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	UniProt_AApos	UniProt_Region	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	ref_context	gc_content	COSMIC_n_overlapping_mutations	ESP_AvgAAsampleReadDepth	ESP_AvgEAsampleReadDepth	ESP_AvgSampleReadDepth	ESP_Chromosome	ESP_Position	ESP_TotalAAsamplesCovered	ESP_TotalEAsamplesCovered	ESP_TotalSamplesCovered	Ensembl_so_accession	Ensembl_so_term	HGNC_AccessionNumbers	HGNC_CCDSIDs	HGNC_Chromosome	HGNC_DateModified	HGNC_DateNameChanged	HGNC_DateSymbolChanged	HGNC_EnsemblGeneID	HGNC_EnsemblIDsuppliedbyEnsembl	HGNC_Genefamilydescription	HGNC_HGNCID	HGNC_LocusGroup	HGNC_LocusType	HGNC_NameSynonyms	HGNC_OMIMIDsuppliedbyNCBI	HGNC_PreviousNames	HGNC_PreviousSymbols	HGNC_PubmedIDs	HGNC_RecordType	HGNC_RefSeqsuppliedbyNCBI	HGNC_Status	HGNC_Synonyms	HGNC_UCSCIDsuppliedbyUCSC	HGNC_UniProtIDsuppliedbyUniProt	HGNC_VEGAIDs	HGVS_coding_DNA_change	HGVS_genomic_change	HGVS_protein_change	UniProt_alt_uniprot_accessions	annotation_transcript	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	gencode_transcript_name	gencode_transcript_status	gencode_transcript_tags	gencode_transcript_type	gene_type	havana_transcript	init_n_lod	init_t_lod	isArtifactMode	n_alt_count	n_ref_count	oxoGCut	pox	pox_cutoff	qox	refseq_mrna_id	t_alt_count	t_lod_fstar	t_ref_count	tumor_f
WDR7	23335	broad.mit.edu	hg19	18	54603067	54603067	+	Silent	SNP	T	T	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr18:54603067T>A	ENST00000254442.3	+	23	3973	c.3762T>A	c.(3760-3762)tcT>tcA	p.S1254S	WDR7_ENST00000589935.1_Intron|WDR7_ENST00000357574.3_Silent_p.S1221S	NM_015285.2	NP_056100.2	Q9Y4E6	WDR7_HUMAN	WD repeat domain 7	1254					NS(1)|breast(5)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(37)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	78				Lung(128;0.0238)|Colorectal(16;0.0296)	CGGCCCGCTCTGCGAGGCATG	0.527	0	84.0	87.0	86.0	18	54603067	2203	4300	6503	SO:0001819	synonymous_variant	AB011113	CCDS11962.1, CCDS11963.1	18q21.31	2013-01-09			ENSG00000091157	ENSG00000091157	"""WD repeat domain containing"""	13490	protein-coding gene	gene with protein product		613473			10828621	Standard	XM_005266674	Approved	KIAA0541, TRAG	uc002lgk.1	Q9Y4E6	OTTHUMG00000132721	ENST00000254442.3:c.3762T>A	18.37:g.54603067T>A		A7E2C8|Q86UX5|Q86VP2|Q96PS7	ENST00000254442.3	37	CCDS11962.1																																																																																			WDR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256062.1		144.178970	0	-22	103	0	0	1	0		45	144.243044	40	0.529412
GAB3	139716	broad.mit.edu	hg19	X	153908520	153908520	+	Silent	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chrX:153908520C>T	ENST00000369575.3	-	9	1564	c.1533G>A	c.(1531-1533)gaG>gaA	p.E511E	GAB3_ENST00000424127.2_Silent_p.E512E|GAB3_ENST00000496390.1_5'UTR	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	511					NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				CTGTTCGGTGCTCCTCCTAGG	0.517	0	123.0	113.0	116.0	X	153908520	2203	4300	6503	SO:0001819	synonymous_variant	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219	"""Pleckstrin homology (PH) domain containing"""	17515	protein-coding gene	gene with protein product	"""DOS/Gab family member 3"", ""Gab3 scaffolding protein"""	300482			11739737	Standard	XM_005274648	Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000424127.2:c.1536G>A	X.37:g.153908520C>T		A6NHF8|E9PB44	ENST00000424127.2	37	CCDS48198.1																																																																																			GAB3-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377380.1		211.806147	0	-91	48	0	0	1	0	NM_001081573	60	220.521757	4	0.937500
SELE	6401	broad.mit.edu	hg19	1	169698468	169698468	+	Missense_Mutation	SNP	A	A	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr1:169698468A>T	ENST00000333360.7	-	7	1088	c.949T>A	c.(949-951)Tgc>Agc	p.C317S	SELE_ENST00000367779.4_Missense_Mutation_p.C317S|SELE_ENST00000367780.4_Missense_Mutation_p.C255S|SELE_ENST00000367781.4_Missense_Mutation_p.C317S|SELE_ENST00000367782.4_Missense_Mutation_p.C317S|SELE_ENST00000367775.1_Missense_Mutation_p.C255S|SELE_ENST00000367774.1_Missense_Mutation_p.C317S|SELE_ENST00000367776.1_Missense_Mutation_p.C317S|SELE_ENST00000367777.1_Missense_Mutation_p.C317S|C1orf112_ENST00000498289.1_Intron	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	317	Sushi 3.	actin filament-based process|activation of phospholipase C activity|calcium-mediated signaling|heterophilic cell-cell adhesion|leukocyte migration involved in inflammatory response|leukocyte tethering or rolling|positive regulation of receptor internalization|regulation of inflammatory response|response to interleukin-1|response to lipopolysaccharide|response to tumor necrosis factor	caveola|coated pit|cortical cytoskeleton|extracellular space|integral to membrane|perinuclear region of cytoplasm	oligosaccharide binding|phospholipase binding|sialic acid binding|transmembrane receptor activity	breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				GAATGGCTGCACCTCACAGAG	0.522	0	61.0	54.0	57.0	1	169698468	2203	4300	6503	SO:0001583	missense	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908	"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM	1375831	Standard	NM_000450	Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.949T>A	1.37:g.169698468A>T	ENSP00000331736:p.Cys317Ser	A2RRD6|P16111	ENST00000333360.7	37	CCDS1283.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.960662	0.53400	.	.	ENSG00000007908	ENST00000367781;ENST00000367782;ENST00000367780;ENST00000367779;ENST00000333360;ENST00000367777;ENST00000367775;ENST00000367776;ENST00000367774	T;T;T;T;T;T;T;T;T	0.73258	1.89;1.89;1.89;-0.73;1.89;1.89;1.89;1.89;-0.73	5.13	5.13	0.70059	Complement control module (2);Sushi/SCR/CCP (3);	0.000000	0.45126	D	0.000386	T	0.81569	0.4850	M	0.85197	2.74	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	D	0.85125	0.0971	10	0.72032	D	0.01	-7.1846	12.9225	0.58241	1.0:0.0:0.0:0.0	.	317	P16581	LYAM2_HUMAN	S	317;317;255;317;317;317;255;317;317	ENSP00000356755:C317S;ENSP00000356756:C317S;ENSP00000356754:C255S;ENSP00000356753:C317S;ENSP00000331736:C317S;ENSP00000356751:C317S;ENSP00000356749:C255S;ENSP00000356750:C317S;ENSP00000356748:C317S	ENSP00000331736:C317S	C	-	1	0	SELE	167965092	1.000000	0.71417	0.113000	0.21522	0.089000	0.18198	6.254000	0.72460	1.928000	0.55862	0.528000	0.53228	TGC	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1		25.867028	0	-2	31	0	0	1	0	NM_000450	9	26.196903	15	0.375000
ABCA12	26154	broad.mit.edu	hg19	2	215865502	215865502	+	Missense_Mutation	SNP	G	G	C			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr2:215865502G>C	ENST00000272895.7	-	22	3325	c.3106C>G	c.(3106-3108)Caa>Gaa	p.Q1036E	ABCA12_ENST00000389661.4_Missense_Mutation_p.Q718E	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1036		cellular homeostasis|lipid transport	integral to membrane	ATP binding|ATPase activity	NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)	CTTCCAGTTTGCAATTCAATG	0.428	0	124.0	130.0	128.0	2	215865502	2203	4300	6503	SO:0001583	missense	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452	"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B	11435397, 12915478, 8845852, 10094194	Standard	NM_015657	Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.3106C>G	2.37:g.215865502G>C	ENSP00000272895:p.Gln1036Glu	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	ENST00000272895.7	37	CCDS33372.1	.	.	.	.	.	.	.	.	.	.	G	15.91	2.972598	0.53614	.	.	ENSG00000144452	ENST00000272895;ENST00000389661	D;D	0.95518	-3.73;-3.73	5.73	4.85	0.62838	.	0.087482	0.49916	D	0.000121	D	0.95762	0.8621	M	0.85197	2.74	0.80722	D	1	P;B	0.40431	0.717;0.237	B;B	0.40534	0.332;0.272	D	0.95485	0.8564	10	0.59425	D	0.04	.	16.2693	0.82607	0.0:0.0:0.8666:0.1333	.	1036;718	Q86UK0;Q86UK0-2	ABCAC_HUMAN;.	E	1036;718	ENSP00000272895:Q1036E;ENSP00000374312:Q718E	ENSP00000272895:Q1036E	Q	-	1	0	ABCA12	215573747	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.530000	0.73816	1.393000	0.46605	0.555000	0.69702	CAA	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1		166.742415	0	15	136	0	0	1	0	NM_173076	53	167.053934	66	0.445378
GNA11	2767	broad.mit.edu	hg19	19	3114962	3114962	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr19:3114962G>A	ENST00000078429.4	+	4	739	c.497G>A	c.(496-498)cGc>cAc	p.R166H		NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	166		activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	GACGTTGACCGCATCGCCACC	0.677	0	92.0	78.0	82.0	19	3114962	2203	4299	6502	SO:0001583	missense	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256		4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2	1302014, 23802516	Standard	NM_002067	Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.497G>A	19.37:g.3114962G>A	ENSP00000078429:p.Arg166His	O15109|Q14350|Q6IB00	ENST00000078429.4	37	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	19.08	3.757625	0.69648	.	.	ENSG00000088256	ENST00000078429	D	0.91996	-2.95	3.62	3.62	0.41486	G protein alpha subunit, helical insertion (2);	0.000000	0.64402	U	0.000002	D	0.97201	0.9085	H	0.96662	3.86	0.54753	D	0.999989	D	0.89917	1.0	D	0.73708	0.981	D	0.98413	1.0573	10	0.87932	D	0	.	14.2446	0.65981	0.0:0.0:1.0:0.0	.	166	P29992	GNA11_HUMAN	H	166	ENSP00000078429:R166H	ENSP00000078429:R166H	R	+	2	0	GNA11	3065962	1.000000	0.71417	1.000000	0.80357	0.207000	0.24258	9.626000	0.98410	1.752000	0.51891	0.556000	0.70494	CGC	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2		-6.224328	0	-14	95	0	0	1	0	NM_002067	3	6.661241	57	0.050000
MGAT4B	11282	broad.mit.edu	hg19	5	179226505	179226505	+	Splice_Site	SNP	C	C	T	rs112845536		TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr5:179226505C>T	ENST00000337755.5	-	8	1973		c.e8+1		MGAT4B_ENST00000292591.7_Splice_Site	NM_054013.3	NP_463459.1	Q9UQ53	MGT4B_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme B			N-glycan processing|post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	13	all_cancers(89;0.000201)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0525)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		CTCTTGCTCACCGCATCCTTC	0.577	0	66.0	66.0	66.0	5	179226505	2203	4300	6503	SO:0001630	splice_region_variant	AB000624	CCDS4448.1, CCDS4449.1	5q35	2013-02-25	2005-11-16		ENSG00000161013	ENSG00000161013	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7048	protein-coding gene	gene with protein product		604561	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme B"""		10372966	Standard	NM_014275	Approved	GnT-Ivb	uc003mks.3	Q9UQ53	OTTHUMG00000130912	ENST00000292591.7:c.1041+1G>A	5.37:g.179226505C>T		A8MPR0|Q86TF1|Q96GH4|Q9NSK6	ENST00000292591.7	37	CCDS4448.1	.	.	.	.	.	.	.	.	.	.	.	15.38	2.817544	0.50633	.	.	ENSG00000161013	ENST00000518778;ENST00000337755;ENST00000292591;ENST00000520969;ENST00000520875;ENST00000518867	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0447	0.80711	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	MGAT4B	179159111	1.000000	0.71417	0.986000	0.45419	0.573000	0.36030	7.590000	0.82653	1.993000	0.58246	0.561000	0.74099	.	MGAT4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253503.3		42.412661	0	15	62	0	0	1	0	NM_014275	15	42.703289	22	0.405405
LPHN3	23284	broad.mit.edu	hg19	4	62599230	62599230	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr4:62599230G>A	ENST00000512091.2	+	7	1900	c.1153G>A	c.(1153-1155)Gtg>Atg	p.V385M	LPHN3_ENST00000514591.1_Missense_Mutation_p.V385M|LPHN3_ENST00000508946.1_Missense_Mutation_p.V385M|LPHN3_ENST00000545650.1_Missense_Mutation_p.V385M|LPHN3_ENST00000504896.1_Missense_Mutation_p.V385M|LPHN3_ENST00000507625.1_Missense_Mutation_p.V453M|LPHN3_ENST00000509896.1_Missense_Mutation_p.V453M|LPHN3_ENST00000506746.1_Missense_Mutation_p.V453M|LPHN3_ENST00000514157.1_Missense_Mutation_p.V385M|LPHN3_ENST00000506720.1_Missense_Mutation_p.V453M|LPHN3_ENST00000511324.1_Missense_Mutation_p.V453M|LPHN3_ENST00000507164.1_Missense_Mutation_p.V453M|LPHN3_ENST00000508693.1_Missense_Mutation_p.V453M|LPHN3_ENST00000506700.1_Missense_Mutation_p.V385M|LPHN3_ENST00000514996.1_Missense_Mutation_p.V385M			Q9HAR2	LPHN3_HUMAN	latrophilin 3		Olfactomedin-like.	neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity|sugar binding	breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125					CTATCACGTCGTGAAATATTC	0.393	0	52.0	47.0	48.0	4	62599230	1838	4095	5933	SO:0001583	missense	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471	"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product					10994649	Standard	NM_015236	Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.1153G>A	4.37:g.62599230G>A	ENSP00000422533:p.Val385Met	E9PE04|O94867|Q9NWK5	ENST00000514591.1	37	CCDS54768.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.904395	0.52333	.	.	ENSG00000150471	ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000534975;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	D	0.93592	0.7954	L	0.55834	1.745	0.48040	D	0.999579	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.991	D	0.93887	0.7176	10	0.72032	D	0.01	.	13.6671	0.62403	0.0:0.1549:0.8451:0.0	.	385;453;385	E9PE04;E7EN28;Q9HAR2-2	.;.;.	M	385;385;453;453;385;385;385;385;385;453;453;453;385;385;385;453;453;385	ENSP00000423388:V385M;ENSP00000422533:V385M;ENSP00000423787:V453M;ENSP00000425033:V453M;ENSP00000424120:V385M;ENSP00000439831:V385M;ENSP00000421476:V453M;ENSP00000424030:V453M;ENSP00000421372:V453M;ENSP00000425201:V385M;ENSP00000423434:V385M;ENSP00000421627:V385M;ENSP00000420931:V453M;ENSP00000425884:V453M;ENSP00000424258:V385M	ENSP00000280009:V385M	V	+	1	0	LPHN3	62281825	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.513000	0.81739	2.471000	0.83476	0.557000	0.71058	GTG	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		25.162415	0	-8	19	0	0	1	0		9	26.383624	22	0.290323
SF3B1	23451	broad.mit.edu	hg19	2	198267483	198267483	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr2:198267483C>T	ENST00000335508.6	-	14	1965	c.1874G>A	c.(1873-1875)cGt>cAt	p.R625H		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa			nuclear mRNA splicing, via spliceosome	catalytic step 2 spliceosome|nuclear speck|U12-type spliceosomal complex	protein binding	NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)		TGTTGTGTTACGGACATACTC	0.438	12	95.0	92.0	93.0	2	198267483	2203	4300	6503	SO:0001583	missense	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524		10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""		9585501	Standard	XM_005246428	Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1874G>A	2.37:g.198267483C>T	ENSP00000335321:p.Arg625His	E9PCH3	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	35	5.485860	0.96323	.	.	ENSG00000115524	ENST00000335508	T	0.74421	-0.84	5.82	5.82	0.92795	Armadillo-like helical (1);Armadillo-type fold (1);	0.053241	0.64402	D	0.000001	D	0.91369	0.7277	H	0.96333	3.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93329	0.6699	10	0.87932	D	0	.	20.0991	0.97865	0.0:1.0:0.0:0.0	.	625	O75533	SF3B1_HUMAN	H	625	ENSP00000335321:R625H	ENSP00000335321:R625H	R	-	2	0	SF3B1	197975728	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.728000	0.84847	2.752000	0.94435	0.655000	0.94253	CGT	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		69.346191	0	-11	44	0	0	1	0		22	69.418623	26	0.458333
CSNK1A1L	122011	broad.mit.edu	hg19	13	37678549	37678549	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr13:37678549C>T	ENST00000379800.3	-	1	1254	c.845G>A	c.(844-846)cGc>cAc	p.R282H		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	282	Protein kinase.	Wnt receptor signaling pathway	cytoplasm	ATP binding|protein serine/threonine kinase activity	NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)	GAAAAGAATGCGGAATAGCTG	0.488	0	167.0	153.0	158.0	13	37678549	2203	4300	6503	SO:0001583	missense	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138		20289	protein-coding gene	gene with protein product						Standard	NM_145203	Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.845G>A	13.37:g.37678549C>T	ENSP00000369126:p.Arg282His	Q5T2N2	ENST00000379800.3	37	CCDS9363.1	.	.	.	.	.	.	.	.	.	.	C	15.22	2.769340	0.49680	.	.	ENSG00000180138	ENST00000379800	T	0.10288	2.89	1.74	1.74	0.24563	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.14184	0.0343	M	0.87682	2.9	0.50813	D	0.999897	P	0.35468	0.503	B	0.24974	0.057	T	0.08006	-1.0743	10	0.62326	D	0.03	.	9.4321	0.38617	0.0:1.0:0.0:0.0	.	282	Q8N752	KC1AL_HUMAN	H	282	ENSP00000369126:R282H	ENSP00000369126:R282H	R	-	2	0	CSNK1A1L	36576549	1.000000	0.71417	0.997000	0.53966	0.992000	0.81027	2.054000	0.41335	0.871000	0.35750	0.561000	0.74099	CGC	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1		-6.229331	0	-2	136	0	0	1	0	NM_145203	6	12.650106	89	0.063158
TRAF3IP1	26146	broad.mit.edu	hg19	2	239237343	239237343	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr2:239237343C>T	ENST00000373327.4	+	4	593	c.371C>T	c.(370-372)gCg>gTg	p.A124V	TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.A124V|TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.A124V	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	124	Abolishes microtubules-binding when missing.		cytoplasm|cytoskeleton	protein binding	breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)	AGTGACGATGCGGTGCGGAGG	0.468	0	81.0	82.0	82.0	2	239237343	2203	4300	6503	SO:0001583	missense	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104	"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380			10791955, 12935900	Standard	NM_015650	Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.371C>T	2.37:g.239237343C>T	ENSP00000362424:p.Ala124Val	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	ENST00000373327.4	37	CCDS33415.1	.	.	.	.	.	.	.	.	.	.	C	19.05	3.752655	0.69533	.	.	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.19394	2.15;2.15;2.15	4.65	4.65	0.58169	.	0.000000	0.85682	D	0.000000	T	0.50480	0.1618	M	0.80982	2.52	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.57694	-0.7767	10	0.66056	D	0.02	-36.9431	17.9082	0.88926	0.0:1.0:0.0:0.0	.	124;124	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	V	124	ENSP00000375851:A124V;ENSP00000362424:A124V;ENSP00000375852:A124V	ENSP00000362424:A124V	A	+	2	0	TRAF3IP1	238902082	1.000000	0.71417	0.120000	0.21714	0.092000	0.18411	5.967000	0.70403	2.301000	0.77427	0.655000	0.94253	GCG	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1		-2.614611	0	8	57	0	0	1	0	NM_015650	3	6.688463	44	0.063830
GNAQ	2776	broad.mit.edu	hg19	9	80409488	80409488	+	Missense_Mutation	SNP	T	T	A	rs121913492		TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr9:80409488T>A	ENST00000286548.4	-	5	848	c.626A>T	c.(625-627)cAa>cTa	p.Q209L	GNAQ_ENST00000397476.3_Missense_Mutation_p.Q7L	NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	209		activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity by dopamine receptor signaling pathway|glutamate signaling pathway|negative regulation of protein kinase activity|platelet activation|protein ADP-ribosylation|protein stabilization|regulation of action potential|regulation of catenin import into nucleus	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activator activity|GTPase activity|signal transducer activity	NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302					CTCTGACCTTTGGCCCCCTAC	0.348	153	108.0	105.0	106.0	9	80409488	2203	4300	6503	SO:0001583	missense		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052		4390	protein-coding gene	gene with protein product		600998			8825633	Standard	NM_002072	Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.626A>T	9.37:g.80409488T>A	ENSP00000286548:p.Gln209Leu	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	ENST00000286548.4	37	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	29.2	4.985495	0.93044	.	.	ENSG00000156052	ENST00000286548;ENST00000397476	D;D	0.91237	-2.81;-2.81	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	D	0.97573	0.9205	H	0.99347	4.525	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.99402	1.0928	10	0.87932	D	0	.	15.9502	0.79827	0.0:0.0:0.0:1.0	.	209	P50148	GNAQ_HUMAN	L	209;7	ENSP00000286548:Q209L;ENSP00000443197:Q7L	ENSP00000286548:Q209L	Q	-	2	0	GNAQ	79599308	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	8.040000	0.89188	2.167000	0.68274	0.460000	0.39030	CAA	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1		118.938182	0	9	121	0	0	1	0	NM_002072	38	119.191543	48	0.441860
DYSF	8291	broad.mit.edu	hg19	2	71797031	71797031	+	Silent	SNP	G	G	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr2:71797031G>A	ENST00000258104.3	+	27	3169	c.2892G>A	c.(2890-2892)caG>caA	p.Q964Q	DYSF_ENST00000409366.1_Silent_p.Q965Q|DYSF_ENST00000409762.1_Silent_p.Q981Q|DYSF_ENST00000394120.2_Silent_p.Q965Q|DYSF_ENST00000409651.1_Silent_p.Q996Q|DYSF_ENST00000409744.1_Silent_p.Q951Q|DYSF_ENST00000409582.3_Silent_p.Q981Q|DYSF_ENST00000413539.2_Silent_p.Q995Q|DYSF_ENST00000410041.1_Silent_p.Q982Q|DYSF_ENST00000410020.3_Silent_p.Q982Q|DYSF_ENST00000429174.2_Silent_p.Q964Q	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	964			cytoplasmic vesicle membrane|integral to membrane|sarcolemma	calcium-dependent phospholipid binding	autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111					CCGGAGGCCAGTGGATCTACA	0.587	0	55.0	57.0	56.0	2	71797031	2203	4300	6503	SO:0001819	synonymous_variant	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636		3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B	8320700	Standard	NM_003494	Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000410020.3:c.2946G>A	2.37:g.71797031G>A		A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	ENST00000410020.3	37	CCDS46328.1																																																																																			DYSF-007	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327477.2		-4.721883	0	-8	75	0	0	1	0	NM_003494	5	8.718728	65	0.071429
ARHGEF17	9828	broad.mit.edu	hg19	11	73073583	73073583	+	Silent	SNP	G	G	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr11:73073583G>A	ENST00000263674.3	+	14	5150	c.4800G>A	c.(4798-4800)gcG>gcA	p.A1600A		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	1600		actin cytoskeleton organization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction	cytosol	Rho guanyl-nucleotide exchange factor activity	endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32					CGACGCTCGCGGAGCCGGGGC	0.731	0	10.0	16.0	14.0	11	73073583	2161	4247	6408	SO:0001819	synonymous_variant	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237	"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""				11559528, 12071859	Standard	NM_014786	Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.4800G>A	11.37:g.73073583G>A		B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	ENST00000263674.3	37	CCDS8221.1																																																																																			ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1		22.690451	0	-6	24	0	0	1	0	NM_014786	8	23.547480	18	0.307692
SNHG14	0	broad.mit.edu	hg19	15	25313008	25313008	+	RNA	SNP	G	G	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr15:25313008G>A	ENST00000549804.2	+	0	538				SNHG14_ENST00000551077.1_RNA|SNORD116-7_ENST00000384404.1_RNA																	TCATACCGTCGTTCTCATCAG	0.507	0	180.0	159.0	165.0	15	25313008	876	1991	2867					15q11.2	2014-01-17	2011-08-22	2011-08-22	ENSG00000224078	ENSG00000224078	"""Long non-coding RNAs"""	37462	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 214"""		"""UBE3A antisense RNA 1 (non-protein coding)"""	UBE3A-AS1	23771028	Standard		Approved	NCRNA00214, UBE3A-AS			OTTHUMG00000056661		15.37:g.25313008G>A			ENST00000549804.2	37																																																																																				SNHG14-012	KNOWN	non_canonical_other|basic	antisense	processed_transcript	OTTHUMT00000408278.2		257.548048	0	3	265	0	0	1	0		81	257.559785	78	0.509434
LRFN2	57497	broad.mit.edu	hg19	6	40400440	40400440	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr6:40400440C>T	ENST00000338305.6	-	2	955	c.413G>A	c.(412-414)gGc>gAc	p.G138D		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	138			cell junction|integral to membrane|postsynaptic membrane		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)				ATCTGCGATGCCGCCCAGCTG	0.597	0	64.0	59.0	61.0	6	40400440	2203	4300	6503	SO:0001583	missense	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1	16495444, 16828986	Standard	NM_020737	Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.413G>A	6.37:g.40400440C>T	ENSP00000345985:p.Gly138Asp	A5PKU3|Q5SYP9	ENST00000338305.6	37	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	C	9.341	1.062997	0.19987	.	.	ENSG00000156564	ENST00000338305	T	0.02737	4.18	5.76	2.45	0.29901	.	0.365256	0.34603	N	0.003827	T	0.00608	0.0020	N	0.13299	0.325	0.32623	N	0.523012	B	0.02656	0.0	B	0.04013	0.001	T	0.45071	-0.9286	10	0.11485	T	0.65	.	11.0243	0.47736	0.0:0.6776:0.245:0.0773	.	138	Q9ULH4	LRFN2_HUMAN	D	138	ENSP00000345985:G138D	ENSP00000345985:G138D	G	-	2	0	LRFN2	40508418	0.396000	0.25262	0.995000	0.50966	0.832000	0.47134	0.911000	0.28584	0.736000	0.32559	0.655000	0.94253	GGC	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1		-8.517509	0	-21	28	0	0	1	0	XM_166372	3	6.315429	64	0.044776
RTDR1	27156	broad.mit.edu	hg19	22	23406237	23406237	+	Missense_Mutation	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr22:23406237C>T	ENST00000216036.4	-	5	692	c.496G>A	c.(496-498)Gag>Aag	p.E166K		NM_014433.2	NP_055248.1	Q9UHP6	RTDR1_HUMAN	rhabdoid tumor deletion region gene 1	166	Poly-Glu.			binding	breast(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	18	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.175)	TCCTGGAACTCCTCCTCCTCC	0.577	0	102.0	90.0	94.0	22	23406237	2203	4300	6503	SO:0001583	missense																									ENST00000216036.4:c.496G>A	22.37:g.23406237C>T	ENSP00000216036:p.Glu166Lys		ENST00000216036.4	37	CCDS13803.1	.	.	.	.	.	.	.	.	.	.	C	4.868	0.161359	0.09287	.	.	ENSG00000100218	ENST00000216036	T	0.51325	0.71	.	.	.	Armadillo-like helical (1);Armadillo-type fold (1);	3.549510	0.00508	N	0.000176	T	0.38852	0.1056	L	0.43923	1.385	0.22562	N	0.998982	P	0.46395	0.877	B	0.43360	0.417	T	0.30909	-0.9962	8	0.07813	T	0.8	0.7507	.	.	.	.	166	Q9UHP6	RTDR1_HUMAN	K	166	ENSP00000216036:E166K	ENSP00000216036:E166K	E	-	1	0	RTDR1	21736237	0.011000	0.17503	0.077000	0.20336	0.028000	0.11728	-0.542000	0.06091	0.064000	0.16427	0.064000	0.15345	GAG	RTDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319049.1		46.690902	0	-7	39	0	0	1	0		16	47.040996	24	0.400000
NBPF10	100132406	broad.mit.edu	hg19	1	145293547	145293547	+	Missense_Mutation	SNP	G	G	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr1:145293547G>T	ENST00000342960.5	+	1	177	c.142G>T	c.(142-144)Gcc>Tcc	p.A48S	NBPF10_ENST00000369339.3_Missense_Mutation_p.A48S|NBPF10_ENST00000369338.1_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN	neuroblastoma breakpoint family, member 10	48					NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	AACTCAACTGGCCGGCTTCCT	0.438	0									SO:0001583	missense	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425	"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000			16079250	Standard	NM_001039703	Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.142G>T	1.37:g.145293547G>T	ENSP00000358345:p.Ala48Ser	Q5RHC0|Q9NWN6	ENST00000369339.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	9.144|9.144	1.014467|1.014467	0.19277|0.19277	.|.	.|.	ENSG00000163386|ENSG00000163386	ENST00000369339;ENST00000342960|ENST00000448873	T|.	0.03801|.	3.8|.	1.0|1.0	-2.0|-2.0	0.07433|0.07433	.|.	.|.	.|.	.|.	.|.	T|T	0.23649|0.23649	0.0572|0.0572	M|M	0.71296|0.71296	2.17|2.17	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.40887|0.40887	-0.9539|-0.9539	7|6	0.56958|0.87932	D|D	0.05|0	.|.	1.9372|1.9372	0.03339|0.03339	0.2412:0.0:0.4556:0.3032|0.2412:0.0:0.4556:0.3032	.|.	.|.	.|.	.|.	S|V	48|7	ENSP00000345684:A48S|.	ENSP00000345684:A48S|ENSP00000414194:G7V	A|G	+|+	1|2	0|0	NBPF10|NBPF10	144004904|144004904	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.898000|-0.898000	0.04105|0.04105	-0.699000|-0.699000	0.05077|0.05077	0.121000|0.121000	0.15741|0.15741	GCC|GGC	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3		69.346321	1	78	746	0	8.87156e-34	1	8.87156e-34	NM_001039703	54	129.235304	380	0.124424
OR6C75	390323	broad.mit.edu	hg19	12	55759765	55759765	+	Nonsense_Mutation	SNP	A	A	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr12:55759765A>T	ENST00000343399.3	+	1	871	c.871A>T	c.(871-873)Aga>Tga	p.R291*		NM_001005497.1	NP_001005497.1	A6NL08	O6C75_HUMAN	olfactory receptor, family 6, subfamily C, member 75	291		sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	endometrium(2)|large_intestine(5)|lung(11)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)	25					ATACACACTGAGAAATAAGCA	0.393	0	69.0	64.0	66.0	12	55759765	2203	4300	6503	SO:0001587	stop_gained		CCDS31820.1	12q13.2	2013-09-23			ENSG00000187857	ENSG00000187857	"""GPCR / Class A : Olfactory receptors"""	31304	protein-coding gene	gene with protein product						Standard	NM_001005497	Approved		uc010spk.2	A6NL08	OTTHUMG00000169886	ENST00000343399.3:c.871A>T	12.37:g.55759765A>T	ENSP00000368987:p.Arg291*		ENST00000343399.3	37	CCDS31820.1	.	.	.	.	.	.	.	.	.	.	a	13.23	2.174605	0.38413	.	.	ENSG00000187857	ENST00000343399	.	.	.	5.22	1.32	0.21799	.	0.000000	0.47455	U	0.000236	.	.	.	.	.	.	0.48571	D	0.999672	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7292	0.62776	0.4857:0.5143:0.0:0.0	.	.	.	.	X	291	.	ENSP00000368987:R291X	R	+	1	2	OR6C75	54046032	0.996000	0.38824	0.059000	0.19551	0.298000	0.27526	2.792000	0.47837	0.069000	0.16605	0.515000	0.50301	AGA	OR6C75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406418.1		-8.732681	0	11	78	0	0	1	0		3	6.394842	65	0.044118
CACNA1D	776	broad.mit.edu	hg19	3	53796064	53796064	+	Missense_Mutation	SNP	A	A	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr3:53796064A>T	ENST00000288139.4	+	31	4004	c.3886A>T	c.(3886-3888)Atc>Ttc	p.I1296F	CACNA1D_ENST00000350061.5_Missense_Mutation_p.I1276F|CACNA1D_ENST00000422281.2_Missense_Mutation_p.I1276F|CACNA1D_ENST00000540742.1_Missense_Mutation_p.I183F	NM_000720.2	NP_000711.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit			axon guidance|energy reserve metabolic process|regulation of insulin secretion	voltage-gated calcium channel complex	voltage-gated calcium channel activity	breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	TGACTCCCTCATCGTAATCGG	0.552	0	174.0	138.0	150.0	3	53796064	2203	4300	6503	SO:0001583	missense	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388	"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2	1664412	Standard	NM_000720	Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000422281.2:c.3826A>T	3.37:g.53796064A>T	ENSP00000409174:p.Ile1276Phe	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	ENST00000422281.2	37	CCDS46849.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.407489	0.83230	.	.	ENSG00000157388	ENST00000350061;ENST00000288139;ENST00000422281;ENST00000540742	D;D;D;D	0.98849	-5.18;-5.18;-5.18;-5.18	5.59	5.59	0.84812	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99260	0.9742	H	0.94771	3.58	0.80722	D	1	D;P;D;D	0.64830	0.994;0.818;0.99;0.974	D;P;D;D	0.69654	0.965;0.776;0.936;0.913	D	0.99253	1.0888	10	0.87932	D	0	.	11.1717	0.48575	0.9283:0.0:0.0717:0.0	.	1276;183;1276;1296	B0FYA3;F5H313;Q01668;Q01668-2	.;.;CAC1D_HUMAN;.	F	1276;1296;1276;183	ENSP00000288133:I1276F;ENSP00000288139:I1296F;ENSP00000409174:I1276F;ENSP00000438229:I183F	ENSP00000288139:I1296F	I	+	1	0	CACNA1D	53771104	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.859000	0.69539	2.254000	0.74563	0.459000	0.35465	ATC	CACNA1D-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000350556.1		103.522898	0	-5	113	0	0	1	0	NM_000720	37	108.476530	90	0.291339
ZNF304	57343	broad.mit.edu	hg19	19	57868113	57868113	+	Silent	SNP	C	C	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr19:57868113C>T	ENST00000391705.3	+	4	1160	c.876C>T	c.(874-876)caC>caT	p.H292H	ZNF304_ENST00000598744.1_Silent_p.H250H|ZNF304_ENST00000443917.2_Silent_p.H339H|ZNF304_ENST00000282286.5_Silent_p.H292H	NM_020657.2	NP_065708.2	Q9HCX3	ZN304_HUMAN	zinc finger protein 304	292		regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)	TTCACTTGCACCACCTAAAAA	0.418	0	95.0	93.0	94.0	19	57868113	2203	4300	6503	SO:0001819	synonymous_variant	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845	"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840				Standard	XM_005259090	Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.876C>T	19.37:g.57868113C>T			ENST00000282286.5	37	CCDS12950.1																																																																																			ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		39.700664	0	6	78	0	0	1	0		15	42.100835	39	0.277778
SAP30BP	29115	broad.mit.edu	hg19	17	73695881	73695881	+	Missense_Mutation	SNP	T	T	C			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr17:73695881T>C	ENST00000584667.1	+	5	583	c.326T>C	c.(325-327)gTt>gCt	p.V109A	SAP30BP_ENST00000579864.1_3'UTR|SAP30BP_ENST00000355423.3_Missense_Mutation_p.V93A	NM_013260.6	NP_037392.1	Q9UHR5	S30BP_HUMAN	SAP30 binding protein	109		apoptosis|induction of apoptosis|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)	17	all_cancers(13;6.42e-08)		all cancers(21;4.25e-07)|Epithelial(20;9.57e-07)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		TCTGAAAGAGTTCGGAACATG	0.453	0	123.0	135.0	131.0	17	73695881	2203	4300	6503	SO:0001583	missense	AY082382	CCDS11726.1	17q25.1	2006-01-05				ENSG00000161526		30785	protein-coding gene	gene with protein product		610218			15496587	Standard	NM_013260	Approved	HCNGP, HTRG, HTRP	uc002jpe.3	Q9UHR5		ENST00000584667.1:c.326T>C	17.37:g.73695881T>C	ENSP00000462116:p.Val109Ala		ENST00000584667.1	37	CCDS11726.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.898561	0.72639	.	.	ENSG00000161526	ENST00000355423;ENST00000542343;ENST00000293208	.	.	.	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.54029	0.1833	L	0.59436	1.845	0.80722	D	1	P;B	0.36837	0.571;0.435	B;B	0.39027	0.288;0.104	T	0.52056	-0.8626	9	0.08179	T	0.78	0.2873	15.7741	0.78198	0.0:0.0:0.0:1.0	.	93;109	Q9UHR5-2;Q9UHR5	.;S30BP_HUMAN	A	109;109;93	.	ENSP00000293208:V93A	V	+	2	0	SAP30BP	71207476	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.455000	0.80726	2.111000	0.64477	0.533000	0.62120	GTT	SAP30BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448227.1		-9.440121	0	-25	139	0	0	1	0	NM_013260	9	20.644623	140	0.060403
ATP8B3	148229	ucsc.edu	hg19	19	1809699	1809699	+	Silent	SNP	G	G	T			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903																										GCCCGTTGTAGGCACGGTTGT	0.632	0	55.0	65.0	62.0	19	1809699	1984	4153	6137	SO:0001819	synonymous_variant	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270	"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""		11015572	Standard	NM_138813	Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.345C>A	19.37:g.1809699G>T		Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	g	7.561	0.664698	0.14710	.	.	ENSG00000130270	ENST00000533993	.	.	.	4.44	2.08	0.27032	.	.	.	.	.	T	0.36963	0.0986	.	.	.	0.19300	N	0.999973	.	.	.	.	.	.	T	0.35425	-0.9789	5	0.87932	D	0	.	3.8307	0.08873	0.2731:0.0:0.536:0.1909	.	.	.	.	H	78	.	ENSP00000444334:P78H	P	-	2	0	ATP8B3	1760699	0.331000	0.24713	0.008000	0.14137	0.005000	0.04900	0.548000	0.23314	0.864000	0.35578	0.561000	0.74099	CCT	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1				17	39					NM_138813	4		16	
OCLN	100506658	broad.mit.edu	hg19	5	68809848	68809848	+	Missense_Mutation	SNP	G	G	A			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr5:68809848G>A	ENST00000355237.2	+	4	1239	c.803G>A	c.(802-804)cGa>cAa	p.R268Q	OCLN_ENST00000380766.2_Intron|OCLN_ENST00000538151.1_Missense_Mutation_p.R17Q|OCLN_ENST00000396442.2_Missense_Mutation_p.R268Q|OCLN_ENST00000542132.1_Intron	NM_002538.3	NP_002529.1	Q16625	OCLN_HUMAN	occludin	268	MARVEL.	cellular component disassembly involved in apoptosis|protein complex assembly	integral to membrane|tight junction	protein binding|structural molecule activity	endometrium(2)|large_intestine(1)|liver(1)|prostate(1)|skin(1)	6		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)	GTGAAAACTCGAAGAAAGATG	0.398	0	116.0	110.0	112.0	5	68809848	2203	4300	6503	SO:0001583	missense	U49184	CCDS4006.1, CCDS54864.1	5q13.1	2014-06-13			ENSG00000197822	ENSG00000197822		8104	protein-coding gene	gene with protein product	"""tight junction protein occludin TM4 minus"", ""phosphatase 1, regulatory subunit 115"""	602876			8601611	Standard	NM_002538	Approved	PPP1R115	uc003jwu.3	Q16625	OTTHUMG00000099356	ENST00000355237.2:c.803G>A	5.37:g.68809848G>A	ENSP00000347379:p.Arg268Gln	B5BU70|D2DU64|D2DU65|D2IGC0|D2IGC1|E2CYV9|Q5U1V4|Q8N6K1	ENST00000355237.2	37	CCDS4006.1	.	.	.	.	.	.	.	.	.	.	G	32	5.110377	0.94292	.	.	ENSG00000197822	ENST00000355237;ENST00000396442;ENST00000538151	T;T	0.60920	0.15;0.15	5.84	4.97	0.65823	Marvel (1);	0.059384	0.64402	N	0.000001	T	0.77315	0.4112	M	0.82323	2.585	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81212	-0.1035	10	0.87932	D	0	-23.569	13.9828	0.64315	0.0741:0.0:0.9259:0.0	.	268	Q16625	OCLN_HUMAN	Q	268;268;17	ENSP00000347379:R268Q;ENSP00000379719:R268Q	ENSP00000347379:R268Q	R	+	2	0	OCLN	68845604	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.407000	0.97325	1.472000	0.48140	0.591000	0.81541	CGA	OCLN-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216794.1		61.189517	0	15	71	0	0	1	0	NM_002538	20	61.795845	32	0.384615
CSMD3	114788	broad.mit.edu	hg19	8	113585861	113585861	+	Missense_Mutation	SNP	G	G	C	rs143652338		TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr8:113585861G>C	ENST00000297405.5	-	24	4155	c.3911C>G	c.(3910-3912)aCt>aGt	p.T1304S	CSMD3_ENST00000455883.2_Missense_Mutation_p.T1200S|CSMD3_ENST00000343508.3_Missense_Mutation_p.T1264S|CSMD3_ENST00000352409.3_Missense_Mutation_p.T1304S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1304	CUB 7.		integral to membrane|plasma membrane		breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646					TAGTAGATGAGTCGTTTTATC	0.328	0	98.0	97.0	98.0	8	113585861	2203	4300	6503	SO:0001583	missense	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796		19291	protein-coding gene	gene with protein product		608399				Standard	NM_052900	Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3911C>G	8.37:g.113585861G>C	ENSP00000297405:p.Thr1304Ser	Q96PZ3	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928516	0.34002	0.0	1.16E-4	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.23950	1.88;1.88;1.88;1.88;1.88	4.85	4.85	0.62838	CUB (5);	0.079522	0.53938	D	0.000058	T	0.06735	0.0172	N	0.00133	-2.03	0.38516	D	0.948603	B;B;B	0.21688	0.059;0.03;0.0	B;B;B	0.23018	0.042;0.043;0.002	T	0.36720	-0.9736	10	0.08837	T	0.75	.	18.1525	0.89678	0.0:0.0:1.0:0.0	.	1200;1304;1264	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	S	1264;1304;644;1200;1304	ENSP00000345799:T1264S;ENSP00000297405:T1304S;ENSP00000341558:T644S;ENSP00000412263:T1200S;ENSP00000343124:T1304S	ENSP00000297405:T1304S	T	-	2	0	CSMD3	113655037	1.000000	0.71417	0.985000	0.45067	0.930000	0.56654	9.411000	0.97342	2.496000	0.84212	0.591000	0.81541	ACT	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1		37.202915	0	13	90	0	0	1	0	NM_052900	20	55.113244	123	0.139860
MBNL2	10150	broad.mit.edu	hg19	13	97986550	97986550	+	Missense_Mutation	SNP	C	C	G			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr13:97986550C>G	ENST00000345429.6	+	3	976	c.195C>G	c.(193-195)aaC>aaG	p.N65K	MBNL2_ENST00000445661.2_Missense_Mutation_p.N65K|MBNL2_ENST00000376673.3_Missense_Mutation_p.N65K|MBNL2_ENST00000343600.4_Missense_Mutation_p.N65K|MBNL2_ENST00000397601.1_Missense_Mutation_p.N65K	NM_144778.3	NP_659002.1	Q5VZF2	MBNL2_HUMAN	muscleblind-like splicing regulator 2	65		mRNA processing|regulation of RNA splicing|RNA splicing	cytoplasm|nucleus	RNA binding|zinc ion binding	endometrium(4)|large_intestine(4)|lung(7)|prostate(1)|skin(1)	17	all_neural(89;0.0982)|Medulloblastoma(90;0.163)|Lung SC(71;0.184)		BRCA - Breast invasive adenocarcinoma(86;0.218)		CGAGAGAGAACTGCAAGTATC	0.398	0	77.0	73.0	74.0	13	97986550	2203	4300	6503	SO:0001583	missense	AF061261	CCDS9483.1, CCDS9484.1	13q31.1	2013-01-18	2012-02-23		ENSG00000139793	ENSG00000139793	"""Zinc fingers, CCCH-type domain containing"""	16746	protein-coding gene	gene with protein product		607327	"""muscleblind-like 2 (Drosophila)"""		11929853	Standard	NM_207304	Approved	MBLL, MBLL39	uc001vmz.4	Q5VZF2	OTTHUMG00000017239	ENST00000345429.6:c.195C>G	13.37:g.97986550C>G	ENSP00000267287:p.Asn65Lys	Q3SXY5|Q58F19|Q8NEV3|Q8TD82	ENST00000345429.6	37	CCDS9484.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357725	0.41801	.	.	ENSG00000139793	ENST00000397601;ENST00000343600;ENST00000345429;ENST00000376673;ENST00000445661	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	5.88	5.03	0.67393	Zinc finger, CCCH-type (2);	0.089398	0.85682	D	0.000000	T	0.49372	0.1553	L	0.28649	0.875	0.41617	D	0.988941	D;B;B;P	0.61080	0.989;0.032;0.007;0.865	D;B;B;P	0.68483	0.958;0.057;0.035;0.799	T	0.39722	-0.9600	10	0.41790	T	0.15	.	12.711	0.57089	0.0:0.8707:0.0:0.1293	.	65;65;65;65	B4E3F7;Q5VZF2;A2A3S3;Q5VZF2-2	.;MBNL2_HUMAN;.;.	K	65	ENSP00000380726:N65K;ENSP00000344214:N65K;ENSP00000267287:N65K;ENSP00000365861:N65K;ENSP00000406842:N65K	ENSP00000344214:N65K	N	+	3	2	MBNL2	96784551	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.191000	0.42640	2.805000	0.96524	0.551000	0.68910	AAC	MBNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045525.1		-3.318080	0	-2	66	0	0	1	0	NM_144778	3	7.078099	48	0.058824
PANK1	53354	broad.mit.edu	hg19	10	91404916	91404916	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr10:91404916delC	ENST00000307534.4	-	1	299	c.144delG	c.(142-144)gggfs	p.G48fs		NM_148977.2	NP_683878.1	Q8TE04	PANK1_HUMAN	pantothenate kinase 1	48		coenzyme A biosynthetic process|pantothenate metabolic process	cytosol|nucleus	ATP binding|pantothenate kinase activity	cervix(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)	11					TCCCCGCGCACCCCCAGCCGG	0.786	0	3.0	4.0	4.0	10	91404916	1257	2904	4161	SO:0001589	frameshift_variant	AF355198	CCDS7405.1, CCDS7406.1, CCDS31244.1	10q23.31	2008-05-14	2002-11-13	2002-11-15	ENSG00000152782	ENSG00000152782		8598	protein-coding gene	gene with protein product		606160	"""pantothenate kinase"""	PANK	11809413	Standard	NM_148977	Approved	MGC24596, PANK1a, PANK1b	uc001kgp.2	Q8TE04	OTTHUMG00000018718	ENST00000307534.4:c.144delG	10.37:g.91404916delC	ENSP00000302108:p.Gly48fs	A6NIP0|Q7RTX6|Q7Z495|Q8TBQ8	ENST00000307534.4	37	CCDS31244.1																																																																																			PANK1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		.	.		-4	6						5		2	0.71
MCRS1	10445	broad.mit.edu	hg19	12	49959401	49959401	+	Frame_Shift_Del	DEL	C	C	-			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr12:49959401delC	ENST00000550165.1	-	5	465	c.199delG	c.(199-201)gcafs	p.A67fs	MCRS1_ENST00000546244.1_5'UTR|MCRS1_ENST00000357123.4_Frame_Shift_Del_p.A80fs|MCRS1_ENST00000343810.4_Frame_Shift_Del_p.A67fs			Q96EZ8	MCRS1_HUMAN	microspherule protein 1	67	Ser-rich.	DNA recombination|DNA repair|protein modification process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|Ino80 complex|MLL1 complex|nucleolus	protein binding	breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)	23					GAAGATTTTGCCAGGCTGCTC	0.562	0	153.0	162.0	159.0	12	49959401	2203	4300	6503	SO:0001589	frameshift_variant	BC011794	CCDS8787.1, CCDS31795.1, CCDS61118.1	12q13.12	2011-07-06				ENSG00000187778	"""INO80 complex subunits"""	6960	protein-coding gene	gene with protein product	"""INO80 complex subunit Q"""	609504			9765390, 9654073	Standard	NM_006337	Approved	ICP22BP, MSP58, P78, MCRS2, INO80Q	uc001rui.1	Q96EZ8		ENST00000550165.1:c.199delG	12.37:g.49959401delC	ENSP00000448056:p.Ala67fs	O14742|O75497|Q6VN53|Q7Z372	ENST00000550165.1	37	CCDS8787.1																																																																																			MCRS1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405102.1	.	.		3	176					NM_006337	67		113	0.37
RP11-114H24.7	0	broad.mit.edu	hg19	15	78215207	78215207	+	RNA	DEL	C	C	-			TCGA-WC-AA9E-01A-11D-A39W-08	TCGA-WC-AA9E-10A-01D-A39Z-08							Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	afccff1a-7b6e-4def-ba95-5e8089668317	7ef509a4-bb46-49f5-9e51-48bf5c4ca903	g.chr15:78215207delC	ENST00000567226.1	-	0	306																					TTCTTCAGGGCCCCAAGGGGA	0.572	0																																				15.37:g.78215207delC			ENST00000565869.1	37																																																																																				RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1	.	.		-4	31						12		11	0.52