#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
RABGGTA	5875	broad.mit.edu	37	14	24738839	24738839	+	Missense_Mutation	SNP	C	C	A			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr14:24738839C>A	ENST00000399409.3	-	5	972	c.489G>T	c.(487-489)gaG>gaT	p.E163D	RABGGTA_ENST00000216840.6_Missense_Mutation_p.E163D|RABGGTA_ENST00000560777.1_5'UTR|RABGGTA_ENST00000559586.1_5'UTR	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN	Rab geranylgeranyltransferase, alpha subunit	163					cellular protein modification process (GO:0006464)|protein geranylgeranylation (GO:0018344)|visual perception (GO:0007601)	Rab-protein geranylgeranyltransferase complex (GO:0005968)	Rab geranylgeranyltransferase activity (GO:0004663)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12				GBM - Glioblastoma multiforme(265;0.0184)		TGAAGGCTAGCTCTTCTGCAG	0.592																																						ENST00000399409.3																			0				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)	12						c.(487-489)gaG>gaT		Rab geranylgeranyltransferase, alpha subunit							52.0	62.0	58.0					14																	24738839		2087	4201	6288	SO:0001583	missense	5875				visual perception		Rab geranylgeranyltransferase activity|zinc ion binding	g.chr14:24738839C>A		CCDS45088.1	14q11.2	2011-06-27				ENSG00000100949		"""Prenyltransferase alpha subunit repeat containing"""	9795	protein-coding gene	gene with protein product	"""protein prenyltransferase alpha subunit repeat containing 3"""	601905				8954794	Standard	NM_182836		Approved	PTAR3	uc001wog.4	Q92696		ENST00000399409.3:c.489G>T	14.37:g.24738839C>A	ENSP00000382341:p.Glu163Asp					RABGGTA_ENST00000216840.6_Missense_Mutation_p.E163D|RABGGTA_ENST00000560777.1_5'UTR|RABGGTA_ENST00000559586.1_5'UTR	p.E163D	NM_004581.5	NP_004572.3	Q92696	PGTA_HUMAN		GBM - Glioblastoma multiforme(265;0.0184)	5	972	-			163					A8K5N2|D3DS69	Missense_Mutation	SNP	ENST00000399409.3	37	c.489G>T	CCDS45088.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.934463	0.73442	.	.	ENSG00000100949	ENST00000216840;ENST00000399409;ENST00000543002	T;T	0.58506	0.33;0.33	5.4	3.4	0.38934	Protein prenyltransferase (1);	0.000000	0.85682	D	0.000000	T	0.77711	0.4171	M	0.92784	3.345	0.80722	D	1	D	0.65815	0.995	D	0.71184	0.972	T	0.77819	-0.2446	10	0.72032	D	0.01	-15.1651	7.9954	0.30265	0.0:0.7003:0.0:0.2997	.	163	Q92696	PGTA_HUMAN	D	163;163;126	ENSP00000216840:E163D;ENSP00000382341:E163D	ENSP00000216840:E163D	E	-	3	2	RABGGTA	23808679	0.998000	0.40836	0.941000	0.38009	0.991000	0.79684	0.530000	0.23036	0.505000	0.28104	0.561000	0.74099	GAG		0.592	RABGGTA-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415308.5	NM_182836		3	52	1	0	1	1	1	3	52				
SPTB	6710	broad.mit.edu	37	14	65260383	65260383	+	Silent	SNP	G	G	C			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr14:65260383G>C	ENST00000389721.5	-	13	2030	c.1998C>G	c.(1996-1998)ggC>ggG	p.G666G	SPTB_ENST00000389722.3_Silent_p.G666G|SPTB_ENST00000556626.1_Silent_p.G666G|SPTB_ENST00000542895.1_Silent_p.G666G|SPTB_ENST00000389720.3_Silent_p.G666G	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	666					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		TCAGGTCTTTGCCATAGTCCA	0.537																																						ENST00000389722.3																			0				breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106						c.(1996-1998)ggC>ggG		spectrin, beta, erythrocytic							122.0	88.0	100.0					14																	65260383		2203	4300	6503	SO:0001819	synonymous_variant	6710				actin filament capping|axon guidance	cell surface|cytosol|intrinsic to internal side of plasma membrane|protein complex|spectrin|spectrin-associated cytoskeleton	actin filament binding|structural constituent of cytoskeleton	g.chr14:65260383G>C		CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.1998C>G	14.37:g.65260383G>C						SPTB_ENST00000389720.3_Silent_p.G666G|SPTB_ENST00000389721.5_Silent_p.G666G|SPTB_ENST00000556626.1_Silent_p.G666G|SPTB_ENST00000542895.1_Silent_p.G666G	p.G666G	NM_001024858.2	NP_001020029.1	P11277	SPTB1_HUMAN		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)	13	2051	-		all_lung(585;4.15e-09)	666					Q15510|Q15519	Silent	SNP	ENST00000389721.5	37	c.1998C>G	CCDS32100.1																																																																																				0.537	SPTB-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000414080.1			3	41	0	0	0	1	0	3	41				
CHEK2P2	646096	broad.mit.edu	37	15	20496770	20496770	+	RNA	SNP	T	T	C	rs3865047		TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr15:20496770T>C	ENST00000555186.1	+	0	823					NR_038836.1				checkpoint kinase 2 pseudogene 2																		TTATAGTGTGTATTTTAATTA	0.353																																						ENST00000555186.1																			0																																																			646096							g.chr15:20496770T>C			15q11.1	2011-11-11			ENSG00000259156	ENSG00000259156			43578	pseudogene	pseudogene							Standard	NR_038836		Approved		uc001ytf.1		OTTHUMG00000171660		15.37:g.20496770T>C								NR_038836.1						0	823	+									RNA	SNP	ENST00000555186.1	37																																																																																						0.353	CHEK2P2-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000414654.1	NR_038836		6	51	0	0	0	1	0	6	51				
CEMIP	57214	broad.mit.edu	37	15	81224299	81224299	+	Silent	SNP	C	C	T	rs375813681		TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr15:81224299C>T	ENST00000394685.3	+	22	3131	c.2712C>T	c.(2710-2712)agC>agT	p.S904S	KIAA1199_ENST00000356249.5_Silent_p.S904S|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000220244.3_Silent_p.S904S			Q8WUJ3	CEMIP_HUMAN		904					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						GGCACACCAGCGCCCTGGCCT	0.557																																						ENST00000394685.3																			0				breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						c.(2710-2712)agC>agT		KIAA1199		C		0,4406		0,0,2203	87.0	98.0	94.0		2712	-3.5	1.0	15		94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1199	NM_018689.1		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		904/1362	81224299	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	57214							g.chr15:81224299C>T																												ENST00000394685.3:c.2712C>T	15.37:g.81224299C>T						KIAA1199_ENST00000356249.5_Silent_p.S904S|KIAA1199_ENST00000220244.3_Silent_p.S904S|RP11-351M8.2_ENST00000560873.1_RNA	p.S904S			Q8WUJ3	K1199_HUMAN			22	3131	+			904					Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	c.2712C>T	CCDS10315.1																																																																																				0.557	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1			14	95	0	0	0	1	0	14	95				
CAPN9	10753	broad.mit.edu	37	1	230914848	230914848	+	Silent	SNP	C	C	G			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr1:230914848C>G	ENST00000271971.2	+	9	1196	c.1083C>G	c.(1081-1083)ggC>ggG	p.G361G	RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000354537.1_Silent_p.G335G|CAPN9_ENST00000366666.2_Silent_p.G298G|RP11-99J16__A.2_ENST00000412344.1_RNA	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	361	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GGGTTCGCGGCTCCACGGCTG	0.582																																						ENST00000354537.1																			0				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25						c.(1003-1005)ggC>ggG		calpain 9							71.0	65.0	67.0					1																	230914848		2203	4300	6503	SO:0001819	synonymous_variant	10753				digestion|proteolysis	intracellular	calcium ion binding|calcium-dependent cysteine-type endopeptidase activity	g.chr1:230914848C>G	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1083C>G	1.37:g.230914848C>G						RP11-99J16__A.2_ENST00000412344.1_RNA|CAPN9_ENST00000366666.2_Silent_p.G298G|RP11-99J16__A.2_ENST00000428480.1_RNA|CAPN9_ENST00000271971.2_Silent_p.G361G|RP11-99J16__A.2_ENST00000452640.1_RNA	p.G335G	NM_016452.1	NP_057536.1	O14815	CAN9_HUMAN			8	1087	+	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)	361			Calpain catalytic.		B1APS1|B1AQI0|Q9NS74	Silent	SNP	ENST00000271971.2	37	c.1005C>G	CCDS1586.1																																																																																				0.582	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615		5	24	0	0	0	1	0	5	24				
FTO	79068	broad.mit.edu	37	16	53859931	53859931	+	Silent	SNP	G	G	A			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr16:53859931G>A	ENST00000471389.1	+	3	501	c.279G>A	c.(277-279)ccG>ccA	p.P93P	FTO_ENST00000394647.3_Intron	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	93	Fe2OG dioxygenase domain.				adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TGCTCACTCCGGTATCTCGCA	0.493																																						ENST00000471389.1																			0				endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						c.(277-279)ccG>ccA		fat mass and obesity associated							97.0	87.0	91.0					16																	53859931		2198	4300	6498	SO:0001819	synonymous_variant	79068				DNA dealkylation involved in DNA repair|oxidative single-stranded DNA demethylation|oxidative single-stranded RNA demethylation|RNA repair	nucleus	DNA-N1-methyladenine dioxygenase activity|ferrous iron binding|oxidative DNA demethylase activity|oxidative RNA demethylase activity|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	g.chr16:53859931G>A	BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.279G>A	16.37:g.53859931G>A						FTO_ENST00000394647.3_Intron	p.P93P	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN			3	501	+			93			Fe2OG dioxygenase domain.		A2RUH1|B2RNS0|Q0P676|Q7Z785	Silent	SNP	ENST00000471389.1	37	c.279G>A	CCDS32448.1																																																																																				0.493	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432		5	41	0	0	0	1	0	5	41				
C2CD3	26005	broad.mit.edu	37	11	73760452	73760452	+	Missense_Mutation	SNP	G	G	C			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr11:73760452G>C	ENST00000334126.7	-	27	5517	c.5291C>G	c.(5290-5292)cCt>cGt	p.P1764R	C2CD3_ENST00000313663.7_Missense_Mutation_p.P1764R			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1764					brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ACTCTCCAAAGGGGAGACAGC	0.483																																						ENST00000334126.7																			0				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64						c.(5290-5292)cCt>cGt		C2 calcium-dependent domain containing 3							140.0	114.0	123.0					11																	73760452		2200	4293	6493	SO:0001583	missense	26005					centrosome		g.chr11:73760452G>C	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5291C>G	11.37:g.73760452G>C	ENSP00000334379:p.Pro1764Arg					C2CD3_ENST00000313663.7_Missense_Mutation_p.P1764R	p.P1764R			Q4AC94	C2CD3_HUMAN			27	5517	-	Breast(11;4.16e-06)		1764					C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37	c.5291C>G		.	.	.	.	.	.	.	.	.	.	G	27.7	4.852098	0.91355	.	.	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.73681	-0.77;-0.57;-0.57	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	D	0.87589	0.6215	M	0.81802	2.56	0.58432	D	0.999997	D	0.89917	1.0	D	0.91635	0.999	D	0.88512	0.3090	10	0.87932	D	0	-12.523	19.3726	0.94495	0.0:0.0:1.0:0.0	.	1764	Q4AC94-1	.	R	1764;1764;1745;572	ENSP00000334379:P1764R;ENSP00000323339:P1764R;ENSP00000388750:P572R	ENSP00000323339:P1764R	P	-	2	0	C2CD3	73438100	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.841000	0.99482	2.680000	0.91292	0.655000	0.94253	CCT		0.483	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531		4	36	0	0	0	1	0	4	36				
SIGLEC5	8778	broad.mit.edu	37	19	52130952	52130952	+	Silent	SNP	G	G	A			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr19:52130952G>A	ENST00000534261.2	-	7	1444	c.1045C>T	c.(1045-1047)Ctg>Ttg	p.L349L	SIGLEC5_ENST00000429354.3_Silent_p.L349L|SIGLEC5_ENST00000222107.4_Silent_p.L349L|SIGLEC5_ENST00000570106.2_Silent_p.L349L|SIGLEC5_ENST00000599649.1_Silent_p.L349L			O15389	SIGL5_HUMAN	sialic acid binding Ig-like lectin 5	349					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27		all_neural(266;0.0726)		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)		CTGCAGTGCAGACCCTCAGCC	0.647																																						ENST00000222107.4																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|large_intestine(4)|lung(9)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27						c.(1045-1047)Ctg>Ttg		sialic acid binding Ig-like lectin 5							11.0	13.0	12.0					19																	52130952		2181	4283	6464	SO:0001819	synonymous_variant	8778				cell adhesion	integral to membrane	sugar binding	g.chr19:52130952G>A	U71383	CCDS33088.1	19q13.41	2013-01-29			ENSG00000105501	ENSG00000105501		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10874	protein-coding gene	gene with protein product		604200		CD33L2		10343116	Standard	NM_003830		Approved	OB-BP2, SIGLEC-5, CD170	uc002pxe.4	O15389	OTTHUMG00000165510	ENST00000534261.2:c.1045C>T	19.37:g.52130952G>A						SIGLEC5_ENST00000534261.2_Silent_p.L349L|SIGLEC5_ENST00000570106.2_Silent_p.L349L|SIGLEC5_ENST00000429354.3_Silent_p.L349L|SIGLEC5_ENST00000599649.1_Silent_p.L349L	p.L349L			O15389	SIGL5_HUMAN		GBM - Glioblastoma multiforme(134;0.00124)|OV - Ovarian serous cystadenocarcinoma(262;0.0218)	6	1183	-		all_neural(266;0.0726)	349						Silent	SNP	ENST00000534261.2	37	c.1045C>T	CCDS33088.1																																																																																				0.647	SIGLEC5-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466897.2	NM_003830		4	7	0	0	0	1	0	4	7				
ALDH1L2	160428	broad.mit.edu	37	12	105433512	105433512	+	Missense_Mutation	SNP	A	A	G			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr12:105433512A>G	ENST00000258494.9	-	17	2164	c.2024T>C	c.(2023-2025)aTt>aCt	p.I675T	C12orf45_ENST00000548583.1_Intron	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN	aldehyde dehydrogenase 1 family, member L2	675	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						CTGTTTGCCAATAGGAGTGGA	0.393																																						ENST00000258494.9																			0				breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(13)|prostate(2)|skin(3)|stomach(2)	35						c.(2023-2025)aTt>aCt		aldehyde dehydrogenase 1 family, member L2							164.0	151.0	155.0					12																	105433512		2203	4300	6503	SO:0001583	missense	160428				10-formyltetrahydrofolate catabolic process|biosynthetic process	mitochondrion	acyl carrier activity|cofactor binding|formyltetrahydrofolate dehydrogenase activity|hydroxymethyl-, formyl- and related transferase activity|methyltransferase activity|phosphopantetheine binding	g.chr12:105433512A>G	AK095827	CCDS31891.1	12q23.3	2014-09-11			ENSG00000136010	ENSG00000136010	1.5.1.6	"""Aldehyde dehydrogenases"""	26777	protein-coding gene	gene with protein product	"""mitochondrial 10-formyltetrahydrofolate dehydrogenase"""	613584				20498374	Standard	NM_001034173		Approved	FLJ38508, mtFDH	uc001tlc.3	Q3SY69	OTTHUMG00000169823	ENST00000258494.9:c.2024T>C	12.37:g.105433512A>G	ENSP00000258494:p.Ile675Thr					C12orf45_ENST00000548583.1_Intron	p.I675T	NM_001034173.3	NP_001029345.2	Q3SY69	AL1L2_HUMAN			17	2164	-			675			Aldehyde dehydrogenase.		Q3SY68|Q68D62|Q6AI55|Q8N922	Missense_Mutation	SNP	ENST00000258494.9	37	c.2024T>C	CCDS31891.1	.	.	.	.	.	.	.	.	.	.	A	14.75	2.629951	0.46944	.	.	ENSG00000136010	ENST00000258494	T	0.73152	-0.72	5.7	5.7	0.88788	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.152930	0.64402	D	0.000016	T	0.31295	0.0792	N	0.00092	-2.175	0.80722	D	1	B	0.06786	0.001	B	0.14578	0.011	T	0.40924	-0.9537	10	0.44086	T	0.13	.	10.6272	0.45514	0.9198:0.0:0.0802:0.0	.	675	Q3SY69	AL1L2_HUMAN	T	675	ENSP00000258494:I675T	ENSP00000258494:I675T	I	-	2	0	ALDH1L2	103957642	1.000000	0.71417	0.724000	0.30704	0.997000	0.91878	7.479000	0.81095	2.167000	0.68274	0.528000	0.53228	ATT		0.393	ALDH1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406098.1	XM_090294		7	33	0	0	0	1	0	7	33				
RP11-423O2.5	0	broad.mit.edu	37	1	142803543	142803543	+	lincRNA	SNP	C	C	T			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr1:142803543C>T	ENST00000423385.1	-	0	1422																											TGTTGGAATTCCTGATGAATC	0.269																																						ENST00000423385.1																			0																																																			0							g.chr1:142803543C>T																													1.37:g.142803543C>T														0	1422	-									RNA	SNP	ENST00000423385.1	37																																																																																						0.269	RP11-423O2.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000193203.1			4	122	0	0	0	1	0	4	122				
EPHX1	2052	broad.mit.edu	37	1	226026489	226026489	+	Missense_Mutation	SNP	C	C	G			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr1:226026489C>G	ENST00000366837.4	+	4	695	c.499C>G	c.(499-501)Ccc>Gcc	p.P167A	EPHX1_ENST00000272167.5_Missense_Mutation_p.P167A|RP11-285F7.2_ENST00000424332.1_RNA	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	167					aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					CCTGACTGACCCCAAGAACCA	0.572																																						ENST00000366837.4																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28						c.(499-501)Ccc>Gcc		epoxide hydrolase 1, microsomal (xenobiotic)							124.0	112.0	116.0					1																	226026489		2203	4300	6503	SO:0001583	missense	2052				aromatic compound catabolic process|response to toxin	endoplasmic reticulum membrane|integral to membrane|microsome	cis-stilbene-oxide hydrolase activity|epoxide hydrolase activity	g.chr1:226026489C>G	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.499C>G	1.37:g.226026489C>G	ENSP00000355802:p.Pro167Ala					EPHX1_ENST00000272167.5_Missense_Mutation_p.P167A	p.P167A	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN			4	695	+	Breast(184;0.197)		167					B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Missense_Mutation	SNP	ENST00000366837.4	37	c.499C>G	CCDS1547.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.344576	0.82022	.	.	ENSG00000143819	ENST00000272167;ENST00000366837	T;T	0.03689	3.84;3.84	5.84	5.84	0.93424	.	0.109027	0.64402	D	0.000006	T	0.10981	0.0268	M	0.72353	2.195	0.80722	D	1	P	0.48294	0.908	P	0.46885	0.53	T	0.01225	-1.1413	9	.	.	.	-22.8053	20.1278	0.97990	0.0:1.0:0.0:0.0	.	167	P07099	HYEP_HUMAN	A	167	ENSP00000272167:P167A;ENSP00000355802:P167A	.	P	+	1	0	EPHX1	224093112	1.000000	0.71417	1.000000	0.80357	0.587000	0.36485	4.443000	0.59994	2.768000	0.95171	0.561000	0.74099	CCC		0.572	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120		6	92	0	0	0	1	0	6	92				
RASSF1	11186	broad.mit.edu	37	3	50369084	50369084	+	Silent	SNP	T	T	A			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr3:50369084T>A	ENST00000357043.2	-	4	713	c.678A>T	c.(676-678)gcA>gcT	p.A226A	RASSF1_ENST00000395126.3_Silent_p.A71A|RASSF1_ENST00000327761.3_Silent_p.A152A|RASSF1_ENST00000359365.4_Silent_p.A222A					Ras association (RalGDS/AF-6) domain family member 1											lung(2)|ovary(1)|skin(1)|urinary_tract(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		TGACTTCACGTGCCCTTGTGC	0.617																																						ENST00000359365.4																			0				lung(2)|ovary(1)|skin(1)|urinary_tract(1)	5						c.(664-666)gcA>gcT		Ras association (RalGDS/AF-6) domain family member 1							85.0	90.0	88.0					3																	50369084		2203	4300	6503	SO:0001819	synonymous_variant	11186				cell cycle arrest|negative regulation of cell cycle arrest|positive regulation of protein ubiquitination|protein stabilization|Ras protein signal transduction|response to DNA damage stimulus	microtubule|microtubule cytoskeleton|microtubule organizing center|nucleus|spindle pole	identical protein binding|protein binding|protein N-terminus binding|zinc ion binding	g.chr3:50369084T>A	AF132675	CCDS2820.1, CCDS2821.1, CCDS2822.1, CCDS43096.1	3p21.3	2008-02-22	2008-02-22		ENSG00000068028	ENSG00000068028			9882	protein-coding gene	gene with protein product		605082					Standard	NM_170713		Approved	NORE2A, REH3P21, RDA32, 123F2	uc003dad.1	Q9NS23	OTTHUMG00000149958	ENST00000357043.2:c.678A>T	3.37:g.50369084T>A						RASSF1_ENST00000395126.3_Silent_p.A71A|RASSF1_ENST00000357043.2_Silent_p.A226A|RASSF1_ENST00000327761.3_Silent_p.A152A	p.A222A	NM_001206957.1|NM_007182.4|NM_170714.1	NP_001193886.1|NP_009113.3|NP_733832.1	Q9NS23	RASF1_HUMAN		BRCA - Breast invasive adenocarcinoma(193;0.000278)|OV - Ovarian serous cystadenocarcinoma(275;0.0015)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)	4	772	-			226			Ras-associating.			Silent	SNP	ENST00000357043.2	37	c.666A>T	CCDS2820.1																																																																																				0.617	RASSF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000314304.1			21	50	0	0	0	1	0	21	50				
AIM1	202	broad.mit.edu	37	6	106975253	106975253	+	Missense_Mutation	SNP	G	G	T			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr6:106975253G>T	ENST00000369066.3	+	5	3749	c.3262G>T	c.(3262-3264)Ggt>Tgt	p.G1088C		NM_001624.2	NP_001615	Q9UMX9	S45A2_HUMAN	absent in melanoma 1	0					developmental pigmentation (GO:0048066)|melanin biosynthetic process (GO:0042438)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)		GGAACTCTCTGGTCTCTGGGG	0.428																																						ENST00000369066.3																			0				breast(8)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(7)|large_intestine(13)|lung(20)|ovary(5)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	69						c.(3262-3264)Ggt>Tgt		absent in melanoma 1							210.0	201.0	204.0					6																	106975253		2203	4300	6503	SO:0001583	missense	202						sugar binding	g.chr6:106975253G>T	U83115	CCDS34506.1	6q21	2014-01-29			ENSG00000112297	ENSG00000112297			356	protein-coding gene	gene with protein product	"""suppression of tumorigenicity 4"", ""beta-gamma crystallin domain containing 1"""	601797	"""suppression of tumorigenicity 4 (malignant melanoma)"""	ST4		1680551, 12693952	Standard	NM_001624		Approved	CRYBG1	uc003prh.3	Q9Y4K1	OTTHUMG00000015302	ENST00000369066.3:c.3262G>T	6.37:g.106975253G>T	ENSP00000358062:p.Gly1088Cys						p.G1088C	NM_001624.2	NP_001615.1	Q9Y4K1	AIM1_HUMAN	Epithelial(6;0.00114)|all cancers(7;0.00726)|BRCA - Breast invasive adenocarcinoma(8;0.0114)|OV - Ovarian serous cystadenocarcinoma(5;0.0305)	all cancers(137;1.73e-50)|Epithelial(106;2.42e-48)|OV - Ovarian serous cystadenocarcinoma(136;1.51e-27)|BRCA - Breast invasive adenocarcinoma(108;0.00104)|GBM - Glioblastoma multiforme(226;0.00858)	5	3749	+	Breast(9;0.0138)|all_epithelial(6;0.169)	all_cancers(87;4.67e-25)|all_epithelial(87;5.46e-21)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|Colorectal(196;3.46e-05)|all_lung(197;5.94e-05)|Lung NSC(302;7.26e-05)|Ovarian(999;0.00473)	1088			Beta/gamma crystallin 'Greek key' 2.		Q6P2P0|Q9BTM3	Missense_Mutation	SNP	ENST00000369066.3	37	c.3262G>T	CCDS34506.1	.	.	.	.	.	.	.	.	.	.	G	16.30	3.083627	0.55861	.	.	ENSG00000112297	ENST00000369066	T	0.76186	-1.0	5.29	4.4	0.53042	Beta/gamma crystallin (4);Gamma-crystallin-related (1);	0.561123	0.20417	N	0.092743	T	0.50446	0.1616	L	0.39633	1.23	0.80722	D	1	B	0.24258	0.1	B	0.25759	0.063	T	0.57825	-0.7744	10	0.72032	D	0.01	.	8.2117	0.31488	0.2431:0.0:0.7569:0.0	.	1088	Q9Y4K1	AIM1_HUMAN	C	1088	ENSP00000358062:G1088C	ENSP00000358062:G1088C	G	+	1	0	AIM1	107081946	1.000000	0.71417	0.991000	0.47740	0.764000	0.43329	1.782000	0.38654	1.331000	0.45412	0.650000	0.86243	GGT		0.428	AIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041669.1			8	102	1	0	0.000274275	1	0.000285703	8	102				
HRAS	3265	broad.mit.edu	37	11	533875	533875	+	Missense_Mutation	SNP	G	G	T	rs28933406		TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr11:533875G>T	ENST00000451590.1	-	3	368	c.181C>A	c.(181-183)Cag>Aag	p.Q61K	HRAS_ENST00000417302.1_Missense_Mutation_p.Q61K|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61K|HRAS_ENST00000311189.7_Missense_Mutation_p.Q61K|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000397594.1_Missense_Mutation_p.Q61K	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	61			Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406). {ECO:0000269|PubMed:12727991}.|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.Q61K(61)|p.Q61R(1)|p.Q61E(1)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TACTCCTCCTGGCCGGCGGTA	0.597		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)																												ENST00000417302.1		6	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	Mis	v-Ha-ras Harvey rat sarcoma viral oncogene homolog			"""E, L, M"""		"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""	"""infrequent sarcomas, rare other types"""		63	Substitution - Missense(63)	p.Q61K(61)|p.Q61R(1)|p.Q61E(1)	thyroid(23)|skin(18)|urinary_tract(8)|upper_aerodigestive_tract(4)|soft_tissue(4)|testis(2)|lung(2)|cervix(1)|kidney(1)	adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901						c.(181-183)Cag>Aag		Harvey rat sarcoma viral oncogene homolog	Sulindac(DB00605)						117.0	102.0	107.0					11																	533875		2203	4300	6503	SO:0001583	missense	3265	Costello syndrome	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding	g.chr11:533875G>T	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.181C>A	11.37:g.533875G>T	ENSP00000407586:p.Gln61Lys	HNSCC(11;0.0054)				HRAS_ENST00000451590.1_Missense_Mutation_p.Q61K|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000397594.1_Missense_Mutation_p.Q61K|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61K|HRAS_ENST00000311189.7_Missense_Mutation_p.Q61K	p.Q61K	NM_176795.3	NP_789765.1	P01112	RASH_HUMAN		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	3	368	-		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)	61		Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406).|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).			B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Missense_Mutation	SNP	ENST00000451590.1	37	c.181C>A	CCDS7698.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.855718	0.51376	.	.	ENSG00000174775	ENST00000397594;ENST00000397596;ENST00000451590;ENST00000417302;ENST00000311189	D;D;D;D;D	0.83506	-1.73;-1.73;-1.73;-1.73;-1.73	3.64	3.64	0.41730	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.88644	0.6492	H	0.96604	3.85	0.80722	D	1	B;B	0.19073	0.033;0.012	B;B	0.19391	0.015;0.025	D	0.89618	0.3846	10	0.62326	D	0.03	.	14.8426	0.70237	0.0:0.0:1.0:0.0	rs28933406	61;61	P01112-2;P01112	.;RASH_HUMAN	K	61	ENSP00000380722:Q61K;ENSP00000380723:Q61K;ENSP00000407586:Q61K;ENSP00000388246:Q61K;ENSP00000309845:Q61K	ENSP00000309845:Q61K	Q	-	1	0	HRAS	523875	1.000000	0.71417	0.987000	0.45799	0.459000	0.32528	9.476000	0.97823	2.045000	0.60652	0.561000	0.74099	CAG		0.597	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795		20	31	1	0	3.8784e-16	1	4.21566e-16	20	31				
C2orf73	129852	broad.mit.edu	37	2	54587376	54587376	+	Missense_Mutation	SNP	G	G	A			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr2:54587376G>A	ENST00000398634.2	+	5	583	c.541G>A	c.(541-543)Ggc>Agc	p.G181S	C2orf73_ENST00000405749.1_Intron|C2orf73_ENST00000491538.1_3'UTR	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN	chromosome 2 open reading frame 73	181										breast(2)	2						GATAAAACCAGGCAGTAGGCC	0.453																																						ENST00000398634.2																			0				breast(2)	2						c.(541-543)Ggc>Agc		chromosome 2 open reading frame 73							50.0	49.0	49.0					2																	54587376		1916	4130	6046	SO:0001583	missense	129852							g.chr2:54587376G>A	BC031669, AK097617	CCDS46285.1	2p16.2	2008-07-07			ENSG00000177994	ENSG00000177994			26861	protein-coding gene	gene with protein product						14702039	Standard	NM_001100396		Approved	FLJ40298	uc002rxt.1	Q8N5S3	OTTHUMG00000151826	ENST00000398634.2:c.541G>A	2.37:g.54587376G>A	ENSP00000381631:p.Gly181Ser					C2orf73_ENST00000491538.1_3'UTR|C2orf73_ENST00000405749.1_Intron	p.G181S	NM_001100396.1	NP_001093866.1	Q8N5S3	CB073_HUMAN			5	583	+			181					A0AV79|A0AV81|Q8N7V4	Missense_Mutation	SNP	ENST00000398634.2	37	c.541G>A	CCDS46285.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.959567	0.53400	.	.	ENSG00000177994	ENST00000486488;ENST00000398634;ENST00000447328	T;T;T	0.49139	0.79;0.79;0.79	5.35	2.52	0.30459	.	0.490355	0.20488	N	0.091347	T	0.39091	0.1065	L	0.39898	1.24	0.33418	D	0.579464	P;P	0.52316	0.952;0.952	P;P	0.46659	0.523;0.523	T	0.45818	-0.9235	10	0.11182	T	0.66	-33.6433	11.0889	0.48104	0.2721:0.0:0.7279:0.0	.	123;181	B7ZM12;Q8N5S3	.;CB073_HUMAN	S	187;181;123	ENSP00000417971:G187S;ENSP00000381631:G181S;ENSP00000389570:G123S	ENSP00000381631:G181S	G	+	1	0	C2orf73	54440880	0.998000	0.40836	1.000000	0.80357	0.997000	0.91878	1.611000	0.36879	0.740000	0.32651	0.650000	0.86243	GGC		0.453	C2orf73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324075.2	NM_001100396		3	6	0	0	0	1	0	3	6				
COL2A1	1280	broad.mit.edu	37	12	48387610	48387610	+	Silent	SNP	C	C	T			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr12:48387610C>T	ENST00000380518.3	-	14	1070	c.906G>A	c.(904-906)gcG>gcA	p.A302A	COL2A1_ENST00000337299.6_Silent_p.A233A	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN	collagen, type II, alpha 1	302	Triple-helical region.		Missing (in STL1). {ECO:0000269|PubMed:7977371}.		axon guidance (GO:0007411)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to BMP stimulus (GO:0071773)|central nervous system development (GO:0007417)|chondrocyte differentiation (GO:0002062)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal joint morphogenesis (GO:0060272)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart morphogenesis (GO:0003007)|inner ear morphogenesis (GO:0042472)|limb bud formation (GO:0060174)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|notochord development (GO:0030903)|otic vesicle development (GO:0071599)|palate development (GO:0060021)|proteoglycan metabolic process (GO:0006029)|regulation of gene expression (GO:0010468)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|tissue homeostasis (GO:0001894)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen type II trimer (GO:0005585)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)			Collagenase(DB00048)	CAGGAGCACCCGCCTCTCCCT	0.542																																						ENST00000380518.3																			0				NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(25)|ovary(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(3)	64	GRCh37	CD001475	COL2A1	D		c.(904-906)gcG>gcA		collagen, type II, alpha 1	Collagenase(DB00048)						70.0	68.0	69.0					12																	48387610		2203	4300	6503	SO:0001819	synonymous_variant	1280				axon guidance|collagen fibril organization|embryonic skeletal joint morphogenesis|sensory perception of sound|visual perception	collagen type II	identical protein binding|platelet-derived growth factor binding	g.chr12:48387610C>T	X16468	CCDS8759.1, CCDS41778.1	12q12-q13.2	2013-11-14	2008-02-04		ENSG00000139219	ENSG00000139219		"""Collagens"""	2200	protein-coding gene	gene with protein product		120140	"""collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)"", ""arthroophthalmopathy, progressive (Stickler syndrome)"""	SEDC, AOM		1677770	Standard	NM_033150		Approved	STL1	uc001rqu.3	P02458	OTTHUMG00000149896	ENST00000380518.3:c.906G>A	12.37:g.48387610C>T						COL2A1_ENST00000337299.6_Silent_p.A233A	p.A302A	NM_001844.4|NM_033150.2	NP_001835.3|NP_149162.2	P02458	CO2A1_HUMAN			14	1070	-		Acute lymphoblastic leukemia(13;0.108)|all_hematologic(14;0.214)	302		Missing (in STL1).	Triple-helical region.		A6NGA0|Q12985|Q14009|Q14044|Q14045|Q14046|Q14047|Q14056|Q14058|Q16672|Q1JQ82|Q2V4X7|Q6LBY1|Q6LBY2|Q6LBY3|Q96IT5|Q99227|Q9UE38|Q9UE39|Q9UE40|Q9UE41|Q9UE42|Q9UE43	Silent	SNP	ENST00000380518.3	37	c.906G>A	CCDS41778.1																																																																																				0.542	COL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313810.2	NM_001844		6	51	0	0	0	1	0	6	51				
COPS5	10987	broad.mit.edu	37	8	67971510	67971510	+	Missense_Mutation	SNP	G	G	C			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr8:67971510G>C	ENST00000357849.4	-	2	634	c.314C>G	c.(313-315)aCc>aGc	p.T105S	COPS5_ENST00000517736.1_Missense_Mutation_p.T41S|AC109335.1_ENST00000578628.1_RNA|PPP1R42_ENST00000517834.1_5'Flank|COPS5_ENST00000519963.1_5'Flank	NM_006837.2	NP_006828.2	Q92905	CSN5_HUMAN	COP9 signalosome subunit 5	105	MPN.				cullin deneddylation (GO:0010388)|exosomal secretion (GO:1990182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein deneddylation (GO:0000338)|protein deubiquitination (GO:0016579)|regulation of cell cycle (GO:0051726)|regulation of JNK cascade (GO:0046328)|transcription from RNA polymerase II promoter (GO:0006366)|translation (GO:0006412)|translational initiation (GO:0006413)	cell junction (GO:0030054)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 3 complex (GO:0005852)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|transcription coactivator activity (GO:0003713)|translation initiation factor activity (GO:0003743)|ubiquitin-specific protease activity (GO:0004843)	p.T105I(1)		endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)			ATTTACTCGGGTTTCAGTGCC	0.418																																						ENST00000517736.1																			1	Substitution - Missense(1)	p.T105I(1)	skin(1)	endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(3)	14						c.(121-123)aCc>aGc		COP9 signalosome subunit 5							150.0	121.0	131.0					8																	67971510		2203	4300	6503	SO:0001583	missense	10987				cullin deneddylation|transcription from RNA polymerase II promoter	eukaryotic translation initiation factor 3 complex|signalosome	metal ion binding|metallopeptidase activity|protein binding|transcription coactivator activity|translation initiation factor activity	g.chr8:67971510G>C	U65928	CCDS6198.1	8q13.1	2013-03-14	2013-03-14		ENSG00000121022	ENSG00000121022			2240	protein-coding gene	gene with protein product		604850	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 5"", ""COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)"""			8837781, 9341143	Standard	NM_006837		Approved	JAB1, SGN5, MOV-34, CSN5	uc003xxe.3	Q92905	OTTHUMG00000164563	ENST00000357849.4:c.314C>G	8.37:g.67971510G>C	ENSP00000350512:p.Thr105Ser					COPS5_ENST00000357849.4_Missense_Mutation_p.T105S	p.T41S			Q92905	CSN5_HUMAN	Epithelial(68;0.00389)|OV - Ovarian serous cystadenocarcinoma(28;0.00691)|all cancers(69;0.0205)|BRCA - Breast invasive adenocarcinoma(89;0.153)		2	683	-	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	105					O15386|Q6AW95|Q86WQ4|Q9BQ17	Missense_Mutation	SNP	ENST00000357849.4	37	c.122C>G	CCDS6198.1	.	.	.	.	.	.	.	.	.	.	G	32	5.137002	0.94517	.	.	ENSG00000121022	ENST00000357849;ENST00000517736;ENST00000518747	T;T;T	0.54866	0.55;0.55;0.55	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.79305	0.4423	M	0.90705	3.14	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.85130	0.993;0.994;0.997	T	0.83080	-0.0138	10	0.87932	D	0	-3.3713	19.7153	0.96115	0.0:0.0:1.0:0.0	.	74;41;105	Q59GH5;E5RHH5;Q92905	.;.;CSN5_HUMAN	S	105;41;41	ENSP00000350512:T105S;ENSP00000429774:T41S;ENSP00000428586:T41S	ENSP00000350512:T105S	T	-	2	0	COPS5	68134064	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	9.703000	0.98714	2.731000	0.93534	0.655000	0.94253	ACC		0.418	COPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379245.2			4	76	0	0	0	1	0	4	76				
KRTAP4-8	728224	broad.mit.edu	37	17	39254054	39254054	+	Missense_Mutation	SNP	A	A	T	rs76270529		TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr17:39254054A>T	ENST00000333822.4	-	1	339	c.283T>A	c.(283-285)Tgc>Agc	p.C95S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	95	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.C95S(4)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						ctggagatgcagcagcTAGGG	0.677																																						ENST00000333822.4																			4	Substitution - Missense(4)	p.C95S(4)	endometrium(3)|kidney(1)	endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						c.(283-285)Tgc>Agc		keratin associated protein 4-8							7.0	11.0	10.0					17																	39254054		685	1582	2267	SO:0001583	missense	728224					keratin filament		g.chr17:39254054A>T	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.283T>A	17.37:g.39254054A>T	ENSP00000328444:p.Cys95Ser						p.C95S	NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN			1	339	-			95			25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].		A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	c.283T>A	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	15.18	2.755714	0.49362	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.02280	4.36	3.11	2.01	0.26516	.	0.000000	0.52532	U	0.000067	T	0.04497	0.0123	M	0.83223	2.63	0.25182	N	0.99019	B	0.21606	0.058	B	0.27887	0.084	T	0.21793	-1.0235	10	0.54805	T	0.06	.	6.3859	0.21559	0.8715:0.0:0.1285:0.0	.	95	Q9BYQ9	KRA48_HUMAN	S	95;80	ENSP00000328444:C95S	ENSP00000414561:C80S	C	-	1	0	KRTAP4-8	36507580	0.999000	0.42202	0.393000	0.26258	0.649000	0.38597	3.122000	0.50446	0.404000	0.25506	0.374000	0.22700	TGC		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960		3	32	0	0	0	1	0	3	32				
COL15A1	1306	broad.mit.edu	37	9	101798452	101798452	+	Splice_Site	SNP	G	G	A			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr9:101798452G>A	ENST00000375001.3	+	20	2713	c.2290G>A	c.(2290-2292)Ggt>Agt	p.G764S		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	764	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ATTTTTCCAGGGTCTCAAAGG	0.483																																						ENST00000375001.3																			0				NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107						c.e20-1		collagen, type XV, alpha 1							68.0	88.0	81.0					9																	101798452		2203	4300	6503	SO:0001630	splice_region_variant	1306				angiogenesis|cell differentiation|signal transduction	collagen type XV|extracellular space|integral to membrane	binding	g.chr9:101798452G>A	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2290-1G>A	9.37:g.101798452G>A							p.G764_splice	NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN			20	2713	+		Acute lymphoblastic leukemia(62;0.0562)	764			Triple-helical region 3 (COL3).		Q5T6J4|Q9UDC5|Q9Y4W4	Splice_Site	SNP	ENST00000375001.3	37	c.2289_splice	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	G	17.53	3.413701	0.62511	.	.	ENSG00000204291	ENST00000375001	D	0.90732	-2.72	5.39	5.39	0.77823	.	0.000000	0.85682	D	0.000000	D	0.96433	0.8836	M	0.93420	3.415	0.45439	D	0.998417	D	0.89917	1.0	D	0.87578	0.998	D	0.97090	0.9790	9	.	.	.	-10.9844	14.9982	0.71449	0.0:0.0:1.0:0.0	.	764	P39059	COFA1_HUMAN	S	764	ENSP00000364140:G764S	.	G	+	1	0	COL15A1	100838273	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	3.325000	0.52030	2.676000	0.91093	0.655000	0.94253	GGT		0.483	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	Missense_Mutation	3	26	0	0	0	1	0	3	26				
ETV6	2120	broad.mit.edu	37	12	12022421	12022421	+	Missense_Mutation	SNP	T	T	C			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr12:12022421T>C	ENST00000396373.4	+	5	801	c.527T>C	c.(526-528)aTt>aCt	p.I176T		NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	176					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				CCTCCCACCATTGAACTGTTG	0.582			T	"""NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"""	"""congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"""																																	ENST00000396373.4				Dom	yes		12	12p13	2120	T	ets variant gene 6 (TEL oncogene)			"""L, E, M"""	"""NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"""		"""congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"""	ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	0				breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						c.(526-528)aTt>aCt		ets variant 6							174.0	180.0	178.0					12																	12022421		2203	4300	6503	SO:0001583	missense	2120					cytoplasm|nucleolus	protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr12:12022421T>C	BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"""TEL oncogene"""	600618	"""ets variant gene 6 (TEL oncogene)"""			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.527T>C	12.37:g.12022421T>C	ENSP00000379658:p.Ile176Thr						p.I176T	NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN			5	801	+		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)	176					A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Missense_Mutation	SNP	ENST00000396373.4	37	c.527T>C	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	T	19.56	3.850418	0.71719	.	.	ENSG00000139083	ENST00000396373	T	0.05139	3.49	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.08403	0.0209	M	0.66939	2.045	0.58432	D	0.999999	P	0.35272	0.493	B	0.29942	0.109	T	0.21109	-1.0255	10	0.12103	T	0.63	.	15.074	0.72063	0.0:0.0:0.0:1.0	.	176	P41212	ETV6_HUMAN	T	176	ENSP00000379658:I176T	ENSP00000379658:I176T	I	+	2	0	ETV6	11913688	1.000000	0.71417	0.999000	0.59377	0.946000	0.59487	7.003000	0.76310	2.035000	0.60131	0.533000	0.62120	ATT		0.582	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2	NM_001987		8	157	0	0	0	1	0	8	157				
MUC7	4589	broad.mit.edu	37	4	71346978	71346978	+	Missense_Mutation	SNP	T	T	C			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr4:71346978T>C	ENST00000304887.5	+	3	707	c.517T>C	c.(517-519)Tct>Cct	p.S173P	MUC7_ENST00000514512.1_3'UTR|MUC7_ENST00000413702.1_Missense_Mutation_p.S173P|MUC7_ENST00000456088.1_Missense_Mutation_p.S173P	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	173	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)		p.S173P(3)		central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			ACCCACACCTTCTGCAACTAC	0.522																																						ENST00000413702.1																			3	Substitution - Missense(3)	p.S173P(3)	lung(2)|kidney(1)	central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42						c.(517-519)Tct>Cct		mucin 7, secreted							341.0	284.0	303.0					4																	71346978		2203	4300	6503	SO:0001583	missense	4589					extracellular region	protein binding	g.chr4:71346978T>C	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.517T>C	4.37:g.71346978T>C	ENSP00000302021:p.Ser173Pro					MUC7_ENST00000456088.1_Missense_Mutation_p.S173P|MUC7_ENST00000304887.5_Missense_Mutation_p.S173P|MUC7_ENST00000514512.1_3'UTR	p.S173P	NM_001145006.1	NP_001138478.1	Q8TAX7	MUC7_HUMAN	Lung(101;0.211)		4	805	+			173			Thr-rich.		Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	c.517T>C	CCDS3541.1	.	.	.	.	.	.	.	.	.	.	T	8.294	0.818323	0.16607	.	.	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.52754	0.65;0.65;0.65	2.59	-1.83	0.07833	.	.	.	.	.	T	0.22360	0.0539	N	0.12182	0.205	0.09310	N	1	B	0.14805	0.011	B	0.10450	0.005	T	0.19451	-1.0305	8	.	.	.	-1.8981	3.858	0.08984	0.0:0.2646:0.3931:0.3423	.	173	Q8TAX7	MUC7_HUMAN	P	173	ENSP00000407422:S173P;ENSP00000400585:S173P;ENSP00000302021:S173P	.	S	+	1	0	MUC7	71381567	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.097000	0.01348	-0.350000	0.08262	-0.605000	0.04089	TCT		0.522	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291		4	83	0	0	0	1	0	4	83				
SRGAP2-AS1	100873165	broad.mit.edu	37	1	121137791	121137793	+	lincRNA	DEL	CCA	CCA	-	rs28552466|rs61625886|rs374710813	byFrequency	TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr1:121137791_121137793delCCA	ENST00000417218.1	+	0	0				RP11-343N15.1_ENST00000437515.1_lincRNA																							ATTTCGCCCTCCACCGCCGCCGC	0.631																																						ENST00000437515.1																			0																																																			100873165							g.chr1:121137791_121137793delCCA																													1.37:g.121137791_121137793delCCA														0	329	-									RNA	DEL	ENST00000417218.1	37																																																																																						0.631	AL592494.5-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000036739.1			3	5						3	5	---	---	---	---
NRM	11270	broad.mit.edu	37	6	30657192	30657192	+	Frame_Shift_Del	DEL	G	G	-			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr6:30657192delG	ENST00000259953.4	-	4	719	c.368delC	c.(367-369)cctfs	p.P123fs	PPP1R18_ENST00000488324.1_5'Flank|NRM_ENST00000470733.1_5'UTR|PPP1R18_ENST00000399199.3_5'Flank|NRM_ENST00000376420.5_Intron|PPP1R18_ENST00000274853.3_5'Flank|NRM_ENST00000376421.5_Frame_Shift_Del_p.P123fs	NM_007243.2	NP_009174.1	Q8IXM6	NRM_HUMAN	nurim (nuclear envelope membrane protein)	123						integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)				large_intestine(1)|lung(2)	3						CCACAACACAGGGCCTTTGGG	0.607																																						ENST00000259953.4																			0				large_intestine(1)|lung(2)	3						c.(367-369)ctfs		nurim (nuclear envelope membrane protein)							42.0	35.0	38.0					6																	30657192		2200	4294	6494	SO:0001589	frameshift_variant	11270					integral to membrane|nuclear inner membrane		g.chr6:30657192delG	AF143676	CCDS4686.1, CCDS59498.1	6p21.3	2010-02-17			ENSG00000137404	ENSG00000137404			8003	protein-coding gene	gene with protein product						10402458, 17517639	Standard	NM_007243		Approved	NRM29	uc031sng.1	Q8IXM6	OTTHUMG00000031223	ENST00000259953.4:c.368delC	6.37:g.30657192delG	ENSP00000259953:p.Pro123fs					NRM_ENST00000470733.1_5'UTR|NRM_ENST00000376420.5_Intron|NRM_ENST00000376421.5_Frame_Shift_Del_p.P123fs	p.P123fs	NM_001270707.1	NP_001257636.1	Q8IXM6	NRM_HUMAN			4	719	-			123					B0S7R0|B0S7R1|I3XIE2|I3XIE3|Q5JP57|Q5JP58|Q5JP59|Q5JP60|Q8WU45|Q9BSX3|Q9UN92	Frame_Shift_Del	DEL	ENST00000259953.4	37	c.368delC	CCDS4686.1																																																																																				0.607	NRM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076466.2			2	4						2	4	---	---	---	---
FJX1	24147	broad.mit.edu	37	11	35640205	35640207	+	In_Frame_Del	DEL	CGC	CGC	-			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr11:35640205_35640207delCGC	ENST00000317811.4	+	1	471_473	c.21_23delCGC	c.(19-24)ggcgcc>ggc	p.A10del		NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	10					retina layer formation (GO:0010842)	extracellular space (GO:0005615)				lung(1)|urinary_tract(1)	2	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				GGATGCGGGGCGCCGCCGCCACC	0.818																																					Melanoma(161;10 2587 27165 47356)	ENST00000317811.4																			0				lung(1)|urinary_tract(1)	2						c.(19-24)ggc>gg		four jointed box 1 (Drosophila)																																				SO:0001651	inframe_deletion	24147					extracellular space		g.chr11:35640205_35640207delCGC	AJ245599	CCDS44570.1	11p13	2012-05-18				ENSG00000179431			17166	protein-coding gene	gene with protein product	"""putative secreted ligand homologous to fjx1"""	612206				7647465, 10072791	Standard	NM_014344		Approved	FLJ22416, FLJ25593	uc001mwh.3	Q86VR8		ENST00000317811.4:c.21_23delCGC	11.37:g.35640211_35640213delCGC	ENSP00000400223:p.Ala10del						p.GA7del	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN			1	471_473	+	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)	7					B2RCA9|Q9UGK6	In_Frame_Del	DEL	ENST00000317811.4	37	c.21_23delCGC	CCDS44570.1																																																																																				0.818	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344		2	4						2	4	---	---	---	---
RBL2	5934	broad.mit.edu	37	16	53476671	53476671	+	Frame_Shift_Del	DEL	T	T	-			TCGA-SP-A6QF-01A-12D-A35I-08	TCGA-SP-A6QF-10A-21D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	88156dd0-256c-499d-ba23-d9c2128f6726	caa96f11-e971-4cb7-9d98-7d55335260ed	g.chr16:53476671delT	ENST00000262133.6	+	3	610	c.473delT	c.(472-474)gttfs	p.V158fs	RNU6-1153P_ENST00000516760.1_RNA	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN	retinoblastoma-like 2	158					chromatin modification (GO:0016568)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of lipid kinase activity (GO:0043550)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						AACTTCACTGTTTCTGCTGTA	0.388																																						ENST00000262133.6																			0				breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						c.(472-474)gtfs		retinoblastoma-like 2 (p130)							55.0	57.0	57.0					16																	53476671		2198	4300	6498	SO:0001589	frameshift_variant	5934				cell cycle|chromatin modification|regulation of cell cycle|regulation of lipid kinase activity|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleolus	DNA binding|protein binding	g.chr16:53476671delT	X74594	CCDS10748.1	16q12.2	2014-03-11	2014-03-11		ENSG00000103479	ENSG00000103479			9894	protein-coding gene	gene with protein product		180203				8361765, 8643454	Standard	NM_005611		Approved	Rb2, p130	uc002ehi.4	Q08999	OTTHUMG00000133198	ENST00000262133.6:c.473delT	16.37:g.53476671delT	ENSP00000262133:p.Val158fs						p.V158fs	NM_005611.3	NP_005602.3	Q08999	RBL2_HUMAN			3	610	+			158					B7Z913|Q15073|Q16084|Q8NE70|Q92812	Frame_Shift_Del	DEL	ENST00000262133.6	37	c.473delT	CCDS10748.1																																																																																				0.388	RBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256908.3	NM_005611		18	28						18	28	---	---	---	---
