#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
CHD5	26038	broad.mit.edu	37	1	6189033	6189033	+	Missense_Mutation	SNP	C	C	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:6189033C>A	ENST00000262450.3	-	23	3583	c.3484G>T	c.(3484-3486)Gcc>Tcc	p.A1162S	CHD5_ENST00000378021.1_Missense_Mutation_p.A19S	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TTGCGCTTGGCCACCTGCGTG	0.642																																						uc001amb.1																			0				central_nervous_system(3)|breast(3)|ovary(2)|upper_aerodigestive_tract(1)|lung(1)|skin(1)|pancreas(1)	12						c.(3484-3486)GCC>TCC		chromodomain helicase DNA binding protein 5							65.0	58.0	60.0					1																	6189033		2203	4300	6503	SO:0001583	missense	26038				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	ATP binding|ATP-dependent helicase activity|DNA binding|zinc ion binding	g.chr1:6189033C>A	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.3484G>T	1.37:g.6189033C>A	ENSP00000262450:p.Ala1162Ser					CHD5_uc001alz.1_Missense_Mutation_p.A19S|CHD5_uc001ama.1_RNA|CHD5_uc001amc.1_RNA|CHD5_uc009vlx.1_RNA	p.A1162S	NM_015557	NP_056372	Q8TDI0	CHD5_HUMAN		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)	23	3584	-	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)	1162			Helicase C-terminal.		A8KAP8|A8MQ44|D3DSH9|O60740	Missense_Mutation	SNP	ENST00000262450.3	37	c.3484G>T	CCDS57.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044221	0.93685	.	.	ENSG00000116254	ENST00000262450;ENST00000378006;ENST00000378021;ENST00000536802;ENST00000538279;ENST00000377999	D;T	0.95412	-3.7;1.08	4.1	4.1	0.47936	Helicase, C-terminal (1);	0.000000	0.64402	D	0.000001	D	0.96821	0.8962	L	0.53561	1.675	0.80722	D	1	D;D	0.89917	0.993;1.0	D;D	0.91635	0.968;0.999	D	0.97400	0.9995	10	0.66056	D	0.02	-21.7686	16.8544	0.86002	0.0:1.0:0.0:0.0	.	1162;19	Q8TDI0;Q5TG85	CHD5_HUMAN;.	S	1162;678;19;570;570;19	ENSP00000262450:A1162S;ENSP00000367260:A19S	ENSP00000262450:A1162S	A	-	1	0	CHD5	6111620	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.662000	0.83803	2.268000	0.75426	0.561000	0.74099	GCC		0.642	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
ESPNP	284729	broad.mit.edu	37	1	17030453	17030453	+	RNA	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:17030453G>A	ENST00000492551.1	-	0	882					NR_026567.1				espin pseudogene																		GGAGGGTGCTGGCCCTTGATG	0.637																																						uc001azn.1																			0					0						c.(769-771)CAG>TAG		RecName: Full=Espin; AltName: Full=Ectoplasmic specialization protein; AltName: Full=Autosomal recessive deafness type 36 protein;																																						284729							g.chr1:17030453G>A	AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17030453G>A							p.Q257*	NR_026567						5	883	-									Nonsense_Mutation	SNP	ENST00000492551.1	37	c.769C>T																																																																																					0.637	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1		
MRTO4	51154	broad.mit.edu	37	1	19584462	19584462	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:19584462C>T	ENST00000330263.4	+	6	774	c.477C>T	c.(475-477)ccC>ccT	p.P159P		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	159					ribosome biogenesis (GO:0042254)	nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGGCCTGCCCACCGCCCTCA	0.607																																					GBM(192;2418 3032 7540 48714)	uc001bbs.2																			0					0						c.(475-477)CCC>CCT		mRNA turnover 4 homolog							34.0	39.0	37.0					1																	19584462		2203	4299	6502	SO:0001819	synonymous_variant	51154				ribosome biogenesis	nuclear membrane|nucleolus		g.chr1:19584462C>T	AK027569	CCDS191.1	1p36.13	2008-02-05	2006-12-21	2007-01-05	ENSG00000053372	ENSG00000053372			18477	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 33"", ""MRT4, mRNA turnover 4, homolog (S. cerevisiae)"""	C1orf33			Standard	NM_016183		Approved	dJ657E11.4, MRT4	uc001bbs.3	Q9UKD2	OTTHUMG00000002496	ENST00000330263.4:c.477C>T	1.37:g.19584462C>T							p.P159P	NM_016183	NP_057267	Q9UKD2	MRT4_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.87e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|GBM - Glioblastoma multiforme(114;0.00301)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	6	732	+		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Breast(348;0.00049)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)	159					B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Silent	SNP	ENST00000330263.4	37	c.477C>T	CCDS191.1																																																																																				0.607	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
HPCAL4	51440	broad.mit.edu	37	1	40149794	40149794	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:40149794C>T	ENST00000372844.3	-	3	584	c.193G>A	c.(193-195)Gcg>Acg	p.A65T		NM_001282396.1|NM_001282397.1|NM_016257.2	NP_001269325.1|NP_001269326.1|NP_057341.1	Q9UM19	HPCL4_HUMAN	hippocalcin like 4	65	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				central nervous system development (GO:0007417)|signal transduction (GO:0007165)	intracellular (GO:0005622)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)	p.A65S(1)		breast(1)|central_nervous_system(1)|lung(5)|stomach(1)	8	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GCGTGCTGCGCGAACTTGGAG	0.682																																						uc001cdr.2																			1	Substitution - Missense(1)		lung(1)	central_nervous_system(1)	1						c.(193-195)GCG>ACG		hippocalcin-like protein 4							38.0	36.0	37.0					1																	40149794		2203	4300	6503	SO:0001583	missense	51440				central nervous system development	intracellular	calcium ion binding	g.chr1:40149794C>T	AB001105	CCDS441.1, CCDS72761.1	1p34.2	2013-01-10			ENSG00000116983	ENSG00000116983		"""EF-hand domain containing"""	18212	protein-coding gene	gene with protein product						10520747	Standard	NM_016257		Approved	HLP4, DKFZp761G122	uc001cdr.3	Q9UM19	OTTHUMG00000009246	ENST00000372844.3:c.193G>A	1.37:g.40149794C>T	ENSP00000361935:p.Ala65Thr					HPCAL4_uc010oix.1_Intron	p.A65T	NM_016257	NP_057341	Q9UM19	HPCL4_HUMAN	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;4.3e-17)|all cancers(16;8.48e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)		3	313	-	all_cancers(7;4.65e-13)|Lung NSC(20;2.88e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	65			EF-hand 2.		B2R5U2|D3DPU1|Q5TG97|Q8N611	Missense_Mutation	SNP	ENST00000372844.3	37	c.193G>A	CCDS441.1	.	.	.	.	.	.	.	.	.	.	C	35	5.424307	0.96111	.	.	ENSG00000116983	ENST00000372844;ENST00000450300	T	0.32023	1.47	3.51	3.51	0.40186	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.46678	0.1405	L	0.59436	1.845	0.80722	D	1	D	0.89917	1.0	P	0.58172	0.834	T	0.54886	-0.8226	10	0.87932	D	0	.	16.3574	0.83241	0.0:1.0:0.0:0.0	.	65	Q9UM19	HPCL4_HUMAN	T	65;57	ENSP00000361935:A65T	ENSP00000361935:A65T	A	-	1	0	HPCAL4	39922381	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.542000	0.82095	2.260000	0.74910	0.462000	0.41574	GCG		0.682	HPCAL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025640.1	NM_016257	
C1orf177	163747	broad.mit.edu	37	1	55277777	55277777	+	Missense_Mutation	SNP	C	C	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:55277777C>A	ENST00000371273.3	+	6	692	c.677C>A	c.(676-678)gCa>gAa	p.A226E	C1orf177_ENST00000358193.3_Missense_Mutation_p.A226E	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	226										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						ACATATGTGGCACGATCCGTC	0.592																																						uc001cyb.3																			0					0						c.(676-678)GCA>GAA		hypothetical protein LOC163747 isoform 2							102.0	102.0	102.0					1																	55277777		2203	4300	6503	SO:0001583	missense	163747							g.chr1:55277777C>A	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.677C>A	1.37:g.55277777C>A	ENSP00000360320:p.Ala226Glu					C1orf177_uc001cya.3_Missense_Mutation_p.A226E	p.A226E	NM_001110533	NP_001104003	Q3ZCV2	CA177_HUMAN			6	731	+			226					B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	c.677C>A	CCDS44153.1	.	.	.	.	.	.	.	.	.	.	C	0.023	-1.401623	0.01165	.	.	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.23348	1.91;1.91	5.06	-2.02	0.07388	.	1.063300	0.07353	N	0.882736	T	0.14313	0.0346	L	0.29908	0.895	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	T	0.36456	-0.9747	10	0.06494	T	0.89	-17.9711	7.7287	0.28775	0.4871:0.2648:0.2481:0.0	.	226;226	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	E	226	ENSP00000350924:A226E;ENSP00000360320:A226E	ENSP00000350924:A226E	A	+	2	0	C1orf177	55050365	0.002000	0.14202	0.033000	0.17914	0.002000	0.02628	-0.310000	0.08135	0.026000	0.15269	-0.521000	0.04368	GCA		0.592	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
GPSM2	29899	broad.mit.edu	37	1	109472462	109472462	+	Missense_Mutation	SNP	G	G	C			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:109472462G>C	ENST00000406462.2	+	16	2728	c.1955G>C	c.(1954-1956)aGa>aCa	p.R652T	AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369969.2_3'UTR|CLCC1_ENST00000415331.1_3'UTR|CLCC1_ENST00000482889.1_5'Flank|CLCC1_ENST00000369971.2_3'UTR|CLCC1_ENST00000369968.2_3'UTR|CLCC1_ENST00000356970.2_3'UTR|GPSM2_ENST00000264126.3_Missense_Mutation_p.R652T			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	652					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CTTTTACAAAGAGATCAAAAC	0.398																																						uc010ovc.1																			0				central_nervous_system(1)	1						c.(1954-1956)AGA>ACA		LGN protein							88.0	87.0	87.0					1																	109472462		2203	4300	6503	SO:0001583	missense	29899				G-protein coupled receptor protein signaling pathway	cell cortex|nucleus	GTPase activator activity|identical protein binding	g.chr1:109472462G>C	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1955G>C	1.37:g.109472462G>C	ENSP00000385510:p.Arg652Thr					AKNAD1_uc010ovb.1_Intron|GPSM2_uc010ovd.1_Missense_Mutation_p.R652T|GPSM2_uc010ove.1_Missense_Mutation_p.R652T|CLCC1_uc001dwe.1_3'UTR|CLCC1_uc001dwf.1_3'UTR|CLCC1_uc001dwg.1_3'UTR	p.R652T	NM_013296	NP_037428	P81274	GPSM2_HUMAN		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)	15	2451	+		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)	652					Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	c.1955G>C	CCDS792.2	.	.	.	.	.	.	.	.	.	.	G	13.75	2.331540	0.41297	.	.	ENSG00000121957	ENST00000406462;ENST00000264126	D;D	0.92911	-3.13;-3.13	5.97	5.97	0.96955	.	0.115109	0.64402	D	0.000020	T	0.75903	0.3913	N	0.08118	0	0.80722	D	1	P	0.45126	0.851	B	0.37550	0.253	T	0.79801	-0.1650	10	0.14656	T	0.56	-21.6606	19.1953	0.93686	0.0:0.0:1.0:0.0	.	652	P81274	GPSM2_HUMAN	T	652	ENSP00000385510:R652T;ENSP00000264126:R652T	ENSP00000264126:R652T	R	+	2	0	GPSM2	109273985	0.963000	0.33076	1.000000	0.80357	0.996000	0.88848	1.239000	0.32719	2.828000	0.97474	0.655000	0.94253	AGA		0.398	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
ZNF697	90874	broad.mit.edu	37	1	120165477	120165477	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:120165477C>T	ENST00000421812.2	-	3	1608	c.1489G>A	c.(1489-1491)Gag>Aag	p.E497K		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	497					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		TTGCCGCACTCGATGCACGTG	0.647																																						uc001ehy.1																			0				ovary(1)	1						c.(1489-1491)GAG>AAG		zinc finger protein 697							31.0	35.0	33.0					1																	120165477		2201	4299	6500	SO:0001583	missense	90874				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr1:120165477C>T	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.1489G>A	1.37:g.120165477C>T	ENSP00000396857:p.Glu497Lys						p.E497K	NM_001080470	NP_001073939	Q5TEC3	ZN697_HUMAN		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)	3	1603	-	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)	497			C2H2-type 10.		Q96IT2	Missense_Mutation	SNP	ENST00000421812.2	37	c.1489G>A	CCDS44202.1	.	.	.	.	.	.	.	.	.	.	C	19.43	3.825465	0.71143	.	.	ENSG00000143067	ENST00000421812	T	0.01152	5.26	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.36972	N	0.002309	T	0.01254	0.0041	N	0.19112	0.55	0.34359	D	0.690765	D	0.76494	0.999	D	0.66351	0.943	T	0.62996	-0.6735	10	0.62326	D	0.03	-23.8521	10.4776	0.44674	0.0:0.9116:0.0:0.0884	.	497	Q5TEC3	ZN697_HUMAN	K	497	ENSP00000396857:E497K	ENSP00000396857:E497K	E	-	1	0	ZNF697	119967000	0.667000	0.27484	1.000000	0.80357	0.525000	0.34531	1.664000	0.37439	2.713000	0.92767	0.655000	0.94253	GAG		0.647	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
PDE4DIP	9659	broad.mit.edu	37	1	144886204	144886204	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:144886204C>T	ENST00000369354.3	-	23	3219	c.3030G>A	c.(3028-3030)agG>agA	p.R1010R	PDE4DIP_ENST00000530740.1_Silent_p.R1147R|PDE4DIP_ENST00000369356.4_Silent_p.R1010R|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Silent_p.R1076R|PDE4DIP_ENST00000369359.4_Silent_p.R1147R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1010					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)	p.R1010S(2)|p.R1010N(2)		NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		GGAACTCAGCCCTCAGGTGGA	0.522			T	PDGFRB	MPD																																	uc001elw.3				Dom	yes		1	1q12	9659	T	phosphodiesterase 4D interacting protein (myomegalin)			L	PDGFRB		MPD		4	Substitution - Missense(4)		lung(4)	ovary(4)|haematopoietic_and_lymphoid_tissue(1)	5						c.(3028-3030)AGG>AGA		phosphodiesterase 4D interacting protein isoform							210.0	204.0	206.0					1																	144886204		2203	4296	6499	SO:0001819	synonymous_variant	9659				cellular protein complex assembly	centrosome|Golgi apparatus|myofibril|nucleus	enzyme binding	g.chr1:144886204C>T	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.3030G>A	1.37:g.144886204C>T						NBPF10_uc009wir.2_Intron|NBPF9_uc010oye.1_Intron|NBPF9_uc010oyf.1_Intron|NBPF9_uc010oyg.1_Intron|PDE4DIP_uc001elk.1_Intron|PDE4DIP_uc001ell.1_Intron|PDE4DIP_uc001elm.3_Intron|PDE4DIP_uc001eln.3_Intron|PDE4DIP_uc001elo.2_Intron|PDE4DIP_uc001elx.3_Silent_p.R1076R|PDE4DIP_uc001elv.3_Silent_p.R17R	p.R1010R	NM_014644	NP_055459	Q5VU43	MYOME_HUMAN		Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)	23	3321	-			1010			Potential.		A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	c.3030G>A	CCDS30824.1																																																																																				0.522	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
LINGO4	339398	broad.mit.edu	37	1	151774395	151774395	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:151774395G>A	ENST00000368820.3	-	2	1723	c.786C>T	c.(784-786)tgC>tgT	p.C262C		NM_001004432.2	NP_001004432.1	Q6UY18	LIGO4_HUMAN	leucine rich repeat and Ig domain containing 4	262						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(4)|large_intestine(5)|lung(4)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGCTCAGATTGCAGCGAGTGA	0.607																																						uc001ezf.1																			0				large_intestine(1)	1						c.(784-786)TGC>TGT		leucine rich repeat and Ig domain containing 4							59.0	63.0	62.0					1																	151774395		2203	4300	6503	SO:0001819	synonymous_variant	339398					integral to membrane		g.chr1:151774395G>A		CCDS30855.1	1q21.3	2013-01-11	2007-02-01	2007-02-01	ENSG00000213171	ENSG00000213171		"""Immunoglobulin superfamily / I-set domain containing"""	31814	protein-coding gene	gene with protein product		609794	"""leucine rich repeat neuronal 6D"""	LRRN6D			Standard	NM_001004432		Approved		uc001ezf.1	Q6UY18	OTTHUMG00000013059	ENST00000368820.3:c.786C>T	1.37:g.151774395G>A							p.C262C	NM_001004432	NP_001004432	Q6UY18	LIGO4_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.181)		2	976	-	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		262			Extracellular (Potential).|LRR 8.			Silent	SNP	ENST00000368820.3	37	c.786C>T	CCDS30855.1																																																																																				0.607	LINGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036639.1	XM_291387	
FLG2	388698	broad.mit.edu	37	1	152329096	152329096	+	Missense_Mutation	SNP	T	T	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:152329096T>G	ENST00000388718.5	-	3	1238	c.1166A>C	c.(1165-1167)cAg>cCg	p.Q389P	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	389	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ACTACAAGACTGGCTACCTCC	0.443																																						uc001ezw.3																			0				ovary(10)|skin(5)|upper_aerodigestive_tract(1)|breast(1)	17						c.(1165-1167)CAG>CCG		filaggrin family member 2							124.0	118.0	120.0					1																	152329096		2203	4300	6503	SO:0001583	missense	388698						calcium ion binding|structural molecule activity	g.chr1:152329096T>G	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1166A>C	1.37:g.152329096T>G	ENSP00000373370:p.Gln389Pro					uc001ezv.2_Intron	p.Q389P	NM_001014342	NP_001014364	Q5D862	FILA2_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	1239	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		389			Ser-rich.		Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	c.1166A>C	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	T	12.19	1.864409	0.32977	.	.	ENSG00000143520	ENST00000388718	T	0.19105	2.17	5.09	1.36	0.22044	.	.	.	.	.	T	0.07548	0.0190	L	0.59436	1.845	0.09310	N	1	P	0.41978	0.767	B	0.39971	0.315	T	0.21793	-1.0235	9	0.33940	T	0.23	-13.0781	4.2415	0.10650	0.0:0.1854:0.174:0.6406	.	389	Q5D862	FILA2_HUMAN	P	389	ENSP00000373370:Q389P	ENSP00000373370:Q389P	Q	-	2	0	FLG2	150595720	0.151000	0.22747	0.797000	0.32132	0.007000	0.05969	0.631000	0.24568	0.390000	0.25115	-0.256000	0.11100	CAG		0.443	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
CRNN	49860	broad.mit.edu	37	1	152383181	152383181	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:152383181G>A	ENST00000271835.3	-	3	439	c.377C>T	c.(376-378)gCg>gTg	p.A126V	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	126					response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCTTTCCCCGCCCTTCCCAC	0.637																																						uc001ezx.2																			0				ovary(2)|skin(1)	3						c.(376-378)GCG>GTG		cornulin							153.0	168.0	163.0					1																	152383181		2203	4300	6503	SO:0001583	missense	49860				cell-cell adhesion|response to heat	cytoplasm|membrane	calcium ion binding	g.chr1:152383181G>A	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"""EF-hand domain containing"""	1230	protein-coding gene	gene with protein product		611312	"""chromosome 1 open reading frame 10"""	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.377C>T	1.37:g.152383181G>A	ENSP00000271835:p.Ala126Val						p.A126V	NM_016190	NP_057274	Q9UBG3	CRNN_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	451	-	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		126					B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	c.377C>T	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947251	0.34377	.	.	ENSG00000143536	ENST00000271835	T	0.04275	3.66	4.63	-1.58	0.08479	.	1.097220	0.07086	N	0.837952	T	0.00906	0.0030	N	0.20986	0.625	0.09310	N	1	B	0.12630	0.006	B	0.10450	0.005	T	0.49204	-0.8964	10	0.46703	T	0.11	.	0.4844	0.00553	0.3946:0.1445:0.241:0.2199	.	126	Q9UBG3	CRNN_HUMAN	V	126	ENSP00000271835:A126V	ENSP00000271835:A126V	A	-	2	0	CRNN	150649805	0.000000	0.05858	0.000000	0.03702	0.576000	0.36127	-1.053000	0.03500	-0.148000	0.11234	0.305000	0.20034	GCG		0.637	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
S100A7A	338324	broad.mit.edu	37	1	153390660	153390660	+	Silent	SNP	G	G	A	rs370692845		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:153390660G>A	ENST00000368729.4	+	2	159	c.102G>A	c.(100-102)acG>acA	p.T34T	S100A7A_ENST00000368728.2_Silent_p.T34T|S100A7A_ENST00000329256.2_Silent_p.T34T	NM_176823.3	NP_789793.1	Q86SG5	S1A7A_HUMAN	S100 calcium binding protein A7A	34	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.					cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|protein self-association (GO:0043621)			cervix(1)|endometrium(3)|kidney(1)|lung(3)|prostate(1)|skin(2)|stomach(1)	12	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.171)			GCCTGCTGACGATGATGAAGG	0.483													G|||	1	0.000199681	0.0	0.0	5008	,	,		20814	0.0		0.001	False		,,,				2504	0.0					uc001fbt.1																			0				skin(1)	1						c.(100-102)ACG>ACA		S100 calcium binding protein A7-like 1		G		0,4406		0,0,2203	205.0	178.0	187.0		102	0.5	0.0	1		187	1,8599		0,1,4299	no	coding-synonymous	S100A7A	NM_176823.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		34/102	153390660	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	338324					cytoplasm	calcium ion binding	g.chr1:153390660G>A	AY189118	CCDS30872.1	1q22	2013-01-10	2006-09-11	2006-09-11	ENSG00000184330	ENSG00000184330		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	21657	protein-coding gene	gene with protein product			"""S100 calcium binding protein A15"", ""S100 calcium binding protein A7-like 1"""	S100A15, S100A7L1		11230159	Standard	NM_176823		Approved	S100A7f	uc001fbt.1	Q86SG5	OTTHUMG00000013122	ENST00000368729.4:c.102G>A	1.37:g.153390660G>A							p.T34T	NM_176823	NP_789793	Q86SG5	S1A7A_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.171)		2	159	+	all_lung(78;2.81e-33)|Lung NSC(65;9.54e-32)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)		34			EF-hand 1.		D3DV38|Q5SY69	Silent	SNP	ENST00000368729.4	37	c.102G>A	CCDS30872.1																																																																																				0.483	S100A7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036786.2	NM_176823	
HMCN1	83872	broad.mit.edu	37	1	186052023	186052023	+	Silent	SNP	C	C	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:186052023C>A	ENST00000271588.4	+	57	9043	c.8814C>A	c.(8812-8814)atC>atA	p.I2938I	HMCN1_ENST00000367492.2_Silent_p.I2938I	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2938	Ig-like C2-type 27.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TAACAGATATCGGCAGGTATG	0.328																																						uc001grq.1																			0				ovary(22)|skin(1)	23						c.(8812-8814)ATC>ATA		hemicentin 1 precursor							52.0	58.0	56.0					1																	186052023		2203	4300	6503	SO:0001819	synonymous_variant	83872				response to stimulus|visual perception	basement membrane	calcium ion binding	g.chr1:186052023C>A	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8814C>A	1.37:g.186052023C>A							p.I2938I	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN			57	9043	+			2938			Ig-like C2-type 27.		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	c.8814C>A	CCDS30956.1																																																																																				0.328	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
HHIPL2	79802	broad.mit.edu	37	1	222713493	222713493	+	Nonsense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:222713493G>A	ENST00000343410.6	-	4	1367	c.1309C>T	c.(1309-1311)Cga>Tga	p.R437*		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	437					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		ATCCGGCCTCGGCCCTGGCGC	0.577																																						uc001hnh.1																			0				ovary(1)	1						c.(1309-1311)CGA>TGA		HHIP-like 2 precursor							71.0	72.0	72.0					1																	222713493		2203	4300	6503	SO:0001587	stop_gained	79802				carbohydrate metabolic process	extracellular region	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor|quinone binding	g.chr1:222713493G>A	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1309C>T	1.37:g.222713493G>A	ENSP00000342118:p.Arg437*						p.R437*	NM_024746	NP_079022	Q6UWX4	HIPL2_HUMAN		GBM - Glioblastoma multiforme(131;0.0185)	4	1367	-			437					Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Nonsense_Mutation	SNP	ENST00000343410.6	37	c.1309C>T	CCDS1530.2	.	.	.	.	.	.	.	.	.	.	G	34	5.367408	0.95900	.	.	ENSG00000143512	ENST00000343410	.	.	.	5.52	4.55	0.56014	.	0.054840	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.7232	11.565	0.50800	0.0:0.0:0.661:0.339	.	.	.	.	X	437	.	ENSP00000342118:R437X	R	-	1	2	HHIPL2	220780116	1.000000	0.71417	1.000000	0.80357	0.078000	0.17371	3.339000	0.52135	2.571000	0.86741	0.591000	0.81541	CGA		0.577	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
RYR2	6262	broad.mit.edu	37	1	237802413	237802413	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr1:237802413C>T	ENST00000366574.2	+	46	7344	c.7027C>T	c.(7027-7029)Ctt>Ttt	p.L2343F	RYR2_ENST00000542537.1_Missense_Mutation_p.L2327F|RYR2_ENST00000360064.6_Missense_Mutation_p.L2341F	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2343	4 X approximate repeats.				BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TGGGAATGGGCTTCTTGCAGC	0.498																																						uc001hyl.1																			0				ovary(17)|large_intestine(6)|central_nervous_system(6)|pancreas(3)|breast(1)	33						c.(7027-7029)CTT>TTT		cardiac muscle ryanodine receptor							126.0	128.0	127.0					1																	237802413		1934	4125	6059	SO:0001583	missense	6262				cardiac muscle contraction|detection of calcium ion|induction of apoptosis by ionic changes|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum|response to caffeine|response to hypoxia|response to redox state	calcium channel complex|cytosol|plasma membrane|plasma membrane enriched fraction|sarcoplasmic reticulum membrane	calcium ion binding|calmodulin binding|identical protein binding|protein kinase A catalytic subunit binding|protein kinase A regulatory subunit binding|receptor activity|ryanodine-sensitive calcium-release channel activity|suramin binding	g.chr1:237802413C>T	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.7027C>T	1.37:g.237802413C>T	ENSP00000355533:p.Leu2343Phe						p.L2343F	NM_001035	NP_001026	Q92736	RYR2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		46	7147	+	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	2343			Cytoplasmic (By similarity).|4 X approximate repeats.		Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	c.7027C>T	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	C	19.45	3.829349	0.71258	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.99311	-5.73;-5.73;-5.73	5.05	5.05	0.67936	.	0.000000	0.50627	D	0.000116	D	0.99327	0.9764	M	0.87180	2.865	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99072	1.0834	10	0.87932	D	0	.	9.0377	0.36298	0.0:0.7907:0.0:0.2093	.	2343	Q92736	RYR2_HUMAN	F	2343;2341;2327	ENSP00000355533:L2343F;ENSP00000353174:L2341F;ENSP00000443798:L2327F	ENSP00000353174:L2341F	L	+	1	0	RYR2	235869036	0.441000	0.25626	0.993000	0.49108	0.975000	0.68041	0.935000	0.28924	2.498000	0.84270	0.561000	0.74099	CTT		0.498	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
Unknown	0	broad.mit.edu	37	10	135491113	135491113	+	IGR	SNP	G	G	A	rs372931654		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr10:135491113G>A								AL845259.1 (17934 upstream) : None (None downstream)																							GGTCGCCTTCGCCCACACCGG	0.776																																						uc010qvi.1																			0					0						c.(724-726)GCC>ACC		double homeobox, 4-like							13.0	15.0	14.0					10																	135491113		1133	2184	3317	SO:0001628	intergenic_variant	653544					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr10:135491113G>A																													10.37:g.135491113G>A							p.A242T	NM_001127389	NP_001120861	F5GZ66	F5GZ66_HUMAN			1	835	+			242						Missense_Mutation	SNP		37	c.724G>A																																																																																				0	0.776								
OR52D1	390066	broad.mit.edu	37	11	5510222	5510222	+	Missense_Mutation	SNP	T	T	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr11:5510222T>A	ENST00000322641.5	+	1	308	c.286T>A	c.(286-288)Tcc>Acc	p.S96T	HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBG2_ENST00000380259.2_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	96					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGGTGAGATTTCCTTTGGTGG	0.498																																						uc010qzg.1																			0				central_nervous_system(1)	1						c.(286-288)TCC>ACC		olfactory receptor, family 52, subfamily D,							142.0	124.0	130.0					11																	5510222		2201	4297	6498	SO:0001583	missense	390066				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:5510222T>A	BK004276	CCDS31384.1	11p15.4	2012-08-09			ENSG00000181609	ENSG00000181609		"""GPCR / Class A : Olfactory receptors"""	15212	protein-coding gene	gene with protein product							Standard	NM_001005163		Approved		uc010qzg.2	Q9H346	OTTHUMG00000066895	ENST00000322641.5:c.286T>A	11.37:g.5510222T>A	ENSP00000326232:p.Ser96Thr					HBG2_uc001mak.1_Intron|HBE1_uc001mam.1_Intron|OR51B5_uc001maq.1_Intron	p.S96T	NM_001005163	NP_001005163	Q9H346	O52D1_HUMAN		Epithelial(150;3.46e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	1	286	+		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)	96			Extracellular (Potential).		B9EGY9|Q6IFI6	Missense_Mutation	SNP	ENST00000322641.5	37	c.286T>A	CCDS31384.1	.	.	.	.	.	.	.	.	.	.	T	11.34	1.610996	0.28712	.	.	ENSG00000181609	ENST00000322641	T	0.00724	5.78	5.57	4.4	0.53042	GPCR, rhodopsin-like superfamily (1);	0.092462	0.48286	D	0.000193	T	0.01029	0.0034	M	0.62266	1.93	0.27290	N	0.957853	B	0.13594	0.008	B	0.19666	0.026	T	0.41787	-0.9489	10	0.30078	T	0.28	.	4.943	0.13975	0.2419:0.0807:0.0:0.6775	.	96	Q9H346	O52D1_HUMAN	T	96	ENSP00000326232:S96T	ENSP00000326232:S96T	S	+	1	0	OR52D1	5466798	0.000000	0.05858	1.000000	0.80357	0.869000	0.49853	-0.155000	0.10115	2.340000	0.79590	0.528000	0.53228	TCC		0.498	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
PRMT3	10196	broad.mit.edu	37	11	20448405	20448405	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr11:20448405G>A	ENST00000331079.6	+	10	1204	c.987G>A	c.(985-987)gaG>gaA	p.E329E	PRMT3_ENST00000437750.2_Silent_p.E267E	NM_001145167.1|NM_005788.3	NP_001138639.1|NP_005779	O60678	ANM3_HUMAN	protein arginine methyltransferase 3	329	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				histone arginine methylation (GO:0034969)|negative regulation of protein ubiquitination (GO:0031397)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|ribosome (GO:0005840)	histone-arginine N-methyltransferase activity (GO:0008469)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|modified amino acid binding (GO:0072341)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|prostate(1)	17						TCATATCTGAGTGGATGGTGA	0.254																																						uc001mqb.2																			0					0						c.(985-987)GAG>GAA		protein arginine methyltransferase 3 isoform 1							55.0	60.0	58.0					11																	20448405		2184	4281	6465	SO:0001819	synonymous_variant	10196						zinc ion binding	g.chr11:20448405G>A	AF059531	CCDS7853.1, CCDS44554.1	11p15.1	2008-02-05	2006-02-16	2006-02-16	ENSG00000185238	ENSG00000185238		"""Protein arginine methyltransferases"""	30163	protein-coding gene	gene with protein product		603190	"""HMT1 hnRNP methyltransferase-like 3 (S. cerevisiae)"""	HRMT1L3		9642256	Standard	NM_005788		Approved		uc001mqb.3	O60678	OTTHUMG00000166022	ENST00000331079.6:c.987G>A	11.37:g.20448405G>A						PRMT3_uc001mqc.2_Silent_p.E252E|PRMT3_uc010rdn.1_Silent_p.E267E	p.E329E	NM_005788	NP_005779	O60678	ANM3_HUMAN			10	1204	+			329					B4DUC7	Silent	SNP	ENST00000331079.6	37	c.987G>A	CCDS7853.1																																																																																				0.254	PRMT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387489.1	NM_005788	
TMPRSS4	56649	broad.mit.edu	37	11	117985881	117985881	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr11:117985881G>A	ENST00000437212.3	+	11	1252	c.1038G>A	c.(1036-1038)gcG>gcA	p.A346A	TMPRSS4_ENST00000534111.1_Silent_p.A344A|TMPRSS4_ENST00000522307.1_Silent_p.A199A|TMPRSS4_ENST00000518413.2_Intron|TMPRSS4_ENST00000523251.1_Silent_p.A306A|TMPRSS4_ENST00000522824.1_Silent_p.A341A			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	346	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		TGCTGCAGGCGTCAGTCCAGG	0.552																																						uc010rxo.1																			0				large_intestine(1)|central_nervous_system(1)	2						c.(1036-1038)GCG>GCA		transmembrane protease, serine 4 isoform 1							90.0	70.0	77.0					11																	117985881		2200	4296	6496	SO:0001819	synonymous_variant	56649				proteolysis	integral to membrane	scavenger receptor activity|serine-type endopeptidase activity	g.chr11:117985881G>A	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.1038G>A	11.37:g.117985881G>A						TMPRSS4_uc010rxp.1_Silent_p.A341A|TMPRSS4_uc010rxq.1_Silent_p.A199A|TMPRSS4_uc010rxr.1_Silent_p.A321A|TMPRSS4_uc010rxs.1_Silent_p.A306A|TMPRSS4_uc009yzu.2_Intron|TMPRSS4_uc010rxt.1_Silent_p.A321A	p.A346A	NM_019894	NP_063947	Q9NRS4	TMPS4_HUMAN		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)	11	1329	+	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)	346			Extracellular (Potential).|Peptidase S1.		A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Silent	SNP	ENST00000437212.3	37	c.1038G>A	CCDS31684.1																																																																																				0.552	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
TECTA	7007	broad.mit.edu	37	11	120998873	120998873	+	Silent	SNP	C	C	T	rs529258973		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr11:120998873C>T	ENST00000392793.1	+	9	2458	c.2187C>T	c.(2185-2187)taC>taT	p.Y729Y	TECTA_ENST00000264037.2_Silent_p.Y729Y			O75443	TECTA_HUMAN	tectorin alpha	729	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)		p.Y729Y(1)	TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		GCGCCTCCTACGCCTTCCCCT	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		17915	0.0		0.0	False		,,,				2504	0.001					uc010rzo.1																			1	Substitution - coding silent(1)		large_intestine(1)	breast(6)|ovary(2)|skin(2)	10						c.(2185-2187)TAC>TAT		tectorin alpha precursor							99.0	87.0	91.0					11																	120998873		2203	4299	6502	SO:0001819	synonymous_variant	7007				cell-matrix adhesion|sensory perception of sound	anchored to membrane|plasma membrane|proteinaceous extracellular matrix		g.chr11:120998873C>T	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.2187C>T	11.37:g.120998873C>T							p.Y729Y	NM_005422	NP_005413	O75443	TECTA_HUMAN		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)	8	2187	+	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)	729			VWFD 2.			Silent	SNP	ENST00000392793.1	37	c.2187C>T	CCDS8434.1																																																																																				0.622	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
C12orf77	196415	broad.mit.edu	37	12	25148921	25148921	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr12:25148921C>T	ENST00000549828.1	-	3	431	c.227G>A	c.(226-228)cGa>cAa	p.R76Q	C12orf77_ENST00000434912.3_Missense_Mutation_p.R21Q|C12orf77_ENST00000549262.1_Missense_Mutation_p.R21Q	NM_001101339.1	NP_001094809.1	C9JDV5	CL097_HUMAN	chromosome 12 open reading frame 77	76										endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)	7						AGGCATCCATCGTATGCTGTC	0.502																																						uc001rgf.2																			0					0						c.(226-228)CGA>CAA		hypothetical protein LOC196415							85.0	89.0	88.0					12																	25148921		1990	4158	6148	SO:0001583	missense	196415							g.chr12:25148921C>T	BC046192	CCDS44846.1	12p12.1	2009-09-30			ENSG00000226397	ENSG00000226397			27282	protein-coding gene	gene with protein product						12477932	Standard	NM_001101339		Approved		uc001rgf.3	C9JDV5	OTTHUMG00000170185	ENST00000549828.1:c.227G>A	12.37:g.25148921C>T	ENSP00000447146:p.Arg76Gln						p.R76Q	NM_001101339	NP_001094809	C9JDV5	CL097_HUMAN			3	432	-			76						Missense_Mutation	SNP	ENST00000549828.1	37	c.227G>A	CCDS44846.1	.	.	.	.	.	.	.	.	.	.	C	7.531	0.658723	0.14645	.	.	ENSG00000226397	ENST00000549828;ENST00000549262;ENST00000434912	T;T;T	0.56776	0.5;0.44;0.44	2.5	1.61	0.23674	.	.	.	.	.	T	0.23766	0.0575	N	0.08118	0	0.09310	N	1	P	0.38800	0.648	B	0.24155	0.051	T	0.11372	-1.0590	9	0.87932	D	0	.	5.4381	0.16492	0.0:0.8385:0.0:0.1615	.	76	C9JDV5	CL097_HUMAN	Q	76;21;21	ENSP00000447146:R76Q;ENSP00000447028:R21Q;ENSP00000403451:R21Q	ENSP00000403451:R21Q	R	-	2	0	C12orf77	25040188	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.721000	0.04963	0.597000	0.29811	-0.137000	0.14449	CGA		0.502	C12orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407827.1	NM_001101339	
ACVRL1	94	broad.mit.edu	37	12	52309923	52309923	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr12:52309923G>A	ENST00000388922.4	+	8	1435	c.1152G>A	c.(1150-1152)caG>caA	p.Q384Q	ACVRL1_ENST00000550683.1_Silent_p.Q398Q|ACVRL1_ENST00000419526.2_Silent_p.Q210Q	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	384	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta receptor activity, type I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	TGGACGAGCAGATCCGCACGG	0.602																																						uc001rzj.2																			0				lung(2)	2						c.(1150-1152)CAG>CAA		activin A receptor type II-like 1 precursor	Adenosine triphosphate(DB00171)						105.0	89.0	95.0					12																	52309923		2203	4300	6503	SO:0001819	synonymous_variant	94	Hereditary_Hemorrhagic_Telangiectasia			blood vessel endothelial cell proliferation involved in sprouting angiogenesis|blood vessel maturation|negative regulation of cell growth|negative regulation of cell proliferation|negative regulation of endothelial cell migration|negative regulation of focal adhesion assembly|positive regulation of BMP signaling pathway|positive regulation of transcription, DNA-dependent|regulation of blood pressure|regulation of blood vessel endothelial cell migration|regulation of DNA replication|regulation of endothelial cell proliferation|transforming growth factor beta receptor signaling pathway|wound healing, spreading of epidermal cells	cell surface|integral to plasma membrane	activin binding|activin receptor activity, type I|ATP binding|metal ion binding|receptor signaling protein serine/threonine kinase activity|SMAD binding|transforming growth factor beta binding|transforming growth factor beta receptor activity	g.chr12:52309923G>A	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.1152G>A	12.37:g.52309923G>A						ACVRL1_uc001rzk.2_Silent_p.Q384Q|ACVRL1_uc010snm.1_Silent_p.Q210Q	p.Q384Q	NM_000020	NP_000011	P37023	ACVL1_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.0991)	8	1435	+			384			Cytoplasmic (Potential).|Protein kinase.		A6NGA8	Silent	SNP	ENST00000388922.4	37	c.1152G>A	CCDS31804.1																																																																																				0.602	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		
ESPL1	9700	broad.mit.edu	37	12	53687195	53687195	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr12:53687195C>T	ENST00000257934.4	+	31	6391	c.6300C>T	c.(6298-6300)ccC>ccT	p.P2100P	PFDN5_ENST00000551018.1_5'Flank|PFDN5_ENST00000351500.3_5'Flank|PFDN5_ENST00000334478.4_5'Flank|PFDN5_ENST00000550846.1_5'Flank|ESPL1_ENST00000552462.1_Silent_p.P2100P	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	2100					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						GCCAAGCTCCCCGACTCAAGT	0.567																																					Colon(53;1069 1201 2587 5382)	uc001sck.2																			0				lung(1)|kidney(1)|skin(1)	3						c.(6298-6300)CCC>CCT		separase							65.0	66.0	65.0					12																	53687195		2203	4300	6503	SO:0001819	synonymous_variant	9700				apoptosis|cytokinesis|establishment of mitotic spindle localization|mitotic sister chromatid segregation|negative regulation of sister chromatid cohesion|positive regulation of mitotic metaphase/anaphase transition|proteolysis	centrosome|nucleus	cysteine-type peptidase activity|protein binding	g.chr12:53687195C>T	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.6300C>T	12.37:g.53687195C>T						ESPL1_uc001scj.2_Silent_p.P1775P|PFDN5_uc001scl.2_5'Flank|PFDN5_uc001scm.2_5'Flank|PFDN5_uc001scn.2_5'Flank|PFDN5_uc001sco.2_5'Flank	p.P2100P	NM_012291	NP_036423	Q14674	ESPL1_HUMAN			31	6391	+			2100						Silent	SNP	ENST00000257934.4	37	c.6300C>T	CCDS8852.1																																																																																				0.567	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
SRRM4	84530	broad.mit.edu	37	12	119568488	119568488	+	Missense_Mutation	SNP	G	G	A	rs532719039		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr12:119568488G>A	ENST00000267260.4	+	8	1008	c.620G>A	c.(619-621)cGc>cAc	p.R207H	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	207	Ser-rich.				cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)	p.R207H(1)		breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CCCAGGCACCGCGGCCGGTCC	0.622													G|||	1	0.000199681	0.0	0.0	5008	,	,		13812	0.001		0.0	False		,,,				2504	0.0					uc001txa.1																			1	Substitution - Missense(1)	p.R207H(1)	ovary(1)	ovary(2)	2						c.(619-621)CGC>CAC		KIAA1853 protein							15.0	18.0	17.0					12																	119568488		1876	4091	5967	SO:0001583	missense	84530				cell differentiation|mRNA processing|nervous system development|regulation of RNA splicing|RNA splicing	nucleus	mRNA binding	g.chr12:119568488G>A	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.620G>A	12.37:g.119568488G>A	ENSP00000267260:p.Arg207His						p.R207H	NM_194286	NP_919262	A7MD48	SRRM4_HUMAN			8	912	+			207			Ser-rich.		A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	c.620G>A	CCDS44994.1	.	.	.	.	.	.	.	.	.	.	G	16.76	3.212125	0.58452	.	.	ENSG00000139767	ENST00000267260	T	0.27402	1.67	5.17	4.27	0.50696	.	0.412269	0.22551	N	0.058589	T	0.41328	0.1154	L	0.47716	1.5	0.34760	D	0.73263	D	0.69078	0.997	P	0.58391	0.838	T	0.53823	-0.8384	10	0.56958	D	0.05	-12.928	11.3983	0.49856	0.0856:0.0:0.9144:0.0	.	207	A7MD48	SRRM4_HUMAN	H	207	ENSP00000267260:R207H	ENSP00000267260:R207H	R	+	2	0	SRRM4	118052871	1.000000	0.71417	1.000000	0.80357	0.740000	0.42216	4.164000	0.58190	2.415000	0.81967	0.448000	0.29417	CGC		0.622	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
CIT	11113	broad.mit.edu	37	12	120138625	120138625	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr12:120138625C>T	ENST00000261833.7	-	43	5474	c.5422G>A	c.(5422-5424)Gga>Aga	p.G1808R	CIT_ENST00000392521.2_Missense_Mutation_p.G1850R|RP1-127H14.3_ENST00000535109.1_3'UTR|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1808	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		ACGAACACTCCAAATTCTGCA	0.547																																						uc001txi.1																			0				ovary(6)|urinary_tract(1)|lung(1)|breast(1)|skin(1)	10						c.(5422-5424)GGA>AGA		citron							140.0	112.0	122.0					12																	120138625		2203	4300	6503	SO:0001583	missense	11113				intracellular signal transduction		ATP binding|metal ion binding|protein serine/threonine kinase activity|SH3 domain binding|small GTPase regulator activity	g.chr12:120138625C>T	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.5422G>A	12.37:g.120138625C>T	ENSP00000261833:p.Gly1808Arg					CIT_uc001txh.1_Missense_Mutation_p.G1327R|CIT_uc001txj.1_Missense_Mutation_p.G1850R	p.G1808R	NM_007174	NP_009105	O14578	CTRO_HUMAN		BRCA - Breast invasive adenocarcinoma(302;0.211)	43	5475	-	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)	1808			CNH.		Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	c.5422G>A	CCDS9192.1	.	.	.	.	.	.	.	.	.	.	C	35	5.518339	0.96416	.	.	ENSG00000122966	ENST00000392521;ENST00000261833	T;T	0.05717	3.4;3.4	5.6	5.6	0.85130	Citron-like (3);	0.000000	0.85682	D	0.000000	T	0.30008	0.0751	M	0.81112	2.525	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.01591	-1.1317	10	0.87932	D	0	.	19.6154	0.95632	0.0:1.0:0.0:0.0	.	1850;1808;1326	Q2M5E1;O14578;O14578-3	.;CTRO_HUMAN;.	R	1850;1808	ENSP00000376306:G1850R;ENSP00000261833:G1808R	ENSP00000261833:G1808R	G	-	1	0	CIT	118623008	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	7.790000	0.85794	2.652000	0.90054	0.650000	0.86243	GGA		0.547	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
PAN3	255967	broad.mit.edu	37	13	28794510	28794510	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr13:28794510C>T	ENST00000380958.3	+	6	1147	c.995C>T	c.(994-996)gCg>gTg	p.A332V	PAN3_ENST00000399613.1_Missense_Mutation_p.A132V	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GCTGGATTAGCGCCAGGTAAG	0.423																																						uc001urz.2																			0				ovary(1)	1						c.(556-558)GCG>GTG		PABP1-dependent poly A-specific ribonuclease							162.0	163.0	163.0					13																	28794510		2203	4300	6503	SO:0001583	missense	255967				nuclear-transcribed mRNA catabolic process, nonsense-mediated decay|nuclear-transcribed mRNA poly(A) tail shortening	centrosome|cytosol	ATP binding|protein kinase activity	g.chr13:28794510C>T	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"""PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.995C>T	13.37:g.28794510C>T	ENSP00000370345:p.Ala332Val					PAN3_uc010tdo.1_Missense_Mutation_p.A332V|PAN3_uc001ury.2_5'UTR|PAN3_uc001urx.2_Missense_Mutation_p.A132V	p.A186V	NM_175854	NP_787050	Q58A45	PAN3_HUMAN	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)	5	565	+	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	332			Interaction with polyadenylate-binding protein.			Missense_Mutation	SNP	ENST00000380958.3	37	c.557C>T	CCDS9329.2	.	.	.	.	.	.	.	.	.	.	C	18.99	3.740449	0.69304	.	.	ENSG00000152520	ENST00000380958;ENST00000399613	T;T	0.47869	0.83;0.87	5.6	5.6	0.85130	.	0.050294	0.85682	D	0.000000	T	0.35098	0.0920	N	0.19112	0.55	0.80722	D	1	P;P;B	0.51791	0.948;0.669;0.44	B;B;B	0.39503	0.301;0.036;0.016	T	0.11567	-1.0582	10	0.29301	T	0.29	-13.567	19.6153	0.95632	0.0:1.0:0.0:0.0	.	332;332;278	Q58A45-4;Q58A45;Q58A45-3	.;PAN3_HUMAN;.	V	332;132	ENSP00000370345:A332V;ENSP00000382522:A132V	ENSP00000370345:A332V	A	+	2	0	PAN3	27692510	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	5.642000	0.67888	2.630000	0.89119	0.555000	0.69702	GCG		0.423	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
TRIP11	9321	broad.mit.edu	37	14	92470681	92470681	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr14:92470681C>T	ENST00000267622.4	-	11	4012	c.3639G>A	c.(3637-3639)aaG>aaA	p.K1213K		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1213					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.K1213N(1)		breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		GCTGTTTTAACTTGTCACGTT	0.428			T	PDGFRB	AML																																Ovarian(84;609 1888 9852 42686)	uc001xzy.2				Dom	yes		14	14q31-q32	9321	T	thyroid hormone receptor interactor 11			L	PDGFRB		AML		1	Substitution - Missense(1)	p.K1213N(1)	breast(1)	ovary(6)|skin(2)|kidney(2)|central_nervous_system(1)|lung(1)|breast(1)	13						c.(3637-3639)AAG>AAA		thyroid hormone receptor interactor 11							86.0	81.0	83.0					14																	92470681		2203	4300	6503	SO:0001819	synonymous_variant	9321				transcription from RNA polymerase II promoter	cytoskeleton|Golgi apparatus|membrane|nucleus	protein binding|transcription coactivator activity	g.chr14:92470681C>T	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.3639G>A	14.37:g.92470681C>T						TRIP11_uc010auf.1_Silent_p.K949K	p.K1213K	NM_004239	NP_004230	Q15643	TRIPB_HUMAN		COAD - Colon adenocarcinoma(157;0.223)	11	4427	-			1213			Potential.		B2RUT2|O14689|O15154|O95949	Silent	SNP	ENST00000267622.4	37	c.3639G>A	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.694849	0.00731	.	.	ENSG00000100815	ENST00000554357	.	.	.	5.46	-4.73	0.03259	.	.	.	.	.	T	0.57431	0.2053	.	.	.	0.39028	D	0.95987	.	.	.	.	.	.	T	0.59852	-0.7376	4	.	.	.	.	13.457	0.61204	0.0:0.5463:0.0:0.4537	.	.	.	.	I	929	.	.	V	-	1	0	TRIP11	91540434	0.022000	0.18835	0.000000	0.03702	0.201000	0.24016	-0.645000	0.05409	-0.919000	0.03803	-0.391000	0.06502	GTT		0.428	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
PRIMA1	145270	broad.mit.edu	37	14	94203651	94203651	+	Missense_Mutation	SNP	C	C	T	rs200260569		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr14:94203651C>T	ENST00000393140.1	-	4	397	c.295G>A	c.(295-297)Gta>Ata	p.V99I	PRIMA1_ENST00000393143.1_Missense_Mutation_p.V99I|PRIMA1_ENST00000316227.3_Missense_Mutation_p.V99I	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	99					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		GCACAGCATACGGCAATGATG	0.532																																						uc001ybw.1																			0				large_intestine(1)|skin(1)	2						c.(295-297)GTA>ATA		proline rich membrane anchor 1 precursor							132.0	122.0	125.0					14																	94203651		2203	4300	6503	SO:0001583	missense	145270				neurotransmitter catabolic process	cell junction|integral to membrane|synapse		g.chr14:94203651C>T		CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"""membrane anchor of acetylcholinesterase"""	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.295G>A	14.37:g.94203651C>T	ENSP00000376848:p.Val99Ile					PRIMA1_uc001ybx.1_RNA	p.V99I	NM_178013	NP_821092	Q86XR5	PRIMA_HUMAN		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)	4	337	-		all_cancers(154;0.127)	99			Helical; (Potential).		Q86XR6	Missense_Mutation	SNP	ENST00000393140.1	37	c.295G>A	CCDS9912.1	.	.	.	.	.	.	.	.	.	.	C	18.82	3.705227	0.68615	.	.	ENSG00000175785	ENST00000393140;ENST00000393143;ENST00000316227	.	.	.	4.95	4.06	0.47325	.	0.194334	0.30584	N	0.009306	T	0.47414	0.1444	N	0.12746	0.255	0.38731	D	0.953673	D	0.67145	0.996	P	0.56563	0.801	T	0.55630	-0.8111	9	0.52906	T	0.07	-7.581	12.1732	0.54169	0.0:0.9193:0.0:0.0807	.	99	Q86XR5	PRIMA_HUMAN	I	99	.	ENSP00000320948:V99I	V	-	1	0	PRIMA1	93273404	0.658000	0.27402	0.127000	0.21898	0.987000	0.75469	2.193000	0.42658	1.219000	0.43474	-0.263000	0.10527	GTA		0.532	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013	
AKT1	207	broad.mit.edu	37	14	105241276	105241276	+	Splice_Site	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr14:105241276G>A	ENST00000554581.1	-	6	2112	c.632C>T	c.(631-633)aCa>aTa	p.T211I	AKT1_ENST00000544168.1_Splice_Site_p.T149I|AKT1_ENST00000555528.1_Splice_Site_p.T211I|AKT1_ENST00000407796.2_Splice_Site_p.T211I|AKT1_ENST00000554848.1_Splice_Site_p.T211I|AKT1_ENST00000349310.3_Splice_Site_p.T211I|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000402615.2_Splice_Site_p.T211I|AKT1_ENST00000554192.1_5'Flank			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	211	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CCCACTCACTGTGAGGAAGGG	0.647		1	Mis		"""breast, colorectal, ovarian, NSCLC"""																																	uc001ypk.2		1		Dom	yes		14	14q32.32	207	Mis	v-akt murine thymoma viral oncogene homolog 1			E			breast|colorectal|ovarian|NSCLC		0				breast(86)|urinary_tract(12)|thyroid(10)|lung(7)|endometrium(5)|large_intestine(4)|skin(4)|prostate(3)|haematopoietic_and_lymphoid_tissue(1)|ovary(1)|NS(1)	134						c.(631-633)ACA>ATA		AKT1 kinase	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)						74.0	69.0	70.0					14																	105241276		2203	4300	6503	SO:0001630	splice_region_variant	207				activation of pro-apoptotic gene products|activation-induced cell death of T cells|endocrine pancreas development|G-protein coupled receptor protein signaling pathway|glucose metabolic process|glycogen biosynthetic process|induction of apoptosis by intracellular signals|insulin receptor signaling pathway|insulin-like growth factor receptor signaling pathway|mRNA metabolic process|negative regulation of fatty acid beta-oxidation|negative regulation of plasma membrane long-chain fatty acid transport|negative regulation of protein kinase activity|nerve growth factor receptor signaling pathway|nitric oxide biosynthetic process|peptidyl-serine phosphorylation|phosphatidylinositol-mediated signaling|platelet activation|positive regulation of blood vessel endothelial cell migration|positive regulation of cell growth|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of establishment of protein localization in plasma membrane|positive regulation of fat cell differentiation|positive regulation of glucose import|positive regulation of glycogen biosynthetic process|positive regulation of lipid biosynthetic process|positive regulation of nitric oxide biosynthetic process|positive regulation of nitric-oxide synthase activity|positive regulation of peptidyl-serine phosphorylation|positive regulation of sequence-specific DNA binding transcription factor activity|protein autophosphorylation|protein import into nucleus, translocation|regulation of neuron projection development|regulation of translation|response to fluid shear stress|response to heat|response to UV-A|T cell costimulation	cytosol|nucleoplasm|plasma membrane	enzyme binding|identical protein binding|nitric-oxide synthase regulator activity|phosphatidylinositol-3,4,5-trisphosphate binding|phosphatidylinositol-3,4-bisphosphate binding|protein serine/threonine kinase activity	g.chr14:105241276G>A	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.633+1C>T	14.37:g.105241276G>A						INF2_uc010tyi.1_Intron|AKT1_uc001ypl.2_Missense_Mutation_p.T211I|AKT1_uc010axa.2_Missense_Mutation_p.T211I|AKT1_uc001ypm.2_Missense_Mutation_p.T211I|AKT1_uc001ypn.2_Missense_Mutation_p.T211I|AKT1_uc010tyk.1_Missense_Mutation_p.T149I	p.T211I	NM_005163	NP_005154	P31749	AKT1_HUMAN	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	7	1186	-		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	211			Protein kinase.		B2RAM5|B7Z5R1|Q9BWB6	Missense_Mutation	SNP	ENST00000554581.1	37	c.632C>T	CCDS9994.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.422472	0.83559	.	.	ENSG00000142208	ENST00000554581;ENST00000407796;ENST00000349310;ENST00000402615;ENST00000555528;ENST00000544168;ENST00000554848	T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06	3.92	3.92	0.45320	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.19927	0.0479	N	0.01729	-0.75	0.80722	D	1	D	0.69078	0.997	D	0.72625	0.978	T	0.47749	-0.9093	10	0.28530	T	0.3	.	16.0891	0.81080	0.0:0.0:1.0:0.0	.	211	P31749	AKT1_HUMAN	I	211;211;211;211;211;149;211	ENSP00000451828:T211I;ENSP00000384293:T211I;ENSP00000270202:T211I;ENSP00000385326:T211I;ENSP00000450688:T211I;ENSP00000443897:T149I;ENSP00000451166:T211I	ENSP00000270202:T211I	T	-	2	0	AKT1	104312321	1.000000	0.71417	0.946000	0.38457	0.892000	0.51952	7.544000	0.82117	2.011000	0.59026	0.491000	0.48974	ACA		0.647	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	Missense_Mutation
GABRB3	2562	broad.mit.edu	37	15	26793162	26793162	+	Silent	SNP	G	G	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr15:26793162G>T	ENST00000311550.5	-	9	1311	c.1200C>A	c.(1198-1200)atC>atA	p.I400I	GABRB3_ENST00000299267.4_Silent_p.I400I|GABRB3_ENST00000545868.1_Silent_p.I315I|GABRB3_ENST00000541819.2_Silent_p.I456I|GABRB3_ENST00000400188.3_Silent_p.I329I	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	400					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCCTGTACTGGATTCCTGAGT	0.512																																						uc001zaz.2																			0				upper_aerodigestive_tract(1)|ovary(1)|lung(1)|liver(1)|central_nervous_system(1)	5						c.(1198-1200)ATC>ATA		gamma-aminobutyric acid (GABA) A receptor, beta	Ethchlorvynol(DB00189)|Flurazepam(DB00690)|Lorazepam(DB00186)|Midazolam(DB00683)						102.0	93.0	96.0					15																	26793162		2203	4300	6503	SO:0001819	synonymous_variant	2562				synaptic transmission	cell junction|chloride channel complex|integral to plasma membrane|postsynaptic membrane	chloride channel activity|extracellular ligand-gated ion channel activity|GABA-A receptor activity	g.chr15:26793162G>T		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1200C>A	15.37:g.26793162G>T						GABRB3_uc010uae.1_Silent_p.I315I|GABRB3_uc001zba.2_Silent_p.I400I|GABRB3_uc001zbb.2_Silent_p.I456I	p.I400I	NM_000814	NP_000805	P28472	GBRB3_HUMAN		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	9	1342	-		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)	400			Cytoplasmic (Probable).		B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Silent	SNP	ENST00000311550.5	37	c.1200C>A	CCDS10019.1																																																																																				0.512	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
OTUD7A	161725	broad.mit.edu	37	15	31776752	31776752	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr15:31776752C>T	ENST00000307050.4	-	11	1618	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H	OTUD7A_ENST00000382902.1_Missense_Mutation_p.R516H	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	509					protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		GGAGTCGGCGCGCGTcttgtc	0.592																																						uc001zfq.2																			0				pancreas(1)|skin(1)	2						c.(1525-1527)CGC>CAC		OTU domain containing 7A							91.0	69.0	77.0					15																	31776752		2201	4300	6501	SO:0001583	missense	161725					cytoplasm|nucleus	cysteine-type peptidase activity|DNA binding|zinc ion binding	g.chr15:31776752C>T	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"""OTU domain containing"""	20718	protein-coding gene	gene with protein product		612024	"""chromosome 15 open reading frame 16"", ""OTU domain containing 7"", ""OTU domain containing 7A"""	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1526G>A	15.37:g.31776752C>T	ENSP00000305926:p.Arg509His					OTUD7A_uc001zfr.2_Missense_Mutation_p.R516H	p.R509H	NM_130901	NP_570971	Q8TE49	OTU7A_HUMAN		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)	11	1619	-		all_lung(180;1.6e-09)	509			Nuclear localization signal (Potential).		Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	c.1526G>A	CCDS10026.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603346	0.87157	.	.	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.40756	1.03;1.02	4.88	4.88	0.63580	.	0.102990	0.64402	D	0.000010	T	0.62612	0.2442	L	0.60455	1.87	0.37374	D	0.911756	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.991	T	0.70303	-0.4909	10	0.72032	D	0.01	-23.749	18.0667	0.89392	0.0:1.0:0.0:0.0	.	516;509	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	H	509;516	ENSP00000305926:R509H;ENSP00000372358:R516H	ENSP00000305926:R509H	R	-	2	0	OTUD7A	29564044	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	7.082000	0.76851	2.241000	0.73720	0.650000	0.86243	CGC		0.592	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901	
RYR3	6263	broad.mit.edu	37	15	33765674	33765674	+	Missense_Mutation	SNP	T	T	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr15:33765674T>A	ENST00000389232.4	+	2	176	c.106T>A	c.(106-108)Ttc>Atc	p.F36I	RYR3_ENST00000415757.3_Missense_Mutation_p.F36I	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	36					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GCAGAGGAAGTTCTGCCTGGC	0.547																																						uc001zhi.2																			0				ovary(5)|central_nervous_system(4)|lung(1)	10						c.(106-108)TTC>ATC		ryanodine receptor 3							99.0	103.0	102.0					15																	33765674		2093	4211	6304	SO:0001583	missense	6263				cellular calcium ion homeostasis	integral to membrane	calcium ion binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr15:33765674T>A		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.106T>A	15.37:g.33765674T>A	ENSP00000373884:p.Phe36Ile					RYR3_uc010bar.2_Missense_Mutation_p.F36I	p.F36I	NM_001036	NP_001027	Q15413	RYR3_HUMAN		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)	2	176	+		all_lung(180;7.18e-09)	36			Cytoplasmic (By similarity).		O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	c.106T>A	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	T	17.07	3.294412	0.60086	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.98192	-4.78;-4.78	4.86	4.86	0.63082	Inositol 1,4,5-trisphosphate/ryanodine receptor (1);	0.000000	0.85682	D	0.000000	D	0.95996	0.8696	N	0.04508	-0.205	0.52099	D	0.999941	D;P	0.57899	0.981;0.897	D;P	0.69142	0.962;0.69	D	0.93439	0.6792	10	0.07990	T	0.79	.	13.5742	0.61864	0.0:0.0:0.0:1.0	.	36;36	Q15413-2;Q15413	.;RYR3_HUMAN	I	36	ENSP00000373884:F36I;ENSP00000399610:F36I	ENSP00000354735:F36I	F	+	1	0	RYR3	31552966	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	5.721000	0.68477	2.029000	0.59856	0.528000	0.53228	TTC		0.547	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
CKMT1A	548596	broad.mit.edu	37	15	43991225	43991225	+	Missense_Mutation	SNP	C	C	T	rs148934583	byFrequency	TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr15:43991225C>T	ENST00000413453.2	+	9	1716	c.1192C>T	c.(1192-1194)Cgg>Tgg	p.R398W	STRC_ENST00000541030.1_Intron|CKMT1A_ENST00000434505.1_Missense_Mutation_p.R398W			P12532	KCRU_HUMAN	creatine kinase, mitochondrial 1A	398	Phosphagen kinase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00843}.				cellular nitrogen compound metabolic process (GO:0034641)|creatine metabolic process (GO:0006600)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|creatine kinase activity (GO:0004111)			lung(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)	Creatine(DB00148)	TGATTGTGAACGGCGTCTGGA	0.493													C|||	25	0.00499201	0.0	0.0	5008	,	,		20163	0.0238		0.0	False		,,,				2504	0.001					uc001zsn.2																			0					0						c.(1192-1194)CGG>TGG		creatine kinase, mitochondrial 1A precursor	Creatine(DB00148)	C	TRP/ARG	1,4395	2.1+/-5.4	0,1,2197	179.0	160.0	166.0		1192	0.5	1.0	15	dbSNP_134	166	0,8588		0,0,4294	no	missense	CKMT1A	NM_001015001.1	101	0,1,6491	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	398/418	43991225	1,12983	2198	4294	6492	SO:0001583	missense	548596				creatine metabolic process	mitochondrial inner membrane	ATP binding|creatine kinase activity	g.chr15:43991225C>T	BC001926, BC006467	CCDS32217.1	15q15	2005-08-09			ENSG00000223572	ENSG00000223572	2.7.3.2		31736	protein-coding gene	gene with protein product		613415	"""creatine kinase, mitochondrial 1 (ubiquitous)"""	CKMT1			Standard	XM_005254498		Approved		uc001zsn.3	P12532	OTTHUMG00000059898	ENST00000413453.2:c.1192C>T	15.37:g.43991225C>T	ENSP00000406577:p.Arg398Trp					CKMT1A_uc010uea.1_Missense_Mutation_p.R429W|CKMT1A_uc001zso.3_Missense_Mutation_p.R398W	p.R398W	NM_001015001	NP_001015001	P12532	KCRU_HUMAN		GBM - Glioblastoma multiforme(94;3.56e-07)	10	1584	+		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)	398			Phosphagen kinase C-terminal.		B4DIT8|B7ZA09|Q0VAM3|Q32NF6|Q53FC4	Missense_Mutation	SNP	ENST00000413453.2	37	c.1192C>T	CCDS32217.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	C	17.78	3.474313	0.63737	2.27E-4	0.0	ENSG00000223572	ENST00000424065;ENST00000434505;ENST00000413453	T;T	0.25250	1.81;1.81	3.71	0.528	0.17089	.	0.108796	0.64402	D	0.000012	T	0.22820	0.0551	.	.	.	0.50813	D	0.999899	.	.	.	.	.	.	T	0.04191	-1.0970	7	0.87932	D	0	8.7535	3.6156	0.08077	0.3386:0.4657:0.0:0.1957	.	.	.	.	W	429;398;398	ENSP00000413165:R398W;ENSP00000406577:R398W	ENSP00000406577:R398W	R	+	1	2	CKMT1A	41778517	1.000000	0.71417	0.985000	0.45067	0.988000	0.76386	2.182000	0.42556	-0.233000	0.09797	0.393000	0.25936	CGG		0.493	CKMT1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133136.1		
DUOX2	50506	broad.mit.edu	37	15	45386398	45386398	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr15:45386398C>T	ENST00000603300.1	-	34	4799	c.4597G>A	c.(4597-4599)Gtc>Atc	p.V1533I	DUOX2_ENST00000389039.6_Missense_Mutation_p.V1533I	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1533					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		TGCCTGTTGACGAGCTGACAG	0.572																																						uc010bea.2																			0				ovary(2)|skin(2)|pancreas(1)	5						c.(4597-4599)GTC>ATC		dual oxidase 2 precursor							140.0	119.0	126.0					15																	45386398		2198	4298	6496	SO:0001583	missense	50506				cuticle development|cytokine-mediated signaling pathway|hormone biosynthetic process|hydrogen peroxide catabolic process|response to cAMP|response to virus	apical plasma membrane|integral to membrane	calcium ion binding|electron carrier activity|flavin adenine dinucleotide binding|heme binding|NAD(P)H oxidase activity|peroxidase activity	g.chr15:45386398C>T	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.4597G>A	15.37:g.45386398C>T	ENSP00000475084:p.Val1533Ile					DUOX2_uc001zun.2_Missense_Mutation_p.V1533I	p.V1533I	NM_014080	NP_054799	Q9NRD8	DUOX2_HUMAN		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)	34	4800	-		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)	1533			Cytoplasmic (Potential).		A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	c.4597G>A	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	1.584	-0.530777	0.04112	.	.	ENSG00000140279	ENST00000389039	.	.	.	5.36	-3.34	0.04943	.	0.553031	0.19529	N	0.112082	T	0.09335	0.0230	N	0.01874	-0.695	0.21445	N	0.999681	B	0.02656	0.0	B	0.04013	0.001	T	0.32481	-0.9905	9	0.05436	T	0.98	-13.3951	8.1402	0.31078	0.0:0.1973:0.1603:0.6423	.	1533	Q9NRD8	DUOX2_HUMAN	I	1533	.	ENSP00000373691:V1533I	V	-	1	0	DUOX2	43173690	0.277000	0.24220	0.163000	0.22734	0.691000	0.40173	0.049000	0.14099	-0.815000	0.04346	-0.783000	0.03347	GTC		0.572	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
CACNA1H	8912	broad.mit.edu	37	16	1262094	1262094	+	Missense_Mutation	SNP	G	G	A	rs541249511	byFrequency	TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr16:1262094G>A	ENST00000348261.5	+	25	4963	c.4715G>A	c.(4714-4716)cGg>cAg	p.R1572Q	CACNA1H_ENST00000565831.1_Missense_Mutation_p.R1572Q|CACNA1H_ENST00000358590.4_Missense_Mutation_p.R1572Q	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1572					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GAGGCGCGGCGGCGAGAGGAG	0.682													G|||	2	0.000399361	0.0	0.0	5008	,	,		12859	0.002		0.0	False		,,,				2504	0.0					uc002cks.2																			0				breast(2)	2						c.(4714-4716)CGG>CAG		calcium channel, voltage-dependent, T type,	Flunarizine(DB04841)|Mibefradil(DB01388)						84.0	89.0	88.0					16																	1262094		2131	4229	6360	SO:0001583	missense	8912				aldosterone biosynthetic process|axon guidance|cellular response to hormone stimulus|cellular response to potassium ion|cortisol biosynthetic process|muscle contraction|myoblast fusion|positive regulation of acrosome reaction|regulation of heart contraction	voltage-gated calcium channel complex	low voltage-gated calcium channel activity	g.chr16:1262094G>A	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.4715G>A	16.37:g.1262094G>A	ENSP00000334198:p.Arg1572Gln					CACNA1H_uc002ckt.2_Missense_Mutation_p.R1572Q|CACNA1H_uc002cku.2_Missense_Mutation_p.R278Q|CACNA1H_uc010brj.2_Missense_Mutation_p.R278Q|CACNA1H_uc002ckv.2_Missense_Mutation_p.R278Q	p.R1572Q	NM_021098	NP_066921	O95180	CAC1H_HUMAN			25	4963	+		Hepatocellular(780;0.00369)	1572			Cytoplasmic (Potential).		B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	c.4715G>A	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.546415	0.65198	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96491	-4.03;-3.94	4.13	3.17	0.36434	.	0.603823	0.16272	N	0.221741	D	0.93949	0.8063	M	0.66378	2.025	0.34466	D	0.702337	P;P;P;P;P	0.47484	0.73;0.896;0.654;0.853;0.642	B;B;B;B;B	0.38264	0.026;0.177;0.048;0.269;0.124	D	0.94078	0.7341	10	0.42905	T	0.14	.	11.0318	0.47779	0.0924:0.0:0.9076:0.0	.	313;313;313;1572;1572	A2SX38;A2SX35;A2SX37;O95180-2;O95180	.;.;.;.;CAC1H_HUMAN	Q	1572	ENSP00000334198:R1572Q;ENSP00000351401:R1572Q	ENSP00000334198:R1572Q	R	+	2	0	CACNA1H	1202095	1.000000	0.71417	0.983000	0.44433	0.807000	0.45602	3.845000	0.55880	1.064000	0.40671	0.467000	0.42956	CGG		0.682	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
PAQR4	124222	broad.mit.edu	37	16	3021625	3021625	+	Silent	SNP	C	C	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr16:3021625C>A	ENST00000318782.8	+	3	928	c.498C>A	c.(496-498)acC>acA	p.T166T	PAQR4_ENST00000576565.1_Silent_p.T99T|PAQR4_ENST00000574988.1_Silent_p.T99T|PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000293978.8_Silent_p.T127T|PAQR4_ENST00000572687.1_Silent_p.T92T|PKMYT1_ENST00000431515.2_Intron	NM_001284513.1|NM_152341.3	NP_001271442.1|NP_689554.2	Q8N4S7	PAQR4_HUMAN	progestin and adipoQ receptor family member IV	166						integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8						GTGCTCTCACCGCCCCCTCCA	0.697																																						uc002csj.3																			0					0						c.(496-498)ACC>ACA		progestin and adipoQ receptor family member IV							31.0	35.0	34.0					16																	3021625		2194	4292	6486	SO:0001819	synonymous_variant	124222					integral to membrane	receptor activity	g.chr16:3021625C>A		CCDS10485.1, CCDS66911.1, CCDS66912.1, CCDS73814.1	16p13	2008-05-02			ENSG00000162073	ENSG00000162073			26386	protein-coding gene	gene with protein product		614578				12477932	Standard	XM_005255112		Approved	FLJ30002	uc002csj.4	Q8N4S7	OTTHUMG00000128977	ENST00000318782.8:c.498C>A	16.37:g.3021625C>A						PAQR4_uc002csk.3_Silent_p.T127T|PAQR4_uc002csl.3_Silent_p.T92T|PAQR4_uc010uwm.1_Silent_p.T97T	p.T166T	NM_152341	NP_689554	Q8N4S7	PAQR4_HUMAN			3	832	+			166			Helical; (Potential).		A8K5Q8|D3DUA2|D3DUA3|Q8NAS6|Q96NW1	Silent	SNP	ENST00000318782.8	37	c.498C>A	CCDS10485.1																																																																																				0.697	PAQR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250966.1	NM_152341	
ZP2	7783	broad.mit.edu	37	16	21213466	21213466	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr16:21213466G>A	ENST00000574002.1	-	12	1728	c.1246C>T	c.(1246-1248)Cgg>Tgg	p.R416W	ZP2_ENST00000574091.1_Missense_Mutation_p.R416W|ZP2_ENST00000219593.4_Missense_Mutation_p.R416W|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	416	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		ATGTGGAACCGTACCAGCCCC	0.507																																						uc002dii.2																			0				central_nervous_system(2)|ovary(1)	3						c.(1246-1248)CGG>TGG		zona pellucida glycoprotein 2 preproprotein							88.0	78.0	81.0					16																	21213466		2200	4300	6500	SO:0001583	missense	7783				binding of sperm to zona pellucida|intracellular protein transport	endoplasmic reticulum|Golgi apparatus|integral to membrane|multivesicular body|plasma membrane|proteinaceous extracellular matrix|stored secretory granule	acrosin binding|coreceptor activity	g.chr16:21213466G>A	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1246C>T	16.37:g.21213466G>A	ENSP00000460971:p.Arg416Trp					ZP2_uc010bwn.1_Missense_Mutation_p.R455W	p.R416W	NM_003460	NP_003451	Q05996	ZP2_HUMAN		GBM - Glioblastoma multiforme(48;0.0573)	11	1246	-			416			Extracellular (Potential).|ZP.		B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	c.1246C>T	CCDS10596.1	.	.	.	.	.	.	.	.	.	.	G	10.56	1.384048	0.25031	.	.	ENSG00000103310	ENST00000219593	D	0.82984	-1.67	5.83	-0.0239	0.13941	Zona pellucida sperm-binding protein (3);	0.917115	0.09272	N	0.824992	T	0.70159	0.3192	L	0.38531	1.155	0.09310	N	1	P;B	0.35844	0.524;0.205	B;B	0.28916	0.096;0.096	T	0.54622	-0.8266	10	0.36615	T	0.2	0.2289	6.6004	0.22697	0.1381:0.0:0.3582:0.5037	.	416;416	Q4VAP1;Q05996	.;ZP2_HUMAN	W	416	ENSP00000219593:R416W	ENSP00000219593:R416W	R	-	1	2	ZP2	21120967	0.000000	0.05858	0.000000	0.03702	0.665000	0.39181	0.200000	0.17257	-0.203000	0.10251	0.467000	0.42956	CGG		0.507	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
NF1	4763	broad.mit.edu	37	17	29556481	29556481	+	Nonsense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr17:29556481C>T	ENST00000358273.4	+	21	3231	c.2848C>T	c.(2848-2850)Cag>Tag	p.Q950*	NF1_ENST00000356175.3_Nonsense_Mutation_p.Q950*	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	950					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		CTCCCAAGGACAGGTAAAGTG	0.348			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												uc002hgg.2			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	D|Mis|N|F|S|O	neurofibromatosis type 1 gene			O		neurofibroma|glioma	neurofibroma|glioma		12	Whole gene deletion(8)|Unknown(4)	p.?(2)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)	soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330						c.(2848-2850)CAG>TAG		neurofibromin isoform 1							78.0	80.0	79.0					17																	29556481		2200	4297	6497	SO:0001587	stop_gained	4763	Neurofibromatosis_type_1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29556481C>T		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2848C>T	17.37:g.29556481C>T	ENSP00000351015:p.Gln950*	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_uc002hgh.2_Nonsense_Mutation_p.Q950*|NF1_uc010csn.1_Nonsense_Mutation_p.Q810*|NF1_uc002hgi.1_5'UTR	p.Q950*	NM_001042492	NP_001035957	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	21	3181	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	950					O00662|Q14284|Q14930|Q14931|Q9UMK3	Nonsense_Mutation	SNP	ENST00000358273.4	37	c.2848C>T	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	.	44	11.090366	0.99514	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	.	.	.	5.48	5.48	0.80851	.	0.057246	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	.	19.3532	0.94398	0.0:1.0:0.0:0.0	.	.	.	.	X	950;950;616	.	ENSP00000348498:Q950X	Q	+	1	0	NF1	26580607	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	7.456000	0.80751	2.594000	0.87642	0.455000	0.32223	CAG		0.348	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
MARCH10	162333	broad.mit.edu	37	17	60865912	60865912	+	Missense_Mutation	SNP	G	G	A	rs146312903	byFrequency	TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr17:60865912G>A	ENST00000311269.5	-	3	413	c.139C>T	c.(139-141)Cgc>Tgc	p.R47C	MARCH10_ENST00000456609.2_Missense_Mutation_p.R47C|MARCH10_ENST00000583600.1_Missense_Mutation_p.R47C|MARCH10_ENST00000544856.2_Missense_Mutation_p.R47C	NM_152598.2	NP_689811.2	Q8NA82	MARHA_HUMAN	membrane-associated ring finger (C3HC4) 10, E3 ubiquitin protein ligase	47					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(11)|liver(1)|lung(15)	38						AACTGATCGCGTTTCTTCTCA	0.443													G|||	5	0.000998403	0.0038	0.0	5008	,	,		17654	0.0		0.0	False		,,,				2504	0.0					uc010ddr.2																			0					0						c.(139-141)CGC>TGC		ring finger protein 190		G	CYS/ARG,CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	143.0	121.0	128.0		139,139	5.2	0.8	17	dbSNP_134	128	0,8600		0,0,4300	yes	missense,missense	MARCH10	NM_001100875.1,NM_152598.2	180,180	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	probably-damaging,probably-damaging	47/809,47/809	60865912	15,12991	2203	4300	6503	SO:0001583	missense	162333						ligase activity|zinc ion binding	g.chr17:60865912G>A	AK093076	CCDS11635.1, CCDS74122.1, CCDS74123.1	17q23.3	2013-01-09	2012-02-23	2007-08-20		ENSG00000173838		"""RING-type (C3HC4) zinc fingers"", ""MARCH membrane-associated ring fingers"""	26655	protein-coding gene	gene with protein product		613337	"""ring finger protein 190"", ""membrane-associated ring finger (C3HC4) 10"""	RNF190		17604280	Standard	XM_005257103		Approved	FLJ35757, MARCH-X	uc002jag.4	Q8NA82		ENST00000311269.5:c.139C>T	17.37:g.60865912G>A	ENSP00000311496:p.Arg47Cys					MARCH10_uc002jag.3_Missense_Mutation_p.R47C|MARCH10_uc010dds.2_Missense_Mutation_p.R47C|MARCH10_uc002jah.2_Missense_Mutation_p.R47C	p.R47C	NM_001100875	NP_001094345	Q8NA82	MARHA_HUMAN			3	377	-			47					D3DU09|Q8IYS7|Q8N7Z7	Missense_Mutation	SNP	ENST00000311269.5	37	c.139C>T	CCDS11635.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.39	1.922300	0.33908	0.003404	0.0	ENSG00000173838	ENST00000456609;ENST00000311269;ENST00000544856	T;T;T	0.23950	1.88;1.88;1.88	5.2	5.2	0.72013	.	0.488505	0.14673	N	0.305231	T	0.47857	0.1468	M	0.63428	1.95	0.32106	N	0.589972	D;D;D	0.89917	1.0;1.0;1.0	P;D;P	0.67231	0.893;0.95;0.893	T	0.56275	-0.8006	10	0.87932	D	0	-0.8947	14.2389	0.65945	0.0:0.0:1.0:0.0	.	47;47;47	B3KVK0;G3V1Q5;Q8NA82	.;.;MARHA_HUMAN	C	47	ENSP00000416177:R47C;ENSP00000311496:R47C;ENSP00000443746:R47C	ENSP00000311496:R47C	R	-	1	0	MARCH10	58219644	0.989000	0.36119	0.782000	0.31804	0.711000	0.40976	2.324000	0.43831	2.422000	0.82143	0.561000	0.74099	CGC		0.443	MARCH10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445252.1	NM_152598	
POTEC	388468	broad.mit.edu	37	18	14542738	14542738	+	Silent	SNP	A	A	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr18:14542738A>G	ENST00000358970.5	-	1	407	c.408T>C	c.(406-408)cgT>cgC	p.R136R	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	136										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GATCTTCTCGACGGACGTGGT	0.607																																						uc010dln.2																			0				skin(3)	3						c.(406-408)CGT>CGC		ANKRD26-like family B, member 2							37.0	50.0	46.0					18																	14542738		692	1590	2282	SO:0001819	synonymous_variant	388468							g.chr18:14542738A>G	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.408T>C	18.37:g.14542738A>G						POTEC_uc010xaj.1_RNA	p.R136R	NM_001137671	NP_001131143	B2RU33	POTEC_HUMAN			1	862	-			136						Silent	SNP	ENST00000358970.5	37	c.408T>C	CCDS45835.1																																																																																				0.607	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
ZNF532	55205	broad.mit.edu	37	18	56587754	56587754	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr18:56587754C>T	ENST00000336078.4	+	4	3011	c.2235C>T	c.(2233-2235)gaC>gaT	p.D745D	ZNF532_ENST00000591230.1_Silent_p.D745D|ZNF532_ENST00000591083.1_Silent_p.D745D|ZNF532_ENST00000591808.1_Silent_p.D745D|ZNF532_ENST00000589288.1_Silent_p.D745D	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	745					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TAGATGAAGACCCCTCCAAAC	0.483																																						uc002lho.2																			0				breast(1)|skin(1)	2						c.(2233-2235)GAC>GAT		zinc finger protein 532							45.0	41.0	42.0					18																	56587754		2203	4300	6503	SO:0001819	synonymous_variant	55205				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr18:56587754C>T	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.2235C>T	18.37:g.56587754C>T						ZNF532_uc002lhp.2_Silent_p.D743D|ZNF532_uc010xeg.1_Silent_p.D743D|ZNF532_uc002lhr.2_Silent_p.D743D|ZNF532_uc002lhs.2_Silent_p.D743D	p.D745D	NM_018181	NP_060651	Q9HCE3	ZN532_HUMAN			4	2782	+			745					Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Silent	SNP	ENST00000336078.4	37	c.2235C>T	CCDS11969.1																																																																																				0.483	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
ZNF516	9658	broad.mit.edu	37	18	74154336	74154336	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr18:74154336G>A	ENST00000443185.2	-	3	992	c.675C>T	c.(673-675)acC>acT	p.T225T	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	225					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		GCCCCTGCGCGGTGATGTGGT	0.697																																						uc010dqx.1																			0				ovary(1)	1						c.(673-675)ACC>ACT		zinc finger protein 516							18.0	20.0	20.0					18																	74154336		2146	4251	6397	SO:0001819	synonymous_variant	9658				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr18:74154336G>A	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.675C>T	18.37:g.74154336G>A						ZNF516_uc002lme.2_RNA	p.T225T	NM_014643	NP_055458	Q92618	ZN516_HUMAN		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)	2	910	-		Prostate(75;0.0869)|Esophageal squamous(42;0.129)	225						Silent	SNP	ENST00000443185.2	37	c.675C>T																																																																																					0.697	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
ACTL9	284382	broad.mit.edu	37	19	8807821	8807821	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:8807821C>T	ENST00000324436.3	-	1	1351	c.1231G>A	c.(1231-1233)Gtg>Atg	p.V411M		NM_178525.3	NP_848620.3	Q8TC94	ACTL9_HUMAN	actin-like 9	411						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(8)|lung(15)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	36						TTGCGGTACACGATATAGGGA	0.632																																						uc002mkl.2																			0				large_intestine(2)|pancreas(1)	3						c.(1231-1233)GTG>ATG		actin-like 9							51.0	49.0	50.0					19																	8807821		2200	4297	6497	SO:0001583	missense	284382					cytoplasm|cytoskeleton		g.chr19:8807821C>T		CCDS12207.1	19p13.2	2014-08-08			ENSG00000181786	ENSG00000181786			28494	protein-coding gene	gene with protein product							Standard	NM_178525		Approved	MGC33407	uc002mkl.2	Q8TC94	OTTHUMG00000182194	ENST00000324436.3:c.1231G>A	19.37:g.8807821C>T	ENSP00000316674:p.Val411Met						p.V411M	NM_178525	NP_848620	Q8TC94	ACTL9_HUMAN			1	1352	-			411					A8K893|Q6X960	Missense_Mutation	SNP	ENST00000324436.3	37	c.1231G>A	CCDS12207.1	.	.	.	.	.	.	.	.	.	.	c	18.19	3.568143	0.65651	.	.	ENSG00000181786	ENST00000324436	D	0.96830	-4.14	4.37	4.37	0.52481	.	0.000000	0.38605	U	0.001638	D	0.98036	0.9353	M	0.83603	2.65	0.51767	D	0.999939	D	0.89917	1.0	D	0.91635	0.999	D	0.98850	1.0758	10	0.87932	D	0	.	16.0135	0.80420	0.0:1.0:0.0:0.0	.	411	Q8TC94	ACTL9_HUMAN	M	411	ENSP00000316674:V411M	ENSP00000316674:V411M	V	-	1	0	ACTL9	8668821	1.000000	0.71417	0.988000	0.46212	0.347000	0.29111	5.446000	0.66600	2.419000	0.82065	0.457000	0.33378	GTG		0.632	ACTL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459953.1	NM_178525	
LDLR	3949	broad.mit.edu	37	19	11224366	11224366	+	Missense_Mutation	SNP	G	G	C			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:11224366G>C	ENST00000558518.1	+	10	1701	c.1514G>C	c.(1513-1515)gGc>gCc	p.G505A	LDLR_ENST00000558013.1_Missense_Mutation_p.G505A|LDLR_ENST00000557933.1_Missense_Mutation_p.G505A|LDLR_ENST00000545707.1_Missense_Mutation_p.G378A|LDLR_ENST00000455727.2_Missense_Mutation_p.G337A|LDLR_ENST00000535915.1_Missense_Mutation_p.G464A	NM_000527.4|NM_001195798.1	NP_000518.1|NP_001182727.1	P01130	LDLR_HUMAN	low density lipoprotein receptor	505					cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|intestinal cholesterol absorption (GO:0030299)|lipid metabolic process (GO:0006629)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|phototransduction, visible light (GO:0007603)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol homeostasis (GO:2000188)|regulation of phosphatidylcholine catabolic process (GO:0010899)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cell surface (GO:0009986)|clathrin-coated endocytic vesicle membrane (GO:0030669)|coated pit (GO:0005905)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|low-density lipoprotein particle (GO:0034362)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|very-low-density lipoprotein particle receptor activity (GO:0030229)	p.?(1)		breast(2)|endometrium(2)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	Porfimer(DB00707)	GATACCAAGGGCGTGAAGAGG	0.592																																					GBM(18;201 575 7820 21545)	uc002mqk.3																			1	Unknown(1)		lung(1)	ovary(2)|skin(2)	4	GRCh37	CM023641	LDLR	M		c.(1513-1515)GGC>GCC		low density lipoprotein receptor precursor	Methyl aminolevulinate(DB00992)|Porfimer(DB00707)						114.0	91.0	99.0					19																	11224366		2203	4300	6503	SO:0001583	missense	3949				cholesterol homeostasis|cholesterol metabolic process|interspecies interaction between organisms|intestinal cholesterol absorption|low-density lipoprotein particle clearance|receptor-mediated endocytosis	clathrin-coated endocytic vesicle membrane|coated pit|early endosome|endosome membrane|external side of plasma membrane|integral to plasma membrane|low-density lipoprotein particle|lysosome	calcium ion binding|low-density lipoprotein receptor activity|protein binding|very-low-density lipoprotein particle receptor activity	g.chr19:11224366G>C	AY114155	CCDS12254.1, CCDS56083.1, CCDS56084.1, CCDS56085.1, CCDS58651.1	19p13.2	2014-09-17	2008-08-01		ENSG00000130164	ENSG00000130164		"""Low density lipoprotein receptors"""	6547	protein-coding gene	gene with protein product	"""familial hypercholesterolemia"""	606945					Standard	NM_000527		Approved	LDLCQ2	uc002mqk.4	P01130		ENST00000558518.1:c.1514G>C	19.37:g.11224366G>C	ENSP00000454071:p.Gly505Ala					LDLR_uc010xlk.1_Missense_Mutation_p.G505A|LDLR_uc010xll.1_Missense_Mutation_p.G464A|LDLR_uc010xlm.1_Missense_Mutation_p.G358A|LDLR_uc010xln.1_Missense_Mutation_p.G378A|LDLR_uc010xlo.1_Missense_Mutation_p.G337A	p.G505A	NM_000527	NP_000518	P01130	LDLR_HUMAN		GBM - Glioblastoma multiforme(1328;1.36e-05)|STAD - Stomach adenocarcinoma(1328;0.000766)|Lung(535;0.197)	10	1682	+		Lung NSC(9;0.000245)|Renal(1328;0.0007)|Hepatocellular(1079;0.0524)	505			Extracellular (Potential).|LDL-receptor class B 3.		B4DII3|B4DJZ8|B4DR00|B4DTQ3|C0JYY8|H0YLU8|H0YNT7|Q53ZD9|Q59FQ1|Q9UDH7	Missense_Mutation	SNP	ENST00000558518.1	37	c.1514G>C	CCDS12254.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.244047	0.59103	.	.	ENSG00000130164	ENST00000252444;ENST00000545707;ENST00000535915;ENST00000455727	D;D;D	0.99232	-5.6;-5.6;-5.6	4.72	4.72	0.59763	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.000000	0.64402	D	0.000015	D	0.99533	0.9833	H	0.94964	3.605	0.80722	D	1	P;D;D;D;D;P	0.58268	0.939;0.982;0.967;0.982;0.967;0.942	P;D;P;P;P;P	0.65233	0.894;0.933;0.904;0.904;0.904;0.904	D	0.98057	1.0391	10	0.62326	D	0.03	.	16.4495	0.83974	0.0:0.0:1.0:0.0	.	337;378;384;464;517;505	B4DR00;B4DJZ8;B4DII3;B4DTQ3;Q59FQ1;P01130	.;.;.;.;.;LDLR_HUMAN	A	505;378;464;337	ENSP00000437639:G378A;ENSP00000440520:G464A;ENSP00000397829:G337A	ENSP00000252444:G505A	G	+	2	0	LDLR	11085366	1.000000	0.71417	0.092000	0.20876	0.008000	0.06430	9.220000	0.95180	2.186000	0.69663	0.555000	0.69702	GGC		0.592	LDLR-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415973.2		
ZNF709	163051	broad.mit.edu	37	19	12575498	12575498	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:12575498G>A	ENST00000397732.3	-	4	1409	c.1238C>T	c.(1237-1239)aCt>aTt	p.T413I	CTD-3105H18.18_ENST00000598753.1_Intron|ZNF709_ENST00000428311.1_Missense_Mutation_p.T413I	NM_152601.3	NP_689814.1	Q8N972	ZN709_HUMAN	zinc finger protein 709	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.T413I(2)		large_intestine(3)|upper_aerodigestive_tract(3)	6						TCCAGTGTGAGTTCTTTCATG	0.418																																					GBM(33;565 669 12371 29134 51667)	uc002mtv.3																			2	Substitution - Missense(2)		kidney(1)|skin(1)		0						c.(1237-1239)ACT>ATT		zinc finger protein 709 isoform a							106.0	111.0	109.0					19																	12575498		2202	4299	6501	SO:0001583	missense	163051				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:12575498G>A	AK095600	CCDS42504.1	19p13.2	2013-01-08			ENSG00000242852	ENSG00000242852		"""Zinc fingers, C2H2-type"", ""-"""	20629	protein-coding gene	gene with protein product							Standard	NM_152601		Approved	FLJ38281	uc002mtv.4	Q8N972	OTTHUMG00000156406	ENST00000397732.3:c.1238C>T	19.37:g.12575498G>A	ENSP00000380840:p.Thr413Ile					ZNF709_uc002mtw.3_Missense_Mutation_p.T381I|ZNF709_uc002mtx.3_Missense_Mutation_p.T413I	p.T413I	NM_152601	NP_689814	Q8N972	ZN709_HUMAN			4	1399	-			413			C2H2-type 11.		A8K4E6	Missense_Mutation	SNP	ENST00000397732.3	37	c.1238C>T	CCDS42504.1	.	.	.	.	.	.	.	.	.	.	G	0.031	-1.333208	0.01298	.	.	ENSG00000242852;ENSG00000196826	ENST00000397732;ENST00000428311	T;T	0.06142	3.34;3.34	3.05	-3.79	0.04320	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35067	N	0.003471	T	0.01976	0.0062	N	0.11000	0.08	0.09310	N	1	B	0.28258	0.205	B	0.25884	0.064	T	0.43814	-0.9368	10	0.02654	T	1	.	5.8441	0.18652	0.2644:0.3999:0.3357:0.0	.	413	Q8N972	ZN709_HUMAN	I	413	ENSP00000380840:T413I;ENSP00000404127:T413I	ENSP00000404127:T413I	T	-	2	0	ZNF709;CTD-2192J16.17	12436498	0.000000	0.05858	0.002000	0.10522	0.972000	0.66771	-2.485000	0.00979	-0.610000	0.05716	0.591000	0.81541	ACT		0.418	ZNF709-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344088.1	NM_152601	
GIPC1	10755	broad.mit.edu	37	19	14591540	14591540	+	Silent	SNP	C	C	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:14591540C>G	ENST00000393033.4	-	5	608	c.339G>C	c.(337-339)ctG>ctC	p.L113L	GIPC1_ENST00000586027.1_Silent_p.L113L|GIPC1_ENST00000393028.1_Silent_p.L16L|GIPC1_ENST00000393029.3_Silent_p.L16L|GIPC1_ENST00000345425.2_Silent_p.L113L|GIPC1_ENST00000591349.1_Silent_p.L16L	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	113					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						TCTGGCCCCCCAGGAGCTTGT	0.612											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									Pancreas(33;78 923 2910 41023 52850)	uc002myt.2																			0					0						c.(337-339)CTG>CTC		regulator of G-protein signalling 19 interacting							121.0	102.0	108.0					19																	14591540		2203	4300	6503	SO:0001819	synonymous_variant	10755				endothelial cell migration|G-protein coupled receptor protein signaling pathway|glutamate secretion|negative regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transforming growth factor beta receptor signaling pathway|protein targeting|regulation of protein stability|regulation of synaptic plasticity|synaptic transmission	cell cortex|dendritic shaft|dendritic spine|membrane fraction|soluble fraction|synaptic vesicle|vesicle membrane	actin binding|myosin binding|protein homodimerization activity|receptor binding	g.chr19:14591540C>G	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.339G>C	19.37:g.14591540C>G			OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	696	GIPC1_uc002myu.2_Silent_p.L113L|GIPC1_uc002myv.2_Silent_p.L16L|GIPC1_uc002myw.2_Silent_p.L16L|GIPC1_uc002myx.2_Silent_p.L113L|GIPC1_uc002myy.2_Silent_p.L16L	p.L113L	NM_005716	NP_005707	O14908	GIPC1_HUMAN			5	609	-			113					A8K4I3|A8MZG3|Q9BTC9	Silent	SNP	ENST00000393033.4	37	c.339G>C	CCDS12310.1																																																																																				0.612	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
LRP3	4037	broad.mit.edu	37	19	33695616	33695616	+	Silent	SNP	A	A	C			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:33695616A>C	ENST00000253193.7	+	4	535	c.333A>C	c.(331-333)ccA>ccC	p.P111P	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	111	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)		p.P111P(1)		breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					CAGCAGCCCCACCCCGCCAGG	0.662																																						uc010edh.2																			1	Substitution - coding silent(1)		lung(1)	pancreas(2)|ovary(1)	3						c.(331-333)CCA>CCC		low density lipoprotein receptor-related protein							56.0	59.0	58.0					19																	33695616		2203	4299	6502	SO:0001819	synonymous_variant	4037				receptor-mediated endocytosis	coated pit|integral to membrane	receptor activity	g.chr19:33695616A>C	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.333A>C	19.37:g.33695616A>C						LRP3_uc010xrp.1_5'UTR|LRP3_uc002nuk.3_5'UTR	p.P111P	NM_002333	NP_002324	O75074	LRP3_HUMAN			4	426	+	Esophageal squamous(110;0.137)		111			Extracellular (Potential).|CUB 1.		B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	c.333A>C	CCDS12430.1																																																																																				0.662	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
ZNF546	339327	broad.mit.edu	37	19	40521654	40521656	+	In_Frame_Del	DEL	ATC	ATC	-			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:40521654_40521656delATC	ENST00000347077.4	+	7	2693_2695	c.2477_2479delATC	c.(2476-2481)aatcat>aat	p.H827del	ZNF546_ENST00000596894.1_Intron|ZNF546_ENST00000600094.1_In_Frame_Del_p.H801del	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	827					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CATCAGAGAAATCATATTAGTGA	0.33																																						uc002oms.2																			0				ovary(1)|breast(1)|skin(1)	3						c.(2476-2481)AATCAT>AAT		zinc finger protein 546																																				SO:0001651	inframe_deletion	339327				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:40521654_40521656delATC	BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"""Zinc fingers, C2H2-type"", ""-"""	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.2477_2479delATC	19.37:g.40521654_40521656delATC	ENSP00000339823:p.His827del					ZNF546_uc002omt.2_In_Frame_Del_p.H801del	p.H827del	NM_178544	NP_848639	Q86UE3	ZN546_HUMAN			7	2733_2735	+	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)		827			C2H2-type 22.		A8K913	In_Frame_Del	DEL	ENST00000347077.4	37	c.2477_2479delATC	CCDS12548.1																																																																																				0.330	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544	
TSKS	60385	broad.mit.edu	37	19	50243159	50243159	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:50243159G>A	ENST00000246801.3	-	11	1735	c.1653C>T	c.(1651-1653)caC>caT	p.H551H	TSKS_ENST00000358830.3_Silent_p.H351H	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	551					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		ACATCTTCAAGTGTAGATGGT	0.592																																						uc002ppm.2																			0				large_intestine(1)|skin(1)	2						c.(1651-1653)CAC>CAT		testis-specific kinase substrate							102.0	93.0	96.0					19																	50243159		2203	4300	6503	SO:0001819	synonymous_variant	60385						protein binding	g.chr19:50243159G>A	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1653C>T	19.37:g.50243159G>A							p.H551H	NM_021733	NP_068379	Q9UJT2	TSKS_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)	11	1664	-		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)	551					Q8WXJ0	Silent	SNP	ENST00000246801.3	37	c.1653C>T	CCDS12780.1																																																																																				0.592	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
ZNF534	147658	broad.mit.edu	37	19	52942411	52942411	+	Silent	SNP	G	G	A	rs113700997	byFrequency	TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:52942411G>A	ENST00000332323.6	+	4	1798	c.1737G>A	c.(1735-1737)gcG>gcA	p.A579A	ZNF534_ENST00000432303.2_Intron|ZNF534_ENST00000301085.4_Intron|ZNF534_ENST00000433050.1_Silent_p.A566A	NM_001143939.1	NP_001137411.1	Q76KX8	ZN534_HUMAN	zinc finger protein 534	579					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A579A(4)		central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	4						CACACCTTGCGCGACATAGGA	0.443																																						uc002pzk.2																			4	Substitution - coding silent(4)		kidney(4)		0						c.(1735-1737)GCG>GCA		zinc finger protein 534 isoform 2							63.0	62.0	62.0					19																	52942411		692	1591	2283	SO:0001819	synonymous_variant	147658				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:52942411G>A	AK058073	CCDS46165.1, CCDS46166.1	19q13.41	2013-01-08	2004-02-06	2004-02-11	ENSG00000198633	ENSG00000198633		"""Zinc fingers, C2H2-type"", ""-"""	26337	protein-coding gene	gene with protein product			"""KRAB domain only 3"""	KRBO3			Standard	NM_001143938		Approved	FLJ25344	uc002pzk.3	Q76KX8	OTTHUMG00000156493	ENST00000332323.6:c.1737G>A	19.37:g.52942411G>A						ZNF534_uc002pzj.1_Intron|ZNF534_uc010epo.1_Intron|ZNF534_uc002pzl.2_Silent_p.A566A	p.A579A	NM_001143939	NP_001137411	Q76KX8	ZN534_HUMAN			4	1798	+			579			C2H2-type 14.		Q76KX9	Silent	SNP	ENST00000332323.6	37	c.1737G>A	CCDS46165.1																																																																																				0.443	ZNF534-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460877.1	NM_182512	
FCAR	2204	broad.mit.edu	37	19	55385635	55385635	+	5'Flank	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr19:55385635C>T	ENST00000355524.3	+	0	0				FCAR_ENST00000359272.4_5'Flank|FCAR_ENST00000345937.4_5'Flank|FCAR_ENST00000391723.3_5'Flank|FCAR_ENST00000391725.3_5'Flank|FCAR_ENST00000469767.1_5'Flank|FCAR_ENST00000353758.4_5'Flank|FCAR_ENST00000391724.3_5'Flank|FCAR_ENST00000391726.3_5'Flank	NM_002000.2	NP_001991.1	P24071	FCAR_HUMAN	Fc fragment of IgA, receptor for						immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(2)	24				GBM - Glioblastoma multiforme(193;0.0443)		AATTCCCTGACGAGGGGCTCT	0.498																																						uc002qhr.1																			0				ovary(1)|skin(1)	2						c.(-112--108)GACGA>GATGA		Fc alpha receptor isoform a precursor																																				SO:0001631	upstream_gene_variant	2204				immune response	extracellular region|integral to plasma membrane	IgA binding|receptor activity	g.chr19:55385635C>T	X54150	CCDS12907.1, CCDS12908.1, CCDS12909.1, CCDS12910.1, CCDS42622.1, CCDS42623.1, CCDS42624.1, CCDS42625.1, CCDS46180.1	19q13.42	2013-01-29			ENSG00000186431	ENSG00000186431		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3608	protein-coding gene	gene with protein product		147045				1577457	Standard	NM_133269		Approved	CD89	uc002qhr.1	P24071	OTTHUMG00000065936		19.37:g.55385635C>T	Exception_encountered					FCAR_uc002qhq.2_Translation_Start_Site|FCAR_uc002qhs.1_RNA|FCAR_uc002qht.1_Translation_Start_Site|FCAR_uc010esi.1_Translation_Start_Site|FCAR_uc002qhu.1_Translation_Start_Site|FCAR_uc002qhv.1_Translation_Start_Site|FCAR_uc002qhw.1_Translation_Start_Site|FCAR_uc002qhx.1_Translation_Start_Site|FCAR_uc002qhy.1_Translation_Start_Site|FCAR_uc002qhz.1_Translation_Start_Site|FCAR_uc002qia.1_Translation_Start_Site		NM_002000	NP_001991	P24071	FCAR_HUMAN		GBM - Glioblastoma multiforme(193;0.0443)	1	87	+								Q13603|Q13604|Q15727|Q15728|Q1AJL7|Q1AJL8|Q1AJL9|Q53X38|Q53X39|Q92587|Q92588|Q92590|Q92592|Q92593|Q9UEK0	Translation_Start_Site	SNP	ENST00000355524.3	37	c.-110C>T	CCDS12907.1																																																																																				0.498	FCAR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141243.1	NM_002000	
RAD51AP2	729475	broad.mit.edu	37	2	17698942	17698942	+	Frame_Shift_Del	DEL	T	T	-			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:17698942delT	ENST00000399080.2	-	1	764	c.741delA	c.(739-741)aaafs	p.K247fs		NM_001099218.2	NP_001092688.1	Q09MP3	R51A2_HUMAN	RAD51 associated protein 2	247										endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(10)|liver(1)|lung(17)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AATAGCTAGGTTTGGCAATTT	0.353																																						uc002rcl.1																			0				ovary(1)	1						c.(739-741)AAAfs		RAD51 associated protein 2							80.0	72.0	74.0					2																	17698942		1814	4082	5896	SO:0001589	frameshift_variant	729475							g.chr2:17698942delT	AK310498	CCDS42656.1	2p24.2	2009-01-13			ENSG00000214842	ENSG00000214842			34417	protein-coding gene	gene with protein product						16990250	Standard	NM_001099218		Approved	FLJ17540	uc002rcl.1	Q09MP3	OTTHUMG00000151761	ENST00000399080.2:c.741delA	2.37:g.17698942delT	ENSP00000382030:p.Lys247fs					RAD51AP2_uc010exn.1_Frame_Shift_Del_p.K238fs	p.K247fs	NM_001099218	NP_001092688	Q09MP3	R51A2_HUMAN			1	765	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)		247						Frame_Shift_Del	DEL	ENST00000399080.2	37	c.741delA	CCDS42656.1																																																																																				0.353	RAD51AP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323801.3	NM_001099218	
ADCY3	109	broad.mit.edu	37	2	25095488	25095489	+	Frame_Shift_Ins	INS	-	-	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:25095488_25095489insG	ENST00000260600.5	-	2	1626_1627	c.775_776insC	c.(775-777)cgcfs	p.R259fs		NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	259					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					CAGCGACTGGCGGGCCTCCAGG	0.634																																						uc002rfs.3																			0				breast(3)|ovary(1)	4						c.(775-777)CGCfs		adenylate cyclase 3																																				SO:0001589	frameshift_variant	109				activation of adenylate cyclase activity by G-protein signaling pathway|activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|inhibition of adenylate cyclase activity by G-protein signaling pathway|nerve growth factor receptor signaling pathway|sensory perception of smell|synaptic transmission|transmembrane transport|water transport	cytoplasm|integral to plasma membrane	ATP binding|calmodulin binding|metal ion binding	g.chr2:25095488_25095489insG	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.776dupC	2.37:g.25095491_25095491dupG	ENSP00000260600:p.Arg259fs					ADCY3_uc010ykm.1_Frame_Shift_Ins_p.R259fs	p.R259fs	NM_004036	NP_004027	O60266	ADCY3_HUMAN			2	974_975	-	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)		259					B3KT86|Q53T54|Q9UDB1	Frame_Shift_Ins	INS	ENST00000260600.5	37	c.775_776insC	CCDS1715.1																																																																																				0.634	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
PLB1	151056	broad.mit.edu	37	2	28761204	28761204	+	Missense_Mutation	SNP	G	G	A	rs149462466		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:28761204G>A	ENST00000327757.5	+	10	618	c.574G>A	c.(574-576)Ggc>Agc	p.G192S	PLB1_ENST00000422425.2_Missense_Mutation_p.G203S	NM_153021.4	NP_694566.4	Q6P1J6	PLB1_HUMAN	phospholipase B1	192	4 X 308-326 AA approximate repeats.				glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phospholipid metabolic process (GO:0006644)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(31)|ovary(6)|prostate(1)|skin(7)|stomach(2)	69	Acute lymphoblastic leukemia(172;0.155)					TGCGGCGGGCGGCGTGGATGA	0.642																																						uc002rmb.1																			0				ovary(4)|large_intestine(2)|skin(2)|breast(1)	9						c.(574-576)GGC>AGC		phospholipase B1 precursor		G	SER/GLY,SER/GLY	0,4406		0,0,2203	41.0	39.0	40.0		607,574	-9.8	0.0	2	dbSNP_134	40	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	PLB1	NM_001170585.1,NM_153021.4	56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign	203/1448,192/1459	28761204	1,13005	2203	4300	6503	SO:0001583	missense	151056				lipid catabolic process|retinoid metabolic process|steroid metabolic process	apical plasma membrane|integral to membrane	lysophospholipase activity|phospholipase A2 activity|retinyl-palmitate esterase activity	g.chr2:28761204G>A		CCDS33168.1, CCDS54340.1	2p23.3	2014-03-14			ENSG00000163803	ENSG00000163803	3.1.1.4, 3.1.1.5		30041	protein-coding gene	gene with protein product		610179				12150957	Standard	NM_153021		Approved	PLB, FLJ30866	uc002rmb.2	Q6P1J6	OTTHUMG00000152014	ENST00000327757.5:c.574G>A	2.37:g.28761204G>A	ENSP00000330442:p.Gly192Ser					PLB1_uc010ezj.1_Missense_Mutation_p.G203S	p.G192S	NM_153021	NP_694566	Q6P1J6	PLB1_HUMAN			10	574	+	Acute lymphoblastic leukemia(172;0.155)		192			4 X 308-326 AA approximate repeats.|Extracellular (Potential).|1.		A8KAX2|Q53S03|Q8IUP7|Q96DP9	Missense_Mutation	SNP	ENST00000327757.5	37	c.574G>A	CCDS33168.1	.	.	.	.	.	.	.	.	.	.	G	8.676	0.903942	0.17760	0.0	1.16E-4	ENSG00000163803	ENST00000416713;ENST00000327757;ENST00000422425	T;T;T	0.20881	2.04;2.82;2.83	4.91	-9.82	0.00484	.	2.123970	0.02270	N	0.068336	T	0.09686	0.0238	N	0.16903	0.455	0.09310	N	1	B;B	0.28760	0.221;0.04	B;B	0.21708	0.036;0.007	T	0.06481	-1.0824	10	0.22109	T	0.4	0.081	7.1501	0.25606	0.6834:0.1:0.1206:0.096	.	203;192	Q6P1J6-3;Q6P1J6	.;PLB1_HUMAN	S	147;192;203	ENSP00000407076:G147S;ENSP00000330442:G192S;ENSP00000416440:G203S	ENSP00000330442:G192S	G	+	1	0	PLB1	28614708	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.968000	0.01507	-2.422000	0.00563	-1.469000	0.01011	GGC		0.642	PLB1-012	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353348.2		
RGPD8	727851	broad.mit.edu	37	2	113127775	113127775	+	Missense_Mutation	SNP	G	G	C	rs370761877		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:113127775G>C	ENST00000302558.3	-	23	5469	c.5278C>G	c.(5278-5280)Cct>Gct	p.P1760A	RGPD8_ENST00000409750.1_Missense_Mutation_p.P1620A	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	1760				P -> A (in Ref. 3; CAI56757). {ECO:0000305}.	protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)	p.P1760A(12)		endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						GAACGGGAAGGATTTTCTTCC	0.308																																						uc002ths.1																			12	Substitution - Missense(12)		prostate(6)|urinary_tract(2)|endometrium(2)|kidney(2)		0						c.(5278-5280)CCT>GCT		RANBP2-like and GRIP domain containing 5 isoform							235.0	168.0	189.0					2																	113127775		686	1558	2244	SO:0001583	missense	84220				intracellular transport	cytoplasm	binding	g.chr2:113127775G>C	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.5278C>G	2.37:g.113127775G>C	ENSP00000306637:p.Pro1760Ala					RGPD8_uc010fkk.1_Missense_Mutation_p.P1620A	p.P1760A	NM_005054	NP_005045	Q99666	RGPD5_HUMAN			23	5355	-			1760					Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	c.5278C>G	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	g	0.008	-1.892319	0.00522	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.36520	1.25;1.25	0.719	0.719	0.18208	.	.	.	.	.	T	0.11239	0.0274	N	0.02011	-0.69	0.58432	D	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.18650	-1.0330	9	0.10902	T	0.67	-6.3628	6.3935	0.21599	0.0:0.6881:0.3119:0.0	.	1760	O14715	RGPD8_HUMAN	A	1760;1620	ENSP00000306637:P1760A;ENSP00000386511:P1620A	ENSP00000306637:P1760A	P	-	1	0	RGPD8	112844246	0.746000	0.28272	0.842000	0.33263	0.015000	0.08874	0.243000	0.18106	-0.105000	0.12132	-1.123000	0.02005	CCT		0.308	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
LRP1B	53353	broad.mit.edu	37	2	141081530	141081530	+	Missense_Mutation	SNP	T	T	C			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:141081530T>C	ENST00000389484.3	-	81	13417	c.12446A>G	c.(12445-12447)gAg>gGg	p.E4149G		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	4149					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)		AGCTAAGTACTCTACTGAACC	0.289										TSP Lung(27;0.18)																											Colon(99;50 2074 2507 20106)	uc002tvj.1																			0		p.E4149*(1)		lung(17)|skin(12)|ovary(12)|pancreas(3)|upper_aerodigestive_tract(2)|central_nervous_system(2)|liver(1)|kidney(1)	50						c.(12445-12447)GAG>GGG		low density lipoprotein-related protein 1B							64.0	73.0	70.0					2																	141081530		2202	4286	6488	SO:0001583	missense	53353				protein transport|receptor-mediated endocytosis	integral to membrane	calcium ion binding	g.chr2:141081530T>C	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.12446A>G	2.37:g.141081530T>C	ENSP00000374135:p.Glu4149Gly	TSP Lung(27;0.18)					p.E4149G	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)	81	13418	-		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)	4149			Extracellular (Potential).		Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	c.12446A>G	CCDS2182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	17.15|17.15	3.314960|3.314960	0.60524|0.60524	.|.	.|.	ENSG00000168702|ENSG00000168702	ENST00000389484;ENST00000544579|ENST00000437977	D|.	0.91068|.	-2.78|.	5.37|5.37	5.37|5.37	0.77165|0.77165	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74794|0.74794	0.3763|0.3763	M|M	0.74647|0.74647	2.275|2.275	0.43771|0.43771	D|D	0.996299|0.996299	B|.	0.21606|.	0.058|.	B|.	0.23419|.	0.046|.	T|T	0.75528|0.75528	-0.3286|-0.3286	10|5	0.44086|.	T|.	0.13|.	.|.	15.6612|15.6612	0.77188|0.77188	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	4149|.	Q9NZR2|.	LRP1B_HUMAN|.	G|G	4149;4087|381	ENSP00000374135:E4149G|.	ENSP00000374135:E4149G|.	E|S	-|-	2|1	0|0	LRP1B|LRP1B	140798000|140798000	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.973000|0.973000	0.67179|0.67179	7.636000|7.636000	0.83301|0.83301	2.164000|2.164000	0.68074|0.68074	0.533000|0.533000	0.62120|0.62120	GAG|AGT		0.289	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
SGOL2	151246	broad.mit.edu	37	2	201437974	201437974	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:201437974G>A	ENST00000357799.4	+	7	3003	c.2905G>A	c.(2905-2907)Gaa>Aaa	p.E969K		NM_001160033.1|NM_001160046.1|NM_152524.5	NP_001153505.1|NP_001153518.1|NP_689737.4	Q562F6	SGOL2_HUMAN	shugoshin-like 2 (S. pombe)	969					meiotic sister chromatid cohesion, centromeric (GO:0051754)|mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic cohesin complex (GO:0030892)|nucleus (GO:0005634)				NS(2)|breast(2)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(7)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	46						CAACAGTAATGAAAAGGAAAG	0.274																																						uc002uvw.2																			0				ovary(2)|skin(2)	4						c.(2905-2907)GAA>AAA		shugoshin-like 2 isoform 1							42.0	42.0	42.0					2																	201437974		1821	4059	5880	SO:0001583	missense	151246				cell division|mitotic prometaphase	condensed chromosome kinetochore|cytosol|mitotic cohesin complex	protein binding	g.chr2:201437974G>A	AY094614	CCDS42796.1	2q33.2	2008-02-05			ENSG00000163535	ENSG00000163535			30812	protein-coding gene	gene with protein product		612425					Standard	NM_001160046		Approved	TRIPIN, FLJ25211	uc002uvw.2	Q562F6	OTTHUMG00000154535	ENST00000357799.4:c.2905G>A	2.37:g.201437974G>A	ENSP00000350447:p.Glu969Lys					SGOL2_uc010zhd.1_Missense_Mutation_p.E969K|SGOL2_uc010zhe.1_Missense_Mutation_p.E969K	p.E969K	NM_152524	NP_689737	Q562F6	SGOL2_HUMAN			7	3018	+			969					Q53RR9|Q53T20|Q86XY4|Q8IWK2|Q8IZK1|Q8N1Q5|Q96LQ3	Missense_Mutation	SNP	ENST00000357799.4	37	c.2905G>A	CCDS42796.1	.	.	.	.	.	.	.	.	.	.	G	11.37	1.617653	0.28801	.	.	ENSG00000163535	ENST00000357799	T	0.10382	2.88	4.98	2.98	0.34508	.	0.738752	0.11953	N	0.513474	T	0.08626	0.0214	L	0.33485	1.01	0.80722	D	1	B;B;B	0.28801	0.223;0.139;0.019	B;B;B	0.28011	0.085;0.085;0.057	T	0.18304	-1.0341	10	0.44086	T	0.13	-8.7081	6.5281	0.22312	0.2255:0.0:0.7745:0.0	.	969;969;969	B7Z7S9;Q562F6-2;Q562F6	.;.;SGOL2_HUMAN	K	969	ENSP00000350447:E969K	ENSP00000350447:E969K	E	+	1	0	SGOL2	201146219	0.643000	0.27269	0.988000	0.46212	0.444000	0.32077	0.737000	0.26144	1.285000	0.44548	0.460000	0.39030	GAA		0.274	SGOL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335834.1	NM_152524	
SP140	11262	broad.mit.edu	37	2	231109774	231109774	+	Missense_Mutation	SNP	A	A	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:231109774A>T	ENST00000392045.3	+	6	757	c.643A>T	c.(643-645)Agc>Tgc	p.S215C	SP140_ENST00000420434.3_Missense_Mutation_p.S215C|SP140_ENST00000343805.6_Missense_Mutation_p.S215C|SP140_ENST00000350136.5_Missense_Mutation_p.S195C|SP140_ENST00000417495.3_Missense_Mutation_p.S215C|SP140_ENST00000486687.2_Missense_Mutation_p.S215C	NM_007237.4	NP_009168.4	Q13342	SP140_HUMAN	SP140 nuclear body protein	215					defense response (GO:0006952)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)	12		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		AGATGCACCCAGCCTACTACC	0.443																																						uc002vql.2																			0					0						c.(643-645)AGC>TGC		SP140 nuclear body protein isoform 1							116.0	108.0	111.0					2																	231109774		1933	4144	6077	SO:0001583	missense	11262				defense response	cytoplasm|nuclear envelope|nucleolus|nucleoplasm	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr2:231109774A>T	U63420	CCDS33392.1, CCDS42831.1, CCDS63149.1, CCDS63150.1, CCDS63151.1	2q37.1	2013-01-28			ENSG00000079263	ENSG00000079263		"""Zinc fingers, PHD-type"""	17133	protein-coding gene	gene with protein product		608602				8695863, 8910577, 12368356	Standard	NM_001005176		Approved	LYSP100-B, LYSP100-A	uc002vql.3	Q13342	OTTHUMG00000153670	ENST00000392045.3:c.643A>T	2.37:g.231109774A>T	ENSP00000375899:p.Ser215Cys					SP140_uc010zma.1_RNA|SP140_uc002vqk.2_Missense_Mutation_p.S215C|SP140_uc002vqn.2_Missense_Mutation_p.S215C|SP140_uc002vqm.2_Missense_Mutation_p.S215C|SP140_uc010fxl.2_Missense_Mutation_p.S215C	p.S215C	NM_007237	NP_009168	Q13342	LY10_HUMAN		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)	6	758	+		Renal(207;0.0112)|all_lung(227;0.0221)|Lung NSC(271;0.0977)|all_hematologic(139;0.103)|Acute lymphoblastic leukemia(138;0.167)	215					E7ESH9|E7EUR5|E9PFJ6|Q0VGE5|Q13341|Q3KR17|Q4ZG66|Q53TG1|Q6NSG4|Q92881|Q96TG3	Missense_Mutation	SNP	ENST00000392045.3	37	c.643A>T	CCDS42831.1	.	.	.	.	.	.	.	.	.	.	A	12.10	1.837542	0.32513	.	.	ENSG00000079263	ENST00000486687;ENST00000392044;ENST00000350136;ENST00000392045;ENST00000417495;ENST00000343805;ENST00000420434	T;T;T;T;T	0.58797	0.55;0.75;0.61;0.31;0.54	2.59	0.15	0.14883	.	.	.	.	.	T	0.52821	0.1758	L	0.27053	0.805	0.09310	N	1	D;D;D;D;D	0.69078	0.989;0.987;0.992;0.997;0.987	P;B;P;P;P	0.61328	0.712;0.334;0.668;0.887;0.468	T	0.41088	-0.9528	9	0.30078	T	0.28	-0.4504	4.578	0.12243	0.6921:0.0:0.3079:0.0	.	215;215;215;215;215	E7EUR5;E7ESH9;E9PFJ6;Q13342;E7EX75	.;.;.;LY10_HUMAN;.	C	215;215;195;215;215;215;215	ENSP00000440107:S215C;ENSP00000345846:S195C;ENSP00000375899:S215C;ENSP00000342096:S215C;ENSP00000398210:S215C	ENSP00000342096:S215C	S	+	1	0	SP140	230818018	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.064000	0.14437	0.026000	0.15269	0.523000	0.50628	AGC		0.443	SP140-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000332015.1	NM_007237	
UGT1A10	54575	broad.mit.edu	37	2	234545195	234545195	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr2:234545195C>T	ENST00000344644.5	+	1	96	c.27C>T	c.(25-27)ccC>ccT	p.P9P	UGT1A1_ENST00000373450.4_Intron|UGT1A10_ENST00000373445.1_Silent_p.P9P	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	9				MARAGWTSPVPLCVCLLLTCGFA -> MAPRRVDQPRSFMC VSTADLWLC (in Ref. 1). {ECO:0000305}.	cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	GGACCAGCCCCGTTCCTTTAT	0.572																																						uc002vur.2																			0				ovary(2)|skin(1)	3						c.(25-27)CCC>CCT		UDP glycosyltransferase 1 family, polypeptide							90.0	87.0	88.0					2																	234545195		2203	4300	6503	SO:0001819	synonymous_variant	54575				flavone metabolic process	endoplasmic reticulum membrane|integral to membrane|microsome	glucuronosyltransferase activity|protein heterodimerization activity|protein homodimerization activity|protein kinase C binding	g.chr2:234545195C>T	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.27C>T	2.37:g.234545195C>T						UGT1A8_uc010zmv.1_Intron|UGT1A8_uc002vup.2_Intron|UGT1A10_uc002vuq.3_Silent_p.P9P	p.P9P	NM_019075	NP_061948	Q9HAW8	UD110_HUMAN		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	1	73	+		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)	9	MARAGWTSPVPLCVCLLLTCGFA -> MAPRRVDQPRSFMC VSTADLWLC (in Ref. 1).				O00474|Q6NT91|Q7Z6H8	Silent	SNP	ENST00000344644.5	37	c.27C>T	CCDS33403.1																																																																																				0.572	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075	
PTPRA	5786	broad.mit.edu	37	20	2969091	2969091	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr20:2969091G>A	ENST00000216877.6	+	8	1082	c.682G>A	c.(682-684)Gac>Aac	p.D228N	PTPRA_ENST00000380393.3_Missense_Mutation_p.D237N|PTPRA_ENST00000399903.2_Missense_Mutation_p.D237N|PTPRA_ENST00000318266.5_Missense_Mutation_p.D228N|PTPRA_ENST00000356147.3_Missense_Mutation_p.D228N|PTPRA_ENST00000425918.2_Missense_Mutation_p.D248N|PTPRA_ENST00000358719.4_Missense_Mutation_p.D93N	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	237					axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)	p.D237N(2)		NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						AATGGCAGACGACAATAAGCT	0.507																																						uc010zqd.1																			2	Substitution - Missense(2)		endometrium(2)	upper_aerodigestive_tract(1)	1						c.(742-744)GAC>AAC		protein tyrosine phosphatase, receptor type, A							111.0	110.0	110.0					20																	2969091		2203	4300	6503	SO:0001583	missense	5786				axon guidance|protein phosphorylation	integral to plasma membrane	transmembrane receptor protein tyrosine phosphatase activity	g.chr20:2969091G>A		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.682G>A	20.37:g.2969091G>A	ENSP00000216877:p.Asp228Asn					PTPRA_uc002whj.2_Missense_Mutation_p.D237N|PTPRA_uc010zqc.1_Missense_Mutation_p.D122N|PTPRA_uc002whk.2_Missense_Mutation_p.D228N|PTPRA_uc002whl.2_Missense_Mutation_p.D228N|PTPRA_uc002whm.2_Missense_Mutation_p.D4N|PTPRA_uc002whn.2_Missense_Mutation_p.D228N|PTPRA_uc002who.2_5'UTR	p.D248N	NM_002836	NP_002827	P18433	PTPRA_HUMAN			8	1059	+			237			Cytoplasmic (Potential).		A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Missense_Mutation	SNP	ENST00000216877.6	37	c.742G>A	CCDS13039.1	.	.	.	.	.	.	.	.	.	.	G	35	5.564551	0.96527	.	.	ENSG00000132670	ENST00000380393;ENST00000455631;ENST00000216877;ENST00000399903;ENST00000358719;ENST00000425918;ENST00000318266;ENST00000356147	T;T;T;T;T;T;T;T	0.70045	2.78;-0.45;2.78;2.78;2.78;2.78;2.78;2.78	5.66	5.66	0.87406	.	0.000000	0.85682	U	0.000000	D	0.82444	0.5038	M	0.81682	2.555	0.80722	D	1	P;P;D;D	0.71674	0.674;0.638;0.996;0.998	B;B;D;P	0.67548	0.079;0.096;0.952;0.861	T	0.80899	-0.1176	10	0.36615	T	0.2	.	19.7589	0.96306	0.0:0.0:1.0:0.0	.	248;237;237;228	B7Z2A4;P18433-3;P18433;P18433-4	.;.;PTPRA_HUMAN;.	N	237;228;228;237;93;248;228;228	ENSP00000369756:D237N;ENSP00000414089:D228N;ENSP00000216877:D228N;ENSP00000382787:D237N;ENSP00000351559:D93N;ENSP00000393553:D248N;ENSP00000314568:D228N;ENSP00000348468:D228N	ENSP00000216877:D228N	D	+	1	0	PTPRA	2917091	1.000000	0.71417	0.997000	0.53966	0.958000	0.62258	9.604000	0.98317	2.662000	0.90505	0.557000	0.71058	GAC		0.507	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
RBPJL	11317	broad.mit.edu	37	20	43936814	43936814	+	Missense_Mutation	SNP	C	C	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr20:43936814C>A	ENST00000343694.3	+	2	126	c.54C>A	c.(52-54)caC>caA	p.H18Q	MATN4_ENST00000342716.4_Splice_Site|MATN4_ENST00000353917.5_Splice_Site|RBPJL_ENST00000372741.3_Missense_Mutation_p.H18Q|MATN4_ENST00000537548.1_Splice_Site|RBPJL_ENST00000372743.1_Missense_Mutation_p.H18Q|MATN4_ENST00000360607.6_Splice_Site|MATN4_ENST00000372751.4_Splice_Site|MATN4_ENST00000372754.1_5'Flank|MATN4_ENST00000372756.1_5'Flank	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	18					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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 (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CTTTGACTCACCTGAGCCTGC	0.627																																						uc002xns.2																			0				ovary(1)	1						c.(52-54)CAC>CAA		recombining binding protein L							77.0	79.0	79.0					20																	43936814		2203	4300	6503	SO:0001583	missense	11317				signal transduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr20:43936814C>A	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.54C>A	20.37:g.43936814C>A	ENSP00000341243:p.His18Gln					MATN4_uc002xnn.2_Intron|MATN4_uc002xno.2_Intron|MATN4_uc002xnp.2_Intron|MATN4_uc010zwr.1_5'Flank|MATN4_uc002xnr.1_Splice_Site|RBPJL_uc002xnt.2_Missense_Mutation_p.H18Q	p.H18Q	NM_014276	NP_055091	Q9UBG7	RBPJL_HUMAN			2	126	+		Myeloproliferative disorder(115;0.0122)	18					O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	c.54C>A	CCDS13349.1	.	.	.	.	.	.	.	.	.	.	C	18.04	3.535333	0.64972	.	.	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	T;T;T	0.60797	1.04;0.16;1.03	4.46	4.46	0.54185	.	0.287431	0.28901	N	0.013768	T	0.51024	0.1650	N	0.24115	0.695	0.31926	N	0.612851	D;D	0.61080	0.989;0.989	P;P	0.53912	0.737;0.737	T	0.49214	-0.8963	10	0.12766	T	0.61	-36.0278	12.7892	0.57523	0.0:1.0:0.0:0.0	.	18;18	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	Q	18	ENSP00000361828:H18Q;ENSP00000361826:H18Q;ENSP00000341243:H18Q	ENSP00000341243:H18Q	H	+	3	2	RBPJL	43370228	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	3.100000	0.50275	2.474000	0.83562	0.462000	0.41574	CAC		0.627	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
NCOA5	57727	broad.mit.edu	37	20	44698964	44698964	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr20:44698964C>T	ENST00000290231.6	-	3	414	c.250G>A	c.(250-252)Gtg>Atg	p.V84M		NM_020967.2	NP_066018.1	Q9HCD5	NCOA5_HUMAN	nuclear receptor coactivator 5	84	Arg/Asp-rich (mixed charge).|Transcription repression.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|extracellular space (GO:0005615)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|skin(2)|urinary_tract(1)	21		Myeloproliferative disorder(115;0.0122)				AGATCCCTCACGTCCCGAACG	0.532																																						uc002xrd.2																			0				central_nervous_system(1)|skin(1)	2						c.(250-252)GTG>ATG		nuclear receptor coactivator 5							133.0	125.0	128.0					20																	44698964		2203	4300	6503	SO:0001583	missense	57727				regulation of transcription, DNA-dependent|transcription, DNA-dependent|translation	nucleus	aminoacyl-tRNA ligase activity|ATP binding	g.chr20:44698964C>T		CCDS13392.1	20q12-q13.12	2008-07-02			ENSG00000124160	ENSG00000124160			15909	protein-coding gene	gene with protein product	"""coactivator independent of AF-2"""					11780052, 11113208	Standard	XM_005260474		Approved	bA465L10.6, CIA	uc002xre.3	Q9HCD5	OTTHUMG00000032639	ENST00000290231.6:c.250G>A	20.37:g.44698964C>T	ENSP00000290231:p.Val84Met					NCOA5_uc002xrc.2_Translation_Start_Site|NCOA5_uc002xre.2_Missense_Mutation_p.V84M	p.V84M	NM_020967	NP_066018	Q9HCD5	NCOA5_HUMAN			2	778	-		Myeloproliferative disorder(115;0.0122)	84			Arg/Asp-rich (mixed charge).|Transcription repression.		B2RTV9|E1P5R0|Q6HA99|Q9H1F2|Q9H2T2|Q9H4Y9	Missense_Mutation	SNP	ENST00000290231.6	37	c.250G>A	CCDS13392.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.709469	0.30322	.	.	ENSG00000124160	ENST00000290231	T	0.47528	0.84	4.97	1.3	0.21679	.	0.329786	0.32002	N	0.006730	T	0.22781	0.0550	N	0.08118	0	0.19575	N	0.999969	B	0.06786	0.001	B	0.01281	0.0	T	0.13980	-1.0489	10	0.30078	T	0.28	-0.1234	7.3092	0.26465	0.0:0.0794:0.4236:0.497	.	84	Q9HCD5	NCOA5_HUMAN	M	84	ENSP00000290231:V84M	ENSP00000290231:V84M	V	-	1	0	NCOA5	44132371	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	0.283000	0.18846	0.048000	0.15891	-0.247000	0.11927	GTG		0.532	NCOA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079559.1	NM_020967	
CHL1	10752	broad.mit.edu	37	3	405060	405060	+	Missense_Mutation	SNP	A	A	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr3:405060A>T	ENST00000256509.2	+	14	2221	c.1579A>T	c.(1579-1581)Att>Ttt	p.I527F	CHL1_ENST00000397491.2_Missense_Mutation_p.I511F|CHL1-AS1_ENST00000608098.1_RNA|CHL1-AS1_ENST00000417612.1_RNA	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		CAATTTGGATATTAGAAGTAT	0.378																																						uc003bou.2																			0				skin(5)|central_nervous_system(4)|large_intestine(2)|ovary(1)	12						c.(1531-1533)ATT>TTT		cell adhesion molecule with homology to L1CAM							104.0	106.0	106.0					3																	405060		2203	4300	6503	SO:0001583	missense	10752				axon guidance|cell adhesion|signal transduction	integral to membrane|plasma membrane|proteinaceous extracellular matrix		g.chr3:405060A>T	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1579A>T	3.37:g.405060A>T	ENSP00000256509:p.Ile527Phe					CHL1_uc003bot.2_Missense_Mutation_p.I527F|CHL1_uc003bow.1_Missense_Mutation_p.I511F|CHL1_uc011asi.1_Missense_Mutation_p.I527F|uc003box.1_RNA	p.I511F	NM_006614	NP_006605	O00533	CHL1_HUMAN		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)	13	1802	+		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)	511			Extracellular (Potential).		Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	c.1531A>T	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	19.42	3.823280	0.71143	.	.	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.31247	1.5;1.5	5.11	3.96	0.45880	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.061471	0.64402	D	0.000003	T	0.55081	0.1898	M	0.86343	2.81	0.44402	D	0.997315	D;D;D	0.69078	0.997;0.997;0.982	D;D;P	0.73708	0.981;0.981;0.907	T	0.57505	-0.7800	10	0.87932	D	0	.	6.875	0.24141	0.816:0.0:0.184:0.0	.	511;511;527	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	F	527;511	ENSP00000256509:I527F;ENSP00000380628:I511F	ENSP00000256509:I527F	I	+	1	0	CHL1	380060	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	2.344000	0.44010	0.888000	0.36160	0.528000	0.53228	ATT		0.378	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
CACNA2D3	55799	broad.mit.edu	37	3	54930849	54930849	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr3:54930849G>A	ENST00000474759.1	+	26	2368	c.2320G>A	c.(2320-2322)Gct>Act	p.A774T	CACNA2D3_ENST00000490478.1_Missense_Mutation_p.A680T|CACNA2D3_ENST00000288197.5_Missense_Mutation_p.A774T|CACNA2D3-AS1_ENST00000471265.1_RNA|CACNA2D3_ENST00000415676.2_Missense_Mutation_p.A774T	NM_018398.2	NP_060868.2	Q8IZS8	CA2D3_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 3	774						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.A774T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(3)	59				KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	Amlodipine(DB00381)|Nilvadipine(DB06712)|Spironolactone(DB00421)	CCGAAGAGCCGCTGAGCAGAT	0.537																																						uc003dhf.2																			1	Substitution - Missense(1)	p.A774T(1)	central_nervous_system(1)	large_intestine(3)|ovary(1)|breast(1)|central_nervous_system(1)|skin(1)	7						c.(2320-2322)GCT>ACT		calcium channel, voltage-dependent, alpha							118.0	118.0	118.0					3																	54930849		1970	4159	6129	SO:0001583	missense	55799					integral to membrane	calcium channel activity|metal ion binding|voltage-gated ion channel activity	g.chr3:54930849G>A	AJ272268	CCDS54598.1	3p21.1	2010-10-05	2008-02-26		ENSG00000157445	ENSG00000157445		"""Calcium channel subunits"""	15460	protein-coding gene	gene with protein product		606399				11245980	Standard	XM_005265318		Approved	HSA272268	uc003dhf.3	Q8IZS8	OTTHUMG00000158580	ENST00000474759.1:c.2320G>A	3.37:g.54930849G>A	ENSP00000419101:p.Ala774Thr					CACNA2D3_uc003dhg.1_Missense_Mutation_p.A680T|CACNA2D3_uc003dhh.1_RNA|uc003dhk.1_RNA	p.A774T	NM_018398	NP_060868	Q8IZS8	CA2D3_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.00287)|Kidney(284;0.00327)	26	2368	+			774			Extracellular (Potential).		B2RPL6|Q9NY16|Q9NY18	Missense_Mutation	SNP	ENST00000474759.1	37	c.2320G>A	CCDS54598.1	.	.	.	.	.	.	.	.	.	.	G	34	5.332900	0.95758	.	.	ENSG00000157445	ENST00000415676;ENST00000474759;ENST00000288197;ENST00000490478;ENST00000398624	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.73	5.73	0.89815	.	0.057226	0.64402	D	0.000001	T	0.51398	0.1672	M	0.72118	2.19	0.58432	D	0.999992	D	0.63880	0.993	P	0.57057	0.812	T	0.50268	-0.8848	10	0.62326	D	0.03	.	18.0478	0.89338	0.0:0.0:1.0:0.0	.	774	Q8IZS8	CA2D3_HUMAN	T	774;774;774;680;680	ENSP00000389506:A774T;ENSP00000419101:A774T;ENSP00000288197:A774T;ENSP00000417279:A680T	ENSP00000288197:A774T	A	+	1	0	CACNA2D3	54905889	1.000000	0.71417	0.234000	0.24042	0.947000	0.59692	9.112000	0.94314	2.861000	0.98227	0.655000	0.94253	GCT		0.537	CACNA2D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351402.1		
PIK3CB	5291	broad.mit.edu	37	3	138417859	138417859	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr3:138417859C>T	ENST00000477593.1	-	12	1733	c.1660G>A	c.(1660-1662)Gaa>Aaa	p.E554K	PIK3CB_ENST00000289153.2_Missense_Mutation_p.E554K|PIK3CB_ENST00000544716.1_5'UTR			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	554	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|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)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	AGATCCATTTCATTTTCACAC	0.383																																						uc011bmq.1																			0				breast(2)|ovary(1)|lung(1)|skin(1)	5						c.(1660-1662)GAA>AAA		catalytic phosphatidylinositol 3-kinase beta							104.0	103.0	103.0					3																	138417859		2203	4300	6503	SO:0001583	missense	5291				activation of MAPK activity|chemotaxis|fibroblast growth factor receptor signaling pathway|G-protein coupled receptor protein signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell receptor signaling pathway	phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:138417859C>T		CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.1660G>A	3.37:g.138417859C>T	ENSP00000418143:p.Glu554Lys					PIK3CB_uc011bmn.1_Missense_Mutation_p.E66K|PIK3CB_uc011bmo.1_5'UTR|PIK3CB_uc011bmp.1_Missense_Mutation_p.E141K	p.E554K	NM_006219	NP_006210	P42338	PK3CB_HUMAN			11	1660	-			554			PI3K helical.		D3DNF0|Q24JU2	Missense_Mutation	SNP	ENST00000477593.1	37	c.1660G>A	CCDS3104.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	32|32	5.171296|5.171296	0.94807|0.94807	.|.	.|.	ENSG00000051382|ENSG00000051382	ENST00000477593;ENST00000289153|ENST00000493568	T;T|.	0.69435|.	-0.4;-0.4|.	5.91|5.91	5.04|5.04	0.67666|0.67666	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);|.	0.095718|.	0.64402|.	D|.	0.000001|.	T|T	0.73976|0.73976	0.3656|0.3656	M|M	0.75085|0.75085	2.285|2.285	0.80722|0.80722	D|D	1|1	P;P|.	0.48407|.	0.91;0.833|.	P;P|.	0.58391|.	0.838;0.6|.	T|T	0.74890|0.74890	-0.3510|-0.3510	10|5	0.46703|.	T|.	0.11|.	-22.153|-22.153	14.825|14.825	0.70104|0.70104	0.0:0.9315:0.0:0.0685|0.0:0.9315:0.0:0.0685	.|.	554;141|.	P42338;B4DZI3|.	PK3CB_HUMAN;.|.	K|I	554|185	ENSP00000418143:E554K;ENSP00000289153:E554K|.	ENSP00000289153:E554K|.	E|M	-|-	1|3	0|0	PIK3CB|PIK3CB	139900549|139900549	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	7.487000|7.487000	0.81328|0.81328	1.513000|1.513000	0.48852|0.48852	0.460000|0.460000	0.39030|0.39030	GAA|ATG		0.383	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358019.1		
LINC00969	440993	broad.mit.edu	37	3	195400814	195400815	+	lincRNA	INS	-	-	TT	rs371598334		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr3:195400814_195400815insTT	ENST00000445430.1	+	0	1410_1411									long intergenic non-protein coding RNA 969																		ACCTGGTTGTCTGGTCAGGCAT	0.574																																						uc003fuw.2																			0					0						c.(109-111)TCTfs		SubName: Full=cDNA FLJ16373 fis, clone THYMU3000269, highly similar to Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial (EC 1.3.5.1);																																						727956							g.chr3:195400814_195400815insTT	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400814_195400815insTT						SDHAP2_uc011btb.1_Frame_Shift_Ins_p.V184fs|SDHAP2_uc011btc.1_RNA|SDHAP2_uc003fuv.2_RNA	p.S37fs							9	1304_1305	+									Frame_Shift_Ins	INS	ENST00000445430.1	37	c.110_111insTT																																																																																					0.574	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1		
IDUA	3425	broad.mit.edu	37	4	995507	995507	+	Silent	SNP	C	C	T	rs376012666		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr4:995507C>T	ENST00000247933.4	+	6	718	c.630C>T	c.(628-630)cgC>cgT	p.R210R	IDUA_ENST00000514224.1_Silent_p.R78R|IDUA_ENST00000453894.1_Silent_p.R163R	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	210					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			AGGGTCTGCGCGCCGCCAGCC	0.716																																						uc003gby.2																			0					0						c.(628-630)CGC>CGT		alpha-L-iduronidase precursor	Laronidase(DB00090)	C		0,4370		0,0,2185	9.0	11.0	11.0		630	-10.3	0.0	4		11	6,8534		0,6,4264	no	coding-synonymous	IDUA	NM_000203.3		0,6,6449	TT,TC,CC		0.0703,0.0,0.0465		210/654	995507	6,12904	2185	4270	6455	SO:0001819	synonymous_variant	3425				disaccharide metabolic process	lysosome	cation binding|L-iduronidase activity	g.chr4:995507C>T	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.630C>T	4.37:g.995507C>T						IDUA_uc003gbz.2_RNA|IDUA_uc003gca.2_Silent_p.R163R	p.R210R	NM_000203	NP_000194	P35475	IDUA_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.0158)		6	718	+			210					B3KWK6	Silent	SNP	ENST00000247933.4	37	c.630C>T	CCDS3343.1																																																																																				0.716	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
TLR10	81793	broad.mit.edu	37	4	38777060	38777060	+	Missense_Mutation	SNP	G	G	A	rs375480992		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr4:38777060G>A	ENST00000308973.4	-	4	757	c.152C>T	c.(151-153)aCg>aTg	p.T51M	TLR10_ENST00000506111.1_Missense_Mutation_p.T51M|TLR10_ENST00000361424.2_Missense_Mutation_p.T51M|TLR10_ENST00000507953.1_5'Flank|TLR10_ENST00000508334.1_Missense_Mutation_p.T51M	NM_001017388.2|NM_001195107.1|NM_030956.3	NP_001017388.1|NP_001182036.1|NP_112218.2	Q9BXR5	TLR10_HUMAN	toll-like receptor 10	51					immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of inflammatory response (GO:0050729)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(2)	25						ATCCAGTGTCGTTGTGGCTGG	0.448																																						uc003gti.2																			0				lung(1)|breast(1)	2						c.(151-153)ACG>ATG		toll-like receptor 10 precursor		G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	84.0	77.0	79.0		152,152,152,110,152	3.5	0.1	4		79	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	TLR10	NM_001017388.2,NM_001195106.1,NM_001195107.1,NM_001195108.1,NM_030956.3	81,81,81,81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	51/812,51/812,51/812,37/798,51/812	38777060	1,13005	2203	4300	6503	SO:0001583	missense	81793				inflammatory response|innate immune response|MyD88-dependent toll-like receptor signaling pathway	integral to membrane|plasma membrane	transmembrane receptor activity	g.chr4:38777060G>A	AF296673	CCDS3445.1	4p14	2009-11-23			ENSG00000174123	ENSG00000174123		"""CD molecules"""	15634	protein-coding gene	gene with protein product		606270				11267672	Standard	NM_030956		Approved	CD290	uc003gtk.3	Q9BXR5	OTTHUMG00000128578	ENST00000308973.4:c.152C>T	4.37:g.38777060G>A	ENSP00000308925:p.Thr51Met					TLR10_uc003gtj.2_Missense_Mutation_p.T51M|TLR10_uc003gtk.2_Missense_Mutation_p.T51M	p.T51M	NM_030956	NP_112218	Q9BXR5	TLR10_HUMAN			2	531	-			51			Extracellular (Potential).|LRR 2.		A8K7L1|B3Y668|D1CS21|D1CS22|Q32MI7|Q32MI8|Q5FWG4|Q6UXL3	Missense_Mutation	SNP	ENST00000308973.4	37	c.152C>T	CCDS3445.1	.	.	.	.	.	.	.	.	.	.	G	9.281	1.048086	0.19827	0.0	1.16E-4	ENSG00000174123	ENST00000308973;ENST00000506111;ENST00000361424;ENST00000508334;ENST00000502321	T;T;T;T;T	0.58797	1.71;1.71;1.71;1.71;0.31	5.23	3.51	0.40186	.	0.455228	0.17294	N	0.179512	T	0.70988	0.3287	M	0.74647	2.275	0.09310	N	1	D	0.76494	0.999	D	0.69307	0.963	T	0.60707	-0.7210	10	0.87932	D	0	.	7.5347	0.27704	0.1382:0.0:0.7183:0.1435	.	51	Q9BXR5	TLR10_HUMAN	M	51;51;51;51;37	ENSP00000308925:T51M;ENSP00000421483:T51M;ENSP00000354459:T51M;ENSP00000424923:T51M;ENSP00000427606:T37M	ENSP00000308925:T51M	T	-	2	0	TLR10	38453455	0.009000	0.17119	0.091000	0.20842	0.332000	0.28634	0.164000	0.16542	0.599000	0.29845	0.655000	0.94253	ACG		0.448	TLR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250430.1		
CCDC158	339965	broad.mit.edu	37	4	77304876	77304876	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr4:77304876C>T	ENST00000388914.3	-	6	894	c.742G>A	c.(742-744)Gaa>Aaa	p.E248K	CCDC158_ENST00000434846.2_Missense_Mutation_p.E248K	NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	248										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						TTCAGTGCTTCAAGTTGATCC	0.368																																						uc003hkb.3																			0				skin(3)|ovary(2)|pancreas(1)	6						c.(742-744)GAA>AAA		coiled-coil domain containing 158							236.0	202.0	213.0					4																	77304876		1836	4085	5921	SO:0001583	missense	339965							g.chr4:77304876C>T	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.742G>A	4.37:g.77304876C>T	ENSP00000373566:p.Glu248Lys					CCDC158_uc003hkd.2_Missense_Mutation_p.E248K	p.E248K	NM_001042784	NP_001036249	Q5M9N0	CD158_HUMAN			6	895	-			248			Potential.		Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	c.742G>A	CCDS43242.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.928541	0.92389	.	.	ENSG00000163749	ENST00000388914;ENST00000318586;ENST00000434846	T;T	0.33654	1.45;1.4	5.78	5.78	0.91487	.	0.000000	0.64402	D	0.000015	T	0.41604	0.1166	N	0.24115	0.695	0.37485	D	0.916137	D;D	0.63880	0.993;0.986	P;P	0.60789	0.879;0.84	T	0.24154	-1.0168	10	0.23891	T	0.37	.	15.5119	0.75789	0.0:1.0:0.0:0.0	.	248;248	Q5M9N0-3;Q5M9N0	.;CD158_HUMAN	K	248	ENSP00000373566:E248K;ENSP00000401742:E248K	ENSP00000316815:E248K	E	-	1	0	CCDC158	77523900	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.284000	0.51708	2.742000	0.94016	0.650000	0.86243	GAA		0.368	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
SPARCL1	8404	broad.mit.edu	37	4	88420673	88420673	+	Splice_Site	SNP	C	C	T	rs11557440		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr4:88420673C>T	ENST00000282470.6	-	2	524	c.54G>A	c.(52-54)ccG>ccA	p.P18P	SPARCL1_ENST00000418378.1_Splice_Site_p.P18P|SPARCL1_ENST00000503414.1_5'UTR	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	18					signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		GGAAATTTACCGGGATTGCAG	0.363																																						uc010ikm.2																			0				ovary(1)	1						c.(52-54)CCG>CCA		SPARC-like 1 precursor							97.0	105.0	102.0					4																	88420673		2203	4300	6503	SO:0001630	splice_region_variant	8404				signal transduction	extracellular space|proteinaceous extracellular matrix	calcium ion binding	g.chr4:88420673C>T	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.54+1G>A	4.37:g.88420673C>T						SPARCL1_uc011cdc.1_Intron|SPARCL1_uc003hqs.3_Silent_p.P18P|SPARCL1_uc011cdd.1_5'UTR|SPARCL1_uc003hqt.2_Silent_p.P18P	p.P18P	NM_001128310	NP_001121782	Q14515	SPRL1_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00118)	3	626	-			18					B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	37	c.54G>A	CCDS3622.1																																																																																				0.363	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		Silent
FGA	2243	broad.mit.edu	37	4	155507297	155507297	+	Nonsense_Mutation	SNP	G	G	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr4:155507297G>T	ENST00000302053.3	-	5	1362	c.1284C>A	c.(1282-1284)taC>taA	p.Y428*	FGA_ENST00000403106.3_Nonsense_Mutation_p.Y428*	NM_000508.3	NP_000499.1	P02671	FIBA_HUMAN	fibrinogen alpha chain	428					blood coagulation (GO:0007596)|blood coagulation, common pathway (GO:0072377)|cell-matrix adhesion (GO:0007160)|cellular protein complex assembly (GO:0043623)|extracellular matrix organization (GO:0030198)|negative regulation of blood coagulation, common pathway (GO:2000261)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of exocytosis (GO:0045921)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of peptide hormone secretion (GO:0090277)|positive regulation of protein secretion (GO:0050714)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive regulation of vasoconstriction (GO:0045907)|protein polymerization (GO:0051258)|response to calcium ion (GO:0051592)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|cell cortex (GO:0005938)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	structural molecule activity (GO:0005198)			NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	73	all_hematologic(180;0.215)	Renal(120;0.0458)			Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)	TTTCTGTGTGGTACTCTCTCC	0.512																																					NSCLC(143;340 1922 20892 22370 48145)	uc003iod.1																			0				ovary(2)|breast(1)	3						c.(1282-1284)TAC>TAA		fibrinogen, alpha polypeptide isoform alpha-E	Alteplase(DB00009)|Anistreplase(DB00029)|Reteplase(DB00015)|Sucralfate(DB00364)|Tenecteplase(DB00031)						184.0	190.0	188.0					4																	155507297		2203	4300	6503	SO:0001587	stop_gained	2243				platelet activation|platelet degranulation|protein polymerization|response to calcium ion|signal transduction	external side of plasma membrane|fibrinogen complex|platelet alpha granule lumen	eukaryotic cell surface binding|protein binding, bridging|receptor binding	g.chr4:155507297G>T		CCDS3787.1, CCDS47152.1	4q28	2014-09-17			ENSG00000171560	ENSG00000171560		"""Fibrinogen C domain containing"", ""Endogenous ligands"""	3661	protein-coding gene	gene with protein product		134820	"""fibrinogen, A alpha polypeptide"""				Standard	NM_000508		Approved		uc003iod.1	P02671	OTTHUMG00000150330	ENST00000302053.3:c.1284C>A	4.37:g.155507297G>T	ENSP00000306361:p.Tyr428*					FGA_uc003ioe.1_Nonsense_Mutation_p.Y428*|FGA_uc003iof.1_Intron	p.Y428*	NM_000508	NP_000499	P02671	FIBA_HUMAN			5	1342	-	all_hematologic(180;0.215)	Renal(120;0.0458)	428			By similarity.		A8K3E4|D3DP14|D3DP15|Q4QQH7|Q9BX62|Q9UCH2	Nonsense_Mutation	SNP	ENST00000302053.3	37	c.1284C>A	CCDS3787.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.961218	0.74016	.	.	ENSG00000171560	ENST00000302053;ENST00000403106	.	.	.	5.89	2.19	0.27852	.	54.872900	0.00166	N	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9346	0.19158	0.2182:0.1401:0.6418:0.0	.	.	.	.	X	428	.	ENSP00000306361:Y428X	Y	-	3	2	FGA	155726747	0.577000	0.26708	0.007000	0.13788	0.404000	0.30871	0.582000	0.23834	0.096000	0.17463	0.655000	0.94253	TAC		0.512	FGA-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317593.1	NM_000508	
THBS4	7060	broad.mit.edu	37	5	79378941	79378941	+	Missense_Mutation	SNP	A	A	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr5:79378941A>G	ENST00000350881.2	+	22	3053	c.2863A>G	c.(2863-2865)Aat>Gat	p.N955D	CTD-2201I18.1_ENST00000503007.1_RNA|THBS4_ENST00000504720.1_3'UTR|CTD-2201I18.1_ENST00000514042.1_RNA|THBS4_ENST00000511733.1_Missense_Mutation_p.N864D	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	955					behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		TCAAACCCAGAATTTCGACCG	0.453											OREG0016685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc003kgh.2																			0					0						c.(2863-2865)AAT>GAT		thrombospondin 4 precursor							90.0	99.0	96.0					5																	79378941		2203	4300	6503	SO:0001583	missense	7060				endothelial cell-cell adhesion|myoblast migration|negative regulation of angiogenesis|positive regulation of endothelial cell proliferation|positive regulation of neutrophil chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation	basement membrane|extracellular space	calcium ion binding|heparin binding|integrin binding|structural molecule activity	g.chr5:79378941A>G		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.2863A>G	5.37:g.79378941A>G	ENSP00000339730:p.Asn955Asp		OREG0016685	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1190	uc003kgi.3_Intron	p.N955D	NM_003248	NP_003239	P35443	TSP4_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)	23	3186	+		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)	955					B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	c.2863A>G	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	A	17.31	3.356531	0.61293	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.86164	-1.95;-2.08	5.91	0.22	0.15279	.	0.360182	0.34652	N	0.003798	T	0.76630	0.4014	L	0.32530	0.975	0.25020	N	0.991348	B	0.02656	0.0	B	0.01281	0.0	T	0.58951	-0.7545	10	0.18276	T	0.48	-7.5648	10.4245	0.44369	0.3282:0.5972:0.0746:0.0	.	955	P35443	TSP4_HUMAN	D	955;864	ENSP00000339730:N955D;ENSP00000422298:N864D	ENSP00000339730:N955D	N	+	1	0	THBS4	79414697	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	1.972000	0.40540	0.095000	0.17434	0.533000	0.62120	AAT		0.453	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
HARS	3035	broad.mit.edu	37	5	140053903	140053903	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr5:140053903C>T	ENST00000504156.1	-	13	2188	c.1469G>A	c.(1468-1470)cGa>cAa	p.R490Q	HARS_ENST00000438307.2_Missense_Mutation_p.R450Q|HARS_ENST00000307633.3_Missense_Mutation_p.R430Q|HARS_ENST00000431330.2_Missense_Mutation_p.R376Q|DND1_ENST00000542735.1_5'Flank|HARS_ENST00000457527.2_Missense_Mutation_p.R470Q|HARS_ENST00000415192.2_Missense_Mutation_p.R416Q|HARS_ENST00000504366.1_Missense_Mutation_p.R421Q|HARS_ENST00000448240.1_Missense_Mutation_p.R295Q	NM_002109.4	NP_002100.2	P12081	SYHC_HUMAN	histidyl-tRNA synthetase	490					gene expression (GO:0010467)|histidyl-tRNA aminoacylation (GO:0006427)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|histidine-tRNA ligase activity (GO:0004821)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	19			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		L-Histidine(DB00117)	GTCTTCTCTTCGGACATCCAC	0.522																																						uc003lgv.2																			0				ovary(1)|skin(1)	2						c.(1468-1470)CGA>CAA		histidyl-tRNA synthetase	L-Histidine(DB00117)						126.0	113.0	117.0					5																	140053903		2203	4300	6503	SO:0001583	missense	3035				histidyl-tRNA aminoacylation	cytosol	ATP binding|histidine-tRNA ligase activity	g.chr5:140053903C>T	AK000498	CCDS4237.1, CCDS58976.1, CCDS58977.1, CCDS58978.1, CCDS75323.1, CCDS75324.1	5q31.3	2012-10-02			ENSG00000170445	ENSG00000170445	6.1.1.21	"""Aminoacyl tRNA synthetases / Class II"""	4816	protein-coding gene	gene with protein product	"""histidine tRNA ligase 1, cytoplasmic"""	142810					Standard	XM_005268428		Approved		uc003lgv.4	P12081	OTTHUMG00000129502	ENST00000504156.1:c.1469G>A	5.37:g.140053903C>T	ENSP00000425634:p.Arg490Gln					DND1_uc003lgt.2_5'Flank|HARS_uc003lgu.2_Missense_Mutation_p.R421Q|HARS_uc011czm.1_Missense_Mutation_p.R450Q|HARS_uc003lgw.2_Missense_Mutation_p.R470Q|HARS_uc011czn.1_Missense_Mutation_p.R430Q|HARS_uc010jfu.2_Missense_Mutation_p.R402Q|HARS_uc011czo.1_Missense_Mutation_p.R416Q|HARS_uc011czp.1_Missense_Mutation_p.R376Q	p.R490Q	NM_002109	NP_002100	P12081	SYHC_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		13	1551	-			490					B4DHQ1|B4DY73|D6REN6|J3KNE5	Missense_Mutation	SNP	ENST00000504156.1	37	c.1469G>A	CCDS4237.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476790	0.44044	.	.	ENSG00000170445	ENST00000504156;ENST00000457527;ENST00000431330;ENST00000504366;ENST00000307633;ENST00000448240;ENST00000438307;ENST00000415192	D;D;D;D;D;D;D;D	0.82255	-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59;-1.59	4.93	3.1	0.35709	Anticodon-binding (3);	0.368895	0.28230	N	0.016109	T	0.73273	0.3566	L	0.49126	1.545	0.33673	D	0.611119	B;B;B;B;B;B	0.31655	0.334;0.11;0.0;0.039;0.039;0.01	B;B;B;B;B;B	0.17979	0.02;0.02;0.001;0.016;0.01;0.003	T	0.76293	-0.3012	10	0.40728	T	0.16	-2.4407	8.3997	0.32579	0.0:0.759:0.1569:0.0842	.	376;416;430;450;470;490	B4E1C5;B4DDD8;B4DHQ1;B4DY73;D6REN6;P12081	.;.;.;.;.;SYHC_HUMAN	Q	490;470;376;421;430;295;450;416	ENSP00000425634:R490Q;ENSP00000387893:R470Q;ENSP00000393244:R376Q;ENSP00000430063:R421Q;ENSP00000304668:R430Q;ENSP00000413605:R295Q;ENSP00000411511:R450Q;ENSP00000411085:R416Q	ENSP00000304668:R430Q	R	-	2	0	HARS	140034087	0.923000	0.31300	1.000000	0.80357	0.992000	0.81027	1.108000	0.31123	1.183000	0.42943	0.655000	0.94253	CGA		0.522	HARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251673.2	NM_002109	
PCDHA2	56146	broad.mit.edu	37	5	140174750	140174750	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr5:140174750G>A	ENST00000526136.1	+	1	201	c.201G>A	c.(199-201)gcG>gcA	p.A67A	PCDHA2_ENST00000378132.1_Silent_p.A67A|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Silent_p.A67A	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	67	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCGGGTGGCGTCCAAAAGAC	0.647																																						uc003lhd.2																			0				ovary(4)	4						c.(199-201)GCG>GCA		protocadherin alpha 2 isoform 1 precursor							55.0	67.0	63.0					5																	140174750		2202	4295	6497	SO:0001819	synonymous_variant	56146				homophilic cell adhesion|nervous system development	integral to plasma membrane	calcium ion binding|protein binding	g.chr5:140174750G>A	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.201G>A	5.37:g.140174750G>A						PCDHA1_uc003lha.2_Intron|PCDHA1_uc003lhb.2_Intron|PCDHA2_uc003lhc.1_Silent_p.A67A|PCDHA2_uc011czy.1_Silent_p.A67A	p.A67A	NM_018905	NP_061728	Q9Y5H9	PCDA2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	307	+			67			Extracellular (Potential).|Cadherin 1.		O75287|Q9BTV3	Silent	SNP	ENST00000526136.1	37	c.201G>A	CCDS54914.1																																																																																				0.647	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905	
PCDHB4	56131	broad.mit.edu	37	5	140503471	140503471	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr5:140503471G>A	ENST00000194152.1	+	1	1891	c.1891G>A	c.(1891-1893)Gag>Aag	p.E631K		NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	631	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTGCTGAGCGAGCGCGACGC	0.687																																						uc003lip.1																			0				upper_aerodigestive_tract(1)|ovary(1)|skin(1)	3						c.(1891-1893)GAG>AAG		protocadherin beta 4 precursor							29.0	29.0	29.0					5																	140503471		1916	3870	5786	SO:0001583	missense	56131				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	cytoplasm|integral to plasma membrane|intermediate filament cytoskeleton	calcium ion binding	g.chr5:140503471G>A	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1891G>A	5.37:g.140503471G>A	ENSP00000194152:p.Glu631Lys						p.E631K	NM_018938	NP_061761	Q9Y5E5	PCDB4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	1891	+			631			Cadherin 6.|Extracellular (Potential).		Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	c.1891G>A	CCDS4246.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823524	0.90873	.	.	ENSG00000081818	ENST00000194152	T	0.50813	0.73	4.12	4.12	0.48240	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.70675	0.3251	M	0.86028	2.79	0.51233	D	0.999918	D	0.69078	0.997	D	0.67548	0.952	T	0.77960	-0.2391	9	0.87932	D	0	.	16.5901	0.84763	0.0:0.0:1.0:0.0	.	631	Q9Y5E5	PCDB4_HUMAN	K	631	ENSP00000194152:E631K	ENSP00000194152:E631K	E	+	1	0	PCDHB4	140483655	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.164000	0.64954	2.307000	0.77673	0.485000	0.47835	GAG		0.687	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
HLA-H	3136	broad.mit.edu	37	6	29856360	29856360	+	IGR	SNP	C	C	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr6:29856360C>A								HLA-G (57458 upstream) : HLA-A (52676 downstream)																							GAACGAGGACCTGCGCTCCTG	0.672																																						uc010jro.2																			0					0						c.(355-357)CTG>ATG		SubName: Full=cDNA FLJ52667, highly similar to HLA class I histocompatibility antigen, alpha chain H;																																				SO:0001628	intergenic_variant	3136							g.chr6:29856360C>A																													6.37:g.29856360C>A						HLA-G_uc011dmb.1_Intron|HLA-H_uc003nod.2_RNA	p.L119M							3	407	+									Missense_Mutation	SNP		37	c.355C>A																																																																																				0	0.672								
PRRT1	80863	broad.mit.edu	37	6	32118160	32118160	+	Silent	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr6:32118160G>A	ENST00000211413.5	-	2	667	c.543C>T	c.(541-543)gtC>gtT	p.V181V	PRRT1_ENST00000375152.2_Silent_p.V100V|PRRT1_ENST00000467780.1_5'Flank|PRRT1_ENST00000375150.2_Silent_p.V100V	NM_030651.3	NP_085154.3	Q99946	PRRT1_HUMAN	proline-rich transmembrane protein 1	181					response to biotic stimulus (GO:0009607)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(2)|endometrium(1)|kidney(1)|lung(2)	6						CCACCGGGTAGACCGGCACGT	0.667																																						uc003nzt.2																			0				breast(1)	1						c.(541-543)GTC>GTT		NG5 protein							34.0	35.0	35.0					6																	32118160		1508	2707	4215	SO:0001819	synonymous_variant	80863				response to biotic stimulus	integral to membrane		g.chr6:32118160G>A	AK054885	CCDS4739.1	6p21.32	2011-10-10	2005-07-24	2005-07-24		ENSG00000204314		"""Proline-rich transmembrane proteins"""	13943	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 7"""		"""chromosome 6 open reading frame 31"""	C6orf31			Standard	XM_006715221		Approved	NG5, IFITMD7	uc003nzt.3	Q99946		ENST00000211413.5:c.543C>T	6.37:g.32118160G>A						PRRT1_uc003nzs.2_Silent_p.V222V|PRRT1_uc003nzu.2_Silent_p.L74L	p.V181V	NM_030651	NP_085154	Q99946	PRRT1_HUMAN			2	659	-			181					A6ND08|A6ND40|B0S869|Q5SSW4|Q5SSX7|Q5STI1|Q96DW3|Q96NQ8	Silent	SNP	ENST00000211413.5	37	c.543C>T	CCDS4739.1																																																																																				0.667	PRRT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076255.2	NM_030651	
ITPR3	3710	broad.mit.edu	37	6	33633622	33633622	+	Nonsense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr6:33633622C>T	ENST00000374316.5	+	15	2480	c.1420C>T	c.(1420-1422)Cag>Tag	p.Q474*	ITPR3_ENST00000605930.1_Nonsense_Mutation_p.Q474*			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	474					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|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)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	GTTTGTCATCCAGCTGCTGGA	0.572																																						uc011drk.1																			0				ovary(6)|lung(5)|central_nervous_system(5)|breast(2)|kidney(1)	19						c.(1420-1422)CAG>TAG		inositol 1,4,5-triphosphate receptor, type 3							137.0	103.0	114.0					6																	33633622		2203	4300	6503	SO:0001587	stop_gained	3710				activation of phospholipase C activity|calcium ion transport into cytosol|energy reserve metabolic process|G-protein coupled receptor protein signaling pathway|nerve growth factor receptor signaling pathway|platelet activation|protein heterooligomerization|protein homooligomerization|regulation of insulin secretion|response to calcium ion	apical part of cell|brush border|endoplasmic reticulum membrane|integral to plasma membrane|myelin sheath|neuronal cell body|nuclear outer membrane|platelet dense tubular network membrane	inositol 1,3,4,5 tetrakisphosphate binding|inositol 1,4,5 trisphosphate binding|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|inositol hexakisphosphate binding|intracellular ligand-gated calcium channel activity|protein binding	g.chr6:33633622C>T	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.1420C>T	6.37:g.33633622C>T	ENSP00000363435:p.Gln474*						p.Q474*	NM_002224	NP_002215	Q14573	ITPR3_HUMAN			14	1639	+			474			Cytoplasmic (Potential).		Q14649|Q5TAQ2	Nonsense_Mutation	SNP	ENST00000374316.5	37	c.1420C>T	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	C	46	12.684424	0.99688	.	.	ENSG00000096433	ENST00000374316	.	.	.	5.4	5.4	0.78164	.	0.058885	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-31.2065	14.0635	0.64815	0.1507:0.8493:0.0:0.0	.	.	.	.	X	474	.	ENSP00000363435:Q474X	Q	+	1	0	ITPR3	33741600	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	6.378000	0.73150	2.539000	0.85634	0.563000	0.77884	CAG		0.572	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
VEGFA	7422	broad.mit.edu	37	6	43748479	43748479	+	Nonsense_Mutation	SNP	C	C	T	rs45533131		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr6:43748479C>T	ENST00000523873.1	+	6	471	c.433C>T	c.(433-435)Cga>Tga	p.R145*	VEGFA_ENST00000372064.4_Intron|VEGFA_ENST00000417285.2_Intron|VEGFA_ENST00000520948.1_Nonsense_Mutation_p.R145*|VEGFA_ENST00000518824.1_Intron|VEGFA_ENST00000523950.1_Intron|VEGFA_ENST00000518689.1_Nonsense_Mutation_p.R145*|VEGFA_ENST00000372077.4_Intron|VEGFA_ENST00000425836.2_Nonsense_Mutation_p.R325*|VEGFA_ENST00000372067.3_Intron|VEGFA_ENST00000413642.3_Nonsense_Mutation_p.R325*|VEGFA_ENST00000324450.6_Intron|VEGFA_ENST00000230480.6_Intron|VEGFA_ENST00000482630.2_Intron|VEGFA_ENST00000372055.4_Nonsense_Mutation_p.R325*|VEGFA_ENST00000457104.2_Intron|VEGFA_ENST00000523125.1_Intron			P15692	VEGFA_HUMAN	vascular endothelial growth factor A	145					activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|artery morphogenesis (GO:0048844)|basophil chemotaxis (GO:0002575)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|camera-type eye morphogenesis (GO:0048593)|cardiac muscle fiber development (GO:0048739)|cardiac vascular smooth muscle cell development (GO:0060948)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to hypoxia (GO:0071456)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|dopaminergic neuron differentiation (GO:0071542)|endothelial cell chemotaxis (GO:0035767)|epithelial cell differentiation (GO:0030855)|eye photoreceptor cell development (GO:0042462)|growth (GO:0040007)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|induction of positive chemotaxis (GO:0050930)|kidney development (GO:0001822)|lactation (GO:0007595)|lung development (GO:0030324)|lymph vessel morphogenesis (GO:0036303)|macrophage differentiation (GO:0030225)|mammary gland alveolus development (GO:0060749)|mesoderm development (GO:0007498)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|outflow tract morphogenesis (GO:0003151)|ovarian follicle development (GO:0001541)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cellular component movement (GO:0051272)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of gene expression (GO:0010628)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell chemotaxis (GO:0060754)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine autophosphorylation (GO:1900086)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein localization to early endosome (GO:1902966)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of receptor internalization (GO:0002092)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of vascular permeability (GO:0043117)|post-embryonic camera-type eye development (GO:0031077)|primitive erythrocyte differentiation (GO:0060319)|regulation of cell shape (GO:0008360)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)|surfactant homeostasis (GO:0043129)|tube formation (GO:0035148)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|VEGF-activated neuropilin signaling pathway (GO:0038190)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|neuropilin binding (GO:0038191)|platelet-derived growth factor receptor binding (GO:0005161)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor agonist activity (GO:0048018)|vascular endothelial growth factor receptor 1 binding (GO:0043183)|vascular endothelial growth factor receptor 2 binding (GO:0043184)|vascular endothelial growth factor receptor binding (GO:0005172)	p.R325*(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		Aflibercept(DB08885)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Dalteparin(DB06779)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Vandetanib(DB05294)	AAAATCAGTTCGAGGAAAGGG	0.532																																						uc003owh.2																			1	Substitution - Nonsense(1)		prostate(1)	ovary(1)|breast(1)	2						c.(973-975)CGA>TGA		vascular endothelial growth factor A isoform a	Atorvastatin(DB01076)|Bevacizumab(DB00112)|Carvedilol(DB01136)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Minocycline(DB01017)|Ranibizumab(DB01270)|Simvastatin(DB00641)						89.0	90.0	90.0					6																	43748479		2203	4300	6503	SO:0001587	stop_gained	7422				basophil chemotaxis|cellular response to hypoxia|induction of positive chemotaxis|induction of positive chemotaxis|platelet activation|platelet degranulation|platelet-derived growth factor receptor signaling pathway|positive regulation of angiogenesis|positive regulation of blood vessel endothelial cell migration|positive regulation of cell adhesion|positive regulation of cell division|positive regulation of endothelial cell proliferation|positive regulation of leukocyte migration|positive regulation of mast cell chemotaxis|positive regulation of peptidyl-tyrosine phosphorylation|positive regulation of vascular endothelial growth factor receptor signaling pathway|positive regulation of vascular permeability|regulation of cell shape|vascular endothelial growth factor receptor signaling pathway|vasculogenesis	cell surface|extracellular space|membrane|platelet alpha granule lumen	cell surface binding|chemoattractant activity|cytokine activity|fibronectin binding|growth factor activity|heparin binding|platelet-derived growth factor receptor binding|protein heterodimerization activity|protein homodimerization activity|vascular endothelial growth factor receptor 1 binding|vascular endothelial growth factor receptor 2 binding|vascular endothelial growth factor receptor binding	g.chr6:43748479C>T	AB021221	CCDS34457.1, CCDS4907.2, CCDS34458.1, CCDS47432.1, CCDS47433.1, CCDS47434.1, CCDS47435.1, CCDS55007.1, CCDS55008.1, CCDS55009.1, CCDS55010.1, CCDS55011.1, CCDS55012.1, CCDS55013.1, CCDS55014.1, CCDS55015.1, CCDS69125.1	6p12	2008-02-05	2006-10-31	2006-10-31	ENSG00000112715	ENSG00000112715			12680	protein-coding gene	gene with protein product		192240	"""vascular endothelial growth factor"""	VEGF		8786112	Standard	NM_001025366		Approved	VEGF-A, VPF	uc003owh.3	P15692	OTTHUMG00000014745	ENST00000523873.1:c.433C>T	6.37:g.43748479C>T	ENSP00000430479:p.Arg145*					VEGFA_uc003owd.2_Intron|VEGFA_uc003owf.2_Nonsense_Mutation_p.R325*|VEGFA_uc003owe.2_Intron|VEGFA_uc003owg.2_Nonsense_Mutation_p.R325*|VEGFA_uc003owi.2_Intron|VEGFA_uc003owj.2_Intron|VEGFA_uc010jyx.2_Intron|VEGFA_uc003owk.2_Intron	p.R325*	NM_001025366	NP_001020537	P15692	VEGFA_HUMAN	all cancers(41;0.000413)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|STAD - Stomach adenocarcinoma(11;0.0742)|OV - Ovarian serous cystadenocarcinoma(102;0.196)		6	1464	+	all_cancers(18;5.46e-07)|all_epithelial(2;5.96e-08)|Lung NSC(15;0.000157)|all_lung(25;0.000486)|Hepatocellular(11;0.00309)		145					B5BU86|H0Y2S8|H0Y407|H0Y414|H0Y462|H0Y8N2|H3BLW7|O60720|O75875|Q074Z4|Q16889|Q5UB46|Q6P0P5|Q96KJ0|Q96L82|Q96NW5|Q9H1W8|Q9H1W9|Q9UH58|Q9UL23	Nonsense_Mutation	SNP	ENST00000523873.1	37	c.973C>T	CCDS55010.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	37|37	6.542237|6.542237	0.97650|0.97650	.|.	.|.	ENSG00000112715|ENSG00000112715	ENST00000413642;ENST00000372055;ENST00000425836;ENST00000520948;ENST00000523873;ENST00000518689|ENST00000519767	.|.	.|.	.|.	4.85|4.85	4.85|4.85	0.62838|0.62838	.|.	4.362100|.	0.00520|.	N|.	0.000187|.	.|T	.|0.66886	.|0.2835	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.66384	.|-0.5937	.|4	0.02654|.	T|.	1|.	-0.4131|-0.4131	17.3086|17.3086	0.87202|0.87202	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs45533131|rs45533131	.|.	.|.	.|.	X|L	325;325;325;145;145;145|296	.|.	ENSP00000361125:R325X|.	R|S	+|+	1|2	2|0	VEGFA|VEGFA	43856457|43856457	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	2.970000|2.970000	0.49240|0.49240	2.387000|2.387000	0.81309|0.81309	0.561000|0.561000	0.74099|0.74099	CGA|TCG		0.532	VEGFA-021	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374460.1	NM_001025366	
GPRC6A	222545	broad.mit.edu	37	6	117128089	117128089	+	Missense_Mutation	SNP	C	C	T	rs368860950		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr6:117128089C>T	ENST00000310357.3	-	3	800	c.779G>A	c.(778-780)cGg>cAg	p.R260Q	GPRC6A_ENST00000368549.3_Missense_Mutation_p.R260Q|GPRC6A_ENST00000530250.1_Missense_Mutation_p.R260Q	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	260					calcium-mediated signaling (GO:0019722)|response to amino acid (GO:0043200)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|liver(1)|lung(24)|ovary(5)|pancreas(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)	65		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)		CTTCAGTGTCCGATTGATTCT	0.363																																						uc003pxj.1																			0				ovary(4)|skin(2)	6						c.(778-780)CGG>CAG		G protein-coupled receptor, family C, group 6,		C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	86.0	90.0	89.0		779	3.8	1.0	6		89	0,8598		0,0,4299	no	missense	GPRC6A	NM_148963.2	43	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign	260/927	117128089	1,13003	2203	4299	6502	SO:0001583	missense	222545				response to amino acid stimulus		G-protein coupled receptor activity	g.chr6:117128089C>T	AF502962	CCDS5112.1, CCDS69184.1, CCDS69185.1	6q22.31	2014-01-30	2014-01-30		ENSG00000173612	ENSG00000173612		"""GPCR / Class C : Calcium-sensing receptors"""	18510	protein-coding gene	gene with protein product			"""G protein-coupled receptor, family C, group 6, member A"""				Standard	NM_001286354		Approved	bA86F4.3	uc003pxj.1	Q5T6X5	OTTHUMG00000015447	ENST00000310357.3:c.779G>A	6.37:g.117128089C>T	ENSP00000309493:p.Arg260Gln					GPRC6A_uc003pxk.1_Missense_Mutation_p.R260Q|GPRC6A_uc003pxl.1_Missense_Mutation_p.R260Q	p.R260Q	NM_148963	NP_683766	Q5T6X5	GPC6A_HUMAN		GBM - Glioblastoma multiforme(226;0.0265)|all cancers(137;0.0554)|OV - Ovarian serous cystadenocarcinoma(136;0.07)	3	801	-		all_cancers(87;0.0314)|all_epithelial(87;0.0216)|Colorectal(196;0.234)	260			Extracellular (Potential).		Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Missense_Mutation	SNP	ENST00000310357.3	37	c.779G>A	CCDS5112.1	.	.	.	.	.	.	.	.	.	.	C	0.027	-1.365791	0.01235	2.27E-4	0.0	ENSG00000173612	ENST00000310357;ENST00000368549;ENST00000530250	D;D;D	0.90955	-1.7;-1.7;-2.76	6.17	3.8	0.43715	Extracellular ligand-binding receptor (1);	0.455997	0.19029	N	0.124602	T	0.56470	0.1987	N	0.08118	0	0.21386	N	0.999708	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.48833	-0.9000	10	0.02654	T	1	.	9.6458	0.39865	0.0:0.2101:0.0:0.7899	.	260;260;260	Q5T6X5-3;Q5T6X5-2;Q5T6X5	.;.;GPC6A_HUMAN	Q	260	ENSP00000309493:R260Q;ENSP00000357537:R260Q;ENSP00000433465:R260Q	ENSP00000309493:R260Q	R	-	2	0	GPRC6A	117234782	0.069000	0.21087	1.000000	0.80357	0.119000	0.20118	0.478000	0.22212	0.559000	0.29153	-0.294000	0.09567	CGG		0.363	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
LPA	4018	broad.mit.edu	37	6	161020531	161020531	+	Splice_Site	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr6:161020531C>T	ENST00000316300.5	-	20	3332		c.e20+1		LPA_ENST00000447678.1_Splice_Site			P08519	APOA_HUMAN	lipoprotein, Lp(a)						blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	CAAAGACGTACGCATTTGGGT	0.483																																						uc003qtl.2																			0				ovary(3)|skin(2)|pancreas(1)	6						c.e21+1		lipoprotein Lp(a) precursor	Aminocaproic Acid(DB00513)						287.0	311.0	303.0					6																	161020531		2200	4299	6499	SO:0001630	splice_region_variant	4018				blood circulation|lipid metabolic process|lipid transport|lipoprotein metabolic process|proteolysis|receptor-mediated endocytosis	plasma lipoprotein particle	apolipoprotein binding|endopeptidase inhibitor activity|fibronectin binding|heparin binding|serine-type endopeptidase activity	g.chr6:161020531C>T	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.3287+1G>A	6.37:g.161020531C>T							p.A1096_splice	NM_005577	NP_005568	P08519	APOA_HUMAN		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	21	3407	-		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)						Q5VTD7|Q9UD88	Splice_Site	SNP	ENST00000316300.5	37	c.3287_splice	CCDS43523.1	.	.	.	.	.	.	.	.	.	.	C	10.78	1.446431	0.25987	.	.	ENSG00000198670	ENST00000316300;ENST00000447678	.	.	.	2.48	2.48	0.30137	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4117	0.32646	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LPA	160940521	1.000000	0.71417	0.930000	0.37139	0.007000	0.05969	3.793000	0.55484	1.361000	0.45981	0.436000	0.28706	.		0.483	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	Intron
EGFR	1956	broad.mit.edu	37	7	55238870	55238870	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr7:55238870G>A	ENST00000275493.2	+	16	2060	c.1883G>A	c.(1882-1884)tGc>tAc	p.C628Y	EGFR_ENST00000442591.1_Missense_Mutation_p.C628Y|EGFR_ENST00000454757.2_Missense_Mutation_p.C575Y|EGFR_ENST00000455089.1_Missense_Mutation_p.C583Y	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	628					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TCCTACAGATGCACTGGGCCA	0.393		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.2		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	A|O|Mis	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	glioma|NSCLC		0				lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(1882-1884)TGC>TAC		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)						134.0	119.0	124.0					7																	55238870		2203	4300	6503	SO:0001583	missense	1956	Lung_Cancer_Familial_Clustering_of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55238870G>A		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1883G>A	7.37:g.55238870G>A	ENSP00000275493:p.Cys628Tyr	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc010kzg.1_Missense_Mutation_p.C583Y|EGFR_uc011kco.1_Missense_Mutation_p.C575Y|EGFR_uc011kcp.1_RNA|EGFR_uc011kcq.1_RNA	p.C628Y	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		16	2129	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		628			Extracellular (Potential).		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	c.1883G>A	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	G	16.25	3.070678	0.55539	.	.	ENSG00000146648	ENST00000455089;ENST00000395504;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.54	5.54	0.83059	Growth factor, receptor (1);	0.087063	0.85682	D	0.000000	T	0.82245	0.4995	H	0.97635	4.045	0.80722	D	1	D;D	0.76494	0.989;0.999	P;D	0.73708	0.765;0.981	D	0.88094	0.2815	10	0.87932	D	0	.	16.5484	0.84457	0.0:0.0:1.0:0.0	.	583;628	Q504U8;P00533	.;EGFR_HUMAN	Y	583;498;628;628;575;422	ENSP00000415559:C583Y;ENSP00000275493:C628Y;ENSP00000410031:C628Y;ENSP00000395243:C575Y	ENSP00000275493:C628Y	C	+	2	0	EGFR	55206364	1.000000	0.71417	0.970000	0.41538	0.066000	0.16364	7.285000	0.78660	2.768000	0.95171	0.561000	0.74099	TGC		0.393	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
CALN1	83698	broad.mit.edu	37	7	71252851	71252851	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr7:71252851C>T	ENST00000329008.5	-	6	867	c.569G>A	c.(568-570)cGg>cAg	p.R190Q	CALN1_ENST00000395275.2_Missense_Mutation_p.R232Q|CALN1_ENST00000395276.2_Missense_Mutation_p.R190Q|CALN1_ENST00000412588.1_Missense_Mutation_p.R232Q|CALN1_ENST00000405452.2_Missense_Mutation_p.R190Q|CALN1_ENST00000431984.1_Missense_Mutation_p.R190Q	NM_001017440.2	NP_001017440.1	Q9BXU9	CABP8_HUMAN	calneuron 1	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	calcium ion binding (GO:0005509)	p.R232Q(1)|p.R190Q(1)		biliary_tract(1)|breast(1)|endometrium(3)|large_intestine(6)|lung(19)|skin(2)	32		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)				GAGGCTCTTCCGGACGCAGGT	0.552																																						uc003twa.3																			2	Substitution - Missense(2)		endometrium(2)	skin(1)	1						c.(568-570)CGG>CAG		calneuron 1 isoform 2							125.0	98.0	107.0					7																	71252851		2203	4300	6503	SO:0001583	missense	83698					Golgi apparatus|integral to membrane|perinuclear region of cytoplasm|plasma membrane	calcium ion binding	g.chr7:71252851C>T	AF282250	CCDS5541.1, CCDS47603.1	7q11	2013-01-10			ENSG00000183166	ENSG00000183166		"""EF-hand domain containing"""	13248	protein-coding gene	gene with protein product	"""calcium-binding protein CABP8"""	607176				11286509	Standard	NM_031468		Approved		uc003twb.4	Q9BXU9	OTTHUMG00000023787	ENST00000329008.5:c.569G>A	7.37:g.71252851C>T	ENSP00000332498:p.Arg190Gln					CALN1_uc003twb.3_Missense_Mutation_p.R232Q|CALN1_uc003twc.3_Missense_Mutation_p.R190Q	p.R190Q	NM_001017440	NP_001017440	Q9BXU9	CABP8_HUMAN			6	1096	-		all_cancers(73;0.069)|Lung NSC(55;0.0658)|all_lung(88;0.0912)|all_epithelial(88;0.161)	190			Cytoplasmic (Potential).		J3KQA7	Missense_Mutation	SNP	ENST00000329008.5	37	c.569G>A	CCDS5541.1	.	.	.	.	.	.	.	.	.	.	C	35	5.581376	0.96565	.	.	ENSG00000183166	ENST00000329008;ENST00000395275;ENST00000395276;ENST00000431984;ENST00000412588;ENST00000405452	T;T;T;T;T;T	0.74526	-0.69;-0.85;-0.69;-0.69;-0.85;-0.69	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.80215	0.4582	L	0.29908	0.895	0.50039	D	0.999846	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.995	T	0.82946	-0.0205	10	0.87932	D	0	-29.6416	17.5493	0.87872	0.0:1.0:0.0:0.0	.	190;190	A4D1Z1;Q9BXU9	.;CABP8_HUMAN	Q	190;232;190;190;232;190	ENSP00000332498:R190Q;ENSP00000378690:R232Q;ENSP00000378691:R190Q;ENSP00000410704:R190Q;ENSP00000391882:R232Q;ENSP00000384354:R190Q	ENSP00000332498:R190Q	R	-	2	0	CALN1	70890787	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.724000	0.84798	2.372000	0.80975	0.561000	0.74099	CGG		0.552	CALN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320044.2	NM_031468	
GRM3	2913	broad.mit.edu	37	7	86415655	86415655	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr7:86415655C>T	ENST00000361669.2	+	3	1646	c.547C>T	c.(547-549)Cgc>Tgc	p.R183C	AC005009.2_ENST00000452471.1_RNA|AC005009.2_ENST00000418031.1_RNA|GRM3_ENST00000536043.1_Missense_Mutation_p.R55C|GRM3_ENST00000546348.1_Intron|GRM3_ENST00000394720.2_Missense_Mutation_p.R181C|GRM3_ENST00000439827.1_Missense_Mutation_p.R183C	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	183					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.R183C(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)					TGATAAGTCGCGCTATGATTA	0.562																																					GBM(52;969 1098 3139 52280)	uc003uid.2																			1	Substitution - Missense(1)		pancreas(1)	lung(4)|ovary(3)|central_nervous_system(2)|skin(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)	13						c.(547-549)CGC>TGC		glutamate receptor, metabotropic 3 precursor	Acamprosate(DB00659)|Nicotine(DB00184)						134.0	129.0	131.0					7																	86415655		2203	4300	6503	SO:0001583	missense	2913				synaptic transmission	integral to plasma membrane		g.chr7:86415655C>T		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.547C>T	7.37:g.86415655C>T	ENSP00000355316:p.Arg183Cys					GRM3_uc010lef.2_Missense_Mutation_p.R181C|GRM3_uc010leg.2_Missense_Mutation_p.R55C|GRM3_uc010leh.2_Intron	p.R183C	NM_000840	NP_000831	Q14832	GRM3_HUMAN			3	1646	+	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)		183			Extracellular (Potential).		Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Missense_Mutation	SNP	ENST00000361669.2	37	c.547C>T	CCDS5600.1	.	.	.	.	.	.	.	.	.	.	C	27.5	4.837511	0.91117	.	.	ENSG00000198822	ENST00000361669;ENST00000454217;ENST00000536043;ENST00000439827;ENST00000394720	D;D;D;D;D	0.85013	-1.93;-1.93;-1.93;-1.93;-1.93	5.83	5.83	0.93111	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.94722	0.8297	M	0.93808	3.46	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;1.0	D	0.95413	0.8500	10	0.87932	D	0	.	19.122	0.93367	0.0:1.0:0.0:0.0	.	55;183;183	F5GYZ2;G5E9K2;Q14832	.;.;GRM3_HUMAN	C	183;55;55;183;181	ENSP00000355316:R183C;ENSP00000405427:R55C;ENSP00000441407:R55C;ENSP00000398767:R183C;ENSP00000378209:R181C	ENSP00000355316:R183C	R	+	1	0	GRM3	86253591	1.000000	0.71417	0.968000	0.41197	0.981000	0.71138	4.667000	0.61561	2.770000	0.95276	0.655000	0.94253	CGC		0.562	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
ABCB4	5244	broad.mit.edu	37	7	87092144	87092144	+	Silent	SNP	G	G	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr7:87092144G>T	ENST00000265723.4	-	4	327	c.216C>A	c.(214-216)ccC>ccA	p.P72P	ABCB4_ENST00000359206.3_Silent_p.P72P|ABCB4_ENST00000545634.1_Silent_p.P72P|ABCB4_ENST00000453593.1_Silent_p.P72P|ABCB4_ENST00000358400.3_Silent_p.P72P	NM_000443.3|NM_018849.2	NP_000434.1|NP_061337.1	P21439	MDR3_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 4	72	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				cellular lipid metabolic process (GO:0044255)|lipid metabolic process (GO:0006629)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|xenobiotic-transporting ATPase activity (GO:0008559)			breast(5)|endometrium(7)|kidney(2)|large_intestine(15)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				Colchicine(DB01394)|Etravirine(DB06414)|Silodosin(DB06207)	TCATCATGAGGGGGAGACCTG	0.383																																						uc003uiv.1																			0				ovary(4)|skin(1)|pancreas(1)	6						c.(214-216)CCC>CCA		ATP-binding cassette, subfamily B, member 4							97.0	88.0	91.0					7																	87092144		2203	4300	6503	SO:0001819	synonymous_variant	5244				cellular lipid metabolic process	apical plasma membrane|Golgi membrane|integral to plasma membrane|intercellular canaliculus|membrane fraction	ATP binding|xenobiotic-transporting ATPase activity	g.chr7:87092144G>T	M23234	CCDS5605.1, CCDS5606.1, CCDS5607.1	7q21	2012-03-14			ENSG00000005471	ENSG00000005471		"""ATP binding cassette transporters / subfamily B"""	45	protein-coding gene	gene with protein product		171060		PGY3, MDR3		2892668, 11313316	Standard	NM_018850		Approved	MDR2, PFIC-3, GBD1	uc003uiv.1	P21439	OTTHUMG00000023396	ENST00000265723.4:c.216C>A	7.37:g.87092144G>T						ABCB4_uc003uiw.1_Silent_p.P72P|ABCB4_uc003uix.1_Silent_p.P72P|ABCB4_uc003uiy.2_Silent_p.P72P	p.P72P	NM_018849	NP_061337	P21439	MDR3_HUMAN			4	292	-	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)		72	IMAIAHGSGLP -> RGSSRVDLQAC (in Ref. 5; CAA84542).		ABC transmembrane type-1 1.|Helical; (By similarity).		A0A2V7|A4D1D3|A4D1D4|A4D1D5|D6W5P3|D6W5P4|Q14813	Silent	SNP	ENST00000265723.4	37	c.216C>A	CCDS5606.1																																																																																				0.383	ABCB4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000336083.1	NM_000443	
AZGP1	563	broad.mit.edu	37	7	99569626	99569626	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr7:99569626C>T	ENST00000292401.4	-	2	216	c.80G>A	c.(79-81)cGt>cAt	p.R27H	AZGP1_ENST00000411734.1_Missense_Mutation_p.R24H	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	27					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					CAGAGAGTAACGACCTGCAAA	0.527																																						uc003ush.2																			0				ovary(1)|central_nervous_system(1)	2						c.(79-81)CGT>CAT		alpha-2-glycoprotein 1, zinc							59.0	58.0	58.0					7																	99569626		2203	4300	6503	SO:0001583	missense	563				antigen processing and presentation|cell adhesion|immune response|lipid catabolic process|negative regulation of cell proliferation	extracellular region|MHC class I protein complex	fatty acid binding|protein transmembrane transporter activity|ribonuclease activity	g.chr7:99569626C>T	BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"""Immunoglobulin superfamily / C1-set domain containing"""	910	protein-coding gene	gene with protein product		194460	"""alpha-2-glycoprotein 1, zinc"""			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.80G>A	7.37:g.99569626C>T	ENSP00000292401:p.Arg27His						p.R27H	NM_001185	NP_001176	P25311	ZA2G_HUMAN			2	124	-	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)		27					D6W5T8|O60386|Q5XKQ4|Q8N4N0	Missense_Mutation	SNP	ENST00000292401.4	37	c.80G>A	CCDS5680.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.328062	0.24080	.	.	ENSG00000160862	ENST00000292401;ENST00000411734	D;D	0.89050	-2.46;-2.46	1.51	-2.22	0.06952	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);	2.353210	0.02490	U	0.089339	T	0.72162	0.3426	N	0.02011	-0.69	0.22468	N	0.999077	B	0.06786	0.001	B	0.01281	0.0	T	0.63492	-0.6625	10	0.87932	D	0	.	3.7112	0.08420	0.0:0.2498:0.305:0.4452	.	27	P25311	ZA2G_HUMAN	H	27;24	ENSP00000292401:R27H;ENSP00000396093:R24H	ENSP00000292401:R27H	R	-	2	0	AZGP1	99407562	0.008000	0.16893	0.130000	0.21974	0.365000	0.29674	-0.562000	0.05950	-0.713000	0.04981	-0.643000	0.03959	CGT		0.527	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4	NM_001185	
ASB15	142685	broad.mit.edu	37	7	123269046	123269046	+	Missense_Mutation	SNP	A	A	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr7:123269046A>G	ENST00000451558.1	+	12	1519	c.998A>G	c.(997-999)gAt>gGt	p.D333G	ASB15_ENST00000275699.3_Missense_Mutation_p.D333G|ASB15_ENST00000434204.1_Missense_Mutation_p.D333G|ASB15_ENST00000540573.1_Missense_Mutation_p.D333G|ASB15_ENST00000451215.1_Missense_Mutation_p.D333G			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	333					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						AATGGTTTTGATGTCAACACT	0.418																																						uc003vku.1																			0				skin(2)|lung(1)	3						c.(997-999)GAT>GGT		ankyrin repeat and SOCS box-containing 15							178.0	164.0	169.0					7																	123269046		2203	4300	6503	SO:0001583	missense	142685				intracellular signal transduction			g.chr7:123269046A>G	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"""Ankyrin repeat domain containing"""	19767	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 15"""			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.998A>G	7.37:g.123269046A>G	ENSP00000397655:p.Asp333Gly					ASB15_uc003vkw.1_Missense_Mutation_p.D333G	p.D333G	NM_080928	NP_563616	Q8WXK1	ASB15_HUMAN			10	1290	+			333			ANK 6.		Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	c.998A>G	CCDS34742.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.514201	0.85389	.	.	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	6.17	6.17	0.99709	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.82637	0.5080	M	0.78916	2.43	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84556	0.0647	10	0.87932	D	0	-8.7552	16.8222	0.85835	1.0:0.0:0.0:0.0	.	333	Q8WXK1	ASB15_HUMAN	G	333;333;333;333;122;333	ENSP00000397655:D333G;ENSP00000390963:D333G;ENSP00000416433:D333G;ENSP00000438643:D333G;ENSP00000275699:D333G	ENSP00000275699:D333G	D	+	2	0	ASB15	123056282	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	8.948000	0.93006	2.371000	0.80710	0.533000	0.62120	GAT		0.418	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
ALDH1A1	216	broad.mit.edu	37	9	75567900	75567900	+	Missense_Mutation	SNP	G	G	A	rs144704960	byFrequency	TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr9:75567900G>A	ENST00000297785.3	-	1	71	c.17C>T	c.(16-18)aCg>aTg	p.T6M	ALDH1A1_ENST00000482210.1_5'Flank|ALDH1A1_ENST00000376939.1_Missense_Mutation_p.T6M	NM_000689.4	NP_000680.2	P00352	AL1A1_HUMAN	aldehyde dehydrogenase 1 family, member A1	6					cellular aldehyde metabolic process (GO:0006081)|ethanol oxidation (GO:0006069)|positive regulation of Ras GTPase activity (GO:0032320)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|androgen binding (GO:0005497)|Ras GTPase activator activity (GO:0005099)|retinal dehydrogenase activity (GO:0001758)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)	17					Tretinoin(DB00755)|Vitamin A(DB00162)	TAAGTCTGGCGTGCCTGAGGA	0.418													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17707	0.0		0.0	False		,,,				2504	0.0					uc004ajd.2																			0				ovary(3)|lung(1)	4						c.(16-18)ACG>ATG		aldehyde dehydrogenase 1A1	NADH(DB00157)|Tretinoin(DB00755)|Vitamin A(DB00162)	G	MET/THR	4,4402	8.1+/-20.4	0,4,2199	117.0	106.0	110.0		17	-9.5	0.0	9	dbSNP_134	110	0,8598		0,0,4299	yes	missense	ALDH1A1	NM_000689.4	81	0,4,6498	AA,AG,GG		0.0,0.0908,0.0308	benign	6/502	75567900	4,13000	2203	4299	6502	SO:0001583	missense	216				cellular aldehyde metabolic process|ethanol oxidation|xenobiotic metabolic process	cytosol	aldehyde dehydrogenase (NAD) activity|androgen binding|Ras GTPase activator activity|retinal dehydrogenase activity	g.chr9:75567900G>A	K03000	CCDS6644.1	9q21.13	2010-08-05			ENSG00000165092	ENSG00000165092	1.2.1.36, 1.2.1.3	"""Aldehyde dehydrogenases"""	402	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 1"""	100640		PUMB1, ALDH1		1709013	Standard	NM_000689		Approved	RALDH1	uc004ajd.3	P00352	OTTHUMG00000020019	ENST00000297785.3:c.17C>T	9.37:g.75567900G>A	ENSP00000297785:p.Thr6Met					ALDH1A1_uc011lsh.1_Intron	p.T6M	NM_000689	NP_000680	P00352	AL1A1_HUMAN			1	70	-			6					O00768|Q5SYR1	Missense_Mutation	SNP	ENST00000297785.3	37	c.17C>T	CCDS6644.1	.	.	.	.	.	.	.	.	.	.	G	4.881	0.163741	0.09287	9.08E-4	0.0	ENSG00000165092	ENST00000297785;ENST00000376939;ENST00000428593;ENST00000419959;ENST00000446946	T;T;T;T	0.76186	-1.0;-0.36;-0.28;-0.01	5.85	-9.48	0.00591	Aldehyde/histidinol dehydrogenase (1);	2.404540	0.01028	N	0.004092	T	0.42720	0.1215	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28235	-1.0050	10	0.25751	T	0.34	.	3.0939	0.06303	0.3042:0.0778:0.1222:0.4958	.	6	P00352	AL1A1_HUMAN	M	6;6;20;6;6	ENSP00000297785:T6M;ENSP00000366138:T6M;ENSP00000388026:T6M;ENSP00000401361:T6M	ENSP00000297785:T6M	T	-	2	0	ALDH1A1	74757720	0.000000	0.05858	0.000000	0.03702	0.048000	0.14542	-0.985000	0.03751	-0.924000	0.03780	-1.252000	0.01501	ACG		0.418	ALDH1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052679.1		
OLFML2A	169611	broad.mit.edu	37	9	127566377	127566377	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr9:127566377C>T	ENST00000373580.3	+	6	924	c.924C>T	c.(922-924)aaC>aaT	p.N308N	OLFML2A_ENST00000288815.5_Silent_p.N94N	NM_182487.2	NP_872293.2	Q68BL7	OLM2A_HUMAN	olfactomedin-like 2A	308					extracellular matrix organization (GO:0030198)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)			endometrium(5)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)	25						CTGCAGACAACACCCTCCAGG	0.637																																						uc004bov.2																			0					0						c.(922-924)AAC>AAT		olfactomedin-like 2A precursor							40.0	40.0	40.0					9																	127566377		2203	4300	6503	SO:0001819	synonymous_variant	169611							g.chr9:127566377C>T	AK092255	CCDS6857.2, CCDS65129.1	9q34.11	2008-02-05			ENSG00000185585	ENSG00000185585			27270	protein-coding gene	gene with protein product		615899				12477932	Standard	NM_001282715		Approved	FLJ00237	uc004bov.3	Q68BL7	OTTHUMG00000020663	ENST00000373580.3:c.924C>T	9.37:g.127566377C>T						OLFML2A_uc010mwr.1_Silent_p.N272N|OLFML2A_uc004bow.2_Silent_p.N94N	p.N308N	NM_182487	NP_872293	Q68BL7	OLM2A_HUMAN			6	1037	+			308					Q5JTM5|Q5JTM6|Q6UXW1|Q7Z5V3	Silent	SNP	ENST00000373580.3	37	c.924C>T	CCDS6857.2	.	.	.	.	.	.	.	.	.	.	C	0.531	-0.857784	0.02630	.	.	ENSG00000185585	ENST00000342100	.	.	.	4.97	-4.5	0.03493	.	.	.	.	.	T	0.48466	0.1501	.	.	.	0.19775	N	0.999952	.	.	.	.	.	.	T	0.55768	-0.8089	5	0.87932	D	0	.	11.979	0.53109	0.0:0.3197:0.0:0.6803	.	.	.	.	I	2	.	ENSP00000339766:T2I	T	+	2	0	OLFML2A	126606198	0.000000	0.05858	0.053000	0.19242	0.160000	0.22226	-2.260000	0.01177	-1.380000	0.02115	-1.202000	0.01658	ACA		0.637	OLFML2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054046.2	NM_182487	
DBH	1621	broad.mit.edu	37	9	136507481	136507481	+	Silent	SNP	C	C	T			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chr9:136507481C>T	ENST00000393056.2	+	3	651	c.639C>T	c.(637-639)acC>acT	p.T213T		NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	213					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	ACGCGTGCACCATGGAGGTCC	0.592																																						uc004cel.2																			0				ovary(2)|central_nervous_system(2)	4						c.(637-639)ACC>ACT		dopamine beta hydroxylase precursor	Dopamine(DB00988)|Vitamin C(DB00126)						70.0	64.0	66.0					9																	136507481		2203	4300	6503	SO:0001819	synonymous_variant	1621				hormone biosynthetic process	chromaffin granule lumen|chromaffin granule membrane|extracellular region|integral to membrane|membrane fraction|soluble fraction|transport vesicle membrane	dopamine beta-monooxygenase activity|L-ascorbic acid binding	g.chr9:136507481C>T	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.639C>T	9.37:g.136507481C>T							p.T213T	NM_000787	NP_000778	P09172	DOPO_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	3	648	+			213			Intragranular (Potential).		Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	37	c.639C>T	CCDS6977.2																																																																																				0.592	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
TLR7	51284	broad.mit.edu	37	X	12904281	12904281	+	Silent	SNP	C	C	T	rs201282415		TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chrX:12904281C>T	ENST00000380659.3	+	3	793	c.654C>T	c.(652-654)gcC>gcT	p.A218A		NM_016562.3	NP_057646.1	Q9NYK1	TLR7_HUMAN	toll-like receptor 7	218					cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)	cytoplasm (GO:0005737)|early phagosome (GO:0032009)|endolysosome membrane (GO:0036020)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	double-stranded RNA binding (GO:0003725)|drug binding (GO:0008144)|single-stranded RNA binding (GO:0003727)|siRNA binding (GO:0035197)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(4)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	44					Hydroxychloroquine(DB01611)|Imiquimod(DB00724)	ATGTCACAGCCGTCCCTACTG	0.343													C|||	1	0.000264901	0.0008	0.0	3775	,	,		15439	0.0		0.0	False		,,,				2504	0.0					uc004cvc.2																			0				ovary(2)|lung(2)|breast(1)	5						c.(652-654)GCC>GCT		toll-like receptor 7 precursor	Imiquimod(DB00724)						66.0	61.0	63.0					X																	12904281		2203	4300	6503	SO:0001819	synonymous_variant	51284				cellular response to mechanical stimulus|defense response to virus|I-kappaB phosphorylation|inflammatory response|innate immune response|positive regulation of chemokine production|positive regulation of interferon-alpha biosynthetic process|positive regulation of interferon-beta biosynthetic process|positive regulation of interferon-gamma biosynthetic process|positive regulation of interleukin-8 biosynthetic process|positive regulation of interleukin-8 production|positive regulation of NF-kappaB import into nucleus	early phagosome|endoplasmic reticulum membrane|endosome membrane|integral to membrane|lysosome|plasma membrane	double-stranded RNA binding|single-stranded RNA binding|siRNA binding|transmembrane receptor activity	g.chrX:12904281C>T	AF240467	CCDS14151.1	Xp22.3	2008-02-05			ENSG00000196664	ENSG00000196664			15631	protein-coding gene	gene with protein product		300365				11022119	Standard	NM_016562		Approved		uc004cvc.3	Q9NYK1	OTTHUMG00000021137	ENST00000380659.3:c.654C>T	X.37:g.12904281C>T							p.A218A	NM_016562	NP_057646	Q9NYK1	TLR7_HUMAN			3	793	+			218			Extracellular (Potential).|LRR 7.		D1CS69|Q9NR98	Silent	SNP	ENST00000380659.3	37	c.654C>T	CCDS14151.1																																																																																				0.343	TLR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055769.1	NM_016562	
ZRSR2	8233	broad.mit.edu	37	X	15840971	15840971	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chrX:15840971G>A	ENST00000307771.7	+	11	1079	c.1055G>A	c.(1054-1056)cGg>cAg	p.R352Q		NM_005089.3	NP_005080.1	Q15696	U2AFM_HUMAN	zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2	352					mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|pre-mRNA 3'-splice site binding (GO:0030628)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(38)|kidney(1)|large_intestine(2)|ovary(2)	48	Hepatocellular(33;0.183)					TCTCCAGATCGGACTGGCTCC	0.502			"""F, S, Mis"""		"""MDS, CLL"""																																NSCLC(197;1631 3042 5741 31152)	uc004cxg.3				Rec	yes		X	Xp22.1	8233		"""zinc finger (CCCH type), RNA-binding motif and serine/arginine rich 2"""			L					0				breast(3)	3						c.(1054-1056)CGG>CAG		U2 small nuclear RNA auxiliary factor 1-like 2							61.0	58.0	59.0					X																	15840971		2203	4300	6503	SO:0001583	missense	8233				spliceosome assembly	U12-type spliceosomal complex	nucleotide binding|pre-mRNA 3'-splice site binding|protein binding|zinc ion binding	g.chrX:15840971G>A	BC050451	CCDS14172.1	Xp22.1	2014-09-17	2006-09-26	2006-09-26	ENSG00000169249	ENSG00000169249		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	23019	protein-coding gene	gene with protein product		300028	"""U2(RNU2) small nuclear RNA auxiliary factor 1-like 2"", ""U2 small nuclear RNA auxiliary factor 1-like 2"""	U2AF1L2		8586425, 9237760, 15146077	Standard	NM_005089		Approved	U2AF1-RS2, URP	uc004cxg.4	Q15696	OTTHUMG00000021184	ENST00000307771.7:c.1055G>A	X.37:g.15840971G>A	ENSP00000303015:p.Arg352Gln						p.R352Q	NM_005089	NP_005080	Q15696	U2AFM_HUMAN			11	1100	+	Hepatocellular(33;0.183)		352					Q14D69	Missense_Mutation	SNP	ENST00000307771.7	37	c.1055G>A	CCDS14172.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.366284	0.61513	.	.	ENSG00000169249	ENST00000307771	.	.	.	5.49	4.63	0.57726	.	0.244651	0.42682	D	0.000667	T	0.47040	0.1424	M	0.68952	2.095	0.80722	D	1	P	0.47409	0.895	B	0.36030	0.216	T	0.47873	-0.9083	9	0.29301	T	0.29	.	13.6489	0.62299	0.0765:0.0:0.9235:0.0	.	352	Q15696	U2AFM_HUMAN	Q	352	.	ENSP00000303015:R352Q	R	+	2	0	ZRSR2	15750892	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	7.588000	0.82629	1.209000	0.43321	0.600000	0.82982	CGG		0.502	ZRSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055889.1	NM_005089	
POF1B	79983	broad.mit.edu	37	X	84634327	84634327	+	Missense_Mutation	SNP	T	T	G			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chrX:84634327T>G	ENST00000262753.4	-	2	278	c.133A>C	c.(133-135)Aaa>Caa	p.K45Q	POF1B_ENST00000373145.3_Missense_Mutation_p.K45Q	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	45						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						ACTACATTTTTTTCTGGAGGC	0.577																																						uc004eer.2																			0					0						c.(133-135)AAA>CAA		premature ovarian failure, 1B							82.0	66.0	72.0					X																	84634327		2203	4300	6503	SO:0001583	missense	79983						actin binding	g.chrX:84634327T>G	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.133A>C	X.37:g.84634327T>G	ENSP00000262753:p.Lys45Gln					POF1B_uc004ees.2_Missense_Mutation_p.K45Q	p.K45Q	NM_024921	NP_079197	Q8WVV4	POF1B_HUMAN			2	279	-			45					A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	c.133A>C	CCDS14452.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.445627	0.43429	.	.	ENSG00000124429	ENST00000262753;ENST00000373145;ENST00000276124	T;T	0.11169	2.8;2.8	5.67	4.49	0.54785	.	0.000000	0.49916	D	0.000130	T	0.09642	0.0237	L	0.47716	1.5	0.27586	N	0.94942	P;P	0.40731	0.728;0.59	B;B	0.36244	0.22;0.22	T	0.18745	-1.0327	10	0.87932	D	0	.	7.7705	0.29006	0.0:0.0988:0.0:0.9012	.	45;45	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	Q	45	ENSP00000262753:K45Q;ENSP00000362238:K45Q	ENSP00000262753:K45Q	K	-	1	0	POF1B	84520983	1.000000	0.71417	1.000000	0.80357	0.166000	0.22503	2.044000	0.41241	1.903000	0.55091	0.437000	0.28790	AAA		0.577	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
THOC2	57187	broad.mit.edu	37	X	122748018	122748020	+	In_Frame_Del	DEL	GGA	GGA	-			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chrX:122748018_122748020delGGA	ENST00000245838.8	-	34	4363_4365	c.4332_4334delTCC	c.(4330-4335)cctcca>cca	p.1444_1445PP>P	THOC2_ENST00000355725.4_In_Frame_Del_p.1444_1445PP>P|THOC2_ENST00000491737.1_In_Frame_Del_p.1329_1330PP>P|THOC2_ENST00000497887.1_5'UTR	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	1444	Lys-rich.				mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						GGACAGTGGTGGAGGAGTATGAT	0.355																																						uc004etu.2																			0				ovary(3)	3						c.(4330-4335)CCTCCA>CCA		THO complex 2																																				SO:0001651	inframe_deletion	57187				intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding	g.chrX:122748018_122748020delGGA	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.4332_4334delTCC	X.37:g.122748021_122748023delGGA	ENSP00000245838:p.Pro1446del					THOC2_uc010nqt.1_RNA|THOC2_uc004etw.1_In_Frame_Del_p.265_266PP>P	p.1444_1445PP>P	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN			34	4364_4366	-			1444_1445			Lys-rich.		A6NM50|Q5JZ12|Q6IN92|Q9H8I6	In_Frame_Del	DEL	ENST00000245838.8	37	c.4332_4334delTCC	CCDS43988.1																																																																																				0.355	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		
STAG2	10735	broad.mit.edu	37	X	123176470	123176471	+	Frame_Shift_Ins	INS	-	-	A			TCGA-14-0789-01A-01W-0424-08	TCGA-14-0789-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	3462087f-f791-43b4-b9d9-b11cc48eaf9e	221ae08d-6862-47d4-9b1d-099cb3dd9e57	g.chrX:123176470_123176471insA	ENST00000371160.1	+	7	727_728	c.437_438insA	c.(436-441)cgaaaafs	p.RK146fs	STAG2_ENST00000371157.3_Frame_Shift_Ins_p.RK146fs|STAG2_ENST00000371145.3_Frame_Shift_Ins_p.RK146fs|STAG2_ENST00000218089.9_Frame_Shift_Ins_p.RK146fs|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000371144.3_Frame_Shift_Ins_p.RK146fs|STAG2_ENST00000354548.5_Frame_Shift_Ins_p.RK77fs	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	146					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						GAGATAATTCGAAAAATGACTG	0.287																																						uc004etz.3																			0				ovary(4)|skin(1)	5						c.(436-438)CGAfs		stromal antigen 2 isoform b																																				SO:0001589	frameshift_variant	10735				cell division|meiosis|mitotic metaphase/anaphase transition|mitotic prometaphase|negative regulation of DNA endoreduplication|sister chromatid cohesion	chromatin|chromosome, centromeric region|nucleoplasm	protein binding	g.chrX:123176470_123176471insA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.442dupA	X.37:g.123176475_123176475dupA	ENSP00000360202:p.Arg146fs					STAG2_uc004eua.2_Frame_Shift_Ins_p.R146fs|STAG2_uc004eub.2_Frame_Shift_Ins_p.R146fs|STAG2_uc004euc.2_Frame_Shift_Ins_p.R146fs|STAG2_uc004eud.2_Frame_Shift_Ins_p.R146fs|STAG2_uc004eue.2_Frame_Shift_Ins_p.R146fs	p.R146fs	NM_006603	NP_006594	Q8N3U4	STAG2_HUMAN			6	776_777	+			146					B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Frame_Shift_Ins	INS	ENST00000371160.1	37	c.437_438insA	CCDS14607.1																																																																																				0.287	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
