#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
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	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_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	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_Transcript_Id	i_Trna_alt1	i_Trna_alt2	i_Trna_ref	i_Trna_tot	i_Trna_var	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ALPL	249	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	21889674	21889674	+	Silent	SNP	C	C	A	rs201342272		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:21889674C>A	ENST00000374840.3	+	5	619	c.369C>A	c.(367-369)gcC>gcA	p.A123A	ALPL_ENST00000374832.1_Silent_p.A123A|ALPL_ENST00000539907.1_Silent_p.A46A|ALPL_ENST00000540617.1_Silent_p.A68A|ALPL_ENST00000425315.2_Silent_p.A123A|ALPL_ENST00000468526.1_3'UTR	NM_000478.4	NP_000469.3	P05186	PPBT_HUMAN	alkaline phosphatase, liver/bone/kidney	123					cellular response to organic cyclic compound (GO:0071407)|cementum mineralization (GO:0071529)|developmental process involved in reproduction (GO:0003006)|endochondral ossification (GO:0001958)|osteoblast differentiation (GO:0001649)|response to antibiotic (GO:0046677)|response to glucocorticoid (GO:0051384)|response to lipopolysaccharide (GO:0032496)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)	anchored component of membrane (GO:0031225)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(11)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	26		all_lung(284;2.19e-05)|Lung NSC(340;2.22e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;8.7e-28)|COAD - Colon adenocarcinoma(152;1.57e-05)|GBM - Glioblastoma multiforme(114;2.66e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000177)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00856)|READ - Rectum adenocarcinoma(331;0.0623)|Lung(427;0.146)	Amifostine(DB01143)|Fospropofol(DB06716)	GGGTGAAGGCCAATGAGGGCA	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		17698	0.0		0.0	False		,,,				2504	0.001				p.A123A		.											.	ALPL-94	0			c.C369A						.						84.0	75.0	78.0					1																	21889674		2203	4300	6503	SO:0001819	synonymous_variant	249	exon5			GAAGGCCAATGAG	BC021289	CCDS217.1, CCDS53274.1, CCDS53275.1	1p36.12	2008-02-05			ENSG00000162551	ENSG00000162551	3.1.3.1		438	protein-coding gene	gene with protein product		171760		HOPS		3532105, 3446011	Standard	NM_001127501		Approved	TNSALP	uc001bet.3	P05186	OTTHUMG00000002949	ENST00000374840.3:c.369C>A	1.37:g.21889674C>A		Somatic	263	0		WXS	Illumina HiSeq	Phase_I	179	71	NM_000478	0	0	2	48	46	A1A4E7|B2RMP8|B7Z387|B7Z4Y6|O75090|Q2TAI7|Q59EJ7|Q5BKZ5|Q5VTG5|Q6NZI8|Q8WU32|Q9UBK0	Silent	SNP	ENST00000374840.3	37	CCDS217.1																																																																																			C|0.999;A|0.001		0.652	ALPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008202.1	NM_000478	
FAM46B	115572	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	27333078	27333078	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:27333078A>T	ENST00000289166.5	-	2	800	c.635T>A	c.(634-636)tTt>tAt	p.F212Y		NM_052943.3	NP_443175.2	Q96A09	FA46B_HUMAN	family with sequence similarity 46, member B	212										breast(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10		all_cancers(24;1.29e-21)|all_epithelial(13;2.35e-19)|Colorectal(325;0.000147)|all_lung(284;0.00122)|Lung NSC(340;0.00128)|Breast(348;0.00131)|Renal(390;0.00211)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0707)|all_neural(195;0.0966)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;7.71e-51)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-29)|Colorectal(126;5.31e-09)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000272)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|STAD - Stomach adenocarcinoma(196;0.00114)|READ - Rectum adenocarcinoma(331;0.0419)		GCTGAATTCAAACTGGCGTCT	0.552																																					p.F212Y		.											.	FAM46B-90	0			c.T635A						.						108.0	110.0	110.0					1																	27333078		2203	4300	6503	SO:0001583	missense	115572	exon2			AATTCAAACTGGC	AK122816	CCDS294.2	1p35.3	2008-02-05			ENSG00000158246	ENSG00000158246			28273	protein-coding gene	gene with protein product						12477932	Standard	NM_052943		Approved	MGC16491	uc010ofj.2	Q96A09	OTTHUMG00000004278	ENST00000289166.5:c.635T>A	1.37:g.27333078A>T	ENSP00000289166:p.Phe212Tyr	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	53	16	NM_052943	0	0	1	6	5		Missense_Mutation	SNP	ENST00000289166.5	37	CCDS294.2	.	.	.	.	.	.	.	.	.	.	A	24.2	4.507004	0.85282	.	.	ENSG00000158246	ENST00000289166	T	0.28454	1.61	5.2	5.2	0.72013	Domain of unknown function DUF1693 (1);	0.045170	0.85682	D	0.000000	T	0.57066	0.2028	M	0.79614	2.46	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.61133	-0.7124	10	0.56958	D	0.05	-1.9476	15.2153	0.73261	1.0:0.0:0.0:0.0	.	212	Q96A09	FA46B_HUMAN	Y	212	ENSP00000289166:F212Y	ENSP00000289166:F212Y	F	-	2	0	FAM46B	27205665	1.000000	0.71417	0.999000	0.59377	0.970000	0.65996	9.135000	0.94478	2.178000	0.69098	0.459000	0.35465	TTT	.		0.552	FAM46B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012347.2	NM_052943	
C1orf94	84970	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	34643683	34643683	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:34643683G>C	ENST00000488417.1	+	1	413	c.293G>C	c.(292-294)aGa>aCa	p.R98T	AC115286.1_ENST00000408126.1_RNA|C1orf94_ENST00000373374.3_Intron	NM_001134734.1	NP_001128206.1	Q6P1W5	CA094_HUMAN	chromosome 1 open reading frame 94	98										central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(15)|skin(4)|upper_aerodigestive_tract(2)	32		Myeloproliferative disorder(586;0.0393)				GGAACTCTAAGAGGCAATGAG	0.537																																					p.R98T		.											.	C1orf94-90	0			c.G293C						.						73.0	69.0	70.0					1																	34643683		692	1591	2283	SO:0001583	missense	84970	exon1			CTCTAAGAGGCAA	AK123355	CCDS381.1, CCDS44108.1	1p34.3	2012-06-26			ENSG00000142698	ENSG00000142698			28250	protein-coding gene	gene with protein product						12477932	Standard	NM_001134734		Approved	MGC15882	uc001bxt.3	Q6P1W5	OTTHUMG00000004012	ENST00000488417.1:c.293G>C	1.37:g.34643683G>C	ENSP00000435634:p.Arg98Thr	Somatic	133	0		WXS	Illumina HiSeq	Phase_I	77	24	NM_001134734	0	0	0	0	0	B3KVT1|D3DPR3|E9PJ76|Q96IC8	Missense_Mutation	SNP	ENST00000488417.1	37	CCDS44108.1	.	.	.	.	.	.	.	.	.	.	G	0.083	-1.180380	0.01633	.	.	ENSG00000142698	ENST00000488417	T	0.44881	0.91	4.99	2.08	0.27032	.	.	.	.	.	T	0.26666	0.0652	N	0.22421	0.69	0.09310	N	1	B	0.12013	0.005	B	0.10450	0.005	T	0.23261	-1.0193	9	0.66056	D	0.02	.	5.0027	0.14273	0.1877:0.173:0.6393:0.0	.	98	Q6P1W5	CA094_HUMAN	T	98	ENSP00000435634:R98T	ENSP00000435634:R98T	R	+	2	0	C1orf94	34416270	0.867000	0.29959	0.005000	0.12908	0.004000	0.04260	1.134000	0.31442	0.277000	0.22141	0.655000	0.94253	AGA	.		0.537	C1orf94-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036845.2	NM_032884	
ZCCHC11	23318	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	52897102	52897102	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:52897102G>T	ENST00000371544.3	-	28	4553	c.4291C>A	c.(4291-4293)Cag>Aag	p.Q1431K	ZCCHC11_ENST00000257177.4_Missense_Mutation_p.Q1432K	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	1431	Gln-rich.|Pro-rich.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						GGAAATGGCTGAGGCTGAGGA	0.393																																					p.Q1432K		.											.	ZCCHC11-93	0			c.C4294A						.						32.0	29.0	30.0					1																	52897102		2203	4298	6501	SO:0001583	missense	23318	exon28			ATGGCTGAGGCTG	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"""Zinc fingers, CCHC domain containing"""	28981	protein-coding gene	gene with protein product	"""TUTase4"""	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.4291C>A	1.37:g.52897102G>T	ENSP00000360599:p.Gln1431Lys	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	60	19	NM_001009881	0	0	3	15	12	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Missense_Mutation	SNP	ENST00000371544.3	37	CCDS30716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.48|15.48	2.847224|2.847224	0.51164|0.51164	.|.	.|.	ENSG00000134744|ENSG00000134744	ENST00000257177;ENST00000371544;ENST00000531722|ENST00000474453	T;T|.	0.46451|.	0.87;0.88|.	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.248184|.	0.35466|.	N|.	0.003196|.	T|.	0.55433|.	0.1920|.	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	D|D	1|1	P|.	0.40144|.	0.704|.	B|.	0.32022|.	0.139|.	T|.	0.50668|.	-0.8801|.	10|.	0.40728|.	T|.	0.16|.	.|.	18.8838|18.8838	0.92367|0.92367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1431|.	Q5TAX3|.	TUT4_HUMAN|.	K|X	1432;1431;269|276	ENSP00000257177:Q1432K;ENSP00000360599:Q1431K|.	ENSP00000257177:Q1432K|.	Q|S	-|-	1|2	0|0	ZCCHC11|ZCCHC11	52669690|52669690	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	5.423000|5.423000	0.66458|0.66458	2.459000|2.459000	0.83118|0.83118	0.557000|0.557000	0.71058|0.71058	CAG|TCA	.		0.393	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288	
HS2ST1	9653	broad.mit.edu	37	1	87570377	87570377	+	Nonstop_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:87570377T>C	ENST00000370550.5	+	7	1432	c.1069T>C	c.(1069-1071)Tga>Cga	p.*357R	RP5-1052I5.2_ENST00000370548.2_Intron|HS2ST1_ENST00000356813.4_Intron	NM_012262.3	NP_036394.1	Q7LGA3	HS2ST_HUMAN	heparan sulfate 2-O-sulfotransferase 1	0					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	sulfotransferase activity (GO:0008146)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)	9		Lung NSC(277;0.153)		all cancers(265;0.00699)|Epithelial(280;0.0261)		TAAGTCGAACTGAGTATAAGG	0.413																																					p.X357R													.	HS2ST1-90	0			c.T1069C						.						29.0	31.0	30.0					1																	87570377		2203	4296	6499	SO:0001578	stop_lost	9653	exon7			TCGAACTGAGTAT	AB007917	CCDS711.1, CCDS44171.1	1p22.3	2008-02-05			ENSG00000153936	ENSG00000153936		"""Sulfotransferases, membrane-bound"""	5193	protein-coding gene	gene with protein product		604844				9455484	Standard	NM_012262		Approved	KIAA0448	uc010osk.2	Q7LGA3	OTTHUMG00000010255	ENST00000370550.5:c.1069T>C	1.37:g.87570377T>C	ENSP00000359581:p.*357Argext*2	Somatic	24	0		WXS	Illumina HiSeq	Phase_I	41	13	NM_012262	0	0	2	3	1	D3DT22|O75036|Q32NB5|Q8TAC5|Q9H441|Q9NUJ9	Missense_Mutation	SNP	ENST00000370550.5	37	CCDS711.1	.	.	.	.	.	.	.	.	.	.	T	14.15	2.450662	0.43531	.	.	ENSG00000153936	ENST00000370550	.	.	.	5.83	4.67	0.58626	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.2373	0.54522	0.1275:0.0:0.0:0.8724	.	.	.	.	R	357	.	.	X	+	1	0	HS2ST1	87342965	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.841000	0.86834	0.986000	0.38683	0.528000	0.53228	TGA	.		0.413	HS2ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028279.2	NM_012262	
RUSC1	23623	broad.mit.edu	37	1	155292770	155292770	+	Silent	SNP	A	A	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:155292770A>C	ENST00000368352.5	+	2	1357	c.1206A>C	c.(1204-1206)ccA>ccC	p.P402P	RUSC1_ENST00000368349.4_5'Flank|RUSC1-AS1_ENST00000446880.1_RNA|RUSC1_ENST00000292254.4_5'Flank|RUSC1-AS1_ENST00000543656.1_RNA|RUSC1-AS1_ENST00000443642.1_RNA|RUSC1_ENST00000368354.3_Silent_p.P402P|RUSC1_ENST00000368347.4_5'Flank|RUSC1-AS1_ENST00000450199.1_RNA	NM_001105203.1	NP_001098673.1	Q9BVN2	RUSC1_HUMAN	RUN and SH3 domain containing 1	402					positive regulation of signal transduction (GO:0009967)|protein polyubiquitination (GO:0000209)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(2)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(2)|skin(1)|urinary_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;1.55e-10)|all cancers(21;4.15e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)			CCCGGCCCCCACCCCCGCCTG	0.726																																					p.P402P													.	RUSC1-92	0			c.A1206C						.																																			SO:0001819	synonymous_variant	23623	exon2			GCCCCCACCCCCG	AB026894	CCDS1112.1, CCDS41410.1, CCDS41411.1, CCDS41412.1	1q21-q22	2011-04-28			ENSG00000160753	ENSG00000160753			17153	protein-coding gene	gene with protein product						10760598	Standard	NM_001105203		Approved	NESCA	uc001fkj.2	Q9BVN2	OTTHUMG00000013910	ENST00000368352.5:c.1206A>C	1.37:g.155292770A>C		Somatic	17	4		WXS	Illumina HiSeq	Phase_I	24	8	NM_001105203	0	0	0	0	0	B3KWM9|Q5T9U9|Q5T9V0|Q5T9V1|Q5T9V2|Q9UPY4|Q9Y4T5	Silent	SNP	ENST00000368352.5	37	CCDS41410.1																																																																																			.		0.726	RUSC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039071.1		
RABIF	5877	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	202850297	202850297	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:202850297C>T	ENST00000367262.3	-	2	217	c.181G>A	c.(181-183)Gac>Aac	p.D61N		NM_002871.4	NP_002862.2	P47224	MSS4_HUMAN	RAB interacting factor	61					membrane fusion (GO:0061025)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)	4			BRCA - Breast invasive adenocarcinoma(75;0.166)			AGATCGCCGTCAGGATTGCTG	0.507																																					p.D61N		.											.	RABIF-227	0			c.G181A						.						68.0	64.0	65.0					1																	202850297		2203	4300	6503	SO:0001583	missense	5877	exon2			CGCCGTCAGGATT	S78873	CCDS1428.1	1q32.1	2008-05-14			ENSG00000183155	ENSG00000183155			9797	protein-coding gene	gene with protein product		603417		RASGRF3		9441742, 7619808	Standard	NM_002871		Approved	mss4	uc001gyl.3	P47224	OTTHUMG00000041400	ENST00000367262.3:c.181G>A	1.37:g.202850297C>T	ENSP00000356231:p.Asp61Asn	Somatic	63	0		WXS	Illumina HiSeq	Phase_I	48	18	NM_002871	0	0	10	14	4	B2R4P4|Q92992	Missense_Mutation	SNP	ENST00000367262.3	37	CCDS1428.1	.	.	.	.	.	.	.	.	.	.	C	10.55	1.382058	0.24944	.	.	ENSG00000183155	ENST00000367262	.	.	.	5.75	4.84	0.62591	Mss4-like (1);Mss4/translationally controlled tumour-associated TCTP (1);	0.332353	0.37136	N	0.002226	T	0.55955	0.1953	L	0.40543	1.245	0.80722	D	1	B	0.25809	0.135	B	0.29176	0.099	T	0.55528	-0.8127	9	0.51188	T	0.08	-57.0511	14.6684	0.68926	0.0:0.9296:0.0:0.0704	.	61	P47224	MSS4_HUMAN	N	61	.	ENSP00000356231:D61N	D	-	1	0	RABIF	201116920	1.000000	0.71417	0.009000	0.14445	0.008000	0.06430	5.492000	0.66893	1.447000	0.47661	-0.254000	0.11334	GAC	.		0.507	RABIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099183.1		
CENPF	1063	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	214826247	214826247	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:214826247T>C	ENST00000366955.3	+	16	8405	c.8237T>C	c.(8236-8238)aTa>aCa	p.I2746T	CENPF_ENST00000467765.1_3'UTR	NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	2842	Sufficient for centromere localization.|Sufficient for self-association.				cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		AAGCTGGAGATAGACCTTTTA	0.328																																					p.I2746T	Colon(80;575 1284 11000 14801 43496)	.											.	CENPF-567	0			c.T8237C						.						91.0	94.0	93.0					1																	214826247		2203	4300	6503	SO:0001583	missense	1063	exon16			TGGAGATAGACCT	U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.8237T>C	1.37:g.214826247T>C	ENSP00000355922:p.Ile2746Thr	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	120	25	NM_016343	0	0	2	2	0	Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	T	11.84	1.757432	0.31137	.	.	ENSG00000117724	ENST00000366955;ENST00000391896	T	0.04234	3.67	3.93	3.93	0.45458	.	.	.	.	.	T	0.05410	0.0143	L	0.47716	1.5	0.20489	N	0.999898	B	0.33694	0.421	B	0.22152	0.038	T	0.28106	-1.0054	9	0.42905	T	0.14	.	11.9872	0.53155	0.0:0.0:0.0:1.0	.	2842	P49454	CENPF_HUMAN	T	2746;145	ENSP00000355922:I2746T	ENSP00000355922:I2746T	I	+	2	0	CENPF	212892870	0.990000	0.36364	0.042000	0.18584	0.923000	0.55619	3.757000	0.55212	1.429000	0.47314	0.418000	0.28097	ATA	.		0.328	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1	NM_016343	
OBSCN	84033	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	228511117	228511117	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:228511117G>A	ENST00000422127.1	+	56	15506	c.15462G>A	c.(15460-15462)atG>atA	p.M5154I	OBSCN_ENST00000570156.2_Missense_Mutation_p.M6111I|OBSCN_ENST00000366707.4_Missense_Mutation_p.M2788I|OBSCN_ENST00000366709.4_Missense_Mutation_p.M2273I|OBSCN_ENST00000284548.11_Missense_Mutation_p.M5154I	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	5154	Ig-like 49.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTCAGCCCATGCCCAGTGTGC	0.522																																					p.M6111I		.											.	OBSCN-403	0			c.G18333A						.						92.0	94.0	93.0					1																	228511117		2155	4253	6408	SO:0001583	missense	84033	exon67			GCCCATGCCCAGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.15462G>A	1.37:g.228511117G>A	ENSP00000409493:p.Met5154Ile	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	102	23	NM_001271223	0	0	1	1	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431705	0.25813	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709	T;T;T;T	0.66638	-0.22;-0.22;-0.22;-0.22	5.07	5.07	0.68467	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.660669	0.14435	N	0.319744	T	0.46034	0.1372	N	0.04959	-0.14	0.27969	N	0.936468	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.13629	-1.0502	10	0.16896	T	0.51	.	15.681	0.77367	0.0:0.2016:0.7984:0.0	.	5154;5154	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	I	5154;5154;2788;2273	ENSP00000284548:M5154I;ENSP00000409493:M5154I;ENSP00000355668:M2788I;ENSP00000355670:M2273I	ENSP00000284548:M5154I	M	+	3	0	OBSCN	226577740	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	1.113000	0.31184	2.629000	0.89072	0.655000	0.94253	ATG	.		0.522	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
OR2W3	343171	hgsc.bcm.edu	37	1	248059782	248059782	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:248059782G>A	ENST00000360358.3	+	1	894	c.894G>A	c.(892-894)aaG>aaA	p.K298K	OR2W3_ENST00000537741.1_Silent_p.K298K	NM_001001957.2	NP_001001957.2	Q7Z3T1	OR2W3_HUMAN	olfactory receptor, family 2, subfamily W, member 3	298						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)	49	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GAGAGGTGAAGGGGGCACTGG	0.537																																					p.K298K		.											.	OR2W3-115	0			c.G894A						.						39.0	40.0	40.0					1																	248059782		2203	4300	6503	SO:0001819	synonymous_variant	343171	exon1			GGTGAAGGGGGCA	N75737	CCDS31099.1	1q44	2012-08-09		2004-03-10	ENSG00000238243	ENSG00000238243		"""GPCR / Class A : Olfactory receptors"""	15021	protein-coding gene	gene with protein product				OR2W8P, OR2W3P		14983052	Standard	NM_001001957		Approved	OST718	uc010pzb.2	Q7Z3T1	OTTHUMG00000040204	ENST00000360358.3:c.894G>A	1.37:g.248059782G>A		Somatic	111	0		WXS	Illumina HiSeq	Phase_I	80	5	NM_001001957	0	0	0	0	0	Q6IF06|Q8NG86	Silent	SNP	ENST00000360358.3	37	CCDS31099.1																																																																																			.		0.537	OR2W3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096861.1	NM_001001957	
MLLT10	8028	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	21970293	21970293	+	Missense_Mutation	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:21970293T>A	ENST00000307729.7	+	12	1832	c.1654T>A	c.(1654-1656)Tgc>Agc	p.C552S	MLLT10_ENST00000377072.3_Missense_Mutation_p.C552S|MLLT10_ENST00000446906.2_Missense_Mutation_p.C552S|MLLT10_ENST00000377059.3_Missense_Mutation_p.C552S			P55197	AF10_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10	552	DNA-binding.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						TGATGGAGcttgcccaacaac	0.428			T	"""MLL, PICALM, CDK6"""	AL																																p.C552S		.		Dom	yes		10	10p12	8028	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 10 (AF10)"""		L	.	MLLT10-658	0			c.T1654A						.						118.0	114.0	115.0					10																	21970293		2203	4300	6503	SO:0001583	missense	8028	exon11			GGAGCTTGCCCAA	U13948	CCDS7135.1, CCDS55706.1, CCDS55707.1, CCDS55708.1	10p12	2013-01-28	2001-11-28		ENSG00000078403	ENSG00000078403		"""Zinc fingers, PHD-type"""	16063	protein-coding gene	gene with protein product		602409	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 10"""			7888665	Standard	NM_004641		Approved	AF10	uc021pny.1	P55197	OTTHUMG00000017799	ENST00000307729.7:c.1654T>A	10.37:g.21970293T>A	ENSP00000307411:p.Cys552Ser	Somatic	88	0		WXS	Illumina HiSeq	Phase_I	97	29	NM_001195626	0	0	0	1	1	B1ANA8|Q5JT37|Q5VX90|Q66K63	Missense_Mutation	SNP	ENST00000307729.7	37	CCDS55708.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.266891	0.23136	.	.	ENSG00000078403	ENST00000377072;ENST00000446906;ENST00000307729;ENST00000396529;ENST00000377059;ENST00000438473;ENST00000538639	T;T;T;T	0.14766	2.5;2.48;2.48;2.48	4.67	4.67	0.58626	.	0.392955	0.33309	N	0.005051	T	0.08670	0.0215	L	0.38175	1.15	0.48135	D	0.999596	B;B;B;B	0.33694	0.008;0.001;0.421;0.0	B;B;B;B	0.21360	0.004;0.0;0.034;0.001	T	0.22034	-1.0228	10	0.13470	T	0.59	.	10.6549	0.45669	0.0:0.0:0.0:1.0	.	247;552;552;552	Q5HYC6;E9PBP4;Q5VX90;P55197	.;.;.;AF10_HUMAN	S	552;552;552;398;552;195;194	ENSP00000366272:C552S;ENSP00000401406:C552S;ENSP00000307411:C552S;ENSP00000366258:C552S	ENSP00000307411:C552S	C	+	1	0	MLLT10	22010299	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	2.116000	0.41930	2.095000	0.63458	0.477000	0.44152	TGC	.		0.428	MLLT10-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047136.1		
ENKUR	219670	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	25288439	25288439	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:25288439G>T	ENST00000331161.4	-	2	333	c.114C>A	c.(112-114)gaC>gaA	p.D38E	ENKUR_ENST00000376363.1_Missense_Mutation_p.D38E	NM_145010.3	NP_659447.1	Q8TC29	ENKUR_HUMAN	enkurin, TRPC channel interacting protein	38						motile cilium (GO:0031514)				endometrium(2)|large_intestine(4)|lung(3)|skin(1)	10						CTTTTTGCATGTCATCTTTTA	0.299																																					p.D38E		.											.	ENKUR-90	0			c.C114A						.						107.0	95.0	99.0					10																	25288439		2201	4297	6498	SO:0001583	missense	219670	exon2			TTGCATGTCATCT	AK095021	CCDS7146.1, CCDS73075.1	10p12.31	2014-08-13	2009-04-28	2009-04-28	ENSG00000151023	ENSG00000151023			28388	protein-coding gene	gene with protein product		611025	"""chromosome 10 open reading frame 63"""	C10orf63		17217053, 15385169	Standard	NM_145010		Approved	MGC26778, enkurin, CFAP106	uc001isg.2	Q8TC29	OTTHUMG00000017827	ENST00000331161.4:c.114C>A	10.37:g.25288439G>T	ENSP00000331044:p.Asp38Glu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	86	19	NM_145010	0	0	0	0	0	A8K8Y0|D3DRV2	Missense_Mutation	SNP	ENST00000331161.4	37	CCDS7146.1	.	.	.	.	.	.	.	.	.	.	G	2.150	-0.394650	0.04899	.	.	ENSG00000151023	ENST00000331161;ENST00000376363	.	.	.	5.98	0.497	0.16902	.	0.090535	0.85682	D	0.000000	T	0.07413	0.0187	N	0.02539	-0.55	0.09310	N	0.999997	B	0.06786	0.001	B	0.01281	0.0	T	0.32079	-0.9920	9	0.02654	T	1	-22.9569	2.4844	0.04595	0.1405:0.2598:0.3993:0.2004	.	38	Q8TC29	ENKUR_HUMAN	E	38	.	ENSP00000331044:D38E	D	-	3	2	ENKUR	25328445	0.018000	0.18449	0.721000	0.30653	0.930000	0.56654	-0.003000	0.12901	0.428000	0.26173	0.591000	0.81541	GAC	.		0.299	ENKUR-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047239.2	NM_145010	
HK1	3098	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	71136714	71136714	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:71136714G>T	ENST00000359426.6	+	8	1004	c.900G>T	c.(898-900)atG>atT	p.M300I	HK1_ENST00000404387.2_Missense_Mutation_p.M304I|HK1_ENST00000298649.3_Missense_Mutation_p.M299I|HK1_ENST00000360289.2_Missense_Mutation_p.M288I|HK1_ENST00000494253.1_3'UTR|HK1_ENST00000448642.2_Missense_Mutation_p.M335I	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	300	Hexokinase type-2 1.|Regulatory.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						TCAGTGGCATGTACTTGGGAG	0.567																																					p.M304I		.											.	HK1-252	0			c.G912T						.						163.0	143.0	150.0					10																	71136714		2203	4300	6503	SO:0001583	missense	3098	exon11			TGGCATGTACTTG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.900G>T	10.37:g.71136714G>T	ENSP00000352398:p.Met300Ile	Somatic	236	0		WXS	Illumina HiSeq	Phase_I	255	59	NM_033498	0	0	20	27	7	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Missense_Mutation	SNP	ENST00000359426.6	37	CCDS7292.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413479	0.62511	.	.	ENSG00000156515	ENST00000360289;ENST00000448642;ENST00000404387;ENST00000298649;ENST00000359426;ENST00000405407	T;T;T;T;T	0.12255	2.7;2.7;2.7;2.7;2.7	4.94	4.94	0.65067	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.26011	0.0634	M	0.86573	2.825	0.80722	D	1	B;B;B;B;B;P	0.39717	0.191;0.191;0.004;0.013;0.05;0.684	B;B;B;B;B;B	0.37267	0.243;0.16;0.012;0.089;0.078;0.245	T	0.30880	-0.9963	10	0.72032	D	0.01	-26.1047	18.1516	0.89676	0.0:0.0:1.0:0.0	.	300;300;299;335;304;288	A8K7J7;P19367;P19367-2;E7ENR4;P19367-3;P19367-4	.;HXK1_HUMAN;.;.;.;.	I	288;335;304;299;300;300	ENSP00000353433:M288I;ENSP00000402103:M335I;ENSP00000384774:M304I;ENSP00000298649:M299I;ENSP00000352398:M300I	ENSP00000298649:M299I	M	+	3	0	HK1	70806720	1.000000	0.71417	1.000000	0.80357	0.561000	0.35649	7.941000	0.87700	2.293000	0.77203	0.585000	0.79938	ATG	.		0.567	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
GBF1	8729	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	104103846	104103846	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr10:104103846T>G	ENST00000369983.3	+	4	462	c.202T>G	c.(202-204)Ttt>Gtt	p.F68V		NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	68					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		CCTTCGACCTTTTCTGGAAGT	0.428																																					p.F68V		.											.	GBF1-91	0			c.T202G						.						163.0	145.0	151.0					10																	104103846		2203	4300	6503	SO:0001583	missense	8729	exon4			CGACCTTTTCTGG	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.202T>G	10.37:g.104103846T>G	ENSP00000359000:p.Phe68Val	Somatic	82	0		WXS	Illumina HiSeq	Phase_I	116	27	NM_001199378	0	0	4	5	1	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	37	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	T	29.0	4.967181	0.92855	.	.	ENSG00000107862	ENST00000369983	T	0.68025	-0.3	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.85741	0.5767	M	0.91663	3.23	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.91635	0.998;0.999;0.994;0.999	D	0.88884	0.3341	10	0.87932	D	0	-13.687	16.3736	0.83374	0.0:0.0:0.0:1.0	.	68;68;68;68	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	68	ENSP00000359000:F68V	ENSP00000359000:F68V	F	+	1	0	GBF1	104093836	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	7.922000	0.87538	2.273000	0.75805	0.482000	0.46254	TTT	.		0.428	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
OR52M1	119772	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	4567069	4567069	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:4567069A>T	ENST00000360213.1	+	1	649	c.649A>T	c.(649-651)Att>Ttt	p.I217F		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		CTCAGTGGCTATTGCTGCATC	0.532																																					p.I217F		.											.	OR52M1-68	0			c.A649T						.						267.0	251.0	257.0					11																	4567069		2201	4298	6499	SO:0001583	missense	119772	exon1			GTGGCTATTGCTG	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.649A>T	11.37:g.4567069A>T	ENSP00000353343:p.Ile217Phe	Somatic	155	0		WXS	Illumina HiSeq	Phase_I	144	32	NM_001004137	0	0	0	0	0		Missense_Mutation	SNP	ENST00000360213.1	37	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	A	15.46	2.838966	0.51057	.	.	ENSG00000197790	ENST00000360213	T	0.00333	8.07	5.01	3.86	0.44501	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47852	D	0.000207	T	0.01092	0.0036	H	0.96916	3.905	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.35450	-0.9788	10	0.87932	D	0	.	5.4232	0.16411	0.7442:0.0:0.0856:0.1702	.	217	Q8NGK5	O52M1_HUMAN	F	217	ENSP00000353343:I217F	ENSP00000353343:I217F	I	+	1	0	OR52M1	4523645	1.000000	0.71417	0.265000	0.24526	0.813000	0.45954	4.973000	0.63763	0.995000	0.38917	0.528000	0.53228	ATT	.		0.532	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137	
RIC3	79608	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	8132577	8132577	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:8132577C>T	ENST00000309737.6	-	6	777	c.778G>A	c.(778-780)Gaa>Aaa	p.E260K	RIC3_ENST00000343202.4_Missense_Mutation_p.E259K|RIC3_ENST00000539720.1_Missense_Mutation_p.E211K|RIC3_ENST00000396677.2_Missense_Mutation_p.E98K|RIC3_ENST00000335425.7_Missense_Mutation_p.E78K|RIC3_ENST00000530060.1_5'UTR|RIC3_ENST00000425599.2_Missense_Mutation_p.E179K			Q7Z5B4	RIC3_HUMAN	RIC3 acetylcholine receptor chaperone	260					cellular protein complex assembly (GO:0043623)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein folding (GO:0006457)|synaptic transmission, cholinergic (GO:0007271)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)	17				Epithelial(150;2.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.204)		TCAGCTATTTCTTCAGCAGAA	0.428																																					p.E260K		.											.	RIC3-155	0			c.G778A						.						112.0	111.0	112.0					11																	8132577		2201	4296	6497	SO:0001583	missense	79608	exon6			CTATTTCTTCAGC		CCDS7788.1, CCDS44533.1, CCDS55741.1, CCDS55742.1	11p15.4	2013-08-05	2013-08-05		ENSG00000166405	ENSG00000166405			30338	protein-coding gene	gene with protein product		610509	"""resistance to inhibitors of cholinesterase 3 homolog (C. elegans)"""			12821669	Standard	NM_024557		Approved	FLJ11608, PRO1385, AYST720	uc001mgd.2	Q7Z5B4	OTTHUMG00000165694	ENST00000309737.6:c.778G>A	11.37:g.8132577C>T	ENSP00000308820:p.Glu260Lys	Somatic	192	0		WXS	Illumina HiSeq	Phase_I	231	47	NM_001206671	0	0	1	4	3	B0B1U0|B2RD25|D3DQU5|Q6UX78|Q7Z5B3|Q86T94|Q8TBJ9|Q9HAH8	Missense_Mutation	SNP	ENST00000309737.6	37	CCDS55742.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.626069	0.87560	.	.	ENSG00000166405	ENST00000396677;ENST00000335425;ENST00000343202;ENST00000309737;ENST00000543346;ENST00000539720;ENST00000425599;ENST00000531450	T;T;T;T;T	0.37752	1.24;1.24;1.26;1.18;1.2	6.06	6.06	0.98353	.	0.154914	0.45606	D	0.000353	T	0.57651	0.2068	M	0.72118	2.19	0.51233	D	0.999912	D;D;D;D;D;D	0.67145	0.996;0.971;0.99;0.99;0.99;0.99	P;P;P;P;P;P	0.62560	0.904;0.651;0.817;0.857;0.857;0.766	T	0.58250	-0.7669	10	0.72032	D	0.01	.	16.0307	0.80574	0.0:0.8665:0.1335:0.0	.	288;179;78;260;259;98	B7Z1U4;B0B1U0;Q7Z5B4-3;Q7Z5B4;Q7Z5B4-5;D3DQU6	.;.;.;RIC3_HUMAN;.;.	K	98;78;259;260;288;211;179;288	ENSP00000344904:E259K;ENSP00000308820:E260K;ENSP00000443871:E211K;ENSP00000395320:E179K;ENSP00000431658:E288K	ENSP00000308820:E260K	E	-	1	0	RIC3	8089153	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.792000	0.62467	2.882000	0.98803	0.655000	0.94253	GAA	.		0.428	RIC3-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385900.1	NM_024557	
LRP4	4038	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	46895104	46895104	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:46895104C>G	ENST00000378623.1	-	29	4512	c.4270G>C	c.(4270-4272)Ggg>Cgg	p.G1424R	LRP4-AS1_ENST00000502049.2_RNA|LRP4-AS1_ENST00000531719.1_RNA	NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	1424					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		AGCCCTCGCCCGATCACTGTC	0.572																																					p.G1424R		.											.	LRP4-94	0			c.G4270C						.						80.0	72.0	75.0					11																	46895104		2201	4299	6500	SO:0001583	missense	4038	exon29			CTCGCCCGATCAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.4270G>C	11.37:g.46895104C>G	ENSP00000367888:p.Gly1424Arg	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	84	25	NM_002334	0	0	3	5	2	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.347774	0.82022	.	.	ENSG00000134569	ENST00000378623	D	0.95690	-3.78	5.91	5.91	0.95273	Six-bladed beta-propeller, TolB-like (1);	0.048798	0.85682	D	0.000000	D	0.91975	0.7458	N	0.12527	0.23	0.80722	D	1	P	0.35107	0.484	B	0.41088	0.347	D	0.89603	0.3836	10	0.22706	T	0.39	.	20.2985	0.98592	0.0:1.0:0.0:0.0	.	1424	O75096	LRP4_HUMAN	R	1424	ENSP00000367888:G1424R	ENSP00000367888:G1424R	G	-	1	0	LRP4	46851680	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	5.943000	0.70211	2.793000	0.96121	0.655000	0.94253	GGG	.		0.572	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
BRMS1	25855	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	11	66108763	66108763	+	Missense_Mutation	SNP	T	T	A	rs199933125	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:66108763T>A	ENST00000359957.3	-	4	432	c.272A>T	c.(271-273)gAg>gTg	p.E91V	RP11-867G23.12_ENST00000526655.1_RNA|BRMS1_ENST00000425825.2_Missense_Mutation_p.E91V	NM_015399.3	NP_056214.1	Q9HCU9	BRMS1_HUMAN	breast cancer metastasis suppressor 1	91					apoptotic process (GO:0006915)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of anoikis (GO:2000210)|positive regulation of protein deacetylation (GO:0090312)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)			large_intestine(1)|liver(1)|lung(1)|prostate(1)|skin(1)	5						CCCCACTTCCTCCAGCCGCAA	0.602																																					p.E91V	GBM(7;55 307 2662 20856 28942)	.											.	BRMS1-90	0			c.A272T						.						32.0	36.0	35.0					11																	66108763		2200	4295	6495	SO:0001583	missense	25855	exon4			ACTTCCTCCAGCC	AF147350	CCDS8135.1, CCDS44654.1	11q13-q13.2	2008-02-05				ENSG00000174744			17262	protein-coding gene	gene with protein product		606259				10850410	Standard	XM_005273883		Approved	DKFZP564A063	uc001oho.1	Q9HCU9		ENST00000359957.3:c.272A>T	11.37:g.66108763T>A	ENSP00000353042:p.Glu91Val	Somatic	80	0		WXS	Illumina HiSeq	Phase_I	72	15	NM_015399	3	0	15	30	12	Q6IAI2	Missense_Mutation	SNP	ENST00000359957.3	37	CCDS8135.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.718118	0.68844	.	.	ENSG00000174744	ENST00000425825;ENST00000359957;ENST00000530756	.	.	.	4.17	4.17	0.49024	.	0.121890	0.53938	D	0.000052	T	0.54431	0.1858	L	0.45228	1.405	0.44175	D	0.99698	B;B	0.31790	0.256;0.34	B;B	0.41135	0.348;0.343	T	0.55075	-0.8197	9	0.38643	T	0.18	-29.1846	11.4756	0.50295	0.0:0.0:0.0:1.0	.	91;91	Q9HCU9;G5E9I4	BRMS1_HUMAN;.	V	91	.	ENSP00000353042:E91V	E	-	2	0	BRMS1	65865339	0.983000	0.35010	1.000000	0.80357	0.998000	0.95712	1.690000	0.37711	1.889000	0.54706	0.460000	0.39030	GAG	T|0.993;C|0.007		0.602	BRMS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392958.2	NM_015399	
CASP1	834	broad.mit.edu;ucsc.edu;bcgsc.ca	37	11	104901192	104901192	+	Silent	SNP	A	A	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:104901192A>C	ENST00000533400.1	-	5	527	c.492T>G	c.(490-492)ctT>ctG	p.L164L	CASP1_ENST00000526568.1_Silent_p.L71L|CASP1_ENST00000594519.1_Silent_p.L71L|CASP1_ENST00000353247.5_Intron|CASP1_ENST00000393136.4_Silent_p.L143L|CASP1_ENST00000534497.1_Silent_p.L71L|CASP1_ENST00000531166.1_Intron|CASP1_ENST00000436863.3_Silent_p.L164L|CASP1_ENST00000527979.1_Silent_p.L127L|CASP1_ENST00000528974.1_Silent_p.L125L|CASP1_ENST00000525825.1_Silent_p.L143L|CASP1_ENST00000598974.1_Silent_p.L164L|CASP1_ENST00000593315.1_Silent_p.L143L|CASP1_ENST00000446369.1_Silent_p.L71L|CASP1_ENST00000415981.2_Intron	NM_001257118.1	NP_001244047.1	P29466	CASP1_HUMAN	caspase 1, apoptosis-related cysteine peptidase	164					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic substance (GO:0071310)|execution phase of apoptosis (GO:0097194)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|membrane hyperpolarization (GO:0060081)|mitochondrial depolarization (GO:0051882)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|programmed necrotic cell death (GO:0097300)|proteolysis (GO:0006508)|pyroptosis (GO:0070269)|regulation of inflammatory response (GO:0050727)|response to ATP (GO:0033198)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|IPAF inflammasome complex (GO:0072557)|NLRP1 inflammasome complex (GO:0072558)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|endopeptidase activity (GO:0004175)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000525)|Epithelial(105;0.0128)|all cancers(92;0.0482)	Minocycline(DB01017)	TAATGAGAGCAAGACGTGTGC	0.403																																					p.L164L	NSCLC(41;1246 1743 4934)												.	CASP1-661	0			c.T492G						.						127.0	112.0	117.0					11																	104901192		2202	4299	6501	SO:0001819	synonymous_variant	834	exon5			GAGAGCAAGACGT	U13697	CCDS8329.1, CCDS8330.1, CCDS8331.1, CCDS8332.1, CCDS53704.1	11q23	2012-02-29	2012-02-29		ENSG00000137752	ENSG00000137752		"""Caspases"""	1499	protein-coding gene	gene with protein product	"""caspase-1"", ""interleukin 1, beta, convertase"""	147678	"""caspase 1, apoptosis-related cysteine protease (interleukin 1, beta, convertase)"", ""caspase 1, apoptosis-related cysteine peptidase (interleukin 1, beta, convertase)"""	IL1BC		1373520, 9250871	Standard	NM_033292		Approved	ICE	uc001pim.5	P29466	OTTHUMG00000048072	ENST00000533400.1:c.492T>G	11.37:g.104901192A>C		Somatic	75	1		WXS	Illumina HiSeq	Phase_I	57	14	NM_001257118	0	0	25	28	3	B5MDZ1|Q53EY6|Q6DMQ1|Q6GSS3|Q6PI75|Q9UCN3	Silent	SNP	ENST00000533400.1	37	CCDS8330.1																																																																																			.		0.403	CASP1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388116.1	NM_033292	
OR10G9	219870	bcgsc.ca	37	11	123894195	123894195	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr11:123894195C>T	ENST00000375024.1	+	1	476	c.476C>T	c.(475-477)aCc>aTc	p.T159I		NM_001001953.1	NP_001001953.1	Q8NGN4	O10G9_HUMAN	olfactory receptor, family 10, subfamily G, member 9	159						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(33)|prostate(2)|skin(4)|stomach(8)|urinary_tract(1)	61		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0399)		GCTGTCCAGACCATATTGACT	0.552																																					p.T159I													.	OR10G9-92	0			c.C476T						.						181.0	158.0	166.0					11																	123894195		2201	4296	6497	SO:0001583	missense	219870	exon1			TCCAGACCATATT	AB065756	CCDS31703.1	11q24.1	2012-08-09			ENSG00000236981	ENSG00000236981		"""GPCR / Class A : Olfactory receptors"""	15129	protein-coding gene	gene with protein product				OR10G10P			Standard	NM_001001953		Approved		uc010sad.2	Q8NGN4	OTTHUMG00000165967	ENST00000375024.1:c.476C>T	11.37:g.123894195C>T	ENSP00000364164:p.Thr159Ile	Somatic	361	2		WXS	Illumina HiSeq	Phase_1	307	81	NM_001001953	0	0	0	0	0		Missense_Mutation	SNP	ENST00000375024.1	37	CCDS31703.1	.	.	.	.	.	.	.	.	.	.	C	6.764	0.509912	0.12883	.	.	ENSG00000236981	ENST00000375024	T	0.00245	8.45	3.48	3.48	0.39840	GPCR, rhodopsin-like superfamily (1);	0.139097	0.33075	N	0.005307	T	0.00328	0.0010	M	0.62088	1.915	0.09310	N	0.999995	D	0.56287	0.975	P	0.62491	0.903	T	0.54029	-0.8354	10	0.13470	T	0.59	.	7.6951	0.28590	0.1822:0.6402:0.1775:0.0	.	159	Q8NGN4	O10G9_HUMAN	I	159	ENSP00000364164:T159I	ENSP00000364164:T159I	T	+	2	0	OR10G9	123399405	0.000000	0.05858	0.704000	0.30370	0.076000	0.17211	0.121000	0.15667	1.938000	0.56188	0.655000	0.94253	ACC	.		0.552	OR10G9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387269.1	NM_001001953	
BCDIN3D	144233	ucsc.edu;bcgsc.ca	37	12	50232259	50232259	+	Missense_Mutation	SNP	G	G	T	rs559976366		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr12:50232259G>T	ENST00000333924.4	-	2	815	c.774C>A	c.(772-774)agC>agA	p.S258R	BCDIN3D-AS1_ENST00000549124.1_RNA|BCDIN3D-AS1_ENST00000548872.1_RNA	NM_181708.2	NP_859059.1	Q7Z5W3	BN3D2_HUMAN	BCDIN3 domain containing	258	Bin3-type SAM. {ECO:0000255|PROSITE- ProRule:PRU00848}.				miRNA metabolic process (GO:0010586)|negative regulation of pre-miRNA processing (GO:2000632)|RNA methylation (GO:0001510)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	O-methyltransferase activity (GO:0008171)|RNA methyltransferase activity (GO:0008173)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)|stomach(1)	9						AGAGCAGAAGGCTTCTGTCCC	0.443																																					p.S258R													.	BCDIN3D-69	0			c.C774A						.						145.0	139.0	141.0					12																	50232259		2203	4300	6503	SO:0001583	missense	144233	exon2			CAGAAGGCTTCTG		CCDS8790.1	12q13.13	2008-03-12				ENSG00000186666			27050	protein-coding gene	gene with protein product							Standard	NM_181708		Approved		uc001rvh.3	Q7Z5W3	OTTHUMG00000169807	ENST00000333924.4:c.774C>A	12.37:g.50232259G>T	ENSP00000335201:p.Ser258Arg	Somatic	41	0		WXS	Illumina HiSeq		38	4	NM_181708	0	0	9	9	0	A8K829	Missense_Mutation	SNP	ENST00000333924.4	37	CCDS8790.1	.	.	.	.	.	.	.	.	.	.	G	13.29	2.193431	0.38707	.	.	ENSG00000186666	ENST00000333924	T	0.45668	0.89	5.44	1.62	0.23740	Bin3-type S-adenosyl-L-methionine binding domain (1);	0.077387	0.85682	D	0.000000	T	0.41442	0.1159	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	P	0.57152	0.814	T	0.09015	-1.0694	10	0.34782	T	0.22	.	8.9521	0.35796	0.3107:0.0:0.6893:0.0	.	258	Q7Z5W3	BN3D2_HUMAN	R	258	ENSP00000335201:S258R	ENSP00000335201:S258R	S	-	3	2	BCDIN3D	48518526	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	0.640000	0.24705	0.099000	0.17552	0.491000	0.48974	AGC	.		0.443	BCDIN3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405982.1	NM_181708	
TAOK3	51347	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	118651868	118651868	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr12:118651868A>T	ENST00000392533.3	-	10	1181	c.691T>A	c.(691-693)Tat>Aat	p.Y231N	TAOK3_ENST00000419821.2_Missense_Mutation_p.Y231N	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	231	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCAATGTGATATAAGGCACTC	0.413																																					p.Y231N		.											.	TAOK3-933	0			c.T691A						.						153.0	148.0	150.0					12																	118651868		2203	4300	6503	SO:0001583	missense	51347	exon10			TGTGATATAAGGC	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.691T>A	12.37:g.118651868A>T	ENSP00000376317:p.Tyr231Asn	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	83	17	NM_016281	0	0	10	14	4	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	37	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.731562	0.89390	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000538601	D;D;D	0.85484	-1.99;-1.99;-1.99	5.24	5.24	0.73138	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.072210	0.64402	D	0.000020	D	0.89245	0.6660	L	0.45228	1.405	0.80722	D	1	D	0.71674	0.998	D	0.74348	0.983	D	0.90431	0.4424	10	0.87932	D	0	.	15.3625	0.74492	1.0:0.0:0.0:0.0	.	231	Q9H2K8	TAOK3_HUMAN	N	231;231;129	ENSP00000416374:Y231N;ENSP00000376317:Y231N;ENSP00000437389:Y129N	ENSP00000376317:Y231N	Y	-	1	0	TAOK3	117136251	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.087000	0.94110	2.210000	0.71456	0.472000	0.43445	TAT	.		0.413	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281	
ATP7B	540	broad.mit.edu;ucsc.edu;bcgsc.ca	37	13	52509756	52509756	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr13:52509756A>G	ENST00000242839.4	-	20	4253	c.4097T>C	c.(4096-4098)gTg>gCg	p.V1366A	ATP7B_ENST00000417240.2_Missense_Mutation_p.V577A|ATP7B_ENST00000344297.5_Missense_Mutation_p.V1159A|ATP7B_ENST00000400366.3_Missense_Mutation_p.V1255A|ATP7B_ENST00000400370.3_Missense_Mutation_p.V936A|ATP7B_ENST00000418097.2_Missense_Mutation_p.V1301A|ATP7B_ENST00000448424.2_Missense_Mutation_p.V1288A	NM_000053.3	NP_000044.2	P35670	ATP7B_HUMAN	ATPase, Cu++ transporting, beta polypeptide	1366					cellular copper ion homeostasis (GO:0006878)|cellular zinc ion homeostasis (GO:0006882)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|intracellular copper ion transport (GO:0015680)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|response to copper ion (GO:0046688)|sequestering of calcium ion (GO:0051208)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|membrane (GO:0016020)|mitochondrion (GO:0005739)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper-exporting ATPase activity (GO:0004008)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(23)|ovary(1)|prostate(3)|skin(4)|stomach(2)	55		Breast(56;0.000207)|Lung NSC(96;0.000845)|Prostate(109;0.0235)|Hepatocellular(98;0.065)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;5.25e-08)	Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGAGAGCACCACAGACACAGA	0.592									Wilson disease																												p.V1366A													.	ATP7B-92	0			c.T4097C	GRCh37	CD033178	ATP7B	D		.						28.0	34.0	32.0					13																	52509756		2120	4230	6350	SO:0001583	missense	540	exon20	Familial Cancer Database		AGCACCACAGACA	U11700	CCDS41892.1, CCDS45049.1, CCDS58293.1	13q14.3	2012-10-22	2005-11-29		ENSG00000123191	ENSG00000123191	3.6.3.4	"""ATPases / P-type"""	870	protein-coding gene	gene with protein product	"""Wilson disease"", ""copper pump 2"", ""copper-transporting ATPase 2"""	606882	"""ATPase, Cu++ transporting, beta polypeptide (Wilson disease)"""	WND		8298641, 8298639	Standard	NM_000053		Approved		uc001vfw.2	P35670	OTTHUMG00000017406	ENST00000242839.4:c.4097T>C	13.37:g.52509756A>G	ENSP00000242839:p.Val1366Ala	Somatic	186	1		WXS	Illumina HiSeq	Phase_I	144	37	NM_000053	0	0	1	5	4	Q16318|Q16319|Q4U3V3|Q59FJ9|Q5T7X7	Missense_Mutation	SNP	ENST00000242839.4	37	CCDS41892.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.100115	0.76983	.	.	ENSG00000123191	ENST00000242839;ENST00000400366;ENST00000344297;ENST00000417240;ENST00000448424;ENST00000400370;ENST00000418097	D;D;D;D;D;D;D	0.99714	-6.5;-6.5;-6.5;-6.5;-6.5;-6.5;-6.5	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.99789	0.9911	H	0.94183	3.505	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.996;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.986;0.995;0.996;0.997;0.996;0.999;0.996;0.999	D	0.96956	0.9698	10	0.87932	D	0	-21.8479	15.2853	0.73822	1.0:0.0:0.0:0.0	.	1288;1318;1301;577;936;1255;1159;1366	E7ET55;B7ZLR4;F5H748;E7EQQ2;F5H562;P35670-3;P35670-2;P35670	.;.;.;.;.;.;.;ATP7B_HUMAN	A	1366;1255;1159;577;1288;936;1301	ENSP00000242839:V1366A;ENSP00000383217:V1255A;ENSP00000342559:V1159A;ENSP00000390360:V577A;ENSP00000416738:V1288A;ENSP00000383221:V936A;ENSP00000393343:V1301A	ENSP00000242839:V1366A	V	-	2	0	ATP7B	51407757	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	8.629000	0.90983	2.201000	0.70794	0.533000	0.62120	GTG	.		0.592	ATP7B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045981.1	NM_000053	
G2E3	55632	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	31081505	31081505	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:31081505G>A	ENST00000206595.6	+	13	1747	c.1593G>A	c.(1591-1593)acG>acA	p.T531T	G2E3_ENST00000553504.1_Silent_p.T561T|G2E3_ENST00000438909.2_Silent_p.T485T	NM_017769.3	NP_060239.2	Q7L622	G2E3_HUMAN	G2/M-phase specific E3 ubiquitin protein ligase	531	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				apoptotic process (GO:0006915)|blastocyst development (GO:0001824)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|protein polyubiquitination (GO:0000209)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23						GACTTATAACGACATTAAGTG	0.313																																					p.T531T		.											.	G2E3-660	0			c.G1593A						.						100.0	103.0	102.0					14																	31081505		2203	4295	6498	SO:0001819	synonymous_variant	55632	exon13			TATAACGACATTA	AK000340	CCDS9638.1	14q12	2013-01-28	2010-09-17	2009-02-03	ENSG00000092140	ENSG00000092140		"""Zinc fingers, PHD-type"""	20338	protein-coding gene	gene with protein product	"""PHD finger protein 7B"""	611299	"""KIAA1333"""	KIAA1333		18511420, 17239372	Standard	NM_017769		Approved	FLJ20333, PHF7B	uc001wqk.2	Q7L622	OTTHUMG00000140204	ENST00000206595.6:c.1593G>A	14.37:g.31081505G>A		Somatic	183	0		WXS	Illumina HiSeq	Phase_I	175	40	NM_017769	0	0	3	3	0	Q9BVR2|Q9H9E9|Q9NXC0|Q9P2L3	Silent	SNP	ENST00000206595.6	37	CCDS9638.1																																																																																			.		0.313	G2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276613.2	NM_017769	
FANCM	57697	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	45645152	45645152	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:45645152C>G	ENST00000267430.5	+	14	3280	c.3195C>G	c.(3193-3195)tgC>tgG	p.C1065W	FANCM_ENST00000542564.2_Missense_Mutation_p.C1039W	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1065					DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAAAAAGTTGCCTTTATGATA	0.299								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.C1065W		.											.	FANCM-569	0			c.C3195G						.						25.0	26.0	25.0					14																	45645152		2203	4296	6499	SO:0001583	missense	57697	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	AAGTTGCCTTTAT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.3195C>G	14.37:g.45645152C>G	ENSP00000267430:p.Cys1065Trp	Somatic	87	0		WXS	Illumina HiSeq	Phase_I	123	31	NM_020937	0	0	1	1	0	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	C	6.697	0.497283	0.12762	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.18657	2.79;2.79;2.2	5.23	-2.33	0.06724	.	1.440870	0.03493	N	0.216880	T	0.30885	0.0779	L	0.56769	1.78	0.09310	N	0.999999	D;D	0.58620	0.964;0.983	P;P	0.53006	0.624;0.715	T	0.38067	-0.9678	10	0.66056	D	0.02	.	5.9826	0.19415	0.0:0.3342:0.137:0.5287	.	1039;1065	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	W	1065;1039;581	ENSP00000267430:C1065W;ENSP00000442493:C1039W;ENSP00000452033:C581W	ENSP00000267430:C1065W	C	+	3	2	FANCM	44714902	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.431000	0.06965	-0.270000	0.09285	-0.229000	0.12294	TGC	.		0.299	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
DLGAP5	9787	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	55642723	55642723	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:55642723C>A	ENST00000247191.2	-	9	1279	c.1063G>T	c.(1063-1065)Gca>Tca	p.A355S	DLGAP5_ENST00000395425.2_Missense_Mutation_p.A355S	NM_014750.4	NP_055565.3	Q15398	DLGP5_HUMAN	discs, large (Drosophila) homolog-associated protein 5	355					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|dephosphorylation (GO:0016311)|mitotic chromosome movement towards spindle pole (GO:0007079)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|spindle pole centrosome (GO:0031616)	phosphoprotein phosphatase activity (GO:0004721)			biliary_tract(1)|breast(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	44						TCTTTTGTTGCTTGAGACTCA	0.313																																					p.A355S		.											.	DLGAP5-92	0			c.G1063T						.						131.0	125.0	127.0					14																	55642723		2203	4297	6500	SO:0001583	missense	9787	exon9			TTGTTGCTTGAGA	D13633	CCDS9723.1, CCDS53897.1	14q22.3	2008-05-30	2008-05-30	2008-05-30	ENSG00000126787	ENSG00000126787			16864	protein-coding gene	gene with protein product			"""discs, large homolog 7 (Drosophila)"""	DLG7		7584026, 7584028	Standard	NM_014750		Approved	KIAA0008, DLG1, HURP	uc001xbs.3	Q15398	OTTHUMG00000140310	ENST00000247191.2:c.1063G>T	14.37:g.55642723C>A	ENSP00000247191:p.Ala355Ser	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	73	10	NM_014750	0	0	0	0	0	A8MTM6|B4DRM8|Q86T11|Q8NG58	Missense_Mutation	SNP	ENST00000247191.2	37	CCDS9723.1	.	.	.	.	.	.	.	.	.	.	C	11.71	1.720936	0.30503	.	.	ENSG00000126787	ENST00000395425;ENST00000247191	T;T	0.15952	2.38;2.38	3.83	2.93	0.34026	.	1.470090	0.03875	N	0.276195	T	0.16342	0.0393	L	0.36672	1.1	0.24747	N	0.993003	B;B	0.26902	0.163;0.095	B;B	0.30105	0.111;0.078	T	0.32798	-0.9893	10	0.13108	T	0.6	.	9.5155	0.39102	0.0:0.7848:0.2152:0.0	.	355;355	A8MTM6;Q15398	.;DLGP5_HUMAN	S	355	ENSP00000378815:A355S;ENSP00000247191:A355S	ENSP00000247191:A355S	A	-	1	0	DLGAP5	54712476	0.784000	0.28713	0.566000	0.28421	0.957000	0.61999	1.018000	0.30002	1.213000	0.43380	0.650000	0.86243	GCA	.		0.313	DLGAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276908.2	NM_014750	
APBA2	321	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	15	29346718	29346718	+	Missense_Mutation	SNP	C	C	T	rs149847107		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:29346718C>T	ENST00000558402.1	+	5	1230	c.631C>T	c.(631-633)Cgc>Tgc	p.R211C	APBA2_ENST00000558259.1_Missense_Mutation_p.R211C|APBA2_ENST00000558330.1_Missense_Mutation_p.R211C|APBA2_ENST00000411764.1_Missense_Mutation_p.R211C|APBA2_ENST00000561069.1_Missense_Mutation_p.R211C			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	211	STXBP1-binding.			DEPSVLEAHDQEEDGHYCASKEGYQDYYPEEANGNTGASPY RLRR -> MSPPSLRPMTRKKMVTMCQQRGLPGLLPRGGQR EHRRLPLPPEA (in Ref. 1; AAC39767). {ECO:0000305}.	in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		CTCCCCCTACCGCCTGAGGCG	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		20367	0.0		0.001	False		,,,				2504	0.0				p.R211C		.											.	APBA2-90	0			c.C631T						.	C	CYS/ARG,CYS/ARG	0,4402		0,0,2201	44.0	34.0	37.0		631,631	2.9	0.1	15	dbSNP_134	37	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	APBA2	NM_001130414.1,NM_005503.3	180,180	0,1,6500	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	211/738,211/750	29346718	1,13001	2201	4300	6501	SO:0001583	missense	321	exon3			CCCTACCGCCTGA	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.631C>T	15.37:g.29346718C>T	ENSP00000453293:p.Arg211Cys	Somatic	210	0		WXS	Illumina HiSeq	Phase_I	162	10	NM_005503	0	0	0	0	0	E9PGI4|O60571|Q5XKC0	Missense_Mutation	SNP	ENST00000558402.1	37	CCDS10022.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.31	1.898247	0.33535	0.0	1.16E-4	ENSG00000034053	ENST00000411764;ENST00000219865	T	0.47177	0.85	4.77	2.89	0.33648	.	0.517876	0.20604	N	0.089082	T	0.42720	0.1215	L	0.54323	1.7	0.18873	N	0.999985	B;D;B	0.63046	0.122;0.992;0.06	B;B;B	0.42916	0.008;0.402;0.006	T	0.35895	-0.9770	10	0.72032	D	0.01	.	10.2679	0.43466	0.0:0.8387:0.0:0.1613	.	211;211;211	Q5XKC0;E9PGI4;Q99767	.;.;APBA2_HUMAN	C	211	ENSP00000409312:R211C	ENSP00000219865:R211C	R	+	1	0	APBA2	27134010	0.000000	0.05858	0.085000	0.20634	0.465000	0.32709	0.245000	0.18142	0.541000	0.28827	-0.142000	0.14014	CGC	C|1.000;T|0.000		0.602	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
AP4E1	23431	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	51285700	51285700	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:51285700G>T	ENST00000261842.5	+	17	2330	c.2224G>T	c.(2224-2226)Gat>Tat	p.D742Y	AP4E1_ENST00000560508.1_Missense_Mutation_p.D667Y	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	742					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GGAGAATGTAGATCAAGCTAT	0.408																																					p.D742Y		.											.	AP4E1-90	0			c.G2224T						.						105.0	92.0	97.0					15																	51285700		2196	4294	6490	SO:0001583	missense	23431	exon17			AATGTAGATCAAG	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2224G>T	15.37:g.51285700G>T	ENSP00000261842:p.Asp742Tyr	Somatic	59	0		WXS	Illumina HiSeq	Phase_I	56	8	NM_007347	0	0	2	2	0	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969624	0.53614	.	.	ENSG00000081014	ENST00000261842	T	0.19250	2.16	5.29	5.29	0.74685	.	0.278842	0.38778	N	0.001568	T	0.22898	0.0553	N	0.24115	0.695	0.35318	D	0.784497	P	0.51653	0.947	P	0.47744	0.556	T	0.19844	-1.0293	10	0.72032	D	0.01	-17.9497	17.9229	0.88973	0.0:0.0:1.0:0.0	.	742	Q9UPM8	AP4E1_HUMAN	Y	742	ENSP00000261842:D742Y	ENSP00000261842:D742Y	D	+	1	0	AP4E1	49072992	0.989000	0.36119	0.774000	0.31636	0.968000	0.65278	3.111000	0.50360	2.455000	0.83008	0.563000	0.77884	GAT	.		0.408	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
PKM	5315	broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	72499107	72499107	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:72499107C>T	ENST00000335181.5	-	8	1205	c.1102G>A	c.(1102-1104)Ggg>Agg	p.G368R	PKM_ENST00000389093.3_Missense_Mutation_p.G368R|PKM_ENST00000568459.1_Missense_Mutation_p.G368R|PKM_ENST00000319622.6_Missense_Mutation_p.G368R|PKM_ENST00000568883.1_Missense_Mutation_p.G203R|PKM_ENST00000449901.2_Missense_Mutation_p.G353R|PKM_ENST00000565184.1_Missense_Mutation_p.G368R|PKM_ENST00000565154.1_Missense_Mutation_p.G368R	NM_002654.4	NP_002645.3	P14618	KPYM_HUMAN	pyruvate kinase, muscle	368	Interaction with POU5F1.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|programmed cell death (GO:0012501)|small molecule metabolic process (GO:0044281)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)			endometrium(1)|lung(7)	8					Pyruvic acid(DB00119)	GGATAGTCCCCTTTGGCTGTT	0.622																																					p.G442R													.	.	0			c.G1324A						.						55.0	51.0	53.0					15																	72499107		2199	4297	6496	SO:0001583	missense	5315	exon9			AGTCCCCTTTGGC	M23725	CCDS32284.1, CCDS32285.1, CCDS55972.1, CCDS73752.1	15q23	2012-10-02		2012-05-23	ENSG00000067225	ENSG00000067225	2.7.1.40		9021	protein-coding gene	gene with protein product		179050		PKM2		2040271	Standard	NM_002654		Approved	THBP1, OIP3, PK3	uc002atr.1	P14618	OTTHUMG00000172709	ENST00000335181.5:c.1102G>A	15.37:g.72499107C>T	ENSP00000334983:p.Gly368Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	36	4	NM_001206796	0	0	492	889	397	A6NFK3|B2R5N8|B3KRY0|B4DFX8|B4DUU6|P14786|Q53GK4|Q96E76|Q9BWB5|Q9UCV6|Q9UPF2	Missense_Mutation	SNP	ENST00000335181.5	37	CCDS32284.1	.	.	.	.	.	.	.	.	.	.	C	34	5.293462	0.95546	.	.	ENSG00000067225	ENST00000319622;ENST00000335181;ENST00000434220;ENST00000327974;ENST00000389093;ENST00000449901	D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61	5.23	5.23	0.72850	Pyruvate/Phosphoenolpyruvate kinase (2);Pyruvate kinase, barrel (1);	0.000000	0.85682	D	0.000000	D	0.95799	0.8633	H	0.99642	4.675	0.80722	D	1	D;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;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.97965	1.0340	10	0.87932	D	0	-24.602	19.1591	0.93524	0.0:1.0:0.0:0.0	.	294;353;348;348;368;368;203;295;203	B4DNK4;B4DUU6;B4DRT3;E7EUQ8;P14618;P14618-2;Q504U3;E9PF79;E7EUJ4	.;.;.;.;KPYM_HUMAN;.;.;.;.	R	368;368;295;203;368;353	ENSP00000320171:G368R;ENSP00000334983:G368R;ENSP00000373745:G368R;ENSP00000403365:G353R	ENSP00000320171:G368R	G	-	1	0	PKM2	70286161	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.818000	0.86416	2.596000	0.87737	0.561000	0.74099	GGG	.		0.622	PKM-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420056.1		
MESP2	145873	broad.mit.edu;ucsc.edu;bcgsc.ca	37	15	90321562	90321562	+	Silent	SNP	C	C	T	rs375171689		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:90321562C>T	ENST00000341735.3	+	2	1191	c.1191C>T	c.(1189-1191)taC>taT	p.Y397Y	MESP2_ENST00000560219.1_Silent_p.Y99Y|MESP2_ENST00000558723.1_3'UTR	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	397					mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			GCATCTTCTACTAAATGGCCT	0.537																																					p.Y397Y													.	MESP2-68	0			c.C1191T						.	T		1,3677		0,1,1838	25.0	28.0	27.0		1191	1.2	0.3	15		27	0,8160		0,0,4080	no	coding-synonymous	MESP2	NM_001039958.1		0,1,5918	TT,TC,CC		0.0,0.0272,0.0084		397/398	90321562	1,11837	1839	4080	5919	SO:0001819	synonymous_variant	145873	exon2			CTTCTACTAAATG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.1191C>T	15.37:g.90321562C>T		Somatic	156	1		WXS	Illumina HiSeq	Phase_I	143	32	NM_001039958	0	0	1	1	0	Q7RTU2	Silent	SNP	ENST00000341735.3	37	CCDS42078.1																																																																																			.		0.537	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261	
CHD2	1106	hgsc.bcm.edu	37	15	93541851	93541851	+	Splice_Site	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr15:93541851G>T	ENST00000394196.4	+	31	5076	c.4008G>T	c.(4006-4008)gaG>gaT	p.E1336D	CHD2_ENST00000557381.1_Splice_Site_p.E1336D	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1336					cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GTGGGGAAGAGGTGAGTACGC	0.552																																					p.E1336D		.											.	CHD2-229	0			c.G4008T						.						92.0	92.0	92.0					15																	93541851		2197	4298	6495	SO:0001630	splice_region_variant	1106	exon31			GGAAGAGGTGAGT	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4008+1G>T	15.37:g.93541851G>T		Somatic	74	0		WXS	Illumina HiSeq	Phase_I	74	4	NM_001271	0	0	1	1	0	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	.	.	.	.	.	.	.	.	.	.	G	15.00	2.702923	0.48412	.	.	ENSG00000173575	ENST00000394196;ENST00000557381	D;D	0.89939	-2.59;-2.58	5.16	5.16	0.70880	.	0.000000	0.34484	U	0.003936	D	0.92410	0.7591	L	0.59436	1.845	0.80722	D	1	D;D	0.67145	0.984;0.996	D;P	0.68192	0.956;0.789	D	0.89962	0.4087	10	0.22109	T	0.4	-32.7161	17.2006	0.86904	0.0:0.0:1.0:0.0	.	1336;1336	O14647;O14647-2	CHD2_HUMAN;.	D	1336	ENSP00000377747:E1336D;ENSP00000451366:E1336D	ENSP00000377747:E1336D	E	+	3	2	CHD2	91342855	1.000000	0.71417	1.000000	0.80357	0.415000	0.31203	8.987000	0.93497	2.578000	0.87016	0.561000	0.74099	GAG	.		0.552	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	Missense_Mutation
CCDC64B	146439	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	3078701	3078701	+	Splice_Site	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3078701T>A	ENST00000572449.1	-	8	1300	c.1238A>T	c.(1237-1239)aAg>aTg	p.K413M	CCDC64B_ENST00000573514.1_Splice_Site_p.K206M|CCDC64B_ENST00000389347.4_Splice_Site_p.K413M			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	413										breast(1)|endometrium(2)|large_intestine(1)	4						TGAGGCTTACTTGTTCACGGC	0.637																																					p.K413M		.											.	.	0			c.A1238T						.						35.0	49.0	44.0					16																	3078701		1994	4127	6121	SO:0001630	splice_region_variant	146439	exon7			GCTTACTTGTTCA	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1238+1A>T	16.37:g.3078701T>A		Somatic	72	0		WXS	Illumina HiSeq	Phase_I	70	16	NM_001103175	0	0	0	0	0	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.656736	0.67586	.	.	ENSG00000162069	ENST00000389347	T	0.39592	1.07	4.28	4.28	0.50868	.	0.067259	0.56097	D	0.000027	T	0.57989	0.2091	M	0.72118	2.19	0.58432	D	0.999993	D	0.76494	0.999	D	0.63192	0.912	T	0.59936	-0.7360	9	.	.	.	-53.638	11.4408	0.50096	0.0:0.0:0.0:1.0	.	413	A1A5D9	BICR2_HUMAN	M	413	ENSP00000373998:K413M	.	K	-	2	0	CCDC64B	3018702	1.000000	0.71417	1.000000	0.80357	0.619000	0.37552	2.792000	0.47837	1.814000	0.52955	0.459000	0.35465	AAG	.		0.637	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		Missense_Mutation
ZNF75A	7627	broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	3367508	3367508	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3367508T>C	ENST00000574298.1	+	6	1003	c.530T>C	c.(529-531)aTt>aCt	p.I177T	ZNF75A_ENST00000498240.2_3'UTR	NM_153028.2	NP_694573.1	Q96N20	ZN75A_HUMAN	zinc finger protein 75a	177					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|large_intestine(3)|lung(7)|prostate(1)	12						TCTGACCTTATTAAGCACCAA	0.378																																					p.I177T													.	ZNF75A-153	0			c.T530C						.						80.0	78.0	79.0					16																	3367508		2197	4300	6497	SO:0001583	missense	7627	exon6			ACCTTATTAAGCA	X91826	CCDS10501.1	16p13.11	2013-01-08			ENSG00000162086	ENSG00000162086		"""Zinc fingers, C2H2-type"", ""-"""	13146	protein-coding gene	gene with protein product		601473				8661144	Standard	NM_153028		Approved	FLJ31529	uc002cut.4	Q96N20	OTTHUMG00000129356	ENST00000574298.1:c.530T>C	16.37:g.3367508T>C	ENSP00000459566:p.Ile177Thr	Somatic	161	1		WXS	Illumina HiSeq	Phase_I	174	43	NM_153028	0	0	7	11	4	Q0VDI8|Q92669	Missense_Mutation	SNP	ENST00000574298.1	37	CCDS10501.1	.	.	.	.	.	.	.	.	.	.	T	9.976	1.226686	0.22542	.	.	ENSG00000162086	ENST00000293995	.	.	.	4.57	3.47	0.39725	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45606	D	0.000353	T	0.12518	0.0304	N	0.04805	-0.155	0.21933	N	0.999462	B	0.18013	0.025	B	0.18561	0.022	T	0.33394	-0.9870	9	0.02654	T	1	.	4.0488	0.09785	0.181:0.0983:0.0:0.7207	.	177	Q96N20	ZN75A_HUMAN	T	177	.	ENSP00000293995:I177T	I	+	2	0	ZNF75A	3307509	0.000000	0.05858	1.000000	0.80357	0.986000	0.74619	0.323000	0.19593	0.889000	0.36185	0.455000	0.32223	ATT	.		0.378	ZNF75A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251506.2	NM_153028	
NLRC3	197358	ucsc.edu	37	16	3593429	3593429	+	RNA	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:3593429G>T	ENST00000301749.7	-	0	3340				NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000448023.2_RNA|LA16c-390H2.4_ENST00000573820.1_RNA|NLRC3_ENST00000419350.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ACTTACTCGAGAATCTCCAAG	0.493																																					p.L979I													.	NLRC3-96	0			c.C2935A						.						42.0	45.0	44.0					16																	3593429		1916	4131	6047			197358	exon18			ACTCGAGAATCTC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3593429G>T		Somatic	36	0		WXS	Illumina HiSeq		44	4	NM_178844	0	0	0	0	0	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	G	16.73	3.203059	0.58234	.	.	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.77229	-1.08;-1.08;-1.08	4.86	3.9	0.45041	.	0.000000	0.64402	D	0.000011	D	0.85336	0.5673	M	0.79011	2.435	0.22001	N	0.999423	D	0.64830	0.994	D	0.74348	0.983	T	0.75563	-0.3274	10	0.87932	D	0	.	8.3586	0.32346	0.104:0.0:0.896:0.0	.	1025	C9JLH9	.	I	979;950;1025	ENSP00000301749:L979I;ENSP00000352039:L950I;ENSP00000414415:L1025I	ENSP00000301749:L979I	L	-	1	0	NLRC3	3533430	1.000000	0.71417	0.986000	0.45419	0.576000	0.36127	3.522000	0.53480	2.675000	0.91044	0.561000	0.74099	CTC	.		0.493	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
TMC5	79838	broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	19474632	19474632	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:19474632G>T	ENST00000396229.2	+	7	1928	c.1179G>T	c.(1177-1179)caG>caT	p.Q393H	TMC5_ENST00000564959.1_Missense_Mutation_p.Q76H|TMC5_ENST00000381414.4_Missense_Mutation_p.Q393H|TMC5_ENST00000542583.2_Missense_Mutation_p.Q393H|TMC5_ENST00000541464.1_Missense_Mutation_p.Q393H|TMC5_ENST00000219821.5_Missense_Mutation_p.Q147H|TMC5_ENST00000561503.1_Missense_Mutation_p.Q34H	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	393					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						AAAGCAAACAGACCCATCGTA	0.393																																					p.Q393H													.	TMC5-91	0			c.G1179T						.						130.0	117.0	121.0					16																	19474632		2197	4300	6497	SO:0001583	missense	79838	exon7			CAAACAGACCCAT	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1179G>T	16.37:g.19474632G>T	ENSP00000379531:p.Gln393His	Somatic	68	2		WXS	Illumina HiSeq	Phase_I	71	18	NM_001105249	0	0	0	0	0	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	9.374	1.071196	0.20147	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	4.52	-3.67	0.04476	.	2.274450	0.01221	N	0.008115	T	0.37919	0.1021	L	0.46157	1.445	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B	0.09377	0.004;0.002;0.004;0.002;0.002;0.004	T	0.04495	-1.0947	10	0.15499	T	0.54	-0.1905	0.9076	0.01288	0.3654:0.2379:0.2531:0.1436	.	393;76;147;147;393;393	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	H	393;393;393;393;147;76	ENSP00000441227:Q393H;ENSP00000370822:Q393H;ENSP00000379531:Q393H;ENSP00000446274:Q393H;ENSP00000219821:Q147H	ENSP00000219821:Q147H	Q	+	3	2	TMC5	19382133	0.001000	0.12720	0.002000	0.10522	0.205000	0.24178	-0.007000	0.12810	-0.220000	0.09988	-0.142000	0.14014	CAG	.		0.393	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
GTF3C1	2975	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	27549611	27549611	+	Silent	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:27549611C>T	ENST00000356183.4	-	3	513	c.498G>A	c.(496-498)gaG>gaA	p.E166E	GTF3C1_ENST00000561623.1_Silent_p.E166E	NM_001520.3	NP_001511.2	Q12789	TF3C1_HUMAN	general transcription factor IIIC, polypeptide 1, alpha 220kDa	166					5S class rRNA transcription from RNA polymerase III type 1 promoter (GO:0042791)|gene expression (GO:0010467)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)|tRNA transcription (GO:0009304)|tRNA transcription from RNA polymerase III promoter (GO:0042797)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|transcription factor TFIIIC complex (GO:0000127)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|liver(3)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	80						CGGGATCCCCCTCCTGGCCTA	0.582																																					p.E166E		.											.	GTF3C1-94	0			c.G498A						.						70.0	66.0	68.0					16																	27549611		2197	4300	6497	SO:0001819	synonymous_variant	2975	exon3			ATCCCCCTCCTGG	U06485	CCDS32414.1, CCDS66988.1	16p12	2010-03-23	2002-08-29			ENSG00000077235		"""General transcription factors"""	4664	protein-coding gene	gene with protein product		603246	"""general transcription factor IIIC, polypeptide 1 (alpha subunit, 220kD )"""			8164661, 8127861	Standard	NM_001520		Approved	TFIIIC220	uc002dov.2	Q12789		ENST00000356183.4:c.498G>A	16.37:g.27549611C>T		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	74	20	NM_001520	0	0	13	18	5	B2RP21|Q12838|Q6DKN9|Q9Y4W9	Silent	SNP	ENST00000356183.4	37	CCDS32414.1	.	.	.	.	.	.	.	.	.	.	C	8.560	0.877594	0.17395	.	.	ENSG00000077235	ENST00000388971	.	.	.	5.5	1.98	0.26296	.	.	.	.	.	T	0.61640	0.2363	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58036	-0.7707	5	0.38643	T	0.18	-3.8349	11.4639	0.50227	0.0:0.6864:0.0:0.3136	.	.	.	.	R	166	.	ENSP00000373623:G166R	G	-	1	0	GTF3C1	27457112	0.875000	0.30112	0.996000	0.52242	0.914000	0.54420	-0.027000	0.12371	0.389000	0.25086	-1.945000	0.00491	GGG	.		0.582	GTF3C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433856.1	NM_001520	
CDH1	999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	68853183	68853183	+	Splice_Site	SNP	A	A	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:68853183A>C	ENST00000261769.5	+	11	1757	c.1566A>C	c.(1564-1566)acA>acC	p.T522T	CDH1_ENST00000562836.1_3'UTR|RP11-354M1.2_ENST00000563916.1_RNA|CDH1_ENST00000422392.2_Splice_Site_p.T461T	NM_004360.3	NP_004351.1	P12830	CADH1_HUMAN	cadherin 1, type 1, E-cadherin (epithelial)	522	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to amino acid stimulus (GO:0071230)|cellular response to indole-3-methanol (GO:0071681)|cellular response to lithium ion (GO:0071285)|cochlea development (GO:0090102)|epithelial cell morphogenesis (GO:0003382)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|homophilic cell adhesion (GO:0007156)|intestinal epithelial cell development (GO:0060576)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of epithelial cell proliferation (GO:0050680)|neuron projection development (GO:0031175)|pituitary gland development (GO:0021983)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|protein metabolic process (GO:0019538)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of immune response (GO:0050776)|regulation of neuron migration (GO:2001222)|regulation of protein localization to cell surface (GO:2000008)|regulation of water loss via skin (GO:0033561)|response to drug (GO:0042493)|response to toxic substance (GO:0009636)|salivary gland cavitation (GO:0060662)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|tight junction assembly (GO:0070830)|trophectodermal cell differentiation (GO:0001829)	actin cytoskeleton (GO:0015629)|aggresome (GO:0016235)|apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|axon terminus (GO:0043679)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell junction (GO:0030054)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|node of Ranvier (GO:0033268)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|trans-Golgi network (GO:0005802)	ankyrin binding (GO:0030506)|beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|gamma-catenin binding (GO:0045295)|glycoprotein binding (GO:0001948)|GTPase activating protein binding (GO:0032794)	p.?(1)		NS(6)|biliary_tract(8)|breast(161)|central_nervous_system(4)|endometrium(9)|kidney(4)|large_intestine(13)|lung(13)|oesophagus(3)|ovary(2)|prostate(3)|soft_tissue(2)|stomach(76)|thyroid(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	311		all_neural(199;0.0189)|Ovarian(137;0.0563)		Epithelial(162;8.44e-05)|all cancers(182;0.000404)|OV - Ovarian serous cystadenocarcinoma(108;0.000426)|BRCA - Breast invasive adenocarcinoma(181;0.0261)		CCCCGTTCAGATATCGGATTT	0.493			"""Mis, N, F, S"""		"""lobular breast, gastric"""	gastric			Hereditary Diffuse Gastric Cancer																												p.T522T		.	yes	Rec	yes	Familial gastric carcinoma	16	16q22.1	999	"""cadherin 1, type 1, E-cadherin (epithelial) (ECAD)"""		E	.	CDH1-3377	1	Unknown(1)	breast(1)	c.A1566C						.						89.0	78.0	82.0					16																	68853183		2198	4300	6498	SO:0001630	splice_region_variant	999	exon11	Familial Cancer Database	HDGC	GTTCAGATATCGG	L08599	CCDS10869.1	16q22.1	2014-09-17			ENSG00000039068	ENSG00000039068		"""CD molecules"", ""Cadherins / Major cadherins"""	1748	protein-coding gene	gene with protein product	"""E-Cadherin"""	192090		UVO		9925936	Standard	NM_004360		Approved	uvomorulin, CD324	uc002ewg.1	P12830	OTTHUMG00000137561	ENST00000261769.5:c.1566-1A>C	16.37:g.68853183A>C		Somatic	116	0		WXS	Illumina HiSeq	Phase_I	92	22	NM_004360	0	0	0	0	0	A8K1U7|Q13799|Q14216|Q15855|Q16194|Q4PJ14|Q9UII8	Silent	SNP	ENST00000261769.5	37	CCDS10869.1																																																																																			.		0.493	CDH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268897.2	NM_004360	Silent
CPNE7	27132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	16	89650107	89650107	+	Silent	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr16:89650107T>A	ENST00000268720.5	+	5	715	c.585T>A	c.(583-585)atT>atA	p.I195I	CPNE7_ENST00000319518.8_Silent_p.I120I	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	195					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		ACTTACAGATTGTGGCCCAGA	0.672																																					p.I195I		.											.	CPNE7-90	0			c.T585A						.						48.0	45.0	46.0					16																	89650107		2198	4300	6498	SO:0001819	synonymous_variant	27132	exon5			ACAGATTGTGGCC	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.585T>A	16.37:g.89650107T>A		Somatic	120	0		WXS	Illumina HiSeq	Phase_I	107	29	NM_014427	0	0	0	0	0		Silent	SNP	ENST00000268720.5	37	CCDS10980.1																																																																																			.		0.672	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
ELP5	23587	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	7157996	7157996	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:7157996T>C	ENST00000396628.2	+	4	548	c.331T>C	c.(331-333)Tgc>Cgc	p.C111R	ELP5_ENST00000356683.2_Missense_Mutation_p.C111R|CTDNEP1_ENST00000572043.1_5'Flank|RP1-4G17.5_ENST00000577138.1_Intron|ELP5_ENST00000354429.2_Missense_Mutation_p.C111R|CTDNEP1_ENST00000318988.6_5'Flank|ELP5_ENST00000396627.2_Missense_Mutation_p.C111R|ELP5_ENST00000574993.1_Missense_Mutation_p.C111R|ELP5_ENST00000573657.1_Missense_Mutation_p.C111R|CTDNEP1_ENST00000573600.1_5'Flank|ELP5_ENST00000574255.1_Missense_Mutation_p.C111R	NM_203414.1	NP_981959.1	Q8TE02	ELP5_HUMAN	elongator acetyltransferase complex subunit 5	111					chromatin organization (GO:0006325)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Elongator holoenzyme complex (GO:0033588)|nucleus (GO:0005634)											GAGAGCCATGTGCAAGAGGAC	0.562																																					p.C111R		.											.	.	0			c.T331C						.						126.0	93.0	104.0					17																	7157996		2203	4300	6503	SO:0001583	missense	23587	exon4			GCCATGTGCAAGA	BC002762	CCDS11094.1, CCDS11095.1	17p13.1	2012-08-14	2012-08-08	2012-08-08	ENSG00000170291	ENSG00000170291		"""Elongator acetyltransferase complex subunits"""	30617	protein-coding gene	gene with protein product	"""dermal papilla derived protein 6"", ""S-phase 2 protein"""	615019	"""chromosome 17 open reading frame 81"""	C17orf81		22854966	Standard	NM_203415		Approved	DERP6	uc002gfi.1	Q8TE02	OTTHUMG00000177974	ENST00000396628.2:c.331T>C	17.37:g.7157996T>C	ENSP00000379869:p.Cys111Arg	Somatic	62	0		WXS	Illumina HiSeq	Phase_I	71	19	NM_203414	1	0	42	129	86	A8K1M5|D3DTN9|Q659B6|Q7Z2T4|Q8TDR9|Q9BUB2|Q9Y2Q4	Missense_Mutation	SNP	ENST00000396628.2	37	CCDS11094.1	.	.	.	.	.	.	.	.	.	.	T	12.68	2.009540	0.35415	.	.	ENSG00000170291	ENST00000354429;ENST00000396628;ENST00000396627;ENST00000356683	T;T;T;T	0.47869	1.54;1.54;1.54;0.83	5.51	0.78	0.18556	.	0.815021	0.11405	N	0.567376	T	0.41858	0.1177	L	0.56769	1.78	0.19575	N	0.999968	B;B;B;B	0.26002	0.029;0.114;0.139;0.021	B;B;B;B	0.31290	0.025;0.053;0.127;0.025	T	0.43925	-0.9361	10	0.56958	D	0.05	-0.1605	4.5046	0.11881	0.0:0.2406:0.3505:0.4089	.	111;111;111;111	Q8TE02-2;Q8TE02-3;A8K1M5;Q8TE02	.;.;.;DERP6_HUMAN	R	111	ENSP00000346412:C111R;ENSP00000379869:C111R;ENSP00000379868:C111R;ENSP00000349111:C111R	ENSP00000346412:C111R	C	+	1	0	C17orf81	7098720	0.003000	0.15002	0.001000	0.08648	0.794000	0.44872	0.167000	0.16602	0.127000	0.18452	0.482000	0.46254	TGC	.		0.562	ELP5-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440111.1	NM_015362	
ATPAF2	91647	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	17	17925092	17925092	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:17925092G>A	ENST00000474627.3	-	6	737	c.583C>T	c.(583-585)Cac>Tac	p.H195Y	ATPAF2_ENST00000469327.1_5'UTR|ATPAF2_ENST00000585101.1_Intron	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	195					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					GATGCCAGGTGGCTGACGAGC	0.547																																					p.H195Y		.											.	ATPAF2-90	0			c.C583T						.						234.0	205.0	215.0					17																	17925092		2203	4300	6503	SO:0001583	missense	91647	exon6			CCAGGTGGCTGAC	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.583C>T	17.37:g.17925092G>A	ENSP00000417190:p.His195Tyr	Somatic	126	0		WXS	Illumina HiSeq	Phase_I	125	34	NM_145691	0	0	31	51	20	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	37	CCDS32585.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.247071	0.59103	.	.	ENSG00000171953	ENST00000474627;ENST00000444058	T;T	0.75821	-0.97;-0.97	5.41	5.41	0.78517	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	T	0.78767	0.4335	L	0.38175	1.15	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.70182	-0.4942	10	0.02654	T	1	4.9557	19.5423	0.95278	0.0:0.0:1.0:0.0	.	195	Q8N5M1	ATPF2_HUMAN	Y	195	ENSP00000417190:H195Y;ENSP00000397198:H195Y	ENSP00000434980:H195Y	H	-	1	0	ATPAF2	17865817	1.000000	0.71417	1.000000	0.80357	0.784000	0.44337	7.369000	0.79578	2.692000	0.91855	0.655000	0.94253	CAC	.		0.547	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691	
KRTAP29-1	100533177	bcgsc.ca	37	17	39458844	39458844	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:39458844G>C	ENST00000391353.1	-	1	259	c.260C>G	c.(259-261)tCc>tGc	p.S87C		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	87	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											GGCTGCGTGGGAGCACATAGG	0.537																																					p.S87C													.	.	0			c.C260G						.																																			SO:0001583	missense	100533177	exon1			GCGTGGGAGCACA		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.260C>G	17.37:g.39458844G>C	ENSP00000375148:p.Ser87Cys	Somatic	65	1		WXS	Illumina HiSeq	Phase_1	78	18	NM_001257309	0	0	0	0	0		Missense_Mutation	SNP	ENST00000391353.1	37		.	.	.	.	.	.	.	.	.	.	G	2.418	-0.333670	0.05278	.	.	ENSG00000212658	ENST00000391353	.	.	.	5.49	2.12	0.27331	.	.	.	.	.	T	0.11922	0.0290	.	.	.	.	.	.	.	.	.	.	.	.	T	0.33979	-0.9847	4	0.02654	T	1	.	4.6973	0.12809	0.1717:0.0:0.5735:0.2548	.	.	.	.	C	87	.	ENSP00000375148:S87C	S	-	2	0	KRTAP29-1	36712370	0.074000	0.21230	0.297000	0.24988	0.104000	0.19210	1.422000	0.34826	1.319000	0.45190	-0.263000	0.10527	TCC	.		0.537	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
TIMP2	7077	hgsc.bcm.edu	37	17	76921135	76921135	+	Silent	SNP	G	G	A	rs577686887	byFrequency	TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:76921135G>A	ENST00000262768.7	-	1	334	c.36C>T	c.(34-36)ctC>ctT	p.L12L	TIMP2_ENST00000536189.2_5'Flank	NM_003255.4	NP_003246.1	P16035	TIMP2_HUMAN	TIMP metallopeptidase inhibitor 2	12					aging (GO:0007568)|cellular response to organic substance (GO:0071310)|central nervous system development (GO:0007417)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of proteolysis (GO:0045861)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neuron differentiation (GO:0045666)|regulation of Rap protein signal transduction (GO:0032487)|response to cytokine (GO:0034097)|response to drug (GO:0042493)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(2)	2			BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.194)			GCAGGAGGCCGAGCGCCAGCC	0.781													G|||	90	0.0179712	0.0098	0.0159	5008	,	,		2705	0.0		0.0398	False		,,,				2504	0.0266				p.L12L		.											.	TIMP2-650	0			c.C36T						.						2.0	2.0	2.0					17																	76921135		972	1756	2728	SO:0001819	synonymous_variant	7077	exon1			GAGGCCGAGCGCC		CCDS11758.1	17q25	2008-07-18	2005-08-08		ENSG00000035862	ENSG00000035862			11821	protein-coding gene	gene with protein product		188825	"""tissue inhibitor of metalloproteinase 2"""			1427908	Standard	NM_003255		Approved	CSC-21K	uc002jwf.3	P16035	OTTHUMG00000154517	ENST00000262768.7:c.36C>T	17.37:g.76921135G>A		Somatic	0	0		WXS	Illumina HiSeq	Phase_I	6	6	NM_003255	0	0	0	4	4	Q16121|Q93006|Q9UDF7	Silent	SNP	ENST00000262768.7	37	CCDS11758.1																																																																																			.		0.781	TIMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335662.1	NM_003255	
DYM	54808	broad.mit.edu;ucsc.edu;bcgsc.ca	37	18	46798650	46798650	+	Silent	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:46798650C>G	ENST00000269445.6	-	11	1606	c.1149G>C	c.(1147-1149)ctG>ctC	p.L383L	DYM_ENST00000442713.2_Silent_p.L193L	NM_017653.3	NP_060123.3	Q7RTS9	DYM_HUMAN	dymeclin	383					bone development (GO:0060348)|Golgi organization (GO:0007030)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	enzyme binding (GO:0019899)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	18						CAACATGATACAGAATCTCAA	0.299																																					p.L383L													.	DYM-226	0			c.G1149C						.						77.0	72.0	74.0					18																	46798650		2203	4299	6502	SO:0001819	synonymous_variant	54808	exon11			ATGATACAGAATC	AK000078	CCDS11937.1	18q21.1	2008-03-12			ENSG00000141627	ENSG00000141627			21317	protein-coding gene	gene with protein product		607461					Standard	NM_017653		Approved	FLJ20071, DMC, SMC	uc002ldi.1	Q7RTS9	OTTHUMG00000132659	ENST00000269445.6:c.1149G>C	18.37:g.46798650C>G		Somatic	151	1		WXS	Illumina HiSeq	Phase_I	123	35	NM_017653	0	0	25	35	10	A8K5I8|B2RCF9|B4DKI7|Q3ZTS8|Q6P2P5|Q8N2M0|Q9BVE9|Q9NPU7	Silent	SNP	ENST00000269445.6	37	CCDS11937.1																																																																																			.		0.299	DYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255912.3	NM_017653	
HMHA1	23526	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	1082889	1082889	+	Silent	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:1082889G>T	ENST00000313093.2	+	20	2799	c.2568G>T	c.(2566-2568)ctG>ctT	p.L856L	HMHA1_ENST00000543365.1_Silent_p.L739L|HMHA1_ENST00000539243.2_Silent_p.L872L|HMHA1_ENST00000536472.1_Silent_p.L724L|HMHA1_ENST00000590577.1_Silent_p.L491L|HMHA1_ENST00000590214.1_Silent_p.L883L|HMHA1_ENST00000586866.1_Silent_p.L860L	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	856	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TCGTAGGGCTGGCCAAGGACA	0.711																																					p.L872L		.											.	HMHA1-91	0			c.G2616T						.						13.0	12.0	12.0					19																	1082889		2193	4288	6481	SO:0001819	synonymous_variant	23526	exon20			AGGGCTGGCCAAG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.2568G>T	19.37:g.1082889G>T		Somatic	49	0		WXS	Illumina HiSeq	Phase_I	49	19	NM_001258328	0	0	33	33	0	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			.		0.711	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
SAFB	6294	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	5653148	5653148	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:5653148C>T	ENST00000292123.5	+	10	1423	c.1316C>T	c.(1315-1317)aCa>aTa	p.T439I	SAFB_ENST00000454510.1_Missense_Mutation_p.T370I|SAFB_ENST00000538656.1_Missense_Mutation_p.T282I|SAFB_ENST00000433404.1_Missense_Mutation_p.T269I|SAFB_ENST00000588852.1_Missense_Mutation_p.T439I|SAFB_ENST00000586934.1_3'UTR|SAFB_ENST00000592224.1_Missense_Mutation_p.T439I	NM_001201338.1|NM_001201339.1|NM_002967.3	NP_001188267.1|NP_001188268.1|NP_002958.2	Q15424	SAFB1_HUMAN	scaffold attachment factor B	439	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				chromatin organization (GO:0006325)|growth (GO:0040007)|hormone metabolic process (GO:0042445)|intracellular estrogen receptor signaling pathway (GO:0030520)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|double-stranded DNA binding (GO:0003690)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(1)	23				UCEC - Uterine corpus endometrioid carcinoma (162;0.000222)		AAGGTTGTGACAAATGCCCGG	0.547																																					p.T439I	Colon(88;338 1345 6184 8214 20897)												.	SAFB-228	0			c.C1316T						.						102.0	86.0	92.0					19																	5653148		2203	4300	6503	SO:0001583	missense	6294	exon10			TTGTGACAAATGC	L43631	CCDS12142.1, CCDS56077.1, CCDS59339.1, CCDS59340.1	19p13.3-p13.2	2013-02-12				ENSG00000160633		"""RNA binding motif (RRM) containing"""	10520	protein-coding gene	gene with protein product	"""Hsp27 ERE-TATA binding protein"""	602895				9605873, 8600450	Standard	NM_002967		Approved	HET, SAFB1	uc002mcg.3	Q15424		ENST00000292123.5:c.1316C>T	19.37:g.5653148C>T	ENSP00000292123:p.Thr439Ile	Somatic	227	1		WXS	Illumina HiSeq	Phase_I	178	57	NM_002967	0	0	34	57	23	A0AV56|B7Z5B6|B7ZLP6|F5H0H3|O60406|Q59HH8	Missense_Mutation	SNP	ENST00000292123.5	37	CCDS12142.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.989341	0.74589	.	.	ENSG00000160633	ENST00000454510;ENST00000540206;ENST00000433404;ENST00000292123;ENST00000538656	T;T;T;T	0.08008	3.14;3.14;3.14;3.14	4.81	4.81	0.61882	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.56097	D	0.000021	T	0.21103	0.0508	L	0.32530	0.975	0.80722	D	1	D;D;D;P;D;D;D	0.89917	1.0;0.998;1.0;0.886;0.998;0.989;0.998	D;D;D;P;D;D;D	0.91635	0.999;0.99;0.999;0.806;0.994;0.963;0.994	T	0.01105	-1.1450	10	0.87932	D	0	-21.1697	18.4417	0.90669	0.0:1.0:0.0:0.0	.	238;282;370;439;439;439;439	B7Z1C7;B7Z2F6;F5H0H3;B7ZLP5;A0AV56;Q15424;B7ZLP6	.;.;.;.;.;SAFB1_HUMAN;.	I	370;334;269;439;282	ENSP00000415895:T370I;ENSP00000404545:T269I;ENSP00000292123:T439I;ENSP00000438880:T282I	ENSP00000292123:T439I	T	+	2	0	SAFB	5604148	1.000000	0.71417	0.967000	0.41034	0.964000	0.63967	7.491000	0.81471	2.654000	0.90174	0.563000	0.77884	ACA	.		0.547	SAFB-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451641.2		
C19orf53	28974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	13883025	13883025	+	5'Flank	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:13883025A>T	ENST00000588234.1	+	0	0				C19orf53_ENST00000593274.1_5'Flank|CTB-5E10.3_ENST00000586894.1_RNA|MRI1_ENST00000040663.6_Missense_Mutation_p.E347V|CTB-5E10.3_ENST00000586297.1_RNA|CTB-5E10.3_ENST00000591826.1_RNA|MRI1_ENST00000319545.8_Missense_Mutation_p.E300V	NM_014047.2	NP_054766.1	Q9UNZ5	L10K_HUMAN	chromosome 19 open reading frame 53											breast(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	6			OV - Ovarian serous cystadenocarcinoma(19;7.7e-24)|Epithelial(5;2.53e-19)			TTTGCCCCTGAGGAGCTCCGG	0.577																																					p.E347V		.											.	MRI1-91	0			c.A1040T						.						95.0	88.0	91.0					19																	13883025		2203	4300	6503	SO:0001631	upstream_gene_variant	84245	exon6			CCCCTGAGGAGCT	AF078852	CCDS12298.1	19p13.2	2011-11-24			ENSG00000104979	ENSG00000104979			24991	protein-coding gene	gene with protein product	"""leydig cell tumor 10 kDa protein homolog"""					11042152	Standard	NM_014047		Approved	HSPC023, LYDG10	uc002mxg.3	Q9UNZ5			19.37:g.13883025A>T	Exception_encountered	Somatic	217	0		WXS	Illumina HiSeq	Phase_I	208	48	NM_001031727	0	0	17	21	4	B2R4J9	Missense_Mutation	SNP	ENST00000588234.1	37	CCDS12298.1	.	.	.	.	.	.	.	.	.	.	A	11.35	1.611851	0.28712	.	.	ENSG00000037757	ENST00000040663;ENST00000319545	T;T	0.31247	1.5;1.5	4.88	3.84	0.44239	.	0.235842	0.36409	N	0.002620	T	0.27900	0.0687	L	0.48986	1.54	0.32290	N	0.566403	B;B	0.29085	0.232;0.011	B;B	0.30251	0.113;0.027	T	0.29518	-1.0009	10	0.42905	T	0.14	-48.5554	10.0893	0.42436	0.8314:0.1686:0.0:0.0	.	300;347	Q9BV20-2;Q9BV20	.;MTNA_HUMAN	V	347;300	ENSP00000040663:E347V;ENSP00000314871:E300V	ENSP00000040663:E347V	E	+	2	0	MRI1	13744025	0.000000	0.05858	0.400000	0.26346	0.621000	0.37620	0.854000	0.27791	0.685000	0.31468	0.397000	0.26171	GAG	.		0.577	C19orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453621.1	NM_014047	
PRKACA	5566	broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	14211641	14211641	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:14211641A>G	ENST00000308677.4	-	5	612	c.416T>C	c.(415-417)tTc>tCc	p.F139S	PRKACA_ENST00000589994.1_Missense_Mutation_p.F131S|PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000350356.3_5'UTR	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	139	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						CGCTTACCTGAACCTTCCGAT	0.592																																					p.F139S													.	PRKACA-978	0			c.T416C						.						101.0	75.0	84.0					19																	14211641		2203	4300	6503	SO:0001583	missense	5566	exon5			TACCTGAACCTTC		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.416T>C	19.37:g.14211641A>G	ENSP00000309591:p.Phe139Ser	Somatic	143	1		WXS	Illumina HiSeq	Phase_I	131	40	NM_002730	0	0	0	0	0	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Missense_Mutation	SNP	ENST00000308677.4	37	CCDS12304.1	.	.	.	.	.	.	.	.	.	.	A	19.18	3.778024	0.70107	.	.	ENSG00000072062	ENST00000308677;ENST00000350356;ENST00000535695;ENST00000536649	T	0.67345	-0.26	4.75	4.75	0.60458	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.283528	0.25267	N	0.031918	D	0.83815	0.5336	M	0.90082	3.085	0.46542	D	0.999096	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.86854	0.2025	10	0.87932	D	0	.	12.2465	0.54574	1.0:0.0:0.0:0.0	.	81;122;139;131	B7Z708;Q15136;P17612;P17612-2	.;.;KAPCA_HUMAN;.	S	139;131;139;81	ENSP00000309591:F139S	ENSP00000309591:F139S	F	-	2	0	PRKACA	14072641	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	9.217000	0.95160	1.796000	0.52611	0.378000	0.23410	TTC	.		0.592	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
USHBP1	83878	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	17366410	17366410	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:17366410G>A	ENST00000252597.3	-	10	1649	c.1476C>T	c.(1474-1476)gcC>gcT	p.A492A	USHBP1_ENST00000431146.2_Silent_p.A428A|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						GGTCCGCCAGGGCCTCCTGTG	0.632																																					p.A492A		.											.	USHBP1-91	0			c.C1476T						.						10.0	12.0	11.0					19																	17366410		2188	4264	6452	SO:0001819	synonymous_variant	83878	exon10			CGCCAGGGCCTCC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1476C>T	19.37:g.17366410G>A		Somatic	79	0		WXS	Illumina HiSeq	Phase_I	79	14	NM_031941	0	0	0	0	0		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			.		0.632	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
CBLC	23624	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	45281521	45281521	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:45281521C>G	ENST00000270279.3	+	1	396	c.333C>G	c.(331-333)ttC>ttG	p.F111L	CBLC_ENST00000341505.4_Missense_Mutation_p.F111L	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	111	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				ACGAGCTCTTCCGGGCGGGCT	0.657			M		AML																																p.F111L		.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC-849	0			c.C333G						.						4.0	5.0	5.0					19																	45281521		1948	3848	5796	SO:0001583	missense	23624	exon1			GCTCTTCCGGGCG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.333C>G	19.37:g.45281521C>G	ENSP00000270279:p.Phe111Leu	Somatic	18	0		WXS	Illumina HiSeq	Phase_I	19	5	NM_001130852	0	0	3	3	0	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	.	.	.	.	.	.	.	.	.	.	.	14.98	2.697608	0.48307	.	.	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.78924	-1.22;-1.22	3.49	3.49	0.39957	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.000000	0.64402	D	0.000016	T	0.78978	0.4369	M	0.81497	2.545	0.39134	D	0.961902	P;D	0.52996	0.939;0.957	P;P	0.45310	0.476;0.469	D	0.83554	0.0103	10	0.66056	D	0.02	-25.9304	10.6934	0.45884	0.0:1.0:0.0:0.0	.	111;111	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	L	111	ENSP00000270279:F111L;ENSP00000340250:F111L	ENSP00000270279:F111L	F	+	3	2	CBLC	49973361	1.000000	0.71417	1.000000	0.80357	0.227000	0.25037	2.404000	0.44539	1.962000	0.57031	0.556000	0.70494	TTC	.		0.657	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
ZNF577	84765	hgsc.bcm.edu;ucsc.edu;bcgsc.ca	37	19	52376955	52376955	+	Silent	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:52376955A>G	ENST00000301399.5	-	7	653	c.288T>C	c.(286-288)ttT>ttC	p.F96F	ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	96					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TCTGGATTACAAAACCTAAAT	0.358																																					p.F96F		.											.	ZNF577-91	0			c.T288C						.						37.0	34.0	35.0					19																	52376955		2203	4299	6502	SO:0001819	synonymous_variant	84765	exon7			GATTACAAAACCT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.288T>C	19.37:g.52376955A>G		Somatic	41	0		WXS	Illumina HiSeq	Phase_I	59	13	NM_032679	0	0	0	0	0	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			.		0.358	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
ZNF606	80095	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	19	58489700	58489700	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:58489700T>C	ENST00000341164.4	-	7	2968	c.2348A>G	c.(2347-2349)cAg>cGg	p.Q783R	ZNF606_ENST00000536132.1_Missense_Mutation_p.Q693R	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	783					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		GTGATTTCTCTGGTGTTGAAG	0.368																																					p.Q783R		.											.	ZNF606-92	0			c.A2348G						.						91.0	84.0	86.0					19																	58489700		2203	4300	6503	SO:0001583	missense	80095	exon7			TTTCTCTGGTGTT	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.2348A>G	19.37:g.58489700T>C	ENSP00000343617:p.Gln783Arg	Somatic	134	0		WXS	Illumina HiSeq	Phase_I	152	39	NM_025027	0	0	5	8	3	A8KAN2|Q8NE04|Q96JH5	Missense_Mutation	SNP	ENST00000341164.4	37	CCDS12968.1	.	.	.	.	.	.	.	.	.	.	T	9.820	1.185460	0.21870	.	.	ENSG00000166704	ENST00000341164;ENST00000536132	T;T	0.25749	1.78;1.78	4.77	2.52	0.30459	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40302	N	0.001121	T	0.18882	0.0453	L	0.39147	1.195	0.23988	N	0.996254	B	0.11235	0.004	B	0.10450	0.005	T	0.16217	-1.0410	10	0.49607	T	0.09	.	7.2862	0.26340	0.0:0.0828:0.145:0.7722	.	783	Q8WXB4	ZN606_HUMAN	R	783;693	ENSP00000343617:Q783R;ENSP00000445624:Q693R	ENSP00000343617:Q783R	Q	-	2	0	ZNF606	63181512	0.000000	0.05858	1.000000	0.80357	0.997000	0.91878	0.272000	0.18644	0.941000	0.37499	0.528000	0.53228	CAG	.		0.368	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
CYP27C1	339761	ucsc.edu	37	2	127950814	127950814	+	Silent	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:127950814G>T	ENST00000335247.7	-	7	988	c.858C>A	c.(856-858)gcC>gcA	p.A286A	CYP27C1_ENST00000409327.1_Silent_p.A286A	NM_001001665.3	NP_001001665.3	Q4G0S4	C27C1_HUMAN	cytochrome P450, family 27, subfamily C, polypeptide 1	286						membrane (GO:0016020)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	16	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.071)		GGAACTCCTTGGCCCGAGGGA	0.542																																					p.A286A													.	CYP27C1-90	0			c.C858A						.						96.0	91.0	93.0					2																	127950814		2203	4300	6503	SO:0001819	synonymous_variant	339761	exon7			CTCCTTGGCCCGA	AC027142	CCDS33285.1	2q14.3	2008-05-14	2007-05-18		ENSG00000186684	ENSG00000186684		"""Cytochrome P450s"""	33480	protein-coding gene	gene with protein product							Standard	NM_001001665		Approved	FLJ16008	uc002tod.2	Q4G0S4	OTTHUMG00000153400	ENST00000335247.7:c.858C>A	2.37:g.127950814G>T		Somatic	137	4		WXS	Illumina HiSeq		124	34	NM_001001665	0	0	0	0	0	Q6ZNI7	Silent	SNP	ENST00000335247.7	37	CCDS33285.1																																																																																			.		0.542	CYP27C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331046.1	NM_001001665	
CHRNA1	1134	broad.mit.edu;ucsc.edu	37	2	175614800	175614800	+	Silent	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:175614800G>A	ENST00000261007.5	-	8	1017	c.951C>T	c.(949-951)ccC>ccT	p.P317P	AC018890.6_ENST00000442996.1_RNA|CHRNA1_ENST00000409542.1_Silent_p.P210P|CHRNA1_ENST00000348749.5_Silent_p.P292P|CHRNA1_ENST00000409219.1_Silent_p.P292P	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	317					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	TTCCAATCAAGGGCACAGCAC	0.517																																					p.P317P													.	CHRNA1-518	0			c.C951T						.						204.0	156.0	172.0					2																	175614800		2203	4300	6503	SO:0001819	synonymous_variant	1134	exon8			AATCAAGGGCACA	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.951C>T	2.37:g.175614800G>A		Somatic	87	2		WXS	Illumina HiSeq	Phase_I	132	22	NM_001039523	0	0	0	0	0	B4DRV6|D3DPE8	Silent	SNP	ENST00000261007.5	37	CCDS33331.1																																																																																			.		0.517	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
SIRPA	140885	bcgsc.ca	37	20	1902142	1902142	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:1902142A>G	ENST00000358771.4	+	3	690	c.538A>G	c.(538-540)Atc>Gtc	p.I180V	SIRPA_ENST00000356025.3_Missense_Mutation_p.I180V|SIRPA_ENST00000400068.3_Missense_Mutation_p.I180V	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	180	Ig-like C1-type 1.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		ACCCAGAGACATCACCCTGAA	0.592																																					p.I180V	GBM(155;1668 1920 5945 42733 48121)												.	SIRPA-227	0			c.A538G						.						80.0	77.0	78.0					20																	1902142		2203	4297	6500	SO:0001583	missense	140885	exon4			AGAGACATCACCC	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.538A>G	20.37:g.1902142A>G	ENSP00000351621:p.Ile180Val	Somatic	383	2		WXS	Illumina HiSeq	Phase_1	316	79	NM_001040022	0	0	32	70	38	A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	A	7.686	0.690124	0.15039	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.02863	4.13;4.13;4.13	4.38	-0.0461	0.13848	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.416111	0.22732	N	0.056306	T	0.05868	0.0153	M	0.77103	2.36	0.26965	N	0.965718	B;P;B	0.34909	0.045;0.475;0.149	B;B;B	0.41619	0.055;0.361;0.081	T	0.11941	-1.0567	10	0.54805	T	0.06	.	6.9109	0.24335	0.6134:0.0:0.3866:0.0	.	160;180;180	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	V	180	ENSP00000382941:I180V;ENSP00000348307:I180V;ENSP00000351621:I180V	ENSP00000348307:I180V	I	+	1	0	SIRPA	1850142	0.954000	0.32549	0.989000	0.46669	0.163000	0.22366	2.005000	0.40864	0.003000	0.14656	-0.475000	0.04921	ATC	.		0.592	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
FRG1B	284802	bcgsc.ca	37	20	29628236	29628236	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:29628236G>C	ENST00000278882.3	+	6	618	c.238G>C	c.(238-240)Gct>Cct	p.A80P	FRG1B_ENST00000358464.4_Missense_Mutation_p.A80P|FRG1B_ENST00000439954.2_Missense_Mutation_p.A85P			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	80								p.A80P(8)		endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						GGGGAAAATGGCTTTGTTGGC	0.363																																					.													.	FRG1B-22	8	Substitution - Missense(8)	prostate(4)|kidney(4)	.						.																																			SO:0001583	missense	284802	.			AAAATGGCTTTGT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.238G>C	20.37:g.29628236G>C	ENSP00000278882:p.Ala80Pro	Somatic	771	12		WXS	Illumina HiSeq	Phase_1	778	17	.	0	0	0	0	0	C4AME5	RNA	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	g	15.73	2.920277	0.52653	.	.	ENSG00000149531	ENST00000278882;ENST00000439954;ENST00000358464	T	0.57595	0.39	2.08	2.08	0.27032	Actin cross-linking (1);	0.052409	0.85682	D	0.000000	T	0.68952	0.3057	.	.	.	0.80722	D	1	D;D	0.64830	0.994;0.988	D;D	0.85130	0.997;0.993	T	0.72766	-0.4194	9	0.87932	D	0	.	10.2211	0.43198	0.0:0.0:1.0:0.0	.	85;80	F5H5R5;Q9BZ01	.;FRG1B_HUMAN	P	80;85;80	ENSP00000408863:A85P	ENSP00000278882:A80P	A	+	1	0	FRG1B	28241897	1.000000	0.71417	1.000000	0.80357	0.334000	0.28698	8.494000	0.90477	1.475000	0.48197	0.423000	0.28283	GCT	.		0.363	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000078494.2	NR_003579	
BPIFB6	128859	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	31627181	31627181	+	Missense_Mutation	SNP	C	C	A	rs370022331		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:31627181C>A	ENST00000349552.1	+	10	929	c.929C>A	c.(928-930)cCc>cAc	p.P310H		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	310						extracellular region (GO:0005576)	lipid binding (GO:0008289)										AAGTCAAAGCCCTTGACGACC	0.522																																					p.P310H		.											.	.	0			c.C929A						.						102.0	107.0	105.0					20																	31627181		2203	4300	6503	SO:0001583	missense	128859	exon10			CAAAGCCCTTGAC	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.929C>A	20.37:g.31627181C>A	ENSP00000344929:p.Pro310His	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	88	33	NM_174897	0	0	0	0	0		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	.	.	.	.	.	.	.	.	.	.	C	11.65	1.703220	0.30232	.	.	ENSG00000167104	ENST00000349552	T	0.08896	3.04	4.44	3.47	0.39725	.	0.000000	0.56097	D	0.000035	T	0.25606	0.0623	M	0.81497	2.545	0.29520	N	0.853577	D	0.71674	0.998	D	0.66716	0.946	T	0.05354	-1.0890	10	0.46703	T	0.11	.	10.1046	0.42526	0.0:0.7964:0.2036:0.0	.	310	Q8NFQ5	BPIB6_HUMAN	H	310	ENSP00000344929:P310H	ENSP00000344929:P310H	P	+	2	0	BPIFB6	31090842	1.000000	0.71417	0.986000	0.45419	0.039000	0.13416	1.937000	0.40193	1.047000	0.40274	0.561000	0.74099	CCC	.		0.522	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
TTPAL	79183	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	43108944	43108944	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43108944A>G	ENST00000372904.3	+	3	448	c.305A>G	c.(304-306)tAc>tGc	p.Y102C	TTPAL_ENST00000372906.2_Missense_Mutation_p.Y102C|TTPAL_ENST00000262605.4_Missense_Mutation_p.Y102C	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	102						intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						CTCGTCAACTACCACAGCTGT	0.567																																					p.Y102C		.											.	TTPAL-153	0			c.A305G						.						51.0	44.0	46.0					20																	43108944		2203	4300	6503	SO:0001583	missense	79183	exon2			TCAACTACCACAG	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 121"""	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.305A>G	20.37:g.43108944A>G	ENSP00000361995:p.Tyr102Cys	Somatic	167	0		WXS	Illumina HiSeq	Phase_I	153	49	NM_001039199	0	0	1	2	1	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	37	CCDS13332.2	.	.	.	.	.	.	.	.	.	.	A	22.6	4.306489	0.81247	.	.	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000372906;ENST00000456317	D;D;D;D	0.86432	-2.12;-2.12;-2.12;-2.12	5.1	5.1	0.69264	Phosphatidylinositol transfer protein-like, N-terminal (1);Cellular retinaldehyde-binding/triple function, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.92886	0.7737	M	0.76328	2.33	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93787	0.7089	10	0.87932	D	0	-22.794	14.903	0.70696	1.0:0.0:0.0:0.0	.	102	Q9BTX7	TTPAL_HUMAN	C	102	ENSP00000262605:Y102C;ENSP00000361995:Y102C;ENSP00000361997:Y102C;ENSP00000412720:Y102C	ENSP00000262605:Y102C	Y	+	2	0	TTPAL	42542358	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.317000	0.96327	1.909000	0.55274	0.533000	0.62120	TAC	.		0.567	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331	
ADA	100	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	20	43251682	43251682	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr20:43251682G>A	ENST00000372874.4	-	7	778	c.644C>T	c.(643-645)gCc>gTc	p.A215V	ADA_ENST00000464097.1_5'UTR|PKIG_ENST00000372887.1_Intron|PKIG_ENST00000372882.3_Intron|ADA_ENST00000537820.1_Intron	NM_000022.2	NP_000013.2	P00813	ADA_HUMAN	adenosine deaminase	215			A -> T (in ADASCID; dbSNP:rs114025668). {ECO:0000269|PubMed:2166947}.		adenosine catabolic process (GO:0006154)|aging (GO:0007568)|cell adhesion (GO:0007155)|dATP catabolic process (GO:0046061)|deoxyadenosine catabolic process (GO:0006157)|embryonic digestive tract development (GO:0048566)|germinal center B cell differentiation (GO:0002314)|histamine secretion (GO:0001821)|hypoxanthine salvage (GO:0043103)|inosine biosynthetic process (GO:0046103)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|negative regulation of adenosine receptor signaling pathway (GO:0060169)|negative regulation of circadian sleep/wake cycle, non-REM sleep (GO:0042323)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mature B cell apoptotic process (GO:0002906)|negative regulation of mucus secretion (GO:0070256)|negative regulation of penile erection (GO:0060407)|negative regulation of thymocyte apoptotic process (GO:0070244)|nucleobase-containing small molecule metabolic process (GO:0055086)|Peyer's patch development (GO:0048541)|placenta development (GO:0001890)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of germinal center formation (GO:0002636)|positive regulation of heart rate (GO:0010460)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of T cell receptor signaling pathway (GO:0050862)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide salvage (GO:0032261)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|purine-containing compound salvage (GO:0043101)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to hypoxia (GO:0001666)|response to morphine (GO:0043278)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|T cell activation (GO:0042110)|trophectodermal cell differentiation (GO:0001829)|xanthine biosynthetic process (GO:0046111)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|lysosome (GO:0005764)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	adenosine deaminase activity (GO:0004000)|purine nucleoside binding (GO:0001883)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(2)|prostate(3)|skin(2)|urinary_tract(1)	18		all_lung(126;1.24e-07)|Lung NSC(126;1.94e-07)|Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)		Adenosine(DB00640)|Dipyridamole(DB00975)|Edetic Acid(DB00974)|Nelarabine(DB01280)|Pentostatin(DB00552)|Theophylline(DB00277)|Vidarabine(DB00194)	CACCTCCCCGGCGTGGACAGT	0.657									Adenosine Deaminase Deficiency																												p.A215V		.											.	ADA-653	0			c.C644T						.						67.0	68.0	68.0					20																	43251682		2203	4300	6503	SO:0001583	missense	100	exon7	Familial Cancer Database	Severe Combined Immunodeficiency (SCID) due to ADA-deficiency	TCCCCGGCGTGGA	X02994	CCDS13335.1	20q13.12	2014-09-17			ENSG00000196839	ENSG00000196839	3.5.4.4		186	protein-coding gene	gene with protein product		608958				6198240, 6090454	Standard	NM_000022		Approved		uc002xmj.3	P00813	OTTHUMG00000033081	ENST00000372874.4:c.644C>T	20.37:g.43251682G>A	ENSP00000361965:p.Ala215Val	Somatic	112	0		WXS	Illumina HiSeq	Phase_I	98	20	NM_000022	0	0	10	14	4	Q53F92|Q6LA59	Missense_Mutation	SNP	ENST00000372874.4	37	CCDS13335.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.377508	0.61735	.	.	ENSG00000196839	ENST00000372874	D	0.97114	-4.25	4.89	3.9	0.45041	Adenosine/AMP deaminase (1);	0.048514	0.85682	D	0.000000	D	0.98466	0.9489	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.63113	0.911	D	0.98951	1.0794	10	0.87932	D	0	-9.5965	15.4157	0.74966	0.0:0.1385:0.8615:0.0	.	215	P00813	ADA_HUMAN	V	215	ENSP00000361965:A215V	ENSP00000361965:A215V	A	-	2	0	ADA	42685096	1.000000	0.71417	0.136000	0.22124	0.136000	0.21042	6.472000	0.73567	2.549000	0.85964	0.563000	0.77884	GCC	.		0.657	ADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080509.2	NM_000022	
KCNE2	9992	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	21	35743124	35743124	+	Missense_Mutation	SNP	C	C	T	rs199473367		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:35743124C>T	ENST00000290310.3	+	2	487	c.347C>T	c.(346-348)gCg>gTg	p.A116V	AP000320.6_ENST00000440403.1_RNA	NM_172201.1	NP_751951.1	Q9Y6J6	KCNE2_HUMAN	potassium voltage-gated channel, Isk-related family, member 2	116					aging (GO:0007568)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cellular protein localization (GO:0034613)|cellular response to drug (GO:0035690)|membrane repolarization (GO:0086009)|membrane repolarization during action potential (GO:0086011)|positive regulation of proteasomal protein catabolic process (GO:1901800)|potassium ion export (GO:0071435)|potassium ion import (GO:0010107)|potassium ion transmembrane transport (GO:0071805)|regulation of cyclic nucleotide-gated ion channel activity (GO:1902159)|regulation of delayed rectifier potassium channel activity (GO:1902259)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of inward rectifier potassium channel activity (GO:1901979)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|tongue development (GO:0043586)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|large_intestine(1)	2						AACATTGGTGCGGCTGGGTTC	0.488																																					p.A116V		.											.	KCNE2-68	0			c.C347T	GRCh37	CM003450	KCNE2	M		.						44.0	40.0	42.0					21																	35743124		2203	4300	6503	SO:0001583	missense	9992	exon2			TTGGTGCGGCTGG	AF071002	CCDS13635.1	21q22.1	2014-09-17			ENSG00000159197	ENSG00000159197		"""Potassium channels"""	6242	protein-coding gene	gene with protein product		603796				10219239	Standard	NM_172201		Approved	MiRP1, LQT6	uc002ytt.1	Q9Y6J6	OTTHUMG00000086189	ENST00000290310.3:c.347C>T	21.37:g.35743124C>T	ENSP00000290310:p.Ala116Val	Somatic	97	0		WXS	Illumina HiSeq	Phase_I	99	26	NM_172201	0	0	4	4	0	A5H1P3|D3DSF8|Q52LJ5	Missense_Mutation	SNP	ENST00000290310.3	37	CCDS13635.1	.	.	.	.	.	.	.	.	.	.	C	19.32	3.805758	0.70682	.	.	ENSG00000159197	ENST00000290310	D	0.93307	-3.2	5.66	5.66	0.87406	.	0.000000	0.64402	D	0.000007	D	0.94686	0.8286	L	0.32530	0.975	0.42882	D	0.994175	D	0.89917	1.0	D	0.78314	0.991	D	0.95265	0.8372	10	0.66056	D	0.02	-27.5208	17.5309	0.87814	0.0:1.0:0.0:0.0	.	116	Q9Y6J6	KCNE2_HUMAN	V	116	ENSP00000290310:A116V	ENSP00000290310:A116V	A	+	2	0	KCNE2	34664994	0.991000	0.36638	0.150000	0.22450	0.102000	0.19082	3.221000	0.51215	2.657000	0.90304	0.655000	0.94253	GCG	.		0.488	KCNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194068.2		
ROBO2	6092	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	77671536	77671536	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:77671536A>T	ENST00000461745.1	+	23	4613	c.3713A>T	c.(3712-3714)gAc>gTc	p.D1238V	ROBO2_ENST00000487694.3_Missense_Mutation_p.D1254V|ROBO2_ENST00000332191.8_Missense_Mutation_p.D1238V	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	1238					apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		AGAGCACTGGACCAGACTCCT	0.463																																					p.D1238V		.											.	ROBO2-328	0			c.A3713T						.						74.0	77.0	76.0					3																	77671536		1902	4120	6022	SO:0001583	missense	6092	exon23			CACTGGACCAGAC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.3713A>T	3.37:g.77671536A>T	ENSP00000417164:p.Asp1238Val	Somatic	70	0		WXS	Illumina HiSeq	Phase_I	48	19	NM_002942	0	0	0	0	0	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.917020	0.52546	.	.	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000461745;ENST00000332191	T;T;T	0.61510	0.1;0.14;0.12	5.56	5.56	0.83823	.	0.299670	0.23303	N	0.049659	T	0.43897	0.1268	N	0.08118	0	0.30052	N	0.811715	B;B;B	0.26512	0.151;0.096;0.151	B;B;B	0.34093	0.086;0.175;0.086	T	0.56667	-0.7941	9	0.56958	D	0.05	.	15.6959	0.77499	1.0:0.0:0.0:0.0	.	1254;1238;1238	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	V	1254;1254;1238;1238	ENSP00000417335:D1254V;ENSP00000417164:D1238V;ENSP00000327536:D1238V	ENSP00000327536:D1238V	D	+	2	0	ROBO2	77754226	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	8.962000	0.93254	2.110000	0.64415	0.528000	0.53228	GAC	.		0.463	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
MRPL3	11222	broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	131190046	131190046	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:131190046G>T	ENST00000264995.3	-	7	854	c.707C>A	c.(706-708)aCc>aAc	p.T236N	MRPL3_ENST00000425847.2_Missense_Mutation_p.T263N	NM_007208.3	NP_009139.1	P09001	RM03_HUMAN	mitochondrial ribosomal protein L3	236					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						TCTCCTGTGGGTTTTCGTTTG	0.418																																					p.T236N													.	MRPL3-90	0			c.C707A						.						123.0	125.0	124.0					3																	131190046		2203	4300	6503	SO:0001583	missense	11222	exon7			CTGTGGGTTTTCG	X06323	CCDS3071.1	3q21-q23	2012-09-13			ENSG00000114686	ENSG00000114686		"""Mitochondrial ribosomal proteins / large subunits"""	10379	protein-coding gene	gene with protein product		607118		RPML3		2891103	Standard	NM_007208		Approved	MRL3	uc003eoh.3	P09001	OTTHUMG00000159607	ENST00000264995.3:c.707C>A	3.37:g.131190046G>T	ENSP00000264995:p.Thr236Asn	Somatic	100	1		WXS	Illumina HiSeq	Phase_I	95	17	NM_007208	0	0	55	95	40	Q6IBT2	Missense_Mutation	SNP	ENST00000264995.3	37	CCDS3071.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.6|25.6	4.650246|4.650246	0.87958|0.87958	.|.	.|.	ENSG00000114686|ENSG00000114686	ENST00000511168|ENST00000264995;ENST00000425847;ENST00000507669	.|T;T;T	.|0.41758	.|0.99;0.99;0.99	5.56|5.56	5.56|5.56	0.83823|0.83823	.|Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.61035|0.61035	0.2315|0.2315	L|L	0.49699|0.49699	1.58|1.58	0.80722|0.80722	D|D	1|1	.|D;D	.|0.65815	.|0.979;0.995	.|D;D	.|0.76575	.|0.976;0.988	T|T	0.61860|0.61860	-0.6976|-0.6976	5|10	.|0.72032	.|D	.|0.01	-16.478|-16.478	18.2922|18.2922	0.90134|0.90134	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|263;236	.|E7ETU7;P09001	.|.;RM03_HUMAN	K|N	250|236;263;131	.|ENSP00000264995:T236N;ENSP00000398536:T263N;ENSP00000422419:T131N	.|ENSP00000264995:T236N	N|T	-|-	3|2	2|0	MRPL3|MRPL3	132672736|132672736	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	8.563000|8.563000	0.90723|0.90723	2.614000|2.614000	0.88457|0.88457	0.650000|0.650000	0.86243|0.86243	AAC|ACC	.		0.418	MRPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356471.3	NM_007208	
AMOTL2	51421	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	134078995	134078995	+	Missense_Mutation	SNP	A	A	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:134078995A>C	ENST00000422605.2	-	7	2002	c.1836T>G	c.(1834-1836)aaT>aaG	p.N612K	AMOTL2_ENST00000514516.1_Missense_Mutation_p.N670K|AMOTL2_ENST00000249883.5_Missense_Mutation_p.N612K|AMOTL2_ENST00000513145.1_Missense_Mutation_p.N610K			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	612					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						GCAGACCCTCATTGAAGCTGC	0.622																																					p.N612K		.											.	AMOTL2-135	0			c.T1836G						.						57.0	50.0	52.0					3																	134078995		2203	4300	6503	SO:0001583	missense	51421	exon7			ACCCTCATTGAAG	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1836T>G	3.37:g.134078995A>C	ENSP00000409999:p.Asn612Lys	Somatic	78	0		WXS	Illumina HiSeq	Phase_I	62	19	NM_016201	0	0	28	50	22	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	37		.	.	.	.	.	.	.	.	.	.	A	16.66	3.183876	0.57800	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.17370	2.29;2.29;2.28;2.29	5.23	-0.975	0.10289	.	0.000000	0.85682	D	0.000000	T	0.26810	0.0656	L	0.57536	1.79	0.58432	D	0.999996	D;D;D	0.64830	0.992;0.992;0.994	P;P;D	0.63793	0.866;0.866;0.918	T	0.14727	-1.0462	10	0.11794	T	0.64	-26.2587	11.2577	0.49063	0.5554:0.0:0.4446:0.0	.	610;612;670	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	K	612;612;670;610	ENSP00000249883:N612K;ENSP00000409999:N612K;ENSP00000424765:N670K;ENSP00000425475:N610K	ENSP00000249883:N612K	N	-	3	2	AMOTL2	135561685	0.461000	0.25783	0.993000	0.49108	0.925000	0.55904	-0.316000	0.08071	-0.263000	0.09378	-0.441000	0.05720	AAT	.		0.622	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201	
SLC25A36	55186	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	140675502	140675502	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:140675502G>A	ENST00000324194.6	+	2	343	c.175G>A	c.(175-177)Gta>Ata	p.V59I	SLC25A36_ENST00000453248.2_Missense_Mutation_p.V59I|SLC25A36_ENST00000507429.1_Missense_Mutation_p.V59I|SLC25A36_ENST00000393015.4_3'UTR|SLC25A36_ENST00000446041.2_Missense_Mutation_p.V59I			Q96CQ1	S2536_HUMAN	solute carrier family 25 (pyrimidine nucleotide carrier ), member 36	59					response to estradiol (GO:0032355)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	6						TGTCAACCGAGTAGTGTCTCC	0.433																																					p.V59I		.											.	SLC25A36-90	0			c.G175A						.						140.0	135.0	137.0					3																	140675502		2203	4300	6503	SO:0001583	missense	55186	exon2			AACCGAGTAGTGT	AK001480	CCDS3114.1, CCDS46927.1	3q23	2013-05-22	2012-03-29		ENSG00000114120	ENSG00000114120		"""Solute carriers"""	25554	protein-coding gene	gene with protein product			"""solute carrier family 25, member 36"""				Standard	NM_001104647		Approved	FLJ10618, PNC2	uc003etr.2	Q96CQ1	OTTHUMG00000160260	ENST00000324194.6:c.175G>A	3.37:g.140675502G>A	ENSP00000320688:p.Val59Ile	Somatic	85	0		WXS	Illumina HiSeq	Phase_I	73	24	NM_018155	0	0	5	10	5	A8MYF7|Q05CY1|Q9H0G8|Q9NVN5	Missense_Mutation	SNP	ENST00000324194.6	37	CCDS46927.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666084	0.29604	.	.	ENSG00000114120	ENST00000446041;ENST00000507429;ENST00000324194;ENST00000453248;ENST00000513887	T;T;T;T	0.78924	-1.22;-1.22;-1.22;-1.17	5.29	-0.772	0.10998	Mitochondrial carrier domain (2);	0.517046	0.21808	N	0.068811	T	0.62551	0.2437	L	0.31578	0.945	0.09310	N	0.999996	B;B;B;B	0.13594	0.0;0.001;0.008;0.0	B;B;B;B	0.13407	0.005;0.003;0.009;0.005	T	0.43130	-0.9410	10	0.23302	T	0.38	-6.1006	11.8956	0.52654	0.3779:0.0:0.6221:0.0	.	59;59;59;59	B4DL01;Q96CQ1-3;Q96CQ1;F6SDC8	.;.;S2536_HUMAN;.	I	59;59;59;59;9	ENSP00000401938:V59I;ENSP00000421470:V59I;ENSP00000320688:V59I;ENSP00000391521:V59I	ENSP00000320688:V59I	V	+	1	0	SLC25A36	142158192	0.994000	0.37717	0.770000	0.31555	0.903000	0.53119	1.349000	0.33998	-0.689000	0.05149	-0.813000	0.03139	GTA	.		0.433	SLC25A36-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359929.1	NM_018155	
MED12L	116931	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	151107816	151107816	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:151107816T>G	ENST00000474524.1	+	36	5434	c.5396T>G	c.(5395-5397)aTc>aGc	p.I1799S	MED12L_ENST00000273432.4_Missense_Mutation_p.I1659S	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1799						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			TACTCGCCTATCTCCTCCCAA	0.468																																					p.I1799S		.											.	MED12L-576	0			c.T5396G						.						175.0	171.0	172.0					3																	151107816		2203	4300	6503	SO:0001583	missense	116931	exon36			CGCCTATCTCCTC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5396T>G	3.37:g.151107816T>G	ENSP00000417235:p.Ile1799Ser	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	88	37	NM_053002	0	0	0	0	0	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	.	.	.	.	.	.	.	.	.	.	T	14.12	2.440148	0.43326	.	.	ENSG00000144893	ENST00000474524;ENST00000273432	T;T	0.60171	0.43;0.21	5.73	5.73	0.89815	.	0.222920	0.46442	D	0.000300	T	0.39682	0.1087	N	0.08118	0	0.32093	N	0.591569	B;B	0.23058	0.005;0.079	B;B	0.19666	0.002;0.026	T	0.52132	-0.8616	10	0.87932	D	0	-5.497	14.2508	0.66019	0.0:0.0:0.0:1.0	.	1659;1799	F8WAE6;Q86YW9	.;MD12L_HUMAN	S	1799;1659	ENSP00000417235:I1799S;ENSP00000273432:I1659S	ENSP00000273432:I1659S	I	+	2	0	MED12L	152590506	0.493000	0.26035	0.865000	0.33974	0.987000	0.75469	3.781000	0.55394	2.186000	0.69663	0.459000	0.35465	ATC	.		0.468	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
MUC4	4585	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	195516343	195516343	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:195516343C>A	ENST00000463781.3	-	2	2567	c.2108G>T	c.(2107-2109)gGt>gTt	p.G703V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G703V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	708					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGTTGTGTGACCATCCCCGGT	0.612																																					p.G703V		.											.	MUC4-90	0			c.G2108T						.						90.0	101.0	97.0					3																	195516343		2126	4247	6373	SO:0001583	missense	4585	exon2			GTGTGACCATCCC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.2108G>T	3.37:g.195516343C>A	ENSP00000417498:p.Gly703Val	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	84	19	NM_018406	0	0	0	0	0	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	3.634	-0.074901	0.07184	.	.	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.59364	0.27;0.3	3.16	0.13	0.14746	.	1.957170	0.02848	N	0.128792	T	0.33673	0.0871	N	0.22421	0.69	0.09310	N	1	P;B	0.43477	0.808;0.316	B;B	0.33568	0.166;0.067	T	0.20174	-1.0283	10	0.13108	T	0.6	0.0732	1.7414	0.02953	0.2123:0.457:0.2069:0.1238	.	703;708	E7ESK3;Q99102	.;MUC4_HUMAN	V	703;703;677	ENSP00000417498:G703V;ENSP00000420243:G703V	ENSP00000376209:G677V	G	-	2	0	MUC4	197000738	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.726000	0.04936	0.016000	0.14998	-0.166000	0.13349	GGT	.		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FAM184B	27146	broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	17635486	17635486	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:17635486C>A	ENST00000265018.3	-	17	3127	c.2915G>T	c.(2914-2916)aGc>aTc	p.S972I	MED28_ENST00000237380.7_3'UTR	NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	972										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						GACCACGCGGCTGGGCACGTC	0.443																																					p.S972I													.	FAM184B-23	0			c.G2915T						.						61.0	64.0	63.0					4																	17635486		692	1591	2283	SO:0001583	missense	27146	exon17			ACGCGGCTGGGCA		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.2915G>T	4.37:g.17635486C>A	ENSP00000265018:p.Ser972Ile	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	82	20	NM_015688	0	0	1	5	4		Missense_Mutation	SNP	ENST00000265018.3	37	CCDS47033.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.767355	0.90020	.	.	ENSG00000047662	ENST00000265018	T	0.37235	1.21	5.5	5.5	0.81552	.	0.116291	0.64402	D	0.000011	T	0.58235	0.2108	L	0.60455	1.87	0.47153	D	0.999337	D	0.89917	1.0	D	0.87578	0.998	T	0.58463	-0.7632	10	0.72032	D	0.01	-17.5063	17.5329	0.87819	0.0:1.0:0.0:0.0	.	972	Q9ULE4	F184B_HUMAN	I	972	ENSP00000265018:S972I	ENSP00000265018:S972I	S	-	2	0	FAM184B	17244584	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.130000	0.50508	2.751000	0.94390	0.655000	0.94253	AGC	.		0.443	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
TLR10	81793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	38776735	38776735	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:38776735G>T	ENST00000308973.4	-	4	1082	c.477C>A	c.(475-477)ttC>ttA	p.F159L	TLR10_ENST00000508334.1_Missense_Mutation_p.F159L|TLR10_ENST00000506111.1_Missense_Mutation_p.F159L|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000361424.2_Missense_Mutation_p.F159L	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	159					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						CAATTTTCTGGAAATCTGATT	0.398																																					p.F159L		.											.	TLR10-522	0			c.C477A						.						57.0	61.0	59.0					4																	38776735		2202	4299	6501	SO:0001583	missense	81793	exon2			TTTCTGGAAATCT	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.477C>A	4.37:g.38776735G>T	ENSP00000308925:p.Phe159Leu	Somatic	41	0		WXS	Illumina HiSeq	Phase_I	43	9	NM_001017388	0	0	0	0	0	A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	1.875	-0.459352	0.04508	.	.	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334	T;T;T;T	0.18338	2.22;2.22;2.22;2.22	5.23	2.42	0.29668	.	0.111310	0.38272	N	0.001753	T	0.07503	0.0189	N	0.17082	0.46	0.41978	D	0.990781	B	0.09022	0.002	B	0.10450	0.005	T	0.20107	-1.0285	10	0.10636	T	0.68	.	4.4622	0.11671	0.1433:0.1228:0.6077:0.1263	.	159	Q9BXR5	TLR10_HUMAN	L	159	ENSP00000308925:F159L;ENSP00000421483:F159L;ENSP00000354459:F159L;ENSP00000424923:F159L	ENSP00000308925:F159L	F	-	3	2	TLR10	38453130	0.010000	0.17322	1.000000	0.80357	0.982000	0.71751	-0.202000	0.09451	1.211000	0.43351	0.655000	0.94253	TTC	.		0.398	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
MUC7	4589	ucsc.edu;bcgsc.ca	37	4	71347168	71347168	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:71347168C>T	ENST00000304887.5	+	3	897	c.707C>T	c.(706-708)gCt>gTt	p.A236V	MUC7_ENST00000456088.1_Missense_Mutation_p.A236V|MUC7_ENST00000413702.1_Missense_Mutation_p.A236V	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	236	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			GAGACCACAGCTGCCCCACCC	0.587																																					p.A236V													.	MUC7-93	0			c.C707T						.						386.0	317.0	340.0					4																	71347168		2203	4300	6503	SO:0001583	missense	4589	exon4			CCACAGCTGCCCC	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.707C>T	4.37:g.71347168C>T	ENSP00000302021:p.Ala236Val	Somatic	689	2		WXS	Illumina HiSeq		547	131	NM_001145007	0	0	0	0	0	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	C	10.12	1.263054	0.23051	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.45668	0.89;0.89;0.89	2.03	2.03	0.26663	.	.	.	.	.	T	0.40767	0.1130	N	0.19112	0.55	0.29493	N	0.855503	D	0.60160	0.987	P	0.58970	0.849	T	0.26258	-1.0108	8	.	.	.	-3.0E-4	10.0947	0.42469	0.0:1.0:0.0:0.0	.	236	Q8TAX7	MUC7_HUMAN	V	236	ENSP00000407422:A236V;ENSP00000400585:A236V;ENSP00000302021:A236V	.	A	+	2	0	MUC7	71381757	0.001000	0.12720	0.167000	0.22817	0.132000	0.20833	0.201000	0.17276	1.420000	0.47138	0.655000	0.94253	GCT	.		0.587	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
SYNPO2	171024	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	119952865	119952865	+	Missense_Mutation	SNP	T	T	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:119952865T>A	ENST00000429713.2	+	4	3117	c.2935T>A	c.(2935-2937)Ttc>Atc	p.F979I	SYNPO2_ENST00000434046.2_Missense_Mutation_p.F979I|SYNPO2_ENST00000448416.2_Intron|SYNPO2_ENST00000307142.4_Missense_Mutation_p.F979I	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	979						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CTTGTTTACTTTCCAACCTCC	0.498																																					p.F979I		.											.	SYNPO2-92	0			c.T2935A						.						96.0	78.0	84.0					4																	119952865		2203	4300	6503	SO:0001583	missense	171024	exon4			TTTACTTTCCAAC	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2935T>A	4.37:g.119952865T>A	ENSP00000395143:p.Phe979Ile	Somatic	129	0		WXS	Illumina HiSeq	Phase_I	140	28	NM_001128934	0	0	2	2	0	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.425277|4.425277	0.83667|0.83667	.|.	.|.	ENSG00000172403|ENSG00000172403	ENST00000307142;ENST00000429713;ENST00000434046|ENST00000504178	T;T;T|.	0.16324|.	2.35;2.39;2.37|.	5.3|5.3	5.3|5.3	0.74995|0.74995	.|.	0.000000|0.000000	0.64402|0.64402	D|D	0.000004|0.000004	T|T	0.75398|0.75398	0.3844|0.3844	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;0.999;0.991|.	D;D;D;D|.	0.80764|.	0.994;0.992;0.991;0.955|.	T|T	0.76713|0.76713	-0.2858|-0.2858	9|6	.|.	.|.	.|.	-21.6986|-21.6986	15.246|15.246	0.73507|0.73507	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	979;979;979;979|.	B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6|.	.;.;.;SYNP2_HUMAN|.	I|Y	979|930	ENSP00000306015:F979I;ENSP00000395143:F979I;ENSP00000390965:F979I|.	.|.	F|F	+|+	1|2	0|0	SYNPO2|SYNPO2	120172313|120172313	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.992000|0.992000	0.81027|0.81027	7.841000|7.841000	0.86834|0.86834	2.013000|2.013000	0.59113|0.59113	0.533000|0.533000	0.62120|0.62120	TTC|TTT	.		0.498	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
TENM3	55714	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	183245385	183245385	+	Missense_Mutation	SNP	C	C	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:183245385C>A	ENST00000511685.1	+	2	335	c.212C>A	c.(211-213)gCa>gAa	p.A71E	TENM3_ENST00000406950.2_Missense_Mutation_p.A71E			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	71	Teneurin N-terminal. {ECO:0000255|PROSITE-ProRule:PRU00694}.				camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CACAGAGAAGCAGACGAGTTC	0.458																																					p.A71E		.											.	.	0			c.C212A						.						98.0	97.0	98.0					4																	183245385		1955	4146	6101	SO:0001583	missense	55714	exon1			GAGAAGCAGACGA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.212C>A	4.37:g.183245385C>A	ENSP00000424226:p.Ala71Glu	Somatic	58	0		WXS	Illumina HiSeq	Phase_I	66	9	NM_001080477	0	0	0	0	0	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	C	16.66	3.184679	0.57909	.	.	ENSG00000218336	ENST00000512480;ENST00000511685;ENST00000406950	T;T;T	0.31769	1.48;1.48;1.48	5.65	5.65	0.86999	Teneurin intracellular, N-terminal (2);	.	.	.	.	T	0.52256	0.1723	L	0.60455	1.87	0.30938	N	0.726181	D;P	0.62365	0.991;0.77	P;B	0.61132	0.884;0.255	T	0.51934	-0.8642	9	0.72032	D	0.01	.	19.9142	0.97043	0.0:1.0:0.0:0.0	.	71;71	D6RGC5;Q9P273	.;TEN3_HUMAN	E	71	ENSP00000421320:A71E;ENSP00000424226:A71E;ENSP00000385276:A71E	ENSP00000385276:A71E	A	+	2	0	ODZ3	183482379	0.995000	0.38212	0.986000	0.45419	0.986000	0.74619	3.658000	0.54482	2.941000	0.99782	0.655000	0.94253	GCA	.		0.458	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
FAT1	2195	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	4	187517964	187517964	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:187517964C>G	ENST00000441802.2	-	25	12939	c.12730G>C	c.(12730-12732)Gac>Cac	p.D4244H	FAT1_ENST00000512347.1_5'Flank	NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4244					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GGTGGTATGTCTGAGTAAATG	0.478										HNSCC(5;0.00058)																											p.D4244H	Colon(197;1040 2055 4143 4984 49344)	.											.	FAT1-34	0			c.G12730C						.						70.0	69.0	69.0					4																	187517964		1861	4100	5961	SO:0001583	missense	2195	exon25			GTATGTCTGAGTA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.12730G>C	4.37:g.187517964C>G	ENSP00000406229:p.Asp4244His	Somatic	90	0		WXS	Illumina HiSeq	Phase_I	97	26	NM_005245	0	0	24	45	21		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.7|23.7	4.443680|4.443680	0.83993|0.83993	.|.	.|.	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.70869|.	-0.52|.	5.39|5.39	5.39|5.39	0.77823|0.77823	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72961|0.72961	0.3526|0.3526	L|L	0.60455|0.60455	1.87|1.87	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.69304|0.69304	-0.5180|-0.5180	10|5	0.66056|.	D|.	0.02|.	.|.	19.3359|19.3359	0.94319|0.94319	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4244|.	Q14517|.	FAT1_HUMAN|.	H|T	4244;4246|11	ENSP00000406229:D4244H|.	ENSP00000260147:D4246H|.	D|R	-|-	1|2	0|0	FAT1|FAT1	187754958|187754958	1.000000|1.000000	0.71417|0.71417	0.831000|0.831000	0.32960|0.32960	0.737000|0.737000	0.42083|0.42083	7.651000|7.651000	0.83577|0.83577	2.809000|2.809000	0.96659|0.96659	0.555000|0.555000	0.69702|0.69702	GAC|AGA	.		0.478	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TRIP13	9319	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	908120	908120	+	Silent	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:908120C>T	ENST00000166345.3	+	8	1046	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_004237.3	NP_004228.1	Q15645	PCH2_HUMAN	thyroid hormone receptor interactor 13	230					double-strand break repair (GO:0006302)|female meiosis I (GO:0007144)|male meiosis I (GO:0007141)|oocyte maturation (GO:0001556)|oogenesis (GO:0048477)|reciprocal meiotic recombination (GO:0007131)|regulation of RNA biosynthetic process (GO:2001141)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|transcription from RNA polymerase II promoter (GO:0006366)	male germ cell nucleus (GO:0001673)|nucleus (GO:0005634)	ATP binding (GO:0005524)|transcription cofactor activity (GO:0003712)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	18			Epithelial(17;0.00147)|OV - Ovarian serous cystadenocarcinoma(19;0.00271)|all cancers(22;0.00622)|Lung(60;0.165)			AGCTGGTAACCAAGATGTTTC	0.498																																					p.T230T		.											.	TRIP13-90	0			c.C690T						.						169.0	149.0	155.0					5																	908120		2203	4300	6503	SO:0001819	synonymous_variant	9319	exon8			GGTAACCAAGATG	L40384	CCDS3858.1	5p15	2010-04-21			ENSG00000071539	ENSG00000071539		"""ATPases / AAA-type"""	12307	protein-coding gene	gene with protein product	"""thyroid receptor interacting protein 13"""	604507				7776974	Standard	NM_004237		Approved	16E1BP	uc003jbr.3	Q15645	OTTHUMG00000090349	ENST00000166345.3:c.690C>T	5.37:g.908120C>T		Somatic	96	0		WXS	Illumina HiSeq	Phase_I	123	38	NM_004237	0	0	0	0	0	C9K0T3|D3DTC0|O15324	Silent	SNP	ENST00000166345.3	37	CCDS3858.1	.	.	.	.	.	.	.	.	.	.	.	8.882	0.951814	0.18431	.	.	ENSG00000071539	ENST00000513435	.	.	.	5.62	-11.2	0.00127	.	.	.	.	.	T	0.41259	0.1151	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	4	.	.	.	-32.367	5.2498	0.15515	0.143:0.5019:0.2154:0.1397	.	.	.	.	L	226	.	.	P	+	2	0	TRIP13	961120	0.006000	0.16342	0.087000	0.20705	0.969000	0.65631	-1.282000	0.02799	-2.592000	0.00456	-0.345000	0.07892	CCA	.		0.498	TRIP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206721.2	NM_004237	
CDH12	1010	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	21752166	21752166	+	Missense_Mutation	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:21752166T>C	ENST00000382254.1	-	15	3151	c.2065A>G	c.(2065-2067)Att>Gtt	p.I689V	CDH12_ENST00000522262.1_Missense_Mutation_p.I649V|CDH12_ENST00000504376.2_Missense_Mutation_p.I689V|RP11-804N13.1_ENST00000522350.1_RNA|CDH12_ENST00000521384.1_5'UTR	NM_004061.3	NP_004052.2	P55289	CAD12_HUMAN	cadherin 12, type 2 (N-cadherin 2)	689					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(19)|lung(75)|ovary(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	120						TCCCTGCGAATTTTGTTCTCC	0.458										HNSCC(59;0.17)																											p.I689V		.											.	CDH12-92	0			c.A2065G						.						188.0	161.0	171.0					5																	21752166		2203	4300	6503	SO:0001583	missense	1010	exon15			TGCGAATTTTGTT	L33477	CCDS3890.1	5p14.3	2010-01-26			ENSG00000154162	ENSG00000154162		"""Cadherins / Major cadherins"""	1751	protein-coding gene	gene with protein product		600562				7731968	Standard	NM_004061		Approved	Br-cadherin, CDHB	uc003jgk.2	P55289	OTTHUMG00000090591	ENST00000382254.1:c.2065A>G	5.37:g.21752166T>C	ENSP00000371689:p.Ile689Val	Somatic	203	0		WXS	Illumina HiSeq	Phase_I	221	60	NM_004061	0	0	0	0	0	B2RBT1|B7Z2U6|Q86UD2	Missense_Mutation	SNP	ENST00000382254.1	37	CCDS3890.1	.	.	.	.	.	.	.	.	.	.	T	5.372	0.253855	0.10185	.	.	ENSG00000154162	ENST00000504376;ENST00000382254;ENST00000522262	T;T;T	0.76186	-1.0;-1.0;-1.0	5.12	3.92	0.45320	Cadherin, cytoplasmic domain (1);	0.479938	0.25538	N	0.029988	T	0.51958	0.1705	N	0.14661	0.345	0.31334	N	0.684456	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.46938	-0.9155	10	0.17369	T	0.5	.	6.6994	0.23217	0.0:0.0776:0.1551:0.7673	.	649;689	B7Z2U6;P55289	.;CAD12_HUMAN	V	689;689;649	ENSP00000423577:I689V;ENSP00000371689:I689V;ENSP00000428786:I649V	ENSP00000371689:I689V	I	-	1	0	CDH12	21787923	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	1.798000	0.38814	0.765000	0.33221	0.383000	0.25322	ATT	.		0.458	CDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207139.1	NM_004061	
IL31RA	133396	broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	55212822	55212822	+	Silent	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:55212822T>C	ENST00000447346.2	+	15	2234	c.2169T>C	c.(2167-2169)ggT>ggC	p.G723G	IL31RA_ENST00000359040.5_Intron|IL31RA_ENST00000396834.1_Intron|IL31RA_ENST00000490985.1_Silent_p.G581G|IL31RA_ENST00000354961.4_Intron	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	691					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				TCTTTTCTGGTCAAAGTTTAG	0.468																																					p.G723G													.	IL31RA-91	0			c.T2169C						.						56.0	63.0	61.0					5																	55212822		2203	4300	6503	SO:0001819	synonymous_variant	133396	exon15			TTCTGGTCAAAGT	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.2169T>C	5.37:g.55212822T>C		Somatic	158	1		WXS	Illumina HiSeq	Phase_I	162	47	NM_139017	0	0	0	0	0	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Silent	SNP	ENST00000447346.2	37	CCDS3970.2																																																																																			.		0.468	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
KIF2A	3796	broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	61662304	61662304	+	Missense_Mutation	SNP	A	A	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:61662304A>T	ENST00000401507.3	+	16	1953	c.1642A>T	c.(1642-1644)Aat>Tat	p.N548Y	KIF2A_ENST00000509663.2_Intron|KIF2A_ENST00000506857.1_Missense_Mutation_p.N502Y|KIF2A_ENST00000381103.2_Missense_Mutation_p.N528Y|KIF2A_ENST00000407818.3_Missense_Mutation_p.N548Y	NM_001243953.1|NM_004520.4	NP_001230882.1|NP_004511.2	O00139	KIF2A_HUMAN	kinesin heavy chain member 2A	548	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|metabolic process (GO:0008152)|microtubule depolymerization (GO:0007019)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|nervous system development (GO:0007399)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	15		Lung NSC(810;8.94e-06)|Prostate(74;0.0132)|Ovarian(174;0.051)|Breast(144;0.077)		Lung(70;0.14)		AAGATATGCAAATAGGTATGA	0.368																																					p.N548Y													.	KIF2A-228	0			c.A1642T						.						47.0	49.0	48.0					5																	61662304		2202	4297	6499	SO:0001583	missense	3796	exon16			TATGCAAATAGGT	BC031828	CCDS3980.2, CCDS47216.1, CCDS58949.1	5q12-q13	2008-02-05	2006-09-26	2006-09-26	ENSG00000068796	ENSG00000068796		"""Kinesins"""	6318	protein-coding gene	gene with protein product		602591	"""kinesin heavy chain member 2"""	KIF2		9177777	Standard	NM_001098511		Approved	HK2	uc003jsz.4	O00139	OTTHUMG00000097755	ENST00000401507.3:c.1642A>T	5.37:g.61662304A>T	ENSP00000385622:p.Asn548Tyr	Somatic	126	1		WXS	Illumina HiSeq	Phase_I	132	31	NM_001098511	0	0	0	0	0	A5YM42|A5YM54|B4DY54|D3DW97|E9PB70|Q7Z5I3|Q8N5Q7	Missense_Mutation	SNP	ENST00000401507.3	37	CCDS3980.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.135292	0.77662	.	.	ENSG00000068796	ENST00000401507;ENST00000381103;ENST00000407818;ENST00000506857	T;T;T;T	0.75589	-0.95;-0.95;-0.95;-0.95	5.95	5.95	0.96441	Kinesin, motor domain (3);	0.000000	0.85682	D	0.000000	T	0.79799	0.4508	L	0.28649	0.875	0.58432	D	0.999997	D;D;D;D	0.58970	0.984;0.98;0.979;0.979	D;D;P;D	0.68353	0.957;0.929;0.905;0.951	T	0.82165	-0.0592	10	0.87932	D	0	.	16.4237	0.83790	1.0:0.0:0.0:0.0	.	548;548;548;528	B4DM85;O00139-4;O00139;E9PB70	.;.;KIF2A_HUMAN;.	Y	548;528;548;502	ENSP00000385622:N548Y;ENSP00000370493:N528Y;ENSP00000385000:N548Y;ENSP00000423772:N502Y	ENSP00000370493:N528Y	N	+	1	0	KIF2A	61698061	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.341000	0.72977	2.279000	0.76181	0.533000	0.62120	AAT	.		0.368	KIF2A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317989.1	NM_004520	
NDST1	3340	broad.mit.edu;ucsc.edu;bcgsc.ca	37	5	149921206	149921206	+	Silent	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:149921206C>T	ENST00000261797.6	+	9	2326	c.1824C>T	c.(1822-1824)ctC>ctT	p.L608L	NDST1_ENST00000523767.1_Silent_p.L608L|snoU13_ENST00000459561.1_RNA	NM_001543.4	NP_001534.1	P52848	NDST1_HUMAN	N-deacetylase/N-sulfotransferase (heparan glucosaminyl) 1	608	Heparan sulfate N-sulfotransferase 1.				carbohydrate metabolic process (GO:0005975)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain development (GO:0030900)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|midbrain development (GO:0030901)|polysaccharide biosynthetic process (GO:0000271)|respiratory gaseous exchange (GO:0007585)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine N-sulfotransferase activity (GO:0015016)|deacetylase activity (GO:0019213)			breast(2)|central_nervous_system(3)|endometrium(5)|kidney(1)|large_intestine(6)|lung(10)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	34		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CAAAGCTCCTCATCATCGGCC	0.552																																					p.L608L													.	NDST1-136	0			c.C1824T						.						84.0	69.0	75.0					5																	149921206		2203	4300	6503	SO:0001819	synonymous_variant	3340	exon9			GCTCCTCATCATC	U18918	CCDS34277.1, CCDS75358.1	5q33.1	2008-02-05				ENSG00000070614		"""Sulfotransferases, membrane-bound"""	7680	protein-coding gene	gene with protein product		600853		HSST		7601448, 9230113	Standard	NM_001543		Approved	NST1	uc003lsk.4	P52848		ENST00000261797.6:c.1824C>T	5.37:g.149921206C>T		Somatic	104	1		WXS	Illumina HiSeq	Phase_I	91	30	NM_001543	0	0	18	23	5	Q96E57	Silent	SNP	ENST00000261797.6	37	CCDS34277.1																																																																																			.		0.552	NDST1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374314.2	NM_001543	
CMAHP	8418	bcgsc.ca	37	6	25108924	25108924	+	RNA	SNP	T	T	C	rs369592727		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:25108924T>C	ENST00000377989.4	-	0	1272							Q9Y471	CMAH_HUMAN	cytidine monophospho-N-acetylneuraminic acid hydroxylase, pseudogene						CMP-N-acetylneuraminate metabolic process (GO:0046381)	cytoplasm (GO:0005737)	2 iron, 2 sulfur cluster binding (GO:0051537)|oxidoreductase activity (GO:0016491)			NS(1)	1						CAGTCTACTATATTGAGTATT	0.413																																					.													.	.	0			.						.																																					8418	.			CTACTATATTGAG			6p23-p22	2011-04-28	2011-04-28	2011-04-28	ENSG00000168405	ENSG00000168405			2098	pseudogene	pseudogene		603209	"""cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMP-N-acetylneuraminate monooxygenase)(pseudogene)"""	CMAH		7608218, 9624188	Standard	NR_002174		Approved		uc003ner.4	Q9Y471	OTTHUMG00000016099		6.37:g.25108924T>C		Somatic	98	0		WXS	Illumina HiSeq	Phase_1	73	4	.	0	0	9	9	0	O95250|Q5TD41|Q5TD42|Q5TD43|Q5TD44|Q68DC3|Q9UEE7	RNA	SNP	ENST00000377989.4	37		.	.	.	.	.	.	.	.	.	.	T	13.55	2.270925	0.40194	.	.	ENSG00000168405	ENST00000377993;ENST00000436589;ENST00000377989;ENST00000424282;ENST00000399346	.	.	.	4.51	4.51	0.55191	.	0.110330	0.64402	D	0.000010	T	0.12944	0.0314	.	.	.	0.21105	N	0.999785	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09122	-1.0689	8	0.23891	T	0.37	-19.5873	12.9696	0.58505	0.0:0.0:0.0:1.0	.	181;181	B7Z8E8;C1K3L2	.;.	V	181	.	ENSP00000367228:I181V	I	-	1	0	CMAHP	25216903	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	6.081000	0.71309	1.892000	0.54788	0.496000	0.49642	ATA	.		0.413	CMAHP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000043292.2	NR_002174	
DST	667	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	56504731	56504731	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:56504731C>T	ENST00000361203.3	-	15	1989	c.1982G>A	c.(1981-1983)aGt>aAt	p.S661N	DST_ENST00000312431.6_Missense_Mutation_p.S661N|DST_ENST00000518935.1_Missense_Mutation_p.S335N|DST_ENST00000370769.4_Missense_Mutation_p.S661N|DST_ENST00000370754.5_Missense_Mutation_p.S839N|DST_ENST00000370788.2_Missense_Mutation_p.S661N|DST_ENST00000370765.6_Missense_Mutation_p.S335N|DST_ENST00000244364.6_Missense_Mutation_p.S335N|DST_ENST00000446842.2_Missense_Mutation_p.S335N|DST_ENST00000421834.2_Missense_Mutation_p.S661N			Q03001	DYST_HUMAN	dystonin	661					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			ACATACCTCACTGATTTTAGC	0.284																																					p.S335N		.											.	DST-523	0			c.G1004A						.						47.0	51.0	50.0					6																	56504731		2203	4299	6502	SO:0001583	missense	667	exon5			ACCTCACTGATTT	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1982G>A	6.37:g.56504731C>T	ENSP00000354508:p.Ser661Asn	Somatic	98	0		WXS	Illumina HiSeq	Phase_I	81	30	NM_001723	0	0	0	0	0	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	C	17.97	3.519255	0.64634	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	T;T;T;T;T;D;T;T;T;D;T;T	0.83992	1.18;0.02;0.02;0.17;0.96;-1.53;0.13;-0.0;-0.3;-1.79;-0.69;-0.14	5.45	4.58	0.56647	.	0.000000	0.64402	D	0.000017	T	0.80486	0.4632	L	0.44542	1.39	0.29528	N	0.852973	P;B;P;B;D;B;B;P;B;B	0.55385	0.899;0.235;0.944;0.354;0.971;0.016;0.115;0.917;0.235;0.277	B;B;D;B;P;B;B;P;B;B	0.63597	0.401;0.149;0.916;0.149;0.73;0.02;0.134;0.897;0.149;0.329	T	0.78265	-0.2271	9	0.17832	T	0.49	.	14.2099	0.65756	0.0:0.9287:0.0:0.0713	.	690;661;661;839;777;335;335;335;661;335	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	N	335;839;661;661;335;661;661;661;335;701;335;335	ENSP00000244364:S335N;ENSP00000359790:S839N;ENSP00000359805:S661N;ENSP00000400883:S661N;ENSP00000393645:S335N;ENSP00000307959:S661N;ENSP00000359824:S661N;ENSP00000354508:S661N;ENSP00000404924:S335N;ENSP00000431030:S701N;ENSP00000359801:S335N;ENSP00000431003:S335N	ENSP00000244364:S335N	S	-	2	0	DST	56612690	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	3.897000	0.56273	1.525000	0.49052	0.655000	0.94253	AGT	.		0.284	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
RIMS1	22999	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	72960096	72960096	+	Missense_Mutation	SNP	C	C	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:72960096C>G	ENST00000521978.1	+	13	2305	c.2305C>G	c.(2305-2307)Cta>Gta	p.L769V	RIMS1_ENST00000520567.1_Missense_Mutation_p.L769V|RIMS1_ENST00000517827.1_Missense_Mutation_p.L228V|RIMS1_ENST00000401910.3_Missense_Mutation_p.L243V|RIMS1_ENST00000517960.1_Missense_Mutation_p.L769V|RIMS1_ENST00000264839.7_Missense_Mutation_p.L769V|RIMS1_ENST00000523963.1_Missense_Mutation_p.L243V|RIMS1_ENST00000522291.1_Missense_Mutation_p.L769V|RIMS1_ENST00000518273.1_Missense_Mutation_p.L769V|RIMS1_ENST00000538414.1_5'Flank|RIMS1_ENST00000491071.2_Missense_Mutation_p.L769V|RIMS1_ENST00000348717.5_Missense_Mutation_p.L769V|RIMS1_ENST00000425662.2_Missense_Mutation_p.L162V	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	769	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				AGCAACAGATCTACCTGCTAG	0.348																																					p.L769V		.											.	RIMS1-144	0			c.C2305G						.						89.0	83.0	84.0					6																	72960096		1846	4102	5948	SO:0001583	missense	22999	exon13			ACAGATCTACCTG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2305C>G	6.37:g.72960096C>G	ENSP00000428417:p.Leu769Val	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	90	14	NM_014989	0	0	0	0	0	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.83|18.83	3.706633|3.706633	0.68615|0.68615	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827|ENST00000517433	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.82344|.	-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6;-1.6|.	5.28|5.28	4.38|4.38	0.52667|0.52667	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);|.	0.000000|.	0.52532|.	D|.	0.000072|.	T|T	0.69663|0.69663	0.3136|0.3136	M|M	0.87971|0.87971	2.92|2.92	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D;D|.	0.76494|.	0.999;0.962;0.99;0.99;0.998;0.994;0.99|.	D;D;D;D;D;D;D|.	0.97110|.	1.0;0.983;0.996;0.996;0.999;0.996;0.996|.	T|T	0.74475|0.74475	-0.3653|-0.3653	10|5	0.87932|.	D|.	0|.	-12.8523|-12.8523	10.4795|10.4795	0.44684|0.44684	0.0:0.8222:0.0:0.1778|0.0:0.8222:0.0:0.1778	.|.	228;243;769;228;243;769;769|.	B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;C9JNW6;Q86UR5|.	.;.;.;.;.;.;RIMS1_HUMAN|.	V|C	769;769;769;769;769;769;769;769;769;769;769;769;243;243;162;162;228|342	ENSP00000430101:L769V;ENSP00000275037:L769V;ENSP00000264839:L769V;ENSP00000429959:L769V;ENSP00000430408:L769V;ENSP00000430502:L769V;ENSP00000430932:L769V;ENSP00000428417:L769V;ENSP00000385649:L243V;ENSP00000428328:L243V;ENSP00000411235:L162V;ENSP00000389503:L162V;ENSP00000428367:L228V|.	ENSP00000264839:L769V|.	L|S	+|+	1|2	2|0	RIMS1|RIMS1	73016817|73016817	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	4.060000|4.060000	0.57477|0.57477	1.279000|1.279000	0.44446|0.44446	0.585000|0.585000	0.79938|0.79938	CTA|TCT	.		0.348	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
VGLL2	245806	hgsc.bcm.edu	37	6	117591730	117591730	+	Missense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:117591730G>T	ENST00000326274.5	+	3	606	c.416G>T	c.(415-417)cGc>cTc	p.R139L	VGLL2_ENST00000352536.3_Intron	NM_182645.3	NP_872586.1	Q8N8G2	VGLL2_HUMAN	vestigial-like family member 2	139					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			central_nervous_system(1)|kidney(1)|lung(3)	5				GBM - Glioblastoma multiforme(226;0.0254)|all cancers(137;0.0676)|OV - Ovarian serous cystadenocarcinoma(136;0.0757)		ATGAGCCAGCGCAGCTTCCCC	0.697																																					p.R139L		.											.	VGLL2-90	0			c.G416T						.						13.0	15.0	14.0					6																	117591730		2195	4285	6480	SO:0001583	missense	245806	exon3			GCCAGCGCAGCTT	AY056583	CCDS5114.1, CCDS5115.1	6q22.31	2014-03-03	2014-03-03		ENSG00000170162	ENSG00000170162			20232	protein-coding gene	gene with protein product		609979	"""vestigial like 2 (Drosophila)"""			12376544	Standard	NM_153453		Approved		uc003pxn.3	Q8N8G2	OTTHUMG00000015451	ENST00000326274.5:c.416G>T	6.37:g.117591730G>T	ENSP00000320957:p.Arg139Leu	Somatic	72	0		WXS	Illumina HiSeq	Phase_I	53	4	NM_182645	0	0	0	0	0	Q8WWX1	Missense_Mutation	SNP	ENST00000326274.5	37	CCDS5115.1	.	.	.	.	.	.	.	.	.	.	G	34	5.331271	0.95733	.	.	ENSG00000170162	ENST00000326274	T	0.54866	0.55	4.86	4.86	0.63082	.	0.056880	0.64402	D	0.000003	T	0.68393	0.2996	M	0.73962	2.25	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.72360	-0.4317	10	0.72032	D	0.01	-24.0493	18.1693	0.89740	0.0:0.0:1.0:0.0	.	139	Q8N8G2	VGLL2_HUMAN	L	139	ENSP00000320957:R139L	ENSP00000320957:R139L	R	+	2	0	VGLL2	117698423	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.078000	0.94023	2.528000	0.85240	0.549000	0.68633	CGC	.		0.697	VGLL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041975.2	NM_153453	
TBC1D32	221322	hgsc.bcm.edu	37	6	121433801	121433801	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:121433801G>T	ENST00000398212.2	-	29	3223	c.3174C>A	c.(3172-3174)tgC>tgA	p.C1058*	TBC1D32_ENST00000275159.6_Nonsense_Mutation_p.C1099*|TBC1D32_ENST00000398197.2_5'UTR	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	1058					cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|lens development in camera-type eye (GO:0002088)|protein localization to cilium (GO:0061512)|retinal pigment epithelium development (GO:0003406)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cilium (GO:0005929)|cytoplasm (GO:0005737)	Rab GTPase activator activity (GO:0005097)										TCCCTTGCAGGCAGACTGAAA	0.274																																					p.C1058X		.											.	C6orf170-92	0			c.C3174A						.						54.0	49.0	50.0					6																	121433801		1803	4070	5873	SO:0001587	stop_gained	221322	exon29			TTGCAGGCAGACT	AK055461	CCDS43501.1	6q22.31	2014-02-20	2013-07-10	2013-07-10	ENSG00000146350	ENSG00000146350			21485	protein-coding gene	gene with protein product	"""broad-minded homolog"""	615867	"""chromosome 6 open reading frame 171"", ""chromosome 6 open reading frame 170"""	C6orf171, C6orf170		20159594, 24285566	Standard	NM_152730		Approved	FLJ30899, dJ310J6.1, FLJ34235, bA57L9.1, BROMI	uc003pyo.1	Q96NH3	OTTHUMG00000015474	ENST00000398212.2:c.3174C>A	6.37:g.121433801G>T	ENSP00000381270:p.Cys1058*	Somatic	54	0		WXS	Illumina HiSeq	Phase_I	67	4	NM_152730	0	0	0	0	0	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Nonsense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	G	33	5.220888	0.95139	.	.	ENSG00000146350	ENST00000275159;ENST00000398212	.	.	.	5.41	3.63	0.41609	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.3109	0.32071	0.3125:0.0:0.6875:0.0	.	.	.	.	X	1099;1058	.	ENSP00000275159:C1099X	C	-	3	2	C6orf170	121475500	1.000000	0.71417	0.998000	0.56505	0.007000	0.05969	2.668000	0.46816	0.674000	0.31244	0.585000	0.79938	TGC	.		0.274	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
FNDC1	84624	broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	159655428	159655428	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:159655428T>G	ENST00000297267.9	+	11	4084	c.3884T>G	c.(3883-3885)aTg>aGg	p.M1295R	FNDC1_ENST00000340366.6_Missense_Mutation_p.M1232R	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1295				M -> K (in Ref. 6; CAE51894). {ECO:0000305}.	cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		ACCACCCCGATGCTGTCCTTG	0.632																																					p.M1295R													.	FNDC1-138	0			c.T3884G						.						25.0	27.0	26.0					6																	159655428		2055	4145	6200	SO:0001583	missense	84624	exon11			CCCCGATGCTGTC	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3884T>G	6.37:g.159655428T>G	ENSP00000297267:p.Met1295Arg	Somatic	199	1		WXS	Illumina HiSeq	Phase_I	136	45	NM_032532	0	0	0	0	0	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	12.10|12.10	1.835380|1.835380	0.32421|0.32421	.|.	.|.	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.08807	.|3.05;3.83	5.56|5.56	5.56|5.56	0.83823|0.83823	.|.	.|0.276491	.|0.34906	.|N	.|0.003600	T|T	0.08044|0.08044	0.0201|0.0201	L|L	0.34521|0.34521	1.04|1.04	0.32639|0.32639	N|N	0.520991|0.520991	.|D;D	.|0.76494	.|0.999;0.998	.|D;P	.|0.74023	.|0.982;0.895	T|T	0.18840|0.18840	-1.0324|-1.0324	5|10	.|0.32370	.|T	.|0.25	-34.3204|-34.3204	8.2561|8.2561	0.31758|0.31758	0.0:0.088:0.0:0.912|0.0:0.088:0.0:0.912	.|.	.|1232;1295	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	E|R	1190|1295;1232	.|ENSP00000297267:M1295R;ENSP00000342460:M1232R	.|ENSP00000297267:M1295R	D|M	+|+	3|2	2|0	FNDC1|FNDC1	159575418|159575418	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.202000|0.202000	0.24057|0.24057	3.172000|3.172000	0.50832|0.50832	2.112000|2.112000	0.64535|0.64535	0.528000|0.528000	0.53228|0.53228	GAT|ATG	.		0.632	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
ACTB	60	broad.mit.edu	37	7	5567474	5567474	+	Missense_Mutation	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:5567474T>G	ENST00000331789.5	-	6	1224	c.1033A>C	c.(1033-1035)Atc>Ctc	p.I345L	AC006483.1_ENST00000579427.1_RNA|ACTB_ENST00000464611.1_5'UTR	NM_001101.3	NP_001092.1	P63261	ACTG_HUMAN	actin, beta	345					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|cellular component movement (GO:0006928)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane organization (GO:0061024)|platelet aggregation (GO:0070527)|retina homeostasis (GO:0001895)|sarcomere organization (GO:0045214)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|membrane (GO:0016020)|myofibril (GO:0030016)|nucleus (GO:0005634)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(2)|prostate(2)	8		Ovarian(82;0.0606)		UCEC - Uterine corpus endometrioid carcinoma (126;0.175)|OV - Ovarian serous cystadenocarcinoma(56;4.24e-37)		GAGGCCAGGATGGAGCCGCCG	0.607																																					p.I345L													.	ACTB-226	0			c.A1033C						.						68.0	71.0	70.0					7																	5567474		2203	4300	6503	SO:0001583	missense	60	exon6			CCAGGATGGAGCC	M28424	CCDS5341.1	7p22	2014-09-17			ENSG00000075624	ENSG00000075624			132	protein-coding gene	gene with protein product		102630				1505215	Standard	NM_001101		Approved		uc003sot.4	P60709	OTTHUMG00000023268	ENST00000331789.5:c.1033A>C	7.37:g.5567474T>G	ENSP00000349960:p.Ile345Leu	Somatic	143	10		WXS	Illumina HiSeq	Phase_I	105	16	NM_001101	3	3	4318	4419	95	A8K7C2|P02571|P14104|P99022|Q5U032|Q96E67	Missense_Mutation	SNP	ENST00000331789.5	37	CCDS5341.1	.	.	.	.	.	.	.	.	.	.	T	14.51	2.555820	0.45487	.	.	ENSG00000075624	ENST00000331789;ENST00000445914;ENST00000400179;ENST00000320713	D	0.95447	-3.71	5.55	5.55	0.83447	.	0.000000	0.64402	D	0.000013	D	0.96528	0.8867	M	0.86740	2.835	0.48975	D	0.999733	B	0.06786	0.001	B	0.35655	0.207	D	0.95309	0.8410	10	0.87932	D	0	.	14.9227	0.70851	0.0:0.0:0.0:1.0	.	345	P60709	ACTB_HUMAN	L	345;321;317;264	ENSP00000349960:I345L	ENSP00000440549:I264L	I	-	1	0	ACTB	5534000	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.747000	0.85070	2.114000	0.64651	0.529000	0.55759	ATC	.		0.607	ACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059589.4	NM_001101	
THSD7A	221981	broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	11500346	11500346	+	Missense_Mutation	SNP	C	C	T	rs199705914		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:11500346C>T	ENST00000423059.4	-	11	2799	c.2548G>A	c.(2548-2550)Gtg>Atg	p.V850M	AC004538.3_ENST00000445839.1_RNA	NM_015204.2	NP_056019.1	Q9UPZ6	THS7A_HUMAN	thrombospondin, type I, domain containing 7A	850					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(5)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(7)|lung(68)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(11)	113				UCEC - Uterine corpus endometrioid carcinoma (126;0.163)		TCTTGTTGCACGCTCCAAGGG	0.552										HNSCC(18;0.044)			C|||	1	0.000199681	0.0	0.0014	5008	,	,		18566	0.0		0.0	False		,,,				2504	0.0				p.V850M													.	THSD7A-71	0			c.G2548A						.	C	MET/VAL	3,3953		0,3,1975	50.0	51.0	50.0		2548	3.4	0.9	7		50	0,8324		0,0,4162	yes	missense	THSD7A	NM_015204.2	21	0,3,6137	TT,TC,CC		0.0,0.0758,0.0244	possibly-damaging	850/1658	11500346	3,12277	1978	4162	6140	SO:0001583	missense	221981	exon11			GTTGCACGCTCCA		CCDS47543.1	7p21.3	2006-10-16			ENSG00000005108	ENSG00000005108			22207	protein-coding gene	gene with protein product		612249					Standard	NM_015204		Approved	KIAA0960	uc021zzn.1	Q9UPZ6	OTTHUMG00000152346	ENST00000423059.4:c.2548G>A	7.37:g.11500346C>T	ENSP00000406482:p.Val850Met	Somatic	68	0		WXS	Illumina HiSeq	Phase_I	62	9	NM_015204	0	0	1	1	0		Missense_Mutation	SNP	ENST00000423059.4	37	CCDS47543.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	15.16	2.752331	0.49362	7.58E-4	0.0	ENSG00000005108	ENST00000262042;ENST00000423059	T	0.60920	0.15	5.2	3.38	0.38709	.	0.257298	0.39834	N	0.001257	T	0.53610	0.1807	L	0.60455	1.87	0.39852	D	0.973256	B	0.28258	0.205	B	0.32624	0.149	T	0.51647	-0.8679	10	0.35671	T	0.21	.	11.4413	0.50099	0.0:0.8729:0.0:0.1271	.	850	Q9UPZ6	THS7A_HUMAN	M	850	ENSP00000406482:V850M	ENSP00000262042:V850M	V	-	1	0	THSD7A	11466871	0.045000	0.20229	0.911000	0.35937	0.977000	0.68977	0.420000	0.21263	0.688000	0.31529	0.655000	0.94253	GTG	C|0.999;T|0.000		0.552	THSD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325944.4	XM_928187.2	
TRIP6	7205	broad.mit.edu;bcgsc.ca	37	7	100466248	100466248	+	Silent	SNP	C	C	T	rs548658866		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:100466248C>T	ENST00000200457.4	+	4	855	c.495C>T	c.(493-495)ggC>ggT	p.G165G		NM_003302.2	NP_003293.2	Q15654	TRIP6_HUMAN	thyroid hormone receptor interactor 6	165					focal adhesion assembly (GO:0048041)|positive regulation of cell migration (GO:0030335)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|kinase binding (GO:0019900)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|liver(1)|lung(5)	14	Lung NSC(181;0.041)|all_lung(186;0.0581)					CCCCGGCTGGCCCAGCCTTCC	0.721													C|||	1	0.000199681	0.0	0.0014	5008	,	,		13231	0.0		0.0	False		,,,				2504	0.0				p.G165G													.	TRIP6-514	0			c.C495T						.						14.0	17.0	16.0					7																	100466248		2149	4196	6345	SO:0001819	synonymous_variant	7205	exon4			GGCTGGCCCAGCC	L40374, AF000974	CCDS5708.1	7q22	2006-09-05			ENSG00000087077	ENSG00000087077			12311	protein-coding gene	gene with protein product		602933				9598321, 7776974	Standard	NM_003302		Approved	ZRP-1, OIP1, MGC10556, MGC10558, MGC29959, MGC3837, MGC4423	uc003uww.3	Q15654	OTTHUMG00000157029	ENST00000200457.4:c.495C>T	7.37:g.100466248C>T		Somatic	54	1		WXS	Illumina HiSeq	Phase_I	78	26	NM_003302	0	0	64	104	40	A4D2E7|F2ZC07|F2ZC08|O15170|O15275|Q9BTB2|Q9BUE5|Q9BXP3|Q9UNT4	Silent	SNP	ENST00000200457.4	37	CCDS5708.1																																																																																			.		0.721	TRIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347151.2	NM_003302	
TMEM67	91147	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	8	94805453	94805453	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:94805453G>C	ENST00000453321.3	+	16	1661	c.1603G>C	c.(1603-1605)Gct>Cct	p.A535P	TMEM67_ENST00000409623.3_Missense_Mutation_p.A454P	NM_153704.5	NP_714915.3	Q5HYA8	MKS3_HUMAN	transmembrane protein 67	535					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of centrosome duplication (GO:0010826)	centrosome (GO:0005813)|ciliary membrane (GO:0060170)|cytoplasmic vesicle membrane (GO:0030659)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|TCTN-B9D complex (GO:0036038)	filamin binding (GO:0031005)|unfolded protein binding (GO:0051082)			breast(3)|endometrium(8)|kidney(5)|large_intestine(4)|liver(2)|lung(15)|ovary(2)|skin(1)|urinary_tract(1)	41	Breast(36;4.14e-07)		BRCA - Breast invasive adenocarcinoma(8;0.00896)			GGGTGGGCTAGCTGTTTTAGC	0.368																																					p.A535P		.											.	TMEM67-92	0			c.G1603C						.						157.0	153.0	154.0					8																	94805453		2203	4300	6503	SO:0001583	missense	91147	exon16			GGGCTAGCTGTTT	BX648768	CCDS6258.2, CCDS47893.1	8q22.1	2014-09-17			ENSG00000164953	ENSG00000164953			28396	protein-coding gene	gene with protein product	"""Meckelin"""	609884	"""Meckel syndrome, type 3"""	MKS3		12384791, 16415887, 19508969	Standard	NM_153704		Approved	MGC26979, JBTS6, NPHP11	uc011lgk.2	Q5HYA8	OTTHUMG00000153119	ENST00000453321.3:c.1603G>C	8.37:g.94805453G>C	ENSP00000389998:p.Ala535Pro	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	116	31	NM_153704	0	0	2	2	0	B3KRU5|B3KT47|G5E9H2|Q3ZCX3|Q7Z5T8|Q8IZ06	Missense_Mutation	SNP	ENST00000453321.3	37	CCDS6258.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.1|26.1	4.706160|4.706160	0.89018|0.89018	.|.	.|.	ENSG00000164953|ENSG00000164953	ENST00000453321;ENST00000409623|ENST00000520680	D;D|.	0.97256|.	-4.31;-4.31|.	5.6|5.6	5.6|5.6	0.85130|0.85130	.|.	0.111849|.	0.64402|.	D|.	0.000016|.	T|T	0.78317|0.78317	0.4264|0.4264	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.83275|.	0.993;0.996;0.992|.	T|T	0.77584|0.77584	-0.2533|-0.2533	10|5	0.66056|.	D|.	0.02|.	-17.8669|-17.8669	19.6017|19.6017	0.95566|0.95566	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	535;454;454|.	Q5HYA8;B3KRU5;G5E9H2|.	MKS3_HUMAN;.;.|.	P|T	535;454|183	ENSP00000389998:A535P;ENSP00000386966:A454P|.	ENSP00000314488:A525P|.	A|S	+|+	1|2	0|0	TMEM67|TMEM67	94874629|94874629	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.997000|0.997000	0.91878|0.91878	6.318000|6.318000	0.72866|0.72866	2.622000|2.622000	0.88805|0.88805	0.655000|0.655000	0.94253|0.94253	GCT|AGC	.		0.368	TMEM67-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329641.2	NM_153704	
FAM91A1	157769	broad.mit.edu	37	8	124796777	124796777	+	Missense_Mutation	SNP	G	G	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:124796777G>C	ENST00000334705.7	+	9	1017	c.771G>C	c.(769-771)aaG>aaC	p.K257N	FAM91A1_ENST00000521166.1_Missense_Mutation_p.K257N	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	257										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			TACTCTATAAGATATTTGTTT	0.328																																					p.K257N													.	FAM91A1-91	0			c.G771C						.						72.0	67.0	69.0					8																	124796777		1806	4060	5866	SO:0001583	missense	157769	exon9			CTATAAGATATTT	AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.771G>C	8.37:g.124796777G>C	ENSP00000335082:p.Lys257Asn	Somatic	40	0		WXS	Illumina HiSeq	Phase_I	32	6	NM_144963	0	0	5	14	9	B6YY23|Q658T5|Q8TE89	Missense_Mutation	SNP	ENST00000334705.7	37	CCDS6346.2	.	.	.	.	.	.	.	.	.	.	G	18.73	3.685454	0.68157	.	.	ENSG00000176853	ENST00000521166;ENST00000334705	T;T	0.53423	0.62;1.19	5.68	1.72	0.24424	.	0.000000	0.85682	D	0.000000	T	0.61035	0.2315	L	0.60455	1.87	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.80764	0.994;0.994	T	0.60084	-0.7332	10	0.72032	D	0.01	.	11.3042	0.49325	0.2407:0.0:0.7593:0.0	.	257;257	E7ER68;Q658Y4	.;F91A1_HUMAN	N	257	ENSP00000429491:K257N;ENSP00000335082:K257N	ENSP00000335082:K257N	K	+	3	2	FAM91A1	124865958	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	1.983000	0.40648	0.089000	0.17243	0.644000	0.83932	AAG	.		0.328	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1	NM_144963	
DNAJC25	548645	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	9	114412019	114412019	+	Missense_Mutation	SNP	A	A	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:114412019A>G	ENST00000313525.3	+	3	832	c.776A>G	c.(775-777)tAt>tGt	p.Y259C	DNAJC25_ENST00000556107.1_Intron|DNAJC25-GNG10_ENST00000374294.3_Intron	NM_001015882.2	NP_001015882.2	Q9H1X3	DJC25_HUMAN	DnaJ (Hsp40) homolog, subfamily C , member 25	259						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|skin(4)	8						CTATGCTCATATATAGTTTGG	0.328																																					p.Y259C		.											.	DNAJC25-22	0			c.A776G						.						48.0	50.0	49.0					9																	114412019		1817	4067	5884	SO:0001583	missense	548645	exon3			GCTCATATATAGT		CCDS43862.1	9q31.3	2011-09-02			ENSG00000059769	ENSG00000059769		"""Heat shock proteins / DNAJ (HSP40)"""	34187	protein-coding gene	gene with protein product							Standard	NM_001015882		Approved	bA16L21.2.1	uc004bfl.3	Q9H1X3	OTTHUMG00000020491	ENST00000313525.3:c.776A>G	9.37:g.114412019A>G	ENSP00000320650:p.Tyr259Cys	Somatic	138	0		WXS	Illumina HiSeq	Phase_I	178	41	NM_001015882	0	0	6	18	12	Q5QTD8|Q96BN9	Missense_Mutation	SNP	ENST00000313525.3	37	CCDS43862.1	.	.	.	.	.	.	.	.	.	.	A	16.14	3.039309	0.55003	.	.	ENSG00000059769	ENST00000313525	T	0.52057	0.68	6.17	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.49729	0.1574	M	0.79475	2.455	0.80722	D	1	B	0.20887	0.049	B	0.19666	0.026	T	0.49244	-0.8960	10	0.56958	D	0.05	-6.1843	11.1739	0.48588	0.9308:0.0:0.0692:0.0	.	259	Q9H1X3	DJC25_HUMAN	C	259	ENSP00000320650:Y259C	ENSP00000320650:Y259C	Y	+	2	0	DNAJC25	113451840	1.000000	0.71417	0.055000	0.19348	0.793000	0.44817	6.943000	0.75934	1.144000	0.42321	0.533000	0.62120	TAT	.		0.328	DNAJC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156218.3	NM_001015882	
ANGPTL2	23452	broad.mit.edu	37	9	129870363	129870363	+	Silent	SNP	T	T	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr9:129870363T>G	ENST00000373425.3	-	2	1265	c.648A>C	c.(646-648)ccA>ccC	p.P216P	RALGPS1_ENST00000424082.2_Intron|RALGPS1_ENST00000373436.1_Intron|ANGPTL2_ENST00000373417.1_Intron|RALGPS1_ENST00000373434.1_Intron|ANGPTL2_ENST00000491991.1_5'Flank|RALGPS1_ENST00000259351.5_Intron|RALGPS1_ENST00000394022.3_Intron	NM_012098.2	NP_036230.1	Q9UKU9	ANGL2_HUMAN	angiopoietin-like 2	216					multicellular organismal development (GO:0007275)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|urinary_tract(1)	18						CAGCGGGGGGTGGCTGGGGGA	0.637																																					p.P216P													.	ANGPTL2-90	0			c.A648C						.						23.0	24.0	24.0					9																	129870363		2203	4300	6503	SO:0001819	synonymous_variant	23452	exon2			GGGGGGTGGCTGG	AF125175	CCDS6868.1	9q34	2013-02-06			ENSG00000136859	ENSG00000136859		"""Fibrinogen C domain containing"""	490	protein-coding gene	gene with protein product		605001				10473614	Standard	NM_012098		Approved	ARP2, HARP	uc004bqr.1	Q9UKU9	OTTHUMG00000020695	ENST00000373425.3:c.648A>C	9.37:g.129870363T>G		Somatic	76	10		WXS	Illumina HiSeq	Phase_I	68	10	NM_012098	0	0	33	35	2	Q5JT58|Q8NCH7	Silent	SNP	ENST00000373425.3	37	CCDS6868.1																																																																																			.		0.637	ANGPTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054129.1	NM_012098	
USP9X	8239	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	41043810	41043810	+	Missense_Mutation	SNP	C	C	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:41043810C>T	ENST00000324545.8	+	23	4073	c.3440C>T	c.(3439-3441)gCc>gTc	p.A1147V	USP9X_ENST00000378308.2_Missense_Mutation_p.A1147V	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1147					axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						CGAAGGGGTGCCTACCTCAAT	0.463																																					p.A1147V	Ovarian(172;1807 2695 35459 49286)	.											.	USP9X-563	0			c.C3440T						.						107.0	99.0	101.0					X																	41043810		2177	4280	6457	SO:0001583	missense	8239	exon23			GGGGTGCCTACCT	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.3440C>T	X.37:g.41043810C>T	ENSP00000316357:p.Ala1147Val	Somatic	154	0		WXS	Illumina HiSeq	Phase_I	143	72	NM_001039591	0	0	4	16	12	O75550|Q8WWT3|Q8WX12	Missense_Mutation	SNP	ENST00000324545.8	37	CCDS43930.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.984913	0.74474	.	.	ENSG00000124486	ENST00000378308;ENST00000324545	T;T	0.11712	2.75;2.75	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.10723	0.0262	L	0.35723	1.085	0.80722	D	1	B;B	0.16802	0.019;0.019	B;B	0.17098	0.017;0.017	T	0.15321	-1.0441	10	0.09843	T	0.71	.	18.7017	0.91623	0.0:1.0:0.0:0.0	.	1147;1147	Q93008-1;Q93008	.;USP9X_HUMAN	V	1147	ENSP00000367558:A1147V;ENSP00000316357:A1147V	ENSP00000316357:A1147V	A	+	2	0	USP9X	40928754	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.729000	0.84864	2.361000	0.80049	0.513000	0.50165	GCC	.		0.463	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
WDR13	64743	ucsc.edu;bcgsc.ca	37	X	48462761	48462761	+	Missense_Mutation	SNP	G	G	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:48462761G>A	ENST00000218056.5	+	8	1761	c.1256G>A	c.(1255-1257)cGc>cAc	p.R419H	WDR13_ENST00000376729.5_Missense_Mutation_p.R419H	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	419						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						ATGTCCTTCCGCCAGGGGGCC	0.632																																					p.R419H													.	WDR13-132	0			c.G1256A						.						55.0	42.0	46.0					X																	48462761		2203	4300	6503	SO:0001583	missense	64743	exon8			CCTTCCGCCAGGG	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.1256G>A	X.37:g.48462761G>A	ENSP00000218056:p.Arg419His	Somatic	67	0		WXS	Illumina HiSeq		40	4	NM_017883	1	0	288	290	1	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Missense_Mutation	SNP	ENST00000218056.5	37	CCDS14302.1	.	.	.	.	.	.	.	.	.	.	G	32	5.118173	0.94385	.	.	ENSG00000101940	ENST00000376729;ENST00000218056	T;T	0.73152	-0.72;-0.72	5.74	5.74	0.90152	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.76863	0.4047	M	0.75264	2.295	0.80722	D	1	D	0.53885	0.963	P	0.48488	0.579	T	0.79855	-0.1627	10	0.56958	D	0.05	-3.1215	16.085	0.81038	0.0:0.0:1.0:0.0	.	419	Q9H1Z4	WDR13_HUMAN	H	419	ENSP00000365919:R419H;ENSP00000218056:R419H	ENSP00000218056:R419H	R	+	2	0	WDR13	48347705	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.978000	0.93450	2.400000	0.81607	0.597000	0.82753	CGC	.		0.632	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
UPF3B	65109	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	118977251	118977251	+	Silent	SNP	T	T	C			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:118977251T>C	ENST00000276201.2	-	5	552	c.483A>G	c.(481-483)agA>agG	p.R161R	UPF3B_ENST00000345865.2_Silent_p.R161R|UPF3B_ENST00000478840.1_5'UTR	NM_080632.2	NP_542199.1	Q9BZI7	REN3B_HUMAN	UPF3 regulator of nonsense transcripts homolog B (yeast)	161	Necessary for interaction with UPF2.|Sufficient for association with EJC core.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|mRNA splicing, via spliceosome (GO:0000398)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(12)|ovary(2)|prostate(1)	30						CCAAAAACTTTCTATATTCTG	0.279																																					p.R161R		.											.	UPF3B-133	0			c.A483G						.						161.0	144.0	150.0					X																	118977251		2202	4300	6502	SO:0001819	synonymous_variant	65109	exon5			AAACTTTCTATAT	AF318576	CCDS14587.1, CCDS14588.1	Xq25-q26	2014-01-31			ENSG00000125351	ENSG00000125351			20439	protein-coding gene	gene with protein product		300298	"""mental retardation, X-linked 62"""	MRX62		11113196, 11163187, 19238151	Standard	NM_023010		Approved	RENT3B, UPF3X, HUPF3B	uc004erz.2	Q9BZI7	OTTHUMG00000022282	ENST00000276201.2:c.483A>G	X.37:g.118977251T>C		Somatic	23	0		WXS	Illumina HiSeq	Phase_I	31	17	NM_023010	0	0	0	0	0	D3DWI3|D3DWI4|Q0VAK8|Q9H1J0	Silent	SNP	ENST00000276201.2	37	CCDS14588.1																																																																																			.		0.279	UPF3B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058068.1		
SPTA1	6708	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	1	158639217	158639217	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr1:158639217delG	ENST00000368147.4	-	14	1994	c.1814delC	c.(1813-1815)gcafs	p.A605fs		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	605					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TTCATCATCTGCCAACTTTTT	0.408																																					p.A605fs		.											.	SPTA1-142	0			c.1814delC						.						285.0	268.0	273.0					1																	158639217		1915	4136	6051	SO:0001589	frameshift_variant	6708	exon14			.	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.1814delC	1.37:g.158639217delG	ENSP00000357129:p.Ala605fs	Somatic	65	0		WXS	Illumina HiSeq	Phase_I	73	19	NM_003126	0	0	0	0	0	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Frame_Shift_Del	DEL	ENST00000368147.4	37	CCDS41423.1																																																																																			.		0.408	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
IL25	64806	broad.mit.edu	37	14	23845057	23845058	+	Frame_Shift_Del	DEL	TG	TG	-	rs569851542		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr14:23845057_23845058delTG	ENST00000329715.2	+	2	760_761	c.502_503delTG	c.(502-504)tgtfs	p.C168fs	CMTM5_ENST00000359320.3_5'Flank|CMTM5_ENST00000555731.1_5'Flank|CMTM5_ENST00000382809.2_5'Flank|IL25_ENST00000397242.2_Frame_Shift_Del_p.C152fs|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000339180.4_5'Flank|CMTM5_ENST00000342473.4_5'Flank	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	168					eosinophil differentiation (GO:0030222)|inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to fungus (GO:0009620)|response to nematode (GO:0009624)	extracellular space (GO:0005615)	interleukin-17E receptor binding (GO:0030380)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)		TTCCTTAGCTTGTGTGTGTGTG	0.604																																					p.168_168del													.	IL25-91	0			c.502_503del						.																																			SO:0001589	frameshift_variant	64806	exon2			TTAGCTTGTGTGT	AF305200	CCDS9597.1, CCDS45086.1	14q11.2	2008-01-07	2006-05-17	2006-05-17	ENSG00000166090	ENSG00000166090		"""Interleukins and interleukin receptors"""	13765	protein-coding gene	gene with protein product		605658	"""interleukin 17E"""	IL17E		11058597, 11754819	Standard	NM_172314		Approved	IL-25, IL-17E	uc001wjq.3	Q9H293	OTTHUMG00000028749	ENST00000329715.2:c.502_503delTG	14.37:g.23845067_23845068delTG	ENSP00000328111:p.Cys168fs	Somatic	179	0		WXS	Illumina HiSeq	Phase_I	138	7	NM_022789	0	0	0	0	0	Q2M3F0|Q8IZV3|Q8WXB0	Frame_Shift_Del	DEL	ENST00000329715.2	37	CCDS9597.1																																																																																			.		0.604	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2		
TNFAIP1	7126	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	17	26675218	26675218	+	IGR	DEL	A	A	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:26675218delA	ENST00000226225.2	+	0	3627				POLDIP2_ENST00000003607.4_5'UTR|POLDIP2_ENST00000540200.1_Frame_Shift_Del_p.F343fs	NM_021137.4	NP_066960.1	Q13829	BACD2_HUMAN	tumor necrosis factor, alpha-induced protein 1 (endothelial)						apoptotic process (GO:0006915)|cell migration (GO:0016477)|DNA replication (GO:0006260)|embryo development (GO:0009790)|immune response (GO:0006955)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of DNA replication (GO:0045740)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein homooligomerization (GO:0051260)|protein ubiquitination (GO:0016567)|stress fiber assembly (GO:0043149)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleolus (GO:0005730)	GTP-Rho binding (GO:0017049)			endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)	12	all_lung(13;0.000294)|Lung NSC(42;0.000964)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		TCCGAACATCAAAGTGGGAGC	0.547																																					.		.											.	.	0			.						.						96.0	97.0	97.0					17																	26675218		1904	4126	6030	SO:0001628	intergenic_variant	26073	.			.		CCDS11227.1	17q22-q23	2013-01-09			ENSG00000109079	ENSG00000109079		"""BTB/POZ domain containing"""	11894	protein-coding gene	gene with protein product		191161		EDP1		2406243, 2233719	Standard	NM_021137		Approved	B61, B12, MGC2317, BTBD34	uc002hay.3	Q13829	OTTHUMG00000132501		17.37:g.26675218delA		Somatic	102	0		WXS	Illumina HiSeq	Phase_I	100	20	.	0	0	0	0	0	B7Z6M4|Q5TZQ1	Targeted_Region	DEL	ENST00000226225.2	37	CCDS11227.1																																																																																			.		0.547	TNFAIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255681.2	NM_021137	
NDC80	10403	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	18	2610806	2610806	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr18:2610806delA	ENST00000261597.4	+	16	1919	c.1737delA	c.(1735-1737)ggafs	p.G579fs		NM_006101.2	NP_006092.1	O14777	NDC80_HUMAN	NDC80 kinetochore complex component	579	Interaction with NEK2 and ZWINT.|Interaction with the C-terminus of CDCA1 and the SPBC24-SPBC25 subcomplex.				attachment of spindle microtubules to kinetochore (GO:0008608)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				NS(1)|biliary_tract(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)|urinary_tract(2)	22						GAAAAGTGGGAAATAACTTGC	0.368																																					p.G579fs		.											.	NDC80-91	0			c.1737delA						.						194.0	172.0	180.0					18																	2610806		2203	4300	6503	SO:0001589	frameshift_variant	10403	exon16			.	AF017790	CCDS11827.1	18p11.31	2013-01-17	2013-01-17	2007-03-02	ENSG00000080986	ENSG00000080986			16909	protein-coding gene	gene with protein product		607272	"""highly expressed in cancer, rich in leucine heptad repeats (yeast)"", ""kinetochore associated 2"", ""NDC80 kinetochore complex component homolog (S. cerevisiae)"""	KNTC2		9315664, 12351790	Standard	NM_006101		Approved	HEC, HEC1, hsNDC80, TID3	uc002kli.3	O14777	OTTHUMG00000131483	ENST00000261597.4:c.1737delA	18.37:g.2610806delA	ENSP00000261597:p.Gly579fs	Somatic	151	0		WXS	Illumina HiSeq	Phase_I	157	36	NM_006101	0	0	0	0	0	Q6PJX2	Frame_Shift_Del	DEL	ENST00000261597.4	37	CCDS11827.1																																																																																			.		0.368	NDC80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254327.1	NM_006101	
NCAN	1463	broad.mit.edu	37	19	19360601	19360603	+	In_Frame_Del	DEL	CAC	CAC	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:19360601_19360603delCAC	ENST00000252575.6	+	15	3946_3948	c.3847_3849delCAC	c.(3847-3849)cacdel	p.H1287del	NCAN_ENST00000538881.1_In_Frame_Del_p.H738del	NM_004386.2	NP_004377.2	O14594	NCAN_HUMAN	neurocan	1287					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|regulation of synapse structural plasticity (GO:0051823)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(32)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64			Epithelial(12;0.00544)		Hyaluronan(DB08818)	GATGCGGCGAcaccaccaccacc	0.596																																					p.1283_1283del													.	NCAN-94	0			c.3847_3849del						.																																			SO:0001651	inframe_deletion	1463	exon15			CGGCGACACCACC	AF026547	CCDS12397.1	19p12	2014-01-30	2007-02-15	2007-02-15	ENSG00000130287	ENSG00000130287		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"", ""Endogenous ligands"""	2465	protein-coding gene	gene with protein product	"""neurocan proteoglycan"""	600826	"""chondroitin sulfate proteoglycan 3"""	CSPG3		1326557, 21353194	Standard	NM_004386		Approved		uc002nlz.3	O14594		ENST00000252575.6:c.3847_3849delCAC	19.37:g.19360610_19360612delCAC	ENSP00000252575:p.His1287del	Somatic	197	0		WXS	Illumina HiSeq	Phase_I	193	7	NM_004386	0	0	0	0	0	Q9UPK6	In_Frame_Del	DEL	ENST00000252575.6	37	CCDS12397.1																																																																																			.		0.596	NCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460111.2	NM_004386	
KCNJ15	3772	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	21	39671646	39671649	+	Frame_Shift_Del	DEL	TTGA	TTGA	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	TTGA	TTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr21:39671646_39671649delTTGA	ENST00000328656.4	+	4	766_769	c.463_466delTTGA	c.(463-468)ttgattfs	p.LI155fs	KCNJ15_ENST00000398930.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398938.2_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398932.1_Frame_Shift_Del_p.LI155fs|KCNJ15_ENST00000398934.1_Frame_Shift_Del_p.LI155fs	NM_001276437.1|NM_001276438.1|NM_001276439.1|NM_002243.3	NP_001263366.1|NP_001263367.1|NP_001263368.1|NP_002234.2	Q99712	KCJ15_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 15	155					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	24					Yohimbine(DB01392)	CATCACGACCTTGATTGAGATCTT	0.515																																					p.155_156del		.											.	KCNJ15-157	0			c.463_466del						.																																			SO:0001589	frameshift_variant	3772	exon4			.	Y10745	CCDS13656.1	21q22.2	2011-07-05			ENSG00000157551	ENSG00000157551		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6261	protein-coding gene	gene with protein product		602106				9299242, 8995301, 16382105	Standard	NM_170736		Approved	Kir4.2, Kir1.3, IRKK	uc002ywx.4	Q99712	OTTHUMG00000090609	ENST00000328656.4:c.463_466delTTGA	21.37:g.39671650_39671653delTTGA	ENSP00000331698:p.Leu155fs	Somatic	115	0		WXS	Illumina HiSeq	Phase_I	105	28	NM_002243	0	0	0	0	0	D3DSH5|O00564|Q96L28|Q99446	Frame_Shift_Del	DEL	ENST00000328656.4	37	CCDS13656.1																																																																																			.		0.515	KCNJ15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207181.2	NM_002243	
SMC4	10051	hgsc.bcm.edu;bcgsc.ca	37	3	160134136	160134136	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr3:160134136delA	ENST00000357388.3	+	10	1821	c.1370delA	c.(1369-1371)gaafs	p.E457fs	SMC4_ENST00000462787.1_Frame_Shift_Del_p.E457fs|RP11-432B6.3_ENST00000483754.1_Intron|SMC4_ENST00000469762.1_Frame_Shift_Del_p.E432fs|SMC4_ENST00000344722.5_Frame_Shift_Del_p.E457fs|SMC4_ENST00000360111.2_Frame_Shift_Del_p.E457fs	NM_001002800.1	NP_001002800.1	Q9NTJ3	SMC4_HUMAN	structural maintenance of chromosomes 4	457					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)|mitotic sister chromatid segregation (GO:0000070)	condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(15)|lung(20)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			GAGAAAGAAGAAAAAAAATTA	0.308																																					p.E457fs		.											.	SMC4-291	0			c.1370delA						.						53.0	62.0	59.0					3																	160134136		2202	4290	6492	SO:0001589	frameshift_variant	10051	exon9			.	AF092564	CCDS3189.1, CCDS75046.1	3q26.1	2006-07-06	2006-07-06	2006-07-06	ENSG00000113810	ENSG00000113810		"""Structural maintenance of chromosomes proteins"""	14013	protein-coding gene	gene with protein product		605575	"""SMC4 (structural maintenance of chromosomes 4, yeast)-like 1"", ""SMC4 structural maintenance of chromosomes 4-like 1 (yeast)"""	SMC4L1		9789013, 10319587	Standard	NM_005496		Approved	hCAP-C, CAP-C	uc003fdh.3	Q9NTJ3	OTTHUMG00000159006	ENST00000357388.3:c.1370delA	3.37:g.160134136delA	ENSP00000349961:p.Glu457fs	Somatic	190	0		WXS	Illumina HiSeq	Phase_I	230	36	NM_005496	0	0	0	0	0	A6NLT9|D3DNL8|O95752|Q8NDL4|Q9UNT9	Frame_Shift_Del	DEL	ENST00000357388.3	37	CCDS3189.1																																																																																			.		0.308	SMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352862.1		
SLC12A2	6558	broad.mit.edu	37	5	127420207	127420209	+	In_Frame_Del	DEL	CGG	CGG	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	CGG	CGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:127420207_127420209delCGG	ENST00000262461.2	+	1	750_752	c.561_563delCGG	c.(559-564)tccggc>tcc	p.G192del	SLC12A2_ENST00000343225.4_In_Frame_Del_p.G192del|CTC-228N24.3_ENST00000501702.2_lincRNA	NM_001046.2	NP_001037.1	P55011	S12A2_HUMAN	solute carrier family 12 (sodium/potassium/chloride transporter), member 2	192	Poly-Gly.				ammonium transmembrane transport (GO:0072488)|ammonium transport (GO:0015696)|branching involved in mammary gland duct morphogenesis (GO:0060444)|chloride transmembrane transport (GO:1902476)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|gamma-aminobutyric acid signaling pathway (GO:0007214)|hyperosmotic response (GO:0006972)|ion transport (GO:0006811)|mammary duct terminal end bud growth (GO:0060763)|multicellular organism growth (GO:0035264)|positive regulation of cell volume (GO:0045795)|potassium ion transport (GO:0006813)|sodium ion transport (GO:0006814)|transepithelial ammonium transport (GO:0070634)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ammonium transmembrane transporter activity (GO:0008519)|sodium:potassium:chloride symporter activity (GO:0008511)			breast(3)|endometrium(5)|kidney(5)|large_intestine(12)|lung(16)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		all_cancers(142;0.0972)|Prostate(80;0.151)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0433)|OV - Ovarian serous cystadenocarcinoma(64;0.0978)	Bumetanide(DB00887)|Potassium Chloride(DB00761)|Quinethazone(DB01325)	GCCTGCACTCCGGCGGCGGCGGC	0.65																																					p.187_188del													.	SLC12A2-94	0			c.561_563del						.																																			SO:0001651	inframe_deletion	6558	exon1			GCACTCCGGCGGC		CCDS4144.1, CCDS58965.1	5q23.3	2014-06-13	2013-07-18		ENSG00000064651	ENSG00000064651		"""Solute carriers"""	10911	protein-coding gene	gene with protein product	"""bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1"", ""basolateral Na-K-Cl symporter"", ""protein phosphatase 1, regulatory subunit 141"""	600840				7629105	Standard	NM_001256461		Approved	NKCC1, BSC, BSC2, PPP1R141	uc003kus.3	P55011	OTTHUMG00000128983	ENST00000262461.2:c.561_563delCGG	5.37:g.127420216_127420218delCGG	ENSP00000262461:p.Gly192del	Somatic	181	0		WXS	Illumina HiSeq	Phase_I	187	9	NM_001046	0	0	0	0	0	Q8N713|Q8WWH7	In_Frame_Del	DEL	ENST00000262461.2	37	CCDS4144.1																																																																																			.		0.650	SLC12A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250972.1	NM_001046	
NCR2	9436	broad.mit.edu	37	6	41303645	41303647	+	In_Frame_Del	DEL	CTG	CTG	-	rs375455161		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:41303645_41303647delCTG	ENST00000373089.5	+	1	119_121	c.31_33delCTG	c.(31-33)ctgdel	p.L15del	NCR2_ENST00000373086.3_In_Frame_Del_p.L15del|NCR2_ENST00000373083.4_In_Frame_Del_p.L15del	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	15					cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					CCCACTGCTACTGCTGCTGCTGC	0.635																																					p.11_11del													.	NCR2-91	0			c.31_33del						.		,,	48,4200		1,46,2077					,,	-2.6	0.0			40	118,8096		0,118,3989	no	coding,coding,coding	NCR2	NM_004828.3,NM_001199510.1,NM_001199509.1	,,	1,164,6066	A1A1,A1R,RR		1.4366,1.1299,1.332	,,	,,		166,12296				SO:0001651	inframe_deletion	9436	exon1			CTGCTACTGCTGC	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.31_33delCTG	6.37:g.41303654_41303656delCTG	ENSP00000362181:p.Leu15del	Somatic	71	0		WXS	Illumina HiSeq	Phase_I	401	8	NM_004828	0	0	0	0	0	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	In_Frame_Del	DEL	ENST00000373089.5	37	CCDS4855.1																																																																																			.		0.635	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3		
AK9	221264	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	6	109977966	109977966	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr6:109977966delG	ENST00000424296.2	-	8	828	c.752delC	c.(751-753)actfs	p.T251fs	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_Frame_Shift_Del_p.T251fs|AK9_ENST00000285397.5_Frame_Shift_Del_p.T251fs	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	251	Adenylate kinase 1.|Glu-rich.				ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TACTTCTAAAGTTTGGAGAAT	0.318																																					p.T251fs		.											.	AKD1-91	0			c.752delC						.						57.0	58.0	58.0					6																	109977966		2203	4294	6497	SO:0001589	frameshift_variant	221264	exon8			.	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.752delC	6.37:g.109977966delG	ENSP00000410186:p.Thr251fs	Somatic	96	0		WXS	Illumina HiSeq	Phase_I	103	32	NM_145025	0	0	0	0	0	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Frame_Shift_Del	DEL	ENST00000424296.2	37	CCDS55048.1																																																																																			.		0.318	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
GPR85	54329	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	112724144	112724146	+	In_Frame_Del	DEL	ATC	ATC	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	ATC	ATC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:112724144_112724146delATC	ENST00000297146.3	-	3	1234_1236	c.631_633delGAT	c.(631-633)gatdel	p.D211del	GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_In_Frame_Del_p.D211del|GPR85_ENST00000449591.1_In_Frame_Del_p.D211del|GPR85_ENST00000501255.2_In_Frame_Del_p.D211del	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	211					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TTTTTCTTCGATCGTGGACGAAA	0.493																																					p.211_211del		.											.	GPR85-91	0			c.631_633del						.																																			SO:0001651	inframe_deletion	54329	exon3			.	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"""GPCR / Class A : Orphans"""	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.631_633delGAT	7.37:g.112724144_112724146delATC	ENSP00000297146:p.Asp211del	Somatic	84	0		WXS	Illumina HiSeq	Phase_I	63	14	NM_001146265	0	0	0	0	0	Q9JHI6|Q9NPD1	In_Frame_Del	DEL	ENST00000297146.3	37	CCDS5758.1																																																																																			.		0.493	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2		
LSM1	27257	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	8	38027436	38027436	+	Splice_Site	DEL	C	C	-			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr8:38027436delC	ENST00000311351.4	-	3	511		c.e3-1		LSM1_ENST00000522515.1_Splice_Site|LSM1_ENST00000520755.1_Intron	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated						exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)			kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					ACTAAGTTTGCTGTAAGTGTA	0.363																																					.		.											.	LSM1-90	0			c.116-1G>-						.						127.0	118.0	121.0					8																	38027436		2203	4300	6503	SO:0001630	splice_region_variant	27257	exon4			.	AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"""LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"""			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.116-1G>-	8.37:g.38027436delC		Somatic	122	0		WXS	Illumina HiSeq	Phase_I	129	33	NM_014462	0	0	0	0	0	B2R5E6	Splice_Site	DEL	ENST00000311351.4	37	CCDS6103.1																																																																																			.		0.363	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1	NM_014462	Intron
GPR174	84636	hgsc.bcm.edu;bcgsc.ca	37	X	78426874	78426874	+	Frame_Shift_Del	DEL	T	T	-	rs137871290		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chrX:78426874delT	ENST00000276077.1	+	1	406	c.370delT	c.(370-372)tttfs	p.F124fs		NM_032553.1	NP_115942.1	Q9BXC1	GP174_HUMAN	G protein-coupled receptor 174	124						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	38						CATGTACCCCTTTCGCTTCCA	0.458										HNSCC(63;0.18)																											p.F124fs		.											.	GPR174-130	0			c.370delT						.						217.0	194.0	202.0					X																	78426874		2203	4300	6503	SO:0001589	frameshift_variant	84636	exon1			.	AF345567	CCDS14443.1	Xq13.3	2012-08-21			ENSG00000147138	ENSG00000147138		"""GPCR / Class A : Orphans"""	30245	protein-coding gene	gene with protein product		300903					Standard	NM_032553		Approved	FKSG79	uc004edg.1	Q9BXC1	OTTHUMG00000021898	ENST00000276077.1:c.370delT	X.37:g.78426874delT	ENSP00000276077:p.Phe124fs	Somatic	128	0		WXS	Illumina HiSeq	Phase_I	144	59	NM_032553	0	0	0	0	0	Q2M3F7	Frame_Shift_Del	DEL	ENST00000276077.1	37	CCDS14443.1																																																																																			.		0.458	GPR174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057327.1	NM_032553	
EFCAB13	124989	hgsc.bcm.edu;bcgsc.ca	37	17	45468874	45468875	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr17:45468874_45468875insG	ENST00000331493.2	+	15	2065_2066	c.1654_1655insG	c.(1654-1656)tgtfs	p.C552fs	EFCAB13_ENST00000517484.1_Frame_Shift_Ins_p.C456fs	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	552	EF-hand 2.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TCTAAATACTTGTCTTCAAAAT	0.327																																					p.C552fs		.											.	.	0			c.1654_1655insG						.																																			SO:0001589	frameshift_variant	124989	exon15			.	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1655dupG	17.37:g.45468875_45468875dupG	ENSP00000332111:p.Cys552fs	Somatic	277	0		WXS	Illumina HiSeq	Phase_I	342	63	NM_152347	0	0	0	0	0	G3V128|Q49AG9	Frame_Shift_Ins	INS	ENST00000331493.2	37	CCDS11512.1																																																																																			.		0.327	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
C19orf40	91442	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	19	33464971	33464972	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr19:33464971_33464972insA	ENST00000588258.1	+	4	359_360	c.249_250insA	c.(250-252)aatfs	p.N84fs	CEP89_ENST00000590597.2_5'Flank|CEP89_ENST00000305768.5_5'Flank|C19orf40_ENST00000590281.1_Frame_Shift_Ins_p.N84fs|CEP89_ENST00000591863.1_5'Flank|C19orf40_ENST00000590179.1_5'UTR|C19orf40_ENST00000589646.1_5'UTR	NM_152266.3	NP_689479.1	Q9BTP7	FAP24_HUMAN	chromosome 19 open reading frame 40	84					DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(2)|prostate(2)	7	Esophageal squamous(110;0.137)					TCAAGTCCAATAATCTTAAAGG	0.406								Direct reversal of damage																													p.N83fs		.											.	C19orf40-90	0			c.249_250insA						.																																			SO:0001589	frameshift_variant	91442	exon4			.	AK128668	CCDS12426.1, CCDS74327.1	19q13.11	2011-11-24			ENSG00000131944	ENSG00000131944			28467	protein-coding gene	gene with protein product	"""Fanconi anemia-associated protein, 24kDa"""	610884				17289582	Standard	XM_005259393		Approved	FLJ46828, MGC32020, FAAP24	uc002nud.4	Q9BTP7		ENST00000588258.1:c.251dupA	19.37:g.33464973_33464973dupA	ENSP00000466121:p.Asn84fs	Somatic	145	0		WXS	Illumina HiSeq	Phase_I	170	43	NM_152266	0	0	0	0	0	B3KY46|Q8WUJ7|Q96FX6	Frame_Shift_Ins	INS	ENST00000588258.1	37	CCDS12426.1																																																																																			.		0.406	C19orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450823.2	NM_152266	
DOK7	285489	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	4	3478120	3478121	+	Frame_Shift_Ins	INS	-	-	GGCTA	rs376659660|rs539942267		TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr4:3478120_3478121insGGCTA	ENST00000340083.5	+	4	448_449	c.383_384insGGCTA	c.(382-387)ccggctfs	p.-129fs	DOK7_ENST00000507039.1_Frame_Shift_Ins_p.-129fs|DOK7_ENST00000389653.2_Frame_Shift_Ins_p.-129fs	NM_173660.4	NP_775931.3	Q18PE1	DOK7_HUMAN	docking protein 7						neuromuscular junction development (GO:0007528)|positive regulation of protein tyrosine kinase activity (GO:0061098)|receptor clustering (GO:0043113)	cell junction (GO:0030054)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|protein kinase binding (GO:0019901)			kidney(1)|large_intestine(1)|skin(2)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		GAGAGCGGCCCGGCTACCCTGC	0.668																																					p.P128fs		.											.	DOK7-91	0			c.383_384insGGCTA						.																																			SO:0001589	frameshift_variant	285489	exon4			.	AK091037	CCDS3370.2, CCDS54717.1	4p16.2	2014-09-17	2006-08-24	2006-08-24	ENSG00000175920	ENSG00000175920			26594	protein-coding gene	gene with protein product		610285	"""chromosome 4 open reading frame 25"""	C4orf25		16794080	Standard	NM_173660		Approved	FLJ33718, FLJ39137, Dok-7	uc003ghd.3	Q18PE1	OTTHUMG00000122087	ENST00000340083.5:c.384_388dupGGCTA	4.37:g.3478121_3478125dupGGCTA	ENSP00000344432:p.Ala129fs	Somatic	91	0		WXS	Illumina HiSeq	Phase_I	86	21	NM_001164673	0	0	0	0	0	A2A499|A2RRD4|E9PB56|Q6P6A6|Q86XG5|Q8N2J3|Q8NBC1	Frame_Shift_Ins	INS	ENST00000340083.5	37	CCDS3370.2																																																																																			.		0.668	DOK7-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313538.1	NM_173660	
SRD5A1	6715	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	5	6663046	6663047	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr5:6663046_6663047insT	ENST00000274192.5	+	4	914_915	c.680_681insT	c.(679-684)tgttttfs	p.CF227fs	SRD5A1_ENST00000537411.1_3'UTR|SRD5A1_ENST00000538824.1_Frame_Shift_Ins_p.CF180fs	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	227					androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)			endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TTCACGTTTTGTTTTTTATCTG	0.396																																					p.C227fs		.											.	SRD5A1-90	0			c.680_681insT						.																																			SO:0001589	frameshift_variant	6715	exon4			.	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.686dupT	5.37:g.6663052_6663052dupT	ENSP00000274192:p.Cys227fs	Somatic	92	0		WXS	Illumina HiSeq	Phase_I	91	23	NM_001047	0	0	0	0	0	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Frame_Shift_Ins	INS	ENST00000274192.5	37	CCDS3870.1																																																																																			.		0.396	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
RBM28	55131	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	7	127958110	127958111	+	In_Frame_Ins	INS	-	-	GAC			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr7:127958110_127958111insGAC	ENST00000223073.2	-	15	1726_1727	c.1612_1613insGTC	c.(1612-1614)cag>cGTCag	p.537_538insR	RBM28_ENST00000481788.1_Intron|RBM28_ENST00000415472.2_In_Frame_Ins_p.396_397insR	NM_018077.2	NP_060547.2	Q9NW13	RBM28_HUMAN	RNA binding motif protein 28	537	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|kidney(7)|large_intestine(3)|lung(8)|ovary(2)	21						GCCCAGGGACTGACCCTTCATG	0.485																																					p.Q538delinsRQ		.											.	RBM28-92	0			c.1613_1614insGTC						.																																			SO:0001652	inframe_insertion	55131	exon15			.	AK001239	CCDS5801.1, CCDS55159.1	7q32.2	2013-02-12			ENSG00000106344	ENSG00000106344		"""RNA binding motif (RRM) containing"""	21863	protein-coding gene	gene with protein product		612074					Standard	NM_018077		Approved	FLJ10377	uc003vmp.2	Q9NW13	OTTHUMG00000157711	ENST00000223073.2:c.1610_1612dupGTC	7.37:g.127958111_127958113dupGAC	ENSP00000223073:p.Gly537_Gln538insArg	Somatic	101	0		WXS	Illumina HiSeq	Phase_I	88	19	NM_018077	0	0	0	0	0	A4D100|B4DU52|E9PDD9|Q53H65|Q96CV3	In_Frame_Ins	INS	ENST00000223073.2	37	CCDS5801.1																																																																																			.		0.485	RBM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349442.2	NM_018077	
LRPPRC	10128	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	44116985	44116986	+	Missense_Mutation	DNP	GC	GC	AG			TCGA-B9-A69E-01A-11D-A31X-10	TCGA-B9-A69E-10A-01D-A31X-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	bc7baae9-8c95-40f5-b778-ca1598e9373d	f4799bdc-b207-4053-9a4b-5a26ebf8ab91	g.chr2:44116985_44116986GC>AG	ENST00000260665.7	-	37	4072_4073	c.4015_4016GC>CT	c.(4015-4017)GCa>CTa	p.A1339L	RNU6-1048P_ENST00000364054.1_RNA	NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	1339	RNA-binding.				mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TTCATACAGTGCTTTAGCAGAT	0.366																																					p.A1339L		.											.	LRPPRC-93	0			c.G4015C						.																																			SO:0001583	missense	10128	exon37			ACAGTGCTTTAGC	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.4015_4016delinsAG	2.37:g.44116985_44116986delinsAG	ENSP00000260665:p.Ala1339Leu	Somatic	244.0	0.0		WXS	Illumina HiSeq	Phase_I	217.0	48.0	NM_133259	0	0	0	0	0	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Missense_Mutation	DNP	ENST00000260665.7	37	CCDS33189.1																																																																																			.		0.366	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
