#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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
KRTAP5-3	387266	broad.mit.edu	37	11	1629156	1629156	+	Missense_Mutation	SNP	T	T	A	rs75371407		TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr11:1629156T>A	ENST00000399685.1	-	1	537	c.460A>T	c.(460-462)Agc>Tgc	p.S154C		NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN	keratin associated protein 5-3	154	11 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)		TGGGAGCAGCTGGGCTTGCAG	0.627																																						ENST00000399685.1																			0				endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	8						c.(460-462)Agc>Tgc		keratin associated protein 5-3							127.0	139.0	135.0					11																	1629156		2202	4299	6501	SO:0001583	missense	387266					keratin filament		g.chr11:1629156T>A	AB126072	CCDS41591.1	11p15.5	2008-02-05			ENSG00000196224	ENSG00000196224		"""Keratin associated proteins"""	23598	protein-coding gene	gene with protein product						15144888	Standard	NM_001012708		Approved	KRTAP5.3, KRTAP5-9	uc001ltw.1	Q6L8H2	OTTHUMG00000057559	ENST00000399685.1:c.460A>T	11.37:g.1629156T>A	ENSP00000382592:p.Ser154Cys						p.S154C	NM_001012708.2	NP_001012726.1	Q6L8H2	KRA53_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000618)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	1	537	-		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	154			11 X 4 AA repeats of C-C-X-P.		Q6PL44|Q701N3	Missense_Mutation	SNP	ENST00000399685.1	37	c.460A>T	CCDS41591.1	.	.	.	.	.	.	.	.	.	.	T	2.139	-0.397181	0.04899	.	.	ENSG00000196224	ENST00000399685	T	0.01084	5.36	3.75	-3.61	0.04556	.	.	.	.	.	T	0.00468	0.0015	N	0.00742	-1.23	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.46331	-0.9199	9	0.51188	T	0.08	.	5.3378	0.15967	0.4233:0.1302:0.0:0.4465	.	154	Q6L8H2	KRA53_HUMAN	C	154	ENSP00000382592:S154C	ENSP00000382592:S154C	S	-	1	0	KRTAP5-3	1585732	.	.	0.594000	0.28785	0.041000	0.13682	.	.	-0.339000	0.08401	-1.270000	0.01421	AGC		0.627	KRTAP5-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127924.1			4	242	0	0	0	1	0	4	242				
AIM2	9447	broad.mit.edu	37	1	159033464	159033464	+	Splice_Site	SNP	C	C	A			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr1:159033464C>A	ENST00000368130.4	-	5	1105	c.817G>T	c.(817-819)Gta>Tta	p.V273L	AIM2_ENST00000411768.1_5'Flank	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN	absent in melanoma 2	273	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				activation of innate immune response (GO:0002218)|apoptotic process (GO:0006915)|cellular response to drug (GO:0035690)|cellular response to interferon-beta (GO:0035458)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity (GO:2001056)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein oligomerization (GO:0032461)|pyroptosis (GO:0070269)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)			breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16	all_hematologic(112;0.0429)					TTTTCTGTTACCTATAAAAGA	0.383																																						ENST00000368130.4																			0				breast(1)|large_intestine(1)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(1)	16						c.e5-1		absent in melanoma 2							85.0	90.0	88.0					1																	159033464		2203	4300	6503	SO:0001630	splice_region_variant	9447				cellular response to drug|immune response|interleukin-1 beta secretion	mitochondrion|nucleus		g.chr1:159033464C>A	AF024714	CCDS1181.1	1q22	2008-07-18			ENSG00000163568	ENSG00000163568			357	protein-coding gene	gene with protein product		604578				9242382	Standard	NM_004833		Approved	PYHIN4	uc001ftj.1	O14862	OTTHUMG00000037183	ENST00000368130.4:c.817-1G>T	1.37:g.159033464C>A						AIM2_ENST00000481829.1_5'UTR	p.V273_splice	NM_004833.1	NP_004824.1	O14862	AIM2_HUMAN			5	1105	-	all_hematologic(112;0.0429)		273			HIN-200.		A8K7M7|Q5T3V9|Q96FG9	Splice_Site	SNP	ENST00000368130.4	37	c.816_splice	CCDS1181.1	.	.	.	.	.	.	.	.	.	.	C	7.947	0.744087	0.15710	.	.	ENSG00000163568	ENST00000368130;ENST00000368129	T;T	0.14022	2.54;2.54	3.92	1.59	0.23543	HIN-200/IF120x (2);Nucleic acid-binding, OB-fold (1);	1.789980	0.03564	N	0.227459	T	0.03136	0.0092	N	0.22421	0.69	0.09310	N	1	B	0.21688	0.059	B	0.16722	0.016	T	0.39860	-0.9593	10	0.54805	T	0.06	-0.0704	5.2747	0.15643	0.0:0.2554:0.0:0.7446	.	273	O14862	AIM2_HUMAN	L	273;136	ENSP00000357112:V273L;ENSP00000357111:V136L	ENSP00000357111:V136L	V	-	1	0	AIM2	157300088	0.031000	0.19500	0.008000	0.14137	0.014000	0.08584	0.008000	0.13197	0.200000	0.20447	-0.367000	0.07326	GTA		0.383	AIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090341.1	NM_004833	Missense_Mutation	4	97	1	0	1	1	1	4	97				
CSGALNACT1	55790	broad.mit.edu	37	8	19263389	19263389	+	Missense_Mutation	SNP	C	C	T			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr8:19263389C>T	ENST00000454498.2	-	10	2514	c.1501G>A	c.(1501-1503)Gag>Aag	p.E501K	CSGALNACT1_ENST00000332246.6_Missense_Mutation_p.E501K|CSGALNACT1_ENST00000522854.1_Missense_Mutation_p.E501K|CSGALNACT1_ENST00000311540.4_Missense_Mutation_p.E501K|CSGALNACT1_ENST00000544602.1_Missense_Mutation_p.E501K	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN	chondroitin sulfate N-acetylgalactosaminyltransferase 1	501					anatomical structure morphogenesis (GO:0009653)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0050653)|dermatan sulfate proteoglycan biosynthetic process (GO:0050651)|endochondral ossification (GO:0001958)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|heparin biosynthetic process (GO:0030210)|nervous system development (GO:0007399)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|UDP-glucuronate metabolic process (GO:0046398)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|intracellular (GO:0005622)	acetylgalactosaminyltransferase activity (GO:0008376)|glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|glucuronosyltransferase activity (GO:0015020)|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047237)|metal ion binding (GO:0046872)|peptidoglycan glycosyltransferase activity (GO:0008955)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31				Colorectal(111;0.182)		TGGGATGCCTCGTTCATGGCC	0.552																																						ENST00000454498.2																			0				NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						c.(1501-1503)Gag>Aag		chondroitin sulfate N-acetylgalactosaminyltransferase 1							160.0	132.0	142.0					8																	19263389		2203	4300	6503	SO:0001583	missense	55790				anatomical structure morphogenesis|cell proliferation|cell recognition|chondroitin sulfate biosynthetic process|chondroitin sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|dermatan sulfate proteoglycan biosynthetic process|extracellular matrix organization|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process|heparin biosynthetic process|nervous system development|UDP-glucuronate metabolic process|UDP-N-acetylgalactosamine metabolic process	Golgi cisterna membrane|integral to Golgi membrane|soluble fraction	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|glucuronosyltransferase activity|glucuronylgalactosylproteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|peptidoglycan glycosyltransferase activity	g.chr8:19263389C>T	AK002126	CCDS6010.1	8p21.3	2013-02-19				ENSG00000147408		"""Beta 4-glycosyltransferases"""	24290	protein-coding gene	gene with protein product	"""chondroitin beta1,4 N-acetylgalactosaminyltransferase"""					17145758, 12446672	Standard	NM_018371		Approved	CSGalNAcT-1, FLJ11264, ChGn	uc011kyo.2	Q8TDX6		ENST00000454498.2:c.1501G>A	8.37:g.19263389C>T	ENSP00000411816:p.Glu501Lys					CSGALNACT1_ENST00000544602.1_Missense_Mutation_p.E501K|CSGALNACT1_ENST00000332246.6_Missense_Mutation_p.E501K|CSGALNACT1_ENST00000311540.4_Missense_Mutation_p.E501K|CSGALNACT1_ENST00000522854.1_Missense_Mutation_p.E501K	p.E501K	NM_001130518.1	NP_001123990.1	Q8TDX6	CGAT1_HUMAN		Colorectal(111;0.182)	10	2514	-			501					B2RBE4|Q6P9G6|Q8IUF9|Q9NSQ7|Q9NUM9	Missense_Mutation	SNP	ENST00000454498.2	37	c.1501G>A	CCDS6010.1	.	.	.	.	.	.	.	.	.	.	C	36	5.871622	0.97049	.	.	ENSG00000147408	ENST00000454498;ENST00000332246;ENST00000311540;ENST00000522854;ENST00000544602	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.43942	0.1270	M	0.76727	2.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.05419	-1.0886	10	0.29301	T	0.29	-43.9703	18.8621	0.92276	0.0:1.0:0.0:0.0	.	501	Q8TDX6	CGAT1_HUMAN	K	501	ENSP00000411816:E501K;ENSP00000330805:E501K;ENSP00000310891:E501K;ENSP00000429809:E501K;ENSP00000442155:E501K	ENSP00000310891:E501K	E	-	1	0	CSGALNACT1	19307669	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.420000	0.80191	2.802000	0.96397	0.655000	0.94253	GAG		0.552	CSGALNACT1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375204.1	NM_018371		6	82	0	0	0	1	0	6	82				
TUBB8P7	197331	broad.mit.edu	37	16	90162620	90162620	+	RNA	SNP	T	T	G	rs567602838	byFrequency	TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr16:90162620T>G	ENST00000564451.1	+	0	1973				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		CTAGGTAAAGTGGGGAAGCAG	0.483													.|||	3	0.000599042	0.0015	0.0	5008	,	,		21669	0.0		0.0	False		,,,				2504	0.001					ENST00000564451.1																			0																																																			197331							g.chr16:90162620T>G			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162620T>G														0	1973	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.483	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		4	139	0	0	0	1	0	4	139				
DNM1P47	100216544	broad.mit.edu	37	15	102293007	102293007	+	RNA	SNP	C	C	G	rs200546955	byFrequency	TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr15:102293007C>G	ENST00000561463.1	+	0	1053									DNM1 pseudogene 47																		CGCGTGGGAACAAGAAGACAC	0.582																																						ENST00000561463.1																			0																																																			100216544							g.chr15:102293007C>G	AJ576276		15q26.3	2013-04-25			ENSG00000259660	ENSG00000259660			35200	pseudogene	pseudogene				DNM1DN14@			Standard	NG_009149		Approved	DNM1DN14-3			OTTHUMG00000172265		15.37:g.102293007C>G														0	1053	+									RNA	SNP	ENST00000561463.1	37																																																																																						0.582	DNM1P47-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417589.1	NG_009149		2	1	0	0	0	1	0	2	1				
SMARCA4	6597	broad.mit.edu	37	19	11136124	11136124	+	Missense_Mutation	SNP	G	G	C	rs1801514		TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr19:11136124G>C	ENST00000429416.3	+	23	3389	c.3108G>C	c.(3106-3108)atG>atC	p.M1036I	SMARCA4_ENST00000413806.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000541122.2_Missense_Mutation_p.M1036I|SMARCA4_ENST00000590574.1_Missense_Mutation_p.M1036I|SMARCA4_ENST00000444061.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000358026.2_Missense_Mutation_p.M1036I|SMARCA4_ENST00000450717.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000344626.4_Missense_Mutation_p.M1036I|SMARCA4_ENST00000589677.1_Missense_Mutation_p.M1036I	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1036			M -> I (in dbSNP:rs1801514).		aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				AGACCCTGATGAACACCATCA	0.637			"""F, N, Mis"""		NSCLC																																	ENST00000358026.2				Rec	yes		19	19p13.2	6597	"""F, N, Mis"""	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""			E			NSCLC		1	Unknown(1)	p.?(1)	lung(1)	adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163						c.(3106-3108)atG>atC		SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4							110.0	90.0	97.0					19																	11136124		2203	4300	6503	SO:0001583	missense	6597				chromatin remodeling|negative regulation of androgen receptor signaling pathway|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of transcription from RNA polymerase II promoter|nervous system development|positive regulation of sequence-specific DNA binding transcription factor activity|positive regulation of transcription from RNA polymerase II promoter|transcription, DNA-dependent	nBAF complex|npBAF complex|nuclear chromatin|SWI/SNF complex|WINAC complex	androgen receptor binding|ATP binding|DNA binding|DNA-dependent ATPase activity|helicase activity|histone acetyl-lysine binding|identical protein binding|p53 binding|protein N-terminus binding|transcription corepressor activity	g.chr19:11136124G>C	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.3108G>C	19.37:g.11136124G>C	ENSP00000395654:p.Met1036Ile					SMARCA4_ENST00000541122.2_Missense_Mutation_p.M1036I|SMARCA4_ENST00000450717.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000444061.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000429416.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000413806.3_Missense_Mutation_p.M1036I|SMARCA4_ENST00000344626.4_Missense_Mutation_p.M1036I|SMARCA4_ENST00000589677.1_Missense_Mutation_p.M1036I|SMARCA4_ENST00000590574.1_Missense_Mutation_p.M1036I	p.M1036I	NM_001128849.1	NP_001122321.1	P51532	SMCA4_HUMAN			22	3392	+		all_lung(6;0.0512)|Lung NSC(9;0.0568)	1036		M -> I (in dbSNP:rs1801514).			B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	c.3108G>C	CCDS12253.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.928688	0.92389	.	.	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	T;T;T;T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91;-0.91;-0.91;-0.91	4.79	4.79	0.61399	SNF2-related (1);	0.000000	0.85682	D	0.000000	T	0.78253	0.4254	L	0.39020	1.185	0.58432	D	0.999999	P;P;P;P;P;B;P;P	0.43094	0.662;0.662;0.662;0.799;0.629;0.151;0.662;0.662	P;P;P;P;B;B;P;P	0.55222	0.643;0.544;0.544;0.771;0.326;0.118;0.643;0.643	T	0.80797	-0.1222	10	0.87932	D	0	-47.5382	16.7568	0.85502	0.0:0.0:1.0:0.0	.	1036;1036;1036;1036;1036;256;1036;1036	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;A7E2E1;P51532	.;.;.;.;.;.;.;SMCA4_HUMAN	I	1036;1036;1100;1036;1036;1036;1036;1036	ENSP00000395654:M1036I;ENSP00000350720:M1036I;ENSP00000343896:M1036I;ENSP00000445036:M1036I;ENSP00000392837:M1036I;ENSP00000397783:M1036I;ENSP00000414727:M1036I	ENSP00000343896:M1036I	M	+	3	0	SMARCA4	10997124	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.565000	0.82337	2.486000	0.83907	0.655000	0.94253	ATG		0.637	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072		4	34	0	0	0	1	0	4	34				
DPY19L2P2	349152	broad.mit.edu	37	7	102912190	102912190	+	RNA	SNP	T	T	G			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr7:102912190T>G	ENST00000312132.4	-	0	2389							Q6ZN68	D19P2_HUMAN	DPY19L2 pseudogene 2							integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)										TCTGGATAAATATGGAAGCGT	0.343																																						ENST00000312132.4																			0																																																			349152							g.chr7:102912190T>G	AL834175		7q22.1	2013-09-12	2013-09-12		ENSG00000170629	ENSG00000170629			21764	pseudogene	pseudogene			"""dpy-19-like 2 pseudogene 2 (C. elegans)"""				Standard	NR_027768		Approved	DKFZp434E092, FLJ36166	uc003vbh.4	Q6ZN68	OTTHUMG00000157200		7.37:g.102912190T>G														0	2389	-								Q8N9V4|Q8ND62	RNA	SNP	ENST00000312132.4	37																																																																																						0.343	DPY19L2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000347877.1	NM_182634		3	36	0	0	0	1	0	3	36				
PRG4	10216	broad.mit.edu	37	1	186276052	186276052	+	Missense_Mutation	SNP	A	A	C	rs542620960	byFrequency	TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr1:186276052A>C	ENST00000445192.2	+	7	1246	c.1201A>C	c.(1201-1203)Acc>Ccc	p.T401P	PRG4_ENST00000367486.3_Missense_Mutation_p.T358P|PRG4_ENST00000367484.3_Missense_Mutation_p.T360P|PRG4_ENST00000367483.4_Missense_Mutation_p.T360P|PRG4_ENST00000367485.4_Missense_Mutation_p.T308P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	401	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.T401P(4)|p.T400>?(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ACCCACCACCACCAAGGAGCC	0.642													-|||	12	0.00239617	0.0083	0.0014	5008	,	,		8994	0.0		0.0	False		,,,				2504	0.0					ENST00000445192.2																			5	Substitution - Missense(4)|Complex(1)	p.T401P(4)|p.T400>?(1)	kidney(2)|prostate(1)|lung(1)|endometrium(1)	NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						c.(1201-1203)Acc>Ccc		proteoglycan 4							95.0	89.0	91.0					1																	186276052		2203	4298	6501	SO:0001583	missense	10216				cell proliferation|immune response	extracellular region	polysaccharide binding|protein binding|scavenger receptor activity	g.chr1:186276052A>C	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1201A>C	1.37:g.186276052A>C	ENSP00000399679:p.Thr401Pro					PRG4_ENST00000367483.4_Missense_Mutation_p.T360P|PRG4_ENST00000367485.4_Missense_Mutation_p.T308P|PRG4_ENST00000367486.3_Missense_Mutation_p.T358P|PRG4_ENST00000367484.3_Missense_Mutation_p.T360P	p.T401P	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN			7	1246	+			401			59 X 8 AA repeats of K-X-P-X-P-T-T-X.		Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	c.1201A>C	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	-	3.851	-0.031771	0.07543	.	.	ENSG00000116690	ENST00000367486;ENST00000367484;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T;T	0.05258	3.54;3.65;3.61;3.47;3.64	3.17	-6.34	0.01982	.	.	.	.	.	T	0.02649	0.0080	N	0.13140	0.3	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.06405	0.002;0.002;0.001;0.002	T	0.46034	-0.9220	8	.	.	.	.	3.639	0.08160	0.4008:0.398:0.0956:0.1055	.	267;308;401;360	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	P	358;360;267;360;308;401	ENSP00000356456:T358P;ENSP00000356454:T360P;ENSP00000356453:T360P;ENSP00000356455:T308P;ENSP00000399679:T401P	.	T	+	1	0	PRG4	184542675	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.209000	0.09358	-1.096000	0.03046	-2.716000	0.00133	ACC		0.642	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807		5	59	0	0	0	1	0	5	59				
SSX3	10214	broad.mit.edu	37	X	48206947	48206947	+	Missense_Mutation	SNP	C	C	A			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chrX:48206947C>A	ENST00000298396.2	-	7	611	c.559G>T	c.(559-561)Gat>Tat	p.D187Y	SSX3_ENST00000376895.1_Missense_Mutation_p.D99Y	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN	synovial sarcoma, X breakpoint 3	187					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(1)|lung(9)	13						AGTTACTCATCATCTTCCTCA	0.502																																					Colon(37;227 826 19399 40970 48007)	ENST00000298396.2																			0				endometrium(3)|large_intestine(1)|lung(9)	13						c.(559-561)Gat>Tat		synovial sarcoma, X breakpoint 3							354.0	305.0	322.0					X																	48206947		2203	4300	6503	SO:0001583	missense	10214				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	nucleic acid binding	g.chrX:48206947C>A	U90840	CCDS14291.1	Xp11.23	2009-06-17			ENSG00000165584	ENSG00000165584			11337	protein-coding gene	gene with protein product		300325				8697803, 9378559	Standard	NM_021014		Approved	CT5.3	uc004djd.1	Q99909	OTTHUMG00000021489	ENST00000298396.2:c.559G>T	X.37:g.48206947C>A	ENSP00000298396:p.Asp187Tyr					SSX3_ENST00000376895.1_Missense_Mutation_p.D99Y	p.D187Y	NM_021014.2	NP_066294.1	Q99909	SSX3_HUMAN			7	611	-			187					O60223|Q5JQZ3|Q9BRW7	Missense_Mutation	SNP	ENST00000298396.2	37	c.559G>T	CCDS14291.1	.	.	.	.	.	.	.	.	.	.	c	11.28	1.592245	0.28357	.	.	ENSG00000165584	ENST00000298396;ENST00000376895	T;T	0.39787	2.46;1.06	1.86	1.86	0.25419	SSXRD motif (1);	0.439796	0.19437	N	0.114282	T	0.51686	0.1689	L	0.50333	1.59	0.18873	N	0.999989	D	0.89917	1.0	D	0.79784	0.993	T	0.23476	-1.0187	10	0.87932	D	0	.	6.5227	0.22285	0.0:1.0:0.0:0.0	.	187	Q99909	SSX3_HUMAN	Y	187;99	ENSP00000298396:D187Y;ENSP00000366092:D99Y	ENSP00000298396:D187Y	D	-	1	0	SSX3	48091891	0.005000	0.15991	0.047000	0.18901	0.036000	0.12997	0.474000	0.22148	1.205000	0.43262	0.358000	0.22013	GAT		0.502	SSX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056486.1	NM_021014		125	159	1	0	9.55279e-52	1	1.05081e-51	125	159				
LOC101927209	101927209	broad.mit.edu	37	1	142713944	142713944	+	lincRNA	SNP	C	C	T	rs199960649		TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr1:142713944C>T	ENST00000610091.1	-	0	1714																											TGATTACCTCCGAAGTTAAAG	0.308																																						ENST00000369381.2																			0																																																			101927209							g.chr1:142713944C>T																													1.37:g.142713944C>T														0	661	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.308	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			4	29	0	0	0	1	0	4	29				
FAM166A	401565	broad.mit.edu	37	9	140139634	140139634	+	Missense_Mutation	SNP	C	C	G			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr9:140139634C>G	ENST00000344774.4	-	4	613	c.559G>C	c.(559-561)Gcc>Ccc	p.A187P	FAM166A_ENST00000388932.2_Missense_Mutation_p.A187P	NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	187						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						TGGCGGCGGGCGGGGGGTGGG	0.662																																						ENST00000344774.4																			0				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						c.(559-561)Gcc>Ccc		family with sequence similarity 166, member A							23.0	29.0	27.0					9																	140139634		2193	4271	6464	SO:0001583	missense	401565							g.chr9:140139634C>G	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.559G>C	9.37:g.140139634C>G	ENSP00000344729:p.Ala187Pro					FAM166A_ENST00000388932.2_Missense_Mutation_p.A187P	p.A187P	NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN			4	613	-			187					A6NND9|Q8N830	Missense_Mutation	SNP	ENST00000344774.4	37	c.559G>C	CCDS35186.1	.	.	.	.	.	.	.	.	.	.	C	9.272	1.045845	0.19748	.	.	ENSG00000188163	ENST00000344774;ENST00000388932;ENST00000484720	.	.	.	5.02	-0.848	0.10727	.	1.387220	0.04677	N	0.411604	T	0.37461	0.1004	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27706	-1.0066	9	0.27082	T	0.32	-1.0629	10.8355	0.46685	0.0:0.599:0.3:0.101	.	187	Q6J272	F166A_HUMAN	P	187;187;214	.	ENSP00000344729:A187P	A	-	1	0	FAM166A	139259455	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.125000	0.10579	-0.114000	0.11936	-0.254000	0.11334	GCC		0.662	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710		5	38	0	0	0	1	0	5	38				
NINL	22981	broad.mit.edu	37	20	25459587	25459587	+	Missense_Mutation	SNP	G	G	A			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr20:25459587G>A	ENST00000278886.6	-	16	2246	c.2173C>T	c.(2173-2175)Cgg>Tgg	p.R725W	NINL_ENST00000422516.1_Missense_Mutation_p.R725W	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN	ninein-like	725					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|microtubule (GO:0005874)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						CTGTGATGCCGCAGGGCCAGG	0.592																																						ENST00000278886.6																			0				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(13)|lung(25)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	57						c.(2173-2175)Cgg>Tgg		ninein-like							32.0	38.0	36.0					20																	25459587		2203	4298	6501	SO:0001583	missense	22981				G2/M transition of mitotic cell cycle	cytosol|microtubule|microtubule organizing center	calcium ion binding	g.chr20:25459587G>A		CCDS33452.1	20p11.22-p11.1	2013-01-10			ENSG00000101004	ENSG00000101004		"""EF-hand domain containing"""	29163	protein-coding gene	gene with protein product	"""ninein-like protein"""	609580				10231032	Standard	XM_005260678		Approved	KIAA0980, NLP	uc002wux.1	Q9Y2I6	OTTHUMG00000032127	ENST00000278886.6:c.2173C>T	20.37:g.25459587G>A	ENSP00000278886:p.Arg725Trp					NINL_ENST00000422516.1_Missense_Mutation_p.R725W	p.R725W	NM_025176.4	NP_079452.3	Q9Y2I6	NINL_HUMAN			16	2246	-			725					A6NJN0|B3V9H6|B7Z1V8|Q5JYP0|Q8NE38|Q9NQE3	Missense_Mutation	SNP	ENST00000278886.6	37	c.2173C>T	CCDS33452.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.31|12.31	1.898391|1.898391	0.33535|0.33535	.|.	.|.	ENSG00000101004|ENSG00000101004	ENST00000336104|ENST00000278886;ENST00000422516	.|T;T	.|0.33438	.|1.51;1.41	4.12|4.12	-0.294|-0.294	0.12831|0.12831	.|.	.|0.459125	.|0.21179	.|N	.|0.078859	T|T	0.13200|0.13200	0.0320|0.0320	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.17465	.|0.022;0.002	.|B;B	.|0.10450	.|0.005;0.001	T|T	0.16424|0.16424	-1.0403|-1.0403	5|10	.|0.52906	.|T	.|0.07	-22.6168|-22.6168	6.5405|6.5405	0.22377|0.22377	0.4812:0.0:0.5188:0.0|0.4812:0.0:0.5188:0.0	.|.	.|725;725	.|Q9Y2I6-2;Q9Y2I6	.|.;NINL_HUMAN	V|W	26|725	.|ENSP00000278886:R725W;ENSP00000410431:R725W	.|ENSP00000278886:R725W	A|R	-|-	2|1	0|2	NINL|NINL	25407587|25407587	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.078000|0.078000	0.17371|0.17371	-0.351000|-0.351000	0.07711|0.07711	-0.015000|-0.015000	0.14150|0.14150	-0.137000|-0.137000	0.14449|0.14449	GCG|CGG		0.592	NINL-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078445.3	NM_025176		3	36	0	0	0	1	0	3	36				
PCDHGA1	56114	broad.mit.edu	37	5	140712578	140712578	+	Missense_Mutation	SNP	C	C	T			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr5:140712578C>T	ENST00000517417.1	+	1	2327	c.2327C>T	c.(2326-2328)gCg>gTg	p.A776V	PCDHGA1_ENST00000378105.3_Missense_Mutation_p.A776V	NM_018912.2	NP_061735.1	Q9Y5H4	PCDG1_HUMAN	protocadherin gamma subfamily A, 1	776					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCCAACTATGCGGACACACTC	0.527																																						ENST00000517417.1																			0				breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|lung(32)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	78						c.(2326-2328)gCg>gTg									115.0	124.0	121.0					5																	140712578		2203	4300	6503	SO:0001583	missense	56114							g.chr5:140712578C>T	AF152318	CCDS54922.1	5q31	2010-01-26				ENSG00000204956		"""Cadherins / Protocadherins : Clustered"""	8696	other	protocadherin		606288				10380929	Standard	NM_018912		Approved	PCDH-GAMMA-A1		Q9Y5H4		ENST00000517417.1:c.2327C>T	5.37:g.140712578C>T	ENSP00000431083:p.Ala776Val					PCDHGA1_ENST00000378105.3_Missense_Mutation_p.A776V	p.A776V	NM_018912.2	NP_061735.1			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	2327	+								Q2M273|Q9Y5D6	Missense_Mutation	SNP	ENST00000517417.1	37	c.2327C>T	CCDS54922.1	.	.	.	.	.	.	.	.	.	.	.	10.69	1.421617	0.25639	.	.	ENSG00000204956	ENST00000517417;ENST00000378105	T;T	0.50548	0.77;0.74	4.04	3.13	0.36017	.	0.814474	0.10297	N	0.691649	T	0.46151	0.1378	M	0.70842	2.15	0.09310	N	1	B;B	0.27380	0.177;0.111	B;B	0.28465	0.09;0.07	T	0.42716	-0.9435	10	0.46703	T	0.11	.	6.5483	0.22418	0.0:0.7109:0.1803:0.1089	.	776;776	Q9Y5H4-2;Q9Y5H4	.;PCDG1_HUMAN	V	776	ENSP00000431083:A776V;ENSP00000367345:A776V	ENSP00000367345:A776V	A	+	2	0	PCDHGA1	140692762	0.001000	0.12720	0.016000	0.15963	0.625000	0.37756	0.311000	0.19380	0.980000	0.38523	0.585000	0.79938	GCG		0.527	PCDHGA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374737.1	NM_018912		4	198	0	0	0	1	0	4	198				
TUBB4A	10382	broad.mit.edu	37	19	6495551	6495551	+	Missense_Mutation	SNP	C	C	T			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr19:6495551C>T	ENST00000264071.2	-	4	1330	c.959G>A	c.(958-960)cGc>cAc	p.R320H	CTD-2396E7.9_ENST00000599292.1_RNA|CTD-2396E7.10_ENST00000596027.1_RNA|TUBB4A_ENST00000540257.1_Missense_Mutation_p.R320H			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	320					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)										CATGGACATGCGGCCCCGGAA	0.637																																						ENST00000264071.2																			0											c.(958-960)cGc>cAc		tubulin, beta 4A class IVa							114.0	97.0	103.0					19																	6495551		2203	4300	6503	SO:0001583	missense	10382				'de novo' posttranslational protein folding|G2/M transition of mitotic cell cycle|microtubule-based movement|protein polymerization	cytosol|microtubule	GTP binding|GTPase activity|protein binding|structural molecule activity	g.chr19:6495551C>T	AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"""Tubulins"""	20774	protein-coding gene	gene with protein product	"""class IVa beta-tubulin"""	602662	"""tubulin, beta 4"", ""tubulin, beta 4 class IVa"", ""dystonia 4, torsion (autosomal dominant)"""	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.959G>A	19.37:g.6495551C>T	ENSP00000264071:p.Arg320His					TUBB4A_ENST00000540257.1_Missense_Mutation_p.R320H	p.R320H			P04350	TBB4_HUMAN			4	1330	-			320					B3KQP4|Q969E5	Missense_Mutation	SNP	ENST00000264071.2	37	c.959G>A	CCDS12168.1	.	.	.	.	.	.	.	.	.	.	C	13.89	2.373060	0.42105	.	.	ENSG00000104833	ENST00000264071;ENST00000540257;ENST00000412858	D;D	0.84298	-1.83;-1.83	3.43	3.43	0.39272	.	0.000000	0.64402	D	0.000001	D	0.82852	0.5127	M	0.64630	1.985	0.52501	D	0.999955	B	0.12630	0.006	B	0.10450	0.005	T	0.82285	-0.0533	10	0.87932	D	0	.	13.6752	0.62449	0.0:1.0:0.0:0.0	.	320	P04350	TBB4A_HUMAN	H	320;320;238	ENSP00000264071:R320H;ENSP00000443590:R320H	ENSP00000264071:R320H	R	-	2	0	TUBB4	6446551	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.580000	0.82523	1.473000	0.48159	0.306000	0.20318	CGC		0.637	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1	NM_006087		4	123	0	0	0	1	0	4	123				
SACS	26278	broad.mit.edu	37	13	23909416	23909416	+	Missense_Mutation	SNP	C	C	A			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr13:23909416C>A	ENST00000382292.3	-	9	8872	c.8599G>T	c.(8599-8601)Gcc>Tcc	p.A2867S	SACS_ENST00000382298.3_Missense_Mutation_p.A2867S|SACS_ENST00000402364.1_Missense_Mutation_p.A2117S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2867					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		AAACAGAAGGCCCTATGGGGT	0.453																																						ENST00000382298.3																			0				NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189						c.(8599-8601)Gcc>Tcc		spastic ataxia of Charlevoix-Saguenay (sacsin)							57.0	62.0	60.0					13																	23909416		2203	4299	6502	SO:0001583	missense	26278				cell death|negative regulation of inclusion body assembly|protein folding	axon|cell body fiber|dendrite|mitochondrion|nucleus	ATP binding|chaperone binding|Hsp70 protein binding|proteasome binding	g.chr13:23909416C>A	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8599G>T	13.37:g.23909416C>A	ENSP00000371729:p.Ala2867Ser					SACS_ENST00000382292.3_Missense_Mutation_p.A2867S|SACS_ENST00000402364.1_Missense_Mutation_p.A2117S	p.A2867S	NM_014363.4	NP_055178.3	Q9NZJ4	SACS_HUMAN		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)	10	9187	-		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)	2867					O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	c.8599G>T	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	C	23.0	4.358185	0.82243	.	.	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.90261	-2.51;-2.64;-2.51	5.4	5.4	0.78164	.	0.115652	0.64402	D	0.000018	D	0.91620	0.7352	M	0.69823	2.125	0.46437	D	0.999047	P	0.40050	0.7	B	0.42625	0.393	D	0.91769	0.5426	10	0.51188	T	0.08	.	19.1639	0.93546	0.0:1.0:0.0:0.0	.	2867	Q9NZJ4	SACS_HUMAN	S	2867;2117;2867	ENSP00000371729:A2867S;ENSP00000385844:A2117S;ENSP00000371735:A2867S	ENSP00000371729:A2867S	A	-	1	0	SACS	22807416	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.487000	0.81328	2.525000	0.85131	0.555000	0.69702	GCC		0.453	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363		27	34	1	0	3.73148e-12	1	3.90917e-12	27	34				
TAS2R60	338398	broad.mit.edu	37	7	143140670	143140670	+	Missense_Mutation	SNP	T	T	C			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr7:143140670T>C	ENST00000332690.1	+	1	125	c.125T>C	c.(124-126)cTg>cCg	p.L42P	EPHA1-AS1_ENST00000429289.1_RNA	NM_177437.1	NP_803186.1	P59551	T2R60_HUMAN	taste receptor, type 2, member 60	42					sensory perception of bitter taste (GO:0050913)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|kidney(1)|large_intestine(2)|lung(17)|prostate(1)|skin(7)|urinary_tract(2)	31	Melanoma(164;0.172)					ACTGCTGCTCTGGGCGTGGAG	0.502																																						ENST00000332690.1																			0				breast(1)|kidney(1)|large_intestine(2)|lung(17)|prostate(1)|skin(7)|urinary_tract(2)	31						c.(124-126)cTg>cCg		taste receptor, type 2, member 60							240.0	216.0	224.0					7																	143140670		2203	4300	6503	SO:0001583	missense	338398				sensory perception of bitter taste	integral to membrane	G-protein coupled receptor activity	g.chr7:143140670T>C	AY114094	CCDS5885.1	7q35	2014-07-10			ENSG00000185899	ENSG00000185899		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	20639	protein-coding gene	gene with protein product		613968				12584440	Standard	NM_177437		Approved	T2R60	uc011ktg.2	P59551	OTTHUMG00000154891	ENST00000332690.1:c.125T>C	7.37:g.143140670T>C	ENSP00000327724:p.Leu42Pro					EPHA1-AS1_ENST00000429289.1_RNA	p.L42P	NM_177437.1	NP_803186.1	P59551	T2R60_HUMAN			1	125	+	Melanoma(164;0.172)		42					A4D2G8|Q645W8|Q7RTR7	Missense_Mutation	SNP	ENST00000332690.1	37	c.125T>C	CCDS5885.1	.	.	.	.	.	.	.	.	.	.	T	11.19	1.566252	0.27915	.	.	ENSG00000185899	ENST00000332690	T	0.44881	0.91	5.68	4.51	0.55191	.	0.849973	0.09990	U	0.729885	T	0.65344	0.2682	M	0.81341	2.54	0.24200	N	0.995511	D	0.89917	1.0	D	0.97110	1.0	T	0.50915	-0.8771	10	0.54805	T	0.06	.	9.0472	0.36354	0.1636:0.0:0.0:0.8364	.	42	P59551	T2R60_HUMAN	P	42	ENSP00000327724:L42P	ENSP00000327724:L42P	L	+	2	0	TAS2R60	142850792	0.046000	0.20272	0.007000	0.13788	0.017000	0.09413	1.989000	0.40707	0.967000	0.38186	0.533000	0.62120	CTG		0.502	TAS2R60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337541.1			14	137	0	0	0	1	0	14	137				
FAM162A	26355	broad.mit.edu	37	3	122103139	122103139	+	Frame_Shift_Del	DEL	G	G	-			TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr3:122103139delG	ENST00000477892.1	+	1	111	c.27delG	c.(25-27)ctgfs	p.L9fs	CCDC58_ENST00000479899.1_5'Flank|CCDC58_ENST00000291458.5_5'Flank|CCDC58_ENST00000497726.1_5'Flank|FAM162A_ENST00000232125.5_5'UTR|FAM162A_ENST00000469967.1_Frame_Shift_Del_p.L9fs	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN	family with sequence similarity 162, member A	9					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to hypoxia (GO:0071456)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|transformed cell apoptotic process (GO:0006927)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						GTCTGCGCCTGGCAGCAGGTG	0.692																																						ENST00000477892.1																			0				breast(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	6						c.(25-27)ctfs		family with sequence similarity 162, member A							13.0	18.0	16.0					3																	122103139		1976	4147	6123	SO:0001589	frameshift_variant	26355					integral to membrane		g.chr3:122103139delG	AF191020	CCDS43139.1	3q21.1	2008-06-05	2008-06-05	2008-06-05	ENSG00000114023	ENSG00000114023			17865	protein-coding gene	gene with protein product		608017	"""chromosome 3 open reading frame 28"""	C3orf28		11085516	Standard	NM_014367		Approved	E2IG5	uc003eez.3	Q96A26	OTTHUMG00000159494	ENST00000477892.1:c.27delG	3.37:g.122103139delG	ENSP00000419088:p.Leu9fs					FAM162A_ENST00000232125.5_5'UTR|FAM162A_ENST00000469967.1_Frame_Shift_Del_p.L9fs	p.L9fs	NM_014367.3	NP_055182.3	Q96A26	F162A_HUMAN			1	111	+			9					Q9NRN6|Q9UJX8	Frame_Shift_Del	DEL	ENST00000477892.1	37	c.27delG	CCDS43139.1																																																																																				0.692	FAM162A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355766.1	NM_014367		2	4						2	4	---	---	---	---
CORO1B	57175	broad.mit.edu	37	11	67209168	67209168	+	Intron	DEL	G	G	-	rs540646391	byFrequency	TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr11:67209168delG	ENST00000341356.5	-	4	565				CORO1B_ENST00000393893.1_Intron|CORO1B_ENST00000539724.1_5'Flank|CORO1B_ENST00000453768.2_Intron|CORO1B_ENST00000545016.1_Frame_Shift_Del_p.H164fs	NM_020441.2	NP_065174.1	Q9BR76	COR1B_HUMAN	coronin, actin binding protein, 1B						actin cytoskeleton organization (GO:0030036)|actin filament branching (GO:0090135)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|endothelial cell chemotaxis (GO:0035767)|negative regulation of Arp2/3 complex-mediated actin nucleation (GO:0034316)|positive regulation of lamellipodium morphogenesis (GO:2000394)|protein localization to cell leading edge (GO:1902463)|ruffle organization (GO:0031529)|wound healing (GO:0042060)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|Arp2/3 complex binding (GO:0071933)|identical protein binding (GO:0042802)			cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(15;3.26e-06)			AGGGGTCCGTGGGGGGGGGGA	0.657													|||unknown(HR)	9	0.00179712	0.0061	0.0014	5008	,	,		10135	0.0		0.0	False		,,,				2504	0.0					ENST00000545016.1																			0				cervix(1)|endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)	13						c.(490-492)acfs		coronin, actin binding protein, 1B			,	246,718,2802		22,17,185,55,591,1013					,	-0.5	0.0			7	285,1558,5707		17,8,243,90,1370,2047	no	intron,intron	CORO1B	NM_020441.2,NM_001018070.2	,	39,25,428,145,1961,3060	A1A1,A1A2,A1R,A2A2,A2R,RR		24.4106,25.5975,24.8056	,	,		531,2276,8509				SO:0001627	intron_variant	57175				actin cytoskeleton organization	actin cytoskeleton|cytoplasm	actin filament binding	g.chr11:67209168delG	AK000860	CCDS8164.1	11q13.1	2013-01-10	2001-11-28		ENSG00000172725	ENSG00000172725		"""Coronins"", ""WD repeat domain containing"""	2253	protein-coding gene	gene with protein product		609849	"""coronin, actin-binding protein, 1B"""			9778037	Standard	NM_001018070		Approved	coronin-2	uc001olk.1	Q9BR76	OTTHUMG00000167775	ENST00000341356.5:c.454+35C>-	11.37:g.67209168delG						CORO1B_ENST00000341356.5_Intron|CORO1B_ENST00000453768.2_Intron|CORO1B_ENST00000393893.1_Intron	p.H164fs			Q9BR76	COR1B_HUMAN	BRCA - Breast invasive adenocarcinoma(15;3.26e-06)		4	575	-			0					B2RD45	Frame_Shift_Del	DEL	ENST00000341356.5	37	c.490delC	CCDS8164.1																																																																																				0.657	CORO1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396220.1	NM_020441		6	12						6	12	---	---	---	---
GOLGA2P9	440518	broad.mit.edu	37	19	22779215	22779215	+	RNA	DEL	G	G	-	rs113336402	byFrequency	TCGA-W2-A7HF-01A-11D-A35I-08	TCGA-W2-A7HF-10C-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	95b7745a-0f8b-4cb5-81b5-12a66d55aeff	bee9bc77-03d3-44a2-9668-fffc359ed20f	g.chr19:22779215delG	ENST00000600260.1	+	0	157					NR_033899.1																						CAGCAGCAAAGAAAAAGGTAC	0.612													?|G|-|unsure	594	0.11861	0.4297	0.0288	5008	,	,		12991	0.0		0.006	False		,,,				2504	0.0					ENST00000600260.1																			0																																																			440518							g.chr19:22779215delG																													19.37:g.22779215delG								NR_033899.1						0	157	+									RNA	DEL	ENST00000600260.1	37																																																																																						0.612	CTC-457E21.3-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000464572.1			4	3						4	3	---	---	---	---
