDE4C_ENST00000447275.3_Missense_Mutation_p.T95M|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594617.3_Missense_Mutation_p.T201M|PDE4C_ENST00000598111.2_Intron|PDE4C_ENST00000594465.3_Missense_Mutation_p.T201M|PDE4C_ENST00000539010.1_De_novo_Start_InFrame			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific			33				Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CTTCTGCCCCGTGTCCTCTGG	0.657000																								0							SO:0001583	missense			ENST00000355502.3	1	1	hg19	CCDS12373.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.513874	0.44763	.	.	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000543547	T;T;T	0.70986	-0.53;-0.52;-0.51	4.2	3.13	0.36017	.	0.547115	0.18791	N	0.131041	T	0.72622	0.3483	M	0.62723	1.935	0.80722	D	1	D;B	0.57571	0.98;0.451	P;B	0.50192	0.634;0.103	T	0.73193	-0.4060	10	0.54805	T	0.06	.	11.2003	0.48736	0.0:0.0:0.8144:0.1855	.	201;169	Q08493;Q08493-3	PDE4C_HUMAN;.	M	280;201;189;169;95;310	ENSP00000347689:T201M;ENSP00000262805:T169M;ENSP00000402091:T95M	ENSP00000262805:T169M	T	-	2	0	PDE4C	18192319	0.897000	0.30589	0.985000	0.45067	0.925000	0.55904	4.944000	0.63561	0.870000	0.35726	-0.513000	0.04457	ACG		TCGA-FB-AAQ3-01A-11D-A40W-08	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1	1	0	1	25	115	0	26		0	0	0	0	26	2		0	0	0	0	0	2	1	1.000000	25	110	0	26	2								-20.000000	1	1	0	0		1	1	2	3	2.057370	0	0.380000	1.890000	0.382347	0.940000	6.400000e-01	1.000000	1.000000	0.908708	0.940000	1	0.780000	1.000000
CILP2	148113	broad.mit.edu	37	19	19656676	19656676	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr19:19656676C>T	ENST00000291495.5	+	8	3407	c.3322C>T	c.(3322-3324)Ccg>Tcg	p.P1108S	CILP2_ENST00000586018.1_Missense_Mutation_p.P1114S	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2			32					CCGGGAGCCACCGGCCGGACG	0.657000																								0							SO:0001583	missense			ENST00000291495.5	0	1	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	C	0.016	-1.516760	0.00975	.	.	ENSG00000160161	ENST00000291495	T	0.49139	0.79	5.57	0.901	0.19284	.	0.431826	0.25919	N	0.027455	T	0.29588	0.0738	L	0.38531	1.155	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.08055	0.003;0.003	T	0.15809	-1.0424	10	0.17832	T	0.49	-2.1441	5.6241	0.17473	0.1343:0.5332:0.2595:0.0731	.	1108;1108	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	S	1108	ENSP00000291495:P1108S	ENSP00000291495:P1108S	P	+	1	0	CILP2	19517676	0.000000	0.05858	0.004000	0.12327	0.089000	0.18198	-0.586000	0.05787	0.035000	0.15519	-0.314000	0.08810	CCG		TCGA-FB-AAQ3-01A-11D-A40W-08	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	1	0	0	12	73	0	20	0	6.330351e-02	0	3	0	20	2		0	0	0	0	0	2	1	0.998984	11	68	0	19	2								-19.955200	1	1	0	0		1	1	2	3	2.057370	0	0.380000	1.890000	0.382347	0.750000	4.200000e-01	1.000000	1.000000	0.761654	0.750000	0	0.570000	0.980000
EEF2	1938	broad.mit.edu	37	19	3976682	3976682	+	Missense_Mutation	SNP	T	T	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08			T	A	T	T		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr19:3976682T>A	ENST00000309311.6	-	15	2535	c.2447A>T	c.(2446-2448)cAc>cTc	p.H816L		NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2			21		Hepatocellular(1079;0.137)			GATCTGCCAGTGGTCAAACAC	0.657000													Colon(165;1804 1908 4071 6587 18799)											0							SO:0001583	missense			ENST00000309311.6	0	1	hg19	CCDS12117.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.780856	0.90195	.	.	ENSG00000167658	ENST00000309311	T	0.64991	-0.13	5.5	4.48	0.54585	Elongation factor G/III/V (1);Translation elongation factor EFG/EF2, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.88343	0.6411	H	0.99890	4.9	0.80722	D	1	D	0.69078	0.997	D	0.81914	0.995	D	0.90917	0.4780	10	0.87932	D	0	-51.5156	11.2148	0.48819	0.1372:0.0:0.0:0.8628	.	816	P13639	EF2_HUMAN	L	816	ENSP00000307940:H816L	ENSP00000307940:H816L	H	-	2	0	EEF2	3927682	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.003000	0.70701	0.899000	0.36444	0.529000	0.55759	CAC		TCGA-FB-AAQ3-01A-11D-A40W-08	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	1	0	1	11	51	0	13	1	1	224	1096	0	13	2	1	1	99	364	0	349	2	1	0.998851	11	51	0	13	2								-20.000000	1	1	0	0		1	1	2	3	2.057370	0	0.380000	1.890000	0.382347	0.940000	5.200000e-01	1.000000	1.000000	0.882859	0.940000	1	0.710000	1.000000
ZIM2	23619	broad.mit.edu	37	19	57335649	57335649	+	Translation_Start_Site	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr19:57335649C>A	ENST00000391708.3	-	0	539				PEG3_ENST00000598410.1_De_novo_Start_OutOfFrame|PEG3_ENST00000594706.1_5'Flank|PEG3_ENST00000423103.2_Missense_Mutation_p.K125N|PEG3_ENST00000326441.9_Missense_Mutation_p.K125N|ZIM2_ENST00000599935.1_De_novo_Start_OutOfFrame|ZIM2_ENST00000593931.1_De_novo_Start_OutOfFrame|ZIM2_ENST00000593711.1_De_novo_Start_OutOfFrame|PEG3_ENST00000593695.1_De_novo_Start_OutOfFrame|ZIM2_ENST00000601070.1_De_novo_Start_OutOfFrame|ZIM2_ENST00000221722.5_De_novo_Start_OutOfFrame	NM_001146326.1|NM_001146327.1	NP_001139798.1|NP_001139799.1	Q9NZV7	ZIM2_HUMAN	zinc finger, imprinted 2			44		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)			GGTACATCTCCTTGTAATTCT	0.547000																								0											ENST00000391708.3	1	0	hg19	CCDS33123.1	.	.	.	.	.	.	.	.	.	.	C	9.895	1.205252	0.22205	.	.	ENSG00000198300	ENST00000326441;ENST00000423103;ENST00000292074	T;T	0.04317	3.65;3.65	4.18	-3.28	0.05033	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.710048	0.12221	N	0.488381	T	0.02012	0.0063	N	0.08118	0	.	.	.	B;B	0.21905	0.032;0.062	B;B	0.23018	0.043;0.043	T	0.42666	-0.9438	9	0.72032	D	0.01	-7.7048	0.944	0.01361	0.1571:0.3297:0.1546:0.3585	.	125;58	Q9GZU2;Q96Q96	PEG3_HUMAN;.	N	125	ENSP00000326581:K125N;ENSP00000403051:K125N	ENSP00000292074:K125N	K	-	3	2	ZIM2	62027461	0.000000	0.05858	0.000000	0.03702	0.405000	0.30901	-0.287000	0.08388	-0.404000	0.07610	-0.142000	0.14014	AAG		TCGA-FB-AAQ3-01A-11D-A40W-08	ZIM2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416094.2	1	0	1	74	315	0	85		0	0	0	0	85	2		0	0	0	0	0	2	1	1.000000	73	311	0	83	2								-2.920372	1	1	0	0		1	1	2	3	2.099934	0	0.380000	1.890000	0.389283	0.990000	8.100000e-01	1.000000	1.000000	0.969574	0.990000	1	0.910000	1.000000
GALNT2	2590	broad.mit.edu	37	1	230338964	230338964	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr1:230338964G>A	ENST00000366672.4	+	3	374	c.302G>A	c.(301-303)cGc>cAc	p.R101H	GALNT2_ENST00000541865.1_Missense_Mutation_p.R11H|GALNT2_ENST00000543760.1_Missense_Mutation_p.R63H	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2			32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)			CCTTACGCCCGCAACAAGTTC	0.547000																								0							SO:0001583	missense			ENST00000366672.4	0	1	hg19	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	G	36	5.625072	0.96671	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000541865	T;T;T	0.56611	0.45;0.45;1.05	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.67571	0.2907	L	0.55017	1.72	0.80722	D	1	D;D	0.76494	0.999;0.999	P;P	0.60609	0.853;0.877	T	0.66862	-0.5816	10	0.56958	D	0.05	.	20.0572	0.97657	0.0:0.0:1.0:0.0	.	101;63	Q10471;G3V1S6	GALT2_HUMAN;.	H	63;101;11	ENSP00000445017:R63H;ENSP00000355632:R101H;ENSP00000444346:R11H	ENSP00000355632:R101H	R	+	2	0	GALNT2	228405587	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	9.792000	0.99085	2.826000	0.97356	0.655000	0.94253	CGC		TCGA-FB-AAQ3-01A-11D-A40W-08	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	0	0	0	7	556	1	115	0	2.243536e-04	0	2	1	115	2		0	0	0	0	0	2	0	0.026503	7	543	1	113	17								-1.897440	0	1	121412	2	41	1	1	2	3	2.064077	0	0.380000	1.890000	0.384676	0.060000	2.000000e-02	1.000000	0.060000	0.101519	0.060000	0	0.040000	0.110000
NIPAL3	57185	broad.mit.edu	37	1	24782657	24782657	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr1:24782657G>A	ENST00000374399.4	+	8	1035	c.667G>A	c.(667-669)Gtg>Atg	p.V223M	NIPAL3_ENST00000339255.2_Missense_Mutation_p.V223M|NIPAL3_ENST00000003912.3_Missense_Mutation_p.V141M	NM_020448.4	NP_065181.1	Q6P499	NPAL3_HUMAN	NIPA-like domain containing 3			14					AGTCAAGGCCGTGGCTGGGAT	0.557000																								0							SO:0001583	missense			ENST00000374399.4	0	1	hg19	CCDS30631.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.1|20.1	3.938783|3.938783	0.73557|0.73557	.|.	.|.	ENSG00000001461|ENSG00000001461	ENST00000432012|ENST00000374399;ENST00000003912;ENST00000339255	.|D;D;D	.|0.91792	.|-2.91;-2.91;-2.91	5.79|5.79	4.87|4.87	0.63330|0.63330	.|.	.|0.107041	.|0.64402	.|D	.|0.000006	D|D	0.95953|0.95953	0.8682|0.8682	M|M	0.87038|0.87038	2.855|2.855	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.998	.|D;D	.|0.66351	.|0.923;0.943	D|D	0.95952|0.95952	0.8955|0.8955	5|10	.|0.62326	.|D	.|0.03	-32.0797|-32.0797	14.3693|14.3693	0.66828|0.66828	0.0723:0.0:0.9277:0.0|0.0723:0.0:0.9277:0.0	.|.	.|223;223	.|Q6P499;A6NN97	.|NPAL3_HUMAN;.	H|M	1|223;141;223	.|ENSP00000363520:V223M;ENSP00000003912:V141M;ENSP00000343549:V223M	.|ENSP00000003912:V141M	R|V	+|+	2|1	0|0	NIPAL3|NIPAL3	24655244|24655244	1.000000|1.000000	0.71417|0.71417	0.912000|0.912000	0.35992|0.35992	0.732000|0.732000	0.41865|0.41865	5.124000|5.124000	0.64709|0.64709	2.745000|2.745000	0.94114|0.94114	0.561000|0.561000	0.74099|0.74099	CGT|GTG		TCGA-FB-AAQ3-01A-11D-A40W-08	NIPAL3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276996.1	0	0	0	9	1284	0	373	0	9.576809e-04	0	6	0	373	2		0	0	0	0	0	2	1	0.993797	9	1265	0	369	2								-2.743427	1	1	0	0		1	0	1	1	1.895110	1	0.380000	1.890000	0.313476	0.030000	0	0.060000	0.030000	0.036782	0.030000	0	0.010000	0.050000
MACF1	23499	broad.mit.edu	37	1	39784230	39784230	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	targeted			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr1:39784230G>A	ENST00000372915.3	+	29	3990	c.3903G>A	c.(3901-3903)atG>atA	p.M1301I	MACF1_ENST00000564288.1_Missense_Mutation_p.M1296I|MACF1_ENST00000476350.1_3'UTR|MACF1_ENST00000361689.2_Missense_Mutation_p.M1301I|MACF1_ENST00000539005.1_Missense_Mutation_p.M1301I|MACF1_ENST00000567887.1_Missense_Mutation_p.M1333I|MACF1_ENST00000317713.7_Missense_Mutation_p.M1301I|MACF1_ENST00000545844.1_Missense_Mutation_p.M1301I			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1			203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)		AGGAAATGATGAAGCCAGGCC	0.512000																								0							SO:0001583	missense			ENST00000372915.3	1	1	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.60|14.60	2.584623|2.584623	0.46110|0.46110	.|.	.|.	ENSG00000127603|ENSG00000127603	ENST00000372925|ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000524432;ENST00000530262	.|T;T;T;T;T;T;T	.|0.33654	.|1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.97|5.97	5.97|5.97	0.96955|0.96955	.|.	.|.	.|.	.|.	.|.	T|T	0.24928|0.24928	0.0605|0.0605	N|N	0.17082|0.17082	0.46|0.46	0.80722|0.80722	D|D	1|1	.|P;B;B	.|0.34587	.|0.458;0.32;0.019	.|B;B;B	.|0.31869	.|0.137;0.077;0.032	T|T	0.05835|0.05835	-1.0861|-1.0861	5|9	.|0.10636	.|T	.|0.68	.|.	20.4387|20.4387	0.99107|0.99107	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|1301;1301;1266	.|F8W8Q1;Q9UPN3-2;Q9UPN3-3	.|.;.;.	K|I	435|1301;1301;1301;1301;1301;1259;1450	.|ENSP00000439537:M1301I;ENSP00000362006:M1301I;ENSP00000354573:M1301I;ENSP00000313438:M1301I;ENSP00000444364:M1301I;ENSP00000435070:M1259I;ENSP00000437059:M1450I	.|ENSP00000313438:M1301I	E|M	+|+	1|3	0|0	MACF1|MACF1	39556817|39556817	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.371000|3.371000	0.52379|0.52379	2.836000|2.836000	0.97738|0.97738	0.655000|0.655000	0.94253|0.94253	GAA|ATG		TCGA-FB-AAQ3-01A-11D-A40W-08	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	1	0	1	18	157	0	26		0	0	0	0	26	2	1	1	91	1149	2	945	9	1	0.999985	18	155	0	26	2								-20.000000	1	1	0	0		1	0	1	1	1.895110	1	0.380000	1.890000	0.313476	0.490000	3.000000e-01	0.720000	0.480000	0.503874	0.490000	0	0.390000	0.610000
AJAP1	55966	broad.mit.edu	37	1	4832475	4832475	+	Silent	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr1:4832475C>T	ENST00000378191.4	+	4	1434	c.1053C>T	c.(1051-1053)aaC>aaT	p.N351N	AJAP1_ENST00000378190.3_Silent_p.N351N	NM_018836.3	NP_061324.1	Q9UKB5	AJAP1_HUMAN	adherens junctions associated protein 1			24	all_cancers(77;0.071)|Ovarian(185;0.0721)	all_cancers(23;1.77e-36)|all_epithelial(116;1.26e-21)|all_lung(118;3.51e-08)|Lung NSC(185;3.47e-06)|all_neural(13;8.84e-06)|all_hematologic(16;7.61e-05)|Breast(487;0.000507)|Renal(390;0.0007)|Colorectal(325;0.00117)|Hepatocellular(190;0.0071)|Glioma(11;0.0155)|Myeloproliferative disorder(586;0.0258)|Ovarian(437;0.0409)|Lung SC(97;0.133)|Medulloblastoma(700;0.215)			CGGCCTATAACGAGACCCTGC	0.597000																								0							SO:0001819	synonymous_variant			ENST00000378191.4	1	1	hg19	CCDS54.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	AJAP1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001542.3	1	0	1	19	154	0	45	0	3.711414e-02	0	3	0	45	2		0	0	0	0	0	2	1	0.999993	19	152	0	45	2								-20.000000	1	1	121412	6	39	1	0	1	1	1.918407	0	0.380000	1.890000	0.330381	0.530000	3.300000e-01	0.780000	0.530000	0.550426	0.530000	0	0.430000	0.660000
GLMN	11146	broad.mit.edu	37	1	92737044	92737044	+	Missense_Mutation	SNP	C	C	G			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr1:92737044C>G	ENST00000370360.3	-	8	982	c.901G>C	c.(901-903)Gat>Cat	p.D301H	GLMN_ENST00000534881.1_Missense_Mutation_p.D301H	NM_053274.2	NP_444504.1	Q92990	GLMN_HUMAN	glomulin, FKBP associated protein			17		all_lung(203;0.00827)|Lung NSC(277;0.0295)			GGAAGCTGATCAATATGGATG	0.318000									Multiple Glomus Tumors (of the Skin), Familial															0							SO:0001583	missense	Familial Cancer Database	Multiple Familial Glomangiomas, Hereditary Multiple Glomus Tumors, Familial Multiple Glomangiomatosis, Inherited Cutaneous Venous Anomalies, incl. Familial Multiple Glomangiomyoma	ENST00000370360.3	0	1	hg19	CCDS738.1	.	.	.	.	.	.	.	.	.	.	C	15.56	2.871104	0.51695	.	.	ENSG00000174842	ENST00000370360;ENST00000534881	T;T	0.50001	0.76;0.78	5.08	4.17	0.49024	.	0.141925	0.64402	D	0.000007	T	0.50616	0.1626	M	0.63843	1.955	0.38063	D	0.936146	D;D	0.89917	0.989;1.0	P;D	0.69824	0.882;0.966	T	0.58064	-0.7702	10	0.87932	D	0	-13.4808	8.206	0.31456	0.0:0.7503:0.0:0.2497	.	301;301	B4DJ85;Q92990	.;GLMN_HUMAN	H	301	ENSP00000359385:D301H;ENSP00000440156:D301H	ENSP00000359385:D301H	D	-	1	0	GLMN	92509632	0.967000	0.33354	0.880000	0.34516	0.924000	0.55760	0.970000	0.29383	1.126000	0.42016	0.591000	0.81541	GAT		TCGA-FB-AAQ3-01A-11D-A40W-08	GLMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028358.1	0	0	0	5	633	0	140	0	2.727419e-03	0	8	0	140	2		0	0	0	0	0	2	1	0.934861	5	622	0	140	2								-2.584876	1	1	0	0		1	0	1	1	1.881734	1	0.380000	1.890000	0.313476	0.030000	0	0.080000	0.040000	0.044373	0.030000	0	0.020000	0.060000
AVP	551	broad.mit.edu	37	20	3065264	3065264	+	Silent	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr20:3065264C>T	ENST00000380293.3	-	1	106	c.57G>A	c.(55-57)gcG>gcA	p.A19A		NM_000490.4	NP_000481.2	P01185	NEU2_HUMAN	arginine vasopressin			3					GGAAGTAGCACGCGGAGGAGA	0.637000																								0							SO:0001819	synonymous_variant			ENST00000380293.3	1	1	hg19	CCDS13045.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	AVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077713.2	1	0	1	127	603	0	143		0	0	0	0	143	2		0	0	0	0	0	2	1	1.000000	124	595	0	139	2								-20.000000	1	1	121412	2	39	1	0	1	1	2.038952	0	0.380000	1.890000	0.378820	0.900000	7.700000e-01	1.000000	1.000000	0.911386	0.900000	1	0.830000	0.990000
ITPA	3704	broad.mit.edu	37	20	3193873	3193873	+	Splice_Site	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr20:3193873G>A	ENST00000380113.3	+	2	316		c.e2+1		ITPA_ENST00000455664.2_Splice_Site|ITPA_ENST00000483354.1_Splice_Site|ITPA_ENST00000399838.3_Intron	NM_033453.3|NM_181493.2	NP_258412.1|NP_852470.1			inosine triphosphatase (nucleoside triphosphate pyrophosphatase)			6					AAAATTGACCGTATGTCTCTG	0.403000																								0							SO:0001630	splice_region_variant			ENST00000380113.3	0	1	hg19	CCDS13051.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987186	0.74589	0.0	1.16E-4	ENSG00000125877	ENST00000380113;ENST00000455664	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.8694	0.70444	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ITPA	3141873	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.722000	0.84778	2.585000	0.87301	0.644000	0.83932	.		TCGA-FB-AAQ3-01A-11D-A40W-08	ITPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077719.2	0	0	0	6	555	0	154		0	0	0	0	154	2		0	0	0	0	0	2	1	0.963750	6	548	0	153	2								-2.520640	1	1	121412	2	40	1	0	1	1	2.038952	0	0.380000	1.890000	0.378820	0.050000	1.000000e-02	0.120000	0.060000	0.065149	0.050000	0	0.030000	0.090000
RBM12	10137	broad.mit.edu	37	20	34241168	34241168	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr20:34241168G>A	ENST00000374114.3	-	3	2340	c.2077C>T	c.(2077-2079)Ccc>Tcc	p.P693S	CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron|CPNE1_ENST00000317677.5_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000374104.3_Missense_Mutation_p.P693S|RBM12_ENST00000359646.1_Missense_Mutation_p.P693S|CPNE1_ENST00000397445.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12			36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)		CCTGCACTGGGCATTCCCGCA	0.557000																								0							SO:0001583	missense			ENST00000374114.3	0	1	hg19	CCDS13261.1	.	.	.	.	.	.	.	.	.	.	G	36	5.653504	0.96724	.	.	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.22336	1.96;1.96;1.96	4.03	4.03	0.46877	.	0.000000	0.64402	D	0.000018	T	0.27663	0.0680	N	0.19112	0.55	0.80722	D	1	D	0.63880	0.993	D	0.70227	0.968	T	0.02365	-1.1170	10	0.19590	T	0.45	-3.377	14.4866	0.67622	0.0:0.0:1.0:0.0	.	693	Q9NTZ6	RBM12_HUMAN	S	693;693;693;492	ENSP00000363228:P693S;ENSP00000352668:P693S;ENSP00000363217:P693S	ENSP00000339879:P492S	P	-	1	0	RBM12	33704582	0.002000	0.14202	0.997000	0.53966	0.903000	0.53119	-0.160000	0.10041	2.528000	0.85240	0.563000	0.77884	CCC		TCGA-FB-AAQ3-01A-11D-A40W-08	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	0	0	0	6	466	0	131	0	8.200116e-03	0	9	0	131	2		0	0	0	0	0	2	1	0.963295	6	458	0	130	2								-2.182804	0	1	0	0		1	0	1	1	2.038952	0	0.380000	1.890000	0.378820	0.060000	2.000000e-02	0.140000	0.060000	0.077326	0.060000	0	0.040000	0.110000
PLEKHM3	389072	broad.mit.edu	37	2	208842157	208842157	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr2:208842157G>A	ENST00000427836.2	-	3	1253	c.764C>T	c.(763-765)gCc>gTc	p.A255V	PLEKHM3_ENST00000457206.1_Missense_Mutation_p.A255V|PLEKHM3_ENST00000389247.4_Missense_Mutation_p.A255V	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	p.A255V(2)		19					CTGGTACGTGGCATAAAGGTT	0.448000																								2	Substitution - Missense(2)						SO:0001583	missense			ENST00000427836.2	0	1	hg19	CCDS42808.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.363231	0.41902	.	.	ENSG00000178385	ENST00000427836;ENST00000389247;ENST00000457206	T;T;T	0.29655	1.56;1.56;1.56	5.96	5.08	0.68730	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.265266	0.36740	N	0.002437	T	0.20700	0.0498	N	0.19112	0.55	0.35452	D	0.795766	B;B	0.32573	0.376;0.1	B;B	0.26770	0.073;0.036	T	0.24977	-1.0145	10	0.59425	D	0.04	-18.8129	14.2231	0.65841	0.0:0.0:0.7279:0.2721	.	255;255	C9J119;Q6ZWE6	.;PKHM3_HUMAN	V	255	ENSP00000417003:A255V;ENSP00000373899:A255V;ENSP00000400150:A255V	ENSP00000373899:A255V	A	-	2	0	PLEKHM3	208550402	1.000000	0.71417	0.996000	0.52242	0.617000	0.37484	4.284000	0.58983	1.516000	0.48900	0.655000	0.94253	GCC		TCGA-FB-AAQ3-01A-11D-A40W-08	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	0	0	0	6	559	1	116		0	0	0	1	116	2		0	0	0	0	0	2	0	0.015086	6	552	1	115	17								-1.845026	0	1	0	0		1	0	1	1	2.039739	0	0.380000	1.890000	0.378820	0.050000	1.000000e-02	0.120000	0.060000	0.064691	0.050000	0	0.030000	0.090000
MREG	55686	broad.mit.edu	37	2	216861118	216861118	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr2:216861118G>A	ENST00000263268.6	-	2	461	c.166C>T	c.(166-168)Ccc>Tcc	p.P56S		NM_018000.2	NP_060470.2	Q8N565	MREG_HUMAN	melanoregulin			3		Renal(323;0.0328)			ACATCATGGGGCATACTCCAT	0.438000																								0							SO:0001583	missense			ENST00000263268.6	0	1	hg19	CCDS46513.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.445649	0.84101	.	.	ENSG00000118242	ENST00000236976;ENST00000263268;ENST00000439791;ENST00000424992;ENST00000420348	T	0.57595	0.39	5.3	5.3	0.74995	.	0.053672	0.85682	D	0.000000	T	0.69602	0.3129	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71388	-0.4608	10	0.87932	D	0	-15.281	16.501	0.84256	0.0:0.0:1.0:0.0	.	56	Q8N565	MREG_HUMAN	S	56;56;2;2;2	ENSP00000263268:P56S	ENSP00000236976:P56S	P	-	1	0	MREG	216569363	1.000000	0.71417	0.943000	0.38184	0.969000	0.65631	5.223000	0.65283	2.759000	0.94783	0.557000	0.71058	CCC		TCGA-FB-AAQ3-01A-11D-A40W-08	MREG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337297.1	0	0	0	5	372	0	69	0	8.626317e-04	0	3	0	69	2		0	0	0	0	0	2	1	0.937502	6	370	0	68	2								-2.604749	1	1	0	0		1	0	1	1	2.039739	0	0.380000	1.890000	0.378820	0.070000	2.000000e-02	0.150000	0.070000	0.082805	0.070000	0	0.040000	0.110000
SETD2	29072	broad.mit.edu	37	3	47098937	47098937	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr3:47098937G>A	ENST00000409792.3	-	15	6379	c.6337C>T	c.(6337-6339)Cgc>Tgc	p.R2113C		NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2			141		Acute lymphoblastic leukemia(5;0.0169)			AGTTTATTGCGGTCTTTAATT	0.403000			N, F, S, Mis		clear cell renal carcinoma										Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0							SO:0001583	missense			ENST00000409792.3	0	1	hg19	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	G	23.2	4.388690	0.82902	.	.	ENSG00000181555	ENST00000451092;ENST00000409792	T	0.24908	1.83	4.84	4.84	0.62591	.	0.000000	0.64402	D	0.000013	T	0.43122	0.1233	L	0.55481	1.735	0.80722	D	1	D;D	0.89917	1.0;0.999	P;P	0.57679	0.825;0.825	T	0.36817	-0.9732	10	0.87932	D	0	.	18.4955	0.90864	0.0:0.0:1.0:0.0	.	2113;2113	F2Z317;Q9BYW2	.;SETD2_HUMAN	C	2113	ENSP00000386759:R2113C	ENSP00000386759:R2113C	R	-	1	0	SETD2	47073941	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.993000	0.70616	2.686000	0.91538	0.561000	0.74099	CGC		TCGA-FB-AAQ3-01A-11D-A40W-08	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2	0	0	0	5	257	0	59	0	6.727365e-02	0	18	0	59	2		0	0	0	0	0	2	1	0.935582	5	253	0	59	2								-4.017868	1	1	0	0		1	0	0	0	2.032035	0	0.380000	1.890000	0.377635	0.100000	3.000000e-02	0.220000	0.100000	0.118417	0.100000	0	0.060000	0.160000
INPP4B	8821	broad.mit.edu	37	4	143033802	143033802	+	Silent	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr4:143033802G>A	ENST00000513000.1	-	23	2602	c.2169C>T	c.(2167-2169)gcC>gcT	p.A723A	INPP4B_ENST00000508116.1_Silent_p.A723A|INPP4B_ENST00000262992.4_Silent_p.A723A|INPP4B_ENST00000308502.4_Silent_p.A723A|INPP4B_ENST00000509777.1_Silent_p.A723A	NM_003866.2	NP_003857.2	O15327	INP4B_HUMAN	inositol polyphosphate-4-phosphatase, type II, 105kDa			58	all_hematologic(180;0.158)				CAAACATTCTGGCTGGAAGCT	0.368000																								0							SO:0001819	synonymous_variant			ENST00000513000.1	1	1	hg19	CCDS3757.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	INPP4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364587.1	1	0	1	91	450	0	109	1	9.999867e-01	39	42	0	109	2		0	0	0	0	0	2	1	1.000000	90	446	0	109	2								-3.236347	1	1	121400	4	37	1	1	2	3	2.067516	0	0.380000	1.890000	0.384676	0.890000	7.300000e-01	1.000000	1.000000	0.893928	0.890000	1	0.800000	0.990000
APBB2	323	broad.mit.edu	37	4	40895355	40895355	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr4:40895355G>A	ENST00000295974.8	-	11	1954	c.1325C>T	c.(1324-1326)gCg>gTg	p.A442V	APBB2_ENST00000513140.1_Missense_Mutation_p.A421V|APBB2_ENST00000508593.1_Missense_Mutation_p.A443V|APBB2_ENST00000506352.1_Missense_Mutation_p.A421V	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	p.A421V(1)		34					GTTGTTGACCGCAACACTACT	0.502000													Ovarian(3;20 75 16686 49997)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000295974.8	0	1	hg19	CCDS54761.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.243991	0.79912	.	.	ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352	T;T;T;T	0.17054	2.3;2.3;2.3;2.3	5.64	5.64	0.86602	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.42921	0.1224	M	0.63428	1.95	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.993;0.999;0.999;0.999	T	0.17198	-1.0377	10	0.66056	D	0.02	-15.5656	19.7013	0.96054	0.0:0.0:1.0:0.0	.	404;443;421;442	B4DJ88;E9PG87;Q92870-2;Q92870	.;.;.;APBB2_HUMAN	V	442;441;421;443;421	ENSP00000295974:A442V;ENSP00000426018:A421V;ENSP00000427211:A443V;ENSP00000421539:A421V	ENSP00000295974:A442V	A	-	2	0	APBB2	40590112	1.000000	0.71417	0.604000	0.28916	0.138000	0.21146	9.771000	0.98977	2.657000	0.90304	0.655000	0.94253	GCG		TCGA-FB-AAQ3-01A-11D-A40W-08	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	0	0	0	6	837	0	168	0	7.833592e-05	0	2	0	168	2		0	0	0	0	0	2	1	0.963175	6	823	0	166	2								-1.861801	0	1	120914	2	35	1	1	2	3	2.067516	0	0.380000	1.890000	0.384676	0.030000	0	1.000000	0.040000	0.071179	0.030000	0	0.020000	0.060000
DCUN1D4	23142	broad.mit.edu	37	4	52777312	52777312	+	Missense_Mutation	SNP	T	T	C			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr4:52777312T>C	ENST00000334635.5	+	9	872	c.692T>C	c.(691-693)cTt>cCt	p.L231P	DCUN1D4_ENST00000381437.4_Missense_Mutation_p.L171P|DCUN1D4_ENST00000381441.3_Intron|DCUN1D4_ENST00000451288.2_Missense_Mutation_p.L275P	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4			9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)		ATCTGGCCCCTTTTTCCAGTT	0.383000																								0							SO:0001583	missense			ENST00000334635.5	0	1	hg19	CCDS33982.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.683870	0.88639	.	.	ENSG00000109184	ENST00000334635;ENST00000381437;ENST00000451288;ENST00000510808	T;T;T	0.69306	-0.39;-0.39;-0.39	5.97	5.97	0.96955	Domain of unknown function DUF298 (2);	0.000000	0.85682	D	0.000000	D	0.86339	0.5909	M	0.93420	3.415	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.89414	0.3705	10	0.62326	D	0.03	-14.1468	15.642	0.77012	0.0:0.0:0.0:1.0	.	275;231	B4DH25;Q92564	.;DCNL4_HUMAN	P	231;171;275;41	ENSP00000334625:L231P;ENSP00000370846:L171P;ENSP00000389900:L275P	ENSP00000334625:L231P	L	+	2	0	DCUN1D4	52472069	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.288000	0.76882	0.533000	0.62120	CTT		TCGA-FB-AAQ3-01A-11D-A40W-08	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	0	0	0	5	491	0	100	0	1.547333e-02	0	15	0	100	2		0	0	0	0	0	2	1	0.934432	5	481	0	100	2								-2.108720	0	1	0	0		1	1	2	3	2.067516	0	0.380000	1.890000	0.384676	0.050000	1.000000e-02	1.000000	0.060000	0.090605	0.050000	0	0.030000	0.090000
SNCAIP	9627	broad.mit.edu	37	5	121786604	121786604	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr5:121786604C>T	ENST00000261368.8	+	10	2324	c.2062C>T	c.(2062-2064)Ccc>Tcc	p.P688S	SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000505546.1_RNA|SNCAIP_ENST00000261367.7_Missense_Mutation_p.P735S|SNCAIP_ENST00000379538.3_Missense_Mutation_p.P322S|CTC-210G5.1_ENST00000509993.1_RNA|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000379533.2_Missense_Mutation_p.P735S|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000542191.1_Missense_Mutation_p.P246S|CTC-210G5.1_ENST00000506053.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.P628S|SNCAIP_ENST00000414317.2_Missense_Mutation_p.P290S	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein			39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)		CTCTGAGGACCCCAAGACTAC	0.547000																								0							SO:0001583	missense			ENST00000261368.8	1	1	hg19	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805916	0.70682	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	T;T;T;T;T;T;T;T	0.12465	4.49;5.02;2.73;2.68;5.02;4.99;2.68;4.71	6.06	6.06	0.98353	.	0.332317	0.35436	N	0.003205	T	0.15825	0.0381	L	0.29908	0.895	0.34659	D	0.72249	B;B;B;B;B;B;B;B	0.32467	0.208;0.354;0.208;0.241;0.312;0.372;0.372;0.156	B;B;B;B;B;B;B;B	0.35550	0.101;0.138;0.101;0.058;0.205;0.058;0.114;0.026	T	0.07731	-1.0757	10	0.56958	D	0.05	-24.3293	20.6208	0.99490	0.0:1.0:0.0:0.0	.	628;316;290;628;322;322;735;688	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	S	246;628;688;735;628;322;735;290;328	ENSP00000441681:P246S;ENSP00000422106:P628S;ENSP00000261368:P688S;ENSP00000368848:P735S;ENSP00000368851:P628S;ENSP00000368854:P322S;ENSP00000261367:P735S;ENSP00000394392:P290S	ENSP00000261367:P735S	P	+	1	0	SNCAIP	121814503	0.992000	0.36948	1.000000	0.80357	0.900000	0.52787	2.147000	0.42226	2.882000	0.98803	0.655000	0.94253	CCC		TCGA-FB-AAQ3-01A-11D-A40W-08	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1	1	0	1	47	199	0	39	0	9.902837e-02	1	2	0	39	2		0	0	0	0	0	2	1	1.000000	45	193	0	39	2								-20.000000	1	1	0	0		1	1	2	3	2.057957	0	0.380000	1.890000	0.382347	0.990000	7.600000e-01	1.000000	1.000000	0.955732	0.990000	1	0.880000	1.000000
FAM13B	51306	broad.mit.edu	37	5	137288332	137288332	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr5:137288332G>A	ENST00000033079.3	-	16	2300	c.1849C>T	c.(1849-1851)Cgg>Tgg	p.R617W	FAM13B_ENST00000425075.2_Missense_Mutation_p.R521W|FAM13B_ENST00000420893.2_Missense_Mutation_p.R617W	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B			11					ATTTGCTTCCGCAGTTTTGTA	0.313000																								0							SO:0001583	missense			ENST00000033079.3	1	1	hg19	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	G	19.67	3.871297	0.72065	2.27E-4	0.0	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	D;T;D	0.95788	-3.81;0.71;-3.81	5.92	3.94	0.45596	.	0.055638	0.64402	D	0.000002	D	0.97356	0.9135	M	0.82517	2.595	0.51482	D	0.999926	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.73708	0.981;0.928;0.957	D	0.97740	1.0208	10	0.87932	D	0	-6.3967	12.1708	0.54157	0.0:0.0:0.4451:0.5549	.	521;617;617	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	W	617;521;617	ENSP00000033079:R617W;ENSP00000394669:R521W;ENSP00000388521:R617W	ENSP00000033079:R617W	R	-	1	2	FAM13B	137316231	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.782000	0.55401	1.460000	0.47911	0.557000	0.71058	CGG		TCGA-FB-AAQ3-01A-11D-A40W-08	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1	1	0	1	74	413	0	105	0	1.146614e-01	1	3	0	105	2		0	0	0	0	0	2	1	1.000000	74	411	0	104	2								-20.000000	1	1	121412	2	34	1	1	2	3	2.057957	0	0.380000	1.890000	0.382347	0.800000	6.400000e-01	1.000000	0.800000	0.808938	0.800000	0	0.710000	0.900000
PCDHA8	56140	broad.mit.edu	37	5	140223264	140223264	+	Silent	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr5:140223264C>T	ENST00000531613.1	+	1	2358	c.2358C>T	c.(2356-2358)ggC>ggT	p.G786G	PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA8_ENST00000378123.3_Silent_p.G786G|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8			78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		TTGATGTAGGCGAAGAGCAAG	0.448000																								0							SO:0001819	synonymous_variant			ENST00000531613.1	1	1	hg19	CCDS54919.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	1	0	1	41	201	0	49		0	0	0	0	49	2		0	0	0	0	0	2	1	1.000000	41	198	0	48	2								-3.377415	1	1	0	0		1	1	2	3	2.057957	0	0.380000	1.890000	0.382347	0.890000	6.600000e-01	1.000000	1.000000	0.887203	0.890000	1	0.770000	1.000000
PCDHGB7	56099	broad.mit.edu	37	5	140798660	140798660	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr5:140798660C>T	ENST00000398594.2	+	1	1234	c.1234C>T	c.(1234-1236)Cgg>Tgg	p.R412W	PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA11_ENST00000398587.2_5'Flank|PCDHGA5_ENST00000518069.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_5'Flank	NM_018927.3	NP_061750.1	Q9Y5F8	PCDGJ_HUMAN	protocadherin gamma subfamily B, 7			56			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		GGCCCTGGATCGGGAGCAGAC	0.473000																								0							SO:0001583	missense			ENST00000398594.2	1	1	hg19	CCDS47293.1	.	.	.	.	.	.	.	.	.	.	c	14.00	2.405532	0.42715	.	.	ENSG00000254122	ENST00000398594	T	0.01685	4.69	5.31	-1.36	0.09085	Cadherin (4);Cadherin-like (1);	0.000000	0.28671	U	0.014540	T	0.19167	0.0460	H	0.97940	4.11	0.22648	N	0.998896	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.44982	-0.9292	10	0.87932	D	0	.	19.8821	0.96901	0.8062:0.1938:0.0:0.0	.	412;412	Q9Y5F8;Q9Y5F8-2	PCDGJ_HUMAN;.	W	412	ENSP00000381594:R412W	ENSP00000381594:R412W	R	+	1	2	PCDHGB7	140778844	0.029000	0.19370	0.019000	0.16419	0.952000	0.60782	-0.448000	0.06820	-0.478000	0.06823	0.561000	0.74099	CGG		TCGA-FB-AAQ3-01A-11D-A40W-08	PCDHGB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376973.1	1	0	0	8	167	0	43		0	0	0	0	43	2		0	0	0	0	0	2	1	0.989392	8	165	0	42	2								-10.743960	1	1	0	0		1	1	2	3	2.057957	0	0.380000	1.890000	0.382347	0.250000	1.100000e-01	0.480000	0.240000	0.273357	0.250000	0	0.170000	0.350000
PRDM13	59336	broad.mit.edu	37	6	100061933	100061933	+	Silent	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr6:100061933G>A	ENST00000369215.4	+	4	1727	c.1422G>A	c.(1420-1422)ccG>ccA	p.P474P		NM_021620.3	NP_067633.2	Q9H4Q3	PRD13_HUMAN	PR domain containing 13			17		all_cancers(76;1.64e-05)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0128)|Colorectal(196;0.069)|Lung NSC(302;0.186)			ACGGCTCACCGGCCACCACCG	0.632000																								0							SO:0001819	synonymous_variant			ENST00000369215.4	1	1	hg19	CCDS43487.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	PRDM13-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041619.2	1	0	0	51	198	0	44		0	0	0	0	44	2		0	0	0	0	0	2	1	1.000000	50	193	0	44	2								-20.000000	1	1	120604	4	33	1	0	1	1	1.665068	1	0.380000	1.890000	0.236359	0.850000	6.600000e-01	1.000000	0.860000	0.851214	0.850000	1	0.750000	0.940000
MAN1A1	4121	broad.mit.edu	37	6	119509656	119509656	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr6:119509656G>A	ENST00000368468.3	-	11	2074	c.1633C>T	c.(1633-1635)Cgg>Tgg	p.R545W		NM_005907.3	NP_005898.2	P33908	MA1A1_HUMAN	mannosidase, alpha, class 1A, member 1	p.R545W(1)		24		all_epithelial(87;0.173)			ACTTCTGGCCGTAAGATGTAG	0.413000													Ovarian(136;8 1825 12608 33541 47587)											1	Substitution - Missense(1)						SO:0001583	missense			ENST00000368468.3	0	1	hg19	CCDS5122.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244459	0.79912	.	.	ENSG00000111885	ENST00000368468	D	0.83837	-1.77	5.92	4.98	0.66077	.	0.000000	0.85682	D	0.000000	D	0.95608	0.8572	H	0.99806	4.795	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97318	0.9942	10	0.87932	D	0	-28.3893	17.0826	0.86603	0.0:0.0:0.8481:0.1519	.	545	P33908	MA1A1_HUMAN	W	545	ENSP00000357453:R545W	ENSP00000357453:R545W	R	-	1	2	MAN1A1	119551355	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	3.615000	0.54167	2.794000	0.96219	0.650000	0.86243	CGG		TCGA-FB-AAQ3-01A-11D-A40W-08	MAN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042015.1	0	0	0	6	469	1	114	0	4.844638e-03	0	7	1	114	2		0	0	0	0	0	2	0	0.036359	6	467	1	114	15								-1.938152	0	1	0	0		1	0	1	1	1.665068	1	0.380000	1.890000	0.236359	0.050000	1.000000e-02	0.110000	0.050000	0.062287	0.050000	0	0.030000	0.080000
LATS1	9113	broad.mit.edu	37	6	149983251	149983251	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr6:149983251C>A	ENST00000543571.1	-	8	3554	c.3007G>T	c.(3007-3009)Gaa>Taa	p.E1003*	LATS1_ENST00000253339.5_Nonsense_Mutation_p.E1003*	NM_004690.3	NP_004681.1			large tumor suppressor kinase 1			6		Ovarian(120;0.0164)			GCTTTTATTTCATCAGCACCA	0.408000																								0							SO:0001587	stop_gained			ENST00000543571.1	0	1	hg19	CCDS34551.1	.	.	.	.	.	.	.	.	.	.	C	41	8.619519	0.98888	.	.	ENSG00000131023	ENST00000543571;ENST00000253339	.	.	.	5.45	5.45	0.79879	.	0.000000	0.52532	D	0.000076	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.2848	0.94066	0.0:1.0:0.0:0.0	.	.	.	.	X	1003	.	.	E	-	1	0	LATS1	150024944	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.442000	0.80503	2.562000	0.86427	0.591000	0.81541	GAA		TCGA-FB-AAQ3-01A-11D-A40W-08	LATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043923.4	1	0	0	115	370	0	140		0	0	0	0	140	2		0	0	0	0	0	2	1	1.000000	111	364	0	138	2								-20.000000	1	1	0	0		1	0	1	1	1.662849	1	0.380000	1.890000	0.236359	0.950000	8.300000e-01	1.000000	1.000000	0.947720	0.950000	1	0.890000	1.000000
HIST1H2AC	8334	broad.mit.edu	37	6	26124629	26124629	+	Missense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08			G	A	G	G		Valid	Somatic	Phase_I	WXS	RNA			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr6:26124629G>A	ENST00000602637.1	+	1	199	c.169G>A	c.(169-171)Gag>Aag	p.E57K	HIST1H2BC_ENST00000396984.1_5'Flank|HIST1H2BC_ENST00000314332.5_5'Flank|HIST1H2AC_ENST00000377791.2_Missense_Mutation_p.E57K			Q93077	H2A1C_HUMAN	histone cluster 1, H2ac			12					GGCGGTGTTAGAGTACCTGAC	0.662000																								0							SO:0001583	missense			ENST00000602637.1	1	1	hg19	CCDS4585.1	.	.	.	.	.	.	.	.	.	.	.	33	5.221276	0.95139	.	.	ENSG00000180573	ENST00000377791;ENST00000314088	T;T	0.61742	0.08;0.08	5.78	5.78	0.91487	Histone-fold (2);Histone core (1);Histone H2A (2);	0.000000	0.44902	D	0.000401	D	0.84124	0.5403	H	0.97516	4.02	0.51767	D	0.999937	D	0.89917	1.0	D	0.97110	1.0	D	0.88700	0.3215	10	0.87932	D	0	.	19.3632	0.94451	0.0:0.0:1.0:0.0	.	57	Q93077	H2A1C_HUMAN	K	57	ENSP00000367022:E57K;ENSP00000321389:E57K	ENSP00000321389:E57K	E	+	1	0	HIST1H2AC	26232608	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	9.460000	0.97641	2.894000	0.99253	0.591000	0.81541	GAG		TCGA-FB-AAQ3-01A-11D-A40W-08	HIST1H2AC-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000468023.1	1	0	1	59	218	0	72	1	9.998886e-01	25	28	0	72	2		0	0	0	0	0	2	1	1.000000	57	212	0	71	2								-20.000000	1	1	0	0		1	0	1	1	2.036596	0	0.380000	1.890000	0.378820	0.990000	8.700000e-01	1.000000	1.000000	0.989328	0.990000	1	0.980000	1.000000
PHIP	55023	broad.mit.edu	37	6	79668316	79668316	+	Splice_Site	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr6:79668316G>A	ENST00000275034.4	-	32	3825	c.3658C>T	c.(3658-3660)Cgg>Tgg	p.R1220W	PHIP_ENST00000479165.1_5'UTR|AL356776.1_ENST00000516160.2_RNA	NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein			68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)			GAAGAAACCCGCCTTAAAAAA	0.328000																								0							SO:0001630	splice_region_variant			ENST00000275034.4	0	1	hg19	CCDS4987.1	.	.	.	.	.	.	.	.	.	.	G	23.2	4.383342	0.82792	.	.	ENSG00000146247	ENST00000275034	T	0.19394	2.15	5.9	5.9	0.94986	Bromodomain (5);	0.000000	0.64402	D	0.000002	T	0.44435	0.1293	M	0.86651	2.83	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.45833	-0.9234	9	.	.	.	-9.9537	14.1372	0.65295	0.0:0.0:0.8502:0.1498	.	1220;1220	A7J992;Q8WWQ0	.;PHIP_HUMAN	W	1220	ENSP00000275034:R1220W	.	R	-	1	2	PHIP	79725035	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.978000	0.88095	2.793000	0.96121	0.563000	0.77884	CGG		TCGA-FB-AAQ3-01A-11D-A40W-08	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2	0	0	0	7	388	1	127		0	0	0	1	127	2		0	0	0	0	0	2	0	0.170877	7	385	1	127	12								-6.585479	1	0	0	0		1	0	1	1	2.039014	0	0.380000	1.890000	0.378820	0.090000	3.000000e-02	0.180000	0.100000	0.105421	0.090000	0	0.060000	0.140000
EEPD1	80820	broad.mit.edu	37	7	36194002	36194002	+	Missense_Mutation	SNP	G	G	C			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr7:36194002G>C	ENST00000242108.4	+	2	787	c.69G>C	c.(67-69)aaG>aaC	p.K23N	EEPD1_ENST00000534978.1_Missense_Mutation_p.K23N	NM_030636.2	NP_085139.2	Q7L9B9	EEPD1_HUMAN	endonuclease/exonuclease/phosphatase family domain containing 1			18					ATAGCCGCAAGTTCAGCGCAG	0.632000																								0							SO:0001583	missense			ENST00000242108.4	1	1	hg19	CCDS34619.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.466389	0.63625	.	.	ENSG00000122547	ENST00000242108;ENST00000534978	T;T	0.25250	1.81;1.81	5.72	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.35451	0.0932	L	0.27053	0.805	0.58432	D	0.999998	D	0.89917	1.0	D	0.85130	0.997	T	0.10660	-1.0620	10	0.49607	T	0.09	-36.8743	10.72	0.46034	0.1452:0.0:0.8548:0.0	.	23	Q7L9B9	EEPD1_HUMAN	N	23	ENSP00000242108:K23N;ENSP00000442692:K23N	ENSP00000242108:K23N	K	+	3	2	EEPD1	36160527	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.540000	0.45727	1.403000	0.46800	0.561000	0.74099	AAG		TCGA-FB-AAQ3-01A-11D-A40W-08	EEPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337602.1	1	0	1	44	220	0	60	0	2.022498e-01	0	5	0	60	2		0	0	0	0	0	2	1	1.000000	44	215	0	60	2								-20.000000	1	1	0	0		1	1	2	3	2.044891	0	0.380000	1.890000	0.381176	0.870000	6.500000e-01	1.000000	1.000000	0.874427	0.870000	1	0.760000	1.000000
DERL1	79139	broad.mit.edu	37	8	124027758	124027758	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr8:124027758G>A	ENST00000259512.4	-	8	985	c.685C>T	c.(685-687)Cga>Tga	p.R229*	DERL1_ENST00000405944.3_Nonsense_Mutation_p.R209*|DERL1_ENST00000523036.1_Nonsense_Mutation_p.R129*|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000519018.1_Nonsense_Mutation_p.R129*|DERL1_ENST00000419562.2_Nonsense_Mutation_p.R129*	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1			8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)		TCAGCAGCTCGCCTCATGCTA	0.627000																								0							SO:0001587	stop_gained			ENST00000259512.4	0	1	hg19	CCDS6337.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943987	0.92593	.	.	ENSG00000136986	ENST00000259512;ENST00000405944;ENST00000419562;ENST00000519018;ENST00000523036	.	.	.	6.17	4.31	0.51392	.	0.060136	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.14656	T	0.56	.	11.4856	0.50352	0.0:0.1048:0.6045:0.2906	.	.	.	.	X	229;209;129;129;129	.	ENSP00000259512:R229X	R	-	1	2	DERL1	124096939	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.468000	0.53086	1.590000	0.49995	0.655000	0.94253	CGA		TCGA-FB-AAQ3-01A-11D-A40W-08	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381714.2	0	0	0	6	403	0	66	1	6.621305e-01	4	141	0	66	2		0	0	0	0	0	2	1	0.960695	6	387	0	66	2								-4.609656	1	1	0	0		1	1	2	3	2.309010	1	0.380000	1.890000	0.451861	0.100000	3.000000e-02	1.000000	0.080000	0.286319	0.100000	0	0.060000	1.000000
BMP1	649	broad.mit.edu	37	8	22037986	22037986	+	Missense_Mutation	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr8:22037986C>A	ENST00000306385.5	+	8	1737	c.1067C>A	c.(1066-1068)cCc>cAc	p.P356H	BMP1_ENST00000397816.3_Missense_Mutation_p.P356H|BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000306349.8_Missense_Mutation_p.P356H|BMP1_ENST00000397814.3_Missense_Mutation_p.P356H	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1			30					TCTGTCACACCCGGGGAGAAG	0.612000																								0							SO:0001583	missense			ENST00000306385.5	0	1	hg19	CCDS6026.1	.	.	.	.	.	.	.	.	.	.	C	18.16	3.561849	0.65538	.	.	ENSG00000168487	ENST00000306385;ENST00000397816;ENST00000306349;ENST00000397814	T;T;T;T	0.19250	2.16;2.16;2.16;2.16	5.66	5.66	0.87406	CUB (5);	0.000000	0.38272	U	0.001746	T	0.45637	0.1352	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.964;0.969	D;D;P;P	0.97110	0.986;1.0;0.864;0.752	T	0.11060	-1.0603	10	0.37606	T	0.19	.	18.5112	0.90917	0.0:1.0:0.0:0.0	.	356;429;356;356	P13497;Q59F71;P13497-2;P13497-6	BMP1_HUMAN;.;.;.	H	356	ENSP00000305714:P356H;ENSP00000380917:P356H;ENSP00000306121:P356H;ENSP00000380915:P356H	ENSP00000306121:P356H	P	+	2	0	BMP1	22093931	1.000000	0.71417	0.727000	0.30756	0.525000	0.34531	7.772000	0.85439	2.665000	0.90641	0.561000	0.74099	CCC		TCGA-FB-AAQ3-01A-11D-A40W-08	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	0	0	0	5	359	0	75	0	3.436077e-02	0	17	0	75	2		0	0	0	0	0	2	1	0.936128	5	355	0	75	2								-2.881535	1	1	0	0		1	0	1	1	1.702097	1	0.380000	1.890000	0.241683	0.060000	1.000000e-02	0.130000	0.060000	0.069934	0.060000	0	0.030000	0.100000
CHMP7	91782	broad.mit.edu	37	8	23114047	23114047	+	Silent	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr8:23114047G>A	ENST00000397677.1	+	5	1380	c.732G>A	c.(730-732)ctG>ctA	p.L244L	CHMP7_ENST00000313219.7_Silent_p.L244L	NM_152272.3	NP_689485.1	Q8WUX9	CHMP7_HUMAN	charged multivesicular body protein 7			11		Prostate(55;0.0513)			TGTACCAGCTGATGCAGAGTG	0.517000																								0							SO:0001819	synonymous_variant			ENST00000397677.1	0	1	hg19	CCDS6040.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	CHMP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254717.1	0	0	0	6	825	0	215	0	3.425244e-03	0	10	0	215	2		0	0	0	0	0	2	1	0.963565	6	814	0	215	2								-2.520252	1	1	0	0		1	0	1	1	1.702097	1	0.380000	1.890000	0.241683	0.020000	0	0.070000	0.030000	0.036035	0.020000	0	0.010000	0.050000
PI15	51050	broad.mit.edu	37	8	75761394	75761394	+	Missense_Mutation	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr8:75761394C>A	ENST00000260113.2	+	6	862	c.683C>A	c.(682-684)cCa>cAa	p.P228Q	RP11-758M4.4_ENST00000523860.1_RNA|RP11-758M4.4_ENST00000522914.1_RNA|RP11-758M4.4_ENST00000518128.1_RNA|PI15_ENST00000523773.1_Missense_Mutation_p.P228Q	NM_015886.3	NP_056970.1	O43692	PI15_HUMAN	peptidase inhibitor 15			30	Breast(64;0.137)		BRCA - Breast invasive adenocarcinoma(89;0.104)|Epithelial(68;0.118)		GTAGGGGTACCATGTTCATCT	0.393000																								0							SO:0001583	missense			ENST00000260113.2	1	1	hg19	CCDS6218.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.692584	0.88735	.	.	ENSG00000137558	ENST00000260113;ENST00000523773	T;T	0.11821	2.74;2.74	5.15	5.15	0.70609	CAP domain (1);	0.051987	0.85682	D	0.000000	T	0.48554	0.1506	M	0.91090	3.175	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.57533	-0.7795	10	0.62326	D	0.03	.	19.1672	0.93562	0.0:1.0:0.0:0.0	.	228	O43692	PI15_HUMAN	Q	228	ENSP00000260113:P228Q;ENSP00000428567:P228Q	ENSP00000260113:P228Q	P	+	2	0	PI15	75923949	1.000000	0.71417	0.997000	0.53966	0.977000	0.68977	7.278000	0.78587	2.833000	0.97629	0.585000	0.79938	CCA		TCGA-FB-AAQ3-01A-11D-A40W-08	PI15-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379115.1	1	0	1	109	525	0	136	0	3.013833e-02	0	2	0	136	2		0	0	0	0	0	2	1	1.000000	109	519	0	135	2								-2.734185	1	1	0	0		1	0	0	0	2.031454	0	0.380000	1.890000	0.377635	0.890000	7.400000e-01	1.000000	1.000000	0.899790	0.890000	1	0.820000	0.980000
OR1L1	26737	broad.mit.edu	37	9	125424096	125424096	+	Silent	SNP	C	C	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chr9:125424096C>A	ENST00000373686.1	+	1	252	c.252C>A	c.(250-252)atC>atA	p.I84I	OR1L1_ENST00000309623.1_Silent_p.I34I			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1			17					TCCTCCCCATCTACCTTATCA	0.493000																								0							SO:0001819	synonymous_variant			ENST00000373686.1	1	1	hg19																																																																																					TCGA-FB-AAQ3-01A-11D-A40W-08	OR1L1-201	KNOWN	basic	protein_coding	protein_coding		1	0	1	63	273	0	84		0	0	0	0	84	2		0	0	0	0	0	2	1	1.000000	63	268	0	84	2								-20.000000	1	1	0	0		1	0	0	0	1.990802	0	0.380000	1.890000	0.363057	0.950000	7.500000e-01	1.000000	1.000000	0.936594	0.950000	1	0.850000	1.000000
STAG2	10735	broad.mit.edu	37	X	123181240	123181240	+	Missense_Mutation	SNP	T	T	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chrX:123181240T>A	ENST00000371160.1	+	9	994	c.704T>A	c.(703-705)cTa>cAa	p.L235Q	STAG2_ENST00000354548.5_Missense_Mutation_p.L166Q|STAG2_ENST00000371157.3_Missense_Mutation_p.L235Q|STAG2_ENST00000218089.9_Missense_Mutation_p.L235Q|STAG2_ENST00000371145.3_Missense_Mutation_p.L235Q|STAG2_ENST00000371144.3_Missense_Mutation_p.L235Q|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2			78					AATGTGGCACTAAATCTTAGC	0.328000																								0							SO:0001583	missense			ENST00000371160.1	0	1	hg19	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.531408	0.85706	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.69	5.69	0.88448	STAG (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.57725	0.2073	M	0.83692	2.655	0.80722	D	1	D;D	0.89917	0.985;1.0	P;D	0.91635	0.891;0.999	T	0.58747	-0.7582	10	0.27082	T	0.32	-12.9753	14.8699	0.70448	0.0:0.0:0.0:1.0	.	235;235	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	Q	235;235;166;235;235;235;235	ENSP00000218089:L235Q;ENSP00000397265:L235Q;ENSP00000346555:L166Q;ENSP00000360202:L235Q;ENSP00000360199:L235Q;ENSP00000360187:L235Q;ENSP00000360186:L235Q	ENSP00000218089:L235Q	L	+	2	0	STAG2	123008921	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.040000	0.89188	1.893000	0.54813	0.486000	0.48141	CTA		TCGA-FB-AAQ3-01A-11D-A40W-08	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	0	0	0	8	431	0	91	0	0	0	1	0	91	2		0	0	0	0	0	2	1	0.988795	8	424	0	91	2								-7.703427	1	1	0	0		1	0	1	1			0.380000	1.890000	0.380000	0.090000	4.000000e-02	0.180000	0.100000	0.106995	0.090000	0	0.060000	0.140000
MCF2	4168	broad.mit.edu	37	X	138678769	138678769	+	Missense_Mutation	SNP	C	C	T			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chrX:138678769C>T	ENST00000370576.4	-	19	2425	c.2216G>A	c.(2215-2217)cGt>cAt	p.R739H	AL033403.1_ENST00000401295.2_RNA|MCF2_ENST00000370573.4_Missense_Mutation_p.R739H|MCF2_ENST00000414978.1_Missense_Mutation_p.R799H|MCF2_ENST00000338585.6_Missense_Mutation_p.R755H|MCF2_ENST00000519895.1_Missense_Mutation_p.R815H|MCF2_ENST00000536274.1_Missense_Mutation_p.R700H|MCF2_ENST00000370578.4_Missense_Mutation_p.R884H|MCF2_ENST00000520602.1_Missense_Mutation_p.R799H	NM_001171879.1|NM_005369.4	NP_001165350.1|NP_005360.3	P10911	MCF2_HUMAN	MCF.2 cell line derived transforming sequence			62	Acute lymphoblastic leukemia(192;0.000127)				ACTTTCAACACGCCTTTTGCA	0.383000																								0							SO:0001583	missense			ENST00000370576.4	1	1	hg19	CCDS14667.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.948071	0.92593	.	.	ENSG00000101977	ENST00000520602;ENST00000370576;ENST00000536274;ENST00000370578;ENST00000414978;ENST00000446225;ENST00000519895;ENST00000370573;ENST00000338585	T;T;T;T;T;T;T;T;T	0.56611	0.99;0.88;0.79;0.99;0.99;0.45;1.05;0.9;0.95	5.67	5.67	0.87782	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.80401	0.4616	M	0.93197	3.39	0.48830	D	0.999716	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	P;D;P;P;P;P;D;P	0.87578	0.834;0.994;0.886;0.834;0.886;0.834;0.998;0.834	D	0.85413	0.1138	10	0.66056	D	0.02	.	17.6181	0.88073	0.0:1.0:0.0:0.0	.	815;884;700;739;739;884;755;739	E9PH77;B7Z3Z2;F5H091;B2R9S6;P10911-2;Q5JYJ7;P10911-4;P10911	.;.;.;.;.;.;.;MCF2_HUMAN	H	799;739;700;884;799;342;815;739;755	ENSP00000427745:R799H;ENSP00000359608:R739H;ENSP00000438155:R700H;ENSP00000359610:R884H;ENSP00000397055:R799H;ENSP00000405848:R342H;ENSP00000430276:R815H;ENSP00000359605:R739H;ENSP00000342204:R755H	ENSP00000342204:R755H	R	-	2	0	MCF2	138506435	1.000000	0.71417	0.719000	0.30619	0.940000	0.58332	6.066000	0.71185	2.376000	0.81061	0.600000	0.82982	CGT		TCGA-FB-AAQ3-01A-11D-A40W-08	MCF2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058560.1	1	0	1	74	366	0	97		0	0	0	0	97	2		0	0	0	0	0	2	1	1.000000	72	360	0	97	2								-20.000000	1	1	121364	1	37	1	0	1	1			0.380000	1.890000	0.380000	0.880000	7.000000e-01	1.000000	1.000000	0.883643	0.880000	1	0.790000	0.980000
MAGEB1	4112	broad.mit.edu	37	X	30269201	30269201	+	Silent	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chrX:30269201G>A	ENST00000378981.3	+	4	912	c.591G>A	c.(589-591)agG>agA	p.R197R	MAGEB1_ENST00000397548.2_Silent_p.R197R|MAGEB1_ENST00000397550.1_Silent_p.R197R	NM_002363.4	NP_002354.2	P43366	MAGB1_HUMAN	melanoma antigen family B, 1			32					ACTTTCCCAGGAATGGGCTTC	0.488000																								0							SO:0001819	synonymous_variant			ENST00000378981.3	1	1	hg19	CCDS14222.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	MAGEB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056160.1	1	0	1	20	86	0	26		0	0	0	0	26	2		0	0	0	0	0	2	1	0.999997	19	86	0	26	2								-20.000000	1	1	0	0		1	0	1	1			0.380000	1.890000	0.380000	0.990000	6.400000e-01	1.000000	1.000000	0.925744	0.990000	1	0.800000	1.000000
PRAF2	11230	broad.mit.edu	37	X	48931491	48931491	+	Silent	SNP	G	G	A			TCGA-FB-AAQ3-01A-11D-A40W-08	TCGA-FB-AAQ3-11A-11D-A40W-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	1978bc24-e7ec-4bb9-a4a8-6152c23c3a57	f9625c44-8f93-4902-a5b2-ecb4206c11da	g.chrX:48931491G>A	ENST00000376390.4	-	1	239	c.156C>T	c.(154-156)ttC>ttT	p.F52F	PRAF2_ENST00000376386.3_Silent_p.F52F|WDR45_ENST00000553851.1_Intron|AF196779.12_ENST00000376358.3_Intron|PRAF2_ENST00000491199.1_5'UTR	NM_007213.1	NP_009144.1	O60831	PRAF2_HUMAN	PRA1 domain family, member 2			8					GGCCGATGCCGAAGCAGAGAA	0.657000																								0							SO:0001819	synonymous_variant			ENST00000376390.4	1	1	hg19	CCDS14317.1																																																																																				TCGA-FB-AAQ3-01A-11D-A40W-08	PRAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083415.2	1	0	0	61	204	0	54	0	9.593851e-01	0	20	0	54	2		0	0	0	0	0	2	1	1.000000	59	201	0	54	2								-20.000000	1	1	121410	3	32	1	0	1	1			0.380000	1.890000	0.380000	0.990000	9.500000e-01	1.000000	1.000000	0.997428	0.990000	1	0.990000	1.000000