#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_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_refseq_mrna_id	i_secondary_variant_classification
CFAP74	85452	broad.mit.edu	37	1	1900084	1900084	+	IGR	SNP	G	G	A	rs150108692	byFrequency	TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr1:1900084G>A								TMEM52 (49372 upstream) : C1orf222 (19478 downstream)																							CAGTGTGTACGTGTTGGTTGG	0.582													g|||	2	0.000399361	0.0	0.0	5008	,	,		21281	0.002		0.0	False		,,,				2504	0.0					uc001aim.1																			0				breast(1)|endometrium(5)|kidney(4)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	32						c.(1234-1236)aCg>aTg		Homo sapiens KIAA1751 (KIAA1751), mRNA.		G	MET/THR	0,4106		0,0,2053	161.0	163.0	163.0		1235	-5.8	0.0	1	dbSNP_134	163	2,8372		0,2,4185	no	missense	KIAA1751	NM_001080484.1	81	0,2,6238	AA,AG,GG		0.0239,0.0,0.016	probably-damaging	412/763	1900084	2,12478	2053	4187	6240	SO:0001628	intergenic_variant	85452							g.chr1:1900084G>A																													1.37:g.1900084G>A						KIAA1751_uc009vkz.1_Missense_Mutation_p.T412M	p.T412M	NM_001080484	NP_001073953	Q9C0B2	K1751_HUMAN		Epithelial(90;8.79e-39)|OV - Ovarian serous cystadenocarcinoma(86;9.61e-25)|GBM - Glioblastoma multiforme(42;1.2e-07)|Colorectal(212;4.84e-05)|COAD - Colon adenocarcinoma(227;0.000214)|Kidney(185;0.00254)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.037)|Lung(427;0.205)	10	1391	-	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)	412						Missense_Mutation	SNP		37	c.1235C>T		2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	g	3.238	-0.155881	0.06544	0.0	2.39E-4	ENSG00000142609	ENST00000270720	.	.	.	2.89	-5.78	0.02362	.	14.379500	0.00166	N	0.000001	T	0.18130	0.0435	N	0.08118	0	0.09310	N	0.999999	B;B	0.18610	0.029;0.003	B;B	0.09377	0.004;0.002	T	0.17806	-1.0357	9	0.48119	T	0.1	.	6.0703	0.19885	0.2922:0.2422:0.4656:0.0	.	412;412	Q9C0B2-2;Q9C0B2	.;K1751_HUMAN	M	412	.	ENSP00000270720:T412M	T	-	2	0	C1orf222	1889944	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.169000	0.01269	-2.280000	0.00675	-1.086000	0.02197	ACG	0	0.582								
MTF1	4520	broad.mit.edu	37	1	38323155	38323155	+	Missense_Mutation	SNP	T	T	C			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr1:38323155T>C	ENST00000373036.4	-	2	316	c.176A>G	c.(175-177)gAg>gGg	p.E59G	MTF1_ENST00000468190.1_5'UTR	NM_005955.2	NP_005946.2	Q14872	MTF1_HUMAN	metal-regulatory transcription factor 1	59					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cadmium ion (GO:0046686)|response to metal ion (GO:0010038)|response to oxidative stress (GO:0006979)	nucleus (GO:0005634)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				ATCTTCATCCTCCAAAGTGCC	0.488																																						uc001cce.1																			0				endometrium(3)|kidney(5)|large_intestine(6)|liver(1)|lung(12)|ovary(2)|pancreas(1)|prostate(1)	31						c.(175-177)gAg>gGg		Homo sapiens metal-regulatory transcription factor 1 (MTF1), mRNA.							140.0	119.0	126.0					1																	38323155		2203	4300	6503	SO:0001583	missense	4520					nucleus	DNA binding|protein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|zinc ion binding	g.chr1:38323155T>C	BC014454	CCDS30676.1	1p33	2008-02-05			ENSG00000188786	ENSG00000188786			7428	protein-coding gene	gene with protein product		600172				8065932	Standard	NM_005955		Approved		uc001cce.1	Q14872	OTTHUMG00000004439	ENST00000373036.4:c.176A>G	1.37:g.38323155T>C	ENSP00000362127:p.Glu59Gly					MTF1_uc009vvj.1_5'UTR	p.E59G	NM_005955	NP_005946	Q14872	MTF1_HUMAN			1	317	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)	59					B2RAK6|Q96CB1	Missense_Mutation	SNP	ENST00000373036.4	37	c.176A>G	CCDS30676.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.752312	0.69533	.	.	ENSG00000188786	ENST00000373036	T	0.11930	2.73	5.62	5.62	0.85841	.	0.051094	0.85682	D	0.000000	T	0.13713	0.0332	L	0.36672	1.1	0.51233	D	0.999915	P	0.39665	0.682	B	0.36534	0.227	T	0.01757	-1.1280	10	0.87932	D	0	.	15.8229	0.78673	0.0:0.0:0.0:1.0	.	59	Q14872	MTF1_HUMAN	G	59	ENSP00000362127:E59G	ENSP00000362127:E59G	E	-	2	0	MTF1	38095742	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.396000	0.79891	2.126000	0.65437	0.528000	0.53228	GAG		0.488	MTF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012984.2	NM_005955	
CFAP57	149465	broad.mit.edu	37	1	43649424	43649424	+	Missense_Mutation	SNP	G	G	A	rs142914910		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr1:43649424G>A	ENST00000372492.4	+	4	961	c.637G>A	c.(637-639)Gtt>Att	p.V213I	WDR65_ENST00000528956.1_Missense_Mutation_p.V213I	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		213										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAAGATTGTCGTTGGCACTGA	0.502																																						uc021omk.1																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						c.(637-639)Gtt>Att		Homo sapiens WD repeat domain 65 (WDR65), transcript variant 5, mRNA.		G	ILE/VAL,ILE/VAL,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	136.0	127.0	130.0		637,637,637	5.2	0.5	1	dbSNP_134	130	0,8600		0,0,4300	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	29,29,29	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	benign,benign,benign	213/699,213/699,213/699	43649424	3,13003	2203	4300	6503	SO:0001583	missense	149465							g.chr1:43649424G>A																												ENST00000372492.4:c.637G>A	1.37:g.43649424G>A	ENSP00000361570:p.Val213Ile					EBNA1BP2_uc001cio.3_Intron|WDR65_uc010ojz.2_Missense_Mutation_p.V202I|WDR65_uc001ciq.2_Missense_Mutation_p.V213I|WDR65_uc001cip.2_Missense_Mutation_p.V213I	p.V213I	NM_001195831	NP_001182760	Q96MR6	WDR65_HUMAN			3	783	+	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)	213					A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37	c.637G>A		.	.	.	.	.	.	.	.	.	.	G	10.12	1.262669	0.23051	6.81E-4	0.0	ENSG00000243710	ENST00000372492;ENST00000528956	T;T	0.07021	4.89;3.23	6.06	5.16	0.70880	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat-like-containing domain (1);	0.177217	0.49916	N	0.000138	T	0.11239	0.0274	M	0.75264	2.295	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.15484	0.003;0.013	T	0.25047	-1.0143	10	0.20046	T	0.44	.	9.5532	0.39324	0.0691:0.0:0.7018:0.2291	.	213;213	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	I	213	ENSP00000361570:V213I;ENSP00000435310:V213I	ENSP00000361570:V213I	V	+	1	0	WDR65	43422011	0.988000	0.35896	0.546000	0.28166	0.630000	0.37929	3.062000	0.49971	1.574000	0.49760	0.650000	0.86243	GTT		0.502	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
RAD54L	8438	broad.mit.edu	37	1	46726266	46726266	+	Missense_Mutation	SNP	C	C	T	rs149141765		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr1:46726266C>T	ENST00000371975.4	+	6	1134	c.460C>T	c.(460-462)Cgg>Tgg	p.R154W	RAD54L_ENST00000442598.1_Missense_Mutation_p.R154W	NM_003579.3	NP_003570.2	Q92698	RAD54_HUMAN	RAD54-like (S. cerevisiae)	154					chromosome organization (GO:0051276)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.R154W(1)		breast(2)|cervix(1)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	25	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)		TAAGGTTTTGCGGCCTCATCA	0.537								Direct reversal of damage;Homologous recombination					C|||	1	0.000199681	0.0	0.0	5008	,	,		22956	0.001		0.0	False		,,,				2504	0.0					uc001cpl.2																			1	Substitution - Missense(1)	p.R154W(2)	cervix(1)	breast(2)|cervix(1)|kidney(3)|large_intestine(5)|liver(1)|lung(6)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	25						c.(460-462)Cgg>Tgg	Direct reversal of damage;Homologous recombination	Homo sapiens RAD54-like (S. cerevisiae) (RAD54L), transcript variant 1, mRNA.		C	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	139.0	128.0	132.0		460,460	3.8	1.0	1	dbSNP_134	132	0,8600		0,0,4300	no	missense,missense	RAD54L	NM_001142548.1,NM_003579.3	101,101	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging,probably-damaging	154/748,154/748	46726266	2,13004	2203	4300	6503	SO:0001583	missense	8438				meiosis	nucleus	ATP binding|DNA binding|helicase activity	g.chr1:46726266C>T	X97795	CCDS532.1	1p32	2008-02-05	2001-11-28		ENSG00000085999	ENSG00000085999			9826	protein-coding gene	gene with protein product		603615	"""RAD54 (S.cerevisiae)-like"""			8805304	Standard	NM_003579		Approved	hHR54, hRAD54, RAD54A	uc009vye.2	Q92698	OTTHUMG00000007772	ENST00000371975.4:c.460C>T	1.37:g.46726266C>T	ENSP00000361043:p.Arg154Trp					RAD54L_uc009vye.2_Missense_Mutation_p.R154W	p.R154W	NM_003579	NP_003570	Q92698	RAD54_HUMAN		KIRC - Kidney renal clear cell carcinoma(1967;0.000896)	5	1171	+	Acute lymphoblastic leukemia(166;0.155)	Breast(1374;0.0634)	154					Q5TE31|Q6IUY3	Missense_Mutation	SNP	ENST00000371975.4	37	c.460C>T	CCDS532.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.614125	0.66672	4.54E-4	0.0	ENSG00000085999	ENST00000442598;ENST00000371975	D;D	0.95205	-3.64;-3.64	5.75	3.8	0.43715	DEAD-like helicase (1);	0.000000	0.85682	D	0.000000	D	0.98327	0.9445	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98550	1.0636	10	0.87932	D	0	-18.6346	13.7348	0.62811	0.4359:0.5641:0.0:0.0	.	154	Q92698	RAD54_HUMAN	W	154	ENSP00000396113:R154W;ENSP00000361043:R154W	ENSP00000361043:R154W	R	+	1	2	RAD54L	46498853	0.999000	0.42202	0.996000	0.52242	0.998000	0.95712	1.055000	0.30467	0.698000	0.31739	0.655000	0.94253	CGG		0.537	RAD54L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021272.1	NM_003579	
LMX1A	4009	broad.mit.edu	37	1	165177351	165177351	+	Nonsense_Mutation	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr1:165177351G>A	ENST00000342310.3	-	7	1148	c.766C>T	c.(766-768)Cga>Tga	p.R256*	LMX1A_ENST00000489443.2_5'UTR|LMX1A_ENST00000367893.4_Nonsense_Mutation_p.R256*|LMX1A_ENST00000294816.2_Nonsense_Mutation_p.R256*|RP11-38C18.2_ENST00000457106.1_RNA	NM_177398.3	NP_796372.1	Q8TE12	LMX1A_HUMAN	LIM homeobox transcription factor 1, alpha	256	Gln-rich.				axon guidance (GO:0007411)|central nervous system neuron differentiation (GO:0021953)|cerebellum development (GO:0021549)|dentate gyrus development (GO:0021542)|dopaminergic neuron differentiation (GO:0071542)|midbrain development (GO:0030901)|negative regulation of neuron differentiation (GO:0045665)|regulation of cell growth (GO:0001558)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35	all_hematologic(923;0.248)					TGCTGCTGTCGCCTGGCCAGC	0.562																																						uc001gcz.2																			0				NS(2)|biliary_tract(1)|central_nervous_system(3)|cervix(2)|endometrium(4)|large_intestine(6)|lung(10)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(4)	35						c.(766-768)Cga>Tga		Homo sapiens LIM homeobox transcription factor 1, alpha (LMX1A), transcript variant 4, mRNA.							69.0	54.0	59.0					1																	165177351		2203	4300	6503	SO:0001587	stop_gained	4009					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr1:165177351G>A	AY078391	CCDS1247.1	1q24.1	2011-06-20			ENSG00000162761	ENSG00000162761		"""Homeoboxes / LIM class"""	6653	protein-coding gene	gene with protein product		600298		LMX1		7698771	Standard	NM_177398		Approved	LMX1.1	uc001gcz.2	Q8TE12	OTTHUMG00000034575	ENST00000342310.3:c.766C>T	1.37:g.165177351G>A	ENSP00000340226:p.Arg256*					LMX1A_uc021pdz.1_Nonsense_Mutation_p.R256*|LMX1A_uc021pdy.1_Nonsense_Mutation_p.R7*|LMX1A_uc001gcw.2_5'UTR	p.R256*	NM_001174069	NP_796372	Q8TE12	LMX1A_HUMAN			6	960	-	all_hematologic(923;0.248)		256			Gln-rich.		B3KXP6|Q0VDB5|Q5VWG4|Q8TE11	Nonsense_Mutation	SNP	ENST00000342310.3	37	c.766C>T	CCDS1247.1	.	.	.	.	.	.	.	.	.	.	G	38	7.181093	0.98118	.	.	ENSG00000162761	ENST00000342310;ENST00000294816;ENST00000367893	.	.	.	5.13	4.19	0.49359	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1.000000	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.8961	0.52658	0.0:0.0:0.6853:0.3147	.	.	.	.	X	256	.	ENSP00000294816:R256X	R	-	1	2	LMX1A	163443975	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.818000	0.39012	1.340000	0.45581	0.655000	0.94253	CGA		0.562	LMX1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083668.2	NM_177398	
AGAP12P	414224	broad.mit.edu	37	10	49218498	49218498	+	IGR	SNP	A	A	G			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr10:49218498A>G								FAM25C (10680 upstream) : RNA5SP315 (29977 downstream)																							GCTGGCCCAGAGACAGCTCAG	0.582																																						uc001jgd.3																			0											c.(1639-1641)tcT>tcC		Homo sapiens uncharacterized LOC399753 (LOC399753), non-coding RNA.																																				SO:0001628	intergenic_variant	414224							g.chr10:49218498A>G																													10.37:g.49218498A>G						DQ588224_uc001jge.1_5'Flank	p.S547S							7	1800	-									Silent	SNP		37	c.1641T>C																																																																																				0	0.582								
AGAP12P	414224	broad.mit.edu	37	10	49218553	49218553	+	IGR	SNP	T	T	C	rs77581903		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr10:49218553T>C								FAM25C (10735 upstream) : RNA5SP315 (29922 downstream)																							ATATTTGGAATGGATCCAGCG	0.567																																						uc001jgd.3																			0											c.(1585-1587)cAt>cGt		Homo sapiens uncharacterized LOC399753 (LOC399753), non-coding RNA.																																				SO:0001628	intergenic_variant	414224							g.chr10:49218553T>C																													10.37:g.49218553T>C						DQ588224_uc001jge.1_5'Flank	p.H529R							7	1745	-									Missense_Mutation	SNP		37	c.1586A>G																																																																																				0	0.567								
KIF20B	9585	broad.mit.edu	37	10	91498196	91498196	+	Missense_Mutation	SNP	A	A	G			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr10:91498196A>G	ENST00000371728.3	+	20	3663	c.3598A>G	c.(3598-3600)Aat>Gat	p.N1200D	KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000416354.1_Missense_Mutation_p.N1230D|KIF20B_ENST00000394289.2_Missense_Mutation_p.N1200D|KIF20B_ENST00000260753.4_Missense_Mutation_p.N1160D	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1200					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|microtubule-based movement (GO:0007018)|mitotic nuclear division (GO:0007067)|neural tube closure (GO:0001843)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization (GO:0070201)|regulation of mitosis (GO:0007088)|regulation of neuron migration (GO:2001222)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|WW domain binding (GO:0050699)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						GCTAGAAAGAAATTTGAAGGA	0.318																																						uc001kgs.1																			0				endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(20)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	58						c.(3598-3600)Aat>Gat		Homo sapiens kinesin family member 20B (KIF20B), mRNA.							51.0	56.0	54.0					10																	91498196		2199	4294	6493	SO:0001583	missense	9585				cell cycle arrest|cell division|microtubule-based movement|mitosis|regulation of mitosis	centrosome|microtubule|nucleolus|nucleoplasm|spindle	ATP binding|ATPase activity|microtubule motor activity|WW domain binding	g.chr10:91498196A>G	L16782	CCDS7407.1, CCDS60590.1	10q23.31	2009-08-06	2008-07-31	2008-07-31	ENSG00000138182	ENSG00000138182			7212	protein-coding gene	gene with protein product	"""cancer/testis antigen 90"""	605498	"""M-phase phosphoprotein 1"""	MPHOSPH1		8885239, 8290587, 11470801	Standard	NM_016195		Approved	MPP1, KRMP1, CT90	uc001kgr.1	Q96Q89	OTTHUMG00000018725	ENST00000371728.3:c.3598A>G	10.37:g.91498196A>G	ENSP00000360793:p.Asn1200Asp					KIF20B_uc001kgr.1_Missense_Mutation_p.N1160D|KIF20B_uc001kgt.1_Missense_Mutation_p.N411D|KIF20B_uc009xtw.1_Non-coding_Transcript	p.N1200D	NM_016195	NP_057279	Q96Q89	KI20B_HUMAN			19	3670	+			1200					A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37	c.3598A>G		.	.	.	.	.	.	.	.	.	.	A	8.970	0.972640	0.18736	.	.	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000394289;ENST00000371728	T;T;T;T	0.69175	-0.29;-0.3;-0.38;-0.31	5.82	3.36	0.38483	.	0.494492	0.18603	N	0.136395	T	0.57917	0.2086	M	0.62723	1.935	0.09310	N	1	B;B	0.14438	0.006;0.01	B;B	0.12156	0.005;0.007	T	0.46048	-0.9219	10	0.27082	T	0.32	-9.7986	6.1432	0.20271	0.6782:0.1326:0.1892:0.0	.	1200;1160	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	D	1160;1230;1200;1200	ENSP00000260753:N1160D;ENSP00000411545:N1230D;ENSP00000377830:N1200D;ENSP00000360793:N1200D	ENSP00000260753:N1160D	N	+	1	0	KIF20B	91488176	0.021000	0.18746	0.007000	0.13788	0.135000	0.20990	1.411000	0.34702	1.025000	0.39708	0.383000	0.25322	AAT		0.318	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
ZNF518A	9849	broad.mit.edu	37	10	97916083	97916083	+	RNA	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr10:97916083C>T	ENST00000534948.1	+	0	861							Q6AHZ1	Z518A_HUMAN	zinc finger protein 518A						transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24		Colorectal(252;0.0815)		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)		TTAAATCATGCCATCTGAACA	0.308																																						uc001klp.3																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	24						c.(4-6)Cca>Tca		Homo sapiens zinc finger protein 518A (ZNF518A), mRNA.							52.0	55.0	54.0					10																	97916083		1788	4056	5844			9849				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr10:97916083C>T	AB002333	CCDS73170.1	10q23.33	2012-08-08	2007-12-07	2007-12-07	ENSG00000177853	ENSG00000177853		"""Zinc fingers, C2H2-type"""	29009	protein-coding gene	gene with protein product			"""zinc finger protein 518"""	ZNF518		9205841	Standard	NM_014803		Approved	KIAA0335	uc001klp.3	Q6AHZ1	OTTHUMG00000018828		10.37:g.97916083C>T						ZNF518A_uc001klo.1_Intron|ZNF518A_uc001klq.3_Missense_Mutation_p.P2S|ZNF518A_uc001klr.3_Missense_Mutation_p.P2S	p.P2S	NM_014803	NP_055618	Q6AHZ1	Z518A_HUMAN		Epithelial(162;4.23e-08)|all cancers(201;1.85e-06)	5	861	+		Colorectal(252;0.0815)	2					A0PJI5|O15044|Q32MP4	Missense_Mutation	SNP	ENST00000534948.1	37	c.4C>T																																																																																					0.308	ZNF518A-202	KNOWN	basic	processed_transcript	processed_transcript		NM_014803	
HEPHL1	341208	broad.mit.edu	37	11	93826783	93826783	+	Missense_Mutation	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr11:93826783G>A	ENST00000315765.9	+	13	2419	c.2411G>A	c.(2410-2412)cGa>cAa	p.R804Q		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	804	Plastocyanin-like 5.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				CGACCACCACGAGAGGAGCAC	0.483																																						uc001pep.2																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61						c.(2410-2412)cGa>cAa		Homo sapiens hephaestin-like 1 (HEPHL1), mRNA.							112.0	109.0	110.0					11																	93826783		1947	4150	6097	SO:0001583	missense	341208				copper ion transport	integral to membrane	copper ion binding|oxidoreductase activity	g.chr11:93826783G>A	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2411G>A	11.37:g.93826783G>A	ENSP00000313699:p.Arg804Gln					AF086184_uc001pen.1_Intron	p.R804Q	NM_001098672	NP_001092142	Q6MZM0	HPHL1_HUMAN			12	2568	+		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)	804			Plastocyanin-like 5.		Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	c.2411G>A	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	G	13.14	2.149052	0.37923	.	.	ENSG00000181333	ENST00000315765	D	0.98914	-5.23	5.68	2.8	0.32819	Cupredoxin (2);	0.452533	0.25347	N	0.031321	D	0.94601	0.8260	N	0.21617	0.685	0.20074	N	0.999933	B	0.13145	0.007	B	0.06405	0.002	D	0.86715	0.1938	10	0.19590	T	0.45	.	7.5294	0.27674	0.471:0.0:0.529:0.0	.	804	Q6MZM0	HPHL1_HUMAN	Q	804	ENSP00000313699:R804Q	ENSP00000313699:R804Q	R	+	2	0	HEPHL1	93466431	0.000000	0.05858	0.691000	0.30163	0.958000	0.62258	0.362000	0.20284	0.338000	0.23692	0.549000	0.68633	CGA		0.483	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
PGR	5241	broad.mit.edu	37	11	100920711	100920711	+	Missense_Mutation	SNP	C	C	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr11:100920711C>A	ENST00000325455.5	-	6	3890	c.2437G>T	c.(2437-2439)Gtt>Ttt	p.V813F	PGR_ENST00000534013.1_Missense_Mutation_p.V219F|PGR_ENST00000263463.5_Missense_Mutation_p.V711F	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	813	Steroid-binding.				cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|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 binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	TCTTGGCTAACTTGAAGCTTG	0.368																																					Pancreas(124;2271 2354 21954 22882)	uc001pgh.2																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36						c.(2437-2439)Gtt>Ttt		Homo sapiens progesterone receptor (PGR), transcript variant 2, mRNA.	Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol Diacetate(DB00823)|Etonogestrel(DB00294)|Levonorgestrel(DB00367)|Medroxyprogesterone(DB00603)|Megestrol(DB00351)|Mifepristone(DB00834)|Norethindrone(DB00717)|Norgestimate(DB00957)|Norgestrel(DB00506)|Progesterone(DB00396)						97.0	91.0	93.0					11																	100920711		2203	4300	6503	SO:0001583	missense	5241				cell-cell signaling|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor	cytoplasm|nucleoplasm	enzyme binding|receptor binding|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|zinc ion binding	g.chr11:100920711C>A	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.2437G>T	11.37:g.100920711C>A	ENSP00000325120:p.Val813Phe					PGR_uc001pgg.2_Missense_Mutation_p.V194F|PGR_uc001pgi.2_Missense_Mutation_p.V711F|PGR_uc009yww.1_Intron|PGR_uc001pgj.2_Non-coding_Transcript|PGR_uc009ywx.1_Non-coding_Transcript	p.V813F	NM_000926	NP_000917	P06401	PRGR_HUMAN		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	5	3180	-		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)	813			Steroid-binding.		A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	c.2437G>T	CCDS8310.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.921177	0.52653	.	.	ENSG00000082175	ENST00000325455;ENST00000534013;ENST00000263463	T;T;D	0.99812	1.19;1.19;-6.88	5.16	2.25	0.28309	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.202566	0.41938	D	0.000794	D	0.99227	0.9731	M	0.64404	1.975	0.49051	D	0.999742	P;D;P	0.52996	0.947;0.957;0.463	P;P;B	0.49451	0.597;0.611;0.158	D	0.97965	1.0340	10	0.87932	D	0	.	8.4736	0.32999	0.0:0.7326:0.1273:0.1401	.	711;813;194	Q8TDS3;P06401;A7LQ08	.;PRGR_HUMAN;.	F	813;219;711	ENSP00000325120:V813F;ENSP00000436561:V219F;ENSP00000263463:V711F	ENSP00000263463:V711F	V	-	1	0	PGR	100425921	1.000000	0.71417	0.909000	0.35828	0.989000	0.77384	3.941000	0.56607	0.286000	0.22352	0.655000	0.94253	GTT		0.368	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
NTF3	4908	broad.mit.edu	37	12	5603770	5603770	+	Silent	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr12:5603770G>A	ENST00000331010.6	+	1	473	c.390G>A	c.(388-390)gcG>gcA	p.A130A	NTF3_ENST00000423158.3_Silent_p.A143A|NTF3_ENST00000535299.1_Intron	NM_002527.4	NP_002518.1	P20783	NTF3_HUMAN	neurotrophin 3	130					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell-cell signaling (GO:0007267)|enteric nervous system development (GO:0048484)|epidermis development (GO:0008544)|glial cell fate determination (GO:0007403)|induction of positive chemotaxis (GO:0050930)|mechanoreceptor differentiation (GO:0042490)|myelination (GO:0042552)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuromuscular synaptic transmission (GO:0007274)|peripheral nervous system development (GO:0007422)|positive chemotaxis (GO:0050918)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of glial cell differentiation (GO:0045687)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of receptor internalization (GO:0002092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of synaptic transmission (GO:0050804)|signal transduction (GO:0007165)|smooth muscle cell differentiation (GO:0051145)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasmic membrane-bounded vesicle (GO:0016023)|extracellular region (GO:0005576)	chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|receptor binding (GO:0005102)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						CCGTGGTGGCGAACAGAACAT	0.602																																					GBM(194;1104 2182 8339 9578 18493)	uc001qnl.4																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(3)|upper_aerodigestive_tract(1)	22						c.(388-390)gcG>gcA		Homo sapiens neurotrophin 3 (NTF3), transcript variant 2, mRNA.							83.0	79.0	80.0					12																	5603770		2203	4300	6503	SO:0001819	synonymous_variant	4908				signal transduction	extracellular region	growth factor activity|neurotrophin receptor binding	g.chr12:5603770G>A		CCDS8538.1, CCDS44806.1	12p13	2014-01-30			ENSG00000185652	ENSG00000185652		"""Endogenous ligands"""	8023	protein-coding gene	gene with protein product		162660				1889806	Standard	NM_002527		Approved	NGF2	uc001qnk.4	P20783	OTTHUMG00000168649	ENST00000331010.6:c.390G>A	12.37:g.5603770G>A						NTF3_uc001qnk.4_Silent_p.A143A	p.A130A	NM_002527	NP_002518	P20783	NTF3_HUMAN			0	473	+			130					B7Z1T5|Q6FH50	Silent	SNP	ENST00000331010.6	37	c.390G>A	CCDS8538.1																																																																																				0.602	NTF3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400486.1		
C1S	716	broad.mit.edu	37	12	7177641	7177641	+	Missense_Mutation	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr12:7177641G>A	ENST00000406697.1	+	15	2381	c.1753G>A	c.(1753-1755)Gca>Aca	p.A585T	C1S_ENST00000360817.5_Missense_Mutation_p.A585T|C1S_ENST00000402681.3_Missense_Mutation_p.A418T|C1S_ENST00000328916.3_Missense_Mutation_p.A585T			P09871	C1S_HUMAN	complement component 1, s subcomponent	585	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	CCTCAAGGCGGCAAGGTTACC	0.512																																					GBM(156;750 1943 12971 24779 31015)	uc001qsj.3																			0				breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33						c.(1753-1755)Gca>Aca		Homo sapiens complement component 1, s subcomponent (C1S), transcript variant 1, mRNA.	Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Immune globulin(DB00028)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)						70.0	69.0	70.0					12																	7177641		2203	4300	6503	SO:0001583	missense	716				complement activation, classical pathway|innate immune response|proteolysis	extracellular region	calcium ion binding|serine-type endopeptidase activity	g.chr12:7177641G>A		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.1753G>A	12.37:g.7177641G>A	ENSP00000385035:p.Ala585Thr					C1S_uc001qsk.3_Missense_Mutation_p.A585T|C1S_uc001qsl.3_Missense_Mutation_p.A585T|C1S_uc009zfr.3_Missense_Mutation_p.A418T|C1S_uc009zfs.3_Non-coding_Transcript	p.A585T	NM_201442	NP_958850	P09871	C1S_HUMAN			14	2472	+			585			Peptidase S1.		D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	c.1753G>A	CCDS31735.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.413703	0.83449	.	.	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000402681	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.01	4.1	0.47936	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.42420	D	0.000716	T	0.77598	0.4154	N	0.21508	0.67	0.47441	D	0.999428	P	0.52577	0.954	P	0.60173	0.87	T	0.78991	-0.1985	10	0.52906	T	0.07	.	13.9749	0.64265	0.0746:0.0:0.9254:0.0	.	585	P09871	C1S_HUMAN	T	585;585;585;579;418	ENSP00000385035:A585T;ENSP00000328173:A585T;ENSP00000354057:A585T;ENSP00000384171:A418T	ENSP00000328173:A585T	A	+	1	0	C1S	7047902	1.000000	0.71417	0.135000	0.22099	0.049000	0.14656	6.912000	0.75753	2.596000	0.87737	0.561000	0.74099	GCA		0.512	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
SPPL2A	84888	broad.mit.edu	37	15	51041869	51041869	+	Silent	SNP	A	A	G	rs536055633		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr15:51041869A>G	ENST00000261854.5	-	2	415	c.141T>C	c.(139-141)ccT>ccC	p.P47P	RP11-507J18.2_ENST00000558317.1_RNA	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	47					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		CTGTCCAATAAGGGTTATAAA	0.418													A|||	1	0.000199681	0.0008	0.0	5008	,	,		20865	0.0		0.0	False		,,,				2504	0.0				Melanoma(50;790 1209 4069 22965 33125)	uc001zyv.3																			0				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15						c.(139-141)ccT>ccC		Homo sapiens signal peptide peptidase-like 2A (SPPL2A), mRNA.							151.0	146.0	148.0					15																	51041869		2196	4294	6490	SO:0001819	synonymous_variant	84888					integral to membrane	aspartic-type endopeptidase activity	g.chr15:51041869A>G		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.141T>C	15.37:g.51041869A>G							p.P47P	NM_032802	NP_116191	Q8TCT8	PSL2_HUMAN		all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)	1	321	-			47					B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	c.141T>C	CCDS10138.1																																																																																				0.418	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
ACAP1	9744	broad.mit.edu	37	17	7250193	7250193	+	Missense_Mutation	SNP	C	C	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr17:7250193C>A	ENST00000158762.3	+	13	1280	c.1074C>A	c.(1072-1074)agC>agA	p.S358R		NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	358	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						TGCAGAGCAGCATTGCTTCTG	0.637																																						uc002ggd.2																			0				NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						c.(1072-1074)agC>agA		Homo sapiens ArfGAP with coiled-coil, ankyrin repeat and PH domains 1 (ACAP1), mRNA.							84.0	80.0	82.0					17																	7250193		2203	4300	6503	SO:0001583	missense	9744				intracellular signal transduction|lipid metabolic process|protein transport|regulation of ARF GTPase activity		ARF GTPase activator activity|phospholipase C activity|protein binding|zinc ion binding	g.chr17:7250193C>A	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.1074C>A	17.37:g.7250193C>A	ENSP00000158762:p.Ser358Arg						p.S358R	NM_014716	NP_055531	Q15027	ACAP1_HUMAN			12	1280	+			358			PH.|Required for formation of endosomal tubules when overexpressed with PIP5K1C.		Q53XN9	Missense_Mutation	SNP	ENST00000158762.3	37	c.1074C>A	CCDS11101.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266624	0.80358	.	.	ENSG00000072818	ENST00000158762	T	0.76186	-1.0	4.6	4.6	0.57074	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.212831	0.53938	D	0.000058	T	0.82135	0.4971	M	0.86178	2.8	0.80722	D	1	P	0.35107	0.484	P	0.44623	0.455	D	0.84756	0.0759	10	0.62326	D	0.03	.	14.9371	0.70964	0.0:1.0:0.0:0.0	.	358	Q15027	ACAP1_HUMAN	R	358	ENSP00000158762:S358R	ENSP00000158762:S358R	S	+	3	2	ACAP1	7190917	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	5.459000	0.66685	2.394000	0.81467	0.448000	0.29417	AGC		0.637	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
TNS4	84951	broad.mit.edu	37	17	38635988	38635988	+	Silent	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr17:38635988C>T	ENST00000254051.6	-	10	2006	c.1848G>A	c.(1846-1848)acG>acA	p.T616T		NM_032865.5	NP_116254.4	Q8IZW8	TENS4_HUMAN	tensin 4	616	Phosphatase tensin-type.				apoptotic process (GO:0006915)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(5;5.91e-05)			CCACGGTGGGCGTGGGGAGGA	0.617																																						uc010cxb.3																			0		p.P615S(1)		NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	30						c.(1846-1848)acG>acA		Homo sapiens tensin 4 (TNS4), mRNA.							129.0	94.0	106.0					17																	38635988		2203	4300	6503	SO:0001819	synonymous_variant	84951				apoptosis|protein localization	cytoplasm|cytoskeleton|focal adhesion	actin binding	g.chr17:38635988C>T	AF417488	CCDS11368.1	17q21.2	2013-02-14			ENSG00000131746	ENSG00000131746		"""SH2 domain containing"""	24352	protein-coding gene	gene with protein product	"""C terminal tensin like"""	608385				12154022, 12711115	Standard	NM_032865		Approved	CTEN	uc010cxb.3	Q8IZW8	OTTHUMG00000133330	ENST00000254051.6:c.1848G>A	17.37:g.38635988C>T						TNS4_uc002huu.4_Intron	p.T616T	NM_032865	NP_116254	Q8IZW8	TENS4_HUMAN	STAD - Stomach adenocarcinoma(5;5.91e-05)		9	2012	-		Breast(137;0.000496)	616			Phosphatase tensin-type.		A6NMJ7|Q71RB7|Q8WV64|Q96JV4	Silent	SNP	ENST00000254051.6	37	c.1848G>A	CCDS11368.1																																																																																				0.617	TNS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257154.3	NM_032865	
KRTAP4-11	653240	broad.mit.edu	37	17	39274446	39274446	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr17:39274446C>T	ENST00000391413.2	-	1	160	c.122G>A	c.(121-123)cGc>cAc	p.R41H		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	41	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			GCAGCTGGGGCGACAGTAGGT	0.667																																						uc002hvz.3																			0				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(121-123)cGc>cAc		Homo sapiens keratin associated protein 4-11 (KRTAP4-11), mRNA.							19.0	22.0	21.0					17																	39274446		691	1591	2282	SO:0001583	missense	653240					keratin filament		g.chr17:39274446C>T	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.122G>A	17.37:g.39274446C>T	ENSP00000375232:p.Arg41His						p.R41H	NM_033059	NP_149048	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		0	161	-		Breast(137;0.000496)	41			27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.122G>A	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	12.23	1.874625	0.33069	.	.	ENSG00000212721	ENST00000391413	T	0.01495	4.83	3.8	-5.77	0.02369	.	1.617350	0.04704	U	0.416336	T	0.03348	0.0097	M	0.85041	2.73	0.09310	N	1	B	0.15141	0.012	B	0.10450	0.005	T	0.47837	-0.9086	10	0.46703	T	0.11	.	5.2821	0.15680	0.6068:0.2018:0.0:0.1915	.	41	Q9BYQ6	KR411_HUMAN	H	41	ENSP00000375232:R41H	ENSP00000375232:R41H	R	-	2	0	KRTAP4-11	36527972	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	-0.653000	0.05360	-0.527000	0.06374	-0.192000	0.12808	CGC		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
ARL4D	379	broad.mit.edu	37	17	41477126	41477126	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr17:41477126C>T	ENST00000320033.4	+	2	233	c.26C>T	c.(25-27)gCg>gTg	p.A9V		NM_001661.3	NP_001652.2	P49703	ARL4D_HUMAN	ADP-ribosylation factor-like 4D	9					GTP catabolic process (GO:0006184)|protein secretion (GO:0009306)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.155)		ACTGAGATGGCGCCCACTGCC	0.572																																						uc002idt.3																			0				endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8						c.(25-27)gCg>gTg		Homo sapiens ADP-ribosylation factor-like 4D (ARL4D), mRNA.							70.0	68.0	68.0					17																	41477126		2203	4300	6503	SO:0001583	missense	379				protein secretion|small GTPase mediated signal transduction	cytoplasm|nucleolus|plasma membrane	GTP binding|GTPase activity|protein binding	g.chr17:41477126C>T	AB060692	CCDS11463.1	17q21.31	2014-05-09	2005-11-03	2005-11-03	ENSG00000175906	ENSG00000175906		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	656	protein-coding gene	gene with protein product		600732	"""ADP-ribosylation factor 4-like"""	ARF4L		7590735	Standard	NM_001661		Approved		uc002idt.3	P49703		ENST00000320033.4:c.26C>T	17.37:g.41477126C>T	ENSP00000322628:p.Ala9Val					ARL4D_uc021txy.1_Missense_Mutation_p.A9V	p.A9V	NM_001661	NP_001652	P49703	ARL4D_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.155)	1	207	+		Breast(137;0.00908)	9					B2RC59|D3DX43	Missense_Mutation	SNP	ENST00000320033.4	37	c.26C>T	CCDS11463.1	.	.	.	.	.	.	.	.	.	.	C	15.64	2.892269	0.52014	.	.	ENSG00000175906	ENST00000320033	T	0.75367	-0.93	4.82	4.82	0.62117	.	0.137736	0.48286	D	0.000187	T	0.62684	0.2448	L	0.52266	1.64	0.58432	D	0.999994	P	0.47253	0.892	B	0.29663	0.105	T	0.67546	-0.5643	10	0.35671	T	0.21	-10.645	15.2659	0.73660	0.0:1.0:0.0:0.0	.	9	P49703	ARL4D_HUMAN	V	9	ENSP00000322628:A9V	ENSP00000322628:A9V	A	+	2	0	ARL4D	38832652	1.000000	0.71417	1.000000	0.80357	0.005000	0.04900	5.008000	0.63991	2.643000	0.89663	0.563000	0.77884	GCG		0.572	ARL4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453481.2	NM_001661	
TUBB4A	10382	broad.mit.edu	37	19	6495656	6495656	+	Missense_Mutation	SNP	G	G	A	rs552079378		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr19:6495656G>A	ENST00000264071.2	-	4	1225	c.854C>T	c.(853-855)aCg>aTg	p.T285M	TUBB4A_ENST00000540257.1_Missense_Mutation_p.T285M|CTD-2396E7.10_ENST00000596027.1_RNA|CTD-2396E7.9_ENST00000599292.1_RNA			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	285					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										CTCGGGCACCGTCAGGGCCCG	0.672																																						uc002mfg.1																			0											c.(853-855)aCg>aTg		Homo sapiens tubulin, beta 4A class IVa (TUBB4A), mRNA.							46.0	47.0	47.0					19																	6495656		2203	4298	6501	SO:0001583	missense	10382				'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity	g.chr19:6495656G>A	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"""Tubulins"""	20774	protein-coding gene	gene with protein product	"""class IVa beta-tubulin"""	602662	"""tubulin, beta 4"", ""tubulin, beta 4 class IVa"", ""dystonia 4, torsion (autosomal dominant)"""	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.854C>T	19.37:g.6495656G>A	ENSP00000264071:p.Thr285Met					TUBB4A_uc002mff.1_Missense_Mutation_p.T213M|JA429441_uc021unq.1_5'Flank	p.T285M	NM_006087	NP_006078	P04350	TBB4_HUMAN			3	961	-			285					B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	37	c.854C>T	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	G	9.991	1.230769	0.22542	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	D;D	0.86030	-2.06;-2.06	3.71	3.71	0.42584	.	0.075274	0.49305	D	0.000159	D	0.93135	0.7814	M	0.93016	3.37	0.48452	D	0.999651	D	0.71674	0.998	D	0.64776	0.929	D	0.94831	0.7996	10	0.87932	D	0	.	14.2842	0.66235	0.0:0.0:1.0:0.0	.	285	P04350	TBB4A_HUMAN	M	285;285;203	ENSP00000264071:T285M;ENSP00000443590:T285M	ENSP00000264071:T285M	T	-	2	0	TUBB4	6446656	1.000000	0.71417	0.704000	0.30370	0.032000	0.12392	7.723000	0.84788	1.639000	0.50556	0.485000	0.47835	ACG		0.672	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087	
VAV1	7409	broad.mit.edu	37	19	6843162	6843162	+	Missense_Mutation	SNP	T	T	C			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr19:6843162T>C	ENST00000602142.1	+	22	2079	c.1997T>C	c.(1996-1998)cTg>cCg	p.L666P	VAV1_ENST00000596764.1_Missense_Mutation_p.L634P|VAV1_ENST00000539284.1_Missense_Mutation_p.L569P|VAV1_ENST00000304076.2_Missense_Mutation_p.L644P|VAV1_ENST00000599806.1_Missense_Mutation_p.L611P	NM_005428.3	NP_005419.2	P15498	VAV_HUMAN	vav 1 guanine nucleotide exchange factor	666					apoptotic signaling pathway (GO:0097190)|blood coagulation (GO:0007596)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|reactive oxygen species metabolic process (GO:0072593)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						CCTCAGGACCTGTCTGTTCAT	0.488																																						uc002mfu.1																			0				biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(16)|lung(18)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	62						c.(1996-1998)cTg>cCg		Homo sapiens vav 1 guanine nucleotide exchange factor (VAV1), mRNA.							223.0	218.0	220.0					19																	6843162		2203	4300	6503	SO:0001583	missense	7409				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|platelet activation|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|T cell costimulation	cytosol|plasma membrane	metal ion binding|protein binding|sequence-specific DNA binding transcription factor activity	g.chr19:6843162T>C		CCDS12174.1, CCDS59341.1, CCDS59342.1	19p13.2	2013-02-14	2007-07-25			ENSG00000141968		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12657	protein-coding gene	gene with protein product		164875	"""vav 1 oncogene"""	VAV		9438848	Standard	NM_005428		Approved		uc010xjh.2	P15498		ENST00000602142.1:c.1997T>C	19.37:g.6843162T>C	ENSP00000472929:p.Leu666Pro					VAV1_uc010xjh.1_Missense_Mutation_p.L634P|VAV1_uc010dva.1_Missense_Mutation_p.L644P|VAV1_uc002mfv.1_Missense_Mutation_p.L611P	p.L666P	NM_005428	NP_005419	P15498	VAV_HUMAN			21	2094	+			666					B4DVK9|M0QXX6|Q15860	Missense_Mutation	SNP	ENST00000602142.1	37	c.1997T>C	CCDS12174.1	.	.	.	.	.	.	.	.	.	.	T	16.72	3.200638	0.58126	.	.	ENSG00000141968	ENST00000304076;ENST00000539284	T	0.70164	-0.46	4.16	4.16	0.48862	Src homology-3 domain (1);SH2 motif (1);	0.086319	0.46145	D	0.000303	T	0.76090	0.3939	L	0.58969	1.84	0.80722	D	1	D;D;B;D	0.64830	0.994;0.992;0.397;0.976	D;D;B;P	0.69479	0.964;0.942;0.366;0.905	T	0.77822	-0.2445	10	0.66056	D	0.02	.	11.1389	0.48392	0.0:0.0:0.0:1.0	.	569;666;611;666	F5H5P4;B2R8B5;Q96D37;P15498	.;.;.;VAV_HUMAN	P	666;569	ENSP00000443242:L569P	ENSP00000302269:L666P	L	+	2	0	VAV1	6794162	1.000000	0.71417	1.000000	0.80357	0.905000	0.53344	4.947000	0.63583	1.512000	0.48834	0.496000	0.49642	CTG		0.488	VAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458475.1		
ZNF701	55762	broad.mit.edu	37	19	53086225	53086228	+	Frame_Shift_Del	DEL	AAGG	AAGG	-			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr19:53086225_53086228delAAGG	ENST00000540331.1	+	5	1336_1339	c.1111_1114delAAGG	c.(1111-1116)aaggttfs	p.KV371fs	CTD-3099C6.7_ENST00000599222.1_RNA|ZNF701_ENST00000301093.2_Frame_Shift_Del_p.KV371fs|ZNF701_ENST00000391785.3_Frame_Shift_Del_p.KV305fs	NM_001172655.1	NP_001166126.1	Q9NV72	ZN701_HUMAN	zinc finger protein 701	371					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14				OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)		TGAATGTGGCAAGGTTTTTAATCA	0.387																																					NSCLC(89;451 1475 9611 20673 52284)	uc010ydn.2																			0				endometrium(5)|kidney(1)|large_intestine(2)|lung(6)	14						c.(1111-1116)aaggttfs		Homo sapiens zinc finger protein 701 (ZNF701), transcript variant 2, mRNA.																																				SO:0001589	frameshift_variant	55762				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:53086225_53086228delAAGG	AK001753	CCDS33092.1, CCDS54311.1	19q13.41	2013-01-08				ENSG00000167562		"""Zinc fingers, C2H2-type"", ""-"""	25597	protein-coding gene	gene with protein product							Standard	NM_018260		Approved	FLJ10891	uc021uyw.1	Q9NV72		ENST00000540331.1:c.1111_1114delAAGG	19.37:g.53086225_53086228delAAGG	ENSP00000444339:p.Lys371fs					ZNF701_uc002pzs.2_Frame_Shift_Del_p.K305fs|ZNF701_uc021uyw.1_Frame_Shift_Del_p.K371fs	p.K371fs	NM_018260	NP_060730	Q9NV72	ZN701_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.0105)|GBM - Glioblastoma multiforme(134;0.0402)	4	1174_1177	+			305					A2RRM8|B9EGF2|F5GZM6|Q66K42	Frame_Shift_Del	DEL	ENST00000540331.1	37	c.1111_1114delAAGG	CCDS54311.1																																																																																				0.387	ZNF701-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463467.1	NM_018260	
CDC42EP3	10602	broad.mit.edu	37	2	37873026	37873026	+	Missense_Mutation	SNP	C	C	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr2:37873026C>A	ENST00000295324.3	-	2	1705	c.705G>T	c.(703-705)caG>caT	p.Q235H	AC006369.2_ENST00000419425.1_RNA	NM_001270436.1|NM_001270437.1|NM_001270438.1|NM_006449.4	NP_001257365.1|NP_001257366.1|NP_001257367.1|NP_006440.2	Q9UKI2	BORG2_HUMAN	CDC42 effector protein (Rho GTPase binding) 3	235					regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|membrane (GO:0016020)	cytoskeletal regulatory protein binding (GO:0005519)			endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|prostate(1)	11		all_hematologic(82;0.172)				CAAGATCAAGCTGCAGGGAGA	0.463																																						uc021vfz.1																			0				endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|prostate(1)	11						c.(703-705)caG>caT		Homo sapiens CDC42 effector protein (Rho GTPase binding) 3 (CDC42EP3), mRNA.							69.0	76.0	73.0					2																	37873026		2203	4300	6503	SO:0001583	missense	10602				regulation of cell shape|signal transduction	actin cytoskeleton|cytoplasm|endomembrane system|membrane	cytoskeletal regulatory protein binding	g.chr2:37873026C>A	AF094521	CCDS1791.1	2p21	2008-05-21			ENSG00000163171	ENSG00000163171			16943	protein-coding gene	gene with protein product		606133				9535835, 11035016	Standard	NM_001270436		Approved	CEP3, UB1, BORG2	uc031rnz.1	Q9UKI2	OTTHUMG00000100971	ENST00000295324.3:c.705G>T	2.37:g.37873026C>A	ENSP00000295324:p.Gln235His					CDC42EP3_uc002rqi.1_Missense_Mutation_p.Q235H	p.Q235H	NM_006449	NP_006440	Q9UKI2	BORG2_HUMAN			0	705	-		all_hematologic(82;0.172)	235					B2R8S0|O95353|Q9UQJ0	Missense_Mutation	SNP	ENST00000295324.3	37	c.705G>T	CCDS1791.1	.	.	.	.	.	.	.	.	.	.	C	11.39	1.625712	0.28889	.	.	ENSG00000163171	ENST00000295324	T	0.27104	1.69	5.91	5.91	0.95273	.	0.051332	0.85682	D	0.000000	T	0.20941	0.0504	N	0.16368	0.405	0.46044	D	0.998839	D	0.61080	0.989	P	0.53912	0.737	T	0.06058	-1.0848	10	0.02654	T	1	.	11.1023	0.48182	0.0:0.9171:0.0:0.0829	.	235	Q9UKI2	BORG2_HUMAN	H	235	ENSP00000295324:Q235H	ENSP00000295324:Q235H	Q	-	3	2	CDC42EP3	37726530	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	1.165000	0.31822	2.793000	0.96121	0.655000	0.94253	CAG		0.463	CDC42EP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218581.3	NM_006449	
LRP1B	53353	broad.mit.edu	37	2	141130669	141130669	+	Missense_Mutation	SNP	C	C	T	rs145915063		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr2:141130669C>T	ENST00000389484.3	-	69	11647	c.10676G>A	c.(10675-10677)cGg>cAg	p.R3559Q		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	3559	LDL-receptor class A 27. {ECO:0000255|PROSITE-ProRule:PRU00124}.				protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ATTGGAACACCGGAACTGATC	0.368										TSP Lung(27;0.18)			c|||	1	0.000199681	0.0	0.0014	5008	,	,		16910	0.0		0.0	False		,,,				2504	0.0				Colon(99;50 2074 2507 20106)	uc002tvj.1																			0				NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606						c.(10675-10677)cGg>cAg		Homo sapiens low density lipoprotein receptor-related protein 1B (LRP1B), mRNA.		C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	160.0	150.0	153.0		10676	3.2	1.0	2	dbSNP_134	153	2,8598	1.2+/-3.3	0,2,4298	yes	missense	LRP1B	NM_018557.2	43	0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384	benign	3559/4600	141130669	5,13001	2203	4300	6503	SO:0001583	missense	53353				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	g.chr2:141130669C>T	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.10676G>A	2.37:g.141130669C>T	ENSP00000374135:p.Arg3559Gln	TSP Lung(27;0.18)					p.R3559Q	NM_018557	NP_061027	Q9NZR2	LRP1B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)	68	11648	-		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)	3559			LDL-receptor class A 27.		Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	c.10676G>A	CCDS2182.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	c	5.199	0.222237	0.09863	6.81E-4	2.33E-4	ENSG00000168702	ENST00000389484;ENST00000544579	T	0.50277	0.75	5.54	3.17	0.36434	.	0.163089	0.41712	N	0.000833	T	0.24509	0.0594	N	0.10945	0.07	0.24874	N	0.992266	B	0.02656	0.0	B	0.01281	0.0	T	0.18935	-1.0321	10	0.12766	T	0.61	.	9.9126	0.41415	0.0:0.1385:0.0:0.8615	.	3559	Q9NZR2	LRP1B_HUMAN	Q	3559;3497	ENSP00000374135:R3559Q	ENSP00000374135:R3559Q	R	-	2	0	LRP1B	140847139	1.000000	0.71417	0.986000	0.45419	0.621000	0.37620	2.081000	0.41596	0.401000	0.25424	-0.404000	0.06349	CGG		0.368	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
DFNB59	494513	broad.mit.edu	37	2	179323290	179323290	+	Silent	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr2:179323290C>T	ENST00000409117.3	+	5	959	c.603C>T	c.(601-603)ttC>ttT	p.F201F	DFNB59_ENST00000605419.1_3'UTR|DFNB59_ENST00000375129.4_Silent_p.F201F	NM_001042702.3	NP_001036167.1	Q0ZLH3	PJVK_HUMAN	deafness, autosomal recessive 59	201					sensory perception of sound (GO:0007605)	neuronal cell body (GO:0043025)				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)			CTATTGTTTTCCCAGCACATA	0.343																																						uc002umi.4																			0				breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|upper_aerodigestive_tract(1)	18						c.(601-603)ttC>ttT		Homo sapiens deafness, autosomal recessive 59 (DFNB59), mRNA.							120.0	119.0	119.0					2																	179323290		1854	4105	5959	SO:0001819	synonymous_variant	494513				sensory perception of sound			g.chr2:179323290C>T	BC020859, BQ887979	CCDS42787.1	2q31.2	2011-07-01			ENSG00000204311	ENSG00000204311			29502	protein-coding gene	gene with protein product		610219				16804542	Standard	NM_001042702		Approved	pejvakin	uc002umi.4	Q0ZLH3	OTTHUMG00000154425	ENST00000409117.3:c.603C>T	2.37:g.179323290C>T						MIR548N_uc021vsx.1_Intron|DFNB59_uc002umj.4_Silent_p.F201F	p.F201F	NM_001042702	NP_001036167	Q0ZLH3	PJVK_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00406)|Epithelial(96;0.0159)|all cancers(119;0.0564)		4	959	+			201					A0PK14|B9EJE2	Silent	SNP	ENST00000409117.3	37	c.603C>T	CCDS42787.1																																																																																				0.343	DFNB59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335160.1		
ITSN1	6453	broad.mit.edu	37	21	35206635	35206635	+	Missense_Mutation	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr21:35206635G>A	ENST00000381318.3	+	28	3664	c.3376G>A	c.(3376-3378)Ggc>Agc	p.G1126S	ITSN1_ENST00000399349.1_Missense_Mutation_p.G1050S|ITSN1_ENST00000399367.3_Missense_Mutation_p.G1121S|ITSN1_ENST00000379960.5_3'UTR|ITSN1_ENST00000381291.4_Missense_Mutation_p.G1126S|ITSN1_ENST00000437442.2_Missense_Mutation_p.G1121S|ITSN1_ENST00000399355.2_Missense_Mutation_p.G1055S|ITSN1_ENST00000381285.4_Missense_Mutation_p.G1126S|ITSN1_ENST00000399326.3_3'UTR|AP000304.12_ENST00000429238.1_Intron|ITSN1_ENST00000399352.1_Missense_Mutation_p.G1121S|ITSN1_ENST00000399353.1_Missense_Mutation_p.G1084S	NM_003024.2	NP_003015.2	Q15811	ITSN1_HUMAN	intersectin 1 (SH3 domain protein)	1126	SH3 4. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic signaling pathway (GO:0097190)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|kinase activator activity (GO:0019209)|proline-rich region binding (GO:0070064)|protein complex scaffold (GO:0032947)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						GCGCCAGATAGGCTGGTTCCC	0.423																																						uc002yta.1																			0				breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(16)|lung(26)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	67						c.(3376-3378)Ggc>Agc		Homo sapiens intersectin 1 (SH3 domain protein) (ITSN1), transcript variant 1, mRNA.							54.0	53.0	53.0					21																	35206635		2203	4300	6503	SO:0001583	missense	6453				apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|regulation of Rho protein signal transduction|small GTPase mediated signal transduction|synaptic vesicle endocytosis	cell junction|coated pit|cytosol|lamellipodium|synapse|synaptosome	calcium ion binding|proline-rich region binding|protein complex scaffold|Rho guanyl-nucleotide exchange factor activity	g.chr21:35206635G>A	AF064244	CCDS33545.1, CCDS33546.1	21q22.1-q22.2	2013-01-10			ENSG00000205726	ENSG00000205726		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""EF-hand domain containing"""	6183	protein-coding gene	gene with protein product	"""SH3 domain protein-1A"", ""human intersectin-SH3 domain-containing protein SH3P17"", ""Src homology 3 domain-containing protein"", ""intersectin 1 short form variant, 11"", ""intersectin 1 short form variant 3"", ""intersectin short variant 12"""	602442		SH3D1A, ITSN		9799604, 9813051	Standard	NM_003024		Approved	SH3P17, MGC134948, MGC134949	uc002yta.1	Q15811	OTTHUMG00000065284	ENST00000381318.3:c.3376G>A	21.37:g.35206635G>A	ENSP00000370719:p.Gly1126Ser					DONSON_uc002ysn.1_Intron|ITSN1_uc010gmj.3_Missense_Mutation_p.G1005S|ITSN1_uc002ysy.3_Missense_Mutation_p.G1121S|ITSN1_uc002ysx.3_Missense_Mutation_p.G1084S|ITSN1_uc002yth.4_Non-coding_Transcript|ITSN1_uc002ysz.3_Missense_Mutation_p.G1050S|ITSN1_uc010gmg.3_Missense_Mutation_p.G1013S|ITSN1_uc010gmh.3_Non-coding_Transcript|ITSN1_uc002ysw.3_Missense_Mutation_p.G1126S|ITSN1_uc010gmi.3_Missense_Mutation_p.G1089S|ITSN1_uc002ytb.1_Missense_Mutation_p.G1121S|ITSN1_uc010gmk.3_Missense_Mutation_p.G1018S|ITSN1_uc010gml.3_Non-coding_Transcript|ITSN1_uc002ytd.3_Non-coding_Transcript|ITSN1_uc002ytj.2_Missense_Mutation_p.G1121S|ITSN1_uc010gmm.1_Non-coding_Transcript|ITSN1_uc002yte.3_Missense_Mutation_p.G989S|ITSN1_uc021wip.1_Missense_Mutation_p.G944S|ITSN1_uc002yti.1_Non-coding_Transcript	p.G1126S	NM_003024	NP_003015	Q15811	ITSN1_HUMAN			27	3644	+			1126			SH3 4.		A7Y322|A8CTX8|A8CTY3|A8CTY7|A8D7D0|A8DCP3|B4DTM2|E7ERJ1|E9PE44|E9PG01|E9PHV2|O95216|Q0PW94|Q0PW95|Q0PW97|Q14BD3|Q1ED40|Q20BK3|Q9UET5|Q9UK60|Q9UNK1|Q9UNK2|Q9UQ92	Missense_Mutation	SNP	ENST00000381318.3	37	c.3376G>A	CCDS33545.1	.	.	.	.	.	.	.	.	.	.	G	36	5.665247	0.96745	.	.	ENSG00000205726	ENST00000399353;ENST00000381318;ENST00000381291;ENST00000381285;ENST00000381288;ENST00000399367;ENST00000399352;ENST00000399355;ENST00000399349;ENST00000437442	T;T;T;T;T;T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33;-1.33	5.28	5.28	0.74379	Src homology-3 domain (3);Variant SH3 (1);	0.055312	0.64402	D	0.000001	D	0.94245	0.8152	H	0.98682	4.3	0.80722	D	1	D;P;D;D;D;P;P;D;D	0.89917	0.999;0.831;1.0;0.974;1.0;0.952;0.952;1.0;0.992	D;P;D;P;D;P;P;D;D	0.97110	0.992;0.792;0.997;0.88;1.0;0.88;0.88;0.995;0.943	D	0.96485	0.9359	10	0.87932	D	0	.	18.9333	0.92576	0.0:0.0:1.0:0.0	.	1018;1089;1013;1121;1055;1121;1126;1050;1084	A8D7D0;A7XZY7;A8CTY7;A8CTY3;F8W7U0;A8CTX8;Q15811;Q15811-3;E7ERJ0	.;.;.;.;.;.;ITSN1_HUMAN;.;.	S	1084;1126;1126;1126;1055;1121;1121;1055;1050;1121	ENSP00000382290:G1084S;ENSP00000370719:G1126S;ENSP00000370691:G1126S;ENSP00000370685:G1126S;ENSP00000382301:G1121S;ENSP00000382289:G1121S;ENSP00000382292:G1055S;ENSP00000382286:G1050S;ENSP00000387377:G1121S	ENSP00000370685:G1126S	G	+	1	0	ITSN1	34128505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.424000	0.97464	2.481000	0.83766	0.643000	0.83706	GGC		0.423	ITSN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000140070.4	NM_003024	
KRTAP10-3	386682	broad.mit.edu	37	21	45978262	45978262	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr21:45978262C>T	ENST00000391620.1	-	1	381	c.337G>A	c.(337-339)Gtc>Atc	p.V113I	TSPEAR_ENST00000397916.1_Intron|TSPEAR_ENST00000323084.4_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	113	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						ttgcagcagacgggcacacag	0.647																																						uc002zfj.1																			0				kidney(1)|lung(4)|prostate(1)|skin(1)	7						c.(337-339)Gtc>Atc		Homo sapiens keratin associated protein 10-3 (KRTAP10-3), mRNA.							142.0	140.0	141.0					21																	45978262		2203	4300	6503	SO:0001583	missense	386682					keratin filament		g.chr21:45978262C>T	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.337G>A	21.37:g.45978262C>T	ENSP00000375478:p.Val113Ile					TSPEAR_uc002zfe.1_Intron|TSPEAR_uc010gpv.1_Intron	p.V113I	NM_198696	NP_941969	P60369	KR103_HUMAN			0	382	-			113			18 X 5 AA repeats of C-C-X(3).		A3KN67|Q70LJ4	Missense_Mutation	SNP	ENST00000391620.1	37	c.337G>A	CCDS42956.1	.	.	.	.	.	.	.	.	.	.	c	1.190	-0.635580	0.03584	.	.	ENSG00000212935	ENST00000391620	T	0.01438	4.89	2.86	1.04	0.20106	.	.	.	.	.	T	0.01627	0.0052	L	0.42245	1.32	0.09310	N	1	B	0.13145	0.007	B	0.12156	0.007	T	0.43734	-0.9373	9	0.45353	T	0.12	.	5.9364	0.19169	0.0:0.7378:0.0:0.2622	.	113	P60369	KR103_HUMAN	I	113	ENSP00000375478:V113I	ENSP00000375478:V113I	V	-	1	0	KRTAP10-3	44802690	0.009000	0.17119	0.099000	0.21106	0.062000	0.15995	-0.330000	0.07925	0.225000	0.20959	-0.712000	0.03635	GTC		0.647	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
P4HTM	54681	broad.mit.edu	37	3	49042445	49042445	+	Missense_Mutation	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr3:49042445G>A	ENST00000383729.4	+	6	1410	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T	WDR6_ENST00000608424.1_5'Flank|WDR6_ENST00000448293.1_5'Flank|WDR6_ENST00000415265.2_5'Flank|WDR6_ENST00000395474.3_5'Flank|P4HTM_ENST00000343546.4_Missense_Mutation_p.A347T	NM_177939.2	NP_808808.1	Q9NXG6	P4HTM_HUMAN	prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum)	347	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21					Vitamin C(DB00126)	CAAGCTGGTAGCCAACGAGTC	0.587																																						uc003cvh.3																			0				NS(1)|breast(2)|kidney(1)|large_intestine(1)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						c.(1039-1041)Gcc>Acc		Homo sapiens prolyl 4-hydroxylase, transmembrane (endoplasmic reticulum) (P4HTM), transcript variant 3, mRNA.	Vitamin C(DB00126)						148.0	110.0	123.0					3																	49042445		2203	4300	6503	SO:0001583	missense	54681					endoplasmic reticulum membrane|integral to membrane	calcium ion binding|iron ion binding|L-ascorbic acid binding|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	g.chr3:49042445G>A		CCDS2781.2, CCDS43089.1	3p21.31	2009-01-14			ENSG00000178467	ENSG00000178467			28858	protein-coding gene	gene with protein product	"""Prolyl hydroxlase domain-containing 4"", ""hypoxia inducible factor prolyl 4 hydroxylase"""	614584				12163023, 17726031	Standard	XR_245139		Approved	P4H-TM, PHD4, PH4, HIFPH4, FLJ20262, EGLN4, PH-4	uc003cvh.3	Q9NXG6	OTTHUMG00000074057	ENST00000383729.4:c.1039G>A	3.37:g.49042445G>A	ENSP00000373235:p.Ala347Thr					P4HTM_uc003cvg.3_Missense_Mutation_p.A347T|WDR6_uc011bbx.1_5'Flank|WDR6_uc003cvj.2_5'Flank|WDR6_uc011bby.1_5'Flank|WDR6_uc010hkn.2_5'Flank|WDR6_uc011bbz.1_5'Flank	p.A347T	NM_177938	NP_808807	Q9NXG6	P4HTM_HUMAN			5	1388	+			347			Fe2OG dioxygenase.		Q6PAG6|Q8TCJ9|Q8WV55|Q96F22|Q9BW77	Missense_Mutation	SNP	ENST00000383729.4	37	c.1039G>A	CCDS43089.1	.	.	.	.	.	.	.	.	.	.	G	16.65	3.181771	0.57800	.	.	ENSG00000178467	ENST00000383729;ENST00000343546	T	0.77620	-1.11	5.32	3.5	0.40072	Oxoglutarate/iron-dependent oxygenase (2);Prolyl 4-hydroxylase, alpha subunit (1);	0.173906	0.50627	D	0.000101	T	0.62405	0.2425	L	0.28014	0.82	0.38375	D	0.944967	B;B	0.31435	0.323;0.17	B;B	0.30943	0.122;0.068	T	0.62959	-0.6743	10	0.31617	T	0.26	-17.1715	9.3798	0.38306	0.2051:0.0:0.7949:0.0	.	347;347	Q9NXG6-3;Q9NXG6	.;P4HTM_HUMAN	T	347	ENSP00000373235:A347T	ENSP00000341422:A347T	A	+	1	0	P4HTM	49017449	0.990000	0.36364	0.994000	0.49952	0.993000	0.82548	2.754000	0.47532	2.495000	0.84180	0.655000	0.94253	GCC		0.587	P4HTM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157211.1	NM_177938	
ATR	545	broad.mit.edu	37	3	142281611	142281611	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr3:142281611C>T	ENST00000350721.4	-	4	754	c.633G>A	c.(631-633)atG>atA	p.M211I	ATR_ENST00000383101.3_Missense_Mutation_p.M211I	NM_001184.3	NP_001175.2	Q13535	ATR_HUMAN	ATR serine/threonine kinase	211			M -> T (in dbSNP:rs2227928).		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						GAGTAAGAACCATTAATAAAG	0.318								Other conserved DNA damage response genes																														uc003eux.4																			0		p.M211T(1)		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						c.(631-633)atG>atA	Other conserved DNA damage response genes	Homo sapiens ataxia telangiectasia and Rad3 related (ATR), mRNA.							56.0	57.0	56.0					3																	142281611		2203	4300	6503	SO:0001583	missense	545				cell cycle|cellular response to gamma radiation|cellular response to UV|DNA damage checkpoint|DNA repair|DNA replication|multicellular organismal development|negative regulation of DNA replication|peptidyl-serine phosphorylation|positive regulation of DNA damage response, signal transduction by p53 class mediator|protein autophosphorylation|replicative senescence	PML body	ATP binding|DNA binding|MutLalpha complex binding|MutSalpha complex binding|protein serine/threonine kinase activity	g.chr3:142281611C>T	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.633G>A	3.37:g.142281611C>T	ENSP00000343741:p.Met211Ile						p.M211I	NM_001184	NP_001175	Q13535	ATR_HUMAN			3	755	-			211		M -> T (in dbSNP:rs2227928).			Q59HB2|Q7KYL3|Q93051|Q9BXK4	Missense_Mutation	SNP	ENST00000350721.4	37	c.633G>A	CCDS3124.1	.	.	.	.	.	.	.	.	.	.	C	9.784	1.176165	0.21704	.	.	ENSG00000175054	ENST00000350721;ENST00000383101	T;T	0.65916	-0.18;-0.18	5.56	-7.95	0.01148	Armadillo-type fold (1);	0.682857	0.14770	N	0.299410	T	0.35068	0.0919	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09314	-1.0680	10	0.52906	T	0.07	-1.8968	5.655	0.17637	0.1271:0.206:0.0768:0.5901	.	211	Q13535	ATR_HUMAN	I	211	ENSP00000343741:M211I;ENSP00000372581:M211I	ENSP00000343741:M211I	M	-	3	0	ATR	143764301	0.001000	0.12720	0.687000	0.30102	0.942000	0.58702	-2.382000	0.01064	-1.295000	0.02357	-0.469000	0.05056	ATG		0.318	ATR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353995.2	NM_001184	
YEATS2	55689	broad.mit.edu	37	3	183525871	183525871	+	Frame_Shift_Del	DEL	G	G	-			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr3:183525871delG	ENST00000305135.5	+	29	4260	c.4065delG	c.(4063-4065)gtgfs	p.V1356fs	YEATS2-AS1_ENST00000425008.3_RNA|YEATS2-AS1_ENST00000609195.1_RNA|YEATS2-AS1_ENST00000609871.1_RNA	NM_018023.4	NP_060493.3	Q9ULM3	YETS2_HUMAN	YEATS domain containing 2	1356					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|mitotic spindle (GO:0072686)	TBP-class protein binding (GO:0017025)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			ATGCGTCCGTGGTGGAGGACA	0.562																																						uc003fly.2																			0				NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(24)|ovary(3)|prostate(2)|skin(3)	49						c.(4063-4065)gtgfs		Homo sapiens YEATS domain containing 2 (YEATS2), mRNA.							37.0	39.0	38.0					3																	183525871		1950	4133	6083	SO:0001589	frameshift_variant	55689				histone H3 acetylation|negative regulation of transcription from RNA polymerase II promoter	Ada2/Gcn5/Ada3 transcription activator complex	TBP-class protein binding	g.chr3:183525871delG	AB033023	CCDS43175.1	3q27.3	2004-08-18			ENSG00000163872	ENSG00000163872			25489	protein-coding gene	gene with protein product		613373				10574462	Standard	NM_018023		Approved	FLJ10201, FLJ12841, FLJ13308, KIAA1197	uc003fly.2	Q9ULM3	OTTHUMG00000156898	ENST00000305135.5:c.4065delG	3.37:g.183525871delG	ENSP00000306983:p.Val1356fs					AX746590_uc003fma.1_5'Flank|YEATS2_uc021xie.1_5'Flank	p.V1355fs	NM_018023	NP_060493	Q9ULM3	YETS2_HUMAN	all cancers(12;2.38e-42)|Epithelial(37;1.9e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		28	4260	+	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		1355					A7E2B9|D3DNS9|Q641P6|Q9NW96	Frame_Shift_Del	DEL	ENST00000305135.5	37	c.4065delG	CCDS43175.1																																																																																				0.562	YEATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346507.2	NM_018023	
PCYT1A	5130	broad.mit.edu	37	3	195965646	195965646	+	Silent	SNP	G	G	A	rs372804569		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr3:195965646G>A	ENST00000292823.2	-	10	1189	c.1017C>T	c.(1015-1017)tcC>tcT	p.S339S	PCYT1A_ENST00000419333.1_Silent_p.S339S|PCYT1A_ENST00000431016.1_Silent_p.S339S	NM_005017.2	NP_005008.2	P49585	PCY1A_HUMAN	phosphate cytidylyltransferase 1, choline, alpha	339	3 X repeats.				CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|glycogen granule (GO:0042587)	choline-phosphate cytidylyltransferase activity (GO:0004105)|lipid binding (GO:0008289)			cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	Choline(DB00122)|Lamivudine(DB00709)	AAGTCTTGCCGGAGAAGGGCC	0.607													G|||	1	0.000199681	0.0	0.0	5008	,	,		16657	0.0		0.0	False		,,,				2504	0.001					uc003fwg.3																			0				cervix(1)|endometrium(3)|large_intestine(8)|lung(5)|ovary(1)	18						c.(1015-1017)tcC>tcT		Homo sapiens phosphate cytidylyltransferase 1, choline, alpha (PCYT1A), mRNA.	Choline(DB00122)	G		1,4405	2.1+/-5.4	0,1,2202	71.0	73.0	72.0		1017	-1.6	1.0	3		72	0,8600		0,0,4300	no	coding-synonymous	PCYT1A	NM_005017.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		339/368	195965646	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	5130					cytosol|soluble fraction	choline-phosphate cytidylyltransferase activity	g.chr3:195965646G>A	L28957	CCDS3315.1	3q29	2010-07-19	2005-09-05		ENSG00000161217	ENSG00000161217	2.7.7.15		8754	protein-coding gene	gene with protein product	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	123695	"""phosphate cytidylyltransferase 1, choline, alpha isoform"""	PCYT1		7918629	Standard	NM_005017		Approved	CT, CTPCT	uc003fwg.3	P49585	OTTHUMG00000155670	ENST00000292823.2:c.1017C>T	3.37:g.195965646G>A						AF088041_uc003fwf.1_5'Flank|PCYT1A_uc003fwh.3_Silent_p.S339S	p.S339S	NM_005017	NP_005008	P49585	PCY1A_HUMAN	Epithelial(36;1.28e-24)|all cancers(36;1.01e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00259)	9	1190	-	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		339			3 X repeats.		A9LYK9|D3DXB1|Q86Y88	Silent	SNP	ENST00000292823.2	37	c.1017C>T	CCDS3315.1																																																																																				0.607	PCYT1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341147.1	NM_005017	
CDH9	1007	broad.mit.edu	37	5	26881547	26881547	+	Missense_Mutation	SNP	G	G	A			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr5:26881547G>A	ENST00000231021.4	-	12	2240	c.2068C>T	c.(2068-2070)Cgg>Tgg	p.R690W		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	690					adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						ATTACATCCCGTCTAAGTTTA	0.408																																					Melanoma(8;187 585 15745 40864 52829)	uc003jgs.1																			0				breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						c.(2068-2070)Cgg>Tgg		Homo sapiens cadherin 9, type 2 (T1-cadherin) (CDH9), mRNA.							194.0	184.0	188.0					5																	26881547		2203	4300	6503	SO:0001583	missense	1007				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:26881547G>A	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.2068C>T	5.37:g.26881547G>A	ENSP00000231021:p.Arg690Trp					CDH9_uc011cnv.1_Missense_Mutation_p.R283W	p.R690W	NM_016279	NP_057363	Q9ULB4	CADH9_HUMAN			11	2237	-			690					Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	c.2068C>T	CCDS3893.1	.	.	.	.	.	.	.	.	.	.	G	15.37	2.812391	0.50527	.	.	ENSG00000113100	ENST00000231021	T	0.78364	-1.17	4.96	2.54	0.30619	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	D	0.89649	0.6776	M	0.93283	3.4	0.46725	D	0.999179	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89704	0.3907	9	.	.	.	.	11.1651	0.48539	0.0:0.0:0.3534:0.6466	.	283;690	B4DFP0;Q9ULB4	.;CADH9_HUMAN	W	690	ENSP00000231021:R690W	.	R	-	1	2	CDH9	26917304	0.991000	0.36638	0.916000	0.36221	0.951000	0.60555	0.843000	0.27640	0.311000	0.23014	0.557000	0.71058	CGG		0.408	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
GDNF	2668	broad.mit.edu	37	5	37815950	37815950	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr5:37815950C>T	ENST00000326524.2	-	3	638	c.439G>A	c.(439-441)Ggc>Agc	p.G147S	GDNF_ENST00000427982.1_Missense_Mutation_p.G164S|GDNF_ENST00000344622.4_Missense_Mutation_p.G121S|GDNF_ENST00000381826.4_Missense_Mutation_p.G138S|GDNF_ENST00000515058.1_Missense_Mutation_p.G121S	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor	147					adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					TCGCAAGAGCCGCTGCAGTAC	0.443																																						uc011cpi.2																			0				NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15						c.(439-441)Ggc>Agc		Homo sapiens glial cell derived neurotrophic factor (GDNF), transcript variant 1, mRNA.							115.0	115.0	115.0					5																	37815950		2203	4300	6503	SO:0001583	missense	2668				adult locomotory behavior|anti-apoptosis|axon guidance|branching involved in ureteric bud morphogenesis|enteric nervous system development|mRNA stabilization|negative regulation of neuron apoptosis|neural crest cell migration|peristalsis|positive regulation of branching involved in ureteric bud morphogenesis|positive regulation of dopamine secretion|positive regulation of monooxygenase activity|positive regulation of transcription from RNA polymerase II promoter|positive regulation of ureteric bud formation|postganglionic parasympathetic nervous system development|regulation of dopamine uptake|signal transduction|sympathetic nervous system development	extracellular region	growth factor activity|protein homodimerization activity	g.chr5:37815950C>T		CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"""Endogenous ligands"""	4232	protein-coding gene	gene with protein product	"""astrocyte-derived trophic factor"", ""glial cell line derived neurotrophic factor"", ""glial derived neurotrophic factor"""	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.439G>A	5.37:g.37815950C>T	ENSP00000317145:p.Gly147Ser					GDNF_uc011cpd.2_Missense_Mutation_p.G95S|GDNF_uc011cpe.2_Missense_Mutation_p.G121S|GDNF_uc011cpf.2_Missense_Mutation_p.G121S|GDNF_uc011cpg.2_Missense_Mutation_p.G164S|GDNF_uc011cph.2_Missense_Mutation_p.G138S	p.G147S	NM_000514	NP_000505	P39905	GDNF_HUMAN			2	639	-	all_lung(31;0.00118)		147					B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Missense_Mutation	SNP	ENST00000326524.2	37	c.439G>A	CCDS3922.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.601715	0.87055	.	.	ENSG00000168621	ENST00000326524;ENST00000344622;ENST00000515058;ENST00000427982;ENST00000381826	D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97	5.76	5.76	0.90799	Transforming growth factor-beta, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.99036	0.9670	M	0.82716	2.605	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.999;0.999	D	0.99802	1.1036	10	0.87932	D	0	-8.8999	19.9576	0.97228	0.0:1.0:0.0:0.0	.	147;138;164;121	P39905;P39905-4;P39905-3;P39905-2	GDNF_HUMAN;.;.;.	S	147;121;121;164;138	ENSP00000317145:G147S;ENSP00000339703:G121S;ENSP00000425928:G121S;ENSP00000409007:G164S;ENSP00000371248:G138S	ENSP00000317145:G147S	G	-	1	0	GDNF	37851707	1.000000	0.71417	0.993000	0.49108	0.960000	0.62799	7.487000	0.81328	2.736000	0.93811	0.655000	0.94253	GGC		0.443	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514	
LNPEP	4012	broad.mit.edu	37	5	96341853	96341853	+	Missense_Mutation	SNP	T	T	C			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr5:96341853T>C	ENST00000231368.5	+	10	2554	c.1862T>C	c.(1861-1863)gTt>gCt	p.V621A	LNPEP_ENST00000395770.3_Missense_Mutation_p.V607A	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	621					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		TTAGTGACTGTTCAAAAGAAA	0.333																																						uc003kmv.1																			0				breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34						c.(1861-1863)gTt>gCt		Homo sapiens leucyl/cystinyl aminopeptidase (LNPEP), transcript variant 1, mRNA.							61.0	65.0	64.0					5																	96341853		2203	4297	6500	SO:0001583	missense	4012				cell-cell signaling|female pregnancy|proteolysis	extracellular region|integral to plasma membrane	aminopeptidase activity|metallopeptidase activity|zinc ion binding	g.chr5:96341853T>C	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.1862T>C	5.37:g.96341853T>C	ENSP00000231368:p.Val621Ala					LNPEP_uc003kmw.1_Missense_Mutation_p.V607A	p.V621A	NM_005575	NP_787116	Q9UIQ6	LCAP_HUMAN		COAD - Colon adenocarcinoma(37;0.072)	9	2376	+		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)	621					O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Missense_Mutation	SNP	ENST00000231368.5	37	c.1862T>C	CCDS4087.1	.	.	.	.	.	.	.	.	.	.	T	16.31	3.088463	0.55968	.	.	ENSG00000113441	ENST00000231368;ENST00000395770	T;T	0.11277	2.79;2.79	5.87	5.87	0.94306	.	0.105582	0.64402	D	0.000005	T	0.11024	0.0269	L	0.42008	1.315	0.54753	D	0.999989	B	0.31485	0.325	B	0.31686	0.134	T	0.05886	-1.0858	10	0.52906	T	0.07	.	10.3205	0.43762	0.0:0.0737:0.0:0.9263	.	621	Q9UIQ6	LCAP_HUMAN	A	621;607	ENSP00000231368:V621A;ENSP00000379117:V607A	ENSP00000231368:V621A	V	+	2	0	LNPEP	96367609	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	5.501000	0.66950	2.248000	0.74166	0.533000	0.62120	GTT		0.333	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
PCDHB5	26167	broad.mit.edu	37	5	140516870	140516870	+	Silent	SNP	G	G	A	rs568545778		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr5:140516870G>A	ENST00000231134.5	+	1	2071	c.1854G>A	c.(1852-1854)gcG>gcA	p.A618A		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	618	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCATGTGGGCGCACAATGGCG	0.687													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14938	0.0		0.0	False		,,,				2504	0.0					uc003liq.3																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81						c.(1852-1854)gcG>gcA		Homo sapiens protocadherin beta 5 (PCDHB5), mRNA.							49.0	52.0	51.0					5																	140516870		2178	4250	6428	SO:0001819	synonymous_variant	26167				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding|protein binding	g.chr5:140516870G>A	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.1854G>A	5.37:g.140516870G>A							p.A618A	NM_015669	NP_056484	Q9Y5E4	PCDB5_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		0	2071	+			618			Cadherin 6.		Q549F4|Q9UFU9	Silent	SNP	ENST00000231134.5	37	c.1854G>A	CCDS4247.1																																																																																				0.687	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
F13A1	2162	broad.mit.edu	37	6	6196068	6196068	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr6:6196068C>T	ENST00000264870.3	-	10	1532	c.1267G>A	c.(1267-1269)Gtc>Atc	p.V423I		NM_000129.3	NP_000120.2	P00488	F13A_HUMAN	coagulation factor XIII, A1 polypeptide	423					blood coagulation (GO:0007596)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62	Ovarian(93;0.0816)	all_hematologic(90;0.152)			L-Glutamine(DB00130)	TGGAAGCAGACATGGCCGTGC	0.498																																						uc003mwv.3																			0				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	62						c.(1267-1269)Gtc>Atc		Homo sapiens coagulation factor XIII, A1 polypeptide (F13A1), mRNA.	L-Glutamine(DB00130)						104.0	83.0	90.0					6																	6196068		2203	4300	6503	SO:0001583	missense	2162				peptide cross-linking|platelet activation|platelet degranulation	extracellular region|platelet alpha granule lumen	acyltransferase activity|metal ion binding|protein-glutamine gamma-glutamyltransferase activity	g.chr6:6196068C>T	M14539	CCDS4496.1	6p24.2-p23	2014-01-24			ENSG00000124491	ENSG00000124491		"""Transglutaminases"""	3531	protein-coding gene	gene with protein product		134570		F13A			Standard	NM_000129		Approved		uc003mwv.3	P00488	OTTHUMG00000014186	ENST00000264870.3:c.1267G>A	6.37:g.6196068C>T	ENSP00000264870:p.Val423Ile					F13A1_uc011dib.2_Missense_Mutation_p.V360I	p.V423I	NM_000129	NP_000120	P00488	F13A_HUMAN			9	1390	-	Ovarian(93;0.0816)	all_hematologic(90;0.152)	423					Q59HA7|Q8N6X2|Q96P24|Q9BX29	Missense_Mutation	SNP	ENST00000264870.3	37	c.1267G>A	CCDS4496.1	.	.	.	.	.	.	.	.	.	.	C	7.303	0.613336	0.14066	.	.	ENSG00000124491	ENST00000264870;ENST00000441301	T	0.51574	0.7	5.49	4.5	0.54988	.	0.311799	0.34200	N	0.004179	T	0.18215	0.0437	L	0.31371	0.925	0.25684	N	0.985769	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.002	T	0.12192	-1.0557	10	0.41790	T	0.15	.	11.9873	0.53155	0.0:0.9051:0.0:0.0949	.	360;423	F5H080;P00488	.;F13A_HUMAN	I	423;360	ENSP00000264870:V423I	ENSP00000264870:V423I	V	-	1	0	F13A1	6141067	0.962000	0.33011	0.331000	0.25455	0.002000	0.02628	2.170000	0.42443	1.178000	0.42870	0.655000	0.94253	GTC		0.498	F13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039756.3	NM_000129	
GPX5	2880	broad.mit.edu	37	6	28497279	28497279	+	Missense_Mutation	SNP	G	G	A	rs60523386	byFrequency	TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr6:28497279G>A	ENST00000412168.2	+	2	228	c.139G>A	c.(139-141)Gca>Aca	p.A47T	GPX5_ENST00000469384.1_Missense_Mutation_p.A47T|GPX5_ENST00000442674.2_3'UTR|GPX6_ENST00000483058.1_5'Flank	NM_001509.2	NP_001500.1	O75715	GPX5_HUMAN	glutathione peroxidase 5 (epididymal androgen-related protein)	47					lipid metabolic process (GO:0006629)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)	glutathione peroxidase activity (GO:0004602)	p.A47T(2)		endometrium(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16					Glutathione(DB00143)	TGAGGCCATCGCACTTAATAA	0.428													G|||	30	0.00599042	0.0182	0.0	5008	,	,		17371	0.0		0.001	False		,,,				2504	0.0051					uc003nll.2																			2	Substitution - Missense(2)	p.A47T(4)	endometrium(2)	endometrium(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						c.(139-141)Gca>Aca		Homo sapiens glutathione peroxidase 5 (epididymal androgen-related protein) (GPX5), transcript variant 1, mRNA.	Glutathione(DB00143)	G	THR/ALA,THR/ALA	38,4368	42.3+/-75.8	0,38,2165	164.0	135.0	145.0		139,139	-0.7	0.0	6	dbSNP_129	145	0,8600		0,0,4300	yes	missense,missense	GPX5	NM_001509.2,NM_003996.3	58,58	0,38,6465	AA,AG,GG		0.0,0.8625,0.2922	benign,benign	47/222,47/101	28497279	38,12968	2203	4300	6503	SO:0001583	missense	2880				lipid metabolic process|response to oxidative stress	extracellular region	glutathione peroxidase activity	g.chr6:28497279G>A	AJ005277	CCDS4652.1, CCDS4653.1	6p22.1	2008-02-05			ENSG00000224586	ENSG00000224586	1.11.1.9		4557	protein-coding gene	gene with protein product		603435				9639555	Standard	NM_001509		Approved		uc003nll.2	O75715	OTTHUMG00000016307	ENST00000412168.2:c.139G>A	6.37:g.28497279G>A	ENSP00000392398:p.Ala47Thr					GPX5_uc003nlm.2_Missense_Mutation_p.A47T|GPX5_uc003nln.2_Non-coding_Transcript	p.A47T	NM_001509	NP_001500	O75715	GPX5_HUMAN			1	141	+			47					A1A4Y0	Missense_Mutation	SNP	ENST00000412168.2	37	c.139G>A	CCDS4652.1	8	0.003663003663003663	7	0.014227642276422764	0	0.0	0	0.0	1	0.0013192612137203166	G	0.003	-2.575670	0.00131	0.008625	0.0	ENSG00000224586	ENST00000412168;ENST00000469384	T;T	0.03580	3.88;3.88	3.65	-0.659	0.11424	Thioredoxin-like fold (2);	0.262995	0.36482	N	0.002570	T	0.00210	0.0006	N	0.00260	-1.75	0.09310	N	1	B;B	0.12630	0.006;0.001	B;B	0.11329	0.006;0.003	T	0.25916	-1.0118	10	0.02654	T	1	-25.4133	3.5103	0.07705	0.6251:0.0:0.2073:0.1677	rs60523386;rs61744383	47;47	A1A4Y0;O75715	.;GPX5_HUMAN	T	47	ENSP00000392398:A47T;ENSP00000419935:A47T	ENSP00000392398:A47T	A	+	1	0	GPX5	28605258	0.018000	0.18449	0.000000	0.03702	0.000000	0.00434	1.347000	0.33975	-0.060000	0.13132	-1.105000	0.02106	GCA		0.428	GPX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043672.2		
PKHD1	5314	broad.mit.edu	37	6	51609339	51609339	+	Splice_Site	SNP	T	T	C			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr6:51609339T>C	ENST00000371117.3	-	60	10275	c.10000A>G	c.(10000-10002)Aaa>Gaa	p.K3334E	PKHD1_ENST00000340994.4_Splice_Site_p.K3334E	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3334					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					CCTAAATCTTTCCTGTGAAGA	0.383																																						uc003pah.1																			0				NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304						c.e60-1		Homo sapiens polycystic kidney and hepatic disease 1 (autosomal recessive) (PKHD1), transcript variant 1, mRNA.							62.0	62.0	62.0					6																	51609339		2203	4300	6503	SO:0001630	splice_region_variant	5314				cell-cell adhesion|cilium assembly|homeostatic process|kidney development|negative regulation of cellular component movement	anchored to external side of plasma membrane|apical plasma membrane|integral to membrane|microtubule basal body	protein binding|receptor activity	g.chr6:51609339T>C	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9999-1A>G	6.37:g.51609339T>C						PKHD1_uc010jzn.1_Splice_Site_p.R1316_splice|PKHD1_uc003pai.3_Splice_Site_p.R3333_splice	p.R3333_splice	NM_138694	NP_619639	P08F94	PKHD1_HUMAN			60	10275	-	Lung NSC(77;0.0605)		3333					Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	c.9999_splice	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	T	6.149	0.395787	0.11638	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.87491	-2.04;-2.26	5.0	2.6	0.31112	.	0.405730	0.25091	N	0.033210	T	0.65575	0.2704	L	0.37561	1.115	0.26411	N	0.976266	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.002;0.003;0.002	T	0.60156	-0.7318	10	0.49607	T	0.09	.	7.2434	0.26109	0.0:0.2536:0.0:0.7464	.	3334;3334;3334	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	E	3334	ENSP00000360158:K3334E;ENSP00000341097:K3334E	ENSP00000341097:K3334E	K	-	1	0	PKHD1	51717298	0.190000	0.23276	1.000000	0.80357	0.173000	0.22820	0.965000	0.29319	0.873000	0.35799	0.528000	0.53228	AAA		0.383	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	Missense_Mutation
COL28A1	340267	broad.mit.edu	37	7	7483281	7483281	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:7483281C>T	ENST00000399429.3	-	20	1725	c.1585G>A	c.(1585-1587)Gaa>Aaa	p.E529K		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	529	Collagen-like 4.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		AGCCCCGCTTCTCCCTAGAGA	0.517																																						uc003src.1																			0				cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42						c.(1585-1587)Gaa>Aaa		Homo sapiens collagen, type XXVIII, alpha 1 (COL28A1), mRNA.							64.0	63.0	64.0					7																	7483281		1932	4149	6081	SO:0001583	missense	340267				cell adhesion	basement membrane|collagen	serine-type endopeptidase inhibitor activity	g.chr7:7483281C>T	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.1585G>A	7.37:g.7483281C>T	ENSP00000382356:p.Glu529Lys					COL28A1_uc011jxe.1_Missense_Mutation_p.E212K|COL28A1_uc003srd.3_Missense_Mutation_p.E84K	p.E529K	NM_001037763	NP_001032852	Q2UY09	COSA1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)	19	1702	-		Ovarian(82;0.0789)	529			Collagen-like 4.		A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	c.1585G>A	CCDS43553.1	.	.	.	.	.	.	.	.	.	.	C	19.49	3.838331	0.71373	.	.	ENSG00000215018	ENST00000399429;ENST00000399419	D	0.93247	-3.19	4.93	4.93	0.64822	.	0.175590	0.34435	U	0.003978	D	0.94221	0.8145	L	0.41961	1.31	0.41537	D	0.988494	D;D;D	0.69078	0.996;0.993;0.997	D;D;D	0.80764	0.99;0.971;0.994	D	0.91652	0.5335	10	0.21014	T	0.42	-19.8684	13.8569	0.63534	0.0:1.0:0.0:0.0	.	529;529;529	Q2UY09-2;B5MDS6;Q2UY09	.;.;COSA1_HUMAN	K	529	ENSP00000382356:E529K	ENSP00000382347:E529K	E	-	1	0	COL28A1	7449806	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	3.569000	0.53827	2.730000	0.93505	0.655000	0.94253	GAA		0.517	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
GRM3	2913	broad.mit.edu	37	7	86415877	86415877	+	Missense_Mutation	SNP	G	G	A	rs571579021		TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:86415877G>A	ENST00000361669.2	+	3	1868	c.769G>A	c.(769-771)Gac>Aac	p.D257N	GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Missense_Mutation_p.D255N|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.D129N|AC005009.2_ENST00000452471.1_RNA|GRM3_ENST00000439827.1_Missense_Mutation_p.D257N	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	257					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)	p.D257H(1)		NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					CAAGTCCTACGACAGCGTGAT	0.647													G|||	1	0.000199681	0.0	0.0	5008	,	,		18791	0.0		0.001	False		,,,				2504	0.0				GBM(52;969 1098 3139 52280)	uc003uid.3																			1	Substitution - Missense(1)	p.D257H(2)|p.Y256Y(1)	lung(1)	NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109						c.(769-771)Gac>Aac		Homo sapiens glutamate receptor, metabotropic 3 (GRM3), mRNA.	Acamprosate(DB00659)|Nicotine(DB00184)						48.0	51.0	50.0					7																	86415877		2203	4300	6503	SO:0001583	missense	2913				synaptic transmission	integral to plasma membrane		g.chr7:86415877G>A		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.769G>A	7.37:g.86415877G>A	ENSP00000355316:p.Asp257Asn					GRM3_uc010lef.3_Missense_Mutation_p.D255N|GRM3_uc010leg.3_Missense_Mutation_p.D129N|GRM3_uc010leh.3_Intron	p.D257N	NM_000840	NP_000831	Q14832	GRM3_HUMAN			2	1868	+	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)		257					Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	c.769G>A	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	G	31	5.093384	0.94149	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73	6.07	6.07	0.98685	Extracellular ligand-binding receptor (1);	0.043778	0.85682	D	0.000000	D	0.89143	0.6631	M	0.70842	2.15	0.80722	D	1	P;D;P	0.55385	0.91;0.971;0.926	P;P;P	0.55577	0.671;0.49;0.779	D	0.88959	0.3392	10	0.62326	D	0.03	.	19.6475	0.95784	0.0:0.0:1.0:0.0	.	129;257;257	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	N	257;129;129;257;255	ENSP00000355316:D257N;ENSP00000405427:D129N;ENSP00000441407:D129N;ENSP00000398767:D257N;ENSP00000378209:D255N	ENSP00000355316:D257N	D	+	1	0	GRM3	86253813	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.756000	0.98918	2.885000	0.99019	0.655000	0.94253	GAC		0.647	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
ABCB1	5243	broad.mit.edu	37	7	87179839	87179839	+	Missense_Mutation	SNP	C	C	G			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:87179839C>G	ENST00000265724.3	-	12	1586	c.1169G>C	c.(1168-1170)gGa>gCa	p.G390A	ABCB1_ENST00000543898.1_Missense_Mutation_p.G326A	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	390					drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	TTCCAAATTTCCCTTAATATT	0.313																																						uc003uiz.2																			0				NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111						c.(1168-1170)gGa>gCa		Homo sapiens ATP-binding cassette, sub-family B (MDR/TAP), member 1 (ABCB1), mRNA.	Adenosine triphosphate(DB00171)|Alfentanil(DB00802)|Arsenic trioxide(DB01169)|Atazanavir(DB01072)|Carvedilol(DB01136)|Colchicine(DB01394)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dipyridamole(DB00975)|Estramustine(DB01196)|Flupenthixol(DB00875)|Imatinib(DB00619)|Itraconazole(DB01167)|Nicardipine(DB00622)|Propafenone(DB01182)|Quinacrine(DB01103)|Quinidine(DB00908)|Ranolazine(DB00243)|Rifampin(DB01045)|Roxithromycin(DB00778)|Saquinavir(DB01232)|Tamoxifen(DB00675)|Vinblastine(DB00570)						101.0	97.0	98.0					7																	87179839		2203	4298	6501	SO:0001583	missense	5243				G2/M transition of mitotic cell cycle|stem cell proliferation	apical plasma membrane|cell surface|Golgi membrane|integral to membrane|intercellular canaliculus|membrane fraction	ATP binding|protein binding|xenobiotic-transporting ATPase activity	g.chr7:87179839C>G	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1169G>C	7.37:g.87179839C>G	ENSP00000265724:p.Gly390Ala					ABCB1_uc011khc.2_Missense_Mutation_p.G326A	p.G390A	NM_000927	NP_000918	P08183	MDR1_HUMAN			11	1662	-	Esophageal squamous(14;0.00164)		390					A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	c.1169G>C	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.010712	0.93346	.	.	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.91237	-2.81;-2.81	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	D	0.95503	0.8539	M	0.75150	2.29	0.80722	D	1	D;D	0.89917	1.0;1.0	P;D	0.97110	0.622;1.0	D	0.95172	0.8291	10	0.87932	D	0	-22.3806	20.4496	0.99125	0.0:1.0:0.0:0.0	.	326;390	B5AK60;P08183	.;MDR1_HUMAN	A	171;390;326	ENSP00000265724:G390A;ENSP00000444095:G326A	ENSP00000265724:G390A	G	-	2	0	ABCB1	87017775	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.047000	0.71038	2.838000	0.97847	0.563000	0.77884	GGA		0.313	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
NPTX2	4885	broad.mit.edu	37	7	98256632	98256632	+	Silent	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:98256632C>T	ENST00000265634.3	+	4	1209	c.1044C>T	c.(1042-1044)ggC>ggT	p.G348G		NM_002523.2	NP_002514.1	P47972	NPTX2_HUMAN	neuronal pentraxin II	348	Pentaxin.				synaptic transmission (GO:0007268)	extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		STAD - Stomach adenocarcinoma(171;0.215)			AGCCCGGGGGCGTGCTGATCC	0.677																																						uc003upl.2																			0				breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	18						c.(1042-1044)ggC>ggT		Homo sapiens neuronal pentraxin II (NPTX2), mRNA.							54.0	45.0	48.0					7																	98256632		2203	4300	6503	SO:0001819	synonymous_variant	4885				synaptic transmission	extracellular region	metal ion binding|sugar binding	g.chr7:98256632C>T		CCDS5657.1	7q21.3-q22.1	2008-04-30			ENSG00000106236	ENSG00000106236			7953	protein-coding gene	gene with protein product	"""apexin"""	600750				8530029	Standard	NM_002523		Approved		uc003upl.2	P47972	OTTHUMG00000154369	ENST00000265634.3:c.1044C>T	7.37:g.98256632C>T							p.G348G	NM_002523	NP_002514	P47972	NPTX2_HUMAN	STAD - Stomach adenocarcinoma(171;0.215)		3	1221	+	all_cancers(62;2.28e-09)|all_epithelial(64;4.86e-10)|Esophageal squamous(72;0.00918)|Lung NSC(181;0.0128)|all_lung(186;0.0142)		348			Pentaxin.		A4D267|Q86XV7|Q96G70	Silent	SNP	ENST00000265634.3	37	c.1044C>T	CCDS5657.1																																																																																				0.677	NPTX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334982.1	NM_002523	
FOXP2	93986	broad.mit.edu	37	7	114282648	114282648	+	Missense_Mutation	SNP	A	A	G			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:114282648A>G	ENST00000393494.2	+	7	1238	c.959A>G	c.(958-960)cAg>cGg	p.Q320R	FOXP2_ENST00000390668.3_Missense_Mutation_p.Q344R|FOXP2_ENST00000393491.3_Missense_Mutation_p.Q228R|FOXP2_ENST00000408937.3_Missense_Mutation_p.Q345R|FOXP2_ENST00000350908.4_Missense_Mutation_p.Q320R|FOXP2_ENST00000393498.2_Missense_Mutation_p.Q299R|FOXP2_ENST00000393489.3_Missense_Mutation_p.Q228R|FOXP2_ENST00000378237.3_Missense_Mutation_p.Q320R|FOXP2_ENST00000403559.4_Missense_Mutation_p.Q337R|FOXP2_ENST00000360232.4_Missense_Mutation_p.Q320R|FOXP2_ENST00000393500.3_Missense_Mutation_p.Q245R			O15409	FOXP2_HUMAN	forkhead box P2	320					camera-type eye development (GO:0043010)|caudate nucleus development (GO:0021757)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|growth (GO:0040007)|lung alveolus development (GO:0048286)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of mesenchymal cell proliferation (GO:0002053)|post-embryonic development (GO:0009791)|putamen development (GO:0021758)|righting reflex (GO:0060013)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|vocal learning (GO:0042297)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|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 negative regulation of transcription (GO:0001078)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						GTGAATGGACAGTCTTCAGTT	0.388																																						uc003vhb.3																			0				breast(3)|endometrium(7)|kidney(4)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	52						c.(958-960)cAg>cGg		Homo sapiens forkhead box P2 (FOXP2), transcript variant 1, mRNA.							183.0	156.0	165.0					7																	114282648		2203	4300	6503	SO:0001583	missense	93986				camera-type eye development|caudate nucleus development|cerebellum development|cerebral cortex development|embryo development|growth|lung alveolus development|negative regulation of transcription, DNA-dependent|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of mesenchymal cell proliferation|post-embryonic development|putamen development|regulation of sequence-specific DNA binding transcription factor activity|righting reflex|skeletal muscle tissue development|smooth muscle tissue development|vocal learning	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr7:114282648A>G	U80741	CCDS5760.1, CCDS5761.1, CCDS43635.1, CCDS5761.2, CCDS55154.1	7q31	2008-07-18			ENSG00000128573	ENSG00000128573		"""Forkhead boxes"""	13875	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 10"", ""forkhead/winged-helix transcription factor"", ""speech and language disorder 1"", ""CAG repeat protein 44"""	605317		TNRC10, SPCH1		11586359, 9225980	Standard	NM_014491		Approved	CAGH44	uc003vgz.3	O15409	OTTHUMG00000023131	ENST00000393494.2:c.959A>G	7.37:g.114282648A>G	ENSP00000377132:p.Gln320Arg					FOXP2_uc003vgu.3_Non-coding_Transcript|FOXP2_uc003vgz.3_Missense_Mutation_p.Q345R|FOXP2_uc003vha.3_Missense_Mutation_p.Q228R|FOXP2_uc011kmv.2_Missense_Mutation_p.Q319R|FOXP2_uc011kmu.2_Missense_Mutation_p.Q337R|FOXP2_uc010ljz.2_Missense_Mutation_p.Q228R|FOXP2_uc003vgx.2_Missense_Mutation_p.Q320R|FOXP2_uc003vhc.3_Missense_Mutation_p.Q345R|FOXP2_uc003vhd.3_Missense_Mutation_p.Q320R	p.Q320R	NM_014491	NP_055306	O15409	FOXP2_HUMAN			6	1333	+			320					A0AUV6|A4D0U8|A6NNW4|B4DLD9|Q6ZND1|Q75MJ3|Q8IZE0|Q8N0W2|Q8N6B7|Q8N6B8|Q8NFQ1|Q8NFQ2|Q8NFQ3|Q8NFQ4|Q8TD74	Missense_Mutation	SNP	ENST00000393494.2	37	c.959A>G	CCDS5760.1	.	.	.	.	.	.	.	.	.	.	A	18.95	3.732695	0.69189	.	.	ENSG00000128573	ENST00000393500;ENST00000393494;ENST00000408937;ENST00000403559;ENST00000350908;ENST00000393498;ENST00000378237;ENST00000393489;ENST00000360232;ENST00000390668;ENST00000393491	T;T;T;T;T;T;T;T;T;T	0.21031	2.07;2.07;2.07;2.07;2.07;2.03;2.07;2.07;2.07;2.07	5.02	5.02	0.67125	.	0.108672	0.64402	D	0.000003	T	0.40932	0.1137	L	0.59436	1.845	0.58432	D	0.999999	P;P;P;P;P;P;P	0.48294	0.851;0.851;0.659;0.769;0.908;0.851;0.908	P;P;P;P;P;P;P	0.61397	0.775;0.775;0.775;0.888;0.888;0.775;0.888	T	0.24119	-1.0169	10	0.66056	D	0.02	.	15.0341	0.71731	1.0:0.0:0.0:0.0	.	319;337;228;320;344;320;345	B7ZLK5;B4DLD9;Q0PRL4;O15409-6;Q8N6B5;O15409;O15409-4	.;.;.;.;.;FOXP2_HUMAN;.	R	245;320;345;337;320;297;320;228;320;344;228	ENSP00000377137:Q245R;ENSP00000377132:Q320R;ENSP00000386200:Q345R;ENSP00000385069:Q337R;ENSP00000265436:Q320R;ENSP00000367482:Q320R;ENSP00000377129:Q228R;ENSP00000353367:Q320R;ENSP00000375084:Q344R;ENSP00000377130:Q228R	ENSP00000265436:Q320R	Q	+	2	0	FOXP2	114069884	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.905000	0.92613	2.012000	0.59069	0.377000	0.23210	CAG		0.388	FOXP2-014	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317366.1	NM_014491	
PLXNA4	91584	broad.mit.edu	37	7	131887591	131887591	+	Missense_Mutation	SNP	G	G	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:131887591G>T	ENST00000359827.3	-	12	3362	c.2400C>A	c.(2398-2400)caC>caA	p.H800Q	PLXNA4_ENST00000321063.4_Missense_Mutation_p.H800Q			Q9HCM2	PLXA4_HUMAN	plexin A4	800					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						ACTTGTAGAGGTGAACTGCAG	0.632																																						uc003vra.4																			0				NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						c.(2398-2400)caC>caA		Homo sapiens plexin A4 (PLXNA4), transcript variant 1, mRNA.							16.0	17.0	17.0					7																	131887591		2146	4273	6419	SO:0001583	missense	91584					integral to membrane|intracellular|plasma membrane		g.chr7:131887591G>T	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2400C>A	7.37:g.131887591G>T	ENSP00000352882:p.His800Gln						p.H800Q	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN			11	2629	-			800					A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	c.2400C>A	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	15.50	2.852075	0.51270	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.64618	-0.11;-0.11	4.41	0.574	0.17368	.	0.099768	0.36778	N	0.002414	T	0.53899	0.1825	M	0.82517	2.595	0.43745	D	0.99624	P	0.38582	0.638	B	0.31614	0.133	T	0.53019	-0.8497	10	0.12766	T	0.61	.	9.663	0.39967	0.4521:0.0:0.5479:0.0	.	800	Q9HCM2	PLXA4_HUMAN	Q	800	ENSP00000323194:H800Q;ENSP00000352882:H800Q	ENSP00000323194:H800Q	H	-	3	2	PLXNA4	131538131	1.000000	0.71417	0.993000	0.49108	0.971000	0.66376	1.862000	0.39448	0.235000	0.21160	0.561000	0.74099	CAC		0.632	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
TRPV6	55503	broad.mit.edu	37	7	142573429	142573429	+	Missense_Mutation	SNP	C	C	T			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:142573429C>T	ENST00000359396.3	-	8	1159	c.914G>A	c.(913-915)cGc>cAc	p.R305H	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	305					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					CAGGATCTGGCGAGCCTGCAA	0.607																																						uc003wbx.2																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42						c.(913-915)cGc>cAc		Homo sapiens transient receptor potential cation channel, subfamily V, member 6 (TRPV6), mRNA.							64.0	67.0	66.0					7																	142573429		2203	4300	6503	SO:0001583	missense	55503				regulation of calcium ion-dependent exocytosis	integral to plasma membrane	calcium channel activity|calmodulin binding	g.chr7:142573429C>T	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.914G>A	7.37:g.142573429C>T	ENSP00000352358:p.Arg305His					TRPV6_uc003wbw.1_Missense_Mutation_p.R91H|TRPV6_uc010lou.1_Missense_Mutation_p.R176H	p.R305H	NM_018646	NP_061116	Q9H1D0	TRPV6_HUMAN			7	1143	-	Melanoma(164;0.059)		305					A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Missense_Mutation	SNP	ENST00000359396.3	37	c.914G>A	CCDS5874.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.946850	0.53186	.	.	ENSG00000165125	ENST00000359396;ENST00000311470	T	0.52057	0.68	4.71	3.84	0.44239	.	0.000000	0.85682	D	0.000000	T	0.39937	0.1097	M	0.65498	2.005	0.80722	D	1	P	0.34757	0.467	B	0.21546	0.035	T	0.28170	-1.0052	10	0.25106	T	0.35	-19.5158	11.8416	0.52357	0.0:0.9162:0.0:0.0838	.	305	Q9H1D0	TRPV6_HUMAN	H	305;137	ENSP00000352358:R305H	ENSP00000310825:R137H	R	-	2	0	TRPV6	142283551	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	4.798000	0.62510	1.222000	0.43521	0.655000	0.94253	CGC		0.607	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
ZYX	7791	broad.mit.edu	37	7	143080299	143080299	+	Missense_Mutation	SNP	T	T	C			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr7:143080299T>C	ENST00000322764.5	+	5	1252	c.907T>C	c.(907-909)Tct>Cct	p.S303P	ZYX_ENST00000392910.2_Missense_Mutation_p.S146P|AC093673.5_ENST00000429630.1_RNA|ZYX_ENST00000477373.1_3'UTR|ZYX_ENST00000449423.2_Missense_Mutation_p.S216P	NM_001010972.1|NM_003461.4	NP_001010972.1|NP_003452.1	Q15942	ZYX_HUMAN	zyxin	303					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|integrin-mediated signaling pathway (GO:0007229)|regulation of inflammatory response (GO:0050727)|signal transduction (GO:0007165)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17	Melanoma(164;0.205)					CGAAGCTCTTTCTGCTGGCAC	0.597																																						uc003wcx.3																			0				breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)	17						c.(907-909)Tct>Cct		Homo sapiens zyxin (ZYX), transcript variant 1, mRNA.							58.0	68.0	65.0					7																	143080299		2203	4300	6503	SO:0001583	missense	7791				cell adhesion|cell-cell signaling|interspecies interaction between organisms|signal transduction	cell-cell adherens junction|cytoplasm|focal adhesion|integral to plasma membrane|nucleus|stress fiber	protein binding|zinc ion binding	g.chr7:143080299T>C	X95735	CCDS5883.1	7q32	2010-02-26			ENSG00000159840	ENSG00000159840			13200	protein-coding gene	gene with protein product		602002				8917469, 8940160	Standard	XM_005250052		Approved		uc003wcx.3	Q15942	OTTHUMG00000023822	ENST00000322764.5:c.907T>C	7.37:g.143080299T>C	ENSP00000324422:p.Ser303Pro					ZYX_uc011ktd.2_Missense_Mutation_p.S146P|ZYX_uc003wcw.3_Missense_Mutation_p.S303P|ZYX_uc011kte.2_Missense_Mutation_p.S272P|ZYX_uc011ktf.2_Missense_Mutation_p.S146P	p.S303P	NM_003461	NP_003452	Q15942	ZYX_HUMAN			4	1065	+	Melanoma(164;0.205)		303					A4D2G6|Q6I9S4	Missense_Mutation	SNP	ENST00000322764.5	37	c.907T>C	CCDS5883.1	.	.	.	.	.	.	.	.	.	.	T	1.811	-0.474725	0.04414	.	.	ENSG00000159840	ENST00000322764;ENST00000354434;ENST00000449423;ENST00000392910	T;T;T;T	0.54675	0.68;0.56;0.56;0.58	4.12	-1.74	0.08056	.	1.837240	0.03455	U	0.211278	T	0.52725	0.1752	L	0.46741	1.465	0.09310	N	1	B;D	0.65815	0.396;0.995	B;P	0.57911	0.099;0.829	T	0.46843	-0.9162	10	0.18710	T	0.47	.	1.0519	0.01582	0.1675:0.2769:0.3338:0.2219	.	216;303	B4DQR8;Q15942	.;ZYX_HUMAN	P	303;271;216;146	ENSP00000324422:S303P;ENSP00000346417:S271P;ENSP00000394158:S216P;ENSP00000376642:S146P	ENSP00000324422:S303P	S	+	1	0	ZYX	142790421	0.000000	0.05858	0.006000	0.13384	0.019000	0.09904	-0.817000	0.04472	0.024000	0.15214	0.460000	0.39030	TCT		0.597	ZYX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156296.2	NM_003461	
ZFAT	57623	broad.mit.edu	37	8	135612748	135612748	+	Silent	SNP	G	G	A	rs144002982	byFrequency	TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr8:135612748G>A	ENST00000377838.3	-	7	2580	c.2406C>T	c.(2404-2406)acC>acT	p.T802T	ZFAT_ENST00000520356.1_Silent_p.T790T|ZFAT_ENST00000520727.1_Silent_p.T790T|ZFAT_ENST00000429442.2_Silent_p.T790T|ZFAT_ENST00000523399.1_Silent_p.T740T|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520214.1_Silent_p.T790T	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	802					hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CACAGCCATCGGTGGGACACT	0.448													G|||	2	0.000399361	0.0008	0.0	5008	,	,		16996	0.0		0.0	False		,,,				2504	0.001					uc003yup.3																			0				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						c.(2404-2406)acC>acT		Homo sapiens zinc finger and AT hook domain containing (ZFAT), transcript variant 1, mRNA.							181.0	178.0	179.0					8																	135612748		1965	4152	6117	SO:0001819	synonymous_variant	57623				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytosol|nucleus	DNA binding|zinc ion binding	g.chr8:135612748G>A	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2406C>T	8.37:g.135612748G>A						ZFAT_uc003yun.3_Silent_p.T790T|ZFAT_uc003yuo.3_Silent_p.T790T|ZFAT_uc010meh.3_Silent_p.T790T|ZFAT_uc010mej.3_Silent_p.T740T|ZFAT_uc010mei.3_Non-coding_Transcript|ZFAT_uc003yuq.3_Silent_p.T790T|ZFAT_uc003yur.3_Silent_p.T790T|ZFAT-AS1_uc003yus.1_Non-coding_Transcript	p.T802T	NM_020863	NP_001161055	Q9P243	ZFAT_HUMAN	BRCA - Breast invasive adenocarcinoma(115;0.0432)		6	2592	-	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		802					B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Silent	SNP	ENST00000377838.3	37	c.2406C>T	CCDS47924.1																																																																																				0.448	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
ERCC6L2	375748	broad.mit.edu	37	9	98683552	98683552	+	Silent	SNP	T	T	G			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chr9:98683552T>G	ENST00000288985.7	+	7	1592	c.1287T>G	c.(1285-1287)ccT>ccG	p.P429P	ERCC6L2_ENST00000437817.1_Silent_p.P240P|ERCC6L2_ENST00000466840.1_3'UTR	NM_001010895.2	NP_001010895.1	Q5T890	ER6L2_HUMAN	excision repair cross-complementation group 6-like 2	429					DNA repair (GO:0006281)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)										CTTCTGAGCCTTGTACCTGTA	0.363																																						uc010mry.1																			0											c.(391-393)ccT>ccG		Homo sapiens chromosome 9 open reading frame 102 (C9orf102), mRNA.							108.0	110.0	109.0					9																	98683552		2203	4300	6503	SO:0001819	synonymous_variant	375748				DNA repair	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding	g.chr9:98683552T>G	BC022957	CCDS35072.1	9q22.32	2014-03-07	2014-03-07	2012-03-30	ENSG00000182150	ENSG00000182150			26922	protein-coding gene	gene with protein product		615667	"""chromosome 9 open reading frame 102"", ""excision repair cross-complementing rodent repair deficiency, complementation group 6-like 2"""	C9orf102			Standard	NM_001010895		Approved	FLJ37706, RAD26L	uc004avt.4	Q5T890	OTTHUMG00000020289	ENST00000288985.7:c.1287T>G	9.37:g.98683552T>G						ERCC6L2_uc010mrx.1_Non-coding_Transcript|ERCC6L2_uc004avt.4_Silent_p.P429P|ERCC6L2_uc011lum.2_Silent_p.P131P|ERCC6L2_uc010mrz.3_Silent_p.P240P|ERCC6L2_uc004avu.3_5'Flank	p.P131P			Q5T890	RAD26_HUMAN			5	1481	+			429					A4D997|B2RTP8|Q49AM9|Q5T892|Q8N663|Q8N9D0|Q9NPM7	Silent	SNP	ENST00000288985.7	37	c.393T>G	CCDS35072.1																																																																																				0.363	ERCC6L2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053247.2	NM_001010895	
XK	7504	broad.mit.edu	37	X	37587132	37587133	+	Frame_Shift_Ins	INS	-	-	C			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chrX:37587132_37587133insC	ENST00000378616.3	+	3	955_956	c.752_753insC	c.(751-756)taccccfs	p.YP251fs	TM4SF2_ENST00000465127.1_Intron	NM_021083.2	NP_066569.1	P51811	XK_HUMAN	X-linked Kx blood group	251					amino acid transport (GO:0006865)|transport (GO:0006810)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15		all_lung(315;0.175)				TTCTTCTTGTACCCCTGGATCC	0.485																																						uc004ddq.3																			0				breast(1)|endometrium(4)|large_intestine(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	15						c.(751-753)tacfs		Homo sapiens X-linked Kx blood group (McLeod syndrome) (XK), mRNA.																																				SO:0001589	frameshift_variant	7504				amino acid transport	integral to membrane	protein binding|transporter activity	g.chrX:37587132_37587133insC	Z32684	CCDS14241.1	Xp21.1	2014-07-19	2014-06-18		ENSG00000047597	ENSG00000047597		"""Blood group antigens"""	12811	protein-coding gene	gene with protein product	"""Kx antigen"", ""McLeod syndrome"""	314850	"""Kell blood group precursor (McLeod phenotype)"", ""XK, Kell blood group complex subunit (McLeod syndrome)"", ""neuroacanthocytosis"", ""neurocanthocytosis"""	NA, NAC		8004674, 11761473	Standard	NM_021083		Approved	XKR1, Kx, X1k	uc004ddq.3	P51811	OTTHUMG00000033171	ENST00000378616.3:c.756dupC	X.37:g.37587136_37587136dupC	ENSP00000367879:p.Tyr251fs						p.Y251fs	NM_021083	NP_066569	P51811	XK_HUMAN			2	834_835	+		all_lung(315;0.175)	251					Q4TTN6|Q8IUK6|Q9UC77	Frame_Shift_Ins	INS	ENST00000378616.3	37	c.752_753insC	CCDS14241.1																																																																																				0.485	XK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080875.1	NM_021083	
SMARCA1	6594	broad.mit.edu	37	X	128621040	128621040	+	Missense_Mutation	SNP	T	T	G			TCGA-12-3653-01A-01D-1495-08	TCGA-12-3653-10A-01D-1495-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	fdc52d48-828e-481f-ba1c-0264f1da38a5	6d1c37a3-4c31-404f-98b5-bc81876f4080	g.chrX:128621040T>G	ENST00000371122.4	-	17	2301	c.2172A>C	c.(2170-2172)caA>caC	p.Q724H	SMARCA1_ENST00000371123.1_Missense_Mutation_p.Q712H|SMARCA1_ENST00000371121.3_Missense_Mutation_p.Q712H	NM_003069.3	NP_003060.2	P28370	SMCA1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1	724					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|DNA strand renaturation (GO:0000733)|neuron differentiation (GO:0030182)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)	CERF complex (GO:0090537)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|NURF complex (GO:0016589)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						TGTATAAACTTTGTTCAATGT	0.348																																						uc011muk.1																			0				biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(13)|ovary(5)|prostate(1)|skin(1)	45						c.(2170-2172)caA>caC		Homo sapiens SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 1 (SMARCA1), transcript variant 1, mRNA.							68.0	62.0	64.0					X																	128621040		2202	4298	6500	SO:0001583	missense	6594				ATP-dependent chromatin remodeling|brain development|neuron differentiation|positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	NURF complex	ATP binding|DNA binding|helicase activity|nucleosome binding|protein binding	g.chrX:128621040T>G	M88163	CCDS14612.1, CCDS76018.1, CCDS76019.1	Xq25	2008-02-05			ENSG00000102038	ENSG00000102038			11097	protein-coding gene	gene with protein product		300012		SNF2L1, SNF2L		1408766, 14609955	Standard	XM_005262461		Approved	SNF2LB, NURF140, ISWI, SWI	uc004eun.4	P28370	OTTHUMG00000022370	ENST00000371122.4:c.2172A>C	X.37:g.128621040T>G	ENSP00000360163:p.Gln724His					SMARCA1_uc004eun.4_Missense_Mutation_p.Q724H|SMARCA1_uc004eup.4_Missense_Mutation_p.Q712H|SMARCA1_uc011mul.1_Missense_Mutation_p.Q712H	p.Q724H	NM_003069	NP_003060	P28370	SMCA1_HUMAN			16	2285	-			724					Q5JV41|Q5JV42	Missense_Mutation	SNP	ENST00000371122.4	37	c.2172A>C	CCDS14612.1	.	.	.	.	.	.	.	.	.	.	T	14.33	2.504034	0.44558	.	.	ENSG00000102038	ENST00000371121;ENST00000371123;ENST00000371122;ENST00000450039	D;D;D;D	0.91351	-2.83;-2.83;-2.83;-2.83	5.79	4.55	0.56014	.	0.284335	0.25500	N	0.030256	T	0.71533	0.3351	N	0.01352	-0.895	0.38086	D	0.936826	B;B;B;B	0.26775	0.099;0.099;0.159;0.099	B;B;B;B	0.23852	0.01;0.013;0.049;0.022	T	0.70791	-0.4776	10	0.56958	D	0.05	-16.4389	4.248	0.10680	0.0:0.1312:0.387:0.4818	.	703;724;712;724	E9PCY3;B7ZLQ5;P28370-2;P28370	.;.;.;SMCA1_HUMAN	H	712;712;724;703	ENSP00000360162:Q712H;ENSP00000360164:Q712H;ENSP00000360163:Q724H;ENSP00000404275:Q703H	ENSP00000360162:Q712H	Q	-	3	2	SMARCA1	128448721	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	1.020000	0.30027	1.941000	0.56285	0.441000	0.28932	CAA		0.348	SMARCA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058206.1	NM_003069	
