#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
MRTO4	51154	broad.mit.edu	37	1	19584431	19584431	+	Missense_Mutation	SNP	T	T	G			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr1:19584431T>G	ENST00000330263.4	+	6	743	c.446T>G	c.(445-447)aTg>aGg	p.M149R		NM_016183.3	NP_057267.2	Q9UKD2	MRT4_HUMAN	mRNA turnover 4 homolog (S. cerevisiae)	149					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)		CCCCACTCCATGGAGCCACAG	0.597																																					GBM(192;2418 3032 7540 48714)	uc001bbs.3																			0				breast(1)|endometrium(1)|large_intestine(1)|liver(2)|ovary(1)|pancreas(1)|stomach(1)	8						c.(445-447)aTg>aGg		Homo sapiens mRNA turnover 4 homolog (S. cerevisiae) (MRTO4), mRNA.							51.0	57.0	55.0					1																	19584431		2203	4300	6503	SO:0001583	missense	51154				ribosome biogenesis	nuclear membrane|nucleolus		g.chr1:19584431T>G	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.446T>G	1.37:g.19584431T>G	ENSP00000364320:p.Met149Arg						p.M149R	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)	5	701	+		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)	149					B3KNB3|Q5TG55|Q96SS6|Q9BPV9	Missense_Mutation	SNP	ENST00000330263.4	37	c.446T>G	CCDS191.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000248	0.74818	.	.	ENSG00000053372	ENST00000330263	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	T	0.71762	0.3378	M	0.87328	2.875	0.80722	D	1	P	0.48640	0.913	P	0.45232	0.474	T	0.78481	-0.2187	9	0.72032	D	0.01	-30.1326	15.1888	0.73025	0.0:0.0:0.0:1.0	.	149	Q9UKD2	MRT4_HUMAN	R	149	.	ENSP00000364320:M149R	M	+	2	0	MRTO4	19457018	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.497000	0.81536	2.263000	0.75096	0.533000	0.62120	ATG		0.597	MRTO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007075.2	NM_016183	
SF3A3	10946	broad.mit.edu	37	1	38435290	38435290	+	Nonsense_Mutation	SNP	C	C	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr1:38435290C>A	ENST00000373019.4	-	13	2078	c.1123G>T	c.(1123-1125)Gag>Tag	p.E375*	SF3A3_ENST00000448721.2_Nonsense_Mutation_p.E322*	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	375					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TAAATGATCTCGTTCTCTTCA	0.468																																						uc001cci.3																			0				breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12						c.(1123-1125)Gag>Tag		Homo sapiens splicing factor 3a, subunit 3, 60kDa (SF3A3), mRNA.							272.0	235.0	248.0					1																	38435290		2203	4300	6503	SO:0001587	stop_gained	10946				nuclear mRNA 3'-splice site recognition	catalytic step 2 spliceosome|nuclear speck	nucleic acid binding|protein binding|zinc ion binding	g.chr1:38435290C>A	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.1123G>T	1.37:g.38435290C>A	ENSP00000362110:p.Glu375*					SF3A3_uc010oik.2_Nonsense_Mutation_p.E322*	p.E375*	NM_006802	NP_006793	Q12874	SF3A3_HUMAN			12	1247	-	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)	375					D3DPT5|Q15460|Q5VT87	Nonsense_Mutation	SNP	ENST00000373019.4	37	c.1123G>T	CCDS428.1	.	.	.	.	.	.	.	.	.	.	C	46	12.495689	0.99672	.	.	ENSG00000183431	ENST00000373019;ENST00000448721	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-25.3599	19.7862	0.96440	0.0:1.0:0.0:0.0	.	.	.	.	X	375;322	.	ENSP00000362110:E375X	E	-	1	0	SF3A3	38207877	1.000000	0.71417	0.991000	0.47740	0.984000	0.73092	7.382000	0.79729	2.769000	0.95229	0.655000	0.94253	GAG		0.468	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
HMCN1	83872	broad.mit.edu	37	1	186099788	186099788	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr1:186099788C>T	ENST00000271588.4	+	85	13418	c.13189C>T	c.(13189-13191)Cgg>Tgg	p.R4397W	HMCN1_ENST00000367492.2_Missense_Mutation_p.R4397W	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4397	Ig-like C2-type 43.				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						CCACAGAATCCGGCAACTGGG	0.507																																						uc001grq.1																			0				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						c.(13189-13191)Cgg>Tgg		Homo sapiens hemicentin 1 (HMCN1), mRNA.							94.0	95.0	95.0					1																	186099788		2203	4300	6503	SO:0001583	missense	83872				response to stimulus|visual perception	basement membrane	calcium ion binding	g.chr1:186099788C>T	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.13189C>T	1.37:g.186099788C>T	ENSP00000271588:p.Arg4397Trp					MIR548F1_uc021pgf.1_Intron|HMCN1_uc001grs.1_5'UTR	p.R4397W	NM_031935	NP_114141	Q96RW7	HMCN1_HUMAN			84	13418	+			4397			Ig-like C2-type 43.		A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	c.13189C>T	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.141667	0.77775	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.68903	-0.36;-0.36	5.48	4.55	0.56014	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.315788	0.35805	N	0.002969	T	0.74397	0.3711	L	0.56199	1.76	0.47153	D	0.99933	D	0.67145	0.996	P	0.60286	0.872	T	0.76719	-0.2856	10	0.62326	D	0.03	.	13.1811	0.59655	0.4111:0.5889:0.0:0.0	.	4397	Q96RW7	HMCN1_HUMAN	W	4397	ENSP00000271588:R4397W;ENSP00000356462:R4397W	ENSP00000271588:R4397W	R	+	1	2	HMCN1	184366411	0.998000	0.40836	0.909000	0.35828	0.747000	0.42532	3.037000	0.49775	1.405000	0.46838	0.591000	0.81541	CGG		0.507	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
DENND1B	163486	broad.mit.edu	37	1	197522236	197522236	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr1:197522236C>T	ENST00000367396.3	-	16	1325	c.1156G>A	c.(1156-1158)Gat>Aat	p.D386N	DENND1B_ENST00000235453.4_Missense_Mutation_p.D356N|DENND1B_ENST00000400967.2_Missense_Mutation_p.D356N	NM_144977.4	NP_659414.2	Q6P3S1	DEN1B_HUMAN	DENN/MADD domain containing 1B	386	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|breast(2)|kidney(2)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	22						AGTCGACCATCGATAAACTAG	0.303																																						uc021pgu.1																			0				NS(2)|breast(2)|kidney(2)|large_intestine(3)|lung(12)|upper_aerodigestive_tract(1)	22						c.(1156-1158)Gat>Aat		Homo sapiens DENN/MADD domain containing 1B (DENND1B), transcript variant 3, mRNA.							78.0	73.0	74.0					1																	197522236		1809	4068	5877	SO:0001583	missense	163486					clathrin-coated vesicle|cytosol	guanyl-nucleotide exchange factor activity	g.chr1:197522236C>T	BC016588	CCDS41452.2, CCDS72996.1, CCDS72997.1	1q31.3	2012-10-03	2005-08-17	2005-08-17	ENSG00000213047	ENSG00000213047		"""DENN/MADD domain containing"""	28404	protein-coding gene	gene with protein product		613292	"""family with sequence similarity 31, member B"", ""chromosome 1 open reading frame 218"""	FAM31B, C1orf218		12477932	Standard	NM_144977		Approved	MGC27044, FLJ20054	uc021pgu.1	Q6P3S1	OTTHUMG00000035653	ENST00000367396.3:c.1156G>A	1.37:g.197522236C>T	ENSP00000356366:p.Asp386Asn					DENND1B_uc010ppf.2_Intron|DENND1B_uc001guf.3_Missense_Mutation_p.D386N|DENND1B_uc001gue.3_Missense_Mutation_p.D356N	p.D386N	NM_001195215	NP_001182144	Q6P3S1	DEN1B_HUMAN			15	1494	-			386			dDENN.		B5MD89|D3PFD5|Q5T3B8|Q5T3B9|Q5T3C1|Q5TAI8|Q6B0I8|Q8NDT1|Q8TBE6|Q9H774|Q9NXU2	Missense_Mutation	SNP	ENST00000367396.3	37	c.1156G>A	CCDS41452.2	.	.	.	.	.	.	.	.	.	.	C	22.0	4.233119	0.79688	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419;ENST00000235453;ENST00000367396;ENST00000400967	T;T;T;T	0.53206	0.63;0.85;0.85;0.85	5.59	5.59	0.84812	dDENN (3);	0.047266	0.85682	D	0.000000	T	0.61627	0.2362	M	0.79258	2.445	0.50039	D	0.999842	P;P;B	0.47841	0.901;0.798;0.314	P;P;B	0.48982	0.597;0.466;0.232	T	0.66674	-0.5864	10	0.87932	D	0	-21.387	18.2005	0.89836	0.0:1.0:0.0:0.0	.	386;386;356	Q6P3S1-5;Q6P3S1;Q6P3S1-4	.;DEN1B_HUMAN;.	N	26;386;366;356;386;356	ENSP00000375839:D26N;ENSP00000235453:D356N;ENSP00000356366:D386N;ENSP00000383751:D356N	ENSP00000235453:D356N	D	-	1	0	DENND1B	195788859	1.000000	0.71417	0.997000	0.53966	0.890000	0.51754	6.582000	0.74049	2.801000	0.96364	0.650000	0.86243	GAT		0.303	DENND1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086539.1	NM_144977	
RYR2	6262	broad.mit.edu	37	1	237791221	237791221	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr1:237791221G>A	ENST00000366574.2	+	41	6598	c.6281G>A	c.(6280-6282)gGc>gAc	p.G2094D	RYR2_ENST00000542537.1_Missense_Mutation_p.G2078D|RYR2_ENST00000360064.6_Missense_Mutation_p.G2092D	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	2094	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)			CAGTATGACGGCATTGGGGGT	0.557																																						uc001hyl.1																			0				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						c.(6280-6282)gGc>gAc		Homo sapiens ryanodine receptor 2 (cardiac) (RYR2), mRNA.							77.0	76.0	76.0					1																	237791221		1974	4143	6117	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.chr1:237791221G>A	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.6281G>A	1.37:g.237791221G>A	ENSP00000355533:p.Gly2094Asp						p.G2094D	NM_001035	NP_001026	Q92736	RYR2_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00606)		40	6401	+	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	2094			4 X approximate repeats.		Q15411|Q546N8|Q5T3P2	Missense_Mutation	SNP	ENST00000366574.2	37	c.6281G>A	CCDS55691.1	.	.	.	.	.	.	.	.	.	.	G	29.0	4.965842	0.92855	.	.	ENSG00000198626	ENST00000366574;ENST00000360064;ENST00000542537	D;D;D	0.97089	-4.24;-4.21;-4.23	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000006	D	0.98623	0.9539	M	0.87269	2.87	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.99564	1.0969	10	0.72032	D	0.01	.	19.0363	0.92980	0.0:0.0:1.0:0.0	.	2094	Q92736	RYR2_HUMAN	D	2094;2092;2078	ENSP00000355533:G2094D;ENSP00000353174:G2092D;ENSP00000443798:G2078D	ENSP00000353174:G2092D	G	+	2	0	RYR2	235857844	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	9.781000	0.99029	2.571000	0.86741	0.591000	0.81541	GGC		0.557	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
KCNK18	338567	broad.mit.edu	37	10	118957199	118957199	+	Missense_Mutation	SNP	G	G	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr10:118957199G>T	ENST00000334549.1	+	1	200	c.200G>T	c.(199-201)aGa>aTa	p.R67I		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	67					cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		GAGCTCTGCAGAATCTTGAAC	0.582																																						uc010qsr.2																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41						c.(199-201)aGa>aTa		Homo sapiens potassium channel, subfamily K, member 18 (KCNK18), mRNA.							90.0	81.0	84.0					10																	118957199		2203	4300	6503	SO:0001583	missense	338567					integral to membrane|plasma membrane		g.chr10:118957199G>T	AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	19439	protein-coding gene	gene with protein product	"""TWIK related spinal cord K+ channel"""	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.200G>T	10.37:g.118957199G>T	ENSP00000334650:p.Arg67Ile						p.R67I	NM_181840	NP_862823	Q7Z418	KCNKI_HUMAN		all cancers(201;0.0211)	0	200	+		Colorectal(252;0.19)	67					Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	c.200G>T	CCDS7598.1	.	.	.	.	.	.	.	.	.	.	G	7.423	0.637174	0.14386	.	.	ENSG00000186795	ENST00000334549	T	0.15603	2.41	4.17	-1.47	0.08772	.	1.224480	0.05198	N	0.504443	T	0.09379	0.0231	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.34502	-0.9826	10	0.35671	T	0.21	.	4.4845	0.11783	0.5221:0.0:0.3178:0.1601	.	67	Q7Z418	KCNKI_HUMAN	I	67	ENSP00000334650:R67I	ENSP00000334650:R67I	R	+	2	0	KCNK18	118947189	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	-0.068000	0.11561	-0.256000	0.09473	0.561000	0.74099	AGA		0.582	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840	
TIAL1	7073	broad.mit.edu	37	10	121341480	121341480	+	Frame_Shift_Del	DEL	T	T	-			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr10:121341480delT	ENST00000436547.2	-	5	369	c.325delA	c.(325-327)acafs	p.T110fs	TIAL1_ENST00000369093.2_Frame_Shift_Del_p.T127fs|TIAL1_ENST00000369092.4_5'UTR	NM_003252.3	NP_003243.1	Q01085	TIAR_HUMAN	TIA1 cytotoxic granule-associated RNA binding protein-like 1	110	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				apoptotic process (GO:0006915)|defense response (GO:0006952)|germ cell development (GO:0007281)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell division (GO:0017145)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)		TCTTCTGTTGTAATTTCTGGA	0.348																																						uc001lei.1																			0				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(3)|ovary(1)	13						c.(325-327)acafs		Homo sapiens TIA1 cytotoxic granule-associated RNA binding protein-like 1 (TIAL1), transcript variant 1, mRNA.							91.0	91.0	91.0					10																	121341480		2203	4300	6503	SO:0001589	frameshift_variant	7073				apoptosis|defense response|induction of apoptosis|regulation of transcription from RNA polymerase II promoter	lysosome|nucleus|stress granule	nucleotide binding|RNA binding	g.chr10:121341480delT	AL833106	CCDS7613.1, CCDS31295.1	10q	2013-02-12	2001-11-28		ENSG00000151923	ENSG00000151923		"""RNA binding motif (RRM) containing"""	11804	protein-coding gene	gene with protein product		603413	"""TIA1 cytotoxic granule-associated RNA-binding protein-like 1"""			1326761	Standard	XM_005270108		Approved	TIAR	uc001lej.1	Q01085	OTTHUMG00000019156	ENST00000436547.2:c.325delA	10.37:g.121341480delT	ENSP00000394902:p.Thr110fs					TIAL1_uc001leh.1_Frame_Shift_Del_p.T87fs|TIAL1_uc001lej.1_Frame_Shift_Del_p.T126fs|TIAL1_uc001lek.1_5'UTR|TIAL1_uc010qtb.1_5'UTR	p.T109fs	NM_003252	NP_003243	Q01085	TIAR_HUMAN		all cancers(201;0.00239)|BRCA - Breast invasive adenocarcinoma(275;0.0932)	4	889	-		Lung NSC(174;0.094)|all_lung(145;0.123)	109			RRM 2.		A8K3T0|A8K4L9	Frame_Shift_Del	DEL	ENST00000436547.2	37	c.325delA	CCDS7613.1																																																																																				0.348	TIAL1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050672.2	NM_022333, NM_003252	
KRTAP5-4	387267	broad.mit.edu	37	11	1642817	1642817	+	Silent	SNP	A	A	G	rs540908783|rs374921824	byFrequency	TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr11:1642817A>G	ENST00000399682.1	-	1	551	c.507T>C	c.(505-507)ggT>ggC	p.G169G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ATGACCCACAACCTGAGGAGG	0.612													a|||	106	0.0211661	0.0393	0.0115	5008	,	,		14637	0.0119		0.0209	False		,,,				2504	0.0133					uc009ycy.1																			0				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20						c.(400-402)ggT>ggC		Homo sapiens keratin associated protein 5-4 (KRTAP5-4), mRNA.							24.0	35.0	32.0					11																	1642817		692	1591	2283	SO:0001819	synonymous_variant	387267					keratin filament		g.chr11:1642817A>G	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.507T>C	11.37:g.1642817A>G						MOB2_uc001ltq.2_Intron	p.G134G	NM_001012709	NP_001012727	Q6L8H1	KRA54_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)	2	489	-		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)	229			9 X 4 AA repeats of C-C-X-P.			Silent	SNP	ENST00000399682.1	37	c.402T>C																																																																																					0.612	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
KRTAP5-4	387267	broad.mit.edu	37	11	1642827	1642827	+	Missense_Mutation	SNP	G	G	C	rs374921824|rs541987207	byFrequency	TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr11:1642827G>C	ENST00000399682.1	-	1	541	c.497C>G	c.(496-498)tCc>tGc	p.S166C		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		ACCTGAGGAGGAGCAGCAGGG	0.607													g|||	148	0.0295527	0.056	0.0187	5008	,	,		15114	0.0188		0.0229	False		,,,				2504	0.0194					uc009ycy.1																			0				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20						c.(391-393)tCc>tGc		Homo sapiens keratin associated protein 5-4 (KRTAP5-4), mRNA.							22.0	35.0	31.0					11																	1642827		692	1590	2282	SO:0001583	missense	387267					keratin filament		g.chr11:1642827G>C	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.497C>G	11.37:g.1642827G>C	ENSP00000382590:p.Ser166Cys					MOB2_uc001ltq.2_Intron	p.S131C	NM_001012709	NP_001012727	Q6L8H1	KRA54_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)	2	479	-		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)	226			9 X 4 AA repeats of C-C-X-P.			Missense_Mutation	SNP	ENST00000399682.1	37	c.392C>G		.	.	.	.	.	.	.	.	.	.	G	2.402	-0.337333	0.05278	.	.	ENSG00000241598	ENST00000399682	T	0.00792	5.69	0.891	-0.0782	0.13716	.	.	.	.	.	T	0.00468	0.0015	N	0.02960	-0.455	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.45056	-0.9287	9	0.51188	T	0.08	.	6.6433	0.22921	0.0:0.5966:0.4034:0.0	.	226	Q6L8H1	KRA54_HUMAN	C	166	ENSP00000382590:S166C	ENSP00000382590:S166C	S	-	2	0	KRTAP5-4	1599403	0.001000	0.12720	0.007000	0.13788	0.001000	0.01503	-0.354000	0.07681	-0.014000	0.14175	-1.289000	0.01358	TCC		0.607	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
DCHS1	8642	broad.mit.edu	37	11	6647232	6647232	+	Missense_Mutation	SNP	C	C	T	rs149822394		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr11:6647232C>T	ENST00000299441.3	-	17	7061	c.6650G>A	c.(6649-6651)cGt>cAt	p.R2217H		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2217	Cadherin 21. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAACAATCCACGTGCCGGCTG	0.602													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20380	0.0		0.0	False		,,,				2504	0.0					uc001mem.1																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103						c.(6649-6651)cGt>cAt		Homo sapiens dachsous 1 (Drosophila) (DCHS1), mRNA.		C	HIS/ARG	1,4401	2.1+/-5.4	0,1,2200	153.0	137.0	142.0		6650	4.0	1.0	11	dbSNP_134	142	1,8591	1.2+/-3.3	0,1,4295	no	missense	DCHS1	NM_003737.2	29	0,2,6495	TT,TC,CC		0.0116,0.0227,0.0154	benign	2217/3299	6647232	2,12992	2201	4296	6497	SO:0001583	missense	8642				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr11:6647232C>T	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.6650G>A	11.37:g.6647232C>T	ENSP00000299441:p.Arg2217His						p.R2217H	NM_003737	NP_003728	Q96JQ0	PCD16_HUMAN		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	16	7051	-		Medulloblastoma(188;0.00263)|all_neural(188;0.026)	2217			Cadherin 21.		O15098	Missense_Mutation	SNP	ENST00000299441.3	37	c.6650G>A	CCDS7771.1	.	.	.	.	.	.	.	.	.	.	C	10.89	1.479059	0.26511	2.27E-4	1.16E-4	ENSG00000166341	ENST00000299441	T	0.52526	0.66	4.9	3.99	0.46301	Cadherin (4);Cadherin-like (1);	0.000000	0.42053	D	0.000771	T	0.32763	0.0840	L	0.37697	1.125	0.27883	N	0.939593	B	0.06786	0.001	B	0.04013	0.001	T	0.14643	-1.0465	10	0.33940	T	0.23	.	5.512	0.16886	0.0:0.6443:0.1779:0.1777	.	2217	Q96JQ0	PCD16_HUMAN	H	2217	ENSP00000299441:R2217H	ENSP00000299441:R2217H	R	-	2	0	DCHS1	6603808	0.994000	0.37717	0.990000	0.47175	0.944000	0.59088	2.976000	0.49289	1.298000	0.44778	-0.244000	0.11960	CGT		0.602	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
OR8J3	81168	broad.mit.edu	37	11	55904448	55904448	+	Silent	SNP	C	C	T	rs529152876		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr11:55904448C>T	ENST00000301529.1	-	1	746	c.747G>A	c.(745-747)acG>acA	p.T249T		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	249						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T249T(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					CATAGAAAACCGTGACTGCTA	0.398													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19498	0.0		0.0	False		,,,				2504	0.0					uc010riz.2																			2	Substitution - coding silent(2)	p.T249T(4)|p.T249K(1)	lung(1)|endometrium(1)	NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59						c.(745-747)acG>acA		Homo sapiens olfactory receptor, family 8, subfamily J, member 3 (OR8J3), mRNA.							131.0	124.0	126.0					11																	55904448		2201	4296	6497	SO:0001819	synonymous_variant	81168				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55904448C>T		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.747G>A	11.37:g.55904448C>T							p.T249T	NM_001004064	NP_001004064	Q8NGG0	OR8J3_HUMAN			0	747	-	Esophageal squamous(21;0.00693)		249					Q6IFB6|Q96RC2	Silent	SNP	ENST00000301529.1	37	c.747G>A	CCDS31520.1																																																																																				0.398	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
GIF	2694	broad.mit.edu	37	11	59610023	59610023	+	Missense_Mutation	SNP	G	G	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr11:59610023G>T	ENST00000257248.2	-	4	451	c.404C>A	c.(403-405)cCc>cAc	p.P135H	GIF_ENST00000541311.1_Missense_Mutation_p.P110H	NM_005142.2	NP_005133.2	P27352	IF_HUMAN	gastric intrinsic factor (vitamin B synthesis)	135					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)	cobalamin binding (GO:0031419)			large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17					Cyanocobalamin(DB00115)	CGCTAGACTGGGCCCATAGAA	0.562																																					NSCLC(53;1139 1245 16872 38474 42853)	uc001noi.3																			0		p.G134E(1)		large_intestine(4)|liver(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	17						c.(403-405)cCc>cAc		Homo sapiens gastric intrinsic factor (vitamin B synthesis) (GIF), mRNA.							84.0	72.0	76.0					11																	59610023		2201	4295	6496	SO:0001583	missense	2694				cobalamin metabolic process|cobalamin transport|cobalt ion transport	apical plasma membrane|endosome|extracellular space|microvillus	cobalamin binding	g.chr11:59610023G>T	X76562	CCDS7977.1	11q12.1	2013-09-20			ENSG00000134812	ENSG00000134812			4268	protein-coding gene	gene with protein product		609342				2071148	Standard	NM_005142		Approved	TCN3, IF, IFMH, INF	uc001noi.3	P27352	OTTHUMG00000167399	ENST00000257248.2:c.404C>A	11.37:g.59610023G>T	ENSP00000257248:p.Pro135His					GIF_uc010rkz.1_3'UTR	p.P135H	NM_005142	NP_005133	P27352	IF_HUMAN			3	452	-			135					B2RAN8|B4DVZ1	Missense_Mutation	SNP	ENST00000257248.2	37	c.404C>A	CCDS7977.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650686	0.87958	.	.	ENSG00000134812	ENST00000257248;ENST00000541311	T;T	0.35973	1.28;1.28	5.63	5.63	0.86233	.	0.169209	0.42420	D	0.000703	T	0.59238	0.2179	M	0.72479	2.2	0.45607	D	0.998541	D	0.89917	1.0	D	0.75484	0.986	T	0.57124	-0.7865	10	0.48119	T	0.1	-29.8799	15.5476	0.76118	0.0:0.0:1.0:0.0	.	135	P27352	IF_HUMAN	H	135;110	ENSP00000257248:P135H;ENSP00000440427:P110H	ENSP00000257248:P135H	P	-	2	0	GIF	59366599	0.995000	0.38212	0.999000	0.59377	0.995000	0.86356	4.371000	0.59523	2.826000	0.97356	0.655000	0.94253	CCC		0.562	GIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394497.1	NM_005142	
Unknown	0	broad.mit.edu	37	12	92000	92000	+	IGR	SNP	A	A	T	rs372724029		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr12:92000A>T								AC215219.1 (18678 upstream) : AC026369.1 (55051 downstream)																							GGTCCTGGCAACACTCTGGAC	0.572																																						uc010sdi.1																			0											c.(310-312)Ttg>Atg		SubName: Full=DEAD/H box polypeptide 11 like 11;																																				SO:0001628	intergenic_variant	100887824							g.chr12:92000A>T																													12.37:g.92000A>T						DDX11L11_uc010sdj.1_Non-coding_Transcript	p.L104M							1	338	-									Missense_Mutation	SNP		37	c.310T>A																																																																																				0	0.572								
SCNN1A	6337	broad.mit.edu	37	12	6464465	6464465	+	Silent	SNP	G	G	A	rs567003433		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr12:6464465G>A	ENST00000228916.2	-	6	1214	c.1116C>T	c.(1114-1116)ggC>ggT	p.G372G	SCNN1A_ENST00000358945.3_Silent_p.G372G|SCNN1A_ENST00000543768.1_Silent_p.G395G|SCNN1A_ENST00000540037.1_Silent_p.G72G|SCNN1A_ENST00000538979.1_5'UTR|SCNN1A_ENST00000360168.3_Silent_p.G431G|SCNN1A_ENST00000396966.2_Silent_p.G372G	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	372					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGGTCTCCACGCCAGGCCGCA	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		17953	0.0		0.0	False		,,,				2504	0.001					uc001qnw.3																			0				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27						c.(1291-1293)ggC>ggT		Homo sapiens sodium channel, nonvoltage-gated 1 alpha (SCNN1A), transcript variant 2, mRNA.	Amiloride(DB00594)|Triamterene(DB00384)						57.0	47.0	50.0					12																	6464465		2203	4300	6503	SO:0001819	synonymous_variant	6337				excretion|response to stimulus|sensory perception of taste	apical plasma membrane	WW domain binding	g.chr12:6464465G>A	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.1116C>T	12.37:g.6464465G>A						SCNN1A_uc001qnv.3_Silent_p.G72G|SCNN1A_uc001qnx.3_Silent_p.G372G|SCNN1A_uc010sfb.2_Silent_p.G395G	p.G431G	NM_001159576	NP_001029	P37088	SCNNA_HUMAN			4	1557	-			372					A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Silent	SNP	ENST00000228916.2	37	c.1293C>T	CCDS8543.1																																																																																				0.612	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
MYO1A	4640	broad.mit.edu	37	12	57424856	57424856	+	Missense_Mutation	SNP	G	G	C			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr12:57424856G>C	ENST00000442789.2	-	24	2739	c.2452C>G	c.(2452-2454)Cag>Gag	p.Q818E	TAC3_ENST00000415231.1_5'Flank|MYO1A_ENST00000300119.3_Missense_Mutation_p.Q818E|MYO1A_ENST00000544473.1_Missense_Mutation_p.Q656E	NM_001256041.1	NP_001242970.1	Q9UBC5	MYO1A_HUMAN	myosin IA	818					microvillus assembly (GO:0030033)|sensory perception of sound (GO:0007605)|vesicle localization (GO:0051648)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|brush border (GO:0005903)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|lateral plasma membrane (GO:0016328)|microvillus (GO:0005902)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						TGCAGCTCCTGATTTGCTGTG	0.517																																						uc001smw.4																			0				breast(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(7)|urinary_tract(3)	50						c.(2452-2454)Cag>Gag		Homo sapiens myosin IA (MYO1A), transcript variant 2, mRNA.							86.0	82.0	83.0					12																	57424856		2203	4300	6503	SO:0001583	missense	4640				sensory perception of sound|vesicle localization	brush border|cortical actin cytoskeleton|filamentous actin|lateral plasma membrane|microvillus|myosin complex	actin binding|ATP binding|calmodulin binding|motor activity	g.chr12:57424856G>C	L29137	CCDS8929.1	12q13-q15	2011-09-27			ENSG00000166866	ENSG00000166866		"""Myosins / Myosin superfamily : Class I"""	7595	protein-coding gene	gene with protein product		601478		MYHL, DFNA48		8884266, 12736868	Standard	NM_001256041		Approved		uc009zpd.3	Q9UBC5	OTTHUMG00000149899	ENST00000442789.2:c.2452C>G	12.37:g.57424856G>C	ENSP00000393392:p.Gln818Glu					MYO1A_uc010sqz.2_Missense_Mutation_p.Q656E|MYO1A_uc009zpd.3_Missense_Mutation_p.Q818E	p.Q818E	NM_005379	NP_005370	Q9UBC5	MYO1A_HUMAN			22	2692	-			818					Q9UQD7	Missense_Mutation	SNP	ENST00000442789.2	37	c.2452C>G	CCDS8929.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.465692	0.00169	.	.	ENSG00000166866	ENST00000300119;ENST00000442789;ENST00000544473	D;D;D	0.86164	-2.03;-2.03;-2.08	4.66	3.76	0.43208	.	0.663219	0.14107	N	0.341014	T	0.79673	0.4486	L	0.43152	1.355	0.30893	N	0.730178	B	0.20368	0.044	B	0.21708	0.036	T	0.65899	-0.6056	10	0.02654	T	1	.	10.7512	0.46211	0.0:0.1935:0.8065:0.0	.	818	Q9UBC5	MYO1A_HUMAN	E	818;818;656	ENSP00000300119:Q818E;ENSP00000393392:Q818E;ENSP00000440514:Q656E	ENSP00000300119:Q818E	Q	-	1	0	MYO1A	55711123	0.984000	0.35163	0.259000	0.24435	0.036000	0.12997	1.190000	0.32126	0.925000	0.37094	-0.300000	0.09419	CAG		0.517	MYO1A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313833.2	NM_005379	
NAV3	89795	broad.mit.edu	37	12	78574731	78574731	+	Silent	SNP	G	G	A	rs200326115		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr12:78574731G>A	ENST00000397909.2	+	30	5771	c.5598G>A	c.(5596-5598)ccG>ccA	p.P1866P	NAV3_ENST00000536525.2_Silent_p.P1844P|NAV3_ENST00000228327.6_Silent_p.P1844P|NAV3_ENST00000552300.1_3'UTR|NAV3_ENST00000266692.7_Silent_p.P1667P			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1866						membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						CTCGGCCACCGTCAGAATCCT	0.433										HNSCC(70;0.22)			G|||	1	0.000199681	0.0	0.0	5008	,	,		17682	0.001		0.0	False		,,,				2504	0.0					uc001syp.3																			0				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						c.(5596-5598)ccG>ccA		Homo sapiens neuron navigator 3 (NAV3), mRNA.							108.0	110.0	110.0					12																	78574731		1997	4165	6162	SO:0001819	synonymous_variant	89795					nuclear outer membrane	ATP binding|nucleoside-triphosphatase activity	g.chr12:78574731G>A	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.5598G>A	12.37:g.78574731G>A		HNSCC(70;0.22)				NAV3_uc001syo.3_Silent_p.P1844P|NAV3_uc010sub.2_Silent_p.P1323P|NAV3_uc009zsf.3_Silent_p.P675P	p.P1866P	NM_014903	NP_055718	Q8IVL0	NAV3_HUMAN			29	5771	+			1866					Q8NFW7|Q9Y2E7	Silent	SNP	ENST00000397909.2	37	c.5598G>A		1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	7.681	0.689077	0.14973	.	.	ENSG00000067798	ENST00000552895	.	.	.	6.02	-12.0	0.00017	.	.	.	.	.	T	0.30885	0.0779	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56727	-0.7931	4	.	.	.	-15.4389	1.3687	0.02206	0.3478:0.2466:0.1052:0.3004	.	.	.	.	I	739	.	.	V	+	1	0	NAV3	77098862	0.000000	0.05858	0.000000	0.03702	0.940000	0.58332	-7.524000	0.00034	-5.000000	0.00024	-0.851000	0.03033	GTC		0.433	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
OR4N2	390429	broad.mit.edu	37	14	20296487	20296487	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr14:20296487G>A	ENST00000315947.1	+	1	880	c.880G>A	c.(880-882)Gtg>Atg	p.V294M	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	294						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CAACCAGGAAGTGAAAGCTTC	0.383																																						uc010tkv.2																			0				breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52						c.(880-882)Gtg>Atg		Homo sapiens olfactory receptor, family 4, subfamily N, member 2 (OR4N2), mRNA.							41.0	44.0	43.0					14																	20296487		2203	4294	6497	SO:0001583	missense	390429				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr14:20296487G>A		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.880G>A	14.37:g.20296487G>A	ENSP00000319601:p.Val294Met						p.V294M	NM_001004723	NP_001004723	Q8NGD1	OR4N2_HUMAN	Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)	0	880	+	all_cancers(95;0.00108)		294					Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	c.880G>A	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	0.009	-1.846683	0.00568	.	.	ENSG00000176294	ENST00000315947	T	0.39229	1.09	4.57	2.72	0.32119	.	0.183411	0.26867	N	0.022087	T	0.21267	0.0512	L	0.33093	0.98	0.24455	N	0.994465	P	0.34639	0.461	B	0.32393	0.145	T	0.17471	-1.0368	10	0.05620	T	0.96	-5.433	4.2847	0.10850	0.2054:0.1914:0.6031:0.0	.	294	Q8NGD1	OR4N2_HUMAN	M	294	ENSP00000319601:V294M	ENSP00000319601:V294M	V	+	1	0	OR4N2	19366327	0.072000	0.21174	0.999000	0.59377	0.088000	0.18126	-0.451000	0.06795	1.273000	0.44346	0.591000	0.81541	GTG		0.383	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
CLEC14A	161198	broad.mit.edu	37	14	38723845	38723845	+	Missense_Mutation	SNP	G	G	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr14:38723845G>T	ENST00000342213.2	-	1	1729	c.1383C>A	c.(1381-1383)aaC>aaA	p.N461K		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	461						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		TCACCCCATTGTTTGTGCAAT	0.607																																						uc001wum.1																			0				breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						c.(1381-1383)aaC>aaA		Homo sapiens C-type lectin domain family 14, member A (CLEC14A), mRNA.							72.0	74.0	73.0					14																	38723845		2203	4300	6503	SO:0001583	missense	161198					integral to membrane	sugar binding	g.chr14:38723845G>T		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"""C-type lectin domain containing"""	19832	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 27"""	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.1383C>A	14.37:g.38723845G>T	ENSP00000353013:p.Asn461Lys						p.N461K	NM_175060	NP_778230	Q86T13	CLC14_HUMAN	Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)	0	1730	-	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		461					Q695G9|Q6PWT6|Q8N5V5	Missense_Mutation	SNP	ENST00000342213.2	37	c.1383C>A	CCDS9667.1	.	.	.	.	.	.	.	.	.	.	G	12.71	2.020619	0.35606	.	.	ENSG00000176435	ENST00000342213	T	0.74002	-0.8	4.72	2.85	0.33270	.	0.570579	0.14668	N	0.305541	T	0.55289	0.1911	N	0.14661	0.345	0.09310	N	1	B	0.21606	0.058	B	0.19946	0.027	T	0.50189	-0.8857	10	0.72032	D	0.01	-5.6055	6.4924	0.22123	0.0956:0.0:0.7254:0.179	.	461	Q86T13	CLC14_HUMAN	K	461	ENSP00000353013:N461K	ENSP00000353013:N461K	N	-	3	2	CLEC14A	37793596	0.001000	0.12720	0.039000	0.18376	0.129000	0.20672	0.396000	0.20867	0.656000	0.30886	-0.214000	0.12660	AAC		0.607	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060	
PYGL	5836	broad.mit.edu	37	14	51387718	51387718	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr14:51387718C>T	ENST00000216392.7	-	6	1060	c.728G>A	c.(727-729)cGc>cAc	p.R243H	PYGL_ENST00000532462.1_Missense_Mutation_p.R243H|PYGL_ENST00000544180.2_Missense_Mutation_p.R209H	NM_002863.4	NP_002854.3	P06737	PYGL_HUMAN	phosphorylase, glycogen, liver	243					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|necroptotic process (GO:0070266)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	AMP binding (GO:0016208)|ATP binding (GO:0005524)|bile acid binding (GO:0032052)|drug binding (GO:0008144)|glucose binding (GO:0005536)|glycogen phosphorylase activity (GO:0008184)|protein homodimerization activity (GO:0042803)|purine nucleobase binding (GO:0002060)|pyridoxal phosphate binding (GO:0030170)|vitamin binding (GO:0019842)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25	all_epithelial(31;0.00825)|Breast(41;0.148)				Adenosine monophosphate(DB00131)	AGACCAGAGGCGCATGGTGTT	0.502																																						uc001wyu.3																			0				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)|skin(3)	25						c.(727-729)cGc>cAc		Homo sapiens phosphorylase, glycogen, liver (PYGL), transcript variant 1, mRNA.	Adenosine monophosphate(DB00131)|Pyridoxal Phosphate(DB00114)|Riboflavin(DB00140)						106.0	104.0	104.0					14																	51387718		2203	4300	6503	SO:0001583	missense	5836				glucose homeostasis|glucose metabolic process|glycogen catabolic process	cytosol|soluble fraction	AMP binding|ATP binding|bile acid binding|drug binding|glucose binding|glycogen phosphorylase activity|protein homodimerization activity|purine base binding|pyridoxal phosphate binding	g.chr14:51387718C>T		CCDS32080.1, CCDS53894.1	14q11.2-q24.3	2013-03-01	2008-07-31		ENSG00000100504	ENSG00000100504	2.4.1.1	"""Glycogen phosphorylases"""	9725	protein-coding gene	gene with protein product	"""Hers disease"", ""glycogen storage disease type VI"", ""glycogen phosphorylase, liver form"""	613741	"""phosphorylase, glycogen; liver"""			2877458	Standard	NM_002863		Approved		uc001wyu.3	P06737	OTTHUMG00000166596	ENST00000216392.7:c.728G>A	14.37:g.51387718C>T	ENSP00000216392:p.Arg243His					PYGL_uc010tqq.2_Missense_Mutation_p.R209H|PYGL_uc010anz.1_Missense_Mutation_p.R46H	p.R243H	NM_002863	NP_002854	P06737	PYGL_HUMAN			5	855	-	all_epithelial(31;0.00825)|Breast(41;0.148)		243					A6NDQ4|B4DUB7|F5H816|O60567|O60752|O60913|Q501V9|Q641R5|Q96G82	Missense_Mutation	SNP	ENST00000216392.7	37	c.728G>A	CCDS32080.1	.	.	.	.	.	.	.	.	.	.	C	36	5.745950	0.96882	.	.	ENSG00000100504	ENST00000532462;ENST00000544180;ENST00000216392	D;D;D	0.96168	-3.93;-3.93;-3.93	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.97739	0.9258	M	0.78049	2.395	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.998;0.999;0.999	D	0.97988	1.0353	10	0.87932	D	0	-0.3184	19.3504	0.94381	0.0:1.0:0.0:0.0	.	209;243;243	F5H816;E9PK47;P06737	.;.;PYGL_HUMAN	H	243;209;243	ENSP00000431657:R243H;ENSP00000443787:R209H;ENSP00000216392:R243H	ENSP00000216392:R243H	R	-	2	0	PYGL	50457468	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	7.750000	0.85110	2.885000	0.99019	0.655000	0.94253	CGC		0.502	PYGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390654.3	NM_002863	
SMOC1	64093	broad.mit.edu	37	14	70442486	70442486	+	Missense_Mutation	SNP	C	C	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr14:70442486C>A	ENST00000381280.4	+	4	686	c.433C>A	c.(433-435)Ccc>Acc	p.P145T	SMOC1_ENST00000361956.3_Missense_Mutation_p.P145T	NM_001034852.2|NM_022137.5	NP_001030024.1|NP_071420.1	Q9H4F8	SMOC1_HUMAN	SPARC related modular calcium binding 1	145	Thyroglobulin type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00500}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|eye development (GO:0001654)|limb development (GO:0060173)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of osteoblast differentiation (GO:0045667)|signal transduction (GO:0007165)	basement membrane (GO:0005604)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21				all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)		GGATGGGAAGCCCATCAGTGG	0.517																																						uc001xlt.2																			0				breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						c.(433-435)Ccc>Acc		Homo sapiens SPARC related modular calcium binding 1 (SMOC1), transcript variant 1, mRNA.							121.0	111.0	115.0					14																	70442486		2203	4300	6503	SO:0001583	missense	64093				cell differentiation|eye development|limb development|regulation of osteoblast differentiation|signal transduction	basement membrane	calcium ion binding	g.chr14:70442486C>A	AJ249900	CCDS9798.1, CCDS32110.1	14q24.1	2010-08-05			ENSG00000198732	ENSG00000198732			20318	protein-coding gene	gene with protein product		608488				12130637	Standard	NM_001034852		Approved		uc001xlt.2	Q9H4F8		ENST00000381280.4:c.433C>A	14.37:g.70442486C>A	ENSP00000370680:p.Pro145Thr					SMOC1_uc001xls.2_Missense_Mutation_p.P145T	p.P145T	NM_001034852	NP_001030024	Q9H4F8	SMOC1_HUMAN		all cancers(60;0.00417)|BRCA - Breast invasive adenocarcinoma(234;0.0119)|OV - Ovarian serous cystadenocarcinoma(108;0.028)	3	715	+			145			Thyroglobulin type-1 1.		A8K1S3|B2R7P5|Q96F78	Missense_Mutation	SNP	ENST00000381280.4	37	c.433C>A	CCDS9798.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740244	0.89573	.	.	ENSG00000198732	ENST00000361956;ENST00000381280	T;T	0.63913	-0.07;-0.07	5.07	5.07	0.68467	Thyroglobulin type-1 (5);	0.000000	0.85682	D	0.000000	T	0.79476	0.4452	M	0.79123	2.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.994;0.999	T	0.79052	-0.1961	10	0.41790	T	0.15	-14.5539	17.3768	0.87394	0.0:1.0:0.0:0.0	.	145;145	Q9H4F8-2;Q9H4F8	.;SMOC1_HUMAN	T	145	ENSP00000355110:P145T;ENSP00000370680:P145T	ENSP00000355110:P145T	P	+	1	0	SMOC1	69512239	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.404000	0.79996	2.637000	0.89404	0.462000	0.41574	CCC		0.517	SMOC1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000412467.1		
NPAP1	23742	broad.mit.edu	37	15	24921536	24921536	+	Silent	SNP	C	C	T	rs368120585		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr15:24921536C>T	ENST00000329468.2	+	1	996	c.522C>T	c.(520-522)gaC>gaT	p.D174D		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	174					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.D174D(2)									GGGAGGATGACGAGAAAAGGA	0.622																																						uc001ywo.3																			2	Substitution - coding silent(2)	p.D174D(4)	ovary(1)|large_intestine(1)	NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(1)|large_intestine(28)|lung(77)|ovary(5)|pancreas(1)|skin(8)	140						c.(520-522)gaC>gaT		Homo sapiens chromosome 15 open reading frame 2 (C15orf2), mRNA.		C		1,4405		0,1,2202	48.0	41.0	43.0		522	-5.4	0.0	15		43	0,8600		0,0,4300	no	coding-synonymous	C15orf2	NM_018958.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		174/1157	24921536	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23742				cell differentiation|multicellular organismal development|spermatogenesis			g.chr15:24921536C>T	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.522C>T	15.37:g.24921536C>T							p.D174D	NM_018958	NP_061831	Q9NZP6	CO002_HUMAN		all cancers(64;3.19e-24)|Epithelial(43;2.67e-17)|GBM - Glioblastoma multiforme(186;7.36e-07)|BRCA - Breast invasive adenocarcinoma(123;0.000273)|Lung(196;0.229)	0	996	+		all_cancers(20;2.14e-21)|all_epithelial(15;4.77e-19)|Lung NSC(15;1.43e-14)|all_lung(15;9.57e-14)|Breast(32;0.00086)	174						Silent	SNP	ENST00000329468.2	37	c.522C>T	CCDS10015.1																																																																																				0.622	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
SEC14L5	9717	broad.mit.edu	37	16	5046964	5046964	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr16:5046964G>A	ENST00000251170.7	+	8	1069	c.889G>A	c.(889-891)Gtg>Atg	p.V297M		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	297						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						GCAGCACCAGGTGGATCTCCT	0.612																																						uc002cye.2																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						c.(889-891)Gtg>Atg		Homo sapiens SEC14-like 5 (S. cerevisiae) (SEC14L5), mRNA.							41.0	40.0	40.0					16																	5046964		1938	4121	6059	SO:0001583	missense	9717					integral to membrane|intracellular	transporter activity	g.chr16:5046964G>A	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.889G>A	16.37:g.5046964G>A	ENSP00000251170:p.Val297Met						p.V297M	NM_014692	NP_055507	O43304	S14L5_HUMAN			7	1069	+			297						Missense_Mutation	SNP	ENST00000251170.7	37	c.889G>A	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.030402	0.93575	.	.	ENSG00000103184	ENST00000251170	T	0.74315	-0.83	4.66	4.66	0.58398	Cellular retinaldehyde-binding/triple function, C-terminal (1);Phosphatidylinositol transfer protein-like, N-terminal (1);	0.101860	0.41712	D	0.000837	D	0.87398	0.6167	M	0.92649	3.33	0.80722	D	1	D	0.56968	0.978	P	0.56612	0.802	D	0.90626	0.4563	10	0.66056	D	0.02	-0.1596	18.0897	0.89471	0.0:0.0:1.0:0.0	.	297	O43304	S14L5_HUMAN	M	297	ENSP00000251170:V297M	ENSP00000251170:V297M	V	+	1	0	SEC14L5	4986965	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.099000	0.94207	2.573000	0.86826	0.491000	0.48974	GTG		0.612	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
ZFP90	146198	broad.mit.edu	37	16	68596966	68596966	+	Missense_Mutation	SNP	A	A	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr16:68596966A>T	ENST00000570495.1	+	5	568	c.276A>T	c.(274-276)gaA>gaT	p.E92D	ZFP90_ENST00000564323.1_3'UTR|ZFP90_ENST00000563169.2_Missense_Mutation_p.E92D|ZFP90_ENST00000398253.2_Missense_Mutation_p.E92D			Q8TF47	ZFP90_HUMAN	ZFP90 zinc finger protein	92					negative regulation of DNA binding (GO:0043392)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)		CCAGGCCTGAAGTCAAATCAT	0.423																																						uc010cff.3																			0				breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27						c.(274-276)gaA>gaT		Homo sapiens zinc finger protein 90 homolog (mouse) (ZFP90), mRNA.							79.0	73.0	75.0					16																	68596966		1898	4127	6025	SO:0001583	missense	146198				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr16:68596966A>T	AK074332	CCDS42183.1	16q22.1	2013-01-08	2012-11-27			ENSG00000184939		"""Zinc fingers, C2H2-type"", ""-"""	23329	protein-coding gene	gene with protein product		609451	"""zinc finger protein 90 homolog (mouse)"""			7576184	Standard	NM_133458		Approved	KIAA1954, NK10, ZNF756	uc002ewc.3	Q8TF47		ENST00000570495.1:c.276A>T	16.37:g.68596966A>T	ENSP00000460547:p.Glu92Asp					ZFP90_uc002ewb.3_5'UTR|ZFP90_uc002ewc.3_5'UTR|ZFP90_uc002ewd.3_Missense_Mutation_p.E92D|ZFP90_uc002ewe.3_Missense_Mutation_p.E92D	p.E92D	NM_133458	NP_597715	Q8TF47	ZFP90_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.00233)|Epithelial(162;0.0184)|all cancers(182;0.0946)	4	568	+		Ovarian(137;0.192)	92					B2RU00|B3KVE7|Q49AD1|Q96MQ6	Missense_Mutation	SNP	ENST00000570495.1	37	c.276A>T	CCDS42183.1	.	.	.	.	.	.	.	.	.	.	A	3.954	-0.011736	0.07727	.	.	ENSG00000184939	ENST00000398253	T	0.06218	3.33	5.85	-4.18	0.03846	.	.	.	.	.	T	0.03651	0.0104	N	0.25485	0.75	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.41980	-0.9478	9	0.37606	T	0.19	-2.8453	2.7769	0.05350	0.3342:0.2113:0.3511:0.1034	.	92	Q8TF47	ZFP90_HUMAN	D	92	ENSP00000381304:E92D	ENSP00000381304:E92D	E	+	3	2	ZFP90	67154467	0.001000	0.12720	0.009000	0.14445	0.150000	0.21749	0.167000	0.16602	-1.111000	0.02988	-1.139000	0.01908	GAA		0.423	ZFP90-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436217.3	XM_085375	
GPR179	440435	broad.mit.edu	37	17	36486234	36486234	+	Missense_Mutation	SNP	T	T	C			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr17:36486234T>C	ENST00000342292.4	-	11	3238	c.3218A>G	c.(3217-3219)cAc>cGc	p.H1073R	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	1073					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				CTTGAGGCTGTGGGATTTAGG	0.567																																						uc002hpz.3																			0				breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60						c.(3217-3219)cAc>cGc		Homo sapiens G protein-coupled receptor 179 (GPR179), mRNA.							69.0	74.0	72.0					17																	36486234		2060	4204	6264	SO:0001583	missense	440435					integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chr17:36486234T>C		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.3218A>G	17.37:g.36486234T>C	ENSP00000345060:p.His1073Arg						p.H1073R	NM_001004334	NP_001004334	Q6PRD1	GP179_HUMAN			10	3239	-	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)	1073						Missense_Mutation	SNP	ENST00000342292.4	37	c.3218A>G	CCDS42308.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.335639	0.41398	.	.	ENSG00000188888	ENST00000342292	T	0.54675	0.56	5.38	5.38	0.77491	.	0.000000	0.64402	D	0.000019	T	0.51924	0.1703	L	0.32530	0.975	0.26131	N	0.980419	D	0.56035	0.974	P	0.51453	0.67	T	0.51458	-0.8703	10	0.59425	D	0.04	-17.4998	13.0156	0.58754	0.0:0.0:0.0:1.0	.	1073	Q6PRD1	GP179_HUMAN	R	1073	ENSP00000345060:H1073R	ENSP00000345060:H1073R	H	-	2	0	GPR179	33739760	0.968000	0.33430	0.998000	0.56505	0.517000	0.34286	1.323000	0.33701	2.263000	0.75096	0.379000	0.24179	CAC		0.567	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
CDH7	1005	broad.mit.edu	37	18	63476948	63476948	+	Silent	SNP	T	T	C			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr18:63476948T>C	ENST00000397968.2	+	3	645	c.219T>C	c.(217-219)tcT>tcC	p.S73S	CDH7_ENST00000323011.3_Silent_p.S73S|CDH7_ENST00000536984.2_Silent_p.S73S	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	73	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				AGCTTCACTCTGATGTTGATA	0.378																																						uc002lkb.3																			0				NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80						c.(217-219)tcT>tcC		Homo sapiens cadherin 7, type 2 (CDH7), transcript variant b, mRNA.							78.0	77.0	77.0					18																	63476948		2203	4300	6503	SO:0001819	synonymous_variant	1005				adherens junction organization|cell junction assembly|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr18:63476948T>C	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.219T>C	18.37:g.63476948T>C						CDH7_uc002ljz.3_Silent_p.S73S|CDH7_uc002lka.3_Silent_p.S73S	p.S73S	NM_004361	NP_387450	Q9ULB5	CADH7_HUMAN			2	645	+		Esophageal squamous(42;0.129)	73			Cadherin 1.		Q9H157	Silent	SNP	ENST00000397968.2	37	c.219T>C	CCDS11993.1																																																																																				0.378	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
NFIC	4782	broad.mit.edu	37	19	3449019	3449019	+	Silent	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr19:3449019G>A	ENST00000443272.2	+	7	1017	c.966G>A	c.(964-966)tcG>tcA	p.S322S	NFIC_ENST00000341919.3_Silent_p.S322S|NFIC_ENST00000586919.1_Silent_p.S289S|NFIC_ENST00000589123.1_Silent_p.S313S|NFIC_ENST00000346156.5_Silent_p.S289S|NFIC_ENST00000395111.3_Silent_p.S313S|NFIC_ENST00000590282.1_Silent_p.S322S	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	322					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		CAGGCATCTCGTCCCCGGTGA	0.632																																						uc010xhi.2																			0				NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21						c.(964-966)tcG>tcA		Homo sapiens nuclear factor I/C (CCAAT-binding transcription factor) (NFIC), transcript variant 1, mRNA.							139.0	117.0	124.0					19																	3449019		2203	4300	6503	SO:0001819	synonymous_variant	4782				DNA replication|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr19:3449019G>A	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.966G>A	19.37:g.3449019G>A						NFIC_uc002lxo.3_Silent_p.S313S|NFIC_uc010xhh.2_Silent_p.S313S|NFIC_uc010xhj.2_Silent_p.S322S|NFIC_uc002lxp.3_Silent_p.S322S	p.S322S	NM_001245002	NP_001231931	P08651	NFIC_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)	6	1036	+		Hepatocellular(1079;0.137)	322					A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Silent	SNP	ENST00000443272.2	37	c.966G>A	CCDS59330.1																																																																																				0.632	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597	
TYK2	7297	broad.mit.edu	37	19	10467283	10467283	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr19:10467283G>A	ENST00000525621.1	-	18	3059	c.2578C>T	c.(2578-2580)Cgc>Tgc	p.R860C	TYK2_ENST00000264818.6_Missense_Mutation_p.R860C|TYK2_ENST00000524462.1_Missense_Mutation_p.R675C	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	860	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			AGGATGGTGCGGAATGATGGC	0.662																																						uc002moc.4																			0				breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64						c.(2578-2580)Cgc>Tgc		Homo sapiens tyrosine kinase 2 (TYK2), mRNA.							130.0	91.0	104.0					19																	10467283		2203	4300	6503	SO:0001583	missense	7297				intracellular protein kinase cascade|regulation of type I interferon-mediated signaling pathway|type I interferon-mediated signaling pathway	cytoskeleton|cytosol|membrane|nucleus	ATP binding|growth hormone receptor binding|non-membrane spanning protein tyrosine kinase activity	g.chr19:10467283G>A		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.2578C>T	19.37:g.10467283G>A	ENSP00000431885:p.Arg860Cys					TYK2_uc010dxe.3_Missense_Mutation_p.R675C	p.R860C	NM_003331	NP_003322	P29597	TYK2_HUMAN	OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)		17	2956	-			860			Protein kinase 1.		Q6QB10|Q96CH0	Missense_Mutation	SNP	ENST00000525621.1	37	c.2578C>T	CCDS12236.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.444112	0.63067	.	.	ENSG00000105397	ENST00000524462;ENST00000525621;ENST00000264818;ENST00000543792	D;D;D	0.83335	-1.71;-1.71;-1.71	5.11	5.11	0.69529	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000084	D	0.91348	0.7271	M	0.90595	3.13	0.80722	D	1	D	0.61080	0.989	P	0.59115	0.852	D	0.92970	0.6397	10	0.87932	D	0	-44.7027	16.0585	0.80822	0.0:0.0:1.0:0.0	.	860	P29597	TYK2_HUMAN	C	675;860;860;607	ENSP00000433203:R675C;ENSP00000431885:R860C;ENSP00000264818:R860C	ENSP00000264818:R860C	R	-	1	0	TYK2	10328283	1.000000	0.71417	1.000000	0.80357	0.373000	0.29922	1.935000	0.40173	2.655000	0.90218	0.655000	0.94253	CGC		0.662	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
SARS2	54938	broad.mit.edu	37	19	39408365	39408365	+	Splice_Site	DEL	G	G	-			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr19:39408365delG	ENST00000221431.6	-	12	1318	c.1159delC	c.(1159-1161)cgg>gg	p.R387fs	CTC-360G5.8_ENST00000599996.1_Splice_Site_p.P456fs|SARS2_ENST00000598831.1_Splice_Site_p.R35fs|SARS2_ENST00000594171.1_Splice_Site_p.R197fs|SARS2_ENST00000448145.2_Splice_Site_p.R387fs|SARS2_ENST00000430193.3_Splice_Site_p.R387fs|SARS2_ENST00000600042.1_Splice_Site_p.R389fs	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	387					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			TCTCCACACCGGAAGTGCAAG	0.637																																						uc010xup.1																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15						c.e13+1		Homo sapiens seryl-tRNA synthetase 2, mitochondrial (SARS2), nuclear gene encoding mitochondrial protein, transcript variant 1, mRNA.							62.0	57.0	58.0					19																	39408365		2203	4300	6503	SO:0001630	splice_region_variant	54938				seryl-tRNA aminoacylation	mitochondrial matrix	ATP binding|protein binding|serine-tRNA ligase activity	g.chr19:39408365delG	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	17697	protein-coding gene	gene with protein product	"""serine tRNA ligase 2, mitochondrial"""	612804	"""serine-tRNA ligase, mitochondrial"", ""seryl-tRNA synthetase 2"""	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.1160+1C>-	19.37:g.39408365delG						SARS2_uc002ojz.2_Splice_Site_p.R197_splice|SARS2_uc002oka.2_Splice_Site_p.R387_splice|SARS2_uc010xuq.1_Splice_Site_p.R387_splice|SARS2_uc010xur.1_Splice_Site	p.R389_splice	NM_001145901	NP_001139373	Q9NP81	SYSM_HUMAN	Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)		13	1326	-	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		387					A6NHW7|B4DE10|Q9BVP3	Frame_Shift_Del	DEL	ENST00000221431.6	37	c.1166_splice	CCDS33017.1																																																																																				0.637	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827	Frame_Shift_Del
ZNF610	162963	broad.mit.edu	37	19	52869863	52869863	+	Missense_Mutation	SNP	G	G	A	rs150692972		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr19:52869863G>A	ENST00000403906.3	+	6	1688	c.1232G>A	c.(1231-1233)cGc>cAc	p.R411H	ZNF610_ENST00000601151.1_Missense_Mutation_p.R368H|ZNF610_ENST00000321287.8_Missense_Mutation_p.R411H|ZNF610_ENST00000327920.8_Missense_Mutation_p.R411H	NM_001161425.1	NP_001154897.1	Q8N9Z0	ZN610_HUMAN	zinc finger protein 610	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34				OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)		GTCTTTGGGCGCAAATTATAC	0.423													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19080	0.0		0.0	False		,,,				2504	0.0					uc002pyx.4																			0				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(8)|liver(2)|lung(9)|ovary(2)|stomach(2)|upper_aerodigestive_tract(2)	34						c.(1231-1233)cGc>cAc		Homo sapiens zinc finger protein 610 (ZNF610), transcript variant 2, mRNA.		G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	2,4404	4.2+/-10.8	0,2,2201	58.0	55.0	56.0		1232,1232,1103,1232	-3.8	0.0	19	dbSNP_134	56	0,8600		0,0,4300	no	missense,missense,missense,missense	ZNF610	NM_001161425.1,NM_001161426.1,NM_001161427.1,NM_173530.2	29,29,29,29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign,benign,benign,benign	411/463,411/463,368/420,411/463	52869863	2,13004	2203	4300	6503	SO:0001583	missense	162963				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr19:52869863G>A	AK093359	CCDS12851.1, CCDS54309.1	19q13.41	2013-01-08			ENSG00000167554	ENSG00000167554		"""Zinc fingers, C2H2-type"", ""-"""	26687	protein-coding gene	gene with protein product						12477932	Standard	NM_001161425		Approved	FLJ36040	uc002pyx.4	Q8N9Z0		ENST00000403906.3:c.1232G>A	19.37:g.52869863G>A	ENSP00000383922:p.Arg411His					ZNF610_uc002pyy.4_Missense_Mutation_p.R411H|ZNF610_uc002pyz.4_Missense_Mutation_p.R368H|ZNF610_uc002pza.3_Missense_Mutation_p.R411H	p.R411H	NM_001161426	NP_775801	Q8N9Z0	ZN610_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00396)|GBM - Glioblastoma multiforme(134;0.00434)	5	1638	+			411					A8K4C3|Q86YH8|Q8NDS9	Missense_Mutation	SNP	ENST00000403906.3	37	c.1232G>A	CCDS12851.1	.	.	.	.	.	.	.	.	.	.	G	1.007	-0.688972	0.03328	4.54E-4	0.0	ENSG00000167554	ENST00000403906;ENST00000321287;ENST00000327920	T;T	0.07327	3.2;3.2	1.88	-3.76	0.04359	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03827	0.0108	L	0.39020	1.185	0.09310	N	1	B;B	0.29378	0.205;0.243	B;B	0.11329	0.004;0.006	T	0.44847	-0.9301	9	0.10636	T	0.68	.	0.1648	0.00107	0.3126:0.152:0.2481:0.2874	.	368;411	Q8N9Z0-2;Q8N9Z0	.;ZN610_HUMAN	H	411;368;411	ENSP00000383922:R411H;ENSP00000327597:R411H	ENSP00000324441:R368H	R	+	2	0	ZNF610	57561675	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.844000	0.04345	-2.397000	0.00581	-1.058000	0.02302	CGC		0.423	ZNF610-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462880.1	NM_173530	
KIR3DL1	3811	broad.mit.edu	37	19	55284986	55284986	+	Intron	SNP	C	C	T	rs687485	byFrequency	TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr19:55284986C>T	ENST00000538269.1	+	2	61				KIR3DL1_ENST00000541392.1_Intron|KIR3DL1_ENST00000402254.2_Intron|KIR2DL4_ENST00000396284.2_Intron|KIR2DL1_ENST00000291633.7_Missense_Mutation_p.T91M|KIR2DL3_ENST00000434419.2_Intron|KIR2DL1_ENST00000336077.6_Missense_Mutation_p.T91M|CTB-61M7.1_ENST00000400864.3_RNA			P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1						immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		AGTCGCATGACGCAAGACCTG	0.532																																						uc010erz.1																			0				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	17						c.(271-273)aCg>aTg		Homo sapiens killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 1 (KIR2DL1), mRNA.							280.0	243.0	256.0					19																	55284986		2172	4212	6384	SO:0001627	intron_variant	3802				immune response|natural killer cell inhibitory signaling pathway	integral to plasma membrane	protein binding|receptor activity	g.chr19:55284986C>T	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000538269.1:c.35-44003C>T	19.37:g.55284986C>T						KIR3DL2_uc010yfj.2_Intron|KIR3DL2_uc010yfk.1_Intron|KIR2DL1_uc010erw.1_Intron|KIR2DL1_uc002qgz.1_Intron|KIR2DL1_uc002qha.1_Intron|GQ422373_uc021vbl.1_5'Flank|KIR2DL1_uc002qhb.1_Missense_Mutation_p.T91M	p.T91M	NM_014218	NP_055033	P43626	KI2L1_HUMAN		GBM - Glioblastoma multiforme(193;0.0192)	2	310	+			91			Ig-like C2-type 1.		O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000538269.1	37	c.272C>T		.	.	.	.	.	.	.	.	.	.	C	0.414	-0.911548	0.02434	.	.	ENSG00000125498	ENST00000336077;ENST00000291633	T;T	0.28666	1.6;1.6	1.24	0.116	0.14647	.	.	.	.	.	T	0.11153	0.0272	N	0.02973	-0.45	0.09310	N	1	P;P	0.42993	0.765;0.797	B;B	0.44163	0.322;0.443	T	0.10064	-1.0646	9	0.07813	T	0.8	.	3.815	0.08812	0.0:0.7435:0.0:0.2565	rs687485;rs17173097	91;91	Q6IST4;Q6H2H3	.;.	M	91	ENSP00000336769:T91M;ENSP00000291633:T91M	ENSP00000291633:T91M	T	+	2	0	KIR2DL1	59976798	0.000000	0.05858	0.004000	0.12327	0.002000	0.02628	-1.126000	0.03254	0.106000	0.17784	-0.552000	0.04208	ACG		0.532	KIR3DL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_013289	
VPS54	51542	broad.mit.edu	37	2	64147109	64147109	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:64147109C>T	ENST00000272322.4	-	15	2226	c.2072G>A	c.(2071-2073)cGc>cAc	p.R691H	VPS54_ENST00000354504.3_Missense_Mutation_p.R538H|VPS54_ENST00000409558.4_Missense_Mutation_p.R679H			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	691					growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						TTGCTTCCAGCGCTCATTGTC	0.393																																						uc002scq.3																			0				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						c.(2071-2073)cGc>cAc		Homo sapiens vacuolar protein sorting 54 homolog (S. cerevisiae) (VPS54), transcript variant 1, mRNA.							69.0	68.0	68.0					2																	64147109		2203	4300	6503	SO:0001583	missense	51542				protein transport|retrograde transport, endosome to Golgi			g.chr2:64147109C>T	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.2072G>A	2.37:g.64147109C>T	ENSP00000272322:p.Arg691His					VPS54_uc002scp.3_Missense_Mutation_p.R679H|VPS54_uc002scn.3_5'UTR|VPS54_uc002sco.3_Missense_Mutation_p.R176H|VPS54_uc010fct.3_Missense_Mutation_p.R538H	p.R691H	NM_016516	NP_057600	Q9P1Q0	VPS54_HUMAN			14	2235	-			691					Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	c.2072G>A	CCDS33208.1	.	.	.	.	.	.	.	.	.	.	C	29.8	5.037125	0.93630	.	.	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.35421	1.31;1.31;1.32	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.63674	0.2531	M	0.81942	2.565	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.76071	0.987;0.943;0.975	T	0.67273	-0.5712	10	0.51188	T	0.08	.	18.417	0.90574	0.0:1.0:0.0:0.0	.	538;691;679	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	H	538;691;679;679;691	ENSP00000346499:R538H;ENSP00000272322:R691H;ENSP00000386980:R679H	ENSP00000272322:R691H	R	-	2	0	VPS54	64000613	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.564000	0.82326	2.332000	0.79248	0.650000	0.86243	CGC		0.393	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
RGPD3	653489	broad.mit.edu	37	2	107049631	107049631	+	Silent	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:107049631C>T	ENST00000409886.3	-	16	2403	c.2316G>A	c.(2314-2316)gcG>gcA	p.A772A	RGPD3_ENST00000304514.7_Silent_p.A772A	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	772					protein targeting to Golgi (GO:0000042)			p.A772A(4)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTTCTGAATCCGCATTTCGCA	0.373																																						uc010ywi.1																			4	Substitution - coding silent(4)	p.A772A(6)	kidney(2)|endometrium(2)	breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						c.(2314-2316)gcG>gcA		Homo sapiens RANBP2-like and GRIP domain containing 3 (RGPD3), mRNA.							81.0	68.0	72.0					2																	107049631		692	1590	2282	SO:0001819	synonymous_variant	653489				intracellular transport		binding	g.chr2:107049631C>T		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.2316G>A	2.37:g.107049631C>T							p.A772A	NM_001144013	NP_001137485	A6NKT7	RGPD3_HUMAN			15	2373	-			772					B8ZZM4	Silent	SNP	ENST00000409886.3	37	c.2316G>A	CCDS46379.1																																																																																				0.373	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
RGPD4	285190	broad.mit.edu	37	2	108455386	108455386	+	Missense_Mutation	SNP	T	T	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:108455386T>A	ENST00000408999.3	+	4	448	c.371T>A	c.(370-372)cTt>cAt	p.L124H	RGPD4_ENST00000354986.4_Missense_Mutation_p.L124H	NM_182588.2	NP_872394.2	Q7Z3J3	RGPD4_HUMAN	RANBP2-like and GRIP domain containing 4	124					protein targeting to Golgi (GO:0000042)					breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						GCAGCAAAACTTTTCCCAGGA	0.333																																						uc010ywk.2																			0				breast(1)|endometrium(7)|kidney(4)|lung(23)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(3)	43						c.(370-372)cTt>cAt		Homo sapiens RANBP2-like and GRIP domain containing 4 (RGPD4), mRNA.							129.0	126.0	127.0					2																	108455386		692	1580	2272	SO:0001583	missense	285190				intracellular transport		binding	g.chr2:108455386T>A	BX537861	CCDS46381.1	2q12.3	2013-01-10			ENSG00000196862	ENSG00000196862		"""Tetratricopeptide (TTC) repeat domain containing"""	32417	protein-coding gene	gene with protein product		612707				15710750, 15815621	Standard	NM_182588		Approved	RGP4, DKFZp686P0288	uc010ywk.2	Q7Z3J3	OTTHUMG00000153208	ENST00000408999.3:c.371T>A	2.37:g.108455386T>A	ENSP00000386810:p.Leu124His					RGPD4_uc002tdu.3_5'UTR	p.L124H	NM_182588	NP_872394	Q7Z3J3	RGPD4_HUMAN			3	453	+			124					B9A029	Missense_Mutation	SNP	ENST00000408999.3	37	c.371T>A	CCDS46381.1	.	.	.	.	.	.	.	.	.	.	t	4.743	0.138218	0.09083	.	.	ENSG00000196862	ENST00000354986;ENST00000408999;ENST00000445751	T;T	0.49720	0.77;0.77	2.5	1.28	0.21552	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.62648	0.2445	M	0.72894	2.215	0.28490	N	0.914545	D	0.76494	0.999	D	0.83275	0.996	T	0.53823	-0.8384	9	0.87932	D	0	-16.4748	6.9047	0.24303	0.2065:0.0:0.0:0.7935	.	124	Q7Z3J3	RGPD4_HUMAN	H	124;124;67	ENSP00000347081:L124H;ENSP00000386810:L124H	ENSP00000347081:L124H	L	+	2	0	RGPD4	107821818	1.000000	0.71417	0.994000	0.49952	0.071000	0.16799	3.191000	0.50981	0.202000	0.20498	-1.436000	0.01078	CTT		0.333	RGPD4-001	NOVEL	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330096.2	XM_496581	
WASH2P	375260	broad.mit.edu	37	2	114355998	114355998	+	RNA	SNP	C	C	G	rs17857355	byFrequency	TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:114355998C>G	ENST00000538033.2	+	0	2178							Q6VEQ5	WASH2_HUMAN	WAS protein family homolog 2 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)										CCAAGGTGGGCACTTGATGTC	0.612																																						uc002tkh.3																			0											c.(616-618)Cac>Gac		Homo sapiens WAS protein family homolog 2 pseudogene (WASH2P), non-coding RNA.																																						375260							g.chr2:114355998C>G			2q13	2010-07-08	2008-01-16	2008-01-16	ENSG00000146556	ENSG00000146556		"""WAS protein homologs"""	33145	pseudogene	pseudogene			"""family with sequence similarity 39, member B"""	FAM39B		18159949	Standard	NR_024077		Approved	MGC52000	uc002tkh.3	Q6VEQ5	OTTHUMG00000047822		2.37:g.114355998C>G						WASH2P_uc002tka.3_Non-coding_Transcript|WASH2P_uc002tkd.3_Non-coding_Transcript	p.H206D							4	674	+									Missense_Mutation	SNP	ENST00000538033.2	37	c.616C>G																																																																																					0.612	WASH2P-002	KNOWN	mRNA_end_NF|basic	retained_intron	pseudogene	OTTHUMT00000467782.1	NM_198943	
GTDC1	79712	broad.mit.edu	37	2	144765034	144765034	+	Missense_Mutation	SNP	A	A	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:144765034A>T	ENST00000392869.2	-	6	742	c.590T>A	c.(589-591)gTt>gAt	p.V197D	GTDC1_ENST00000542155.1_Missense_Mutation_p.V197D|GTDC1_ENST00000409298.1_Intron|GTDC1_ENST00000241391.5_Missense_Mutation_p.V197D|GTDC1_ENST00000344850.4_Missense_Mutation_p.V197D|GTDC1_ENST00000392867.3_Missense_Mutation_p.V197D|GTDC1_ENST00000409214.1_Missense_Mutation_p.V197D|GTDC1_ENST00000463875.2_Missense_Mutation_p.V68D	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	197					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		CATGGACAGAACCGCACCGCC	0.403																																						uc002tvp.3																			0				central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25						c.(589-591)gTt>gAt		Homo sapiens glycosyltransferase-like domain containing 1 (GTDC1), transcript variant 1, mRNA.							75.0	75.0	75.0					2																	144765034		2203	4300	6503	SO:0001583	missense	79712				biosynthetic process		transferase activity, transferring glycosyl groups	g.chr2:144765034A>T	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.590T>A	2.37:g.144765034A>T	ENSP00000376608:p.Val197Asp					GTDC1_uc002tvo.3_Missense_Mutation_p.V197D|GTDC1_uc021vqf.1_Missense_Mutation_p.V197D|GTDC1_uc010fnn.3_Missense_Mutation_p.V197D|GTDC1_uc002tvs.3_Missense_Mutation_p.V165D|GTDC1_uc021vqg.1_Intron|GTDC1_uc002tvr.3_Missense_Mutation_p.V197D|GTDC1_uc010fno.3_Missense_Mutation_p.V68D|GTDC1_uc002tvt.2_Missense_Mutation_p.V197D	p.V197D	NM_001006636	NP_001158101	Q4AE62	GTDC1_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0914)	6	869	-			197					A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Missense_Mutation	SNP	ENST00000392869.2	37	c.590T>A	CCDS33300.1	.	.	.	.	.	.	.	.	.	.	A	11.60	1.686865	0.29962	.	.	ENSG00000121964	ENST00000392869;ENST00000409214;ENST00000392867;ENST00000542155;ENST00000241391;ENST00000344850;ENST00000463875	T;T;T;T;T;T;T	0.42513	0.98;0.98;0.99;0.98;0.99;0.98;0.97	5.42	4.53	0.55603	.	0.978113	0.08441	N	0.945510	T	0.32102	0.0818	L	0.36672	1.1	0.09310	N	1	B;B;B;B	0.30973	0.095;0.302;0.009;0.302	B;B;B;B	0.24155	0.032;0.043;0.004;0.051	T	0.17531	-1.0366	10	0.34782	T	0.22	-3.2237	8.1806	0.31309	0.0841:0.0:0.7508:0.165	.	197;197;197;197	G1UFN1;Q4AE62-2;Q4AE62;Q4AE62-3	.;.;GTDC1_HUMAN;.	D	197;197;197;197;197;197;68	ENSP00000376608:V197D;ENSP00000386581:V197D;ENSP00000376606:V197D;ENSP00000438323:V197D;ENSP00000241391:V197D;ENSP00000339750:V197D;ENSP00000437964:V68D	ENSP00000241391:V197D	V	-	2	0	GTDC1	144481504	0.002000	0.14202	0.004000	0.12327	0.030000	0.12068	0.703000	0.25646	1.391000	0.46566	-0.242000	0.12053	GTT		0.403	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659	
ALS2CR11	151254	broad.mit.edu	37	2	202401017	202401017	+	Silent	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:202401017G>A	ENST00000286195.3	-	13	1277	c.1233C>T	c.(1231-1233)ggC>ggT	p.G411G	ALS2CR11_ENST00000439140.1_Silent_p.G411G|ALS2CR11_ENST00000439802.1_Intron|ALS2CR11_ENST00000450242.1_Silent_p.G411G	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	411										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						GTATAGTCAGGCCTTTCTCAG	0.338																																						uc002uyf.3																			0				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						c.(1231-1233)ggC>ggT		Homo sapiens amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 (ALS2CR11), transcript variant 1, mRNA.							116.0	110.0	112.0					2																	202401017		2203	4300	6503	SO:0001819	synonymous_variant	151254							g.chr2:202401017G>A	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.1233C>T	2.37:g.202401017G>A						ALS2CR11_uc002uye.3_Silent_p.G411G|ALS2CR11_uc010fti.3_Intron|ALS2CR11_uc021vvc.1_Silent_p.G411G	p.G411G	NM_001168221	NP_001161693	Q53TS8	AL2SA_HUMAN			12	1285	-			411					C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Silent	SNP	ENST00000286195.3	37	c.1233C>T	CCDS2349.1																																																																																				0.338	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
ALS2CR11	151254	broad.mit.edu	37	2	202483675	202483675	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:202483675G>A	ENST00000286195.3	-	1	223	c.179C>T	c.(178-180)aCg>aTg	p.T60M	ALS2CR11_ENST00000439140.1_Missense_Mutation_p.T60M|ALS2CR11_ENST00000439802.1_Missense_Mutation_p.T60M|ALS2CR11_ENST00000450242.1_Missense_Mutation_p.T60M	NM_152525.5	NP_689738.3	Q53TS8	AL2SA_HUMAN	amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11	60										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						AGGCAGGGCCGTCGTGCCCTG	0.642																																						uc002uyf.3																			0				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(11)|ovary(1)|skin(5)|urinary_tract(3)	33						c.(178-180)aCg>aTg		Homo sapiens amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 11 (ALS2CR11), transcript variant 1, mRNA.							54.0	53.0	54.0					2																	202483675		2203	4300	6503	SO:0001583	missense	151254							g.chr2:202483675G>A	AB053313	CCDS2349.1, CCDS54430.1, CCDS54428.1, CCDS54429.1	2q33	2007-12-07			ENSG00000155754	ENSG00000155754			14438	protein-coding gene	gene with protein product						11586298	Standard	NM_152525		Approved	FLJ25351	uc002uyf.3	Q53TS8	OTTHUMG00000132830	ENST00000286195.3:c.179C>T	2.37:g.202483675G>A	ENSP00000286195:p.Thr60Met					ALS2CR11_uc002uye.3_Missense_Mutation_p.T60M|ALS2CR11_uc010fti.3_Missense_Mutation_p.T60M|ALS2CR11_uc021vvc.1_Missense_Mutation_p.T60M	p.T60M	NM_001168221	NP_001161693	Q53TS8	AL2SA_HUMAN			0	231	-			60					C9IZH7|E9PGG4|Q8NCN6|Q96LN4	Missense_Mutation	SNP	ENST00000286195.3	37	c.179C>T	CCDS2349.1	.	.	.	.	.	.	.	.	.	.	G	6.906	0.536719	0.13188	.	.	ENSG00000155754	ENST00000286195;ENST00000439802;ENST00000439140;ENST00000450242	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	3.54	-4.13	0.03904	.	5.904740	0.00424	N	0.000069	T	0.22589	0.0545	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.14805	0.011;0.003;0.003	B;B;B	0.11329	0.006;0.002;0.002	T	0.10428	-1.0630	10	0.33141	T	0.24	.	4.7902	0.13245	0.0977:0.4305:0.35:0.1218	.	60;60;60	Q53TS8-2;E9PGG4;Q53TS8	.;.;AL2SA_HUMAN	M	60	ENSP00000286195:T60M;ENSP00000400672:T60M;ENSP00000409937:T60M;ENSP00000399016:T60M	ENSP00000286195:T60M	T	-	2	0	ALS2CR11	202191920	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.739000	0.04866	-0.994000	0.03463	-1.486000	0.00981	ACG		0.642	ALS2CR11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256296.2	NM_152525	
FAM124B	79843	broad.mit.edu	37	2	225266256	225266256	+	Missense_Mutation	SNP	G	G	A	rs149161165		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:225266256G>A	ENST00000409685.3	-	1	495	c.230C>T	c.(229-231)cCg>cTg	p.P77L	FAM124B_ENST00000243806.2_Missense_Mutation_p.P77L|FAM124B_ENST00000389874.3_Missense_Mutation_p.P77L	NM_001122779.1	NP_001116251.1	Q9H5Z6	F124B_HUMAN	family with sequence similarity 124B	77										endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)		ATCCTCTCCCGGGCTTTCGTG	0.572																																						uc002vnx.3																			0				endometrium(2)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	16						c.(229-231)cCg>cTg		Homo sapiens family with sequence similarity 124B (FAM124B), transcript variant 1, mRNA.							59.0	57.0	58.0					2																	225266256		2203	4300	6503	SO:0001583	missense	79843						protein binding	g.chr2:225266256G>A	AK075126	CCDS2461.1, CCDS46527.1	2q36.2	2008-02-05			ENSG00000124019	ENSG00000124019			26224	protein-coding gene	gene with protein product						12477932	Standard	NM_001122779		Approved	FLJ22746	uc002vnx.3	Q9H5Z6	OTTHUMG00000133168	ENST00000409685.3:c.230C>T	2.37:g.225266256G>A	ENSP00000386895:p.Pro77Leu					FAM124B_uc002vnw.3_Missense_Mutation_p.P77L	p.P77L	NM_001122779	NP_001116251	Q9H5Z6	F124B_HUMAN		Epithelial(121;4.4e-10)|all cancers(144;2.02e-07)|Lung(261;0.00766)|LUSC - Lung squamous cell carcinoma(224;0.00825)	0	456	-		Renal(207;0.0112)|all_lung(227;0.0126)|Lung NSC(271;0.0161)|all_hematologic(139;0.138)	77					A6NNC7|Q8NBZ4|Q8TAV7	Missense_Mutation	SNP	ENST00000409685.3	37	c.230C>T	CCDS46527.1	.	.	.	.	.	.	.	.	.	.	G	0.007	-1.939343	0.00484	.	.	ENSG00000124019	ENST00000389874;ENST00000409685;ENST00000243806	T;T;T	0.35973	1.28;1.28;1.28	5.39	1.54	0.23209	.	0.354583	0.30850	N	0.008746	T	0.04907	0.0132	N	0.00058	-2.35	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39901	-0.9591	10	0.02654	T	1	-4.9059	4.4304	0.11524	0.6821:0.1283:0.0671:0.1225	.	77;77	Q9H5Z6;Q9H5Z6-2	F124B_HUMAN;.	L	77	ENSP00000374524:P77L;ENSP00000386895:P77L;ENSP00000243806:P77L	ENSP00000243806:P77L	P	-	2	0	FAM124B	224974500	0.921000	0.31238	0.000000	0.03702	0.001000	0.01503	1.979000	0.40608	0.078000	0.16900	-0.238000	0.12139	CCG		0.572	FAM124B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330873.1	NM_024785	
ANO7	50636	broad.mit.edu	37	2	242142864	242142864	+	Silent	SNP	C	C	T	rs565229836	byFrequency	TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr2:242142864C>T	ENST00000274979.8	+	9	1105	c.1002C>T	c.(1000-1002)caC>caT	p.H334H	ANO7_ENST00000402430.3_Silent_p.H333H	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	334					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						CCCTGGACCACGTGCGCAGGT	0.692													C|||	4	0.000798722	0.0008	0.0	5008	,	,		12846	0.0		0.0	False		,,,				2504	0.0031					uc002wax.2																			0				NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						c.(1000-1002)caC>caT		Homo sapiens anoctamin 7 (ANO7), transcript variant NGEP-L, mRNA.							35.0	28.0	31.0					2																	242142864		2189	4298	6487	SO:0001819	synonymous_variant	50636					cell junction|chloride channel complex|cytosol	chloride channel activity	g.chr2:242142864C>T	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1002C>T	2.37:g.242142864C>T							p.H334H	NM_001001891	NP_001001891	Q6IWH7	ANO7_HUMAN			8	1105	+			334					Q6IWH6	Silent	SNP	ENST00000274979.8	37	c.1002C>T	CCDS33423.1																																																																																				0.692	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
APOBEC3A	200315	broad.mit.edu	37	22	39357613	39357613	+	Silent	SNP	C	C	T	rs141631289		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr22:39357613C>T	ENST00000402255.1	+	4	600	c.396C>T	c.(394-396)taC>taT	p.Y132Y	APOBEC3A_ENST00000249116.2_Silent_p.Y132Y			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	132					cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)	p.Y132Y(1)		large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					TCTATGATTACGACCCCCTAT	0.572																																						uc003awn.2																			1	Substitution - coding silent(1)	p.Y132Y(1)	lung(1)	cervix(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	13						c.(394-396)taC>taT		Homo sapiens apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A (APOBEC3A), transcript variant 1, mRNA.		C		1,4245		0,1,2122	59.0	66.0	64.0		396	-0.6	0.0	22	dbSNP_134	64	2,8136		0,2,4067	no	coding-synonymous	APOBEC3A	NM_145699.3		0,3,6189	TT,TC,CC		0.0246,0.0236,0.0242		132/200	39357613	3,12381	2123	4069	6192	SO:0001819	synonymous_variant	200315				negative regulation of transposition		hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines|RNA binding|zinc ion binding	g.chr22:39357613C>T	U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"""Apolipoprotein B mRNA editing enzymes"""	17343	protein-coding gene	gene with protein product	"""phorbolin I"""	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.396C>T	22.37:g.39357613C>T						APOBEC3B_uc011aob.1_Silent_p.Y114Y|APOBEC3B_uc011aoc.1_Silent_p.Y132Y	p.Y132Y	NM_145699	NP_663745	Q9UH17	ABC3B_HUMAN			2	566	+	Melanoma(58;0.04)		315					A0AVM1|Q12807|Q5JZ93|Q9UH18	Silent	SNP	ENST00000402255.1	37	c.396C>T	CCDS13981.1																																																																																				0.572	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699	
FRYL	285527	broad.mit.edu	37	4	48569356	48569356	+	Silent	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr4:48569356C>T	ENST00000503238.1	-	25	3077	c.3078G>A	c.(3076-3078)ctG>ctA	p.L1026L	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507711.1_Silent_p.L1026L|FRYL_ENST00000537810.1_Silent_p.L1026L|FRYL_ENST00000358350.4_Silent_p.L1026L			O94915	FRYL_HUMAN	FRY-like	1026					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TTTCTGCTTCCAGGAGTTGTC	0.343																																						uc003gyh.1																			0				breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						c.(3076-3078)ctG>ctA		Homo sapiens FRY-like (FRYL), mRNA.							127.0	115.0	119.0					4																	48569356		1866	4102	5968	SO:0001819	synonymous_variant	285527				regulation of transcription, DNA-dependent|transcription, DNA-dependent		protein binding	g.chr4:48569356C>T	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.3078G>A	4.37:g.48569356C>T						FRYL_uc003gyk.3_Silent_p.L1026L|FRYL_uc003gyi.1_5'Flank	p.L1026L	NM_015030	NP_055845	O94915	FRYL_HUMAN			27	3683	-			1026					O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	c.3078G>A	CCDS43227.1																																																																																				0.343	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
USO1	8615	broad.mit.edu	37	4	76722293	76722293	+	Silent	SNP	A	A	G			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr4:76722293A>G	ENST00000538159.1	+	18	1953	c.1953A>G	c.(1951-1953)aaA>aaG	p.K651K	USO1_ENST00000514213.2_Silent_p.K627K			O60763	USO1_HUMAN	USO1 vesicle transport factor	642					ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi vesicle docking (GO:0048211)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|mitotic cell cycle (GO:0000278)|transcytosis (GO:0045056)|vesicle fusion with Golgi apparatus (GO:0048280)	endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AAGAGGTGAAAAAAACATTAG	0.294																																						uc003hiu.3																			0				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						c.(1771-1773)aaA>aaG		Homo sapiens USO1 vesicle docking protein homolog (yeast) (USO1), mRNA.							80.0	72.0	74.0					4																	76722293		1829	4074	5903	SO:0001819	synonymous_variant	8615				intracellular protein transport|vesicle fusion with Golgi apparatus	cytosol|Golgi membrane	protein binding|protein transporter activity	g.chr4:76722293A>G	AL832010	CCDS75144.1	4q21.1	2012-12-10	2012-12-10		ENSG00000138768	ENSG00000138768			30904	protein-coding gene	gene with protein product	"""vesicle docking protein"", ""transcytosis associated protein"""	603344	"""USO1 homolog, vesicle docking protein (yeast)"", ""USO1 vesicle docking protein homolog (yeast)"""			9478999, 9150144, 12077354, 15979508, 14736916	Standard	XM_006714395		Approved	TAP, VDP, p115	uc003hiu.3	O60763	OTTHUMG00000160952	ENST00000538159.1:c.1953A>G	4.37:g.76722293A>G						USO1_uc003hiv.3_Silent_p.K484K|USO1_uc003hiw.3_Silent_p.K477K	p.K591K	NM_003715	NP_003706	O60763	USO1_HUMAN	Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)		15	1948	+			642			Globular head.		B2RAQ0|Q6PK63|Q86TB8|Q8N592	Silent	SNP	ENST00000538159.1	37	c.1773A>G		.	.	.	.	.	.	.	.	.	.	A	7.934	0.741271	0.15642	.	.	ENSG00000138768	ENST00000441296	T	0.67345	-0.26	5.6	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.63224	0.2493	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57452	-0.7809	7	0.19590	T	0.45	.	10.6186	0.45465	0.1484:0.0:0.8516:0.0	.	.	.	.	R	318	ENSP00000411698:K318R	ENSP00000411698:K318R	K	+	2	0	USO1	76941317	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.618000	0.54188	1.353000	0.45828	-0.321000	0.08615	AAA		0.294	USO1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_003715	
CCDC125	202243	broad.mit.edu	37	5	68590723	68590723	+	Missense_Mutation	SNP	G	G	A			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr5:68590723G>A	ENST00000396496.2	-	9	928	c.821C>T	c.(820-822)gCg>gTg	p.A274V	CCDC125_ENST00000396499.1_Missense_Mutation_p.A274V|CCDC125_ENST00000511257.1_Missense_Mutation_p.A149V|CCDC125_ENST00000383374.2_Intron|CCDC125_ENST00000460090.1_5'UTR			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	274						cytoplasm (GO:0005737)		p.A274V(2)		breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		TCCGAGGACCGCAAGCTTTAA	0.488																																						uc003jvv.1																			2	Substitution - Missense(2)	p.A274V(4)	lung(1)|kidney(1)	breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19						c.(820-822)gCg>gTg		Homo sapiens coiled-coil domain containing 125 (CCDC125), mRNA.							83.0	85.0	85.0					5																	68590723		2203	4300	6503	SO:0001583	missense	202243					cytoplasm		g.chr5:68590723G>A	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.821C>T	5.37:g.68590723G>A	ENSP00000379754:p.Ala274Val					CCDC125_uc003jvx.1_Missense_Mutation_p.A273V|CCDC125_uc003jvy.1_Non-coding_Transcript|CCDC125_uc003jvw.2_Missense_Mutation_p.A149V	p.A274V	NM_176816	NP_789786	Q86Z20	CC125_HUMAN		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)	7	861	-		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)	274					Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	c.821C>T	CCDS4000.1	.	.	.	.	.	.	.	.	.	.	G	16.12	3.032379	0.54790	.	.	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000511257	T;T;T	0.58210	0.35;0.35;0.35	5.1	3.3	0.37823	.	0.283555	0.39146	N	0.001444	T	0.45216	0.1331	M	0.64404	1.975	0.09310	N	1	P;P	0.47841	0.862;0.901	B;B	0.39771	0.309;0.187	T	0.42050	-0.9474	10	0.49607	T	0.09	7.2848	7.4586	0.27280	0.0859:0.0:0.7482:0.1659	.	149;274	Q86Z20-2;Q86Z20	.;CC125_HUMAN	V	274;274;149	ENSP00000379754:A274V;ENSP00000379756:A274V;ENSP00000426795:A149V	ENSP00000379754:A274V	A	-	2	0	CCDC125	68626479	1.000000	0.71417	0.013000	0.15412	0.609000	0.37215	3.984000	0.56923	0.722000	0.32252	0.650000	0.86243	GCG		0.488	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816	
VCAN	1462	broad.mit.edu	37	5	82849273	82849273	+	Missense_Mutation	SNP	G	G	A	rs145625752		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr5:82849273G>A	ENST00000265077.3	+	11	10149	c.9584G>A	c.(9583-9585)cGg>cAg	p.R3195Q	VCAN_ENST00000502527.2_Missense_Mutation_p.R454Q|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000343200.5_Missense_Mutation_p.R2208Q|VCAN_ENST00000342785.4_Missense_Mutation_p.R1441Q|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Missense_Mutation_p.R1393Q|VCAN-AS1_ENST00000513899.1_RNA	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	3195	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GCAGCTGAACGGGAATGCCGT	0.473																																						uc003kii.3																			0				NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190						c.(9583-9585)cGg>cAg		Homo sapiens versican (VCAN), transcript variant 1, mRNA.		G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	160.0	138.0	145.0		1361,6623,4322,9584	6.1	1.0	5	dbSNP_134	145	0,8600		0,0,4300	no	missense,missense,missense,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	43,43,43,43	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	454/656,2208/2410,1441/1643,3195/3397	82849273	1,13005	2203	4300	6503	SO:0001583	missense	1462				cell adhesion|cell recognition|glial cell migration	extracellular space|proteinaceous extracellular matrix	calcium ion binding|hyaluronic acid binding|sugar binding	g.chr5:82849273G>A	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.9584G>A	5.37:g.82849273G>A	ENSP00000265077:p.Arg3195Gln					VCAN_uc003kij.3_Missense_Mutation_p.R2208Q|VCAN_uc010jau.2_Missense_Mutation_p.R1441Q|VCAN_uc003kik.3_Missense_Mutation_p.R454Q|VCAN_uc003kil.3_Missense_Mutation_p.R1859Q	p.R3195Q	NM_004385	NP_004376	P13611	CSPG2_HUMAN		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	10	9940	+		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)	3195			C-type lectin.		P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	c.9584G>A	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	G	37	6.280649	0.97440	2.27E-4	0.0	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000342785;ENST00000512590;ENST00000502527	T;T;T;T;T	0.16743	2.32;2.32;2.32;2.32;2.32	6.06	6.06	0.98353	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.64402	D	0.000015	T	0.26774	0.0655	N	0.10664	0.02	0.53005	D	0.999969	D;D;P;D	0.89917	1.0;1.0;0.73;1.0	D;D;B;D	0.83275	0.993;0.977;0.28;0.996	T	0.30534	-0.9975	10	0.59425	D	0.04	.	20.6208	0.99490	0.0:0.0:1.0:0.0	.	1441;454;2208;3195	P13611-3;P13611-4;P13611-2;P13611	.;.;.;CSPG2_HUMAN	Q	3195;2208;1441;1393;454	ENSP00000265077:R3195Q;ENSP00000340062:R2208Q;ENSP00000342768:R1441Q;ENSP00000425959:R1393Q;ENSP00000421362:R454Q	ENSP00000265077:R3195Q	R	+	2	0	VCAN	82885029	1.000000	0.71417	0.980000	0.43619	0.992000	0.81027	8.009000	0.88606	2.882000	0.98803	0.655000	0.94253	CGG		0.473	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
FAT2	2196	broad.mit.edu	37	5	150922879	150922879	+	Silent	SNP	C	C	T	rs368590845		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr5:150922879C>T	ENST00000261800.5	-	9	7821	c.7809G>A	c.(7807-7809)ccG>ccA	p.P2603P		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2603	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CCTGGATAACCGGAGAGTCTT	0.443																																						uc003lue.4																			0				NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196						c.(7807-7809)ccG>ccA		Homo sapiens FAT tumor suppressor homolog 2 (Drosophila) (FAT2), mRNA.		C		2,4404	4.2+/-10.8	0,2,2201	205.0	205.0	205.0		7809	-10.7	0.0	5		205	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAT2	NM_001447.2		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		2603/4350	150922879	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2196				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding	g.chr5:150922879C>T	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.7809G>A	5.37:g.150922879C>T							p.P2603P	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		8	7822	-		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	2603			Cadherin 23.		O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	c.7809G>A	CCDS4317.1																																																																																				0.443	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
HK3	3101	broad.mit.edu	37	5	176314737	176314737	+	Missense_Mutation	SNP	C	C	T	rs367991681		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr5:176314737C>T	ENST00000292432.5	-	11	1406	c.1315G>A	c.(1315-1317)Gtc>Atc	p.V439I		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	439	Hexokinase type-2 1.|Regulatory.			V -> I (in Ref. 4; AAC50422). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CCCTGCAGGACGCTGCAGAAC	0.622																																						uc003mfa.3																			0				breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						c.(1315-1317)Gtc>Atc		Homo sapiens hexokinase 3 (white cell) (HK3), nuclear gene encoding mitochondrial protein, mRNA.		C	ILE/VAL	0,4406		0,0,2203	50.0	42.0	45.0		1315	-3.2	0.0	5		45	3,8591	3.0+/-9.4	0,3,4294	no	missense	HK3	NM_002115.2	29	0,3,6497	TT,TC,CC		0.0349,0.0,0.0231	benign	439/924	176314737	3,12997	2203	4297	6500	SO:0001583	missense	3101				glucose transport|glycolysis|transmembrane transport	cytosol|membrane	ATP binding|glucokinase activity	g.chr5:176314737C>T		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.1315G>A	5.37:g.176314737C>T	ENSP00000292432:p.Val439Ile					HK3_uc003mez.3_5'UTR	p.V439I	NM_002115	NP_002106	P52790	HXK3_HUMAN	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		10	1407	-	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	439	V -> I (in Ref. 4; AAC50422).		Regulatory.		Q8N1E7	Missense_Mutation	SNP	ENST00000292432.5	37	c.1315G>A	CCDS4407.1	.	.	.	.	.	.	.	.	.	.	C	0.278	-0.988506	0.02162	0.0	3.49E-4	ENSG00000160883	ENST00000292432	D	0.98075	-4.7	4.43	-3.18	0.05186	Hexokinase, C-terminal (1);	0.687783	0.13203	N	0.405767	D	0.87164	0.6109	N	0.01464	-0.85	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.82246	-0.0552	10	0.17832	T	0.49	.	5.2039	0.15279	0.0:0.2438:0.2681:0.4882	.	439	P52790	HXK3_HUMAN	I	439	ENSP00000292432:V439I	ENSP00000292432:V439I	V	-	1	0	HK3	176247343	0.001000	0.12720	0.023000	0.16930	0.002000	0.02628	-0.416000	0.07097	-0.955000	0.03636	-0.415000	0.06103	GTC		0.622	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
CARD11	84433	broad.mit.edu	37	7	2963984	2963984	+	Missense_Mutation	SNP	C	C	T	rs587778150		TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr7:2963984C>T	ENST00000396946.4	-	15	2226	c.1823G>A	c.(1822-1824)cGc>cAc	p.R608H		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	608					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		GAAGGAGTAGCGTTCGTGACT	0.642			Mis		DLBCL																																	uc003smv.3				Dom	yes		7	7p22	84433	Mis	"""caspase recruitment domain family, member 11"""			L			DLBCL		0				NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150						c.(1822-1824)cGc>cAc		Homo sapiens caspase recruitment domain family, member 11 (CARD11), mRNA.							94.0	78.0	83.0					7																	2963984		2203	4300	6503	SO:0001583	missense	84433				positive regulation of cytokine production|positive regulation of NF-kappaB transcription factor activity|regulation of apoptosis|T cell costimulation|T cell receptor signaling pathway	cytosol|membrane raft|plasma membrane	CARD domain binding|guanylate kinase activity	g.chr7:2963984C>T	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1823G>A	7.37:g.2963984C>T	ENSP00000380150:p.Arg608His						p.R608H	NM_032415	NP_115791	Q9BXL7	CAR11_HUMAN		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)	14	2157	-		Ovarian(82;0.0115)	608					A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	c.1823G>A	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	C	8.620	0.891212	0.17613	.	.	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.33654	1.4;2.34	5.15	3.35	0.38373	.	0.374846	0.25009	N	0.033857	T	0.28267	0.0698	N	0.08118	0	0.18873	N	0.999985	D	0.69078	0.997	P	0.55667	0.781	T	0.10870	-1.0611	10	0.27785	T	0.31	-19.9497	9.7146	0.40268	0.0:0.84:0.0:0.16	.	608	Q9BXL7	CAR11_HUMAN	H	608;79	ENSP00000380150:R608H;ENSP00000347695:R79H	ENSP00000347695:R79H	R	-	2	0	CARD11	2930510	0.498000	0.26075	0.028000	0.17463	0.523000	0.34469	0.699000	0.25586	0.583000	0.29574	0.555000	0.69702	CGC		0.642	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
PON3	5446	broad.mit.edu	37	7	95019499	95019499	+	Silent	SNP	A	A	G			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr7:95019499A>G	ENST00000265627.5	-	3	178	c.168T>C	c.(166-168)gaT>gaC	p.D56D	PON1_ENST00000542556.1_Intron|PON3_ENST00000451904.1_Silent_p.D56D|PON3_ENST00000475439.1_5'UTR|PON3_ENST00000427422.1_Silent_p.D56D	NM_000940.2	NP_000931.1	Q15166	PON3_HUMAN	paraoxonase 3	56					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|coumarin catabolic process (GO:0046226)|phenylacetate catabolic process (GO:0010124)|response to external stimulus (GO:0009605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	3,4-dihydrocoumarin hydrolase activity (GO:0018733)|aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|dihydrocoumarin hydrolase activity (GO:0047856)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	24	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0151)		Edetic Acid(DB00974)|Lovastatin(DB00227)	TAGGAAGTATATCAATATCTT	0.378																																						uc003unt.3																			0				autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27						c.(166-168)gaT>gaC		Homo sapiens paraoxonase 3 (PON3), mRNA.	Atorvastatin(DB01076)|Cefazolin(DB01327)						203.0	214.0	210.0					7																	95019499		2203	4300	6503	SO:0001819	synonymous_variant	5446				aromatic compound catabolic process|carboxylic acid catabolic process|organophosphate catabolic process|phosphatidylcholine metabolic process|positive regulation of binding|positive regulation of cholesterol efflux|positive regulation of transporter activity|response to external stimulus	spherical high-density lipoprotein particle	aryldialkylphosphatase activity|arylesterase activity|calcium ion binding|phospholipid binding|protein homodimerization activity	g.chr7:95019499A>G	L48516, AF320003	CCDS5639.1	7q21.3	2014-03-14			ENSG00000105852	ENSG00000105852	3.1.1.2	"""Paraoxonases"""	9206	protein-coding gene	gene with protein product	"""arylesterase 3"""	602720				8661009	Standard	NM_000940		Approved			Q15166	OTTHUMG00000153917	ENST00000265627.5:c.168T>C	7.37:g.95019499A>G						PON1_uc011kih.2_Intron|PON1_uc011kii.2_Silent_p.D56D	p.D56D	NM_000940	NP_000931	P27169	PON1_HUMAN	STAD - Stomach adenocarcinoma(171;0.0031)		2	193	-	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		56					A4D1H8|O75855|O76060|Q6IRU9|Q8IX97|Q9BZH9	Silent	SNP	ENST00000265627.5	37	c.168T>C	CCDS5639.1																																																																																				0.378	PON3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333007.1	NM_000940	
PLXNA4	91584	broad.mit.edu	37	7	131872361	131872361	+	Silent	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr7:131872361C>T	ENST00000359827.3	-	15	3824	c.2862G>A	c.(2860-2862)ctG>ctA	p.L954L	PLXNA4_ENST00000321063.4_Silent_p.L954L			Q9HCM2	PLXA4_HUMAN	plexin A4	954	IPT/TIG 2.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CTGAGAGAGTCAGTGTCTGTG	0.617																																						uc003vra.4																			0				NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						c.(2860-2862)ctG>ctA		Homo sapiens plexin A4 (PLXNA4), transcript variant 1, mRNA.							128.0	138.0	135.0					7																	131872361		2062	4199	6261	SO:0001819	synonymous_variant	91584					integral to membrane|intracellular|plasma membrane		g.chr7:131872361C>T	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.2862G>A	7.37:g.131872361C>T							p.L954L	NM_020911	NP_065962	Q9HCM2	PLXA4_HUMAN			14	3091	-			954			IPT/TIG 2.		A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	c.2862G>A	CCDS43646.1																																																																																				0.617	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
SSPO	23145	broad.mit.edu	37	7	149493732	149493732	+	RNA	SNP	G	G	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr7:149493732G>T	ENST00000378016.2	+	0	6728							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGCTGTGCCAGTGGTGAGTGT	0.652																																						uc010lpk.3																			0											c.(6718-6720)aGt>aTt		Homo sapiens SCO-spondin homolog (Bos taurus) (SSPO), mRNA.							97.0	100.0	99.0					7																	149493732		2120	4224	6344			23145				cell adhesion	extracellular space	peptidase inhibitor activity	g.chr7:149493732G>T	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149493732G>T							p.S2240I	NM_198455	NP_940857	A2VEC9	SSPO_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.00625)		44	6719	+	Melanoma(164;0.165)|Ovarian(565;0.177)		2243			LDL-receptor class A 8.		Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37	c.6719G>T																																																																																					0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TBC1D31	93594	broad.mit.edu	37	8	124109565	124109565	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr8:124109565C>T	ENST00000287380.1	+	6	805	c.715C>T	c.(715-717)Cat>Tat	p.H239Y	TBC1D31_ENST00000378080.2_Missense_Mutation_p.H134Y|TBC1D31_ENST00000522420.1_Missense_Mutation_p.H134Y|TBC1D31_ENST00000521676.1_Missense_Mutation_p.H134Y|TBC1D31_ENST00000327098.5_Missense_Mutation_p.H239Y|TBC1D31_ENST00000309336.3_Missense_Mutation_p.H239Y	NM_145647.3	NP_663622.2	Q96DN5	TBC31_HUMAN	TBC1 domain family, member 31	239						centrosome (GO:0005813)	Rab GTPase activator activity (GO:0005097)										AAATCATCTTCATTTGTGGTG	0.423																																						uc003ypp.2																			0				NS(1)|breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(21)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						c.(715-717)Cat>Tat		Homo sapiens WD repeat domain 67 (WDR67), transcript variant 1, mRNA.							134.0	121.0	126.0					8																	124109565		2203	4300	6503	SO:0001583	missense	93594					centrosome	Rab GTPase activator activity	g.chr8:124109565C>T	AK094612	CCDS6338.1, CCDS47916.1	8q24.13	2013-07-10	2013-07-10	2013-07-10	ENSG00000156787	ENSG00000156787		"""WD repeat domain containing"""	30888	protein-coding gene	gene with protein product			"""WD repeat domain 67"""	WDR67		12477932	Standard	NM_001145088		Approved	MGC21654, Gm85	uc003ypp.2	Q96DN5	OTTHUMG00000165081	ENST00000287380.1:c.715C>T	8.37:g.124109565C>T	ENSP00000287380:p.His239Tyr					WDR67_uc011lig.2_Missense_Mutation_p.H239Y|WDR67_uc011lih.2_Missense_Mutation_p.H129Y|WDR67_uc003ypq.2_Non-coding_Transcript|WDR67_uc003ypo.1_Missense_Mutation_p.H239Y|WDR67_uc003ypr.3_Non-coding_Transcript	p.H239Y	NM_145647	NP_663622	Q96DN5	WDR67_HUMAN	STAD - Stomach adenocarcinoma(47;0.00527)		5	805	+	Lung NSC(37;7e-10)|Ovarian(258;0.0205)		239					B7ZL19|Q2M2J9|Q3MIR6|Q8TBP9	Missense_Mutation	SNP	ENST00000287380.1	37	c.715C>T	CCDS6338.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.653258	0.67472	.	.	ENSG00000156787	ENST00000287380;ENST00000309336;ENST00000543408;ENST00000327098;ENST00000522420;ENST00000521676;ENST00000378080;ENST00000522276	T;T;T;T;T;T;T	0.69685	-0.09;1.66;1.66;1.65;1.65;1.65;-0.42	5.73	5.73	0.89815	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.70176	0.3194	M	0.78637	2.42	0.80722	D	1	B;B;B	0.21452	0.002;0.006;0.056	B;B;B	0.20184	0.002;0.016;0.028	T	0.65664	-0.6113	10	0.31617	T	0.26	-24.9716	19.8949	0.96954	0.0:1.0:0.0:0.0	.	239;239;239	B7ZL19;Q96DN5;Q3KRB0	.;WDR67_HUMAN;.	Y	239;239;118;239;134;134;134;229	ENSP00000287380:H239Y;ENSP00000308358:H239Y;ENSP00000312701:H239Y;ENSP00000429334:H134Y;ENSP00000430628:H134Y;ENSP00000367320:H134Y;ENSP00000428891:H229Y	ENSP00000287380:H239Y	H	+	1	0	WDR67	124178746	1.000000	0.71417	0.987000	0.45799	0.954000	0.61252	5.534000	0.67167	2.712000	0.92718	0.484000	0.47621	CAT		0.423	TBC1D31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381721.1	NM_145647	
INPP5E	56623	broad.mit.edu	37	9	139327520	139327520	+	Missense_Mutation	SNP	C	C	G			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chr9:139327520C>G	ENST00000371712.3	-	5	1569	c.1167G>C	c.(1165-1167)gaG>gaC	p.E389D		NM_019892.4	NP_063945.2	Q10713	MPPA_HUMAN	inositol polyphosphate-5-phosphatase, 72 kDa	0					cellular protein metabolic process (GO:0044267)|protein targeting to mitochondrion (GO:0006626)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			NS(1)|endometrium(1)|lung(4)|skin(3)	9		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)		CCGTGGAGCACTCCACCTCTG	0.627																																						uc004cho.3																			0				NS(1)|endometrium(1)|lung(4)|skin(3)	9						c.(1165-1167)gaG>gaC		Homo sapiens inositol polyphosphate-5-phosphatase, 72 kDa (INPP5E), mRNA.							141.0	133.0	136.0					9																	139327520		2202	4300	6502	SO:0001583	missense	56623					cilium axoneme|cytoskeleton|Golgi cisterna membrane	inositol-polyphosphate 5-phosphatase activity|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity	g.chr9:139327520C>G	AF187891	CCDS7000.1	9q34.3	2011-02-11			ENSG00000148384	ENSG00000148384			21474	protein-coding gene	gene with protein product		613037	"""Joubert syndrome 1"""	JBTS1		10764818, 10577920, 19668216	Standard	NM_019892		Approved	PPI5PIV, CORS1	uc004cho.3	Q9NRR6	OTTHUMG00000020927	ENST00000371712.3:c.1167G>C	9.37:g.139327520C>G	ENSP00000360777:p.Glu389Asp					INPP5E_uc010nbm.3_Missense_Mutation_p.E389D	p.E389D	NM_019892	NP_063945	Q9NRR6	INP5E_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;8.36e-06)|Epithelial(140;1.4e-05)	4	1552	-		Myeloproliferative disorder(178;0.0511)	389					B4DKL3|E7ET61|Q16639|Q5SXM9|Q8N513	Missense_Mutation	SNP	ENST00000371712.3	37	c.1167G>C	CCDS7000.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.494299	0.44352	.	.	ENSG00000148384	ENST00000371712	T	0.79749	-1.3	4.82	3.65	0.41850	Endonuclease/exonuclease/phosphatase (2);Inositol polyphosphate-related phosphatase (1);	0.000000	0.85682	D	0.000000	T	0.74741	0.3756	M	0.65677	2.01	0.58432	D	0.999999	B;B	0.30584	0.286;0.044	B;B	0.29598	0.104;0.047	T	0.75587	-0.3266	10	0.56958	D	0.05	-38.1068	6.7077	0.23260	0.0:0.714:0.0:0.286	.	355;389	Q9NRR6-2;Q9NRR6	.;INP5E_HUMAN	D	389	ENSP00000360777:E389D	ENSP00000360777:E389D	E	-	3	2	INPP5E	138447341	1.000000	0.71417	1.000000	0.80357	0.786000	0.44442	1.267000	0.33050	2.387000	0.81309	0.561000	0.74099	GAG		0.627	INPP5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055058.1	NM_019892	
RLIM	51132	broad.mit.edu	37	X	73811411	73811411	+	Missense_Mutation	SNP	C	C	T			TCGA-14-0787-01A-01W-0424-08	TCGA-14-0787-10A-01W-0424-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	184b240c-ebf1-4ecf-87eb-aae0718cd81f	160d43cf-950b-4476-aaec-6d9be41de861	g.chrX:73811411C>T	ENST00000332687.6	-	4	1957	c.1739G>A	c.(1738-1740)gGc>gAc	p.G580D	RLIM_ENST00000349225.2_Missense_Mutation_p.G580D	NM_016120.3	NP_057204.2	Q9NVW2	RNF12_HUMAN	ring finger protein, LIM domain interacting	580					negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|protein ubiquitination (GO:0016567)|random inactivation of X chromosome (GO:0060816)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	ligase activity (GO:0016874)|transcription corepressor activity (GO:0003714)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						AAGTTTGTTGCCTTCTGTATA	0.408																																					Esophageal Squamous(169;1899 1923 14997 18818 32118)	uc004ebu.3																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						c.(1738-1740)gGc>gAc		Homo sapiens ring finger protein, LIM domain interacting (RLIM), transcript variant 2, mRNA.							133.0	104.0	114.0					X																	73811411		2203	4300	6503	SO:0001583	missense	51132				random inactivation of X chromosome|transcription, DNA-dependent|ubiquitin-dependent protein catabolic process	cytoplasm|transcriptional repressor complex	transcription corepressor activity|ubiquitin-protein ligase activity|zinc ion binding	g.chrX:73811411C>T	AF155109	CCDS14427.1	Xq13-q21	2013-01-09	2009-02-17	2009-02-17	ENSG00000131263	ENSG00000131263		"""RING-type (C3HC4) zinc fingers"""	13429	protein-coding gene	gene with protein product	"""ring zinc finger protein NY-REN-43antigen"", ""LIM domain interacting ring finger protein"""	300379	"""ring finger protein 12"""	RNF12		10508479	Standard	NM_016120		Approved	NY-REN-43, MGC15161	uc004ebw.3	Q9NVW2	OTTHUMG00000021859	ENST00000332687.6:c.1739G>A	X.37:g.73811411C>T	ENSP00000328059:p.Gly580Asp					RLIM_uc004ebw.3_Missense_Mutation_p.G580D	p.G580D	NM_183353	NP_899196	Q9NVW2	RNF12_HUMAN			4	2029	-			580					B2RBQ1|D3DTE0|Q96D38|Q9Y598	Missense_Mutation	SNP	ENST00000332687.6	37	c.1739G>A	CCDS14427.1	.	.	.	.	.	.	.	.	.	.	C	17.52	3.408930	0.62399	.	.	ENSG00000131263	ENST00000332687;ENST00000349225	T;T	0.46819	0.86;0.86	5.41	5.41	0.78517	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, RING-H2-type (1);	0.000000	0.85682	D	0.000000	T	0.60470	0.2271	L	0.32530	0.975	0.80722	D	1	D	0.65815	0.995	D	0.83275	0.996	T	0.61753	-0.6998	10	0.51188	T	0.08	-11.6683	18.3591	0.90368	0.0:1.0:0.0:0.0	.	580	Q9NVW2	RNF12_HUMAN	D	580	ENSP00000328059:G580D;ENSP00000253571:G580D	ENSP00000328059:G580D	G	-	2	0	RLIM	73728136	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.442000	0.80503	2.275000	0.75901	0.600000	0.82982	GGC		0.408	RLIM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057268.1	NM_016120	
