#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
SYBU	55638	broad.mit.edu	37	8	110590198	110590198	+	Silent	SNP	G	G	T			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr8:110590198G>T	ENST00000422135.1	-	7	1298	c.783C>A	c.(781-783)ccC>ccA	p.P261P	SYBU_ENST00000532779.1_Silent_p.P193P|SYBU_ENST00000276646.9_Silent_p.P261P|SYBU_ENST00000529690.1_Silent_p.P131P|SYBU_ENST00000408889.3_Silent_p.P142P|SYBU_ENST00000527707.1_5'UTR|SYBU_ENST00000533065.1_Silent_p.P142P|SYBU_ENST00000424158.2_Silent_p.P266P|SYBU_ENST00000446070.2_Silent_p.P260P|SYBU_ENST00000440310.1_Silent_p.P261P|SYBU_ENST00000533171.1_Silent_p.P261P|SYBU_ENST00000399066.3_Silent_p.P258P|SYBU_ENST00000419099.1_Silent_p.P260P|SYBU_ENST00000408908.2_Silent_p.P261P|SYBU_ENST00000528647.1_Silent_p.P260P|SYBU_ENST00000528331.1_Silent_p.P142P|SYBU_ENST00000533895.1_Silent_p.P260P|SYBU_ENST00000529175.1_Silent_p.P55P|SYBU_ENST00000433638.1_Silent_p.P261P	NM_001099744.1	NP_001093214.1	Q9NX95	SYBU_HUMAN	syntabulin (syntaxin-interacting)	261	Sufficient for interaction with KIF5B.				regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|dense body (GO:0097433)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						CTGGGTTTGGGGGTCTGACAC	0.453																																						ENST00000399066.3																			0				NS(1)|breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	30						c.(772-774)ccC>ccA		syntabulin (syntaxin-interacting)							201.0	194.0	196.0					8																	110590198		1986	4174	6160	SO:0001819	synonymous_variant	55638					cytoplasmic membrane-bounded vesicle|cytoskeleton|Golgi membrane|integral to membrane		g.chr8:110590198G>T	AB040905	CCDS43763.1, CCDS43764.1, CCDS47912.1, CCDS55271.1	8q23.2	2010-08-27				ENSG00000147642			26011	protein-coding gene	gene with protein product	"""syntaphilin-like"""	611568				17611281, 16750881, 16157705, 15656992, 15459722	Standard	NM_001099743		Approved	FLJ20366, GOLSYN, KIAA1472, OCSYN, SNPHL	uc003ynj.4	Q9NX95		ENST00000422135.1:c.783C>A	8.37:g.110590198G>T			Somatic				SYBU_ENST00000408889.3_Silent_p.P142P|SYBU_ENST00000422135.1_Silent_p.P261P|SYBU_ENST00000529690.1_Silent_p.P131P|SYBU_ENST00000446070.2_Silent_p.P260P|SYBU_ENST00000533171.1_Silent_p.P261P|SYBU_ENST00000408908.2_Silent_p.P261P|SYBU_ENST00000433638.1_Silent_p.P261P|SYBU_ENST00000528331.1_Silent_p.P142P|SYBU_ENST00000533065.1_Silent_p.P142P|SYBU_ENST00000529175.1_Silent_p.P55P|SYBU_ENST00000276646.9_Silent_p.P261P|SYBU_ENST00000424158.2_Silent_p.P266P|SYBU_ENST00000533895.1_Silent_p.P260P|SYBU_ENST00000440310.1_Silent_p.P261P|SYBU_ENST00000532779.1_Silent_p.P193P|SYBU_ENST00000528647.1_Silent_p.P260P|SYBU_ENST00000419099.1_Silent_p.P260P|SYBU_ENST00000527707.1_5'UTR	p.P258P	NM_001099756.1	NP_001093226.1	WXS	Illumina GAIIx	Phase_I	Q9NX95	SYBU_HUMAN			5	1501	-			261			Sufficient for interaction with KIF5B.		A8K354|B3KQX3|B3KU61|Q5R1T1|Q5R1T2|Q5R1T3|Q5Y2M6|Q8ND49|Q8TCR6|Q96D80|Q9P256	Silent	SNP	ENST00000422135.1	37	c.774C>A	CCDS47912.1																																																																																				0.453	SYBU-204	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000385501.1	NM_017786		96	57	1	0	3.78979e-47	1	4.09297e-47	96	57				
TMEM2	23670	broad.mit.edu	37	9	74324303	74324303	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr9:74324303T>C	ENST00000377044.4	-	17	3396	c.2857A>G	c.(2857-2859)Att>Gtt	p.I953V	TMEM2_ENST00000377066.5_Missense_Mutation_p.I890V	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	Q9UHN6	TMEM2_HUMAN	transmembrane protein 2	953					multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)		GAGCCATCAATGTCATGGAAT	0.448																																						ENST00000377044.4																			0				central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(15)|liver(1)|lung(19)|ovary(2)|prostate(5)|skin(1)|stomach(1)|urinary_tract(2)	56						c.(2857-2859)Att>Gtt		transmembrane protein 2							219.0	184.0	195.0					9																	74324303		2203	4300	6503	SO:0001583	missense	23670					integral to membrane		g.chr9:74324303T>C		CCDS6638.1, CCDS47979.1	9q21.13	2011-07-19			ENSG00000135048	ENSG00000135048			11869	protein-coding gene	gene with protein product		605835					Standard	NM_013390		Approved		uc011lsa.1	Q9UHN6	OTTHUMG00000020000	ENST00000377044.4:c.2857A>G	9.37:g.74324303T>C	ENSP00000366243:p.Ile953Val		Somatic				TMEM2_ENST00000377066.5_Missense_Mutation_p.I890V	p.I953V	NM_001135820.1|NM_013390.2	NP_001129292.1|NP_037522.1	WXS	Illumina GAIIx	Phase_I	Q9UHN6	TMEM2_HUMAN		GBM - Glioblastoma multiforme(74;7.45e-21)|OV - Ovarian serous cystadenocarcinoma(323;1.02e-16)	17	3396	-		all_epithelial(88;4.56e-14)|Myeloproliferative disorder(762;0.0255)	953					A6H8W9|B2RTQ6|Q5T838|Q5T839|Q5T840|Q5T841|Q8NBP6|Q9P2D5	Missense_Mutation	SNP	ENST00000377044.4	37	c.2857A>G	CCDS6638.1	.	.	.	.	.	.	.	.	.	.	T	0.803	-0.754578	0.03041	.	.	ENSG00000135048	ENST00000377044;ENST00000377066;ENST00000377043	T;T;T	0.42900	0.96;0.96;0.96	5.67	-5.47	0.02600	Pectin lyase fold/virulence factor (1);	0.901261	0.09718	N	0.764883	T	0.08758	0.0217	N	0.00224	-1.81	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44034	-0.9354	10	0.02654	T	1	.	13.5683	0.61832	0.0:0.6285:0.1083:0.2632	.	953;890	Q9UHN6;Q9UHN6-2	TMEM2_HUMAN;.	V	953;890;54	ENSP00000366243:I953V;ENSP00000366266:I890V;ENSP00000366242:I54V	ENSP00000366242:I54V	I	-	1	0	TMEM2	73514123	0.000000	0.05858	0.001000	0.08648	0.904000	0.53231	-1.121000	0.03270	-0.943000	0.03691	-0.479000	0.04858	ATT		0.448	TMEM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052618.2	NM_013390		28	34	0	0	0	1	0	28	34				
LRRC37A4P	55073	broad.mit.edu	37	17	43587730	43587730	+	RNA	SNP	A	A	C			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr17:43587730A>C	ENST00000579913.1	-	0	1394				RP11-798G7.5_ENST00000253803.2_RNA	NR_002940.2				leucine rich repeat containing 37, member A4, pseudogene																		GTATTGATTCATTTTATTCAT	0.343																																						ENST00000253803.2																			0																																																			0							g.chr17:43587730A>C	AK000982		17q21.31	2014-04-01	2012-03-07	2012-03-07	ENSG00000214425	ENSG00000214425			25479	pseudogene	pseudogene			"""leucine rich repeat containing 37, member A4 (pseudogene)"""	LRRC37A4			Standard	NR_002940		Approved	FLJ10120	uc031rhd.1		OTTHUMG00000179212		17.37:g.43587730A>C			Somatic				LRRC37A4P_ENST00000579913.1_RNA				WXS	Illumina GAIIx	Phase_I					0	267	+									RNA	SNP	ENST00000579913.1	37																																																																																						0.343	LRRC37A4P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445300.1	NR_002940		3	43	0	0	0	1	0	3	43				
ALG1	56052	broad.mit.edu	37	16	5121851	5121851	+	Start_Codon_SNP	SNP	A	A	G			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr16:5121851A>G	ENST00000262374.5	+	1	32	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	ALG1_ENST00000588623.1_Intron|ALG1_ENST00000544428.1_5'Flank	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	1					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				GCCAGCCAAGATGGCGGCCTC	0.721																																						ENST00000262374.5																			0				breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						c.(1-3)Atg>Gtg		ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase							13.0	14.0	14.0					16																	5121851		2188	4285	6473	SO:0001582	initiator_codon_variant	56052				dolichol-linked oligosaccharide biosynthetic process|lipopolysaccharide biosynthetic process|post-translational protein modification|protein N-linked glycosylation via asparagine	endoplasmic reticulum membrane|integral to membrane	chitobiosyldiphosphodolichol beta-mannosyltransferase activity	g.chr16:5121851A>G	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.1A>G	16.37:g.5121851A>G	ENSP00000262374:p.Met1Val		Somatic				ALG1_ENST00000588623.1_Intron	p.M1V	NM_019109.4	NP_061982.3	WXS	Illumina GAIIx	Phase_I	Q9BT22	ALG1_HUMAN			1	32	+		Ovarian(90;0.0164)	1					B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Translation_Start_Site	SNP	ENST00000262374.5	37	c.1A>G	CCDS10528.1	.	.	.	.	.	.	.	.	.	.	A	11.97	1.797087	0.31777	.	.	ENSG00000033011	ENST00000262374	T	0.75367	-0.93	4.81	4.81	0.61882	.	0.309916	0.36591	N	0.002506	T	0.66446	0.2790	.	.	.	0.80722	D	1	B	0.15141	0.012	B	0.11329	0.006	T	0.65961	-0.6041	9	0.87932	D	0	-29.8406	10.8028	0.46497	1.0:0.0:0.0:0.0	.	1	Q9BT22	ALG1_HUMAN	V	1	ENSP00000262374:M1V	ENSP00000262374:M1V	M	+	1	0	ALG1	5061852	.	.	1.000000	0.80357	0.109000	0.19521	.	.	1.816000	0.52996	0.454000	0.30748	ATG		0.721	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	Missense_Mutation	8	10	0	0	0	1	0	8	10				
TMEM35	59353	broad.mit.edu	37	X	100349757	100349757	+	Nonsense_Mutation	SNP	C	C	T			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chrX:100349757C>T	ENST00000372930.4	+	2	599	c.316C>T	c.(316-318)Cag>Tag	p.Q106*	TMEM35_ENST00000478351.1_3'UTR|TRMT2B-AS1_ENST00000443801.2_RNA	NM_021637.2	NP_067650.1	Q53FP2	TMM35_HUMAN	transmembrane protein 35	106						cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|peroxisome (GO:0005777)				NS(1)|large_intestine(3)|liver(1)|skin(1)|urinary_tract(1)	7						CTTCTTCCACCAGCTGGTCGG	0.577																																						ENST00000372930.4																			0				NS(1)|large_intestine(3)|liver(1)|skin(1)|urinary_tract(1)	7						c.(316-318)Cag>Tag		transmembrane protein 35							250.0	183.0	206.0					X																	100349757		2203	4300	6503	SO:0001587	stop_gained	59353					cytoplasmic membrane-bounded vesicle|integral to membrane|peroxisomal membrane		g.chrX:100349757C>T	AK024146	CCDS14478.1	Xq22	2008-02-05			ENSG00000126950	ENSG00000126950			25864	protein-coding gene	gene with protein product							Standard	NM_021637		Approved	FLJ14084	uc004egw.3	Q53FP2	OTTHUMG00000022016	ENST00000372930.4:c.316C>T	X.37:g.100349757C>T	ENSP00000362021:p.Gln106*		Somatic				TMEM35_ENST00000478351.1_3'UTR	p.Q106*	NM_021637.2	NP_067650.1	WXS	Illumina GAIIx	Phase_I	Q53FP2	TMM35_HUMAN			2	599	+			106					Q9H7Y3	Nonsense_Mutation	SNP	ENST00000372930.4	37	c.316C>T	CCDS14478.1	.	.	.	.	.	.	.	.	.	.	C	37	6.294758	0.97449	.	.	ENSG00000126950	ENST00000372930;ENST00000444892	.	.	.	5.51	5.51	0.81932	.	0.052538	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-34.3831	18.3931	0.90490	0.0:1.0:0.0:0.0	.	.	.	.	X	106;65	.	ENSP00000362021:Q106X	Q	+	1	0	TMEM35	100236413	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.267000	0.78462	2.284000	0.76573	0.594000	0.82650	CAG		0.577	TMEM35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057508.1	NM_021637		47	52	0	0	0	1	0	47	52				
TUBB8P7	197331	broad.mit.edu	37	16	90162513	90162513	+	RNA	SNP	T	T	C			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	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																																						ENST00000564451.1																			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			Somatic				TUBB8P7_ENST00000567960.1_RNA				WXS	Illumina GAIIx	Phase_I					0	1866	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.537	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		5	104	0	0	0	1	0	5	104				
SLC13A5	284111	broad.mit.edu	37	17	6594096	6594096	+	Splice_Site	SNP	A	A	T			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr17:6594096A>T	ENST00000433363.2	-	10	1671		c.e10+1		SLC13A5_ENST00000293800.6_Splice_Site|SLC13A5_ENST00000573648.1_Splice_Site|SLC13A5_ENST00000381074.4_Splice_Site	NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	Q86YT5	S13A5_HUMAN	solute carrier family 13 (sodium-dependent citrate transporter), member 5						transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	citrate transmembrane transporter activity (GO:0015137)|sodium:dicarboxylate symporter activity (GO:0017153)|succinate transmembrane transporter activity (GO:0015141)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						CAGGTTACTTACCATGGAGGC	0.552																																						ENST00000433363.2																			0				breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(9)|prostate(5)|skin(3)|urinary_tract(1)	26						c.e10+1		solute carrier family 13 (sodium-dependent citrate transporter), member 5							211.0	187.0	195.0					17																	6594096		2203	4300	6503	SO:0001630	splice_region_variant	284111					integral to membrane	citrate transmembrane transporter activity	g.chr17:6594096A>T	AJ489980	CCDS11079.1, CCDS45593.1, CCDS67136.1, CCDS67137.1	17p13.1	2013-05-22			ENSG00000141485	ENSG00000141485		"""Solute carriers"""	23089	protein-coding gene	gene with protein product		608305				12445824	Standard	NM_001284510		Approved	NACT	uc002gdj.3	Q86YT5	OTTHUMG00000102052	ENST00000433363.2:c.1437+1T>A	17.37:g.6594096A>T			Somatic				SLC13A5_ENST00000293800.6_Splice_Site|SLC13A5_ENST00000573648.1_Splice_Site|SLC13A5_ENST00000381074.4_Splice_Site		NM_001284510.1|NM_177550.3	NP_001271439.1|NP_808218.1	WXS	Illumina GAIIx	Phase_I	Q86YT5	S13A5_HUMAN			10	1671	-								B3KXR0|B7Z4P2|B7ZLB4|F8W7N2|Q6ZMG1	Splice_Site	SNP	ENST00000433363.2	37		CCDS11079.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.942801	0.73672	.	.	ENSG00000141485	ENST00000293800;ENST00000433363;ENST00000381074	.	.	.	4.8	4.8	0.61643	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.606	0.56523	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC13A5	6534820	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	8.396000	0.90190	1.920000	0.55613	0.533000	0.62120	.		0.552	SLC13A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219853.2	NM_177550	Intron	39	56	0	0	0	1	0	39	56				
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	AC005262.2_ENST00000585980.1_RNA|AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4				Dom	yes		19	19p13.3	2767	Mis	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""			E			uveal melanoma		82	Substitution - Missense(82)	p.Q209L(80)|p.Q209P(2)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg		guanine nucleotide binding protein (G protein), alpha 11 (Gq class)							104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767				activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256			4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	Standard	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		Somatic				GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA	p.Q209L	NM_002067.2	NP_002058.2	WXS	Illumina GAIIx	Phase_I	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209					O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2	NM_002067		32	42	0	0	0	1	0	32	42				
RAB33A	9363	broad.mit.edu	37	X	129318341	129318341	+	Missense_Mutation	SNP	T	T	C			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chrX:129318341T>C	ENST00000257017.4	+	2	755	c.341T>C	c.(340-342)gTc>gCc	p.V114A		NM_004794.2	NP_004785.1	Q14088	RB33A_HUMAN	RAB33A, member RAS oncogene family	114					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(5)	11						CATGCCGTGGTCTTCGTCTAT	0.502																																						ENST00000257017.4																			0				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(5)	11						c.(340-342)gTc>gCc		RAB33A, member RAS oncogene family							162.0	122.0	135.0					X																	129318341		2203	4300	6503	SO:0001583	missense	9363				protein transport|small GTPase mediated signal transduction	plasma membrane	GTP binding|GTPase activity|protein binding	g.chrX:129318341T>C	D14889	CCDS14621.1	Xq26	2008-02-05			ENSG00000134594	ENSG00000134594		"""RAB, member RAS oncogene"""	9773	protein-coding gene	gene with protein product		300333				7688322, 9512502	Standard	NM_004794		Approved	RabS10	uc004evl.3	Q14088	OTTHUMG00000022391	ENST00000257017.4:c.341T>C	X.37:g.129318341T>C	ENSP00000257017:p.Val114Ala		Somatic					p.V114A	NM_004794.2	NP_004785.1	WXS	Illumina GAIIx	Phase_I	Q14088	RB33A_HUMAN			2	755	+			114					Q5JUZ6|Q92465	Missense_Mutation	SNP	ENST00000257017.4	37	c.341T>C	CCDS14621.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.298518	0.81025	.	.	ENSG00000134594	ENST00000257017	D	0.81996	-1.56	4.71	4.71	0.59529	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.89753	0.6806	M	0.69523	2.12	0.80722	D	1	D	0.76494	0.999	D	0.79784	0.993	D	0.90910	0.4775	10	0.87932	D	0	-19.3113	13.6381	0.62233	0.0:0.0:0.0:1.0	.	114	Q14088	RB33A_HUMAN	A	114	ENSP00000257017:V114A	ENSP00000257017:V114A	V	+	2	0	RAB33A	129146022	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.997000	0.88414	1.663000	0.50791	0.350000	0.21858	GTC		0.502	RAB33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058246.1	NM_004794		23	32	0	0	0	1	0	23	32				
FAM13B	51306	broad.mit.edu	37	5	137288386	137288386	+	Missense_Mutation	SNP	C	C	A			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr5:137288386C>A	ENST00000033079.3	-	16	2246	c.1795G>T	c.(1795-1797)Gat>Tat	p.D599Y	FAM13B_ENST00000425075.2_Missense_Mutation_p.D503Y|FAM13B_ENST00000420893.2_Missense_Mutation_p.D599Y	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B	599					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			endometrium(4)|kidney(2)|lung(5)	11						GCAGCAATATCACTGTAGGAG	0.333																																						ENST00000033079.3																			0				endometrium(4)|kidney(2)|lung(5)	11						c.(1795-1797)Gat>Tat		family with sequence similarity 13, member B							96.0	101.0	99.0					5																	137288386		2203	4300	6503	SO:0001583	missense	0				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr5:137288386C>A	AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.1795G>T	5.37:g.137288386C>A	ENSP00000033079:p.Asp599Tyr		Somatic				FAM13B_ENST00000420893.2_Missense_Mutation_p.D599Y|FAM13B_ENST00000425075.2_Missense_Mutation_p.D503Y	p.D599Y	NM_016603.2	NP_057687.2	WXS	Illumina GAIIx	Phase_I	Q9NYF5	FA13B_HUMAN			16	2246	-			599					D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	c.1795G>T	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.716476	0.89205	.	.	ENSG00000031003	ENST00000033079;ENST00000425075;ENST00000420893	D;T;D	0.95756	-3.8;0.53;-3.8	6.05	6.05	0.98169	.	0.048468	0.85682	D	0.000000	D	0.97892	0.9307	M	0.82056	2.57	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	D	0.98027	1.0374	10	0.87932	D	0	-16.9519	20.2037	0.98272	0.0:1.0:0.0:0.0	.	503;599;599	G3V0H9;Q9NYF5-2;Q9NYF5	.;.;FA13B_HUMAN	Y	599;503;599	ENSP00000033079:D599Y;ENSP00000394669:D503Y;ENSP00000388521:D599Y	ENSP00000033079:D599Y	D	-	1	0	FAM13B	137316285	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.784000	0.75084	2.866000	0.98385	0.650000	0.86243	GAT		0.333	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			42	3	1	0	1.51926e-22	1	1.51926e-22	42	3				
TUBB8P7	197331	broad.mit.edu	37	16	90162579	90162579	+	RNA	SNP	C	C	T			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr16:90162579C>T	ENST00000564451.1	+	0	1932				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7																		AGGAGTATGCCGAGGAGGAGG	0.512																																						ENST00000564451.1																			0																																																			0							g.chr16:90162579C>T			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162579C>T			Somatic				TUBB8P7_ENST00000567960.1_RNA				WXS	Illumina GAIIx	Phase_I					0	1932	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.512	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		5	122	0	0	0	1	0	5	122				
BRCA1	672	broad.mit.edu	37	17	41244681	41244681	+	Missense_Mutation	SNP	G	G	C	rs80357961|rs80357819		TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr17:41244681G>C	ENST00000357654.3	-	10	2985	c.2867C>G	c.(2866-2868)tCt>tGt	p.S956C	BRCA1_ENST00000471181.2_Missense_Mutation_p.S956C|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.S956C|BRCA1_ENST00000309486.4_Missense_Mutation_p.S660C|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.S909C|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000354071.3_Missense_Mutation_p.S956C|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000351666.3_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	956					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		TCTGAACTGAGATGATAGACA	0.393			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																												ENST00000309486.4			yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	"""D, Mis, N, F, S"""	familial breast/ovarian cancer gene 1			E		"""breast, ovarian"""	ovarian		0				NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120						c.(1978-1980)tCt>tGt	Homologous recombination	breast cancer 1, early onset							120.0	119.0	120.0					17																	41244681		2203	4300	6503	SO:0001583	missense	672	Hereditary Breast-Ovarian Cancer, BRCA1 type	Familial Cancer Database		androgen receptor signaling pathway|apoptosis|cellular response to indole-3-methanol|chromosome segregation|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator|DNA damage response, signal transduction resulting in induction of apoptosis|double-strand break repair via homologous recombination|fatty acid biosynthetic process|G2/M transition DNA damage checkpoint|negative regulation of centriole replication|negative regulation of fatty acid biosynthetic process|negative regulation of histone H3-K9 methylation|negative regulation of transcription, DNA-dependent|positive regulation of cell cycle arrest|positive regulation of DNA repair|positive regulation of histone acetylation|positive regulation of histone H3-K4 methylation|positive regulation of histone H4-K20 methylation|positive regulation of protein ubiquitination|positive regulation of transcription from RNA polymerase II promoter|postreplication repair|protein autoubiquitination|protein K6-linked ubiquitination|regulation of cell motility|regulation of cell proliferation|regulation of transcription from RNA polymerase III promoter|response to estrogen stimulus|response to ionizing radiation|substrate adhesion-dependent cell spreading	BRCA1-A complex|BRCA1-BARD1 complex|gamma-tubulin ring complex|nucleoplasm|plasma membrane|ribonucleoprotein complex|ruffle	androgen receptor binding|identical protein binding|protein binding|RNA binding|transcription coactivator activity|transcription regulatory region DNA binding|tubulin binding|ubiquitin protein ligase binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr17:41244681G>C	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.2867C>G	17.37:g.41244681G>C	ENSP00000350283:p.Ser956Cys	TCGA Ovarian(2;0.000030)	Somatic				BRCA1_ENST00000354071.3_Missense_Mutation_p.S956C|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000357654.3_Missense_Mutation_p.S956C|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000346315.3_Missense_Mutation_p.S956C|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000493795.1_Missense_Mutation_p.S909C|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000591534.1_Intron|BRCA1_ENST00000471181.2_Missense_Mutation_p.S956C|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591849.1_Intron	p.S660C	NM_007297.3	NP_009228.2	WXS	Illumina GAIIx	Phase_I	P38398	BRCA1_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.126)	9	3006	-		Breast(137;0.000717)	956					O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Missense_Mutation	SNP	ENST00000357654.3	37	c.1979C>G	CCDS11453.1	.	.	.	.	.	.	.	.	.	.	G	8.488	0.861394	0.17178	.	.	ENSG00000012048	ENST00000357654;ENST00000412061;ENST00000354071;ENST00000346315;ENST00000309486;ENST00000471181;ENST00000493795	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.04	1.78	0.24846	.	0.847511	0.10115	N	0.714129	D	0.88209	0.6375	M	0.90922	3.16	0.09310	N	1	D;D;D;D;D;P	0.76494	0.999;0.999;0.999;0.974;0.996;0.819	D;D;D;P;P;P	0.75484	0.921;0.921;0.986;0.854;0.908;0.464	T	0.73392	-0.3997	10	0.87932	D	0	.	4.9292	0.13909	0.1682:0.0:0.5368:0.295	.	956;915;956;956;956;956	E7EMP0;E7ERL4;Q5YLB2;E9PFC7;P38398;P38398-2	.;.;.;.;BRCA1_HUMAN;.	C	956;956;956;956;660;956;909	ENSP00000350283:S956C;ENSP00000326002:S956C;ENSP00000246907:S956C;ENSP00000310938:S660C;ENSP00000418960:S956C;ENSP00000418775:S909C	ENSP00000310938:S660C	S	-	2	0	BRCA1	38498207	0.003000	0.15002	0.176000	0.23000	0.009000	0.06853	-0.005000	0.12855	0.699000	0.31761	-0.188000	0.12872	TCT		0.393	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294		4	143	0	0	0	1	0	4	143				
OSGIN1	29948	broad.mit.edu	37	16	83999242	83999242	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr16:83999242A>G	ENST00000343939.2	+	7	1696	c.1313A>G	c.(1312-1314)tAt>tGt	p.Y438C	OSGIN1_ENST00000393306.1_Missense_Mutation_p.Y355C|NECAB2_ENST00000305202.4_5'Flank|OSGIN1_ENST00000361711.3_Missense_Mutation_p.Y355C			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	438					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						CCCAGCCCCTATGAGGGTTAC	0.617																																						ENST00000343939.2																			0				autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						c.(1312-1314)tAt>tGt		oxidative stress induced growth inhibitor 1							87.0	79.0	82.0					16																	83999242		2200	4300	6500	SO:0001583	missense	29948				cell differentiation|multicellular organismal development|negative regulation of cell growth		growth factor activity	g.chr16:83999242A>G	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1313A>G	16.37:g.83999242A>G	ENSP00000343376:p.Tyr438Cys		Somatic				OSGIN1_ENST00000361711.3_Missense_Mutation_p.Y355C|OSGIN1_ENST00000393306.1_Missense_Mutation_p.Y355C	p.Y438C			WXS	Illumina GAIIx	Phase_I	Q9UJX0	OSGI1_HUMAN			7	1696	+			438					Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37	c.1313A>G		.	.	.	.	.	.	.	.	.	.	A	16.91	3.253680	0.59212	.	.	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.48201	0.82;0.82;0.82	4.8	3.65	0.41850	.	0.125086	0.56097	D	0.000023	T	0.59252	0.2180	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.64042	0.921	T	0.59182	-0.7502	10	0.42905	T	0.14	-24.9902	10.0644	0.42295	0.85:0.0:0.0:0.1499	.	438	Q9UJX0	OSGI1_HUMAN	C	438;355;355	ENSP00000343376:Y438C;ENSP00000355374:Y355C;ENSP00000376983:Y355C	ENSP00000343376:Y438C	Y	+	2	0	OSGIN1	82556743	1.000000	0.71417	1.000000	0.80357	0.789000	0.44602	5.901000	0.69861	1.794000	0.52575	0.383000	0.25322	TAT		0.617	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370		18	15	0	0	0	1	0	18	15				
DNAH17	8632	broad.mit.edu	37	17	76563118	76563118	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr17:76563118G>A	ENST00000585328.1	-	10	1539	c.1415C>T	c.(1414-1416)gCc>gTc	p.A472V	DNAH17_ENST00000389840.5_Missense_Mutation_p.A472V	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	472	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TTTGCAGTCGGCAAAAACCTT	0.567																																						ENST00000389840.5																			0				NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116						c.(1414-1416)gCc>gTc		dynein, axonemal, heavy chain 17							68.0	57.0	61.0					17																	76563118		2203	4300	6503	SO:0001583	missense	8632							g.chr17:76563118G>A	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.1415C>T	17.37:g.76563118G>A	ENSP00000465516:p.Ala472Val		Somatic				DNAH17_ENST00000585328.1_Missense_Mutation_p.A472V	p.A472V			WXS	Illumina GAIIx	Phase_I			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)		10	1539	-								O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	37	c.1415C>T		.	.	.	.	.	.	.	.	.	.	G	8.418	0.845762	0.16963	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.56275	0.47	4.92	2.93	0.34026	.	0.643900	0.13370	N	0.393012	T	0.46092	0.1375	L	0.54323	1.7	0.24140	N	0.995735	B	0.13145	0.007	B	0.16722	0.016	T	0.34428	-0.9829	10	0.30078	T	0.28	.	9.5094	0.39067	0.168:0.0:0.832:0.0	.	174	Q9UFH2-4	.	V	472	ENSP00000374490:A472V	ENSP00000300671:A472V	A	-	2	0	DNAH17	74074713	0.865000	0.29922	0.042000	0.18584	0.248000	0.25809	3.514000	0.53422	0.609000	0.30018	0.561000	0.74099	GCC		0.567	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628		4	21	0	0	0	1	0	4	21				
CTDSP1	58190	broad.mit.edu	37	2	219268127	219268127	+	Missense_Mutation	SNP	A	A	G			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr2:219268127A>G	ENST00000273062.2	+	6	980	c.644A>G	c.(643-645)cAt>cGt	p.H215R	MIR26B_ENST00000362251.2_RNA|CTDSP1_ENST00000488627.1_3'UTR|CTDSP1_ENST00000443891.1_Missense_Mutation_p.H214R	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	Q9GZU7	CTDS1_HUMAN	CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1	215	FCP1 homology. {ECO:0000255|PROSITE- ProRule:PRU00336}.				negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|protein dephosphorylation (GO:0006470)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	CTD phosphatase activity (GO:0008420)|metal ion binding (GO:0046872)			NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8		Renal(207;0.0915)		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TATGTCTTCCATCCAGACAAT	0.607																																						ENST00000273062.2																			0				NS(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	8						c.(643-645)cAt>cGt		CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase 1							61.0	63.0	62.0					2																	219268127		2203	4300	6503	SO:0001583	missense	58190				protein dephosphorylation|regulation of transcription from RNA polymerase II promoter	nucleus	CTD phosphatase activity|metal ion binding|protein binding	g.chr2:219268127A>G	AF229162	CCDS2416.1, CCDS56166.1	2q35	2010-06-21			ENSG00000144579	ENSG00000144579		"""Serine/threonine phosphatases / CTD aspartate-based phosphatases"""	21614	protein-coding gene	gene with protein product	"""nuclear LIM interactor-interacting factor"", ""small CTD phosphatase 1"""	605323				11950066, 12721286	Standard	NM_021198		Approved	NLIIF, SCP1	uc021vwv.1	Q9GZU7	OTTHUMG00000133109	ENST00000273062.2:c.644A>G	2.37:g.219268127A>G	ENSP00000273062:p.His215Arg		Somatic				CTDSP1_ENST00000488627.1_3'UTR|CTDSP1_ENST00000443891.1_Missense_Mutation_p.H214R	p.H215R	NM_021198.2|NM_182642.2	NP_067021.1|NP_872580.1	WXS	Illumina GAIIx	Phase_I	Q9GZU7	CTDS1_HUMAN		Epithelial(149;9.96e-07)|all cancers(144;0.00017)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	6	980	+		Renal(207;0.0915)	215			FCP1 homology.		C9IYG0|Q7Z5Q3|Q7Z5Q4	Missense_Mutation	SNP	ENST00000273062.2	37	c.644A>G	CCDS2416.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.22|19.22	3.786513|3.786513	0.70337|0.70337	.|.	.|.	ENSG00000144579|ENSG00000144579	ENST00000443891;ENST00000273062|ENST00000452977;ENST00000428361	T;T|.	0.17691|.	2.26;2.26|.	4.64|4.64	4.64|4.64	0.57946|0.57946	NLI interacting factor (3);Dullard phosphatase domain, eukaryotic (1);HAD-like domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.88243|0.88243	0.6384|0.6384	H|H	0.98664|0.98664	4.295|4.295	0.80722|0.80722	D|D	1|1	P;P|.	0.46277|.	0.875;0.875|.	P;P|.	0.59288|.	0.855;0.855|.	D|D	0.92137|0.92137	0.5717|0.5717	10|5	0.72032|.	D|.	0.01|.	-21.5941|-21.5941	13.051|13.051	0.58954|0.58954	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	215;214|.	Q9GZU7;C9IYG0|.	CTDS1_HUMAN;.|.	R|V	214;215|208;216	ENSP00000392248:H214R;ENSP00000273062:H215R|.	ENSP00000273062:H215R|.	H|I	+|+	2|1	0|0	CTDSP1|CTDSP1	218976371|218976371	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.763000|0.763000	0.43281|0.43281	9.273000|9.273000	0.95719|0.95719	1.724000|1.724000	0.51502|0.51502	0.402000|0.402000	0.26972|0.26972	CAT|ATC		0.607	CTDSP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256774.1	NM_182642, NM_021198		14	24	0	0	0	1	0	14	24				
TUBB8P7	197331	broad.mit.edu	37	16	90162462	90162462	+	RNA	SNP	A	A	G			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr16:90162462A>G	ENST00000564451.1	+	0	1815				TUBB8P7_ENST00000567960.1_RNA					tubulin, beta 8 class VIII pseudogene 7									p.T398T(1)									ACTGGTACACAGGCGAGGGCA	0.522																																						ENST00000564451.1																			1	Substitution - coding silent(1)	p.T398T(1)	kidney(1)																																																0							g.chr16:90162462A>G			16q24.3	2013-02-18			ENSG00000261812	ENSG00000261812			42345	pseudogene	pseudogene							Standard	NG_002334		Approved				OTTHUMG00000172847		16.37:g.90162462A>G			Somatic				TUBB8P7_ENST00000567960.1_RNA				WXS	Illumina GAIIx	Phase_I					0	1815	+									RNA	SNP	ENST00000564451.1	37																																																																																						0.522	TUBB8P7-004	KNOWN	basic	processed_transcript	polymorphic_pseudogene	OTTHUMT00000420856.1	NG_002334		5	105	0	0	0	1	0	5	105				
TWF2	11344	broad.mit.edu	37	3	52263159	52263159	+	Missense_Mutation	SNP	G	G	C			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr3:52263159G>C	ENST00000305533.5	-	9	1184	c.941C>G	c.(940-942)cCc>cGc	p.P314R	TLR9_ENST00000597542.1_Intron|TLR9_ENST00000360658.2_5'Flank|TLR9_ENST00000494383.1_Intron|TWF2_ENST00000499914.2_3'UTR	NM_007284.3	NP_009215.1	Q6IBS0	TWF2_HUMAN	twinfilin actin-binding protein 2	314					barbed-end actin filament capping (GO:0051016)|cell projection organization (GO:0030030)|cellular response to growth factor stimulus (GO:0071363)|cellular response to retinoic acid (GO:0071300)|negative regulation of actin filament polymerization (GO:0030837)|positive regulation of axon extension (GO:0045773)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of microvillus length (GO:0032532)|sequestering of actin monomers (GO:0042989)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|myofibril (GO:0030016)|perinuclear region of cytoplasm (GO:0048471)|stereocilium (GO:0032420)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|poly(A) RNA binding (GO:0044822)|protein kinase C binding (GO:0005080)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)		GTGTTGCTTGGGGTGCACCTC	0.642																																						ENST00000305533.5																			0				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|stomach(1)|urinary_tract(1)	15						c.(940-942)cCc>cGc		twinfilin actin-binding protein 2							119.0	106.0	110.0					3																	52263159		2203	4300	6503	SO:0001583	missense	11344							g.chr3:52263159G>C	Y17169	CCDS2849.1	3p21.1	2013-04-25	2013-04-25	2006-11-13	ENSG00000247596	ENSG00000247596			9621	protein-coding gene	gene with protein product		607433	"""protein tyrosine kinase 9-like (A6-related protein)"", ""PTK9L protein tyrosine kinase 9-like (A6-related protein)"", ""twinfilin, actin-binding protein, homolog 2 (Drosophila)"""	PTK9L		10406962, 12807912	Standard	NM_007284		Approved	A6RP, A6r		Q6IBS0	OTTHUMG00000158105	ENST00000305533.5:c.941C>G	3.37:g.52263159G>C	ENSP00000303908:p.Pro314Arg		Somatic				TWF2_ENST00000499914.2_3'UTR|TLR9_ENST00000494383.1_Intron|TLR9_ENST00000597542.1_Intron	p.P314R	NM_007284.3	NP_009215.1	WXS	Illumina GAIIx	Phase_I				BRCA - Breast invasive adenocarcinoma(193;2.43e-05)|Kidney(197;0.000539)|KIRC - Kidney renal clear cell carcinoma(197;0.000716)	9	1184	-								Q9Y3F5	Missense_Mutation	SNP	ENST00000305533.5	37	c.941C>G	CCDS2849.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.442530	0.83993	.	.	ENSG00000247596	ENST00000305533	T	0.31769	1.48	5.04	4.16	0.48862	.	.	.	.	.	T	0.59838	0.2223	M	0.86864	2.845	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67538	-0.5645	9	0.87932	D	0	.	13.3672	0.60692	0.0764:0.0:0.9236:0.0	.	314	Q6IBS0	TWF2_HUMAN	R	314	ENSP00000303908:P314R	ENSP00000303908:P314R	P	-	2	0	TWF2	52238199	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.824000	0.99380	1.120000	0.41904	0.561000	0.74099	CCC		0.642	TWF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350199.2			29	2	0	0	0	1	0	29	2				
C8orf31	286122	broad.mit.edu	37	8	144124604	144124604	+	Silent	SNP	G	G	A			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr8:144124604G>A	ENST00000395172.1	+	3	463	c.111G>A	c.(109-111)ggG>ggA	p.G37G	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	37										breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					GGGCCCAGGGGCTGCTGGCTG	0.642																																						ENST00000395172.1																			0				breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10						c.(109-111)ggG>ggA		chromosome 8 open reading frame 31							36.0	39.0	38.0					8																	144124604		2203	4300	6503	SO:0001819	synonymous_variant	286122							g.chr8:144124604G>A		CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.111G>A	8.37:g.144124604G>A			Somatic				C8orf31_ENST00000517653.1_3'UTR	p.G37G	NM_173687.2	NP_775958.1	WXS	Illumina GAIIx	Phase_I	Q8N9H6	CH031_HUMAN			3	463	+	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)		37					Q6GMU7	Silent	SNP	ENST00000395172.1	37	c.111G>A	CCDS6395.1																																																																																				0.642	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687		23	16	0	0	0	1	0	23	16				
DCAF8L2	347442	broad.mit.edu	37	X	27766141	27766141	+	Missense_Mutation	SNP	G	G	A			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chrX:27766141G>A	ENST00000451261.2	+	5	1528	c.1129G>A	c.(1129-1131)Gcc>Acc	p.A377T		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	377										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTGAATCCCGCCAATACCTA	0.408																																						ENST00000451261.2																			0				central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						c.(1129-1131)Gcc>Acc		DDB1 and CUL4 associated factor 8-like 2							107.0	80.0	89.0					X																	27766141		692	1591	2283	SO:0001583	missense	347442							g.chrX:27766141G>A		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1129G>A	X.37:g.27766141G>A	ENSP00000462745:p.Ala377Thr		Somatic					p.A377T	NM_001136533.1	NP_001130005.1	WXS	Illumina GAIIx	Phase_I					5	1528	+								B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	c.1129G>A	CCDS59162.1																																																																																				0.408	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354		3	38	0	0	0	1	0	3	38				
ZNF446	55663	broad.mit.edu	37	19	58991009	58991009	+	Splice_Site	SNP	G	G	C			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr19:58991009G>C	ENST00000594369.1	+	5	1008		c.e5-1		ZNF446_ENST00000596341.1_Splice_Site|ZNF446_ENST00000335841.4_Intron	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446						regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.?(1)		endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		CACATCCGCAGGAGGAGTGGG	0.582																																						ENST00000596341.1																			1	Unknown(1)	p.?(1)	endometrium(1)	endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8						c.e5-1		zinc finger protein 446							93.0	78.0	83.0					19																	58991009		2203	4300	6503	SO:0001630	splice_region_variant	55663				viral reproduction	nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:58991009G>C		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.628-1G>C	19.37:g.58991009G>C			Somatic				ZNF446_ENST00000335841.4_Intron|ZNF446_ENST00000594369.1_Splice_Site				WXS	Illumina GAIIx	Phase_I	Q9NWS9	ZN446_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)	5	2847	+		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)							Splice_Site	SNP	ENST00000594369.1	37		CCDS12982.1	.	.	.	.	.	.	.	.	.	.	G	16.47	3.131978	0.56828	.	.	ENSG00000083838	ENST00000335841;ENST00000540481;ENST00000391694	.	.	.	4.35	4.35	0.52113	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.5628	0.56293	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ZNF446	63682821	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	2.745000	0.47459	2.423000	0.82170	0.561000	0.74099	.		0.582	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	Intron	7	6	0	0	0	1	0	7	6				
UBA7	7318	broad.mit.edu	37	3	49842221	49842221	+	IGR	SNP	C	C	A			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr3:49842221C>A	ENST00000333486.3	-	0	3299				MIR5193_ENST00000584510.1_RNA|FAM212A_ENST00000333323.4_Missense_Mutation_p.P222H	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7						cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		CGTGCTCGGCCCCCTCAGTTC	0.657																																						ENST00000333323.4																			0											c.(664-666)cCc>cAc		family with sequence similarity 212, member A							78.0	84.0	82.0					3																	49842221		2203	4300	6503	SO:0001628	intergenic_variant	389119							g.chr3:49842221C>A	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267		3.37:g.49842221C>A			Somatic					p.P222H	NM_203370.1	NP_976248.1	WXS	Illumina GAIIx	Phase_I	Q96EL1	CC054_HUMAN			2	798	+			220					Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	c.665C>A	CCDS2805.1	.	.	.	.	.	.	.	.	.	.	C	19.48	3.836245	0.71373	.	.	ENSG00000185614	ENST00000333323	.	.	.	5.14	5.14	0.70334	.	0.000000	0.51477	D	0.000095	T	0.74253	0.3692	L	0.44542	1.39	0.51233	D	0.999919	D	0.89917	1.0	D	0.91635	0.999	T	0.76061	-0.3097	9	0.72032	D	0.01	.	18.4034	0.90525	0.0:1.0:0.0:0.0	.	220	Q96EL1	CC054_HUMAN	H	222	.	ENSP00000329735:P222H	P	+	2	0	C3orf54	49817225	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.950000	0.63603	2.686000	0.91538	0.561000	0.74099	CCC		0.657	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335		48	4	1	0	6.9144e-35	1	7.18033e-35	48	4				
GARS	2617	broad.mit.edu	37	7	30634583	30634585	+	In_Frame_Del	DEL	CTG	CTG	-	rs150213018		TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr7:30634583_30634585delCTG	ENST00000389266.3	+	1	287_289	c.46_48delCTG	c.(46-48)ctgdel	p.L20del	AC005154.6_ENST00000581665.1_RNA|AC005154.6_ENST00000584199.1_RNA|AC005154.6_ENST00000580440.1_RNA|AC005154.6_ENST00000579174.1_RNA|AC005154.6_ENST00000583664.1_RNA|AC005154.6_ENST00000584372.1_RNA|AC005154.6_ENST00000578994.1_RNA|AC005154.6_ENST00000582549.1_RNA	NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	20					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	TCGCGCCGCTCTGCTGCTGCTGC	0.749																																						ENST00000389266.3																			0				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24						c.(46-48)ctgdel		glycyl-tRNA synthetase	Glycine(DB00145)			181,3387		9,163,1612						-3.2	0.0		dbSNP_134	8	497,6929		13,471,3229	no	coding	GARS	NM_002047.2		22,634,4841	A1A1,A1R,RR		6.6927,5.0729,6.167				678,10316				SO:0001651	inframe_deletion	2617				cell death|diadenosine tetraphosphate biosynthetic process|glycyl-tRNA aminoacylation	cytosol|mitochondrial matrix|soluble fraction	ATP binding|glycine-tRNA ligase activity|protein dimerization activity	g.chr7:30634583_30634585delCTG	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"""Aminoacyl tRNA synthetases / Class II"""	4162	protein-coding gene	gene with protein product	"""glycine tRNA ligase"""	600287	"""Charcot-Marie-Tooth neuropathy 2D"""	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.46_48delCTG	7.37:g.30634592_30634594delCTG	ENSP00000373918:p.Leu20del		Somatic					p.L20del	NM_002047.2	NP_002038.2	WXS	Illumina GAIIx	Phase_I	P41250	SYG_HUMAN			1	287_289	+			20					B3KQA2|B4DIA0|Q969Y1	In_Frame_Del	DEL	ENST00000389266.3	37	c.46_48delCTG	CCDS43564.1																																																																																				0.749	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047		6	11						6	11	---	---	---	---
HEBP1	50865	broad.mit.edu	37	12	13154583	13154583	+	5'Flank	DEL	G	G	-	rs398076428|rs59113920	byFrequency	TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr12:13154583delG	ENST00000014930.4	-	0	0				HEBP1_ENST00000536942.1_5'Flank|RP11-377D9.3_ENST00000543321.1_lincRNA	NM_015987.4	NP_057071.2	Q9NRV9	HEBP1_HUMAN	heme binding protein 1						circadian rhythm (GO:0007623)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	heme binding (GO:0020037)			breast(1)|endometrium(1)|large_intestine(3)|lung(1)|urinary_tract(1)	7		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.153)		TCTGCTGAGCGGGGGCCCCCG	0.731													GGGG|GGGGG|GGGG|insertion	2433	0.485823	0.3949	0.4986	5008	,	,		11429	0.378		0.6064	False		,,,				2504	0.5869					ENST00000543321.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr12:13154583delG	AF117615	CCDS31749.1	12p13.2	2014-01-30			ENSG00000013583	ENSG00000013583		"""Endogenous ligands"""	17176	protein-coding gene	gene with protein product		605826				10640688	Standard	NM_015987		Approved	HEBP, HBP	uc001rbd.3	Q9NRV9	OTTHUMG00000168771		12.37:g.13154583delG	Exception_encountered		Somatic								WXS	Illumina GAIIx	Phase_I					0	31	+								A8K1G2|Q9Y5Z5	RNA	DEL	ENST00000014930.4	37		CCDS31749.1																																																																																				0.731	HEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401001.1			5	3						5	3	---	---	---	---
GFRA4	64096	broad.mit.edu	37	20	3644008	3644010	+	In_Frame_Del	DEL	CAG	CAG	-			TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr20:3644008_3644010delCAG	ENST00000319242.3	-	1	36_38	c.37_39delCTG	c.(37-39)ctgdel	p.L15del	GFRA4_ENST00000290417.2_In_Frame_Del_p.L15del			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	15					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						CACCCAGTAACAGCAGCAGCAGC	0.621																																						ENST00000290417.2																			0				large_intestine(1)|lung(2)	3						c.(37-39)ctgdel		GDNF family receptor alpha 4																																				SO:0001651	inframe_deletion	64096					anchored to membrane|extracellular region|plasma membrane	receptor activity	g.chr20:3644008_3644010delCAG	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.37_39delCTG	20.37:g.3644017_3644019delCAG	ENSP00000313423:p.Leu15del		Somatic				GFRA4_ENST00000319242.3_In_Frame_Del_p.L15del	p.L15del	NM_022139.3|NM_145762.2	NP_071422.1|NP_665705.1	WXS	Illumina GAIIx	Phase_I	Q9GZZ7	GFRA4_HUMAN			1	36_38	-			15					Q5JT74|Q9H191|Q9H192	In_Frame_Del	DEL	ENST00000319242.3	37	c.37_39delCTG	CCDS13056.1																																																																																				0.621	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762		2	4						2	4	---	---	---	---
CDH4	1002	broad.mit.edu	37	20	60470052	60470065	+	Frame_Shift_Del	DEL	CATCACGGTGACAG	CATCACGGTGACAG	-	rs149375024|rs145754297		TCGA-VD-AA8P-01A-11D-A39W-08	TCGA-VD-AA8P-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5e4ed9fe-6d1c-495a-8ae6-ade952d0fec2	9c561355-ff26-452d-9ed3-870d5a6fdb1e	g.chr20:60470052_60470065delCATCACGGTGACAG	ENST00000360469.5	+	8	1225_1238	c.1137_1150delCATCACGGTGACAG	c.(1135-1152)atcatcacggtgacagatfs	p.ITVTD380fs	CDH4_ENST00000543233.1_Frame_Shift_Del_p.ITVTD306fs	NM_001794.3	NP_001785.2	P55283	CADH4_HUMAN	cadherin 4, type 1, R-cadherin (retinal)	380	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74			BRCA - Breast invasive adenocarcinoma(19;2.36e-08)			CCACAGCCATCATCACGGTGACAGATGTGAATGA	0.547																																						ENST00000360469.5																			0				NS(2)|breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|liver(2)|lung(25)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74						c.(1135-1152)atcatcacggtgacagatfs		cadherin 4, type 1, R-cadherin (retinal)																																				SO:0001589	frameshift_variant	1002				adherens junction organization|cell junction assembly		calcium ion binding	g.chr20:60470052_60470065delCATCACGGTGACAG	L34059	CCDS13488.1, CCDS58784.1	20q13.3	2010-01-26			ENSG00000179242	ENSG00000179242		"""Cadherins / Major cadherins"""	1763	protein-coding gene	gene with protein product	"""R-Cadherin"""	603006				10191097, 10516427	Standard	NM_001794		Approved		uc002ybn.2	P55283	OTTHUMG00000032890	ENST00000360469.5:c.1137_1150delCATCACGGTGACAG	20.37:g.60470052_60470065delCATCACGGTGACAG	ENSP00000353656:p.Ile380fs		Somatic				CDH4_ENST00000543233.1_Frame_Shift_Del_p.ITVTD306fs	p.ITVTD380fs	NM_001794.3	NP_001785.2	WXS	Illumina GAIIx	Phase_I	P55283	CADH4_HUMAN	BRCA - Breast invasive adenocarcinoma(19;2.36e-08)		8	1225_1238	+			380			Cadherin 2.		B3KWB8|G3V1P8|Q2M208|Q5VZ44|Q9BZ05	Frame_Shift_Del	DEL	ENST00000360469.5	37	c.1137_1150delCATCACGGTGACAG	CCDS13488.1																																																																																				0.547	CDH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079965.2	NM_001794		28	73						28	73	---	---	---	---
