#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
CCDC62	84660	broad.mit.edu	37	12	123276650	123276650	+	Missense_Mutation	SNP	G	G	T	rs375333901		TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr12:123276650G>T	ENST00000253079.6	+	6	1098	c.754G>T	c.(754-756)Gat>Tat	p.D252Y	CCDC62_ENST00000392440.2_Intron|CCDC62_ENST00000537566.1_Intron|CCDC62_ENST00000392441.4_Missense_Mutation_p.D252Y	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN	coiled-coil domain containing 62	252					cellular response to estradiol stimulus (GO:0071392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)	p.D252N(2)		breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)		TTGCCTGCACGATGAATTGCT	0.393																																						ENST00000253079.6																			2	Substitution - Missense(2)	p.D252N(2)	lung(2)	breast(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	20						c.(754-756)Gat>Tat		coiled-coil domain containing 62							103.0	99.0	100.0					12																	123276650		2203	4300	6503	SO:0001583	missense	84660					cytoplasm|nucleus		g.chr12:123276650G>T		CCDS9238.1	12q24.31	2009-08-18			ENSG00000130783	ENSG00000130783			30723	protein-coding gene	gene with protein product	"""cancer/testis antigen 109"""	613481				18563714, 19126643	Standard	NM_201435		Approved	TSP-NY, FLJ40344, CT109, ERAP75	uc001udc.3	Q6P9F0	OTTHUMG00000168764	ENST00000253079.6:c.754G>T	12.37:g.123276650G>T	ENSP00000253079:p.Asp252Tyr					CCDC62_ENST00000392440.2_Intron|CCDC62_ENST00000392441.4_Missense_Mutation_p.D252Y|CCDC62_ENST00000537566.1_Intron	p.D252Y	NM_201435.4	NP_958843.2	Q6P9F0	CCD62_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;6.51e-06)|Epithelial(86;2.65e-05)|BRCA - Breast invasive adenocarcinoma(302;0.206)	6	1098	+	all_neural(191;0.0837)|Medulloblastoma(191;0.163)		252					A8K8V1|B3KUP3|Q6ZVF2|Q86VJ0|Q9BYZ5	Missense_Mutation	SNP	ENST00000253079.6	37	c.754G>T	CCDS9238.1	.	.	.	.	.	.	.	.	.	.	G	18.37	3.608830	0.66558	.	.	ENSG00000130783	ENST00000253079;ENST00000392441	T;T	0.34472	1.37;1.36	5.11	5.11	0.69529	.	0.220251	0.33792	N	0.004556	T	0.57066	0.2028	M	0.62723	1.935	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.993;0.999	T	0.59225	-0.7494	10	0.72032	D	0.01	-23.1263	14.4063	0.67083	0.0:0.0:1.0:0.0	.	252;252	Q6P9F0-2;Q6P9F0	.;CCD62_HUMAN	Y	252	ENSP00000253079:D252Y;ENSP00000376236:D252Y	ENSP00000253079:D252Y	D	+	1	0	CCDC62	121842603	0.998000	0.40836	0.850000	0.33497	0.971000	0.66376	3.653000	0.54446	2.529000	0.85273	0.585000	0.79938	GAT		0.393	CCDC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400930.1	NM_032573		17	85	1	0	7.05477e-17	0.520397	7.78457e-17	17	85				
KCNAB3	9196	broad.mit.edu	37	17	7829388	7829388	+	Silent	SNP	G	G	A			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr17:7829388G>A	ENST00000303790.2	-	5	437	c.438C>T	c.(436-438)agC>agT	p.S146S	RP11-1099M24.7_ENST00000573621.1_3'UTR	NM_004732.3	NP_004723.2	O43448	KCAB3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 3	146					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	8		Prostate(122;0.157)				TCCAACCTTTGCTCTTGAGGA	0.478																																						ENST00000303790.2																			0				breast(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(1)	8						c.(436-438)agC>agT		potassium voltage-gated channel, shaker-related subfamily, beta member 3							135.0	122.0	126.0					17																	7829388		2203	4300	6503	SO:0001819	synonymous_variant	9196					cytoplasm|integral to membrane	oxidoreductase activity|potassium channel regulator activity|voltage-gated potassium channel activity	g.chr17:7829388G>A	AF016411	CCDS11124.1	17p13.1	2006-11-29			ENSG00000170049	ENSG00000170049		"""Potassium channels"", ""Aldo-keto reductases"""	6230	protein-coding gene	gene with protein product		604111				9857044	Standard	NM_004732		Approved	AKR6A9, KCNA3B	uc002gjm.2	O43448	OTTHUMG00000108170	ENST00000303790.2:c.438C>T	17.37:g.7829388G>A						RP11-1099M24.7_ENST00000573621.1_3'UTR	p.S146S	NM_004732.3	NP_004723.2	O43448	KCAB3_HUMAN			5	437	-		Prostate(122;0.157)	146					Q4VAW0	Silent	SNP	ENST00000303790.2	37	c.438C>T	CCDS11124.1																																																																																				0.478	KCNAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226974.1	NM_004732		11	118	0	0	0	0.387290	0	11	118				
LRSAM1	90678	broad.mit.edu	37	9	130224635	130224635	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr9:130224635C>T	ENST00000323301.4	+	8	1115	c.511C>T	c.(511-513)Cac>Tac	p.H171Y	LRSAM1_ENST00000373322.1_Missense_Mutation_p.H171Y|LRSAM1_ENST00000373324.4_Missense_Mutation_p.H171Y|LRSAM1_ENST00000300417.6_Missense_Mutation_p.H171Y	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	171					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						GATGCTGGCTCACGTTCGAAC	0.577																																						ENST00000323301.4																			0				central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						c.(511-513)Cac>Tac		leucine rich repeat and sterile alpha motif containing 1							159.0	127.0	138.0					9																	130224635		2203	4300	6503	SO:0001583	missense	90678				negative regulation of endocytosis|non-lytic virus budding|protein autoubiquitination|protein catabolic process|protein polyubiquitination|protein transport|ubiquitin-dependent endocytosis	cytoplasm|extracellular region|membrane part	hormone activity|ubiquitin-protein ligase activity|zinc ion binding	g.chr9:130224635C>T	AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"""Sterile alpha motif (SAM) domain containing"""	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.511C>T	9.37:g.130224635C>T	ENSP00000322937:p.His171Tyr					LRSAM1_ENST00000373324.4_Missense_Mutation_p.H171Y|LRSAM1_ENST00000300417.6_Missense_Mutation_p.H171Y|LRSAM1_ENST00000373322.1_Missense_Mutation_p.H171Y	p.H171Y	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN			8	1115	+			171					Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Missense_Mutation	SNP	ENST00000323301.4	37	c.511C>T	CCDS6873.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.665309	0.47677	.	.	ENSG00000148356	ENST00000300417;ENST00000373324;ENST00000323301;ENST00000373322	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	5.75	5.75	0.90469	.	0.221750	0.46758	D	0.000264	T	0.49558	0.1564	N	0.13043	0.29	0.41182	D	0.986245	D;D	0.69078	0.992;0.997	P;D	0.79108	0.811;0.992	T	0.40021	-0.9585	10	0.15499	T	0.54	-21.0994	15.4523	0.75282	0.0:1.0:0.0:0.0	.	171;171	Q6UWE0-2;Q6UWE0	.;LRSM1_HUMAN	Y	171	ENSP00000300417:H171Y;ENSP00000362421:H171Y;ENSP00000322937:H171Y;ENSP00000362419:H171Y	ENSP00000300417:H171Y	H	+	1	0	LRSAM1	129264456	0.956000	0.32656	0.702000	0.30337	0.997000	0.91878	2.438000	0.44837	2.725000	0.93324	0.655000	0.94253	CAC		0.577	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361		14	52	0	0	0	0.457914	0	14	52				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr16:90162513T>C	ENST00000564451.1	+	0	1866				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.N415N(2)									GCAACATGAATGACCTGGTGT	0.537																																						ENST00000567960.1																			2	Substitution - coding silent(2)	p.N415N(2)	prostate(1)|kidney(1)																																																0							g.chr16:90162513T>C			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162513T>C						TUBB8P7_ENST00000564451.1_RNA								0	1249	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		6	102	0	0	0	0.248553	0	6	102				
KRTAP4-6	81871	broad.mit.edu	37	17	39296599	39296599	+	Silent	SNP	T	T	C			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr17:39296599T>C	ENST00000345847.4	-	1	140	c.141A>G	c.(139-141)agA>agG	p.R47R		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	47	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						AGCACTGGGGTCTGCAGCAGC	0.682																																						ENST00000345847.4																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						c.(139-141)agA>agG		keratin associated protein 4-6																																				SO:0001819	synonymous_variant	81871					keratin filament		g.chr17:39296599T>C	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.141A>G	17.37:g.39296599T>C							p.R47R	NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN			1	140	-			47			29 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].		Q9BYR1	Silent	SNP	ENST00000345847.4	37	c.141A>G	CCDS54125.1																																																																																				0.682	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1			5	128	0	0	0	0.411799	0	5	128				
BMS1P20	96610	broad.mit.edu	37	22	22664115	22664115	+	RNA	SNP	A	A	T	rs376271028		TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr22:22664115A>T	ENST00000426066.1	+	0	638					NR_027293.1				BMS1 pseudogene 20																		TGTTTAATTCAGCCTTGGAAG	0.413																																						ENST00000426066.1																			0																																																			0							g.chr22:22664115A>T			22q11.22	2013-09-20			ENSG00000236850	ENSG00000236850			49153	pseudogene	pseudogene							Standard	XR_430414		Approved				OTTHUMG00000151046		22.37:g.22664115A>T								NR_027293.1						0	638	+									RNA	SNP	ENST00000426066.1	37																																																																																						0.413	BMS1P20-001	KNOWN	basic|readthrough_transcript	processed_transcript	processed_transcript	OTTHUMT00000473090.1			6	74	0	0	0	0.435327	0	6	74				
TSHR	7253	broad.mit.edu	37	14	81609809	81609809	+	Silent	SNP	C	C	A	rs372224556		TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr14:81609809C>A	ENST00000541158.2	+	11	1729	c.1407C>A	c.(1405-1407)ctC>ctA	p.L469L	TSHR_ENST00000298171.2_Silent_p.L469L|RP11-114N19.3_ENST00000557775.1_RNA			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	469					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	ACCTGCTCCTCATCGCCTCTG	0.537			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																															ENST00000541158.2			yes	Dom	yes		14	14q31	7253	Mis	thyroid stimulating hormone receptor	yes	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism	E		thyroid  adenoma	toxic thyroid adenoma		0				breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337						c.(1405-1407)ctC>ctA		thyroid stimulating hormone receptor	Thyrotropin Alfa(DB00024)						683.0	525.0	578.0					14																	81609809		2203	4300	6503	SO:0001819	synonymous_variant	7253				cell-cell signaling|positive regulation of cell proliferation	integral to plasma membrane	protein binding|thyroid-stimulating hormone receptor activity	g.chr14:81609809C>A	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.1407C>A	14.37:g.81609809C>A						TSHR_ENST00000298171.2_Silent_p.L469L|RP11-114N19.3_ENST00000557775.1_RNA	p.L469L			P16473	TSHR_HUMAN		BRCA - Breast invasive adenocarcinoma(234;0.0402)	11	1729	+			469					A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Silent	SNP	ENST00000541158.2	37	c.1407C>A	CCDS9872.1																																																																																				0.537	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369		42	69	1	0	1.38162e-09	0.840704	1.47373e-09	42	69				
QSER1	79832	broad.mit.edu	37	11	32953853	32953853	+	Missense_Mutation	SNP	T	T	G			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr11:32953853T>G	ENST00000399302.2	+	4	997	c.662T>G	c.(661-663)gTa>gGa	p.V221G	QSER1_ENST00000527788.1_Missense_Mutation_p.V221G	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN	glutamine and serine rich 1	221	Ser-rich.									breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48	Breast(20;0.158)					AATTCAAGTGTAGTTAATTTT	0.438																																						ENST00000399302.2																			0				breast(5)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	48						c.(661-663)gTa>gGa		glutamine and serine rich 1							61.0	57.0	58.0					11																	32953853		1882	4100	5982	SO:0001583	missense	79832							g.chr11:32953853T>G	AL834141	CCDS41631.1	11p13	2014-02-12			ENSG00000060749	ENSG00000060749			26154	protein-coding gene	gene with protein product							Standard	XM_006718323		Approved	FLJ21924	uc001mty.3	Q2KHR3		ENST00000399302.2:c.662T>G	11.37:g.32953853T>G	ENSP00000382241:p.Val221Gly					QSER1_ENST00000527788.1_Missense_Mutation_p.V221G	p.V221G	NM_001076786.1	NP_001070254.1	Q2KHR3	QSER1_HUMAN			4	997	+	Breast(20;0.158)		221			Ser-rich.		Q6ZU30|Q6ZUR5	Missense_Mutation	SNP	ENST00000399302.2	37	c.662T>G	CCDS41631.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.798916	0.31777	.	.	ENSG00000060749	ENST00000399302;ENST00000078652;ENST00000527788	T;T	0.23552	2.28;1.9	4.98	3.83	0.44106	.	0.499077	0.17421	N	0.174833	T	0.12732	0.0309	N	0.04880	-0.145	0.27417	N	0.954405	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.19943	-1.0290	10	0.23302	T	0.38	.	11.87	0.52515	0.0:0.0:0.468:0.532	.	221;221	Q2KHR3-2;Q2KHR3	.;QSER1_HUMAN	G	221	ENSP00000382241:V221G;ENSP00000432766:V221G	ENSP00000078652:V221G	V	+	2	0	QSER1	32910429	1.000000	0.71417	0.968000	0.41197	0.944000	0.59088	2.934000	0.48956	0.830000	0.34757	0.533000	0.62120	GTA		0.438	QSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388448.1	NM_024774		9	37	0	0	0	0.307466	0	9	37				
KRTAP4-6	81871	broad.mit.edu	37	17	39296600	39296600	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr17:39296600C>T	ENST00000345847.4	-	1	139	c.140G>A	c.(139-141)aGa>aAa	p.R47K		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	47	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)		p.R47K(1)		endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GCACTGGGGTCTGCAGCAGCT	0.682																																						ENST00000345847.4																			1	Substitution - Missense(1)	p.R47K(1)	prostate(1)	endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						c.(139-141)aGa>aAa		keratin associated protein 4-6																																				SO:0001583	missense	81871					keratin filament		g.chr17:39296600C>T	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.140G>A	17.37:g.39296600C>T	ENSP00000328270:p.Arg47Lys						p.R47K	NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN			1	139	-			47			29 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].		Q9BYR1	Missense_Mutation	SNP	ENST00000345847.4	37	c.140G>A	CCDS54125.1	.	.	.	.	.	.	.	.	.	.	.	6.616	0.482131	0.12581	.	.	ENSG00000198090	ENST00000345847	T	0.00590	6.36	5.01	2.62	0.31277	.	2.335370	0.02364	N	0.077186	T	0.00875	0.0029	M	0.67625	2.065	0.09310	N	1	.	.	.	.	.	.	T	0.62435	-0.6855	8	0.05959	T	0.93	.	4.9322	0.13923	0.1734:0.6205:0.0:0.2061	.	.	.	.	K	47	ENSP00000328270:R47K	ENSP00000328270:R47K	R	-	2	0	KRTAP4-6	36550126	0.019000	0.18553	0.192000	0.23308	0.098000	0.18820	1.906000	0.39887	1.096000	0.41439	0.650000	0.86243	AGA		0.682	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1			5	128	0	0	0	0.411799	0	5	128				
SDHAP1	255812	broad.mit.edu	37	3	195711423	195711423	+	RNA	SNP	A	A	G	rs201502468		TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr3:195711423A>G	ENST00000427841.1	-	0	524					NR_003264.2				succinate dehydrogenase complex, subunit A, flavoprotein pseudogene 1																		CTCTTGTACTAGAAACAGACC	0.552																																					Ovarian(67;1158 1227 12109 20189 43170)	ENST00000427841.1																			0																																																			0							g.chr3:195711423A>G	BC071730		3q29	2009-12-02	2006-11-21	2009-12-02	ENSG00000185485	ENSG00000185485			32455	pseudogene	pseudogene			"""succinate dehydrogenase complex, subunit A, flavoprotein-like 1"""	SDHAL1, SDHALP1			Standard	NR_003264		Approved		uc003fvy.3		OTTHUMG00000155716		3.37:g.195711423A>G								NR_003264.2						0	524	-									RNA	SNP	ENST00000427841.1	37																																																																																						0.552	SDHAP1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341367.1			3	37	0	0	0	0.150653	0	3	37				
BTAF1	9044	broad.mit.edu	37	10	93748982	93748982	+	Silent	SNP	T	T	C			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr10:93748982T>C	ENST00000265990.6	+	20	2807	c.2499T>C	c.(2497-2499)agT>agC	p.S833S	BTAF1_ENST00000471217.1_3'UTR	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN	BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa	833					negative regulation of chromatin binding (GO:0035562)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59		Colorectal(252;0.0846)				AGTTAGATAGTAAACGACAGC	0.378																																						ENST00000265990.6																			0				central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(17)|ovary(1)|prostate(1)|skin(2)|urinary_tract(6)	59						c.(2497-2499)agT>agC		BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170kDa							77.0	75.0	76.0					10																	93748982		2203	4300	6503	SO:0001819	synonymous_variant	9044				negative regulation of transcription, DNA-dependent	nucleus	ATP binding|DNA binding|helicase activity|sequence-specific DNA binding transcription factor activity	g.chr10:93748982T>C	AJ001017	CCDS7419.1	10q22-q23	2013-05-01	2013-05-01		ENSG00000095564	ENSG00000095564			17307	protein-coding gene	gene with protein product	"""Mot1 homolog (S. cerevisiae)"""	605191	"""BTAF1 RNA polymerase II, B-TFIID transcription factor-associated, 170 kD (Mot1 homolog, S. cerevisiae)"""			9342322, 9488487	Standard	NM_003972		Approved	TAFII170, TAF172, MOT1, TAF-172, TAF(II)170	uc001khr.3	O14981	OTTHUMG00000018752	ENST00000265990.6:c.2499T>C	10.37:g.93748982T>C						BTAF1_ENST00000471217.1_3'UTR	p.S833S	NM_003972.2	NP_003963.1	O14981	BTAF1_HUMAN			20	2807	+		Colorectal(252;0.0846)	833					B4E0W6|O43578	Silent	SNP	ENST00000265990.6	37	c.2499T>C	CCDS7419.1																																																																																				0.378	BTAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049380.4	NM_003972		23	44	0	0	0	0.639603	0	23	44				
GPR112	139378	broad.mit.edu	37	X	135427194	135427194	+	Silent	SNP	C	C	T			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chrX:135427194C>T	ENST00000394143.1	+	6	1620	c.1329C>T	c.(1327-1329)gcC>gcT	p.A443A	GPR112_ENST00000287534.4_Silent_p.A380A|GPR112_ENST00000394141.1_Silent_p.A238A|GPR112_ENST00000412101.1_Silent_p.A238A|GPR112_ENST00000370652.1_Silent_p.A443A	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN	G protein-coupled receptor 112	443					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199	Acute lymphoblastic leukemia(192;0.000127)					CTACAGCTGCCGGAACTGTAC	0.478																																						ENST00000394143.1																			0				NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(33)|lung(97)|ovary(5)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(1)|urinary_tract(2)	199						c.(1327-1329)gcC>gcT		G protein-coupled receptor 112							79.0	72.0	74.0					X																	135427194		2203	4300	6503	SO:0001819	synonymous_variant	139378				neuropeptide signaling pathway	integral to membrane|plasma membrane	G-protein coupled receptor activity	g.chrX:135427194C>T	AY140954	CCDS35409.1	Xq26.3	2014-08-08			ENSG00000156920	ENSG00000156920		"""-"", ""GPCR / Class B : Orphans"""	18992	protein-coding gene	gene with protein product						12435584	Standard	XM_005262367		Approved	RP1-299I16, PGR17	uc004ezu.1	Q8IZF6	OTTHUMG00000022508	ENST00000394143.1:c.1329C>T	X.37:g.135427194C>T						GPR112_ENST00000412101.1_Silent_p.A238A|GPR112_ENST00000394141.1_Silent_p.A238A|GPR112_ENST00000370652.1_Silent_p.A443A|GPR112_ENST00000287534.4_Silent_p.A380A	p.A443A	NM_153834.3	NP_722576.3	Q8IZF6	GP112_HUMAN			6	1620	+	Acute lymphoblastic leukemia(192;0.000127)		443					A2A2J1|A2A2J2|Q5EGP2|Q86SM6	Silent	SNP	ENST00000394143.1	37	c.1329C>T	CCDS35409.1																																																																																				0.478	GPR112-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000286639.1			23	66	0	0	0	0.608945	0	23	66				
C5orf42	65250	broad.mit.edu	37	5	37176053	37176053	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr5:37176053G>A	ENST00000508244.1	-	30	6029	c.5936C>T	c.(5935-5937)aCt>aTt	p.T1979I	C5orf42_ENST00000425232.2_Missense_Mutation_p.T1979I|C5orf42_ENST00000274258.7_Missense_Mutation_p.T859I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1979						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			TGATTGAGGAGTGGTATGCCC	0.333																																						ENST00000274258.7																			0				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79						c.(2575-2577)aCt>aTt		chromosome 5 open reading frame 42							207.0	220.0	216.0					5																	37176053		2203	4300	6503	SO:0001583	missense	65250							g.chr5:37176053G>A		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5936C>T	5.37:g.37176053G>A	ENSP00000421690:p.Thr1979Ile					C5orf42_ENST00000508244.1_Missense_Mutation_p.T1979I|C5orf42_ENST00000425232.2_Missense_Mutation_p.T1979I	p.T859I			E9PH94	E9PH94_HUMAN	COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)		31	6163	-	all_lung(31;0.000616)		1979					A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	c.2576C>T	CCDS34146.2	.	.	.	.	.	.	.	.	.	.	G	0.764	-0.768349	0.02974	.	.	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.20463	2.07;2.07;2.08;2.07	5.25	-1.26	0.09376	.	1.673320	0.03314	N	0.190925	T	0.13030	0.0316	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.01281	0.0;0.0	T	0.28396	-1.0045	10	0.09338	T	0.73	.	9.2095	0.37309	0.6025:0.0:0.3975:0.0	.	1979;859	E9PH94;Q9H799	.;CE042_HUMAN	I	1979;1979;859;1027;859	ENSP00000421690:T1979I;ENSP00000389014:T1979I;ENSP00000274258:T859I;ENSP00000424223:T1027I	ENSP00000274258:T859I	T	-	2	0	C5orf42	37211810	0.065000	0.20965	0.000000	0.03702	0.144000	0.21451	0.471000	0.22100	-0.362000	0.08113	-0.150000	0.13652	ACT		0.333	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073		8	159	0	0	0	0.278610	0	8	159				
SH3KBP1	30011	broad.mit.edu	37	X	19560130	19560130	+	Missense_Mutation	SNP	G	G	A	rs369126109		TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chrX:19560130G>A	ENST00000397821.3	-	16	2095	c.1805C>T	c.(1804-1806)gCg>gTg	p.A602V	SH3KBP1_ENST00000379698.4_Missense_Mutation_p.A565V|SH3KBP1_ENST00000541422.1_Missense_Mutation_p.A341V|SH3KBP1_ENST00000379716.1_Missense_Mutation_p.A364V	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN	SH3-domain kinase binding protein 1	602					apoptotic process (GO:0006915)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|cytoskeleton organization (GO:0007010)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|regulation of cell shape (GO:0008360)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						GCTGCTGGCCGCAGGCTCCAT	0.627																																						ENST00000397821.3																			0				breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|skin(4)	29						c.(1804-1806)gCg>gTg		SH3-domain kinase binding protein 1		G	VAL/ALA,VAL/ALA,VAL/ALA	0,3835		0,0,1632,571	79.0	77.0	78.0		1694,1091,1805	-6.8	0.0	X		78	1,6727		0,1,2427,1872	no	missense,missense,missense	SH3KBP1	NM_001024666.2,NM_001184960.1,NM_031892.2	64,64,64	0,1,4059,2443	AA,AG,GG,G		0.0149,0.0,0.0095	benign,benign,benign	565/629,364/428,602/666	19560130	1,10562	2203	4300	6503	SO:0001583	missense	30011				apoptosis|cell-cell signaling|endocytosis|epidermal growth factor receptor signaling pathway|negative regulation of epidermal growth factor receptor signaling pathway	cytoplasmic vesicle membrane|cytoskeleton|cytosol|focal adhesion|nucleus|synapse|synaptosome	SH3 domain binding	g.chrX:19560130G>A	AF230904	CCDS14193.1, CCDS35213.1, CCDS55383.1	Xp22.1-p21.3	2008-02-05			ENSG00000147010	ENSG00000147010			13867	protein-coding gene	gene with protein product		300374				8889549, 7566098	Standard	NM_031892		Approved	CIN85	uc004czm.3	Q96B97	OTTHUMG00000021227	ENST00000397821.3:c.1805C>T	X.37:g.19560130G>A	ENSP00000380921:p.Ala602Val					SH3KBP1_ENST00000541422.1_Missense_Mutation_p.A341V|SH3KBP1_ENST00000379698.4_Missense_Mutation_p.A565V|SH3KBP1_ENST00000379716.1_Missense_Mutation_p.A364V	p.A602V	NM_031892.2	NP_114098.1	Q96B97	SH3K1_HUMAN			16	2095	-			602					B7Z1D5|Q5JPT4|Q5JPT5|Q8IWX6|Q8IX98|Q96RN4|Q9NYR0	Missense_Mutation	SNP	ENST00000397821.3	37	c.1805C>T	CCDS14193.1	.	.	.	.	.	.	.	.	.	.	G	12.73	2.024828	0.35701	0.0	1.49E-4	ENSG00000147010	ENST00000379702;ENST00000397821;ENST00000379716;ENST00000379698;ENST00000541422;ENST00000379726	T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41	5.54	-6.8	0.01709	.	2.813160	0.00921	N	0.002593	T	0.24699	0.0599	L	0.36672	1.1	0.09310	N	1	B;B;B	0.33073	0.226;0.396;0.396	B;B;B	0.25614	0.041;0.038;0.062	T	0.10636	-1.0621	10	0.30078	T	0.28	3.0863	17.2325	0.86988	0.8718:0.0:0.1282:0.0	.	364;602;565	Q5JPT4;Q96B97;Q5JPT5	.;SH3K1_HUMAN;.	V	587;602;364;565;341;582	ENSP00000380921:A602V;ENSP00000369039:A364V;ENSP00000369020:A565V;ENSP00000442499:A341V;ENSP00000369049:A582V	ENSP00000369020:A565V	A	-	2	0	SH3KBP1	19470051	0.000000	0.05858	0.005000	0.12908	0.995000	0.86356	0.034000	0.13776	-1.809000	0.01232	0.529000	0.55759	GCG		0.627	SH3KBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055992.1	NM_031892		43	75	0	0	0	0.859065	0	43	75				
SYT5	6861	broad.mit.edu	37	19	55687427	55687427	+	Silent	SNP	C	C	T	rs11668445	byFrequency	TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr19:55687427C>T	ENST00000354308.3	-	4	687	c.318G>A	c.(316-318)aaG>aaA	p.K106K	SYT5_ENST00000590851.1_Silent_p.K103K|SYT5_ENST00000537500.1_Silent_p.K106K|CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000592935.1_5'Flank	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	synaptotagmin V	106					calcium ion-dependent exocytosis (GO:0017156)|energy reserve metabolic process (GO:0006112)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|dense core granule (GO:0031045)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|metal ion binding (GO:0046872)|transporter activity (GO:0005215)			kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)		CTAGCTCATGCTTGTCTGCCA	0.602													c|||	17	0.00339457	0.0015	0.0072	5008	,	,		21078	0.0		0.0089	False		,,,				2504	0.001					ENST00000354308.3																			0				kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	18						c.(316-318)aaG>aaA		synaptotagmin V		C		8,4398	14.3+/-33.2	0,8,2195	141.0	136.0	138.0		318	3.4	1.0	19	dbSNP_120	138	92,8508	51.5+/-111.7	0,92,4208	no	coding-synonymous	SYT5	NM_003180.2		0,100,6403	TT,TC,CC		1.0698,0.1816,0.7689		106/387	55687427	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	6861				energy reserve metabolic process|regulation of insulin secretion|synaptic transmission	cell junction|integral to membrane|recycling endosome membrane|synaptic vesicle membrane	metal ion binding|transporter activity	g.chr19:55687427C>T	X96783	CCDS12919.1, CCDS74455.1	19q13.42	2014-07-02			ENSG00000129990	ENSG00000129990		"""Synaptotagmins"""	11513	protein-coding gene	gene with protein product	"""synaptotagmin 5"""	600782				9177789	Standard	XM_006723338		Approved		uc002qjn.1	O00445	OTTHUMG00000180669	ENST00000354308.3:c.318G>A	19.37:g.55687427C>T						CTD-2587H24.5_ENST00000591665.1_RNA|SYT5_ENST00000590851.1_Silent_p.K103K|SYT5_ENST00000537500.1_Silent_p.K106K	p.K106K	NM_003180.2	NP_003171.2	O00445	SYT5_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0452)	4	687	-			106					B3KWJ8|B7Z300|Q86X72	Silent	SNP	ENST00000354308.3	37	c.318G>A	CCDS12919.1																																																																																				0.602	SYT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452501.1	NM_003180		6	126	0	0	0	0.248553	0	6	126				
EDAR	10913	broad.mit.edu	37	2	109527373	109527373	+	Intron	SNP	A	A	G	rs587776352|rs260630	byFrequency	TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr2:109527373A>G	ENST00000258443.2	-	7	1086				EDAR_ENST00000376651.1_Missense_Mutation_p.F229L|EDAR_ENST00000409271.1_Missense_Mutation_p.F229L	NM_022336.3	NP_071731.1	Q9UNE0	EDAR_HUMAN	ectodysplasin A receptor						apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|epidermis development (GO:0008544)|hair follicle development (GO:0001942)|odontogenesis of dentin-containing tooth (GO:0042475)|pigmentation (GO:0043473)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|salivary gland cavitation (GO:0060662)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						GAGTCCAGGAAGCAGGGCACC	0.627													G|||	4645	0.927516	0.8979	0.9308	5008	,	,		18246	0.994		0.9085	False		,,,				2504	0.9162					ENST00000409271.1																			0				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	16						c.(685-687)Ttc>Ctc		ectodysplasin A receptor		G		4019,387	193.3+/-218.5	1835,349,19	65.0	62.0	63.0			-3.7	0.0	2	dbSNP_79	63	7759,841	193.1+/-238.9	3496,767,37	no	intron	EDAR	NM_022336.3		5331,1116,56	GG,GA,AA		9.7791,8.7835,9.4418			109527373	11778,1228	2203	4300	6503	SO:0001627	intron_variant	10913				apoptosis|cell differentiation	integral to membrane	protein binding|transmembrane receptor activity	g.chr2:109527373A>G	AF130988	CCDS2081.1	2q13	2013-05-22	2004-08-09		ENSG00000135960	ENSG00000135960		"""Tumor necrosis factor receptor superfamily"""	2895	protein-coding gene	gene with protein product		604095	"""ectodysplasin 1, anhidrotic receptor"""	ED3, DL		10431241, 9375732	Standard	NM_022336		Approved	ED5, EDA3, Edar, ED1R, EDA1R	uc002teq.4	Q9UNE0	OTTHUMG00000130982	ENST00000258443.2:c.655+29T>C	2.37:g.109527373A>G						EDAR_ENST00000258443.2_Intron|EDAR_ENST00000376651.1_Missense_Mutation_p.F229L	p.F229L			Q9UNE0	EDAR_HUMAN			8	1128	-			217					B2R9H2|B4DLC5|D3DX74|E9PC98|Q52LL5|Q9UND9	Missense_Mutation	SNP	ENST00000258443.2	37	c.685T>C	CCDS2081.1	2042	0.934981684981685	438	0.8902439024390244	340	0.9392265193370166	571	0.9982517482517482	693	0.9142480211081794	G	4.499	0.092523	0.08632	0.912165	0.902209	ENSG00000135960	ENST00000409271;ENST00000376651	D;D	0.89415	-2.51;-2.51	5.11	-3.69	0.04450	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28713	-1.0035	7	0.27785	T	0.31	.	3.4135	0.07366	0.5629:0.123:0.1897:0.1244	rs260630;rs262074;rs59696490	229	E9PC98	.	L	229	ENSP00000386371:F229L;ENSP00000365839:F229L	ENSP00000365839:F229L	F	-	1	0	EDAR	108893805	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.900000	0.04097	-1.281000	0.02399	-0.215000	0.12644	TTC		0.627	EDAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253595.1			3	30	0	0	0	0.150653	0	3	30				
LOC645752	645752	broad.mit.edu	37	15	78211648	78211648	+	lincRNA	SNP	A	A	G	rs577974396	byFrequency	TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr15:78211648A>G	ENST00000565869.1	+	0	111				RP11-114H24.2_ENST00000567226.1_RNA|RN7SL214P_ENST00000487317.2_RNA																							CGCCAGGGATAGGGGCTCAGC	0.522																																						ENST00000565869.1																			0																																																			0							g.chr15:78211648A>G																													15.37:g.78211648A>G						RP11-114H24.2_ENST00000567226.1_RNA								0	111	+									RNA	SNP	ENST00000565869.1	37																																																																																						0.522	RP11-114H24.7-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000421587.1			4	76	0	0	0	0.184627	0	4	76				
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	G	A			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr9:20414340G>A	ENST00000380338.4	-	5	790	c.504C>T	c.(502-504)agC>agT	p.S168S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	168	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S168S(5)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctgctactgctgc	0.537			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		5	Substitution - coding silent(5)	p.S168S(5)	lung(2)|urinary_tract(1)|endometrium(1)|kidney(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(502-504)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							9.0	16.0	13.0					9																	20414340		1646	3412	5058	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414340G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.504C>T	9.37:g.20414340G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000355930.6_5'UTR	p.S168S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	790	-			168			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.504C>T	CCDS6494.1																																																																																				0.537	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		6	56	0	0	0	0.248553	0	6	56				
GOLGB1	2804	broad.mit.edu	37	3	121415620	121415620	+	Silent	SNP	G	G	A			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr3:121415620G>A	ENST00000340645.5	-	13	3860	c.3735C>T	c.(3733-3735)gaC>gaT	p.D1245D	GOLGB1_ENST00000393667.3_Silent_p.D1250D	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	1245					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)	p.D1245D(1)		NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		GGAGTTTTCCGTCTATGGATT	0.438																																						ENST00000393667.3																			1	Substitution - coding silent(1)	p.D1245D(1)	central_nervous_system(1)	NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119						c.(3748-3750)gaC>gaT		golgin B1							204.0	184.0	191.0					3																	121415620		2203	4300	6503	SO:0001819	synonymous_variant	2804				Golgi organization	ER-Golgi intermediate compartment|Golgi membrane|Golgi stack|integral to membrane	protein binding	g.chr3:121415620G>A	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.3735C>T	3.37:g.121415620G>A						GOLGB1_ENST00000340645.5_Silent_p.D1245D	p.D1250D	NM_001256486.1	NP_001243415.1	Q14789	GOGB1_HUMAN		GBM - Glioblastoma multiforme(114;0.0989)	13	3860	-			1245					B2ZZ91|D3DN92|E7EP74|Q14398	Silent	SNP	ENST00000340645.5	37	c.3750C>T	CCDS3004.1																																																																																				0.438	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487		21	72	0	0	0	0.592651	0	21	72				
HNRNPC	3183	broad.mit.edu	37	14	21679622	21679623	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr14:21679622_21679623delAG	ENST00000320084.7	-	7	1018_1019	c.779_780delCT	c.(778-780)tctfs	p.S260fs	HNRNPC_ENST00000553753.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000430246.2_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000556513.1_Intron|HNRNPC_ENST00000554455.1_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000556142.1_Intron|HNRNPC_ENST00000420743.2_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000556897.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000557201.1_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000336053.6_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000556628.1_Frame_Shift_Del_p.S180fs|HNRNPC_ENST00000554969.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000553300.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000449098.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000555914.1_Frame_Shift_Del_p.S246fs|HNRNPC_ENST00000555883.1_Frame_Shift_Del_p.S204fs|HNRNPC_ENST00000555309.1_Frame_Shift_Del_p.S259fs	NM_001077442.1	NP_001070910.1	P07910	HNRPC_HUMAN	heterogeneous nuclear ribonucleoprotein C (C1/C2)	260	Asp/Glu-rich (acidic).				3'-UTR-mediated mRNA stabilization (GO:0070935)|ATP-dependent chromatin remodeling (GO:0043044)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|spliceosomal complex (GO:0005681)	identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleosomal DNA binding (GO:0031492)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)			breast(1)|liver(1)|lung(6)|skin(1)	9	all_cancers(95;0.00176)		Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)		CCTCCTCAGCAGAGTCATCTGC	0.51																																					NSCLC(108;607 2244 12726 38757)	ENST00000430246.2																			0				breast(1)|liver(1)|lung(6)|skin(1)	9						c.(739-741)tfs		heterogeneous nuclear ribonucleoprotein C (C1/C2)																																				SO:0001589	frameshift_variant	3183					catalytic step 2 spliceosome|nucleoplasm	identical protein binding|nucleotide binding|RNA binding	g.chr14:21679622_21679623delAG		CCDS41915.1, CCDS45079.1	14q11.2	2013-06-12		2007-08-16	ENSG00000092199	ENSG00000092199		"""RNA binding motif (RRM) containing"""	5035	protein-coding gene	gene with protein product		164020		HNRPC		3457372	Standard	NM_031314		Approved	hnRNPC	uc001waa.3	P07910	OTTHUMG00000170757	ENST00000320084.7:c.779_780delCT	14.37:g.21679624_21679625delAG	ENSP00000319690:p.Ser260fs					HNRNPC_ENST00000557201.1_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000449098.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000556897.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000556628.1_Frame_Shift_Del_p.S180fs|HNRNPC_ENST00000556513.1_Intron|HNRNPC_ENST00000556142.1_Intron|HNRNPC_ENST00000555883.1_Frame_Shift_Del_p.S204fs|HNRNPC_ENST00000555914.1_Frame_Shift_Del_p.S246fs|HNRNPC_ENST00000555309.1_Frame_Shift_Del_p.S259fs|HNRNPC_ENST00000553300.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000554455.1_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000320084.7_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000554969.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000420743.2_Frame_Shift_Del_p.S260fs|HNRNPC_ENST00000553753.1_Frame_Shift_Del_p.S247fs|HNRNPC_ENST00000336053.6_Frame_Shift_Del_p.S247fs	p.S247fs			P07910	HNRPC_HUMAN	Epithelial(56;1.08e-06)|all cancers(55;8.95e-06)	GBM - Glioblastoma multiforme(265;0.00783)	7	3691_3692	-	all_cancers(95;0.00176)		260			Asp/Glu-rich (acidic).		D3DS19|D3DS22|P22628|Q53EX2|Q59FD3|Q5FWE8|Q86SF8|Q86U45|Q96HK7|Q96HM4|Q96IY5|Q9BTS3	Frame_Shift_Del	DEL	ENST00000320084.7	37	c.740_741delCT	CCDS41915.1																																																																																				0.510	HNRNPC-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410235.1			25	69						25	69	---	---	---	---
PPM1E	22843	broad.mit.edu	37	17	56833644	56833646	+	In_Frame_Del	DEL	GAG	GAG	-	rs544816257		TCGA-ET-A3DS-01A-11D-A19J-08	TCGA-ET-A3DS-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	e02fad9d-940c-45dc-829b-39c38d2f6f76	0ed6611d-ccc7-4403-a1b0-6e56cd147e8f	g.chr17:56833644_56833646delGAG	ENST00000308249.2	+	1	415_417	c.286_288delGAG	c.(286-288)gagdel	p.E100del		NM_014906.4	NP_055721.3	Q96MI6	PPM1M_HUMAN	protein phosphatase, Mg2+/Mn2+ dependent, 1E	0	PP2C-like.				protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|manganese ion binding (GO:0030145)			biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33	Medulloblastoma(34;0.127)|all_neural(34;0.237)		BRCA - Breast invasive adenocarcinoma(1;5.76e-11)			ggttgagggtgaggaggaggagg	0.783																																						ENST00000308249.2																			0				biliary_tract(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)	33						c.(286-288)del		protein phosphatase, Mg2+/Mn2+ dependent, 1E				173,3033		18,137,1448						0.3	0.0			5	371,5843		38,295,2774	no	coding	PPM1E	NM_014906.3		56,432,4222	A1A1,A1R,RR		5.9704,5.3961,5.7749				544,8876				SO:0001651	inframe_deletion	22843				protein dephosphorylation	cytoplasm|nucleolus|protein serine/threonine phosphatase complex	metal ion binding|protein serine/threonine phosphatase activity	g.chr17:56833644_56833646delGAG	AB028995	CCDS11613.1	17q24.2	2012-04-17	2010-03-05		ENSG00000175175	ENSG00000175175		"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	19322	protein-coding gene	gene with protein product	"""partner of PIX 1"", ""nuclear calmodulin-dependent protein kinase phosphatase"""		"""protein phosphatase 1E (PP2C domain containing)"""			11864573, 10470851	Standard	NR_048561		Approved	POPX1, KIAA1072, PP2CH, CaMKP-N	uc002iwx.4	Q8WY54		ENST00000308249.2:c.286_288delGAG	17.37:g.56833653_56833655delGAG	ENSP00000312411:p.Glu100del						p.E100del	NM_014906.4	NP_055721.3	Q8WY54	PPM1E_HUMAN	BRCA - Breast invasive adenocarcinoma(1;5.76e-11)		1	415_417	+	Medulloblastoma(34;0.127)|all_neural(34;0.237)		100			Glu-rich.|Pro-rich.		Q8N8J9|Q96DB8	In_Frame_Del	DEL	ENST00000308249.2	37	c.286_288delGAG	CCDS11613.1																																																																																				0.783	PPM1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445458.1	NM_014906		2	4						2	4	---	---	---	---
