#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_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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_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_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AATK	9625	broad.mit.edu;hgsc.bcm.edu	37	17	79098648	79098648	+	Splice_Site	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:79098648C>T	ENST00000326724.4	-	9	865	c.841G>A	c.(841-843)Gag>Aag	p.E281K	AATK_ENST00000417379.1_Splice_Site_p.E178K|AATK_ENST00000572339.1_5'Flank|MIR657_ENST00000385003.1_RNA|MIR338_ENST00000390137.2_RNA	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.E281K(2)		endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AAGTAGTCCTCCTGTTGGCAC	0.667																																																	2	Substitution - Missense(2)	kidney(2)											33.0	39.0	37.0					17																	79098648		2151	4247	6398	SO:0001630	splice_region_variant	9625			AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.841-1G>A	17.37:g.79098648C>T		Somatic		WXS	Illumina HiSeq	Phase_I	O75136|Q6ZN31|Q86X28	Missense_Mutation	SNP	ENST00000326724.4	37	CCDS45807.1	.	.	.	.	.	.	.	.	.	.	C	23.7	4.442987	0.83993	.	.	ENSG00000181409	ENST00000326724;ENST00000374792	D;D	0.82255	-1.59;-1.59	3.66	3.66	0.41972	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.130939	0.48286	D	0.000183	D	0.85124	0.5625	L	0.41824	1.3	0.50039	D	0.999846	D	0.63046	0.992	P	0.60286	0.872	D	0.86976	0.2101	10	0.66056	D	0.02	.	14.6471	0.68769	0.0:1.0:0.0:0.0	.	281	Q6ZMQ8	LMTK1_HUMAN	K	281	ENSP00000324196:E281K;ENSP00000363924:E281K	ENSP00000324196:E281K	E	-	1	0	AATK	76713243	1.000000	0.71417	0.998000	0.56505	0.272000	0.26649	7.002000	0.76304	2.041000	0.60428	0.591000	0.81541	GAG		0.667	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1		NM_004920	Missense_Mutation
ADAM21	8747	broad.mit.edu;hgsc.bcm.edu	37	14	70925009	70925009	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr14:70925009A>T	ENST00000603540.1	+	2	1051	c.793A>T	c.(793-795)Aat>Tat	p.N265Y	ADAM21_ENST00000267499.3_Missense_Mutation_p.N265Y|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	265	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.N265Y(2)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GAATCAAGGAAATGTTTTCCC	0.368																																																	2	Substitution - Missense(2)	kidney(2)											63.0	64.0	64.0					14																	70925009		2203	4300	6503	SO:0001583	missense	8747			AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.793A>T	14.37:g.70925009A>T	ENSP00000474385:p.Asn265Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	O43507|Q2VPC6|Q32MR0	Missense_Mutation	SNP	ENST00000603540.1	37	CCDS9804.1	.	.	.	.	.	.	.	.	.	.	A	12.44	1.938438	0.34189	.	.	ENSG00000139985	ENST00000267499	T	0.68025	-0.3	4.1	2.97	0.34412	Metallopeptidase, catalytic domain (1);Peptidase M12B, ADAM/reprolysin (2);	0.000000	0.46758	D	0.000275	D	0.82728	0.5100	M	0.92507	3.315	0.09310	N	0.999999	D	0.76494	0.999	D	0.77557	0.99	T	0.72469	-0.4284	10	0.87932	D	0	.	8.5619	0.33516	0.9052:0.0:0.0948:0.0	.	265	Q9UKJ8	ADA21_HUMAN	Y	265	ENSP00000267499:N265Y	ENSP00000267499:N265Y	N	+	1	0	ADAM21	69994762	0.970000	0.33590	0.967000	0.41034	0.715000	0.41141	5.263000	0.65507	1.839000	0.53478	0.455000	0.32223	AAT		0.368	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3			
AFTPH	54812	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	64779884	64779884	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:64779884G>C	ENST00000422803.1	+	2	1590	c.1276G>C	c.(1276-1278)Gat>Cat	p.D426H	AFTPH_ENST00000238855.7_Missense_Mutation_p.D426H|AFTPH_ENST00000409933.1_Missense_Mutation_p.D426H|AFTPH_ENST00000238856.4_Missense_Mutation_p.D426H|AFTPH_ENST00000409183.1_Missense_Mutation_p.D57H			Q6ULP2	AFTIN_HUMAN	aftiphilin	426					protein transport (GO:0015031)	AP-1 adaptor complex (GO:0030121)|cytosol (GO:0005829)	clathrin binding (GO:0030276)	p.D426H(2)		breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	35						GACTTGCAATGATATCAATGA	0.378																																																	2	Substitution - Missense(2)	kidney(2)											164.0	158.0	160.0					2																	64779884		2203	4300	6503	SO:0001583	missense	54812			AB073356	CCDS1878.1, CCDS46303.1	2p14	2008-02-05			ENSG00000119844	ENSG00000119844			25951	protein-coding gene	gene with protein product						14665628, 15758025, 15811338	Standard	NM_017657		Approved	MGC33965, FLJ20080, FLJ23793, Nbla10388	uc002scz.3	Q6ULP2	OTTHUMG00000129539	ENST00000422803.1:c.1276G>C	2.37:g.64779884G>C	ENSP00000397726:p.Asp426His	Somatic		WXS	Illumina HiSeq	Phase_I	D6W5E9|Q6ZM66|Q86VW3|Q8TCF3|Q9H7E3|Q9HAB9|Q9NXS4	Missense_Mutation	SNP	ENST00000422803.1	37		.	.	.	.	.	.	.	.	.	.	G	10.90	1.480957	0.26598	.	.	ENSG00000119844	ENST00000238856;ENST00000422803;ENST00000238855;ENST00000409933;ENST00000409183	T;T;T;T;T	0.47869	1.65;1.65;1.8;1.8;0.83	5.65	3.78	0.43462	.	0.354390	0.28482	N	0.015182	T	0.55625	0.1932	M	0.62723	1.935	0.09310	N	1	P;P;D;D	0.69078	0.729;0.729;0.997;0.997	B;P;P;P	0.59761	0.345;0.545;0.863;0.863	T	0.47636	-0.9102	10	0.54805	T	0.06	-2.257	6.042	0.19740	0.2194:0.1398:0.6408:0.0	.	426;426;426;426	Q6ULP2;Q6ULP2-2;Q6ULP2-5;Q6ULP2-4	AFTIN_HUMAN;.;.;.	H	426;426;426;426;57	ENSP00000238856:D426H;ENSP00000397726:D426H;ENSP00000238855:D426H;ENSP00000387071:D426H;ENSP00000386913:D57H	ENSP00000238855:D426H	D	+	1	0	AFTPH	64633388	0.104000	0.21937	0.742000	0.31022	0.715000	0.41141	1.306000	0.33505	1.381000	0.46364	0.650000	0.86243	GAT		0.378	AFTPH-202	KNOWN	basic	protein_coding	protein_coding			NM_017657	
ARID1A	8289	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	27099852	27099852	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:27099852C>A	ENST00000324856.7	+	15	4102	c.3731C>A	c.(3730-3732)cCc>cAc	p.P1244H	ARID1A_ENST00000457599.2_Missense_Mutation_p.P1244H|ARID1A_ENST00000540690.1_5'UTR|ARID1A_ENST00000374152.2_Missense_Mutation_p.P861H	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1244					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)	p.P1244H(1)	ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		GGGAGTGATCCCTTCATGTCC	0.592			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																			Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	1	Substitution - Missense(1)	kidney(1)											61.0	62.0	62.0					1																	27099852		2203	4300	6503	SO:0001583	missense	8289			AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.3731C>A	1.37:g.27099852C>A	ENSP00000320485:p.Pro1244His	Somatic		WXS	Illumina HiSeq	Phase_I	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Missense_Mutation	SNP	ENST00000324856.7	37	CCDS285.1	.	.	.	.	.	.	.	.	.	.	C	15.42	2.826931	0.50739	.	.	ENSG00000117713	ENST00000324856;ENST00000457599;ENST00000374152	T;T;T	0.02709	4.43;4.19;4.24	5.02	5.02	0.67125	.	0.055152	0.85682	D	0.000000	T	0.04497	0.0123	L	0.40543	1.245	0.80722	D	1	B;B;B;B	0.18461	0.004;0.016;0.028;0.016	B;B;B;B	0.14578	0.006;0.005;0.011;0.005	T	0.44128	-0.9348	10	0.62326	D	0.03	-4.3543	18.5413	0.91029	0.0:1.0:0.0:0.0	.	861;1244;1244;897	O14497-3;O14497;O14497-2;Q4LE49	.;ARI1A_HUMAN;.;.	H	1244;1244;861	ENSP00000320485:P1244H;ENSP00000387636:P1244H;ENSP00000363267:P861H	ENSP00000320485:P1244H	P	+	2	0	ARID1A	26972439	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.709000	0.68384	2.627000	0.88993	0.655000	0.94253	CCC		0.592	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2		NM_139135	
ATR	545	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	142168328	142168328	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:142168328delT	ENST00000350721.4	-	47	7999	c.7878delA	c.(7876-7878)gaafs	p.E2626fs	XRN1_ENST00000465074.1_5'Flank|ATR_ENST00000383101.3_Frame_Shift_Del_p.E2562fs|XRN1_ENST00000264951.4_5'Flank|XRN1_ENST00000392981.2_5'Flank|XRN1_ENST00000463916.1_5'Flank|XRN1_ENST00000544157.1_5'Flank	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	2626	FATC. {ECO:0000255|PROSITE- ProRule:PRU00534, ECO:0000255|PROSITE- ProRule:PRU00535}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|multicellular organismal development (GO:0007275)|negative regulation of DNA replication (GO:0008156)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|protein autophosphorylation (GO:0046777)|regulation of protein binding (GO:0043393)|replicative senescence (GO:0090399)|response to drug (GO:0042493)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|XY body (GO:0001741)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|MutLalpha complex binding (GO:0032405)|MutSalpha complex binding (GO:0032407)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(10)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|liver(2)|lung(45)|ovary(3)|skin(10)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(4)	122						CATCAGTAGCTTCCTGTATAA	0.348								Other conserved DNA damage response genes																																									0													121.0	117.0	118.0					3																	142168328		2203	4300	6503	SO:0001589	frameshift_variant	545			U76308	CCDS3124.1	3q23	2014-06-17	2014-06-17		ENSG00000175054	ENSG00000175054			882	protein-coding gene	gene with protein product	"""MEC1, mitosis entry checkpoint 1, homolog (S. cerevisiae)"""	601215	"""ataxia telangiectasia and Rad3 related"""			8978690, 8610130	Standard	NM_001184		Approved	FRP1, SCKL, SCKL1, MEC1	uc003eux.4	Q13535	OTTHUMG00000159234	ENST00000350721.4:c.7878delA	3.37:g.142168328delT	ENSP00000343741:p.Glu2626fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q59HB2|Q7KYL3|Q93051|Q9BXK4	Frame_Shift_Del	DEL	ENST00000350721.4	37	CCDS3124.1																																																																																				0.348	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2		NM_001184	
GPANK1	7918	broad.mit.edu;ucsc.edu	37	6	31632107	31632107	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr6:31632107T>C	ENST00000375906.1	-	3	833	c.149A>G	c.(148-150)gAt>gGt	p.D50G	CSNK2B_ENST00000375885.4_5'Flank|CSNK2B_ENST00000375865.2_5'Flank|CSNK2B_ENST00000375866.2_5'Flank|CSNK2B-LY6G5B-1181_ENST00000375880.2_5'Flank|CSNK2B_ENST00000375882.2_5'Flank|GPANK1_ENST00000375893.2_Missense_Mutation_p.D50G|GPANK1_ENST00000375896.4_Missense_Mutation_p.D50G|GPANK1_ENST00000375895.2_Missense_Mutation_p.D50G|Y_RNA_ENST00000364337.1_RNA|GPANK1_ENST00000375900.4_Missense_Mutation_p.D50G	NM_001199237.1	NP_001186166.1	O95872	GPAN1_HUMAN	G patch domain and ankyrin repeats 1	50							nucleic acid binding (GO:0003676)	p.D50G(1)		central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(7)	12						GCTGCTCTCATCCCCAATCAG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											49.0	53.0	52.0					6																	31632107		2203	4300	6503	SO:0001583	missense	0				CCDS4711.1	6p21.3	2013-01-28	2010-11-24	2010-11-24	ENSG00000204438	ENSG00000204438		"""Ankyrin repeat domain containing"", ""G patch domain containing"""	13920	protein-coding gene	gene with protein product	"""G patch domain containing 10"", ""ankyrin repeat domain 59"""	142610	"""HLA-B associated transcript 4"""	BAT4		2911734, 2813433	Standard	NM_001199237		Approved	G5, D6S54E, GPATCH10, ANKRD59	uc021yuu.1	O95872	OTTHUMG00000031174	ENST00000375906.1:c.149A>G	6.37:g.31632107T>C	ENSP00000365071:p.Asp50Gly	Somatic		WXS	Illumina GAIIx	Phase_I	A6NG25|B0UXA2|Q5SQ49	Missense_Mutation	SNP	ENST00000375906.1	37	CCDS4711.1	.	.	.	.	.	.	.	.	.	.	T	11.11	1.541956	0.27563	.	.	ENSG00000204438	ENST00000375906;ENST00000375896;ENST00000375893;ENST00000375895;ENST00000375900;ENST00000440842;ENST00000458083;ENST00000445768;ENST00000432291;ENST00000456540	T;T;T;T;T;T;T;T	0.53206	3.05;3.05;3.05;3.05;3.05;1.39;1.39;0.63	4.94	-2.59	0.06209	.	1.181720	0.05945	N	0.637746	T	0.12347	0.0300	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.23583	-1.0184	10	0.34782	T	0.22	-0.8462	3.359	0.07179	0.1463:0.4892:0.1496:0.2149	.	50	O95872	GPAN1_HUMAN	G	50	ENSP00000365071:D50G;ENSP00000365060:D50G;ENSP00000365057:D50G;ENSP00000365059:D50G;ENSP00000365065:D50G;ENSP00000395307:D50G;ENSP00000409349:D50G;ENSP00000395484:D50G	ENSP00000365057:D50G	D	-	2	0	GPANK1	31740086	0.000000	0.05858	0.001000	0.08648	0.599000	0.36880	0.163000	0.16520	-0.046000	0.13446	-0.366000	0.07423	GAT		0.557	GPANK1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144445.2		NM_033177	
BCAR1	9564	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	75276901	75276902	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr16:75276901_75276902CC>AA	ENST00000162330.5	-	2	225_226	c.99_100GG>TT	c.(97-102)ctGGag>ctTTag	p.E34*	BCAR1_ENST00000538440.2_Nonsense_Mutation_p.E34*|BCAR1_ENST00000546196.1_Nonsense_Mutation_p.E5*|BCAR1_ENST00000393422.2_Nonsense_Mutation_p.E52*|BCAR1_ENST00000418647.3_Nonsense_Mutation_p.E80*|BCAR1_ENST00000542031.2_Nonsense_Mutation_p.E32*|BCAR1_ENST00000535626.2_Nonsense_Mutation_p.E34*|BCAR1_ENST00000420641.3_Nonsense_Mutation_p.E52*|BCAR1_ENST00000393420.6_Nonsense_Mutation_p.E34*	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	34	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)	p.E34*(4)|p.E80*(2)|p.L33L(2)|p.L79L(1)		breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GTGTCCTGCTCCAGCACCGTCA	0.629																																																	9	Substitution - Nonsense(6)|Substitution - coding silent(3)	kidney(9)																																								SO:0001587	stop_gained	9564			AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.99_100delinsAA	16.37:g.75276901_75276902delinsAA	ENSP00000162330:p.Glu34*	Somatic		WXS	Illumina HiSeq	Phase_I	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Nonsense_Mutation|Silent	SNP	ENST00000162330.5	37	CCDS10915.1																																																																																				0.629	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1		NM_014567	
BCORL1	63035	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	129148444	129148444	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:129148444C>A	ENST00000218147.7	+	4	1893	c.1696C>A	c.(1696-1698)Cct>Act	p.P566T	BCORL1_ENST00000359304.2_Missense_Mutation_p.P566T|BCORL1_ENST00000303743.5_Missense_Mutation_p.P566T|BCORL1_ENST00000540052.1_Missense_Mutation_p.P566T			Q5H9F3	BCORL_HUMAN	BCL6 corepressor-like 1	566	Pro-rich.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.P566T(1)		breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|liver(3)|lung(30)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	75						AACTCCACAGCCTCTGCTGCC	0.632																																																	1	Substitution - Missense(1)	kidney(1)											62.0	63.0	63.0					X																	129148444		2203	4300	6503	SO:0001583	missense	63035			AL136450	CCDS14616.1	Xq25-q26.1	2014-09-17	2010-06-10		ENSG00000085185	ENSG00000085185		"""Ankyrin repeat domain containing"""	25657	protein-coding gene	gene with protein product		300688	"""chromosome X open reading frame 10"", ""BCL6 co-repressor-like 1"""	CXorf10			Standard	NM_021946		Approved	FLJ11362	uc022cdu.1	Q5H9F3	OTTHUMG00000022379	ENST00000218147.7:c.1696C>A	X.37:g.129148444C>A	ENSP00000218147:p.Pro566Thr	Somatic		WXS	Illumina HiSeq	Phase_I	B5MDQ8|Q5H9F2|Q5H9F4|Q6ZVE0|Q8TEN3|Q9Y528	Missense_Mutation	SNP	ENST00000218147.7	37	CCDS14616.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	13.06|13.06	2.124434|2.124434	0.37533|0.37533	.|.	.|.	ENSG00000085185|ENSG00000085185	ENST00000441294|ENST00000218147;ENST00000303743;ENST00000359304;ENST00000540052;ENST00000456822	.|T;T;T;T;T	.|0.39787	.|1.08;1.45;1.06;1.08;1.53	5.68|5.68	4.82|4.82	0.62117|0.62117	.|.	.|0.226622	.|0.22716	.|N	.|0.056518	T|T	0.24774|0.24774	0.0601|0.0601	N|N	0.24115|0.24115	0.695|0.695	0.30479|0.30479	N|N	0.772511|0.772511	.|B;P	.|0.43094	.|0.015;0.799	.|B;B	.|0.38378	.|0.013;0.272	T|T	0.14337|0.14337	-1.0476|-1.0476	5|10	.|0.32370	.|T	.|0.25	-3.5471|-3.5471	5.7611|5.7611	0.18201|0.18201	0.1233:0.6012:0.1987:0.0768|0.1233:0.6012:0.1987:0.0768	.|.	.|566;566	.|Q5H9F3-2;Q5H9F3	.|.;BCORL_HUMAN	D|T	1|566;566;566;566;166	.|ENSP00000218147:P566T;ENSP00000307541:P566T;ENSP00000352253:P566T;ENSP00000437775:P566T;ENSP00000399483:P166T	.|ENSP00000218147:P566T	A|P	+|+	2|1	0|0	BCORL1|BCORL1	128976125|128976125	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.981000|0.981000	0.71138|0.71138	0.698000|0.698000	0.25571|0.25571	1.183000|1.183000	0.42943|0.42943	0.525000|0.525000	0.51046|0.51046	GCC|CCT		0.632	BCORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058223.1		NM_021946	
METTL21C	196541	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	103343225	103343226	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr13:103343225_103343226insA	ENST00000267273.6	-	2	224_225	c.219_220insT	c.(217-222)tttgcafs	p.A74fs		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	74					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						TCCTTTCCTGCAAACCGATAAT	0.46																																																	0																																										SO:0001589	frameshift_variant	0				CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"""chromosome 13 open reading frame 39"""	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.220dupT	13.37:g.103343228_103343228dupA	ENSP00000267273:p.Ala74fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Ins	INS	ENST00000267273.6	37	CCDS32003.1																																																																																				0.460	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2		NM_001010977	
C1orf168	199920	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	57258476	57258476	+	Splice_Site	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:57258476C>A	ENST00000343433.6	-	2	90	c.10G>T	c.(10-12)Gaa>Taa	p.E4*	C1orf168_ENST00000484327.1_5'UTR	NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	4								p.E4*(1)		NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						CTTACCCCTTCCTAAGGCAAA	0.353																																																	1	Substitution - Nonsense(1)	kidney(1)											86.0	92.0	90.0					1																	57258476		2202	4290	6492	SO:0001630	splice_region_variant	199920			BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.10-1G>T	1.37:g.57258476C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q63HM3|Q6ZUY6	Nonsense_Mutation	SNP	ENST00000343433.6	37	CCDS30729.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.400431	0.83120	.	.	ENSG00000187889	ENST00000343433	.	.	.	4.65	3.74	0.42951	.	0.099220	0.43416	D	0.000562	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33141	T	0.24	-16.547	8.8314	0.35087	0.0:0.8977:0.0:0.1023	.	.	.	.	X	4	.	ENSP00000345972:E4X	E	-	1	0	C1orf168	57031064	1.000000	0.71417	1.000000	0.80357	0.620000	0.37586	2.133000	0.42093	1.318000	0.45170	-0.253000	0.11424	GAA		0.353	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2		NM_001004303	Nonsense_Mutation
SSUH2	51066	hgsc.bcm.edu	37	3	8675505	8675506	+	Frame_Shift_Ins	INS	-	-	G	rs201775949	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:8675505_8675506insG	ENST00000317371.4	-	11	1344_1345	c.119_120insC	c.(118-120)ccgfs	p.P40fs	SSUH2_ENST00000415132.1_Frame_Shift_Ins_p.P40fs|SSUH2_ENST00000341795.3_Frame_Shift_Ins_p.P40fs|SSUH2_ENST00000544814.1_Intron			Q9Y2M2	SSUH2_HUMAN	ssu-2 homolog (C. elegans)	40						cytoplasm (GO:0005737)											AACAGAGAGGCGGGGGCTTCTG	0.639																																																	0																																										SO:0001589	frameshift_variant	0			AB024705	CCDS2568.1, CCDS58815.1	3p25.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000125046	ENSG00000125046			24809	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 32"""	C3orf32		20205943	Standard	NM_001256748		Approved	fls485, ssu-2	uc011atg.3	Q9Y2M2	OTTHUMG00000122075	ENST00000317371.4:c.120dupC	3.37:g.8675510_8675510dupG	ENSP00000324551:p.Pro40fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFA9|B3KS84|B7Z6E3|F5H2S5|Q7Z7K4	Frame_Shift_Ins	INS	ENST00000317371.4	37	CCDS2568.1																																																																																				0.639	SSUH2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337900.1		NM_015931	
NREP	9315	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	111071196	111071196	+	Nonsense_Mutation	SNP	G	G	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr5:111071196G>T	ENST00000379671.3	-	4	276	c.12C>A	c.(10-12)taC>taA	p.Y4*	NREP_ENST00000450761.2_Nonsense_Mutation_p.Y4*|NREP_ENST00000508870.1_Nonsense_Mutation_p.Y4*|NREP_ENST00000507742.1_5'UTR|NREP_ENST00000509427.1_Nonsense_Mutation_p.Y4*|NREP_ENST00000453526.2_Nonsense_Mutation_p.Y4*|NREP_ENST00000509025.1_Nonsense_Mutation_p.Y4*|NREP_ENST00000509979.1_Nonsense_Mutation_p.Y4*|NREP_ENST00000447165.2_Nonsense_Mutation_p.Y4*|NREP_ENST00000446294.2_Nonsense_Mutation_p.Y4*|NREP_ENST00000257435.7_Nonsense_Mutation_p.Y4*|NREP_ENST00000395634.3_Nonsense_Mutation_p.Y48*|STARD4-AS1_ENST00000500779.2_RNA|NREP_ENST00000515855.1_Nonsense_Mutation_p.Y4*|NREP_ENST00000455559.2_Nonsense_Mutation_p.Y4*|NREP_ENST00000419114.2_Nonsense_Mutation_p.Y4*	NM_001142478.1	NP_001135950.1	Q16612	NREP_HUMAN	neuronal regeneration related protein	4					axon regeneration (GO:0031103)|regulation of neuron differentiation (GO:0045664)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.Y4*(1)|p.Y48*(1)									AGAGTTCTGGGTAATAAACCT	0.403																																																	2	Substitution - Nonsense(2)	kidney(2)											88.0	89.0	89.0					5																	111071196		2202	4300	6502	SO:0001587	stop_gained	0			AF119859	CCDS4105.1, CCDS47255.1	5q22.1	2012-12-07	2012-12-07	2012-01-23	ENSG00000134986	ENSG00000134986			16834	protein-coding gene	gene with protein product	"""neuronal protein 3.1"""	607332	"""chromosome 5 open reading frame 13"", ""neuronal regeneration related protein homolog (rat)"""	C5orf13		8261136, 10981724, 15485502	Standard	NM_004772		Approved	P311, D4S114, PRO1873, PTZ17, SEZ17	uc011cvr.2	Q16612	OTTHUMG00000128795	ENST00000379671.3:c.12C>A	5.37:g.111071196G>T	ENSP00000368993:p.Tyr4*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RDN8|B7Z5D2|D3DSZ8	Nonsense_Mutation	SNP	ENST00000379671.3	37	CCDS4105.1	.	.	.	.	.	.	.	.	.	.	G	34	5.332428	0.95733	.	.	ENSG00000134986	ENST00000509025;ENST00000379671;ENST00000257435;ENST00000447165;ENST00000446294;ENST00000395634;ENST00000515855;ENST00000509979;ENST00000450761;ENST00000419114;ENST00000509427;ENST00000453526;ENST00000455559;ENST00000508870;ENST00000513100;ENST00000508161;ENST00000507032	.	.	.	5.55	4.62	0.57501	.	0.398139	0.21371	N	0.075628	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.824	8.9943	0.36043	0.0:0.171:0.6742:0.1548	.	.	.	.	X	4;4;4;4;4;48;4;4;4;4;4;4;4;4;4;4;4	.	ENSP00000257435:Y4X	Y	-	3	2	C5orf13	111099095	1.000000	0.71417	0.997000	0.53966	0.618000	0.37518	0.900000	0.28431	2.773000	0.95371	0.655000	0.94253	TAC		0.403	NREP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250722.1		NM_004772	
CA10	56934	broad.mit.edu;hgsc.bcm.edu	37	17	49726541	49726541	+	Splice_Site	SNP	A	A	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:49726541A>G	ENST00000285273.4	-	7	1746		c.e7+1		CA10_ENST00000442502.2_Splice_Site|CA10_ENST00000340813.6_Splice_Site|CA10_ENST00000570565.1_Splice_Site|CA10_ENST00000571918.1_Splice_Site|CA10_ENST00000451037.2_Splice_Site	NM_001082533.1	NP_001076002.1	Q9NS85	CAH10_HUMAN	carbonic anhydrase X						brain development (GO:0007420)			p.?(1)		cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|ovary(1)|skin(3)|stomach(2)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(22;4.74e-06)		Zonisamide(DB00909)	AACCAAACTTACTTTTATATG	0.383																																																	1	Unknown(1)	kidney(1)											121.0	126.0	124.0					17																	49726541		2203	4300	6503	SO:0001630	splice_region_variant	56934			AF288385	CCDS32684.1	17q21	2012-08-21			ENSG00000154975	ENSG00000154975		"""Carbonic anhydrases"""	1369	protein-coding gene	gene with protein product		604642				8673298, 9921901	Standard	NM_020178		Approved	CARPX, CA-RPX, HUCEP-15	uc002itx.4	Q9NS85	OTTHUMG00000177544	ENST00000285273.4:c.634+1T>C	17.37:g.49726541A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2R7J0|B4DGL6	Splice_Site	SNP	ENST00000285273.4	37	CCDS32684.1	.	.	.	.	.	.	.	.	.	.	A	23.0	4.358044	0.82243	.	.	ENSG00000154975	ENST00000442502;ENST00000285273;ENST00000451037;ENST00000340813	.	.	.	5.37	5.37	0.77165	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5469	0.68038	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CA10	47081540	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.546000	0.90661	2.018000	0.59344	0.482000	0.46254	.		0.383	CA10-003	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000437480.1		NM_020178	Intron
CCNA1	8900	hgsc.bcm.edu	37	13	37012869	37012873	+	Frame_Shift_Del	DEL	AGGTT	AGGTT	-	rs200577481	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	AGGTT	AGGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr13:37012869_37012873delAGGTT	ENST00000255465.4	+	5	1022_1026	c.758_762delAGGTT	c.(757-762)gaggttfs	p.EV253fs	CCNA1_ENST00000440264.1_Frame_Shift_Del_p.EV209fs|CCNA1_ENST00000449823.1_Frame_Shift_Del_p.EV209fs|CCNA1_ENST00000418263.1_Frame_Shift_Del_p.EV252fs			P78396	CCNA1_HUMAN	cyclin A1	253					G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|male meiosis I (GO:0007141)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				breast(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(2)|urinary_tract(1)	35		Breast(139;0.014)|Lung SC(185;0.0548)|Prostate(109;0.174)	KIRC - Kidney renal clear cell carcinoma(5;0.119)|Kidney(79;0.169)	all cancers(112;1.91e-07)|Epithelial(112;1.22e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0119)|GBM - Glioblastoma multiforme(144;0.0242)		TGGCTGGTGGAGGTTGGGGAAGAAT	0.502																																																	0																																										SO:0001589	frameshift_variant	8900			U66838	CCDS9357.1, CCDS45031.1	13q12.3-q13	2014-01-21			ENSG00000133101	ENSG00000133101			1577	protein-coding gene	gene with protein product		604036				9041194	Standard	NM_003914		Approved	CT146	uc001uvr.4	P78396	OTTHUMG00000016733	ENST00000255465.4:c.758_762delAGGTT	13.37:g.37012869_37012873delAGGTT	ENSP00000255465:p.Glu253fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z7E3|Q5T3V0|Q5U0G2|Q8IY91	Frame_Shift_Del	DEL	ENST00000255465.4	37	CCDS9357.1																																																																																				0.502	CCNA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044514.2		NM_003914	
CEP164	22897	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	117280582	117280582	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:117280582C>A	ENST00000278935.3	+	30	4144	c.3997C>A	c.(3997-3999)Caa>Aaa	p.Q1333K	CEP164_ENST00000533706.1_3'UTR	NM_001271933.1|NM_014956.4	NP_001258862.1|NP_055771.4	Q9UPV0	CE164_HUMAN	centrosomal protein 164kDa	1333					cilium assembly (GO:0042384)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)		p.Q1333K(1)		breast(3)|central_nervous_system(1)|kidney(7)|large_intestine(12)|lung(18)|ovary(3)|prostate(3)	47	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;4e-05)|Epithelial(105;0.0008)		CACGTCCACCCAATGGGCCTG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											95.0	95.0	95.0					11																	117280582		2201	4296	6497	SO:0001583	missense	22897			AB028975	CCDS31683.1	11q23.3	2014-02-20			ENSG00000110274	ENSG00000110274			29182	protein-coding gene	gene with protein product		614848				10470851, 14654843	Standard	NM_014956		Approved	KIAA1052, NPHP15	uc001prc.3	Q9UPV0	OTTHUMG00000167070	ENST00000278935.3:c.3997C>A	11.37:g.117280582C>A	ENSP00000278935:p.Gln1333Lys	Somatic		WXS	Illumina HiSeq	Phase_I	Q6PKH9|Q7Z2X9|Q9NVS0|Q9UFJ6	Missense_Mutation	SNP	ENST00000278935.3	37	CCDS31683.1	.	.	.	.	.	.	.	.	.	.	C	5.579	0.291711	0.10567	.	.	ENSG00000110274	ENST00000278935	T	0.24350	1.86	4.61	3.69	0.42338	.	1.025460	0.07784	N	0.953829	T	0.29126	0.0724	M	0.68952	2.095	0.30857	N	0.733919	B;B	0.32829	0.386;0.386	B;B	0.28139	0.086;0.086	T	0.23833	-1.0177	10	0.41790	T	0.15	0.0	10.9183	0.47150	0.0:0.9097:0.0:0.0903	.	1333;1328	Q9UPV0;Q9UPV0-2	CE164_HUMAN;.	K	1333	ENSP00000278935:Q1333K	ENSP00000278935:Q1333K	Q	+	1	0	CEP164	116785792	0.534000	0.26362	0.988000	0.46212	0.173000	0.22820	3.017000	0.49615	0.914000	0.36822	0.561000	0.74099	CAA		0.617	CEP164-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392893.1		NM_014956	
CHPT1	56994	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	102107933	102107933	+	Silent	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr12:102107933T>A	ENST00000229266.3	+	2	574	c.339T>A	c.(337-339)atT>atA	p.I113I	CHPT1_ENST00000549872.1_Silent_p.I113I|CHPT1_ENST00000550385.1_3'UTR	NM_020244.2	NP_064629.2	Q8WUD6	CHPT1_HUMAN	choline phosphotransferase 1	113					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|regulation of cell growth (GO:0001558)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	diacylglycerol binding (GO:0019992)|diacylglycerol cholinephosphotransferase activity (GO:0004142)|metal ion binding (GO:0046872)	p.I113I(1)		kidney(2)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	10						TGGATGCTATTGATGGGAAAC	0.383																																																	1	Substitution - coding silent(1)	kidney(1)											155.0	167.0	163.0					12																	102107933		2203	4300	6503	SO:0001819	synonymous_variant	56994				CCDS9086.1	12q	2010-07-08				ENSG00000111666	2.7.8.2		17852	protein-coding gene	gene with protein product	"""phosphatidylcholine synthesizing enzyme"""					10893425	Standard	NM_020244		Approved	CPT1	uc001tin.3	Q8WUD6		ENST00000229266.3:c.339T>A	12.37:g.102107933T>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KQM2|Q7Z7H0|Q7Z7H1|Q7Z7H2|Q8IWQ4|Q8IWQ5|Q8WYI4|Q9NRQ6|Q9NRQ7|Q9Y6M6	Silent	SNP	ENST00000229266.3	37	CCDS9086.1																																																																																				0.383	CHPT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409173.1		NM_020244	
CNBP	7555	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	128890023	128890023	+	Silent	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:128890023G>A	ENST00000422453.2	-	4	475	c.315C>T	c.(313-315)ggC>ggT	p.G105G	CNBP_ENST00000504813.1_Silent_p.G95G|CNBP_ENST00000441626.2_Silent_p.G107G|CNBP_ENST00000446936.2_Silent_p.G100G|CNBP_ENST00000500450.2_Silent_p.G88G|CNBP_ENST00000451728.2_Silent_p.G106G|CNBP_ENST00000502976.1_Silent_p.G98G	NM_001127192.1|NM_001127193.1|NM_003418.4	NP_001120664.1|NP_001120665.1|NP_003409.1	P62633	CNBP_HUMAN	CCHC-type zinc finger, nucleic acid binding protein	105					cholesterol biosynthetic process (GO:0006695)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)	p.G105G(1)		biliary_tract(1)|endometrium(1)|kidney(1)|lung(2)	5						GAGCCAGATGGCCTGGTTTGC	0.502																																																	1	Substitution - coding silent(1)	kidney(1)											116.0	97.0	103.0					3																	128890023		2203	4300	6503	SO:0001819	synonymous_variant	7555			U19765	CCDS3056.1, CCDS46906.1, CCDS46907.1, CCDS46908.1, CCDS54637.1	3q21	2013-01-09	2006-06-29	2006-06-29				"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, CCHC domain containing"""	13164	protein-coding gene	gene with protein product		116955	"""zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)"", ""zinc finger protein 9"""	DM2, ZNF9		2249857, 11486088	Standard	NM_003418		Approved	RNF163, ZCCHC22, CNBP1	uc021xdw.1	P62633		ENST00000422453.2:c.315C>T	3.37:g.128890023G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7V4|B2RAV9|B4DP17|D3DNB9|D3DNC0|D3DNC1|E9PDR7|P20694|Q4JGY0|Q4JGY1|Q5QJR0|Q5U0E9|Q6PJI7|Q96NV3	Silent	SNP	ENST00000422453.2	37	CCDS3056.1	.	.	.	.	.	.	.	.	.	.	G	8.013	0.757872	0.15846	.	.	ENSG00000169714	ENST00000512338	.	.	.	5.52	4.65	0.58169	.	.	.	.	.	T	0.64416	0.2596	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66980	-0.5786	5	0.87932	D	0	-13.9427	7.7781	0.29049	0.0866:0.1637:0.7496:0.0	.	.	.	.	V	110	.	ENSP00000424787:A110V	A	-	2	0	CNBP	130372713	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.951000	0.40333	1.352000	0.45808	0.591000	0.81541	GCC		0.502	CNBP-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358419.1		NM_003418	
COL5A2	1290	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	189914113	189914113	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:189914113G>A	ENST00000374866.3	-	44	3381	c.3107C>T	c.(3106-3108)cCc>cTc	p.P1036L		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1036					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)	p.P1036L(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GGAGCCTGGGGGCCCCACAGG	0.458																																																	1	Substitution - Missense(1)	kidney(1)											58.0	56.0	57.0					2																	189914113		2203	4300	6503	SO:0001583	missense	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.3107C>T	2.37:g.189914113G>A	ENSP00000364000:p.Pro1036Leu	Somatic		WXS	Illumina HiSeq	Phase_I	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Missense_Mutation	SNP	ENST00000374866.3	37	CCDS33350.1	.	.	.	.	.	.	.	.	.	.	G	12.45	1.941279	0.34283	.	.	ENSG00000204262	ENST00000374866;ENST00000452536	D	0.96685	-4.09	5.6	5.6	0.85130	.	0.328616	0.22606	N	0.057889	D	0.93220	0.7840	L	0.50847	1.595	0.21782	N	0.999545	B;B	0.06786	0.0;0.001	B;B	0.11329	0.001;0.006	T	0.82176	-0.0587	9	.	.	.	.	9.0076	0.36122	0.0749:0.0:0.767:0.1581	.	676;1036	Q5PR22;P05997	.;CO5A2_HUMAN	L	1036;676	ENSP00000364000:P1036L	.	P	-	2	0	COL5A2	189622358	1.000000	0.71417	0.992000	0.48379	0.854000	0.48673	3.770000	0.55310	2.932000	0.99384	0.644000	0.83932	CCC		0.458	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1		NM_000393	
CPSF1	29894	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	145623927	145623927	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr8:145623927T>A	ENST00000349769.3	-	18	1834	c.1740A>T	c.(1738-1740)gaA>gaT	p.E580D	MIR1234_ENST00000408875.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	580					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)	p.E580D(1)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			TGGTGGAGTCTTCCCGGCTCA	0.682																																					NSCLC(133;1088 1848 27708 34777 35269)												1	Substitution - Missense(1)	kidney(1)											90.0	94.0	92.0					8																	145623927		2203	4300	6503	SO:0001583	missense	29894			U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.1740A>T	8.37:g.145623927T>A	ENSP00000339353:p.Glu580Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	T	16.66	3.184937	0.57909	.	.	ENSG00000071894	ENST00000349769	T	0.43294	0.95	5.84	0.0524	0.14302	.	0.000000	0.85682	D	0.000000	T	0.33323	0.0859	L	0.42245	1.32	0.45899	D	0.998747	B	0.28470	0.213	B	0.35278	0.199	T	0.05835	-1.0861	10	0.25751	T	0.34	-13.851	9.3829	0.38325	0.1427:0.6922:0.0:0.1651	.	580	Q10570	CPSF1_HUMAN	D	580	ENSP00000339353:E580D	ENSP00000339353:E580D	E	-	3	2	CPSF1	145594735	0.905000	0.30787	0.993000	0.49108	0.789000	0.44602	-0.064000	0.11636	-0.353000	0.08224	0.533000	0.62120	GAA		0.682	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2		NM_013291	
LRRC7	57554	broad.mit.edu;hgsc.bcm.edu	37	1	70144085	70144085	+	Silent	SNP	A	A	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:70144085A>G	ENST00000370958.1	+	2	214	c.24A>G	c.(22-24)ggA>ggG	p.G8G	LRRC7_ENST00000310961.5_5'UTR			Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	0						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.G8G(1)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TAATAAGGGGAAGGAATCCCC	0.383																																																	1	Substitution - coding silent(1)	kidney(1)											20.0	19.0	19.0					1																	70144085		876	1991	2867	SO:0001819	synonymous_variant	0				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000370958.1:c.24A>G	1.37:g.70144085A>G		Somatic		WXS	Illumina HiSeq	Phase_I	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	IGR	SNP	ENST00000370958.1	37																																																																																					0.383	LRRC7-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000131263.1		NM_020794	
ACAA1	30	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	38163910	38163910	+	IGR	SNP	G	G	A	rs369229329		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:38163910G>A	ENST00000333167.8	-	0	1785				DLEC1_ENST00000346219.3_Silent_p.P1717P|DLEC1_ENST00000308059.6_3'UTR|Y_RNA_ENST00000365095.1_RNA|ACAA1_ENST00000480865.1_5'Flank|DLEC1_ENST00000452631.2_3'UTR	NM_001607.3	NP_001598.1	P09110	THIK_HUMAN	acetyl-CoA acyltransferase 1						alpha-linolenic acid metabolic process (GO:0036109)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acetyl-CoA C-acyltransferase activity (GO:0003988)|palmitoyl-CoA oxidase activity (GO:0016401)	p.P1717P(2)		endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	9				KIRC - Kidney renal clear cell carcinoma(284;0.0523)|Kidney(284;0.0657)		CTGAGGCTCCGCCCCAGCCCT	0.612																																																	2	Substitution - coding silent(2)	large_intestine(1)|kidney(1)						G	,	0,3872		0,0,1936	43.0	47.0	46.0		,5151	1.3	0.1	3		46	1,8297		0,1,4148	no	utr-3,coding-synonymous	DLEC1	NM_007335.2,NM_007337.2	,	0,1,6084	AA,AG,GG		0.0121,0.0,0.0082	,	,1717/1779	38163910	1,12169	1936	4149	6085	SO:0001628	intergenic_variant	9940			X14813	CCDS2673.1, CCDS46794.1	3p22.2	2012-05-16	2010-04-30		ENSG00000060971	ENSG00000060971	2.3.1.16		82	protein-coding gene	gene with protein product	"""peroxisomal 3-oxoacyl-Coenzyme A thiolase"""	604054	"""acetyl-Coenzyme A acyltransferase 1"""				Standard	NM_001607		Approved		uc003cht.3	P09110	OTTHUMG00000131087		3.37:g.38163910G>A		Somatic		WXS	Illumina HiSeq	Phase_I	G5E935|Q96CA6	Silent	SNP	ENST00000333167.8	37	CCDS2673.1																																																																																				0.612	ACAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342980.1		NM_001607	
DNAH17	8632	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	76482488	76482488	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:76482488G>T	ENST00000585328.1	-	45	7028	c.6904C>A	c.(6904-6906)Cgc>Agc	p.R2302S	DNAH17_ENST00000389840.5_Missense_Mutation_p.R2293S|DNAH17_ENST00000586052.1_5'UTR|RP11-559N14.5_ENST00000585969.1_RNA|RP11-559N14.5_ENST00000588565.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2293					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)	p.R2302S(1)		NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			AACCCAAAGCGCAACTTGTCC	0.582																																																	1	Substitution - Missense(1)	kidney(1)											74.0	80.0	78.0					17																	76482488		2184	4266	6450	SO:0001583	missense	8632			AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.6904C>A	17.37:g.76482488G>T	ENSP00000465516:p.Arg2302Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.331226	0.60853	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.26957	1.7	5.01	3.92	0.45320	.	.	.	.	.	T	0.53029	0.1771	M	0.92412	3.305	0.30878	N	0.731709	.	.	.	.	.	.	T	0.62025	-0.6941	7	0.87932	D	0	.	10.6149	0.45445	0.0:0.0:0.5769:0.4231	.	.	.	.	S	2302;2293	ENSP00000374490:R2293S	ENSP00000300671:R2302S	R	-	1	0	DNAH17	73994083	0.962000	0.33011	0.992000	0.48379	0.972000	0.66771	2.248000	0.43160	2.505000	0.84491	0.561000	0.74099	CGC		0.582	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2		NM_173628	
EIF4E	1977	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	99823113	99823113	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr4:99823113A>T	ENST00000450253.2	-	2	1563	c.39T>A	c.(37-39)aaT>aaA	p.N13K	EIF4E_ENST00000280892.6_Missense_Mutation_p.N33K|EIF4E_ENST00000504432.1_Missense_Mutation_p.N41K|EIF4E_ENST00000505992.1_Missense_Mutation_p.N13K|EIF4E_ENST00000504472.1_5'UTR	NM_001968.3	NP_001959.1	P06730	IF4E_HUMAN	eukaryotic translation initiation factor 4E	13					cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of mitotic cell cycle (GO:0045931)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|extracellular vesicular exosome (GO:0070062)|mRNA cap binding complex (GO:0005845)|RISC complex (GO:0016442)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation initiation factor activity (GO:0003743)	p.N13K(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.7e-07)|LUSC - Lung squamous cell carcinoma(721;0.00227)		TAGTCGGGGGATTAGGAGTAG	0.373																																																	1	Substitution - Missense(1)	kidney(1)											123.0	129.0	127.0					4																	99823113		2203	4299	6502	SO:0001583	missense	1977			M15353	CCDS34031.1, CCDS47109.1, CCDS54779.1	4q21-q25	2008-02-05			ENSG00000151247	ENSG00000151247			3287	protein-coding gene	gene with protein product		133440		EIF4EL1, EIF4F		9330633, 1916814	Standard	NM_001968		Approved	EIF4E1	uc011cea.1	P06730	OTTHUMG00000161090	ENST00000450253.2:c.39T>A	4.37:g.99823113A>T	ENSP00000389624:p.Asn13Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z6V1|D6RCQ6|Q96E95	Missense_Mutation	SNP	ENST00000450253.2	37	CCDS34031.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	15.33|15.33	2.802047|2.802047	0.50315|0.50315	.|.	.|.	ENSG00000151247|ENSG00000151247	ENST00000450253;ENST00000280892;ENST00000504432;ENST00000505992|ENST00000511644	T;T;T;T|.	0.43688|.	0.94;0.94;0.94;0.94|.	5.85|5.85	2.11|2.11	0.27256|0.27256	Translation Initiation factor eIF- 4e-like  domain (2);|.	0.510486|.	0.23281|.	N|.	0.049912|.	T|T	0.32526|0.32526	0.0832|0.0832	N|N	0.08118|0.08118	0|0	0.58432|0.58432	D|D	0.999999|0.999999	P;D;D;P|.	0.67145|.	0.908;0.996;0.967;0.76|.	D;D;D;P|.	0.75484|.	0.947;0.986;0.964;0.82|.	T|T	0.04386|0.04386	-1.0955|-1.0955	10|5	0.18276|.	T|.	0.48|.	-14.8551|-14.8551	10.0348|10.0348	0.42122|0.42122	0.7354:0.0:0.2646:0.0|0.7354:0.0:0.2646:0.0	.|.	13;13;33;13|.	B7Z2T1;P06730-2;B7Z6V1;P06730|.	.;.;.;IF4E_HUMAN|.	K|T	13;33;41;13|10	ENSP00000389624:N13K;ENSP00000280892:N33K;ENSP00000423977:N41K;ENSP00000425561:N13K|.	ENSP00000280892:N33K|.	N|S	-|-	3|1	2|0	EIF4E|EIF4E	100042136|100042136	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.974000|0.974000	0.67602|0.67602	3.081000|3.081000	0.50120|0.50120	0.563000|0.563000	0.29222|0.29222	0.523000|0.523000	0.50628|0.50628	AAT|TCC		0.373	EIF4E-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363739.1		NM_001968	
FAM166A	401565	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	140139965	140139965	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr9:140139965G>A	ENST00000344774.4	-	3	370	c.316C>T	c.(316-318)Ccc>Tcc	p.P106S	FAM166A_ENST00000388932.2_Missense_Mutation_p.P106S	NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	106						nucleus (GO:0005634)		p.P106S(1)		kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						ACCTCCAAGGGTGGGAGCTGG	0.637																																																	1	Substitution - Missense(1)	kidney(1)											60.0	75.0	70.0					9																	140139965		2187	4294	6481	SO:0001583	missense	401565			BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.316C>T	9.37:g.140139965G>A	ENSP00000344729:p.Pro106Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A6NND9|Q8N830	Missense_Mutation	SNP	ENST00000344774.4	37	CCDS35186.1	.	.	.	.	.	.	.	.	.	.	G	3.404	-0.121586	0.06838	.	.	ENSG00000188163	ENST00000344774;ENST00000388932;ENST00000484720	.	.	.	5.1	2.05	0.26809	.	0.837236	0.10612	N	0.654333	T	0.30696	0.0773	L	0.35723	1.085	0.09310	N	1	B	0.14438	0.01	B	0.10450	0.005	T	0.28870	-1.0030	9	0.17832	T	0.49	-3.014	9.0131	0.36153	0.0874:0.5167:0.3959:0.0	.	106	Q6J272	F166A_HUMAN	S	106;106;133	.	ENSP00000344729:P106S	P	-	1	0	FAM166A	139259786	0.012000	0.17670	0.098000	0.21074	0.014000	0.08584	0.836000	0.27545	0.089000	0.17243	0.462000	0.41574	CCC		0.637	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1		NM_001001710	
TVP23C	201158	broad.mit.edu;hgsc.bcm.edu	37	17	15449215	15449215	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:15449215T>A	ENST00000225576.3	-	5	441	c.346A>T	c.(346-348)Aat>Tat	p.N116Y	TVP23C_ENST00000584811.1_Missense_Mutation_p.N52Y|TVP23C_ENST00000438826.3_Missense_Mutation_p.N116Y|TVP23C_ENST00000519970.1_Missense_Mutation_p.N30Y|TVP23C_ENST00000518321.1_Missense_Mutation_p.N116Y|TVP23C-CDRT4_ENST00000522212.2_Missense_Mutation_p.N116Y|TVP23C_ENST00000428082.2_Missense_Mutation_p.N116Y	NM_145301.2	NP_660344.2	Q96ET8	TV23C_HUMAN	trans-golgi network vesicle protein 23 homolog C (S. cerevisiae)	116						integral component of membrane (GO:0016021)		p.N116Y(2)									ACAGTTTTATTCTCTTGAGAG	0.323																																																	2	Substitution - Missense(2)	kidney(2)											101.0	100.0	101.0					17																	15449215		2203	4297	6500	SO:0001583	missense	0			BC011952	CCDS11170.1, CCDS45617.1	17p12	2012-11-29	2012-11-29	2012-11-29	ENSG00000175106	ENSG00000175106			30453	protein-coding gene	gene with protein product			"""family with sequence similarity 18, member B2"""	FAM18B2			Standard	NM_001135036		Approved	MGC8763	uc002goq.2	Q96ET8	OTTHUMG00000171461	ENST00000225576.3:c.346A>T	17.37:g.15449215T>A	ENSP00000225576:p.Asn116Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q3LIC7	Missense_Mutation	SNP	ENST00000225576.3	37	CCDS11170.1	.	.	.	.	.	.	.	.	.	.	.	8.538	0.872660	0.17322	.	.	ENSG00000259024;ENSG00000259024;ENSG00000259024;ENSG00000175106;ENSG00000175106;ENSG00000175106;ENSG00000175106;ENSG00000175106	ENST00000522212;ENST00000557349;ENST00000481756;ENST00000519970;ENST00000225576;ENST00000428082;ENST00000438826;ENST00000419890	T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93	5.05	2.82	0.32997	.	0.657654	0.15767	N	0.245641	T	0.55194	0.1905	M	0.68317	2.08	0.09310	N	0.999999	B;P;B;P	0.51791	0.178;0.948;0.122;0.473	B;P;B;P	0.59595	0.091;0.86;0.096;0.532	T	0.44907	-0.9297	10	0.72032	D	0.01	.	8.7142	0.34401	0.0:0.1612:0.0:0.8388	.	116;30;116;116	Q96ET8-2;B4E0Q0;Q96ET8-3;Q96ET8	.;.;.;F18B2_HUMAN	Y	116;30;30;30;116;116;116;52	ENSP00000429865:N116Y;ENSP00000428961:N30Y;ENSP00000225576:N116Y;ENSP00000406387:N116Y;ENSP00000413355:N116Y;ENSP00000409988:N52Y	ENSP00000225576:N116Y	N	-	1	0	RP11-726O12.1;FAM18B2	15389940	0.427000	0.25514	0.003000	0.11579	0.227000	0.25037	2.274000	0.43390	0.348000	0.23949	0.528000	0.53228	AAT		0.323	TVP23C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000130705.2		NM_145301	
FLG	2312	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	152279938	152279938	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:152279938C>G	ENST00000368799.1	-	3	7459	c.7424G>C	c.(7423-7425)gGa>gCa	p.G2475A	FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2475	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.G2475A(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTAGTGGGATCCCTGCCTTCC	0.577									Ichthyosis																																								1	Substitution - Missense(1)	kidney(1)											368.0	340.0	349.0					1																	152279938		2203	4300	6503	SO:0001583	missense	2312	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.7424G>C	1.37:g.152279938C>G	ENSP00000357789:p.Gly2475Ala	Somatic		WXS	Illumina HiSeq	Phase_I	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	10.04	1.241438	0.22711	.	.	ENSG00000143631	ENST00000368799	T	0.07114	3.22	3.41	-0.305	0.12784	.	.	.	.	.	T	0.05914	0.0154	M	0.82517	2.595	0.09310	N	1	D	0.55172	0.97	P	0.48704	0.587	T	0.28522	-1.0041	9	0.22109	T	0.4	.	6.3157	0.21188	0.0:0.5924:0.0:0.4076	.	2475	P20930	FILA_HUMAN	A	2475	ENSP00000357789:G2475A	ENSP00000357789:G2475A	G	-	2	0	FLG	150546562	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.244000	0.00542	0.000000	0.14550	0.306000	0.20318	GGA		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1		NM_002016	
FLRT2	23768	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	86089641	86089641	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr14:86089641A>T	ENST00000330753.4	+	2	2550	c.1783A>T	c.(1783-1785)Aag>Tag	p.K595*	FLRT2_ENST00000554746.1_Nonsense_Mutation_p.K595*	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	595					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.K595*(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		AGGCACCAAGAAGGACAACTC	0.478																																																	1	Substitution - Nonsense(1)	kidney(1)											111.0	118.0	116.0					14																	86089641		2203	4300	6503	SO:0001587	stop_gained	23768			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1783A>T	14.37:g.86089641A>T	ENSP00000332879:p.Lys595*	Somatic		WXS	Illumina HiSeq	Phase_I	A0AV84|B7ZLP3	Nonsense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	.	.	.	.	.	.	.	.	.	.	A	46	12.291422	0.99654	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	.	.	.	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.5994	16.8222	0.85835	1.0:0.0:0.0:0.0	.	.	.	.	X	595;595;248	.	ENSP00000332879:K595X	K	+	1	0	FLRT2	85159394	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.338000	0.96553	2.371000	0.80710	0.533000	0.62120	AAG		0.478	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1			
GCNT3	9245	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	59910566	59910566	+	Silent	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr15:59910566G>A	ENST00000396065.1	+	3	577	c.129G>A	c.(127-129)gaG>gaA	p.E43E	GCNT3_ENST00000560585.1_Silent_p.E43E	NM_004751.2	NP_004742.1	O95395	GCNT3_HUMAN	glucosaminyl (N-acetyl) transferase 3, mucin type	43					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|immunoglobulin production in mucosal tissue (GO:0002426)|intestinal absorption (GO:0050892)|kidney morphogenesis (GO:0060993)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|tissue morphogenesis (GO:0048729)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0047225)|beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase activity (GO:0003829)|N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)	p.E43E(1)		central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						TGGGTCTGGAGTCCAGGGAAT	0.488																																																	1	Substitution - coding silent(1)	kidney(1)											98.0	102.0	101.0					15																	59910566		2190	4290	6480	SO:0001819	synonymous_variant	9245			AF102542	CCDS10172.1	15q22	2013-02-25			ENSG00000140297	ENSG00000140297	2.4.1.102, 2.4.1.150	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4205	protein-coding gene	gene with protein product		606836				9915862, 9988682	Standard	NM_004751		Approved	C2GnT-M, C2/4GnT, C2GnT2	uc002age.3	O95395	OTTHUMG00000132726	ENST00000396065.1:c.129G>A	15.37:g.59910566G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000396065.1	37	CCDS10172.1																																																																																				0.488	GCNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256068.1		NM_004751	
GRIN3B	116444	broad.mit.edu;ucsc.edu	37	19	1004979	1004979	+	Silent	SNP	C	C	T	rs369027881		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:1004979C>T	ENST00000234389.3	+	3	1498	c.1479C>T	c.(1477-1479)ttC>ttT	p.F493F	GRIN3B_ENST00000588335.1_3'UTR|AC004528.4_ENST00000588380.1_RNA	NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	493					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)	p.F493F(1)		breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	ACACGCCCTTCGACTTCGAGC	0.721																																																	1	Substitution - coding silent(1)	kidney(1)						C		0,4404		0,0,2202	27.0	28.0	28.0		1479	-1.0	1.0	19		28	1,8593		0,1,4296	no	coding-synonymous	GRIN3B	NM_138690.1		0,1,6498	TT,TC,CC		0.0116,0.0,0.0077		493/1044	1004979	1,12997	2202	4297	6499	SO:0001819	synonymous_variant	116444				CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.1479C>T	19.37:g.1004979C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q5EAK7|Q7RTW9	Silent	SNP	ENST00000234389.3	37	CCDS32861.1																																																																																				0.721	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2			
HERC1	8925	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	63915942	63915942	+	Silent	SNP	G	G	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr15:63915942G>T	ENST00000443617.2	-	73	13680	c.13593C>A	c.(13591-13593)acC>acA	p.T4531T		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4531	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)	p.T4531T(2)		NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						TCTCTGTGATGGTGTCATCAA	0.522																																																	2	Substitution - coding silent(2)	kidney(2)											122.0	122.0	122.0					15																	63915942		2066	4225	6291	SO:0001819	synonymous_variant	8925			U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.13593C>A	15.37:g.63915942G>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q8IW65	Silent	SNP	ENST00000443617.2	37	CCDS45277.1																																																																																				0.522	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1		NM_003922	
HLA-DPB1	3115	hgsc.bcm.edu	37	6	33054014	33054014	+	Stop_Codon_Del	DEL	A	A	-	rs67523850	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr6:33054014delA	ENST00000418931.2	+	0	892					NM_002121.5	NP_002112.3	P04440	DPB1_HUMAN	major histocompatibility complex, class II, DP beta 1						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell proliferation (GO:0042102)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	peptide antigen binding (GO:0042605)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	11						GGATCTGCATAAACAGGTAAT	0.423													|||unknown(NO_COVERAGE)	391	0.0780751	0.0968	0.0677	5008	,	,		20380	0.0863		0.0437	False		,,,				2504	0.0869																0										358,3906		18,322,1792	167.0	183.0	177.0			-2.0	0.0	6	dbSNP_130	185	318,7936		7,304,3816	no	frameshift	HLA-DPB1	NM_002121.5		25,626,5608	A1A1,A1R,RR		3.8527,8.3959,5.4002			33054014	676,11842	2202	4299	6501	SO:0001567	stop_retained_variant	3115				CCDS4765.1	6p21.3	2013-01-11			ENSG00000223865	ENSG00000223865		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4940	protein-coding gene	gene with protein product		142858		HLA-DP1B			Standard	NM_002121		Approved		uc003ocu.2	P04440	OTTHUMG00000031076	Exception_encountered	6.37:g.33054014delA		Somatic		WXS	Illumina HiSeq	Phase_I	A0PFJ7|A5I886|A8YPB3|B5U8B4|B7VF80|B7VF87|B8ZX68|B8ZYT0|B9W5S8|B9W6F7|B9W6F9|C0MPP5|C0MPQ2|C0MPQ3|C0MPQ5|C0MPQ6|C0MPQ7|C4R9J5|C5IZL1|O00259|O19698|O19700|O19702|O19749|O46884|O77952|O98215|O98216|O98217|O98218|O98219|O98222|O98223|P01916|P04232|P13763|P79493|P79608|Q0P0L4|Q0ZFN3|Q14279|Q27S71|Q29682|Q29684|Q29698|Q29714|Q29775|Q29776|Q29778|Q29779|Q29781|Q29827|Q29828|Q29879|Q29880|Q29898|Q29977|Q2MGW3|Q30015|Q30031|Q30032|Q30033|Q30034|Q30050|Q30051|Q30052|Q30053|Q30054|Q30055|Q30174|Q4GY31|Q4JHD8|Q5ENE0|Q5ENE1|Q5ENW3|Q5EP46|Q5EP47|Q5EP49|Q5EP51|Q5EP52|Q5EP53|Q5EP56|Q5I4H8|Q5I4H9|Q5ISH4|Q5ISH5|Q5SQ73|Q5STP2|Q5YLA6|Q6IVX1|Q6LBX2|Q6LBX3|Q6LBX4|Q6LBX5|Q6LBX6|Q6LBX7|Q6PWX6|Q6TAS4|Q714U1|Q714U2|Q7YQ10|Q860Z7|Q8HWL7|Q8HWT5|Q8SNC4|Q95HC1|Q95IT7|Q95IT8|Q9BD13|Q9GIM2|Q9GIM4|Q9GIX6|Q9GJ41|Q9MY67|Q9TNT7|Q9TQE2|Q9XS11|Q9XS12	Frame_Shift_Del	DEL	ENST00000418931.2	37	CCDS4765.1																																																																																				0.423	HLA-DPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076106.2		NM_002121	
HNRNPCL1	343069	broad.mit.edu;hgsc.bcm.edu	37	1	12907356	12907356	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:12907356C>T	ENST00000317869.6	-	2	1012	c.787G>A	c.(787-789)Ggg>Agg	p.G263R		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	263						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.G263R(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						TGGTCATCCCCCTGATCTTCA	0.502																																																	1	Substitution - Missense(1)	kidney(1)											143.0	156.0	151.0					1																	12907356		2203	4300	6503	SO:0001583	missense	343069			BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.787G>A	1.37:g.12907356C>T	ENSP00000365370:p.Gly263Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	10.96	1.499023	0.26861	.	.	ENSG00000179172	ENST00000317869	T	0.10192	2.9	1.09	1.09	0.20402	.	0.336255	0.26442	U	0.024359	T	0.25269	0.0614	M	0.65498	2.005	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01099	-1.1452	10	0.72032	D	0.01	.	8.1133	0.30928	0.0:1.0:0.0:0.0	.	263	O60812	HNRCL_HUMAN	R	263	ENSP00000365370:G263R	ENSP00000365370:G263R	G	-	1	0	HNRNPCL1	12829943	0.252000	0.23972	0.006000	0.13384	0.002000	0.02628	3.306000	0.51881	0.916000	0.36871	0.416000	0.27883	GGG		0.502	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1		NM_001013631	
ILDR1	286676	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	121724198	121724198	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:121724198T>A	ENST00000344209.5	-	3	398	c.272A>T	c.(271-273)gAc>gTc	p.D91V	ILDR1_ENST00000273691.3_Missense_Mutation_p.D91V|ILDR1_ENST00000462014.1_Missense_Mutation_p.D103V|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.D91V	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	91	Ig-like V-type.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)	p.D91V(2)		central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		GTCGTTGCAGTCATTGGATGG	0.577																																																	2	Substitution - Missense(2)	kidney(2)											65.0	64.0	64.0					3																	121724198		2203	4300	6503	SO:0001583	missense	286676			BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.272A>T	3.37:g.121724198T>A	ENSP00000345667:p.Asp91Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	.	.	.	.	.	.	.	.	.	.	T	25.0	4.591922	0.86953	.	.	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000383663;ENST00000393631;ENST00000462014	T;T;T;T	0.53857	0.6;0.6;0.6;0.6	5.62	5.62	0.85841	Immunoglobulin subtype (1);	0.000000	0.85682	D	0.000000	T	0.72724	0.3496	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.998;0.999;1.0	T	0.76556	-0.2916	10	0.87932	D	0	-26.7101	14.0659	0.64828	0.0:0.0:0.0:1.0	.	91;91;91;103	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	V	91;91;91;91;103	ENSP00000273691:D91V;ENSP00000345667:D91V;ENSP00000377251:D91V;ENSP00000419414:D103V	ENSP00000273691:D91V	D	-	2	0	ILDR1	123206888	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	7.651000	0.83577	2.257000	0.74773	0.455000	0.32223	GAC		0.577	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1		NM_175924	
IPO13	9670	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	44425962	44425962	+	Silent	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:44425962G>A	ENST00000372343.3	+	12	2732	c.2070G>A	c.(2068-2070)aaG>aaA	p.K690K		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	690					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.K690K(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TTATCCAGAAGGTGCTGAGCA	0.562																																																	1	Substitution - coding silent(1)	kidney(1)											324.0	267.0	286.0					1																	44425962		2203	4300	6503	SO:0001819	synonymous_variant	9670			AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.2070G>A	1.37:g.44425962G>A		Somatic		WXS	Illumina HiSeq	Phase_I	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																				0.562	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1		NM_014652	
ITGB4	3691	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73745083	73745083	+	Silent	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:73745083C>T	ENST00000200181.3	+	27	3460	c.3273C>T	c.(3271-3273)caC>caT	p.H1091H	ITGB4_ENST00000449880.2_Silent_p.H1091H|ITGB4_ENST00000339591.3_Silent_p.H1091H|ITGB4_ENST00000579662.1_Silent_p.H1091H|ITGB4_ENST00000450894.3_Silent_p.H1091H	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1091					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)	p.H1091H(1)		breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TTGGGGCCCACCTGGGCCAGC	0.642																																																	1	Substitution - coding silent(1)	kidney(1)											29.0	33.0	32.0					17																	73745083		2203	4300	6503	SO:0001819	synonymous_variant	3691				CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3273C>T	17.37:g.73745083C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Silent	SNP	ENST00000200181.3	37	CCDS11727.1																																																																																				0.642	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1			
ITIH6	347365	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	54785300	54785300	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:54785300C>T	ENST00000218436.6	-	8	1236	c.1207G>A	c.(1207-1209)Ggc>Agc	p.G403S		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	403	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.G403S(1)									GTCGTCACGCCGGCCGTGGGC	0.597																																																	1	Substitution - Missense(1)	kidney(1)											56.0	44.0	48.0					X																	54785300		2203	4300	6503	SO:0001583	missense	0			AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.1207G>A	X.37:g.54785300C>T	ENSP00000218436:p.Gly403Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	C	11.43	1.637957	0.29157	.	.	ENSG00000102313	ENST00000218436	T	0.03745	3.82	3.78	1.99	0.26369	von Willebrand factor, type A (3);	0.069948	0.56097	U	0.000027	T	0.07188	0.0182	M	0.77406	2.37	0.21697	N	0.999583	P	0.40970	0.734	B	0.42112	0.376	T	0.12528	-1.0544	10	0.49607	T	0.09	.	8.4301	0.32753	0.0:0.7908:0.0:0.2092	.	403	Q6UXX5	ITH5L_HUMAN	S	403	ENSP00000218436:G403S	ENSP00000218436:G403S	G	-	1	0	ITIH5L	54802025	0.809000	0.29036	0.000000	0.03702	0.000000	0.00434	2.195000	0.42677	0.038000	0.15604	-0.180000	0.13094	GGC		0.597	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2		NM_198510	
KIAA0368	23392	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	114134741	114134741	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr9:114134741A>T	ENST00000338205.5	-	41	4715	c.4496T>A	c.(4495-4497)tTa>tAa	p.L1499*	KIAA0368_ENST00000259335.4_Nonsense_Mutation_p.L1677*|KIAA0368_ENST00000465499.1_5'Flank|KIAA0368_ENST00000374378.3_5'UTR			Q5VYK3	ECM29_HUMAN	KIAA0368	1505					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)		p.L1677*(1)		NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TTCGGTCCATAAATTACATTC	0.398																																																	1	Substitution - Nonsense(1)	kidney(1)											124.0	118.0	120.0					9																	114134741		1864	4105	5969	SO:0001587	stop_gained	23392			AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.4496T>A	9.37:g.114134741A>T	ENSP00000339889:p.Leu1499*	Somatic		WXS	Illumina HiSeq	Phase_I	O15074|Q8WU82	Nonsense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	A	47	13.839404	0.99766	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000543827	.	.	.	5.94	5.94	0.96194	.	0.083486	0.50627	D	0.000103	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	16.4075	0.83691	1.0:0.0:0.0:0.0	.	.	.	.	X	1499;1677;974	.	ENSP00000259335:L1677X	L	-	2	0	KIAA0368	113174562	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	8.767000	0.91732	2.275000	0.75901	0.528000	0.53228	TTA		0.398	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000053637.2		NM_014686	
KANSL1	284058	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	44127972	44127981	+	Frame_Shift_Del	DEL	GTGAATTTCG	GTGAATTTCG	-	rs371047711|rs587780998	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	GTGAATTTCG	GTGAATTTCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:44127972_44127981delGTGAATTTCG	ENST00000262419.6	-	7	2408_2417	c.1938_1947delCGAAATTCAC	c.(1936-1947)cccgaaattcacfs	p.PEIH646fs	KANSL1_ENST00000432791.1_Frame_Shift_Del_p.PEIH646fs|KANSL1_ENST00000393476.3_Frame_Shift_Del_p.PEIH3fs|KANSL1_ENST00000574590.1_Frame_Shift_Del_p.PEIH646fs|KANSL1_ENST00000575318.1_Frame_Shift_Del_p.PEIH646fs|KANSL1_ENST00000572904.1_Frame_Shift_Del_p.PEIH646fs	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	646					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GGGCTTCATAGTGAATTTCGGGAGGCATGG	0.495																																																	0																																										SO:0001589	frameshift_variant	0			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.1938_1947delCGAAATTCAC	17.37:g.44127972_44127981delGTGAATTTCG	ENSP00000262419:p.Pro646fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Frame_Shift_Del	DEL	ENST00000262419.6	37	CCDS11503.1																																																																																				0.495	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1		NM_015443	
LHX2	9355	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	126783560	126783560	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr9:126783560G>T	ENST00000373615.4	+	4	1649	c.910G>T	c.(910-912)Ggc>Tgc	p.G304C		NM_004789.3	NP_004780.3	P50458	LHX2_HUMAN	LIM homeobox 2	304					axon extension (GO:0048675)|axon guidance (GO:0007411)|cerebral cortex development (GO:0021987)|dorsal/ventral pattern formation (GO:0009953)|mesoderm development (GO:0007498)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|neural tube closure (GO:0001843)|olfactory bulb development (GO:0021772)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|retina development in camera-type eye (GO:0060041)|telencephalon regionalization (GO:0021978)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.G304C(1)		endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|prostate(1)	10						GCAAAAGACGGGCCTCACCAA	0.632																																																	1	Substitution - Missense(1)	kidney(1)											59.0	54.0	55.0					9																	126783560		2203	4300	6503	SO:0001583	missense	9355			U11701	CCDS6853.1	9q33.3	2011-06-20			ENSG00000106689	ENSG00000106689		"""Homeoboxes / LIM class"""	6594	protein-coding gene	gene with protein product		603759				8649822, 10051612	Standard	NM_004789		Approved	LH-2, hLhx2	uc004boe.1	P50458	OTTHUMG00000020647	ENST00000373615.4:c.910G>T	9.37:g.126783560G>T	ENSP00000362717:p.Gly304Cys	Somatic		WXS	Illumina HiSeq	Phase_I	O95860|Q52M57|Q8N1Z3	Missense_Mutation	SNP	ENST00000373615.4	37	CCDS6853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	24.9|24.9	4.579194|4.579194	0.86645|0.86645	.|.	.|.	ENSG00000106689|ENSG00000106689	ENST00000373615|ENST00000446480	D|.	0.96856|.	-4.15|.	4.98|4.98	4.98|4.98	0.66077|0.66077	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.78717|0.78717	0.4327|0.4327	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.81046|0.81046	-0.1110|-0.1110	10|6	0.87932|.	D|.	0|.	.|.	17.2507|17.2507	0.87041|0.87041	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	304;304|.	B3KNJ5;P50458|.	.;LHX2_HUMAN|.	C|V	304|309	ENSP00000362717:G304C|.	ENSP00000362717:G304C|.	G|G	+|+	1|2	0|0	LHX2|LHX2	125823381|125823381	1.000000|1.000000	0.71417|0.71417	0.942000|0.942000	0.38095|0.38095	0.993000|0.993000	0.82548|0.82548	9.471000|9.471000	0.97696|0.97696	2.291000|2.291000	0.77112|0.77112	0.561000|0.561000	0.74099|0.74099	GGC|GGG		0.632	LHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054010.2			
MAST4	375449	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	66462356	66462356	+	Missense_Mutation	SNP	G	G	A	rs576028127		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr5:66462356G>A	ENST00000403625.2	+	29	7644	c.7349G>A	c.(7348-7350)cGa>cAa	p.R2450Q	MAST4_ENST00000404260.3_Missense_Mutation_p.R2453Q|MAST4_ENST00000405643.1_Missense_Mutation_p.R2271Q|MAST4_ENST00000403666.1_Missense_Mutation_p.R2261Q|MAST4_ENST00000261569.7_Missense_Mutation_p.R2256Q	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2453						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.R2453Q(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		AGTTCTTTCCGATCCACGGCC	0.632											OREG0016638	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											17.0	22.0	20.0					5																	66462356		1984	4166	6150	SO:0001583	missense	375449			AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.7349G>A	5.37:g.66462356G>A	ENSP00000385727:p.Arg2450Gln	Somatic	1092	WXS	Illumina HiSeq	Phase_I	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	37	CCDS54861.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.581313	0.28180	.	.	ENSG00000069020	ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	T;T;T;T;T	0.67171	-0.24;-0.24;-0.25;-0.25;-0.23	4.94	1.98	0.26296	.	0.203577	0.25004	N	0.033884	T	0.63815	0.2543	L	0.29908	0.895	0.09310	N	1	D;D	0.67145	0.993;0.996	P;P	0.56398	0.632;0.797	T	0.56141	-0.8028	10	0.72032	D	0.01	-4.7524	9.3882	0.38356	0.2608:0.0:0.7392:0.0	.	2453;2261	O15021;O15021-3	MAST4_HUMAN;.	Q	2453;2450;2261;2271;2271;2256	ENSP00000385048:R2453Q;ENSP00000385727:R2450Q;ENSP00000384313:R2261Q;ENSP00000384099:R2271Q;ENSP00000261569:R2256Q	ENSP00000261569:R2256Q	R	+	2	0	MAST4	66498112	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	0.113000	0.15499	0.686000	0.31488	0.462000	0.41574	CGA		0.632	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2			
MEI1	150365	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	42180387	42180387	+	Silent	SNP	T	T	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr22:42180387T>C	ENST00000401548.3	+	25	3172	c.3132T>C	c.(3130-3132)gcT>gcC	p.A1044A	MEI1_ENST00000300398.4_Silent_p.A52A|MEI1_ENST00000400107.1_Silent_p.A377A|MEI1_ENST00000476893.1_3'UTR	NM_152513.3	NP_689726.3			meiosis inhibitor 1									p.A1050A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						TATTGAAGGCTCTCAGCTTTC	0.493																																																	1	Substitution - coding silent(1)	kidney(1)											73.0	72.0	72.0					22																	42180387		1889	4109	5998	SO:0001819	synonymous_variant	150365			AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.3132T>C	22.37:g.42180387T>C		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000401548.3	37	CCDS46718.1																																																																																				0.493	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3		NM_152513	
MYOF	26509	broad.mit.edu;hgsc.bcm.edu	37	10	95093560	95093560	+	Silent	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr10:95093560G>A	ENST00000359263.4	-	42	4673	c.4674C>T	c.(4672-4674)taC>taT	p.Y1558Y	MYOF_ENST00000371502.4_Silent_p.Y1577Y|MYOF_ENST00000371501.4_Silent_p.Y1558Y|MYOF_ENST00000358334.5_Silent_p.Y1545Y	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1558	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)	p.Y1558Y(1)		NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						CTCGAACAATGTAAATCCTAA	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											85.0	88.0	87.0					10																	95093560		2007	4192	6199	SO:0001819	synonymous_variant	26509			AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.4674C>T	10.37:g.95093560G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Silent	SNP	ENST00000359263.4	37	CCDS41551.1																																																																																				0.547	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2		NM_013451	
NFE2L2	4780	broad.mit.edu;hgsc.bcm.edu	37	2	178097099	178097099	+	Intron	SNP	A	A	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:178097099A>G	ENST00000397062.3	-	4	1149				NFE2L2_ENST00000464747.1_Intron|NFE2L2_ENST00000423513.1_3'UTR|NFE2L2_ENST00000397063.4_Intron|NFE2L2_ENST00000446151.2_Intron	NM_006164.4	NP_006155.2	Q16236	NF2L2_HUMAN	nuclear factor, erythroid 2-like 2						cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to tumor necrosis factor (GO:0071356)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|positive regulation of blood coagulation (GO:0030194)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of embryonic development (GO:0045995)|regulation of removal of superoxide radicals (GO:2000121)|transcription from RNA polymerase II promoter (GO:0006366)	centrosome (GO:0005813)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(4)|endometrium(14)|kidney(5)|large_intestine(4)|liver(13)|lung(71)|oesophagus(29)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	158			Epithelial(96;0.00442)|OV - Ovarian serous cystadenocarcinoma(117;0.00739)|all cancers(119;0.0195)|LUSC - Lung squamous cell carcinoma(2;0.036)|Lung(16;0.0935)			AATCTCCAGTATTACATTCTA	0.358			Mis		"""NSCLC, HNSCC"""					HNSCC(56;0.16)																														Dom	yes		2	2q31	4780	nuclear factor (erythroid-derived 2)-like 2 (NRF2)		E	0													26.0	25.0	25.0					2																	178097099		1834	4071	5905	SO:0001627	intron_variant	4780				CCDS42782.1, CCDS46457.1, CCDS46458.1	2q31	2013-08-23	2013-08-23		ENSG00000116044	ENSG00000116044		"""basic leucine zipper proteins"""	7782	protein-coding gene	gene with protein product	"""NF-E2-related factor 2"""	600492	"""nuclear factor (erythroid-derived 2)-like 2"""			7937919	Standard	NM_006164		Approved	NRF2	uc002ulh.5	Q16236	OTTHUMG00000133620	ENST00000397062.3:c.594+20T>C	2.37:g.178097099A>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2RBU2|B4E338|E9PGJ7|Q53RW6|Q59HH2|Q96F71	Intron	SNP	ENST00000397062.3	37	CCDS42782.1																																																																																				0.358	NFE2L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257752.4		NM_006164	
NPAS1	4861	broad.mit.edu;ucsc.edu	37	19	47539306	47539306	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:47539306C>A	ENST00000602212.1	+	6	827	c.607C>A	c.(607-609)Ccg>Acg	p.P203T	NPAS1_ENST00000449844.2_Missense_Mutation_p.P203T|NPAS1_ENST00000602189.1_Missense_Mutation_p.P27T|NPAS1_ENST00000439365.2_Missense_Mutation_p.P27T			Q99742	NPAS1_HUMAN	neuronal PAS domain protein 1	203	PAS 1. {ECO:0000255|PROSITE- ProRule:PRU00140}.			P -> T (in Ref. 1; AAB47248). {ECO:0000305}.	central nervous system development (GO:0007417)|maternal behavior (GO:0042711)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.P203T(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(1)	6		all_cancers(25;4.31e-08)|all_epithelial(76;2.96e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.102)		all cancers(93;6.02e-05)|OV - Ovarian serous cystadenocarcinoma(262;7.35e-05)|Epithelial(262;0.00389)|GBM - Glioblastoma multiforme(486;0.0252)		GCTGCGGACGCCGACGCCCGG	0.642											OREG0025586	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											15.0	16.0	16.0					19																	47539306		2200	4297	6497	SO:0001583	missense	4861			U77968	CCDS12694.1	19q13.2-q13.3	2013-05-21				ENSG00000130751		"""Basic helix-loop-helix proteins"""	7894	protein-coding gene	gene with protein product	"""neuronal PAS1"", ""member of PAS superfamily 5"""	603346				9012850, 9079689	Standard	NM_002517		Approved	MOP5, PASD5, bHLHe11	uc002pfy.3	Q99742		ENST00000602212.1:c.607C>A	19.37:g.47539306C>A	ENSP00000469142:p.Pro203Thr	Somatic	947	WXS	Illumina GAIIx	Phase_I	B4DR69|Q99632|Q9BY83	Missense_Mutation	SNP	ENST00000602212.1	37	CCDS12694.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.101161	0.37048	.	.	ENSG00000130751	ENST00000449844;ENST00000439365	T;T	0.22336	1.96;1.96	5.13	1.62	0.23740	PAS (1);	0.861618	0.09650	N	0.773784	T	0.21674	0.0522	M	0.67397	2.05	0.09310	N	1	B;B	0.22146	0.065;0.007	B;B	0.21917	0.037;0.007	T	0.32981	-0.9886	10	0.25106	T	0.35	.	7.0061	0.24838	0.0:0.5535:0.3508:0.0956	.	27;203	B4DR69;Q99742	.;NPAS1_HUMAN	T	203;27	ENSP00000405290:P203T;ENSP00000398689:P27T	ENSP00000398689:P27T	P	+	1	0	NPAS1	52231146	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	0.079000	0.14782	0.138000	0.18790	0.561000	0.74099	CCG		0.642	NPAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466658.1		NM_002517	
NR1H3	10062	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	47289515	47289515	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:47289515A>C	ENST00000467728.1	+	7	2278	c.1040A>C	c.(1039-1041)aAt>aCt	p.N347T	NR1H3_ENST00000527949.1_Missense_Mutation_p.N196T|MADD_ENST00000311027.5_5'Flank|MADD_ENST00000406482.1_5'Flank|MADD_ENST00000395344.3_5'Flank|MADD_ENST00000402799.1_5'Flank|NR1H3_ENST00000405853.3_Missense_Mutation_p.N287T|MADD_ENST00000342922.4_5'Flank|NR1H3_ENST00000405576.1_Missense_Mutation_p.N242T|MADD_ENST00000402192.2_5'Flank|MADD_ENST00000349238.3_5'Flank|RP11-17G12.3_ENST00000545474.1_RNA|NR1H3_ENST00000441012.2_Missense_Mutation_p.N347T|NR1H3_ENST00000407404.1_Missense_Mutation_p.N287T|NR1H3_ENST00000529540.1_3'UTR|NR1H3_ENST00000395397.3_Missense_Mutation_p.N302T|NR1H3_ENST00000481889.2_Missense_Mutation_p.N366T|RP11-17G12.3_ENST00000543925.1_RNA|MADD_ENST00000407859.3_5'Flank|MADD_ENST00000395336.3_5'Flank			Q13133	NR1H3_HUMAN	nuclear receptor subfamily 1, group H, member 3	347	Ligand-binding. {ECO:0000255}.				apoptotic cell clearance (GO:0043277)|cellular lipid metabolic process (GO:0044255)|cellular response to lipopolysaccharide (GO:0071222)|cholesterol homeostasis (GO:0042632)|gene expression (GO:0010467)|lipid homeostasis (GO:0055088)|negative regulation of cholesterol storage (GO:0010887)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of lipid transport (GO:0032369)|negative regulation of macrophage activation (GO:0043031)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of pinocytosis (GO:0048550)|negative regulation of proteolysis (GO:0045861)|negative regulation of secretion of lysosomal enzymes (GO:0090341)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of receptor biosynthetic process (GO:0010870)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|response to progesterone (GO:0032570)|sterol homeostasis (GO:0055092)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid hormone receptor activity (GO:0003707)|sterol response element binding (GO:0032810)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.N347T(1)		endometrium(1)|kidney(2)|large_intestine(6)|lung(6)|ovary(5)	20						AGGGCCATGAATGAGCTGCAA	0.537																																																	1	Substitution - Missense(1)	kidney(1)											135.0	114.0	121.0					11																	47289515		2201	4298	6499	SO:0001583	missense	10062			U22662	CCDS7929.1, CCDS44584.1, CCDS44585.1, CCDS73285.1	11p11.2	2013-01-16			ENSG00000025434	ENSG00000025434		"""Nuclear hormone receptors"""	7966	protein-coding gene	gene with protein product	"""liver X receptor-alpha"""	602423				8621574, 7744246	Standard	NM_005693		Approved	LXR-a, RLD-1	uc009ylm.3	Q13133	OTTHUMG00000150628	ENST00000467728.1:c.1040A>C	11.37:g.47289515A>C	ENSP00000420656:p.Asn347Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3J9|D3DQR1|Q8IW13|Q96H87	Missense_Mutation	SNP	ENST00000467728.1	37	CCDS7929.1	.	.	.	.	.	.	.	.	.	.	A	16.62	3.173791	0.57692	.	.	ENSG00000025434	ENST00000395397;ENST00000405576;ENST00000481889;ENST00000531660;ENST00000407404;ENST00000441012;ENST00000467728;ENST00000405853;ENST00000527949	D;D;D;D;D;D;D;D;D	0.96651	-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08;-4.08	5.32	5.32	0.75619	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.000000	0.85682	D	0.000000	D	0.95749	0.8617	L	0.52126	1.63	0.58432	D	0.999996	B;P;D;P;P	0.55605	0.073;0.757;0.972;0.48;0.762	B;P;P;B;B	0.56563	0.12;0.566;0.801;0.393;0.352	D	0.93685	0.7002	10	0.22706	T	0.39	.	10.009	0.41975	0.9243:0.0:0.0757:0.0	.	353;242;347;366;287	B4DXU5;B5MBY7;Q13133;E9PLL4;Q13133-2	.;.;NR1H3_HUMAN;.;.	T	302;242;366;153;287;347;347;287;196	ENSP00000378793:N302T;ENSP00000385073:N242T;ENSP00000433271:N366T;ENSP00000434650:N153T;ENSP00000385801:N287T;ENSP00000387946:N347T;ENSP00000420656:N347T;ENSP00000384745:N287T;ENSP00000432073:N196T	ENSP00000378793:N302T	N	+	2	0	NR1H3	47246091	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.997000	0.76270	2.139000	0.66308	0.533000	0.62120	AAT		0.537	NR1H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319214.3			
OIT3	170392	hgsc.bcm.edu	37	10	74684103	74684103	+	Nonsense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr10:74684103C>A	ENST00000334011.5	+	7	1286	c.1068C>A	c.(1066-1068)tgC>tgA	p.C356*		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	356	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.					nucleus (GO:0005634)	calcium ion binding (GO:0005509)	p.C356*(1)		autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					CGGTGACCTGCGAGTTTCCAC	0.552																																					Colon(7;19 345 13446 17537)												1	Substitution - Nonsense(1)	kidney(1)											74.0	72.0	73.0					10																	74684103		2203	4300	6503	SO:0001587	stop_gained	170392				CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.1068C>A	10.37:g.74684103C>A	ENSP00000333900:p.Cys356*	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVP3|Q8N1M8	Nonsense_Mutation	SNP	ENST00000334011.5	37	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	C	37	6.220752	0.97390	.	.	ENSG00000138315	ENST00000334011	.	.	.	5.72	1.29	0.21616	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.3497	10.998	0.47589	0.0:0.519:0.0:0.481	.	.	.	.	X	356	.	ENSP00000333900:C356X	C	+	3	2	OIT3	74354109	0.001000	0.12720	1.000000	0.80357	0.994000	0.84299	-1.560000	0.02160	0.221000	0.20879	0.655000	0.94253	TGC		0.552	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1		NM_152635	
OR52N2	390077	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	5841740	5841740	+	Silent	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:5841740C>A	ENST00000317037.2	+	1	197	c.175C>A	c.(175-177)Cgg>Agg	p.R59R	TRIM5_ENST00000380027.1_Intron	NM_001005174.1	NP_001005174.1	Q8NGI0	O52N2_HUMAN	olfactory receptor, family 52, subfamily N, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.H53_F64del(1)|p.R59G(1)|p.R59R(1)		autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|pancreas(1)|skin(3)|stomach(1)|urinary_tract(1)	32		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.49e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCCCTGCACCGGCCCATGTA	0.522																																																	3	Substitution - Missense(1)|Substitution - coding silent(1)|Deletion - In frame(1)	ovary(1)|lung(1)|kidney(1)											138.0	119.0	125.0					11																	5841740		2201	4296	6497	SO:0001819	synonymous_variant	390077			AB065816	CCDS31399.1	11p15.4	2012-08-09			ENSG00000180988	ENSG00000180988		"""GPCR / Class A : Olfactory receptors"""	15228	protein-coding gene	gene with protein product							Standard	NM_001005174		Approved		uc010qzp.2	Q8NGI0	OTTHUMG00000168801	ENST00000317037.2:c.175C>A	11.37:g.5841740C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q6IFF9	Silent	SNP	ENST00000317037.2	37	CCDS31399.1																																																																																				0.522	OR52N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401143.1		NM_001005174	
P2RY11	5032	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	10225224	10225224	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:10225224T>C	ENST00000321826.4	+	2	1119	c.935T>C	c.(934-936)cTg>cCg	p.L312P	PPAN_ENST00000556468.1_Missense_Mutation_p.L732P|PPAN-P2RY11_ENST00000428358.1_3'UTR|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.L732P	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11	312					activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)	p.L312P(1)|p.L732P(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			CTCATGCCCCTGGCCTTCTGT	0.672																																																	2	Substitution - Missense(2)	kidney(2)											45.0	50.0	48.0					19																	10225224		2203	4300	6503	SO:0001583	missense	5032			AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166	ENST00000321826.4:c.935T>C	19.37:g.10225224T>C	ENSP00000323872:p.Leu312Pro	Somatic		WXS	Illumina HiSeq	Phase_I	B2R8X9|O43190|Q9BYU4|Q9H170	Missense_Mutation	SNP	ENST00000321826.4	37	CCDS12226.1	.	.	.	.	.	.	.	.	.	.	t	18.08	3.543504	0.65198	.	.	ENSG00000243207;ENSG00000130810;ENSG00000244165	ENST00000393796;ENST00000556468;ENST00000321826	T;T;T	0.44881	0.91;0.91;0.91	3.9	3.9	0.45041	GPCR, rhodopsin-like superfamily (1);	0.211174	0.31268	U	0.007948	T	0.64800	0.2631	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.74348	0.983	T	0.70410	-0.4879	10	0.87932	D	0	-9.7896	10.7491	0.46198	0.0:0.0:0.0:1.0	.	312	Q96G91	P2Y11_HUMAN	P	732;732;312	ENSP00000377385:L732P;ENSP00000450710:L732P;ENSP00000323872:L312P	ENSP00000323872:L312P	L	+	2	0	PPAN;P2RY11;PPAN-P2RY11	10086224	0.993000	0.37304	0.971000	0.41717	0.805000	0.45488	2.280000	0.43443	1.645000	0.50612	0.454000	0.30748	CTG		0.672	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2		NM_002566	
P2RY13	53829	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	151045862	151045862	+	Missense_Mutation	SNP	G	G	T	rs368054575		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:151045862G>T	ENST00000325602.5	-	2	1001	c.982C>A	c.(982-984)Cta>Ata	p.L328I	MED12L_ENST00000491549.1_Intron|MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron	NM_176894.2	NP_795713.2	Q9BPV8	P2Y13_HUMAN	purinergic receptor P2Y, G-protein coupled, 13	328					negative regulation of adenylate cyclase activity (GO:0007194)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)	p.L307I(1)|p.L328I(1)		biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(72;0.0189)|Lung(72;0.0278)			ATACATGGTAGCTTTTCTGTG	0.363																																																	2	Substitution - Missense(2)	kidney(2)											174.0	161.0	166.0					3																	151045862		2203	4300	6503	SO:0001583	missense	53829			AF295368	CCDS3158.2	3q24	2012-08-08	2004-07-12	2004-07-14	ENSG00000181631	ENSG00000181631		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	4537	protein-coding gene	gene with protein product		606380	"""G protein-coupled receptor 86"""	GPR94, GPR86		11273702, 11574155	Standard	NM_176894		Approved	FKSG77, P2Y13	uc003eyv.2	Q9BPV8	OTTHUMG00000155745	ENST00000325602.5:c.982C>A	3.37:g.151045862G>T	ENSP00000320376:p.Leu328Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B2R827|Q05C50|Q6DKN4|Q8IUT5|Q8TDU7|Q9BY61	Missense_Mutation	SNP	ENST00000325602.5	37	CCDS3158.2	.	.	.	.	.	.	.	.	.	.	G	11.23	1.577121	0.28092	.	.	ENSG00000181631	ENST00000325602	T	0.34275	1.37	5.81	1.96	0.26148	.	0.168906	0.39985	N	0.001210	T	0.17408	0.0418	N	0.08118	0	0.09310	N	1	B	0.31859	0.343	B	0.34138	0.176	T	0.12863	-1.0531	10	0.52906	T	0.07	-1.5033	5.3757	0.16164	0.1286:0.3931:0.3762:0.102	.	328	Q9BPV8	P2Y13_HUMAN	I	328	ENSP00000320376:L328I	ENSP00000320376:L328I	L	-	1	2	P2RY13	152528552	0.295000	0.24389	0.003000	0.11579	0.612000	0.37316	1.028000	0.30128	0.077000	0.16863	0.655000	0.94253	CTA		0.363	P2RY13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341468.1		NM_023914	
PCGF5	84333	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	93011143	93011144	+	Frame_Shift_Del	DEL	TA	TA	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr10:93011143_93011144delTA	ENST00000336126.5	+	6	652_653	c.420_421delTA	c.(418-423)gctatcfs	p.I141fs	PCGF5_ENST00000543648.1_Frame_Shift_Del_p.I141fs	NM_001257101.1|NM_032373.4	NP_001244030.1|NP_115749.2	Q86SE9	PCGF5_HUMAN	polycomb group ring finger 5	141					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)	zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)	12						CACAAATTGCTATCTGTCTAGA	0.337																																					Colon(178;732 2696 46441 50370)												0																																										SO:0001589	frameshift_variant	84333			AL832003	CCDS7413.1	10q23.33	2013-01-09	2005-01-17	2005-01-19	ENSG00000180628	ENSG00000180628		"""RING-type (C3HC4) zinc fingers"", ""Polycomb group ring fingers"""	28264	protein-coding gene	gene with protein product			"""ring finger protein (C3HC4 type) 159"""	RNF159		8076819	Standard	NM_001256549		Approved	MGC16202	uc001khh.4	Q86SE9	OTTHUMG00000018740	ENST00000336126.5:c.420_421delTA	10.37:g.93011143_93011144delTA	ENSP00000337500:p.Ile141fs	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z892|D3DR33|Q6PK47|Q86TD0	Frame_Shift_Del	DEL	ENST00000336126.5	37	CCDS7413.1																																																																																				0.337	PCGF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049363.1		NM_032373	
PDE11A	50940	hgsc.bcm.edu	37	2	178576587	178576587	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:178576587A>T	ENST00000286063.6	-	13	2380	c.2063T>A	c.(2062-2064)aTt>aAt	p.I688N	PDE11A_ENST00000409504.1_Missense_Mutation_p.I330N|PDE11A_ENST00000497003.1_5'UTR|AC012499.1_ENST00000412133.1_RNA|AC012499.1_ENST00000450227.1_RNA|PDE11A_ENST00000449286.2_Missense_Mutation_p.I330N|PDE11A_ENST00000389683.3_Missense_Mutation_p.I244N|PDE11A_ENST00000358450.4_Missense_Mutation_p.I438N	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	688	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	CTCGGTCAGAATGTCTTGAAA	0.498									Primary Pigmented Nodular Adrenocortical Disease, Familial																																								0													96.0	79.0	85.0					2																	178576587		2203	4300	6503	SO:0001583	missense	50940	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.2063T>A	2.37:g.178576587A>T	ENSP00000286063:p.Ile688Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Missense_Mutation	SNP	ENST00000286063.6	37	CCDS33334.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	13.88|13.88	2.368364|2.368364	0.42003|0.42003	.|.	.|.	ENSG00000128655|ENSG00000128655	ENST00000433879|ENST00000286063;ENST00000358450;ENST00000409504;ENST00000389683;ENST00000449286	.|D;D;D;D;D	.|0.81739	.|-1.53;-1.53;-1.53;-1.53;-1.53	5.63|5.63	5.63|5.63	0.86233|0.86233	.|Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	.|0.314095	.|0.38164	.|N	.|0.001781	T|T	0.70351|0.70351	0.3214|0.3214	N|N	0.17594|0.17594	0.5|0.5	0.80722|0.80722	D|D	1|1	.|B;B	.|0.34015	.|0.435;0.418	.|B;B	.|0.34242	.|0.076;0.178	T|T	0.73266|0.73266	-0.4037|-0.4037	5|10	.|0.59425	.|D	.|0.04	.|.	16.1307|16.1307	0.81436|0.81436	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|438;688	.|Q9HCR9-2;Q9HCR9	.|.;PDE11_HUMAN	I|N	296|688;438;330;244;330	.|ENSP00000286063:I688N;ENSP00000351232:I438N;ENSP00000386539:I330N;ENSP00000374333:I244N;ENSP00000390599:I330N	.|ENSP00000286063:I688N	F|I	-|-	1|2	0|0	PDE11A|PDE11A	178284833|178284833	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	4.071000|4.071000	0.57556|0.57556	2.263000|2.263000	0.75096|0.75096	0.533000|0.533000	0.62120|0.62120	TTC|ATT		0.498	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2			
PGK1	5230	broad.mit.edu;hgsc.bcm.edu	37	X	77380396	77380396	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:77380396G>A	ENST00000373316.4	+	9	1129	c.962G>A	c.(961-963)aGc>aAc	p.S321N	PGK1_ENST00000537456.1_Missense_Mutation_p.S293N|PGK1_ENST00000442431.1_Missense_Mutation_p.S185N	NM_000291.3	NP_000282.1	P00558	PGK1_HUMAN	phosphoglycerate kinase 1	321					carbohydrate metabolic process (GO:0005975)|epithelial cell differentiation (GO:0030855)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphoglycerate kinase activity (GO:0004618)	p.S321N(1)		breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	24					Lamivudine(DB00709)	CCTGAAAGCAGCAAGAAGTAT	0.502																																																	1	Substitution - Missense(1)	kidney(1)											124.0	121.0	122.0					X																	77380396		2203	4296	6499	SO:0001583	missense	5230			L00159	CCDS14438.1	Xq13.3	2011-03-17			ENSG00000102144	ENSG00000102144	2.7.2.3		8896	protein-coding gene	gene with protein product		311800				6188151, 6099325	Standard	NM_000291		Approved		uc004ecz.4	P00558	OTTHUMG00000021888	ENST00000373316.4:c.962G>A	X.37:g.77380396G>A	ENSP00000362413:p.Ser321Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4W6|B7Z7A9|Q5J7W1|Q6IBT6|Q8NI87	Missense_Mutation	SNP	ENST00000373316.4	37	CCDS14438.1	.	.	.	.	.	.	.	.	.	.	G	7.592	0.670976	0.14776	.	.	ENSG00000102144	ENST00000373316;ENST00000442431;ENST00000450919;ENST00000537456	D;D;D	0.91945	-2.94;-2.94;-2.94	5.0	4.13	0.48395	Phosphoglycerate kinase, C-terminal (1);	0.319059	0.38164	N	0.001783	T	0.81498	0.4835	N	0.17594	0.5	0.24273	N	0.995231	B	0.02656	0.0	B	0.04013	0.001	T	0.64257	-0.6450	10	0.13470	T	0.59	-25.0944	6.4138	0.21705	0.0937:0.0:0.6195:0.2868	.	321	P00558	PGK1_HUMAN	N	321;185;146;293	ENSP00000362413:S321N;ENSP00000405452:S185N;ENSP00000444708:S293N	ENSP00000362413:S321N	S	+	2	0	PGK1	77267052	0.994000	0.37717	1.000000	0.80357	0.993000	0.82548	1.406000	0.34646	0.990000	0.38787	0.513000	0.50165	AGC		0.502	PGK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057310.1			
PGLYRP3	114771	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	153274993	153274993	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	A	G	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:153274993A>G	ENST00000290722.1	-	5	672	c.620T>C	c.(619-621)aTc>aCc	p.I207T		NM_052891.1	NP_443123.1	Q96LB9	PGRP3_HUMAN	peptidoglycan recognition protein 3	207					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptidoglycan catabolic process (GO:0009253)	extracellular region (GO:0005576)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)	p.I207T(1)		breast(3)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(1)|liver(1)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	28	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCGGTGTGGATGATGATGAC	0.483																																																	1	Substitution - Missense(1)	kidney(1)											301.0	276.0	285.0					1																	153274993		2203	4300	6503	SO:0001583	missense	114771			AY035376	CCDS1035.1	1q21	2008-02-05			ENSG00000159527	ENSG00000159527			30014	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein I alpha precursor"""	608197				11461926	Standard	NM_052891		Approved	PGRPIA, PGLYRPIalpha, PGRP-Ialpha	uc001fbn.1	Q96LB9	OTTHUMG00000014044	ENST00000290722.1:c.620T>C	1.37:g.153274993A>G	ENSP00000290722:p.Ile207Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A1A4U8|Q5SY65	Missense_Mutation	SNP	ENST00000290722.1	37	CCDS1035.1	.	.	.	.	.	.	.	.	.	.	A	11.24	1.580587	0.28180	.	.	ENSG00000159527	ENST00000290722	T	0.13089	2.62	4.49	3.31	0.37934	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.216602	0.32041	N	0.006662	T	0.08447	0.0210	L	0.39566	1.225	0.29036	N	0.885413	P	0.52692	0.955	P	0.54889	0.763	T	0.10613	-1.0622	10	0.33940	T	0.23	-25.4653	6.8729	0.24131	0.8916:0.0:0.1084:0.0	.	207	Q96LB9	PGRP3_HUMAN	T	207	ENSP00000290722:I207T	ENSP00000290722:I207T	I	-	2	0	PGLYRP3	151541617	1.000000	0.71417	1.000000	0.80357	0.466000	0.32739	1.620000	0.36976	1.891000	0.54761	0.533000	0.62120	ATC		0.483	PGLYRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039488.1		NM_052891	
POLR3H	171568	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	41926704	41926704	+	Frame_Shift_Del	DEL	G	G	-	rs372733493		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr22:41926704delG	ENST00000355209.4	-	5	891	c.548delC	c.(547-549)ccgfs	p.P183fs	POLR3H_ENST00000396504.2_Frame_Shift_Del_p.P183fs|POLR3H_ENST00000337566.5_Frame_Shift_Del_p.P154fs|POLR3H_ENST00000407461.1_Frame_Shift_Del_p.P183fs|POLR3H_ENST00000420561.1_5'Flank	NM_001018050.2	NP_001018060.1	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)	183					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|nucleobase-containing compound metabolic process (GO:0006139)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|lung(5)|skin(1)|urinary_tract(1)	8						AAGCGTGTACGGAGCCTCCTT	0.622																																																	0													70.0	63.0	65.0					22																	41926704		2203	4300	6503	SO:0001589	frameshift_variant	171568			AB051452	CCDS14018.1, CCDS33651.1	22q13	2013-01-21			ENSG00000100413	ENSG00000100413		"""RNA polymerase subunits"""	30349	protein-coding gene	gene with protein product						11258795, 12391170	Standard	XR_244356		Approved	RPC8, KIAA1665	uc003baf.3	Q9Y535	OTTHUMG00000150971	ENST00000355209.4:c.548delC	22.37:g.41926704delG	ENSP00000347345:p.Pro183fs	Somatic		WXS	Illumina HiSeq	Phase_I	B0QYH9|Q5M7Y8|Q96AE3|Q9BY95	Frame_Shift_Del	DEL	ENST00000355209.4	37	CCDS14018.1																																																																																				0.622	POLR3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320701.1		NM_138338	
PPFIA1	8500	broad.mit.edu;ucsc.edu	37	11	70184559	70184559	+	Splice_Site	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:70184559G>A	ENST00000253925.7	+	13	1786	c.1571G>A	c.(1570-1572)gGc>gAc	p.G524D	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Splice_Site_p.G524D	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	524					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)	p.G524D(1)		breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CTTCATCATGGGTATGGTATT	0.478																																																	1	Substitution - Missense(1)	kidney(1)											103.0	97.0	99.0					11																	70184559		2200	4294	6494	SO:0001630	splice_region_variant	8500			U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.1571+1G>A	11.37:g.70184559G>A		Somatic		WXS	Illumina GAIIx	Phase_I	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	16.36|16.36	3.100327|3.100327	0.56183|0.56183	.|.	.|.	ENSG00000131626|ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950|ENST00000530798	T;T|.	0.36340|.	1.26;1.26|.	4.45|4.45	4.45|4.45	0.53987|0.53987	.|.	0.309756|.	0.32068|.	U|.	0.006635|.	T|.	0.58235|.	0.2108|.	L|L	0.36672|0.36672	1.1|1.1	0.53688|0.53688	D|D	0.999971|0.999971	B;B|.	0.20164|.	0.042;0.003|.	B;B|.	0.22601|.	0.04;0.002|.	T|.	0.55256|.	-0.8169|.	10|.	0.42905|.	T|.	0.14|.	.|.	16.0826|16.0826	0.81014|0.81014	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	524;524|.	Q13136;Q13136-2|.	LIPA1_HUMAN;.|.	D|X	524;524;11|75	ENSP00000253925:G524D;ENSP00000374198:G524D|.	ENSP00000253925:G524D|.	G|W	+|+	2|3	0|0	PPFIA1|PPFIA1	69862207|69862207	1.000000|1.000000	0.71417|0.71417	0.715000|0.715000	0.30552|0.30552	0.893000|0.893000	0.52053|0.52053	7.818000|7.818000	0.86416|0.86416	2.217000|2.217000	0.71921|0.71921	0.655000|0.655000	0.94253|0.94253	GGC|TGG		0.478	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1		NM_003626	Missense_Mutation
PRMT7	54496	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	68386205	68386205	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr16:68386205delA	ENST00000339507.5	+	15	2298	c.1468delA	c.(1468-1470)aacfs	p.N490fs	PRMT7_ENST00000441236.1_Frame_Shift_Del_p.N440fs|PRMT7_ENST00000449359.3_Frame_Shift_Del_p.N440fs|PRMT7_ENST00000348497.4_Frame_Shift_Del_p.N342fs			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	490	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		GCCGTGGCACAACCTCTACTT	0.647																																																	0													100.0	82.0	88.0					16																	68386205		2198	4300	6498	SO:0001589	frameshift_variant	54496			AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1468delA	16.37:g.68386205delA	ENSP00000343103:p.Asn490fs	Somatic		WXS	Illumina HiSeq	Phase_I	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Frame_Shift_Del	DEL	ENST00000339507.5	37	CCDS10866.1																																																																																				0.647	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3		NM_019023	
PTGDS	5730	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	139873535	139873535	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr9:139873535G>A	ENST00000371625.3	+	2	279	c.205G>A	c.(205-207)Gtg>Atg	p.V69M	PTGDS_ENST00000224167.2_Missense_Mutation_p.V69M|RP11-229P13.19_ENST00000413913.2_RNA|PTGDS_ENST00000460340.1_3'UTR	NM_000954.5	NP_000945.3	P41222	PTGDS_HUMAN	prostaglandin D2 synthase 21kDa (brain)	69					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|prostaglandin biosynthetic process (GO:0001516)|regulation of circadian sleep/wake cycle, sleep (GO:0045187)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|rough endoplasmic reticulum (GO:0005791)	fatty acid binding (GO:0005504)|prostaglandin-D synthase activity (GO:0004667)|retinoid binding (GO:0005501)|transporter activity (GO:0005215)	p.V69M(1)		endometrium(2)|kidney(1)|lung(3)|ovary(1)	7	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CAAGTCTGTGGTGGCCCCTGC	0.672																																																	1	Substitution - Missense(1)	kidney(1)											69.0	69.0	69.0					9																	139873535		2203	4299	6502	SO:0001583	missense	5730			AA621632	CCDS7019.1	9q34.2-q34.3	2011-11-15	2002-08-29		ENSG00000107317	ENSG00000107317	5.3.99.2	"""Lipocalins"""	9592	protein-coding gene	gene with protein product	"""lipocalin-type prostaglandin D synthase"""	176803	"""prostaglandin D2 synthase (21kD, brain)"""			1902577	Standard	NM_000954		Approved	PGDS, L-PGDS	uc004cke.3	P41222	OTTHUMG00000020957	ENST00000371625.3:c.205G>A	9.37:g.139873535G>A	ENSP00000360687:p.Val69Met	Somatic		WXS	Illumina HiSeq	Phase_I	B2R727|Q5SQ10|Q7M4P3|Q9UC22|Q9UCC9|Q9UCD9	Missense_Mutation	SNP	ENST00000371625.3	37	CCDS7019.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	22.1|22.1	4.246538|4.246538	0.80024|0.80024	.|.	.|.	ENSG00000107317|ENSG00000107317	ENST00000446677|ENST00000224167;ENST00000457950;ENST00000371625;ENST00000371623	.|T;T;T;T	.|0.09073	.|3.02;3.02;3.02;3.02	4.28|4.28	1.18|1.18	0.20946|0.20946	.|Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	.|0.280362	.|0.24779	.|N	.|0.035664	T|T	0.18676|0.18676	0.0448|0.0448	M|M	0.70903|0.70903	2.155|2.155	0.09310|0.09310	N|N	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.79784	.|0.993	T|T	0.05162|0.05162	-1.0902|-1.0902	5|10	.|0.42905	.|T	.|0.14	-11.7164|-11.7164	2.3977|2.3977	0.04394|0.04394	0.2006:0.1563:0.5008:0.1422|0.2006:0.1563:0.5008:0.1422	.|.	.|69	.|P41222	.|PTGDS_HUMAN	D|M	91|69	.|ENSP00000224167:V69M;ENSP00000392633:V69M;ENSP00000360687:V69M;ENSP00000360685:V69M	.|ENSP00000224167:V69M	G|V	+|+	2|1	0|0	PTGDS|PTGDS	138993356|138993356	0.001000|0.001000	0.12720|0.12720	0.075000|0.075000	0.20258|0.20258	0.771000|0.771000	0.43674|0.43674	-0.003000|-0.003000	0.12901|0.12901	0.783000|0.783000	0.33636|0.33636	0.436000|0.436000	0.28706|0.28706	GGT|GTG		0.672	PTGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055188.1		NM_000954	
PTK2	5747	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	141727751	141727751	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr8:141727751T>A	ENST00000522684.1	-	23	2317	c.2088A>T	c.(2086-2088)agA>agT	p.R696S	PTK2_ENST00000430260.2_Missense_Mutation_p.R6S|PTK2_ENST00000517887.1_Missense_Mutation_p.R740S|PTK2_ENST00000519465.1_Missense_Mutation_p.R324S|PTK2_ENST00000538769.1_Missense_Mutation_p.R364S|PTK2_ENST00000519419.1_Missense_Mutation_p.R740S|PTK2_ENST00000340930.3_Missense_Mutation_p.R696S|PTK2_ENST00000535192.1_Missense_Mutation_p.R696S|PTK2_ENST00000395218.2_Missense_Mutation_p.R696S|PTK2_ENST00000521059.1_Missense_Mutation_p.R696S	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	696					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)	p.R718S(1)|p.R696S(1)|p.R648S(1)		breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TGGCCTGTCTTCTGGACTCCA	0.537																																																	3	Substitution - Missense(3)	kidney(3)											169.0	141.0	151.0					8																	141727751		2203	4300	6503	SO:0001583	missense	5747			L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2088A>T	8.37:g.141727751T>A	ENSP00000429911:p.Arg696Ser	Somatic		WXS	Illumina HiSeq	Phase_I	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	26.8|26.8	4.776662|4.776662	0.90195|0.90195	.|.	.|.	ENSG00000169398|ENSG00000169398	ENST00000519654|ENST00000522684;ENST00000535192;ENST00000519465;ENST00000517887;ENST00000521059;ENST00000395214;ENST00000395218;ENST00000354438;ENST00000395221;ENST00000523539;ENST00000340930;ENST00000538769;ENST00000519419;ENST00000430260;ENST00000521986;ENST00000522424;ENST00000521562;ENST00000523388	.|T;T;T;T;T;T;T;T;T;T;T;T	.|0.76839	.|-1.04;-1.05;-1.01;-1.05;-1.04;-1.05;-1.01;-1.05;-1.01;-1.05;0.26;-1.02	5.62|5.62	2.03|2.03	0.26663|0.26663	.|Protein kinase-like domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	.|D	.|0.83138	.|0.5189	M|M	0.75777|0.75777	2.31|2.31	0.52099|0.52099	D|D	0.99994|0.99994	.|P;B;P;D;D;D;P;P;D;D	.|0.67145	.|0.594;0.444;0.952;0.994;0.996;0.993;0.952;0.846;0.991;0.991	.|B;B;P;D;D;P;P;P;P;P	.|0.74348	.|0.164;0.206;0.703;0.983;0.94;0.777;0.703;0.687;0.885;0.885	.|T	.|0.79438	.|-0.1803	.|10	.|0.51188	.|T	.|0.08	.|.	4.2646|4.2646	0.10757|0.10757	0.0:0.368:0.1854:0.4466|0.0:0.368:0.1854:0.4466	.|.	.|696;391;616;696;718;696;648;544;364;324	.|B4E2N6;B4DH13;Q59GN8;Q05397;Q658W2;Q8IYN9;Q59GM6;Q05397-2;Q8N9D7;E9PEI4	.|.;.;.;FAK1_HUMAN;.;.;.;.;.;.	X|S	707|696;696;324;740;696;648;696;617;391;368;696;364;740;6;394;6;6;6	.|ENSP00000429911:R696S;ENSP00000438009:R696S;ENSP00000429170:R324S;ENSP00000429082:R740S;ENSP00000429474:R696S;ENSP00000378644:R696S;ENSP00000428492:R368S;ENSP00000341189:R696S;ENSP00000445742:R364S;ENSP00000429129:R740S;ENSP00000403416:R6S;ENSP00000430603:R394S	.|ENSP00000341189:R696S	K|R	-|-	1|3	0|2	PTK2|PTK2	141796933|141796933	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.183000|2.183000	0.42565|0.42565	0.423000|0.423000	0.26033|0.26033	0.528000|0.528000	0.53228|0.53228	AAG|AGA		0.537	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5		NM_005607	
RAB3D	9545	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	11436252	11436252	+	Missense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:11436252A>T	ENST00000222120.3	-	5	742	c.482T>A	c.(481-483)tTc>tAc	p.F161Y	TSPAN16_ENST00000316737.1_Intron|CTC-510F12.6_ENST00000586051.1_RNA|RAB3D_ENST00000589655.1_Missense_Mutation_p.F161Y|CTC-510F12.4_ENST00000586356.1_RNA	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	161					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)	p.F161Y(1)		cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						GGCTTCAAAGAACTCGAAACC	0.527																																																	1	Substitution - Missense(1)	kidney(1)											135.0	125.0	128.0					19																	11436252		2203	4300	6503	SO:0001583	missense	9545			AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"""RAB, member RAS oncogene"""	9779	protein-coding gene	gene with protein product	"""Rab3D upregulated with myeloid differentiation"", ""glioblastoma overexpressed"""	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.482T>A	19.37:g.11436252A>T	ENSP00000222120:p.Phe161Tyr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000222120.3	37	CCDS12257.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.959934	0.53400	.	.	ENSG00000105514	ENST00000222120	T	0.77620	-1.11	4.76	4.76	0.60689	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.68256	0.2981	L	0.31120	0.905	0.80722	D	1	B	0.16166	0.016	B	0.20577	0.03	T	0.66952	-0.5793	10	0.59425	D	0.04	.	13.3691	0.60703	1.0:0.0:0.0:0.0	.	161	O95716	RAB3D_HUMAN	Y	161	ENSP00000222120:F161Y	ENSP00000222120:F161Y	F	-	2	0	RAB3D	11297252	1.000000	0.71417	1.000000	0.80357	0.687000	0.40016	4.870000	0.63035	2.004000	0.58718	0.454000	0.30748	TTC		0.527	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1		NM_004283	
RCOR2	283248	broad.mit.edu;hgsc.bcm.edu	37	11	63679957	63679957	+	Silent	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:63679957C>T	ENST00000301459.4	-	11	1464	c.1077G>A	c.(1075-1077)ggG>ggA	p.G359G	RCOR2_ENST00000473926.2_5'Flank	NM_173587.3	NP_775858.2	Q8IZ40	RCOR2_HUMAN	REST corepressor 2	359	SANT 2. {ECO:0000255|PROSITE- ProRule:PRU00624}.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.G359G(1)		kidney(2)|large_intestine(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	17						GAGTCTTGTTCCCAATCACCT	0.542																																																	1	Substitution - coding silent(1)	kidney(1)											73.0	86.0	81.0					11																	63679957		2200	4297	6497	SO:0001819	synonymous_variant	283248			BC010608	CCDS8052.1	11q13.1	2008-02-05			ENSG00000167771	ENSG00000167771			27455	protein-coding gene	gene with protein product						12477932	Standard	NM_173587		Approved		uc001nyc.3	Q8IZ40	OTTHUMG00000150472	ENST00000301459.4:c.1077G>A	11.37:g.63679957C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q96FP3	Silent	SNP	ENST00000301459.4	37	CCDS8052.1																																																																																				0.542	RCOR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318233.1		NM_173587	
RGS19	10287	hgsc.bcm.edu	37	20	62707927	62707928	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr20:62707927_62707928insG	ENST00000395042.1	-	3	368_369	c.102_103insC	c.(100-105)cccagcfs	p.S35fs	RGS19_ENST00000493165.1_5'UTR|RGS19_ENST00000332298.5_Frame_Shift_Ins_p.S35fs	NM_005873.2	NP_005864.1	P49795	RGS19_HUMAN	regulator of G-protein signaling 19	35					autophagy (GO:0006914)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	brush border (GO:0005903)|clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			lung(1)|prostate(1)|skin(1)	3	all_cancers(38;3.45e-11)|all_epithelial(29;9.12e-13)|Lung NSC(23;2e-09)|all_lung(23;6.77e-09)					GGGTTGCGGCTGGGGGCCGCTG	0.663																																																	0									,	24,4238		0,24,2107					,	-0.5	1.0			62	27,8215		0,27,4094	no	frameshift,frameshift	RGS19	NM_005873.2,NM_001039467.1	,	0,51,6201	A1A1,A1R,RR		0.3276,0.5631,0.4079	,	,		51,12453				SO:0001589	frameshift_variant	10287			X91809	CCDS13555.1	20q13.33	2007-08-14	2007-08-14		ENSG00000171700	ENSG00000171700		"""Regulators of G-protein signaling"""	13735	protein-coding gene	gene with protein product		605071	"""regulator of G-protein signalling 19"""			8524874	Standard	XM_005260183		Approved	GAIP, RGSGAIP	uc002yib.3	P49795	OTTHUMG00000033024	ENST00000395042.1:c.103dupC	20.37:g.62707932_62707932dupG	ENSP00000378483:p.Ser35fs	Somatic		WXS	Illumina HiSeq	Phase_I	A8K216|E1P5G9|Q53XN0|Q8TD60	Frame_Shift_Ins	INS	ENST00000395042.1	37	CCDS13555.1																																																																																				0.663	RGS19-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080273.1		NM_005873	
RSPO4	343637	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	948634	948634	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr20:948634C>G	ENST00000217260.4	-	2	323	c.227G>C	c.(226-228)gGg>gCg	p.G76A	RSPO4_ENST00000400634.2_Missense_Mutation_p.G76A	NM_001029871.3	NP_001025042.2	Q2I0M5	RSPO4_HUMAN	R-spondin 4	76					Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)	heparin binding (GO:0008201)	p.G76A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7						GCCGAAGTACCCAGGGGGACA	0.602																																																	1	Substitution - Missense(1)	kidney(1)											84.0	87.0	86.0					20																	948634		2023	4166	6189	SO:0001583	missense	343637			AK122609	CCDS42845.1, CCDS42846.1	20p13	2014-01-30	2011-06-29	2005-08-08	ENSG00000101282	ENSG00000101282		"""Endogenous ligands"""	16175	protein-coding gene	gene with protein product		610573	"""chromosome 20 open reading frame 182"", ""R-spondin family, member 4"""	C20orf182		15469841	Standard	NM_001029871		Approved	dJ824F16.3	uc002wej.3	Q2I0M5	OTTHUMG00000031651	ENST00000217260.4:c.227G>C	20.37:g.948634C>G	ENSP00000217260:p.Gly76Ala	Somatic		WXS	Illumina HiSeq	Phase_I	A2A2I6|Q9UGB2	Missense_Mutation	SNP	ENST00000217260.4	37	CCDS42846.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.834762	0.91036	.	.	ENSG00000101282	ENST00000217260;ENST00000400634	D;D	0.91577	-2.87;-2.87	5.28	5.28	0.74379	Growth factor, receptor (1);	0.177470	0.36409	N	0.002604	D	0.96225	0.8769	M	0.90595	3.13	0.53688	D	0.999971	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.96883	0.9647	10	0.72032	D	0.01	-3.1168	17.4895	0.87699	0.0:1.0:0.0:0.0	.	76;76	Q2I0M5-2;Q2I0M5	.;RSPO4_HUMAN	A	76	ENSP00000217260:G76A;ENSP00000383475:G76A	ENSP00000217260:G76A	G	-	2	0	RSPO4	896634	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	7.238000	0.78173	2.473000	0.83533	0.563000	0.77884	GGG		0.602	RSPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077492.3		XM_297816	
SEC16A	9919	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	139369264	139369264	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr9:139369264T>C	ENST00000371706.3	-	1	2303	c.2270A>G	c.(2269-2271)gAg>gGg	p.E757G	SEC16A_ENST00000431893.2_Missense_Mutation_p.E757G|SEC16A_ENST00000290037.6_Missense_Mutation_p.E757G|SEC16A_ENST00000313050.7_Missense_Mutation_p.E935G			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	757					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.E935G(2)		breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		AACCAAGTTCTCTGGAACTGG	0.473																																																	2	Substitution - Missense(2)	kidney(2)											99.0	97.0	98.0					9																	139369264		1885	4129	6014	SO:0001583	missense	9919			AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.2270A>G	9.37:g.139369264T>C	ENSP00000360771:p.Glu757Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000371706.3	37		.	.	.	.	.	.	.	.	.	.	T	8.556	0.876585	0.17395	.	.	ENSG00000148396	ENST00000313050;ENST00000371706;ENST00000290037;ENST00000431893	T;T;T;T	0.24350	1.86;1.87;1.87;1.87	4.88	-1.92	0.07618	.	1.636150	0.03170	N	0.170525	T	0.15522	0.0374	L	0.29908	0.895	0.09310	N	0.999999	B;B;B	0.09022	0.001;0.002;0.002	B;B;B	0.11329	0.002;0.006;0.006	T	0.12863	-1.0531	10	0.23302	T	0.38	-1.4176	0.6289	0.00791	0.2987:0.2887:0.1224:0.2902	.	935;757;757	F1T0I1;O15027-5;O15027-4	.;.;.	G	935;757;757;757	ENSP00000325827:E935G;ENSP00000360771:E757G;ENSP00000290037:E757G;ENSP00000387583:E757G	ENSP00000290037:E757G	E	-	2	0	SEC16A	138489085	0.011000	0.17503	0.000000	0.03702	0.385000	0.30292	0.273000	0.18662	-0.408000	0.07565	-0.256000	0.11100	GAG		0.473	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1		XM_088459	
SIM1	6492	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	100841464	100841464	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr6:100841464C>A	ENST00000369208.3	-	11	2251	c.1469G>T	c.(1468-1470)tGg>tTg	p.W490L	SIM1_ENST00000262901.4_Missense_Mutation_p.W490L			P81133	SIM1_HUMAN	single-minded family bHLH transcription factor 1	490	Single-minded C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00632}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)	p.W490L(1)		breast(1)|central_nervous_system(4)|endometrium(5)|kidney(1)|large_intestine(15)|lung(34)|ovary(4)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(5)	79		all_cancers(76;9.88e-06)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(107;0.0248)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0774)		GCGAGAGCCCCACCAGGGCTC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											65.0	69.0	68.0					6																	100841464		2203	4300	6503	SO:0001583	missense	6492			U70212	CCDS5045.1	6q16.3	2013-10-17	2013-10-17		ENSG00000112246	ENSG00000112246		"""Basic helix-loop-helix proteins"""	10882	protein-coding gene	gene with protein product		603128	"""single-minded (Drosophila) homolog 1"", ""single-minded homolog 1 (Drosophila)"""			9199934, 11448938	Standard	NM_005068		Approved	bHLHe14	uc003pqj.4	P81133	OTTHUMG00000015275	ENST00000369208.3:c.1469G>T	6.37:g.100841464C>A	ENSP00000358210:p.Trp490Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TDP7	Missense_Mutation	SNP	ENST00000369208.3	37	CCDS5045.1	.	.	.	.	.	.	.	.	.	.	C	32	5.186202	0.94885	.	.	ENSG00000112246	ENST00000369208;ENST00000262901	T;T	0.64085	-0.08;-0.08	5.78	5.78	0.91487	Single-minded, C-terminal (2);	0.105625	0.64402	D	0.000002	T	0.65196	0.2668	L	0.34521	1.04	0.80722	D	1	D	0.71674	0.998	D	0.66196	0.942	T	0.64063	-0.6495	10	0.45353	T	0.12	.	20.0086	0.97443	0.0:1.0:0.0:0.0	.	490	P81133	SIM1_HUMAN	L	490	ENSP00000358210:W490L;ENSP00000262901:W490L	ENSP00000262901:W490L	W	-	2	0	SIM1	100948185	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.487000	0.81328	2.731000	0.93534	0.655000	0.94253	TGG		0.607	SIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041628.3		NM_005068	
SLC13A4	26266	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	135370277	135370277	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr7:135370277C>T	ENST00000354042.4	-	14	2287	c.1598G>A	c.(1597-1599)tGc>tAc	p.C533Y	SLC13A4_ENST00000491630.1_5'UTR|C7orf73_ENST00000422968.1_Intron	NM_012450.2	NP_036582.2	Q9UKG4	S13A4_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 4	533					sodium ion transmembrane transport (GO:0035725)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)	p.C533Y(1)		breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	24						CACCAGGCTGCACAGGATGGG	0.612																																																	1	Substitution - Missense(1)	kidney(1)											123.0	107.0	112.0					7																	135370277		2203	4300	6503	SO:0001583	missense	26266			AF169301	CCDS5840.1	7q33	2013-07-18	2013-07-18		ENSG00000164707	ENSG00000164707		"""Solute carriers"""	15827	protein-coding gene	gene with protein product	"""sulphate transporter 1"""	604309	"""solute carrier family 13 (sodium/sulphate symporters), member 4"""			10535998	Standard	NM_012450		Approved	SUT-1, SUT1	uc003vta.3	Q9UKG4	OTTHUMG00000155539	ENST00000354042.4:c.1598G>A	7.37:g.135370277C>T	ENSP00000297282:p.Cys533Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1Q4|Q8N631	Missense_Mutation	SNP	ENST00000354042.4	37	CCDS5840.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.071970	0.76301	.	.	ENSG00000164707	ENST00000354042	T	0.02737	4.18	6.03	6.03	0.97812	.	0.047245	0.85682	D	0.000000	T	0.12092	0.0294	L	0.45581	1.43	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.76071	0.987;0.975	T	0.00081	-1.2106	10	0.87932	D	0	.	18.0507	0.89347	0.0:1.0:0.0:0.0	.	402;533	Q59HF0;Q9UKG4	.;S13A4_HUMAN	Y	533	ENSP00000297282:C533Y	ENSP00000297282:C533Y	C	-	2	0	SLC13A4	135020817	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.070000	0.64376	2.861000	0.98227	0.655000	0.94253	TGC		0.612	SLC13A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340558.1		NM_012450	
SLC33A1	9197	broad.mit.edu;hgsc.bcm.edu	37	3	155546088	155546088	+	Nonsense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:155546088C>A	ENST00000392845.3	-	6	1941	c.1561G>T	c.(1561-1563)Gga>Tga	p.G521*	SLC33A1_ENST00000359479.3_Nonsense_Mutation_p.G521*			O00400	ACATN_HUMAN	solute carrier family 33 (acetyl-CoA transporter), member 1	521					acetyl-CoA transport (GO:0015876)|cell death (GO:0008219)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	acetyl-CoA transporter activity (GO:0008521)	p.G521*(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	22			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CAACCAAATCCAATGAAAACA	0.338																																																	1	Substitution - Nonsense(1)	kidney(1)											80.0	80.0	80.0					3																	155546088		2203	4297	6500	SO:0001587	stop_gained	9197			D88152	CCDS3173.1	3q25.31	2013-05-22		2002-12-06	ENSG00000169359	ENSG00000169359		"""Solute carriers"""	95	protein-coding gene	gene with protein product		603690	"""acetyl-Coenzyme A transporter"", ""spastic paraplegia 42 (autosomal dominant)"""	ACATN, SPG42		9096318, 19061983	Standard	NM_004733		Approved	AT-1, AT1	uc003fao.2	O00400	OTTHUMG00000158481	ENST00000392845.3:c.1561G>T	3.37:g.155546088C>A	ENSP00000376587:p.Gly521*	Somatic		WXS	Illumina HiSeq	Phase_I	B2R5Q2|D3DNK4	Nonsense_Mutation	SNP	ENST00000392845.3	37	CCDS3173.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	40|40	8.164472|8.164472	0.98686|0.98686	.|.	.|.	ENSG00000169359|ENSG00000169359	ENST00000392845;ENST00000359479;ENST00000496772|ENST00000475842	.|.	.|.	.|.	5.78|5.78	4.89|4.89	0.63831|0.63831	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	.|T	.|0.66297	.|0.2775	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.69273	.|-0.5188	.|3	0.87932|.	D|.	0|.	-13.5195|-13.5195	15.2806|15.2806	0.73781|0.73781	0.0:0.9316:0.0:0.0684|0.0:0.9316:0.0:0.0684	.|.	.|.	.|.	.|.	X|L	521;521;157|240	.|.	ENSP00000352456:G521X|.	G|W	-|-	1|2	0|0	SLC33A1|SLC33A1	157028782|157028782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	5.971000|5.971000	0.70440|0.70440	2.741000|2.741000	0.93983|0.93983	0.650000|0.650000	0.86243|0.86243	GGA|TGG		0.338	SLC33A1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351130.3		NM_004733	
SLC7A8	23428	broad.mit.edu;hgsc.bcm.edu	37	14	23597394	23597394	+	Silent	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr14:23597394C>G	ENST00000316902.7	-	10	2000	c.1275G>C	c.(1273-1275)ctG>ctC	p.L425L	SLC7A8_ENST00000529705.2_Silent_p.L320L|SLC7A8_ENST00000469263.1_Intron|SLC7A8_ENST00000453702.1_Silent_p.L222L|SLC7A8_ENST00000422941.2_Silent_p.L201L	NM_012244.3	NP_036376.2	Q9UHI5	LAT2_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 8	425					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|metal ion homeostasis (GO:0055065)|neutral amino acid transport (GO:0015804)|organic cation transport (GO:0015695)|response to toxic substance (GO:0009636)|toxin transport (GO:1901998)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|organic cation transmembrane transporter activity (GO:0015101)|peptide antigen binding (GO:0042605)|toxin transporter activity (GO:0019534)	p.L425L(1)		autonomic_ganglia(1)|endometrium(6)|kidney(4)|large_intestine(6)|lung(5)|ovary(1)|skin(1)	24	all_cancers(95;4.6e-05)			GBM - Glioblastoma multiforme(265;0.00809)	L-Alanine(DB00160)|L-DOPA(DB01235)|L-Glutamine(DB00130)|L-Phenylalanine(DB00120)	TGATGGGGAACAGCAGGTTGA	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											160.0	138.0	145.0					14																	23597394		2203	4300	6503	SO:0001819	synonymous_variant	23428			Y18483	CCDS9590.1, CCDS41924.1, CCDS58304.1, CCDS58305.1	14q11.2	2013-05-22	2011-07-12		ENSG00000092068	ENSG00000092068		"""Solute carriers"""	11066	protein-coding gene	gene with protein product		604235				10080183, 10391915	Standard	NM_001267036		Approved	LPI-PC1, LAT2	uc001wiz.4	Q9UHI5	OTTHUMG00000028720	ENST00000316902.7:c.1275G>C	14.37:g.23597394C>G		Somatic		WXS	Illumina HiSeq	Phase_I	B2R8Q4|B4DKT4|B4DTV6|D3DS46|F2Z2J4|Q86U05|Q9UKQ6|Q9UKQ7|Q9UKQ8|Q9Y445	Silent	SNP	ENST00000316902.7	37	CCDS9590.1																																																																																				0.582	SLC7A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071718.3			
SLC9A4	389015	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	103095413	103095413	+	Silent	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:103095413C>A	ENST00000295269.4	+	2	829	c.372C>A	c.(370-372)gtC>gtA	p.V124V		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	124					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)	p.V124V(1)		NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CGCCTCCGGTCATGGACTCCA	0.612																																																	1	Substitution - coding silent(1)	kidney(1)											71.0	66.0	68.0					2																	103095413		2203	4300	6503	SO:0001819	synonymous_variant	389015				CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.372C>A	2.37:g.103095413C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																				0.612	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1		NM_001011552.3	
CAPN15	6650	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	596909	596909	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr16:596909C>A	ENST00000219611.2	+	4	434	c.71C>A	c.(70-72)tCc>tAc	p.S24Y	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	24					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.S24Y(1)									CGCCAGTGCTCCATCTGCGAG	0.682																																																	1	Substitution - Missense(1)	kidney(1)											26.0	24.0	24.0					16																	596909		2187	4290	6477	SO:0001583	missense	6650			U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.71C>A	16.37:g.596909C>A	ENSP00000219611:p.Ser24Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	29.1	4.980588	0.92982	.	.	ENSG00000103326	ENST00000219611;ENST00000397687	T	0.55588	0.51	5.1	5.1	0.69264	Zinc finger, RanBP2-type (4);	0.506262	0.20012	N	0.101112	T	0.70107	0.3186	L	0.59436	1.845	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.72214	-0.4358	10	0.66056	D	0.02	.	17.0758	0.86586	0.0:1.0:0.0:0.0	.	24	O75808	CAN15_HUMAN	Y	24	ENSP00000219611:S24Y	ENSP00000219611:S24Y	S	+	2	0	SOLH	536910	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.661000	0.83786	2.359000	0.80004	0.556000	0.70494	TCC		0.682	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1		NM_005632	
SORL1	6653	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	121437700	121437700	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:121437700C>A	ENST00000260197.7	+	22	3230	c.3101C>A	c.(3100-3102)gCc>gAc	p.A1034D	SORL1_ENST00000525532.1_5'UTR	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	1034	EGF-like.				cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)	p.A1034D(1)		NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CTGCCCAAGGCCAACAACAGT	0.567																																																	1	Substitution - Missense(1)	kidney(1)											121.0	93.0	102.0					11																	121437700		2203	4299	6502	SO:0001583	missense	6653			Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.3101C>A	11.37:g.121437700C>A	ENSP00000260197:p.Ala1034Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	C	15.14	2.745872	0.49151	.	.	ENSG00000137642	ENST00000260197	D	0.91577	-2.87	4.38	3.47	0.39725	Epidermal growth factor-like (1);	0.343623	0.29822	N	0.011111	D	0.85915	0.5808	L	0.57536	1.79	0.80722	D	1	P	0.40144	0.704	B	0.32762	0.152	D	0.84713	0.0735	10	0.66056	D	0.02	.	9.917	0.41442	0.0:0.8329:0.0:0.1671	.	1034	Q92673	SORL_HUMAN	D	1034	ENSP00000260197:A1034D	ENSP00000260197:A1034D	A	+	2	0	SORL1	120942910	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.310000	0.65780	0.960000	0.38005	-0.373000	0.07131	GCC		0.567	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2		NM_003105	
SPIRE2	84501	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	89929985	89929985	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr16:89929985C>A	ENST00000378247.3	+	11	1720	c.1677C>A	c.(1675-1677)aaC>aaA	p.N559K	SPIRE2_ENST00000393062.2_Missense_Mutation_p.N559K	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	559					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.N559K(1)		central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TTTTGCAGAACAAGGAGCTCT	0.617																																																	1	Substitution - Missense(1)	kidney(1)											81.0	70.0	74.0					16																	89929985		2197	4300	6497	SO:0001583	missense	84501			AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"""spire homolog 2 (Drosophila)"", ""spire family actin nucleation factor 2"""			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.1677C>A	16.37:g.89929985C>A	ENSP00000367494:p.Asn559Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	37	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.323569	0.41096	.	.	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.75704	-0.96;0.98	5.5	0.781	0.18561	Zinc finger, FYVE/PHD-type (1);	0.402149	0.31772	N	0.007093	T	0.59211	0.2177	L	0.38838	1.175	0.80722	D	1	P;B;P;B	0.38504	0.493;0.132;0.634;0.013	B;B;B;B	0.36845	0.116;0.209;0.234;0.007	T	0.50508	-0.8820	10	0.17832	T	0.49	-32.2363	10.9923	0.47557	0.0:0.6936:0.0:0.3064	.	426;559;511;559	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	K	559	ENSP00000367494:N559K;ENSP00000376782:N559K	ENSP00000367494:N559K	N	+	3	2	SPIRE2	88457486	1.000000	0.71417	0.942000	0.38095	0.986000	0.74619	1.875000	0.39578	0.294000	0.22547	0.313000	0.20887	AAC		0.617	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1		XM_047462	
SYT15	83849	hgsc.bcm.edu;ucsc.edu	37	10	46967610	46967611	+	Frame_Shift_Ins	INS	-	-	C	rs201388422		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr10:46967610_46967611insC	ENST00000374321.4	-	4	532_533	c.466_467insG	c.(466-468)gaafs	p.E156fs	SYT15_ENST00000374325.3_Frame_Shift_Ins_p.E156fs|SYT15_ENST00000374323.4_Frame_Shift_Ins_p.E209fs|SYT15_ENST00000503753.1_Frame_Shift_Ins_p.E156fs|RP11-38L15.3_ENST00000506914.1_RNA	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	156	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						CTGCTCATATTCCACCGAGAAC	0.624																																					Ovarian(57;1152 1428 19651 37745)												0																																										SO:0001589	frameshift_variant	83849			AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.467dupG	10.37:g.46967612_46967612dupC	ENSP00000363441:p.Glu156fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Frame_Shift_Ins	INS	ENST00000374321.4	37	CCDS44376.1																																																																																				0.624	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1		NM_031912	
TCAP	8557	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	37821618	37821618	+	Silent	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:37821618T>A	ENST00000309889.2	+	1	1179	c.6T>A	c.(4-6)gcT>gcA	p.A2A	PNMT_ENST00000269582.2_5'Flank|TCAP_ENST00000578283.1_Silent_p.A2A|PNMT_ENST00000394246.1_5'Flank			O15273	TELT_HUMAN	titin-cap	2					adult heart development (GO:0007512)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of mechanical stimulus (GO:0050982)|detection of muscle stretch (GO:0035995)|muscle filament sliding (GO:0030049)|otic vesicle formation (GO:0030916)|protein complex assembly (GO:0006461)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle contraction (GO:0003009)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)	cytosol (GO:0005829)|I band (GO:0031674)|Z disc (GO:0030018)	FATZ binding (GO:0051373)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)	p.A2A(1)		kidney(1)|lung(1)	2	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TGATCATGGCTACCTCAGAGC	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											97.0	100.0	99.0					17																	37821618		2203	4300	6503	SO:0001819	synonymous_variant	8557			AJ000491	CCDS11342.1	17q12	2014-09-17	2012-09-20		ENSG00000173991	ENSG00000173991			11610	protein-coding gene	gene with protein product	"""19 kDa sarcomeric protein"""	604488	"""limb girdle muscular dystrophy 2G (autosomal recessive)"", ""titin-cap (telethonin)"""	LGMD2G		9350988, 9817758	Standard	NM_003673		Approved	T-cap, TELE, telethonin, CMD1N	uc002hsh.3	O15273	OTTHUMG00000133215	ENST00000309889.2:c.6T>A	17.37:g.37821618T>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q96L27	Silent	SNP	ENST00000309889.2	37	CCDS11342.1																																																																																				0.602	TCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256942.1		NM_003673	
TMCO4	255104	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	20009748	20009748	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:20009748C>G	ENST00000294543.6	-	16	1931	c.1690G>C	c.(1690-1692)Ggt>Cgt	p.G564R	TMCO4_ENST00000375122.2_Missense_Mutation_p.G524R|TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375127.1_Intron	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	564						integral component of membrane (GO:0016021)		p.G564R(1)		biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		GATATGGGACCCTGGGTTTGC	0.667																																																	1	Substitution - Missense(1)	kidney(1)											63.0	68.0	66.0					1																	20009748		2203	4300	6503	SO:0001583	missense	255104				CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.1690G>C	1.37:g.20009748C>G	ENSP00000294543:p.Gly564Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.920717	0.52653	.	.	ENSG00000162542	ENST00000294543;ENST00000375122	T;T	0.32753	1.47;1.44	4.61	4.61	0.57282	.	0.600243	0.14714	N	0.302780	T	0.23532	0.0569	L	0.29908	0.895	0.36908	D	0.890732	B;P	0.40107	0.435;0.703	B;B	0.37508	0.128;0.252	T	0.14448	-1.0472	10	0.22109	T	0.4	-12.8024	14.5439	0.68015	0.0:1.0:0.0:0.0	.	564;524	Q5TGY1;Q5TGY1-2	TMCO4_HUMAN;.	R	564;524	ENSP00000294543:G564R;ENSP00000364264:G524R	ENSP00000294543:G564R	G	-	1	0	TMCO4	19882335	0.000000	0.05858	0.539000	0.28077	0.235000	0.25334	-0.105000	0.10907	2.264000	0.75181	0.655000	0.94253	GGT		0.667	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1		NM_181719	
TNKS1BP1	85456	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	57077336	57077336	+	Frame_Shift_Del	DEL	T	T	-			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:57077336delT	ENST00000532437.1	-	5	3160	c.2849delA	c.(2848-2850)cagfs	p.Q950fs	TNKS1BP1_ENST00000358252.3_Frame_Shift_Del_p.Q950fs|TNKS1BP1_ENST00000530920.1_5'UTR			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	950	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CCCAAACTCCTGTTCCTGTGG	0.592																																																	0													92.0	105.0	100.0					11																	57077336		2201	4296	6497	SO:0001589	frameshift_variant	85456			AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.2849delA	11.37:g.57077336delT	ENSP00000437271:p.Gln950fs	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2F8|Q6PJ35|Q6ZV74	Frame_Shift_Del	DEL	ENST00000532437.1	37	CCDS7951.1																																																																																				0.592	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1		NM_033396	
TMEM132A	54972	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	60701064	60701064	+	Silent	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr11:60701064C>A	ENST00000453848.2	+	8	1565	c.1407C>A	c.(1405-1407)ggC>ggA	p.G469G	TMEM132A_ENST00000005286.4_Silent_p.G470G			Q24JP5	T132A_HUMAN	transmembrane protein 132A	469						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)		p.G470G(2)		breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						AGAGCCGGGGCGCCCGGGGGG	0.692																																																	2	Substitution - coding silent(2)	kidney(2)											17.0	25.0	22.0					11																	60701064		2194	4290	6484	SO:0001819	synonymous_variant	54972			AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.1407C>A	11.37:g.60701064C>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Silent	SNP	ENST00000453848.2	37	CCDS44618.1	.	.	.	.	.	.	.	.	.	.	C	0.374	-0.932586	0.02359	.	.	ENSG00000006118	ENST00000536409	.	.	.	4.75	-9.5	0.00584	.	.	.	.	.	T	0.31888	0.0811	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46062	-0.9218	4	.	.	.	.	0.4611	0.00516	0.3682:0.1886:0.149:0.2941	.	.	.	.	S	61	.	.	R	+	1	0	TMEM132A	60457640	0.000000	0.05858	0.010000	0.14722	0.058000	0.15608	-4.824000	0.00181	-3.555000	0.00142	-1.683000	0.00735	CGC		0.692	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1		NM_017870	
TPTE2	93492	broad.mit.edu;hgsc.bcm.edu	37	13	19999143	19999143	+	Nonsense_Mutation	SNP	G	G	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr13:19999143G>C	ENST00000400230.2	-	19	1454	c.1410C>G	c.(1408-1410)taC>taG	p.Y470*	TPTE2_ENST00000390680.2_Nonsense_Mutation_p.Y393*|TPTE2_ENST00000382977.4_Nonsense_Mutation_p.Y470*|TPTE2_ENST00000382978.1_Nonsense_Mutation_p.Y430*|TPTE2_ENST00000255310.6_Nonsense_Mutation_p.Y393*|TPTE2_ENST00000400103.2_Nonsense_Mutation_p.Y359*|TPTE2_ENST00000457266.2_Nonsense_Mutation_p.Y359*|TPTE2_ENST00000382975.4_Nonsense_Mutation_p.Y430*			Q6XPS3	TPTE2_HUMAN	transmembrane phosphoinositide 3-phosphatase and tensin homolog 2	470	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.Y470*(1)|p.Y393*(1)		NS(2)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(8)|lung(21)|pancreas(1)|prostate(8)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		all_cancers(29;1.23e-20)|all_lung(29;1.97e-20)|all_epithelial(30;5.86e-20)|Lung NSC(5;3.36e-17)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;1.73e-05)|Epithelial(112;7.42e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000785)|Lung(94;0.0176)|LUSC - Lung squamous cell carcinoma(192;0.089)		AATTGTCATAGTATTTAGGAA	0.279																																																	2	Substitution - Nonsense(2)	kidney(2)											37.0	37.0	37.0					13																	19999143		2074	4247	6321	SO:0001587	stop_gained	93492			AJ421032	CCDS9285.1, CCDS45013.1, CCDS45014.1	13q12.11	2012-12-10			ENSG00000132958	ENSG00000132958		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	17299	protein-coding gene	gene with protein product		606791				11716755, 12717346, 15057823	Standard	NM_130785		Approved	TPIP	uc001umd.3	Q6XPS3	OTTHUMG00000016493	ENST00000400230.2:c.1410C>G	13.37:g.19999143G>C	ENSP00000383089:p.Tyr470*	Somatic		WXS	Illumina HiSeq	Phase_I	A1A4X0|A1A4X1|A8MX64|B1AQ16|B4DWZ2|Q5VUH2|Q8WWL4|Q8WWL5	Nonsense_Mutation	SNP	ENST00000400230.2	37	CCDS45014.1	.	.	.	.	.	.	.	.	.	.	g	25.7	4.666488	0.88251	.	.	ENSG00000132958	ENST00000382978;ENST00000400103;ENST00000400230;ENST00000255310;ENST00000390680;ENST00000382977;ENST00000382975;ENST00000457266	.	.	.	2.17	2.17	0.27698	.	0.365001	0.25104	U	0.033109	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.1665	10.4642	0.44598	0.0:0.0:1.0:0.0	.	.	.	.	X	430;359;470;393;393;470;430;359	.	.	Y	-	3	2	TPTE2	18897143	1.000000	0.71417	0.968000	0.41197	0.665000	0.39181	1.352000	0.34033	1.526000	0.49068	0.194000	0.17425	TAC		0.279	TPTE2-205	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_199254	
TST	7263	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	37414210	37414210	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr22:37414210G>C	ENST00000403892.3	-	1	1298	c.564C>G	c.(562-564)ttC>ttG	p.F188L	TST_ENST00000249042.3_Missense_Mutation_p.F188L|MPST_ENST00000397129.1_5'Flank|MPST_ENST00000341116.3_5'Flank|MPST_ENST00000404393.1_5'Flank|MPST_ENST00000404802.3_5'Flank|MPST_ENST00000429360.2_5'Flank|MPST_ENST00000401419.3_5'Flank	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	188	Rhodanese 2. {ECO:0000255|PROSITE- ProRule:PRU00173}.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)	p.F188L(1)		kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						CGGTGCCCAGGAACCGCCCTT	0.592																																																	1	Substitution - Missense(1)	kidney(1)											31.0	29.0	30.0					22																	37414210		2203	4300	6503	SO:0001583	missense	7263			Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.564C>G	22.37:g.37414210G>C	ENSP00000385828:p.Phe188Leu	Somatic		WXS	Illumina HiSeq	Phase_I	B3KRM1|Q6IB06	Missense_Mutation	SNP	ENST00000403892.3	37	CCDS13938.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.245532	0.80024	.	.	ENSG00000128311	ENST00000403892;ENST00000249042;ENST00000413912	T;T	0.31247	1.5;1.5	4.93	4.93	0.64822	Rhodanese-like (5);	0.108407	0.64402	D	0.000007	T	0.70570	0.3239	H	0.99143	4.445	0.53005	D	0.999968	D	0.65815	0.995	D	0.69479	0.964	T	0.82182	-0.0584	10	0.87932	D	0	-22.303	12.0764	0.53647	0.0908:0.0:0.9092:0.0	.	188	Q16762	THTR_HUMAN	L	188	ENSP00000385828:F188L;ENSP00000249042:F188L	ENSP00000249042:F188L	F	-	3	2	TST	35744156	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.763000	0.55257	2.262000	0.75019	0.511000	0.50034	TTC		0.592	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1			
TTC22	55001	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	55251692	55251692	+	Silent	SNP	T	T	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:55251692T>C	ENST00000371276.4	-	5	1087	c.984A>G	c.(982-984)ccA>ccG	p.P328P	TTC22_ENST00000371274.4_Silent_p.P328P	NM_001114108.1	NP_001107580.1	Q5TAA0	TTC22_HUMAN	tetratricopeptide repeat domain 22	328								p.P328P(2)		kidney(1)|large_intestine(1)|lung(7)|skin(1)	10						AGTTGAGTTCTGGATCTCGTA	0.552																																																	2	Substitution - coding silent(2)	kidney(2)											77.0	71.0	73.0					1																	55251692		2203	4300	6503	SO:0001819	synonymous_variant	55001			AK000626	CCDS598.1, CCDS44152.1	1p32.3	2013-01-11			ENSG00000006555	ENSG00000006555		"""Tetratricopeptide (TTC) repeat domain containing"""	26067	protein-coding gene	gene with protein product							Standard	NM_017904		Approved	FLJ20619	uc009vzt.1	Q5TAA0	OTTHUMG00000009916	ENST00000371276.4:c.984A>G	1.37:g.55251692T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q9NWT4	Silent	SNP	ENST00000371276.4	37	CCDS44152.1																																																																																				0.552	TTC22-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027438.1		NM_017904	
TTN	7273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	179582323	179582323	+	Silent	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:179582323G>A	ENST00000591111.1	-	85	24551	c.24327C>T	c.(24325-24327)caC>caT	p.H8109H	TTN_ENST00000342992.6_Silent_p.H7182H|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342175.6_Intron|TTN_ENST00000589042.1_Silent_p.H8426H			Q8WZ42	TITIN_HUMAN	titin	12300	Ig-like 63.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.H7182H(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ACTGCCCTATGTGGCTCTGGT	0.423																																																	1	Substitution - coding silent(1)	kidney(1)											79.0	80.0	80.0					2																	179582323		1882	4122	6004	SO:0001819	synonymous_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24327C>T	2.37:g.179582323G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																					0.423	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179633434	179633435	+	Frame_Shift_Ins	INS	-	-	C	rs113275222	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr2:179633434_179633435insC	ENST00000591111.1	-	38	9352_9353	c.9128_9129insG	c.(9127-9129)ggafs	p.G3043fs	TTN_ENST00000342992.6_Frame_Shift_Ins_p.G3043fs|TTN-AS1_ENST00000610005.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000360870.5_Frame_Shift_Ins_p.G3043fs|TTN_ENST00000359218.5_Frame_Shift_Ins_p.G2997fs|TTN_ENST00000460472.2_Frame_Shift_Ins_p.G2997fs|TTN_ENST00000342175.6_Frame_Shift_Ins_p.G2997fs|TTN_ENST00000589042.1_Frame_Shift_Ins_p.G3043fs			Q8WZ42	TITIN_HUMAN	titin	13375	Ig-like 17.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			ATGTTGCTTTTCCAGCCACAAA	0.386																																																	0																																										SO:0001589	frameshift_variant	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.9129dupG	2.37:g.179633436_179633436dupC	ENSP00000465570:p.Gly3043fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Frame_Shift_Ins	INS	ENST00000591111.1	37																																																																																					0.386	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
TXLNA	200081	hgsc.bcm.edu;ucsc.edu	37	1	32660776	32660776	+	Missense_Mutation	SNP	C	C	T	rs77692511	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:32660776C>T	ENST00000373609.1	+	10	1902	c.1621C>T	c.(1621-1623)Ccc>Tcc	p.P541S	TXLNA_ENST00000373610.3_Missense_Mutation_p.P541S			P40222	TXLNA_HUMAN	taxilin alpha	541					B cell activation (GO:0042113)|cell proliferation (GO:0008283)|exocytosis (GO:0006887)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	cytokine activity (GO:0005125)|high molecular weight B cell growth factor receptor binding (GO:0030372)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				GCCTCAAGAGCCCACCTCCGC	0.657													C|||	9	0.00179712	0.0068	0.0	5008	,	,		17771	0.0		0.0	False		,,,				2504	0.0																0								C	SER/PRO	23,4383		0,23,2180	23.0	26.0	25.0		1621	4.3	1.0	1	dbSNP_131	25	0,8600		0,0,4300	yes	missense	TXLNA	NM_175852.3	74	0,23,6480	TT,TC,CC		0.0,0.522,0.1768	benign	541/547	32660776	23,12983	2203	4300	6503	SO:0001583	missense	200081			AF516206	CCDS353.1	1p35	2012-02-21			ENSG00000084652	ENSG00000084652			30685	protein-coding gene	gene with protein product		608676				15184072, 14623251	Standard	NM_175852		Approved	DKFZp451J0118	uc001bui.3	P40222	OTTHUMG00000004423	ENST00000373609.1:c.1621C>T	1.37:g.32660776C>T	ENSP00000362711:p.Pro541Ser	Somatic		WXS	Illumina HiSeq	Phase_I	D3DPP6|Q5TFJ6|Q66K62|Q86T54|Q86T85|Q86T86|Q86Y86|Q86YW3|Q8N2Y3	Missense_Mutation	SNP	ENST00000373609.1	37	CCDS353.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	10.51	1.371731	0.24857	0.00522	0.0	ENSG00000084652	ENST00000373610;ENST00000373609	T;T	0.40225	1.04;1.04	5.27	4.3	0.51218	.	0.112829	0.40554	N	0.001069	T	0.23965	0.0580	N	0.24115	0.695	0.29013	N	0.886746	B	0.25667	0.131	B	0.22386	0.039	T	0.32134	-0.9918	10	0.72032	D	0.01	-17.694	15.7851	0.78297	0.0:0.8094:0.1906:0.0	.	541	P40222	TXLNA_HUMAN	S	541	ENSP00000362712:P541S;ENSP00000362711:P541S	ENSP00000362711:P541S	P	+	1	0	TXLNA	32433363	0.955000	0.32602	1.000000	0.80357	0.199000	0.23934	0.655000	0.24933	2.651000	0.90000	0.655000	0.94253	CCC		0.657	TXLNA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012844.1		NM_175852	
UHRF1BP1	54887	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	34789455	34789455	+	Nonsense_Mutation	SNP	A	A	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr6:34789455A>T	ENST00000192788.5	+	2	241	c.70A>T	c.(70-72)Aaa>Taa	p.K24*	Y_RNA_ENST00000383990.1_RNA|UHRF1BP1_ENST00000452449.2_Nonsense_Mutation_p.K24*	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	24							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)	p.K24*(1)		breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						TTCCCCAGACAAAATCAACCT	0.453																																																	1	Substitution - Nonsense(1)	kidney(1)											46.0	47.0	47.0					6																	34789455		1861	4108	5969	SO:0001587	stop_gained	54887			AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.70A>T	6.37:g.34789455A>T	ENSP00000192788:p.Lys24*	Somatic		WXS	Illumina HiSeq	Phase_I	Q9NXE0	Nonsense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	A	37	6.283819	0.97440	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	.	.	.	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.4368	16.1267	0.81400	1.0:0.0:0.0:0.0	.	.	.	.	X	24	.	ENSP00000192788:K24X	K	+	1	0	UHRF1BP1	34897433	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.299000	0.78831	2.205000	0.71048	0.455000	0.32223	AAA		0.453	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1		NM_017754	
WDR47	22911	broad.mit.edu;hgsc.bcm.edu	37	1	109554267	109554267	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr1:109554267T>C	ENST00000369962.3	-	5	623	c.401A>G	c.(400-402)tAt>tGt	p.Y134C	WDR47_ENST00000369965.4_Missense_Mutation_p.Y134C|WDR47_ENST00000357672.3_Missense_Mutation_p.Y106C|WDR47_ENST00000361054.3_Missense_Mutation_p.Y106C|WDR47_ENST00000400794.3_Missense_Mutation_p.Y141C			O94967	WDR47_HUMAN	WD repeat domain 47	134					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|microtubule (GO:0005874)		p.Y134C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20		all_lung(203;0.00519)|all_epithelial(167;0.00611)|Lung NSC(277;0.00822)		Colorectal(144;0.0165)|Lung(183;0.0484)|COAD - Colon adenocarcinoma(174;0.128)|Epithelial(280;0.168)|all cancers(265;0.201)|LUSC - Lung squamous cell carcinoma(189;0.244)		GAGCTTACTATAGTCATCTTT	0.398																																																	1	Substitution - Missense(1)	kidney(1)											131.0	131.0	131.0					1																	109554267		2203	4296	6499	SO:0001583	missense	22911			AB020700	CCDS30787.1, CCDS44186.1, CCDS44187.1	1p13.3	2013-01-09			ENSG00000085433	ENSG00000085433		"""WD repeat domain containing"""	29141	protein-coding gene	gene with protein product		615734				10048485	Standard	NM_014969		Approved	KIAA0893	uc001dwl.3	O94967	OTTHUMG00000011734	ENST00000369962.3:c.401A>G	1.37:g.109554267T>C	ENSP00000358979:p.Tyr134Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A8MX09|Q5TYV7|Q5TYV8|Q5TYV9|Q8IXT7|Q8IYU9	Missense_Mutation	SNP	ENST00000369962.3	37	CCDS44187.1	.	.	.	.	.	.	.	.	.	.	T	18.45	3.627740	0.66901	.	.	ENSG00000085433	ENST00000400794;ENST00000369962;ENST00000361054;ENST00000369965;ENST00000357672;ENST00000530772;ENST00000529074;ENST00000531337	T;T;T;T;T	0.76060	-0.81;-0.77;-0.99;-0.81;-0.99	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.81809	0.4901	M	0.69358	2.11	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.986;0.997;0.997	D	0.84745	0.0753	10	0.87932	D	0	-12.7322	15.3075	0.74004	0.0:0.0:0.0:1.0	.	106;141;134;134	O94967-2;A8MX09;O94967;O94967-3	.;.;WDR47_HUMAN;.	C	141;134;106;134;106;134;61;34	ENSP00000383599:Y141C;ENSP00000358979:Y134C;ENSP00000354339:Y106C;ENSP00000358982:Y134C;ENSP00000350301:Y106C	ENSP00000350301:Y106C	Y	-	2	0	WDR47	109355790	1.000000	0.71417	0.978000	0.43139	0.975000	0.68041	7.673000	0.83973	2.008000	0.58898	0.460000	0.39030	TAT		0.398	WDR47-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000032414.2		NM_014969	
WDR90	197335	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	700616	700616	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr16:700616C>G	ENST00000293879.4	+	5	466	c.466C>G	c.(466-468)Ctg>Gtg	p.L156V	AL022341.3_ENST00000455294.1_RNA|WDR90_ENST00000549091.1_Missense_Mutation_p.L156V			Q96KV7	WDR90_HUMAN	WD repeat domain 90	156								p.L156V(1)		endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCTGGTCTACCTGAACCGGTG	0.627																																																	1	Substitution - Missense(1)	kidney(1)											48.0	56.0	54.0					16																	700616		2057	4184	6241	SO:0001583	missense	197335			AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.466C>G	16.37:g.700616C>G	ENSP00000293879:p.Leu156Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	C	13.47	2.247660	0.39697	.	.	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.37584	1.19;1.19	5.18	3.21	0.36854	.	0.111883	0.37012	N	0.002300	T	0.44705	0.1306	M	0.62723	1.935	0.80722	D	1	D;P;P	0.56521	0.976;0.896;0.75	P;B;B	0.52823	0.71;0.416;0.292	T	0.33727	-0.9857	10	0.51188	T	0.08	.	9.9148	0.41427	0.0:0.6666:0.2599:0.0735	.	156;156;156	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	V	156	ENSP00000448122:L156V;ENSP00000293879:L156V	ENSP00000293879:L156V	L	+	1	2	WDR90	640617	1.000000	0.71417	0.216000	0.23742	0.070000	0.16714	1.863000	0.39459	0.572000	0.29383	0.563000	0.77884	CTG		0.627	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1		NM_145294	
XKR7	343702	broad.mit.edu;hgsc.bcm.edu	37	20	30556225	30556225	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr20:30556225C>G	ENST00000562532.2	+	1	421	c.247C>G	c.(247-249)Ctg>Gtg	p.L83V		NM_001011718.1	NP_001011718.1	Q5GH72	XKR7_HUMAN	XK, Kell blood group complex subunit-related family, member 7	83						integral component of membrane (GO:0016021)		p.L83V(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	34			Colorectal(19;0.00306)|COAD - Colon adenocarcinoma(19;0.0347)			CTCCTACTACCTGCAGAATCA	0.622																																																	1	Substitution - Missense(1)	kidney(1)											68.0	56.0	60.0					20																	30556225		2203	4300	6503	SO:0001583	missense	343702			AY534245	CCDS33459.1	20q11.21	2014-07-16	2006-01-12		ENSG00000260903	ENSG00000260903			23062	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 7"", ""chromosome 20 open reading frame 159"""	C20orf159			Standard	NM_001011718		Approved	dJ310O13.4	uc002wxe.3	Q5GH72	OTTHUMG00000032198	ENST00000562532.2:c.247C>G	20.37:g.30556225C>G	ENSP00000477059:p.Leu83Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q9NUG5	Missense_Mutation	SNP	ENST00000562532.2	37	CCDS33459.1	.	.	.	.	.	.	.	.	.	.	C	14.19	2.460296	0.43736	.	.	ENSG00000101321	ENST00000217299	T	0.64803	-0.12	3.41	2.42	0.29668	.	0.236341	0.27289	N	0.020049	T	0.58148	0.2102	M	0.71581	2.175	0.41522	D	0.988403	P	0.41475	0.751	B	0.42138	0.377	T	0.53961	-0.8364	10	0.16896	T	0.51	-8.897	9.5646	0.39391	0.2278:0.7721:0.0:0.0	.	83	Q5GH72	XKR7_HUMAN	V	83	ENSP00000217299:L83V	ENSP00000217299:L83V	L	+	1	2	XKR7	30019886	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.466000	0.35310	0.716000	0.32124	0.637000	0.83480	CTG		0.622	XKR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078597.3		NM_001011718	
XPO5	57510	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	43515440	43515440	+	Silent	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr6:43515440G>A	ENST00000265351.7	-	19	2275	c.2065C>T	c.(2065-2067)Ctg>Ttg	p.L689L		NM_020750.2	NP_065801.1	Q9HAV4	XPO5_HUMAN	exportin 5	689					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|protein export from nucleus (GO:0006611)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|RNA binding (GO:0003723)|tRNA binding (GO:0000049)	p.L689L(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(4)|lung(10)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	34	all_cancers(18;2.08e-05)|Lung NSC(15;0.000907)|all_lung(25;0.00243)		all cancers(41;0.000321)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|OV - Ovarian serous cystadenocarcinoma(102;0.0524)			ACATCTGACAGCACTCTGAAG	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											90.0	85.0	87.0					6																	43515440		1956	4154	6110	SO:0001819	synonymous_variant	57510			AB033117	CCDS47430.1	6p21.1	2011-04-13			ENSG00000124571	ENSG00000124571		"""Exportins"""	17675	protein-coding gene	gene with protein product		607845				11777942, 12426392	Standard	NM_020750		Approved	KIAA1291	uc003ovp.3	Q9HAV4	OTTHUMG00000014742	ENST00000265351.7:c.2065C>T	6.37:g.43515440G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q5JTE6|Q96G48|Q96HN3|Q9BWM6|Q9BZV5|Q9H9M4|Q9NT89|Q9NW39|Q9ULC9	Silent	SNP	ENST00000265351.7	37	CCDS47430.1																																																																																				0.463	XPO5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040657.2		NM_020750	
ZCCHC5	203430	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	77913051	77913051	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:77913051C>A	ENST00000321110.1	-	2	1162	c.867G>T	c.(865-867)tgG>tgT	p.W289C		NM_152694.2	NP_689907.1	Q8N8U3	ZCHC5_HUMAN	zinc finger, CCHC domain containing 5	289							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.W289C(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(18)|ovary(1)|prostate(1)|skin(1)	37						GCTGGAACCACCATCCTGCCC	0.468																																																	1	Substitution - Missense(1)	kidney(1)											41.0	38.0	39.0					X																	77913051		2203	4299	6502	SO:0001583	missense	203430			AK096184	CCDS14440.1	Xq13.3	2008-02-05			ENSG00000179300	ENSG00000179300		"""Zinc fingers, CCHC domain containing"""	22997	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_152694		Approved	FLJ38865, Mar3, Mart3, ZHC5	uc004edc.1	Q8N8U3	OTTHUMG00000021892	ENST00000321110.1:c.867G>T	X.37:g.77913051C>A	ENSP00000316794:p.Trp289Cys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RMZ0|Q5JQE9	Missense_Mutation	SNP	ENST00000321110.1	37	CCDS14440.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.438295	0.01098	.	.	ENSG00000179300	ENST00000321110	T	0.17370	2.28	3.36	-3.53	0.04667	.	0.761213	0.10696	U	0.644579	T	0.04998	0.0134	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30416	-0.9979	10	0.56958	D	0.05	.	3.6209	0.08096	0.3214:0.2004:0.0:0.4781	.	289	Q8N8U3	ZCHC5_HUMAN	C	289	ENSP00000316794:W289C	ENSP00000316794:W289C	W	-	3	0	ZCCHC5	77799707	0.001000	0.12720	0.000000	0.03702	0.156000	0.22039	-0.537000	0.06128	-1.209000	0.02631	-0.324000	0.08512	TGG		0.468	ZCCHC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057319.1		NM_152694	
ZDHHC8	29801	hgsc.bcm.edu	37	22	20130989	20130990	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr22:20130989_20130990insG	ENST00000334554.7	+	10	1977_1978	c.1836_1837insG	c.(1837-1839)gggfs	p.G613fs	ZDHHC8_ENST00000405930.3_Frame_Shift_Ins_p.G613fs|ZDHHC8_ENST00000320602.7_Frame_Shift_Ins_p.G521fs	NM_013373.3	NP_037505.1	Q9ULC8	ZDHC8_HUMAN	zinc finger, DHHC-type containing 8	613					locomotory behavior (GO:0007626)|protein palmitoylation (GO:0018345)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	20	Colorectal(54;0.0993)					ACCTTGTGGCTGGGCCCGGCTT	0.698																																																	0																																										SO:0001589	frameshift_variant	29801			AB033118	CCDS13776.1, CCDS54502.1	22q11.21	2009-10-06		2003-02-28	ENSG00000099904	ENSG00000099904		"""Zinc fingers, DHHC-type"""	18474	protein-coding gene	gene with protein product		608784				10574462, 15184899	Standard	NM_013373		Approved	ZNF378, KIAA1292	uc002zrr.2	Q9ULC8	OTTHUMG00000150499	ENST00000334554.7:c.1839dupG	22.37:g.20130992_20130992dupG	ENSP00000334490:p.Gly613fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q2TGE9|Q6ICL1|Q6ZNF5|Q7Z6L9	Frame_Shift_Ins	INS	ENST00000334554.7	37	CCDS13776.1																																																																																				0.698	ZDHHC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318564.1		NM_013373	
ZNF714	148206	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	21300402	21300402	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:21300402C>A	ENST00000596143.1	+	5	1257	c.932C>A	c.(931-933)tCt>tAt	p.S311Y	ZNF714_ENST00000601416.1_3'UTR|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000596053.1_Intron	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	311					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.S416Y(1)|p.S311Y(1)		endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						GGAGAGAAATCTTACAAATGT	0.333																																																	2	Substitution - Missense(2)	kidney(2)											24.0	27.0	26.0					19																	21300402		2167	4284	6451	SO:0001583	missense	148206			AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.932C>A	19.37:g.21300402C>A	ENSP00000472368:p.Ser311Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	37	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	4.413	0.076323	0.08485	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.955	0.955	0.19602	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.40423	0.1116	L	0.51914	1.62	0.26359	N	0.977078	P;P;P	0.40360	0.534;0.714;0.589	B;B;B	0.43386	0.196;0.418;0.405	T	0.32877	-0.9890	8	0.87932	D	0	.	8.8708	0.35314	0.0:1.0:0.0:0.0	.	312;311;312	Q96N38-2;A6NEM4;Q96N38	.;.;ZN714_HUMAN	Y	311	.	ENSP00000291770:S311Y	S	+	2	0	ZNF714	21092242	0.001000	0.12720	0.060000	0.19600	0.054000	0.15201	0.841000	0.27613	0.446000	0.26666	0.449000	0.29647	TCT		0.333	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1		NM_182515	
ZNF749	388567	broad.mit.edu;hgsc.bcm.edu	37	19	57955937	57955937	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:57955937A>G	ENST00000334181.4	+	3	1671	c.1421A>G	c.(1420-1422)aAg>aGg	p.K474R	AC004076.9_ENST00000596831.1_Intron	NM_001023561.2	NP_001018855.2	O43361	ZN749_HUMAN	zinc finger protein 749	474					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K387R(1)|p.K474R(1)		breast(1)|endometrium(6)|kidney(2)|lung(3)|prostate(1)	13		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)|Lung(386;0.177)		ATTCAACACAAGAGGATTGAC	0.448																																																	2	Substitution - Missense(2)	kidney(2)											85.0	79.0	81.0					19																	57955937		2203	4300	6503	SO:0001583	missense	388567			AK122740	CCDS33132.2	19q13.43	2013-01-08			ENSG00000186230	ENSG00000186230		"""Zinc fingers, C2H2-type"", ""-"""	32783	protein-coding gene	gene with protein product							Standard	NM_001023561		Approved	FLJ16360	uc002qoq.2	O43361	OTTHUMG00000150372	ENST00000334181.4:c.1421A>G	19.37:g.57955937A>G	ENSP00000333980:p.Lys474Arg	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000334181.4	37	CCDS33132.2	.	.	.	.	.	.	.	.	.	.	A	8.042	0.763991	0.15914	.	.	ENSG00000186230	ENST00000334181	T	0.15017	2.46	0.894	0.894	0.19242	.	.	.	.	.	T	0.07728	0.0194	N	0.11364	0.135	0.09310	N	1	B	0.13594	0.008	B	0.04013	0.001	T	0.31364	-0.9946	9	0.42905	T	0.14	.	3.7157	0.08437	0.5932:0.4067:0.0:1.0E-4	.	474	O43361	ZN749_HUMAN	R	474	ENSP00000333980:K474R	ENSP00000333980:K474R	K	+	2	0	ZNF749	62647749	0.187000	0.23238	0.002000	0.10522	0.001000	0.01503	-0.365000	0.07573	0.639000	0.30564	0.377000	0.23210	AAG		0.448	ZNF749-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317879.1		NM_001023561	
ATP8B5P	158381	broad.mit.edu	37	9	35449946	35449946	+	RNA	SNP	G	G	C			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr9:35449946G>C	ENST00000430846.1	+	0	2796									ATPase, class I, type 8B, member 5, pseudogene																		CAGTGTCCCAGAAGCCCAGTC	0.403																																																	0																																												158381					9p13.3	2010-09-22			ENSG00000179766	ENSG00000179766		"""ATPases / P-type"""	27245	pseudogene	pseudogene	"""flippase expressed in testis splicing form A pseudogene"""					20210903, 19657017	Standard	NR_003582		Approved	FetA	uc010mkn.2		OTTHUMG00000019862		9.37:g.35449946G>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000430846.1	37																																																																																					0.403	ATP8B5P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000052312.1		NR_003581.1	
FMN1	342184	broad.mit.edu	37	15	33358779	33358779	+	Intron	SNP	T	T	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr15:33358779T>G	ENST00000559047.1	-	3	2043				FMN1_ENST00000559150.1_Intron|FMN1_ENST00000334528.9_Missense_Mutation_p.E436A|FMN1_ENST00000561249.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.E436A			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)		p.E436A(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TCTTAGCGACTCCTTCTCATG	0.488																																																	1	Substitution - Missense(1)	kidney(1)											54.0	54.0	54.0					15																	33358779		1967	4163	6130	SO:0001627	intron_variant	342184			AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-1504A>C	15.37:g.33358779T>G		Somatic		WXS	Illumina GAIIx	Phase_I	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		.	.	.	.	.	.	.	.	.	.	T	18.18	3.566143	0.65651	.	.	ENSG00000248905	ENST00000334528	T	0.60299	0.2	5.96	5.96	0.96718	.	0.269242	0.41823	D	0.000805	T	0.74351	0.3705	.	.	.	.	.	.	D;D	0.89917	1.0;0.999	D;D	0.77004	0.989;0.984	T	0.71909	-0.4450	8	0.29301	T	0.29	.	16.4484	0.83959	0.0:0.0:0.0:1.0	.	436;436	Q68DA7-3;Q68DA7-5	.;.	A	436	ENSP00000333950:E436A	ENSP00000333950:E436A	E	-	2	0	FMN1	31146071	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.996000	0.76263	2.285000	0.76669	0.533000	0.62120	GAG		0.488	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1		NM_001103184	
GGN	199720	broad.mit.edu	37	19	38876474	38876474	+	Silent	SNP	C	C	T	rs183192050	byFrequency	TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr19:38876474C>T	ENST00000334928.6	-	3	1560	c.1428G>A	c.(1426-1428)ctG>ctA	p.L476L	SPRED3_ENST00000587013.1_5'Flank|GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	476	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)		p.L476L(1)		breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			cggtgggagccagggctgACT	0.761													C|||	103	0.0205671	0.0174	0.0144	5008	,	,		9849	0.0		0.0338	False		,,,				2504	0.0368																1	Substitution - coding silent(1)	kidney(1)						C		23,3623		0,23,1800	3.0	4.0	4.0		1428	1.5	0.2	19		4	134,7106		0,134,3486	no	coding-synonymous	GGN	NM_152657.3		0,157,5286	TT,TC,CC		1.8508,0.6308,1.4422		476/653	38876474	157,10729	1823	3620	5443	SO:0001819	synonymous_variant	199720			AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.1428G>A	19.37:g.38876474C>T		Somatic		WXS	Illumina GAIIx	Phase_I	Q7RTU6|Q86UU4|Q8NAA1	Silent	SNP	ENST00000334928.6	37	CCDS12516.1																																																																																				0.761	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1		NM_152657	
KIF19	124602	broad.mit.edu	37	17	72343936	72343936	+	Silent	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr17:72343936C>T	ENST00000389916.4	+	9	1083	c.945C>T	c.(943-945)agC>agT	p.S315S		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	315	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)	p.S315S(1)		autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GAGGAAACAGCCGCACAGTGA	0.612																																																	1	Substitution - coding silent(1)	kidney(1)											87.0	50.0	63.0					17																	72343936		2201	4287	6488	SO:0001819	synonymous_variant	124602			AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.945C>T	17.37:g.72343936C>T		Somatic		WXS	Illumina GAIIx	Phase_I	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																				0.612	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2		NM_153209	
OFD1	8481	broad.mit.edu	37	X	13776512	13776512	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:13776512G>T	ENST00000340096.6	+	15	1926	c.1599G>T	c.(1597-1599)aaG>aaT	p.K533N	OFD1_ENST00000380567.1_Missense_Mutation_p.K393N|OFD1_ENST00000380550.3_Missense_Mutation_p.K493N|OFD1_ENST00000490265.1_3'UTR	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	533					axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)	p.K533N(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CTTCTGTAAAGAGTTTAACTA	0.343																																																	1	Substitution - Missense(1)	kidney(1)											56.0	56.0	56.0					X																	13776512		2203	4300	6503	SO:0001583	missense	8481			Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.1599G>T	X.37:g.13776512G>T	ENSP00000344314:p.Lys533Asn	Somatic		WXS	Illumina GAIIx	Phase_I	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	37	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	.	8.374	0.835930	0.16820	.	.	ENSG00000046651	ENST00000380550;ENST00000340096;ENST00000380567	D;D;D	0.96522	-2.34;-4.04;-1.94	5.46	2.64	0.31445	.	0.279998	0.38492	N	0.001662	D	0.91253	0.7243	L	0.34521	1.04	0.80722	D	1	B;B;B;B;B	0.27140	0.125;0.125;0.169;0.169;0.125	B;B;B;B;B	0.28553	0.067;0.037;0.091;0.091;0.037	T	0.83287	-0.0035	10	0.33141	T	0.24	-15.7207	5.6009	0.17353	0.2387:0.1395:0.6219:0.0	.	533;493;201;393;533	A8K2T9;O75665-3;B4DLQ3;A6NF31;O75665	.;.;.;.;OFD1_HUMAN	N	493;533;393	ENSP00000369923:K493N;ENSP00000344314:K533N;ENSP00000369941:K393N	ENSP00000344314:K533N	K	+	3	2	OFD1	13686433	0.999000	0.42202	0.407000	0.26434	0.247000	0.25773	0.884000	0.28214	0.186000	0.20125	0.600000	0.82982	AAG		0.343	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1		NM_003611	
MAGEB16	139604	broad.mit.edu	37	X	35821205	35821205	+	Missense_Mutation	SNP	C	C	A	rs370569797		TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:35821205C>A	ENST00000399989.1	+	2	1171	c.892C>A	c.(892-894)Cat>Aat	p.H298N	MAGEB16_ENST00000399992.1_Missense_Mutation_p.H330N|MAGEB16_ENST00000399988.1_Missense_Mutation_p.H298N|MAGEB16_ENST00000399987.1_Missense_Mutation_p.H298N|MAGEB16_ENST00000399985.1_Missense_Mutation_p.H298N	NM_001099921.1	NP_001093391.1	A2A368	MAGBG_HUMAN	melanoma antigen family B, 16	298	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.							p.H465N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31						GGCCAAAGTTCATGGGTCTTA	0.498																																																	1	Substitution - Missense(1)	kidney(1)											32.0	32.0	32.0					X																	35821205		2195	4300	6495	SO:0001583	missense	139604				CCDS43927.1	Xp21.1	2010-05-26	2005-11-07		ENSG00000189023	ENSG00000189023			21188	protein-coding gene	gene with protein product		300762	"""melanoma antigen family B, 16 (pseudogene)"""			11454705	Standard	NM_001099921		Approved		uc010ngt.1	A2A368	OTTHUMG00000021348	ENST00000399989.1:c.892C>A	X.37:g.35821205C>A	ENSP00000382871:p.His298Asn	Somatic		WXS	Illumina GAIIx	Phase_I	A8MU30	Missense_Mutation	SNP	ENST00000399989.1	37	CCDS43927.1	.	.	.	.	.	.	.	.	.	.	C	0.099	-1.155053	0.01700	.	.	ENSG00000189023	ENST00000399988;ENST00000399992;ENST00000399987;ENST00000399989;ENST00000399985	T;T;T;T;T	0.01422	4.92;4.91;4.92;4.92;4.92	3.13	0.0902	0.14462	.	0.825002	0.11170	N	0.592149	T	0.01156	0.0038	L	0.42245	1.32	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.50346	-0.8839	10	0.02654	T	1	.	3.3512	0.07153	0.4513:0.4087:0.0:0.1399	.	298	A2A368	MAGBG_HUMAN	N	298;330;298;298;298	ENSP00000382870:H298N;ENSP00000382874:H330N;ENSP00000382869:H298N;ENSP00000382871:H298N;ENSP00000382867:H298N	ENSP00000382867:H298N	H	+	1	0	MAGEB16	35731126	0.000000	0.05858	0.120000	0.21714	0.201000	0.24016	-0.364000	0.07583	-0.080000	0.12685	0.521000	0.50471	CAT		0.498	MAGEB16-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251034.1			
PBRM1	55193	broad.mit.edu	37	3	52649373	52649373	+	Nonsense_Mutation	SNP	T	T	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	T	T	T	A	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr3:52649373T>A	ENST00000296302.7	-	15	1919	c.1918A>T	c.(1918-1920)Aag>Tag	p.K640*	PBRM1_ENST00000409767.1_Nonsense_Mutation_p.K655*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.K640*|PBRM1_ENST00000409057.1_Nonsense_Mutation_p.K640*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.K640*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.K640*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.K655*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.K608*			Q86U86	PB1_HUMAN	polybromo 1	640					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.K640*(2)|p.K608*(1)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTACTCAGCTTGAGTTTGGGA	0.363			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	3	Substitution - Nonsense(3)	kidney(3)											104.0	92.0	96.0					3																	52649373		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1918A>T	3.37:g.52649373T>A	ENSP00000296302:p.Lys640*	Somatic		WXS	Illumina GAIIx	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	T	41	8.978253	0.99023	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	.	.	.	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-65.5612	16.19	0.81981	0.0:0.0:0.0:1.0	.	.	.	.	X	608;640;640;640;640;640;655;655;640;599	.	ENSP00000296302:K640X	K	-	1	0	PBRM1	52624413	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	8.040000	0.89188	2.225000	0.72522	0.460000	0.39030	AAG		0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PGAM1	5223	broad.mit.edu	37	10	99186086	99186086	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr10:99186086C>G	ENST00000334828.5	+	1	170	c.22C>G	c.(22-24)Ctg>Gtg	p.L8V	AL355490.1_ENST00000439965.2_5'Flank	NM_002629.2	NP_002620.1	P18669	PGAM1_HUMAN	phosphoglycerate mutase 1 (brain)	8					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|regulation of glycolytic process (GO:0006110)|regulation of pentose-phosphate shunt (GO:0043456)|respiratory burst (GO:0045730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)|protein kinase binding (GO:0019901)	p.L8V(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(252;0.162)		Epithelial(162;8.36e-10)|all cancers(201;5.62e-08)		CAAACTGGTGCTGATCCGGCA	0.711																																																	1	Substitution - Missense(1)	kidney(1)											13.0	16.0	15.0					10																	99186086		2062	4132	6194	SO:0001583	missense	5223			BC010038	CCDS7458.1	10q25.3	2012-10-02			ENSG00000171314	ENSG00000171314	5.4.2.1		8888	protein-coding gene	gene with protein product	"""Phosphoglycerate mutase A, nonmuscle form"""	172250		PGAMA		2846553	Standard	NM_002629		Approved	PGAM-B	uc001knh.3	P18669	OTTHUMG00000018846	ENST00000334828.5:c.22C>G	10.37:g.99186086C>G	ENSP00000359991:p.Leu8Val	Somatic		WXS	Illumina GAIIx	Phase_I	Q9BWC0	Missense_Mutation	SNP	ENST00000334828.5	37	CCDS7458.1	.	.	.	.	.	.	.	.	.	.	C	13.27	2.186030	0.38609	.	.	ENSG00000171314	ENST00000334828	D	0.88896	-2.44	5.03	5.03	0.67393	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.56097	U	0.000032	D	0.87325	0.6149	M	0.69463	2.115	0.44373	D	0.997276	B;B	0.14012	0.009;0.008	B;B	0.20184	0.028;0.021	D	0.84921	0.0854	10	0.87932	D	0	-5.0477	11.3764	0.49730	0.0:0.9128:0.0:0.0872	.	8;8	Q0D2Q6;P18669	.;PGAM1_HUMAN	V	8	ENSP00000359991:L8V	ENSP00000359991:L8V	L	+	1	2	PGAM1	99176076	0.015000	0.18098	1.000000	0.80357	0.318000	0.28184	0.194000	0.17135	2.612000	0.88384	0.484000	0.47621	CTG		0.711	PGAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049652.1		NM_002629	
SYTL4	94121	broad.mit.edu	37	X	99941139	99941139	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chrX:99941139G>A	ENST00000372989.1	-	15	1628	c.1297C>T	c.(1297-1299)Cca>Tca	p.P433S	SYTL4_ENST00000263033.5_Missense_Mutation_p.P433S|SYTL4_ENST00000372981.1_3'UTR|SYTL4_ENST00000276141.6_Missense_Mutation_p.P433S|SYTL4_ENST00000454200.2_Missense_Mutation_p.P435S|SYTL4_ENST00000455616.1_Missense_Mutation_p.P433S	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	433	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)	p.P433S(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AGAGATTCTGGGATCTCATAC	0.453																																																	1	Substitution - Missense(1)	kidney(1)											47.0	41.0	43.0					X																	99941139		2202	4300	6502	SO:0001583	missense	94121				CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.1297C>T	X.37:g.99941139G>A	ENSP00000362080:p.Pro433Ser	Somatic		WXS	Illumina GAIIx	Phase_I	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Missense_Mutation	SNP	ENST00000372989.1	37	CCDS14472.1	.	.	.	.	.	.	.	.	.	.	G	2.808	-0.247608	0.05867	.	.	ENSG00000102362	ENST00000372989;ENST00000455616;ENST00000454200;ENST00000276141;ENST00000263033	T;T;T;T;T	0.08193	3.12;3.12;3.12;3.12;3.12	5.88	2.12	0.27331	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);Synaptotagmin (1);	0.688831	0.15876	N	0.240296	T	0.03136	0.0092	N	0.04275	-0.24	0.32121	N	0.588037	B	0.02656	0.0	B	0.01281	0.0	T	0.38672	-0.9650	9	.	.	.	0.214	4.8068	0.13325	0.3245:0.0:0.494:0.1816	.	433	Q96C24	SYTL4_HUMAN	S	433;433;435;433;433	ENSP00000362080:P433S;ENSP00000390252:P433S;ENSP00000403556:P435S;ENSP00000276141:P433S;ENSP00000263033:P433S	.	P	-	1	0	SYTL4	99827795	0.998000	0.40836	0.995000	0.50966	0.987000	0.75469	1.115000	0.31209	0.227000	0.20999	0.600000	0.82982	CCA		0.453	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1		NM_080737	
Unknown	0	broad.mit.edu	37	15	82620366	82620366	+	IGR	SNP	C	C	T			TCGA-A3-3320-01A-01D-0966-08	TCGA-A3-3320-11A-01D-0966-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5c4cc718-d7b5-453c-89d8-186ab0869e68	94726a4b-14cf-4592-b63c-22a8f994631d	g.chr15:82620366C>T								RP13-98N21.3 (22214 upstream) : GOLGA6L10 (14763 downstream)																							CTCGGGCACACGCCTGAGCCT	0.652																																																	0																																										SO:0001628	intergenic_variant	0																															15.37:g.82620366C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.652									
