#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
PSAT1	29968	broad.mit.edu	37	9	80919787	80919787	+	Missense_Mutation	SNP	A	A	C			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr9:80919787A>C	ENST00000376588.3	+	4	396	c.328A>C	c.(328-330)Aag>Cag	p.K110Q	PSAT1_ENST00000347159.2_Missense_Mutation_p.K110Q	NM_058179.2	NP_478059.1	Q9Y617	SERC_HUMAN	phosphoserine aminotransferase 1	110					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-serine biosynthetic process (GO:0006564)|pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	O-phospho-L-serine:2-oxoglutarate aminotransferase activity (GO:0004648)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						TTGGTCAGCTAAGGCCGCAGA	0.507																																					Colon(34;187 791 10662 18313 37609)	uc004ala.3																			0				breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|urinary_tract(1)	20						c.(328-330)Aag>Cag		Homo sapiens phosphoserine aminotransferase 1 (PSAT1), transcript variant 1, mRNA.	L-Glutamic Acid(DB00142)|Pyridoxal Phosphate(DB00114)|Pyridoxine(DB00165)						112.0	103.0	106.0					9																	80919787		2203	4300	6503	SO:0001583	missense	29968				L-serine biosynthetic process|pyridoxine biosynthetic process		O-phospho-L-serine:2-oxoglutarate aminotransferase activity|pyridoxal phosphate binding	g.chr9:80919787A>C	BC004863	CCDS6659.1, CCDS6660.1	9q21.2	2008-08-11			ENSG00000135069	ENSG00000135069			19129	protein-coding gene	gene with protein product		610936				12633500, 3651428	Standard	NM_058179		Approved	PSA	uc004ala.3	Q9Y617	OTTHUMG00000020066	ENST00000376588.3:c.328A>C	9.37:g.80919787A>C	ENSP00000365773:p.Lys110Gln		Somatic				PSAT1_uc004alb.3_Missense_Mutation_p.K110Q	p.K110Q	NM_058179	NP_478059	WXS	Illumina GAIIx	Phase_I	Q9Y617	SERC_HUMAN			3	396	+			110					Q5T7G5|Q5T7G6|Q96AW2|Q9BQ12	Missense_Mutation	SNP	ENST00000376588.3	37	c.328A>C	CCDS6660.1	.	.	.	.	.	.	.	.	.	.	A	20.6	4.019948	0.75275	.	.	ENSG00000135069	ENST00000347159;ENST00000376588	T;T	0.66280	-0.2;-0.2	5.65	5.65	0.86999	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);Aminotransferase, class V/Cysteine desulfurase (1);	0.046935	0.85682	D	0.000000	T	0.80691	0.4671	M	0.85945	2.785	0.58432	D	0.999999	D;P	0.69078	0.997;0.86	D;B	0.67382	0.951;0.266	D	0.84230	0.0466	10	0.87932	D	0	-25.9967	15.8828	0.79216	1.0:0.0:0.0:0.0	.	110;110	Q9Y617-2;Q9Y617	.;SERC_HUMAN	Q	110	ENSP00000317606:K110Q;ENSP00000365773:K110Q	ENSP00000317606:K110Q	K	+	1	0	PSAT1	80109607	1.000000	0.71417	0.995000	0.50966	0.989000	0.77384	8.923000	0.92808	2.152000	0.67230	0.533000	0.62120	AAG		0.507	PSAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052777.1	NM_021154		4	50	0	0	0	1	0	4	50				
UBQLN3	50613	broad.mit.edu	37	11	5530553	5530553	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr11:5530553C>T	ENST00000311659.4	-	2	383	c.236G>A	c.(235-237)tGt>tAt	p.C79Y	HBG2_ENST00000380259.2_Intron	NM_017481.2	NP_059509.1	Q9H347	UBQL3_HUMAN	ubiquilin 3	79	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.									NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCGCACTCCACACTGTGCCAG	0.562																																					Ovarian(72;684 1260 12332 41642 52180)	uc001may.1																			0				NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(16)|ovary(4)|prostate(1)|skin(2)	39						c.(235-237)tGt>tAt		Homo sapiens ubiquilin 3 (UBQLN3), mRNA.							118.0	113.0	114.0					11																	5530553		2201	4297	6498	SO:0001583	missense	50613							g.chr11:5530553C>T	AF230481	CCDS7758.1	11p15	2013-02-12			ENSG00000175520	ENSG00000175520		"""Ubiquilin family"""	12510	protein-coding gene	gene with protein product		605473				10831842	Standard	NM_017481		Approved	TUP-1	uc001may.1	Q9H347	OTTHUMG00000066886	ENST00000311659.4:c.236G>A	11.37:g.5530553C>T	ENSP00000347997:p.Cys79Tyr		Somatic				HBG1_uc001mak.1_Intron|UBQLN3_uc021qcw.1_Missense_Mutation_p.C79Y	p.C79Y	NM_017481	NP_059509	WXS	Illumina GAIIx	Phase_I	Q9H347	UBQL3_HUMAN		Epithelial(150;1.74e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)	1	322	-		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)	79			Ubiquitin-like.		Q9NRE0	Missense_Mutation	SNP	ENST00000311659.4	37	c.236G>A	CCDS7758.1	.	.	.	.	.	.	.	.	.	.	C	15.82	2.947576	0.53186	.	.	ENSG00000175520	ENST00000311659;ENST00000445998	T;T	0.64618	-0.11;-0.11	5.24	5.24	0.73138	Ubiquitin supergroup (1);Ubiquitin (2);	0.000000	0.49916	D	0.000139	T	0.47303	0.1438	N	0.01431	-0.87	0.43039	D	0.994627	B	0.29085	0.232	P	0.48795	0.59	T	0.53989	-0.8360	10	0.25106	T	0.35	-24.9506	10.1835	0.42984	0.0:0.9088:0.0:0.0912	.	79	Q9H347	UBQL3_HUMAN	Y	79	ENSP00000347997:C79Y;ENSP00000412561:C79Y	ENSP00000347997:C79Y	C	-	2	0	UBQLN3	5487129	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.843000	0.55865	2.629000	0.89072	0.484000	0.47621	TGT		0.562	UBQLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143348.1	NM_017481		50	25	0	0	0	1	0	50	25				
OR5D18	219438	broad.mit.edu	37	11	55587399	55587399	+	Missense_Mutation	SNP	C	C	G	rs147156620		TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr11:55587399C>G	ENST00000333976.4	+	1	314	c.294C>G	c.(292-294)tgC>tgG	p.C98W		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55		all_epithelial(135;0.208)				TTTTAGGATGCGTAGTACAAT	0.433																																						uc010rin.2																			0				NS(2)|breast(1)|endometrium(3)|large_intestine(6)|lung(33)|ovary(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						c.(292-294)tgC>tgG		Homo sapiens olfactory receptor, family 5, subfamily D, member 18 (OR5D18), mRNA.							203.0	203.0	203.0					11																	55587399		2200	4296	6496	SO:0001583	missense	219438				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55587399C>G	AB065781	CCDS31510.1	11q11	2012-08-09			ENSG00000186119	ENSG00000186119		"""GPCR / Class A : Olfactory receptors"""	15285	protein-coding gene	gene with protein product							Standard	NM_001001952		Approved		uc010rin.2	Q8NGL1	OTTHUMG00000166811	ENST00000333976.4:c.294C>G	11.37:g.55587399C>G	ENSP00000335025:p.Cys98Trp		Somatic					p.C98W	NM_001001952	NP_001001952	WXS	Illumina GAIIx	Phase_I	Q8NGL1	OR5DI_HUMAN			0	294	+		all_epithelial(135;0.208)	98					Q6IF67|Q6IFD3|Q96RB3	Missense_Mutation	SNP	ENST00000333976.4	37	c.294C>G	CCDS31510.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	8.592	0.884887	0.17540	.	.	ENSG00000186119	ENST00000333976	T	0.00551	6.65	4.94	-5.17	0.02849	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	D	0.000680	T	0.03263	0.0095	H	0.98701	4.305	0.37293	D	0.908355	D	0.89917	1.0	D	0.97110	1.0	T	0.10706	-1.0618	10	0.87932	D	0	-31.9624	9.597	0.39580	0.0:0.5212:0.1199:0.3589	.	98	Q8NGL1	OR5DI_HUMAN	W	98	ENSP00000335025:C98W	ENSP00000335025:C98W	C	+	3	2	OR5D18	55343975	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.983000	0.03759	-0.871000	0.04042	-1.111000	0.02071	TGC		0.433	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952		39	156	0	0	0	1	0	39	156				
CSPG4	1464	broad.mit.edu	37	15	75969141	75969141	+	Missense_Mutation	SNP	C	C	T	rs368180303		TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr15:75969141C>T	ENST00000308508.5	-	10	5811	c.5719G>A	c.(5719-5721)Gtg>Atg	p.V1907M	AC105020.1_ENST00000435356.1_5'Flank|CTD-2026K11.1_ENST00000569467.1_RNA	NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1907	Cysteine-containing.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CCGTTGGCCACGAAGGCCAGC	0.672																																						uc002baw.3																			0		p.F1906F(1)		breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						c.(5719-5721)Gtg>Atg		Homo sapiens chondroitin sulfate proteoglycan 4 (CSPG4), mRNA.		C	MET/VAL	0,4394		0,0,2197	29.0	30.0	30.0		5719	0.3	0.9	15		30	1,8583		0,1,4291	no	missense	CSPG4	NM_001897.4	21	0,1,6488	TT,TC,CC		0.0116,0.0,0.0077	benign	1907/2323	75969141	1,12977	2197	4292	6489	SO:0001583	missense	1464				angiogenesis|cell differentiation|intracellular signal transduction|positive regulation of peptidyl-tyrosine phosphorylation|tissue remodeling	apical plasma membrane|cell surface|integral to plasma membrane|intracellular|lamellipodium membrane	protein kinase binding|signal transducer activity	g.chr15:75969141C>T	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.5719G>A	15.37:g.75969141C>T	ENSP00000312506:p.Val1907Met		Somatic					p.V1907M	NM_001897	NP_001888	WXS	Illumina GAIIx	Phase_I	Q6UVK1	CSPG4_HUMAN			9	5812	-			1907			Cysteine-containing.|Neurite growth inhibition (By similarity).		D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	c.5719G>A	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	C	10.95	1.495977	0.26774	0.0	1.16E-4	ENSG00000173546	ENST00000308508	T	0.24538	1.85	5.04	0.347	0.16022	.	0.969624	0.08452	N	0.943773	T	0.23210	0.0561	L	0.56769	1.78	0.09310	N	0.999999	B	0.27656	0.184	B	0.18871	0.023	T	0.27191	-1.0081	10	0.59425	D	0.04	.	6.5275	0.22309	0.0:0.5446:0.1265:0.3288	.	1907	Q6UVK1	CSPG4_HUMAN	M	1907	ENSP00000312506:V1907M	ENSP00000312506:V1907M	V	-	1	0	CSPG4	73756196	0.002000	0.14202	0.943000	0.38184	0.961000	0.63080	-0.078000	0.11375	0.161000	0.19458	0.555000	0.69702	GTG		0.672	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897		4	11	0	0	0	1	0	4	11				
MAP3K1	4214	broad.mit.edu	37	5	56180602	56180602	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr5:56180602G>T	ENST00000399503.3	+	16	3931	c.3931G>T	c.(3931-3933)Gga>Tga	p.G1311*		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	1311	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TAGGATGTTGGGAGCCACGTG	0.363																																						uc003jqw.4																			0				NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57						c.(3931-3933)Gga>Tga		Homo sapiens mitogen-activated protein kinase kinase kinase 1 (MAP3K1), mRNA.							108.0	100.0	103.0					5																	56180602		1913	4136	6049	SO:0001587	stop_gained	4214				MyD88-dependent toll-like receptor signaling pathway|Toll signaling pathway|cellular response to mechanical stimulus|innate immune response|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 4 signaling pathway	cytosol	ATP binding|zinc ion binding	g.chr5:56180602G>T	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.3931G>T	5.37:g.56180602G>T	ENSP00000382423:p.Gly1311*		Somatic					p.G1311*	NM_005921	NP_005912	WXS	Illumina GAIIx	Phase_I	Q13233	M3K1_HUMAN		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)	15	4432	+		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)	1311			Protein kinase.			Nonsense_Mutation	SNP	ENST00000399503.3	37	c.3931G>T	CCDS43318.1	.	.	.	.	.	.	.	.	.	.	G	42	9.532869	0.99198	.	.	ENSG00000095015	ENST00000399503	.	.	.	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.7403	0.96228	0.0:0.0:1.0:0.0	.	.	.	.	X	1311	.	ENSP00000382423:G1311X	G	+	1	0	MAP3K1	56216359	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.549000	0.90672	2.652000	0.90054	0.655000	0.94253	GGA		0.363	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066		3	49	0	0	0	1	0	3	49				
SYNPO2	171024	broad.mit.edu	37	4	119944588	119944588	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr4:119944588C>T	ENST00000429713.2	+	2	291	c.109C>T	c.(109-111)Cga>Tga	p.R37*	SYNPO2_ENST00000448416.2_Nonsense_Mutation_p.R37*|SYNPO2_ENST00000307142.4_Nonsense_Mutation_p.R37*|SYNPO2_ENST00000434046.2_Nonsense_Mutation_p.R37*	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	37	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.					actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CACTCAGATTCGAAATCAGAG	0.428																																						uc010inb.3																			0				breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						c.(109-111)Cga>Tga		Homo sapiens synaptopodin 2 (SYNPO2), transcript variant 1, mRNA.							66.0	57.0	60.0					4																	119944588		2203	4300	6503	SO:0001587	stop_gained	171024					Z disc|nucleus	14-3-3 protein binding|actin binding|muscle alpha-actinin binding	g.chr4:119944588C>T	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.109C>T	4.37:g.119944588C>T	ENSP00000395143:p.Arg37*		Somatic				SYNPO2_uc010ina.3_Nonsense_Mutation_p.R37*|SYNPO2_uc003icm.4_Nonsense_Mutation_p.R37*|SYNPO2_uc011cgh.2_Nonsense_Mutation_p.R37*|SYNPO2_uc010inc.3_5'UTR	p.R37*	NM_133477	NP_597734	WXS	Illumina GAIIx	Phase_I	Q9UMS6	SYNP2_HUMAN			1	305	+			37			PDZ.		B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Nonsense_Mutation	SNP	ENST00000429713.2	37	c.109C>T	CCDS47129.1	.	.	.	.	.	.	.	.	.	.	C	37	6.399451	0.97537	.	.	ENSG00000172403	ENST00000307142;ENST00000448416;ENST00000429713;ENST00000434046	.	.	.	5.66	4.81	0.61882	.	0.000000	0.53938	D	0.000044	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.6151	14.345	0.66654	0.1484:0.8516:0.0:0.0	.	.	.	.	X	37	.	ENSP00000306015:R37X	R	+	1	2	SYNPO2	120164036	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	2.696000	0.47052	1.365000	0.46057	0.650000	0.86243	CGA		0.428	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1			10	15	0	0	0	1	0	10	15				
ULK4	54986	broad.mit.edu	37	3	41723024	41723024	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr3:41723024G>A	ENST00000301831.4	-	29	3415	c.2953C>T	c.(2953-2955)Ctc>Ttc	p.L985F		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	985					cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		TCTCGAATGAGAGCCAGAAGA	0.473																																						uc003ckv.4																			0				breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22						c.(2953-2955)Ctc>Ttc		Homo sapiens unc-51-like kinase 4 (C. elegans) (ULK4), mRNA.							125.0	121.0	123.0					3																	41723024		1969	4147	6116	SO:0001583	missense	54986						ATP binding|protein serine/threonine kinase activity	g.chr3:41723024G>A	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.2953C>T	3.37:g.41723024G>A	ENSP00000301831:p.Leu985Phe		Somatic					p.L985F	NM_017886	NP_060356	WXS	Illumina GAIIx	Phase_I	Q96C45	ULK4_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.214)	28	3154	-			985					A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	c.2953C>T	CCDS43071.1	.	.	.	.	.	.	.	.	.	.	g	19.41	3.822539	0.71028	.	.	ENSG00000168038	ENST00000301831	T	0.65916	-0.18	5.75	5.75	0.90469	Armadillo-type fold (1);	0.103984	0.39341	U	0.001390	T	0.70928	0.3280	L	0.50333	1.59	0.80722	D	1	D	0.65815	0.995	P	0.61533	0.89	T	0.71354	-0.4618	10	0.54805	T	0.06	.	13.1821	0.59660	0.0727:0.0:0.9273:0.0	.	985	Q96C45	ULK4_HUMAN	F	985	ENSP00000301831:L985F	ENSP00000301831:L985F	L	-	1	0	ULK4	41698028	1.000000	0.71417	0.946000	0.38457	0.857000	0.48899	5.133000	0.64764	2.716000	0.92895	0.655000	0.94253	CTC		0.473	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989		3	45	0	0	0	1	0	3	45				
ARAP2	116984	broad.mit.edu	37	4	36069767	36069767	+	Missense_Mutation	SNP	C	C	T	rs149183264		TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr4:36069767C>T	ENST00000303965.4	-	33	5366	c.4877G>A	c.(4876-4878)cGa>cAa	p.R1626Q		NM_015230.3	NP_056045.2	Q8WZ64	ARAP2_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2	1626					regulation of ARF GTPase activity (GO:0032312)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						TTTTCGGGGTCGATTTCGAAG	0.502													C|||	1	0.000199681	0.0	0.0	5008	,	,		18475	0.001		0.0	False		,,,				2504	0.0					uc003gsq.2																			0				breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(32)|ovary(2)|pancreas(1)|prostate(3)|skin(7)|urinary_tract(1)	82						c.(4876-4878)cGa>cAa		Homo sapiens ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 2 (ARAP2), mRNA.		C	GLN/ARG	0,4406		0,0,2203	125.0	121.0	123.0		4877	6.0	0.7	4	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ARAP2	NM_015230.3	43	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1626/1705	36069767	1,13005	2203	4300	6503	SO:0001583	missense	116984				regulation of ARF GTPase activity|small GTPase mediated signal transduction	cytosol	ARF GTPase activator activity|phosphatidylinositol-3,4,5-trisphosphate binding|zinc ion binding	g.chr4:36069767C>T	AF411982	CCDS3441.1	4p15.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000047365	ENSG00000047365		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16924	protein-coding gene	gene with protein product		606645	"""centaurin, delta 1"""	CENTD1			Standard	NM_015230		Approved	PARX	uc003gsq.2	Q8WZ64	OTTHUMG00000097811	ENST00000303965.4:c.4877G>A	4.37:g.36069767C>T	ENSP00000302895:p.Arg1626Gln		Somatic				ARAP2_uc003gso.3_Intron	p.R1626Q	NM_015230	NP_056045	WXS	Illumina GAIIx	Phase_I	Q8WZ64	ARAP2_HUMAN			32	5215	-			1626					Q4W5D2|Q7Z2L5|Q96L70|Q96P49|Q9Y4E4	Missense_Mutation	SNP	ENST00000303965.4	37	c.4877G>A	CCDS3441.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	21.7	4.182936	0.78677	0.0	1.16E-4	ENSG00000047365	ENST00000303965	T	0.10192	2.9	5.98	5.98	0.97165	.	0.075779	0.51477	D	0.000092	T	0.12987	0.0315	L	0.32530	0.975	0.34803	D	0.736885	D	0.63046	0.992	P	0.45794	0.493	T	0.03249	-1.1056	10	0.62326	D	0.03	.	15.9435	0.79776	0.0:1.0:0.0:0.0	.	1626	Q8WZ64	ARAP2_HUMAN	Q	1626	ENSP00000302895:R1626Q	ENSP00000302895:R1626Q	R	-	2	0	ARAP2	35746162	0.986000	0.35501	0.674000	0.29902	0.456000	0.32438	2.834000	0.48167	2.838000	0.97847	0.655000	0.94253	CGA		0.502	ARAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215074.2	NM_015230		5	100	0	0	0	1	0	5	100				
KARS	3735	broad.mit.edu	37	16	75662486	75662486	+	Missense_Mutation	SNP	G	G	A			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr16:75662486G>A	ENST00000302445.3	-	13	1715	c.1676C>T	c.(1675-1677)aCg>aTg	p.T559M	KARS_ENST00000319410.5_Missense_Mutation_p.T587M|KARS_ENST00000568378.1_Intron	NM_005548.2	NP_005539.1	Q15046	SYK_HUMAN	lysyl-tRNA synthetase	559					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|lysyl-tRNA aminoacylation (GO:0006430)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)|viral process (GO:0016032)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|microtubule cytoskeleton (GO:0015630)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid binding (GO:0016597)|ATP binding (GO:0005524)|lysine-tRNA ligase activity (GO:0004824)|metal ion binding (GO:0046872)|tRNA binding (GO:0000049)			kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18					L-Lysine(DB00123)	GTTGGAGTCCGTGAGAAACAT	0.552																																						uc002fer.3																			0				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	18						c.(1759-1761)aCg>aTg		Homo sapiens lysyl-tRNA synthetase (KARS), transcript variant 1, mRNA.	L-Lysine(DB00123)						109.0	104.0	106.0					16																	75662486		2198	4300	6498	SO:0001583	missense	3735				interspecies interaction between organisms|lysyl-tRNA aminoacylation|tRNA processing	cytosol|extracellular region|mitochondrial matrix|nucleus|plasma membrane|soluble fraction	ATP binding|lysine-tRNA ligase activity|metal ion binding|tRNA binding	g.chr16:75662486G>A	AF285758	CCDS10923.1, CCDS45532.1	16q23.1	2014-09-17			ENSG00000065427	ENSG00000065427	6.1.1.6	"""Aminoacyl tRNA synthetases / Class II"""	6215	protein-coding gene	gene with protein product	"""lysine tRNA ligase"""	601421	"""deafness, autosomal recessive 89"""	DFNB89		8812440, 9278442, 23768514	Standard	NM_005548		Approved	KARS2, KARS1	uc002fer.3	Q15046	OTTHUMG00000137609	ENST00000302445.3:c.1676C>T	16.37:g.75662486G>A	ENSP00000303043:p.Thr559Met		Somatic				KARS_uc002feq.3_Missense_Mutation_p.T559M	p.T587M	NM_001130089	NP_001123561	WXS	Illumina GAIIx	Phase_I	Q15046	SYK_HUMAN			13	1904	-			559					A8MSK1|D3DUK4|O14946|Q96J25|Q9HB23	Missense_Mutation	SNP	ENST00000302445.3	37	c.1760C>T	CCDS10923.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.746502	0.89663	.	.	ENSG00000065427	ENST00000319410;ENST00000302445	T;T	0.81330	-1.48;-1.48	6.16	6.16	0.99307	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.000000	0.85682	D	0.000000	D	0.94810	0.8324	H	0.99261	4.49	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.96283	0.9208	10	0.87932	D	0	-5.1885	19.4379	0.94804	0.0:0.0:1.0:0.0	.	587;559	Q15046-2;Q15046	.;SYK_HUMAN	M	587;559	ENSP00000325448:T587M;ENSP00000303043:T559M	ENSP00000303043:T559M	T	-	2	0	KARS	74219987	1.000000	0.71417	0.992000	0.48379	0.878000	0.50629	9.747000	0.98863	2.937000	0.99478	0.650000	0.86243	ACG		0.552	KARS-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269023.1	NM_005548		3	53	0	0	0	1	0	3	53				
LETMD1	25875	broad.mit.edu	37	12	51442144	51442144	+	Missense_Mutation	SNP	C	C	T			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr12:51442144C>T	ENST00000262055.4	+	1	44	c.5C>T	c.(4-6)gCg>gTg	p.A2V	LETMD1_ENST00000380123.2_Missense_Mutation_p.A2V|LETMD1_ENST00000552739.1_Missense_Mutation_p.A2V|LETMD1_ENST00000548516.1_3'UTR|LETMD1_ENST00000418425.2_Missense_Mutation_p.A2V|LETMD1_ENST00000550929.1_5'UTR|LETMD1_ENST00000547008.1_Missense_Mutation_p.A2V	NM_015416.4	NP_056231.3	Q6P1Q0	LTMD1_HUMAN	LETM1 domain containing 1	2	Required and sufficient for mitochondrial import.					integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						GTGAAGATGGCGCTCTCCAGG	0.592											OREG0021818	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc009zlw.3																			0				central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(3)	16						c.(4-6)gCg>gTg		Homo sapiens LETM1 domain containing 1 (LETMD1), nuclear gene encoding mitochondrial protein, transcript variant 3, mRNA.							90.0	99.0	96.0					12																	51442144		2203	4300	6503	SO:0001583	missense	25875					integral to membrane|mitochondrial outer membrane	protein binding	g.chr12:51442144C>T	AF195651	CCDS8806.1, CCDS58231.1, CCDS73469.1	12q13.13	2006-04-12				ENSG00000050426			24241	protein-coding gene	gene with protein product	"""cervical cancer 1 protooncogene"""					12879013, 12061725	Standard	NM_015416		Approved	HCCR1	uc009zlw.3	Q6P1Q0	OTTHUMG00000169538	ENST00000262055.4:c.5C>T	12.37:g.51442144C>T	ENSP00000262055:p.Ala2Val		Somatic	OREG0021818	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	977	LETMD1_uc010smz.2_Missense_Mutation_p.A2V|LETMD1_uc010sna.2_Missense_Mutation_p.A2V|LETMD1_uc001rxm.3_Missense_Mutation_p.A2V|LETMD1_uc001rxn.3_5'UTR|LETMD1_uc001rxo.3_Non-coding_Transcript|LETMD1_uc001rxr.3_Non-coding_Transcript|LETMD1_uc001rxl.3_5'UTR|LETMD1_uc001rxt.3_5'Flank	p.A2V	NM_001243689	NP_001230618	WXS	Illumina GAIIx	Phase_I	Q6P1Q0	LTMD1_HUMAN			0	63	+			2			Required and sufficient for mitochondrial import.		A6NER7|B3KXK7|Q6X2E4|Q6X2E5|Q7L2G9|Q7L690|Q8WXW6|Q96PK7|Q9BY59|Q9Y3X3	Missense_Mutation	SNP	ENST00000262055.4	37	c.5C>T	CCDS8806.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045931	0.75846	.	.	ENSG00000050426	ENST00000262055;ENST00000550442;ENST00000549340;ENST00000548209;ENST00000548251;ENST00000380123;ENST00000548401;ENST00000418425;ENST00000448283;ENST00000547008;ENST00000552739	T;T;T;T;T;T;T;T;T	0.60672	0.58;0.48;0.17;0.35;0.29;0.39;0.48;0.56;0.35	4.69	4.69	0.59074	.	0.340919	0.29246	N	0.012712	T	0.65565	0.2703	L	0.34521	1.04	0.36848	D	0.887753	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.995;1.0;0.999;1.0;0.998	D;D;P;D;D;D;P	0.87578	0.998;0.996;0.695;0.996;0.991;0.996;0.771	T	0.71144	-0.4678	10	0.87932	D	0	-6.7628	13.4282	0.61039	0.0:1.0:0.0:0.0	.	2;2;2;2;2;2;2	B7Z9A7;F8VVQ3;B3KXK7;F8W6J0;F8W1Z2;F8VP71;Q6P1Q0	.;.;.;.;.;.;LTMD1_HUMAN	V	2	ENSP00000262055:A2V;ENSP00000448110:A2V;ENSP00000449896:A2V;ENSP00000450275:A2V;ENSP00000447166:A2V;ENSP00000369466:A2V;ENSP00000450082:A2V;ENSP00000389903:A2V;ENSP00000447419:A2V	ENSP00000262055:A2V	A	+	2	0	LETMD1	49728411	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.133000	0.50531	2.885000	0.99019	0.655000	0.94253	GCG		0.592	LETMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404710.1	NM_015416		87	59	0	0	0	1	0	87	59				
INO80D	54891	broad.mit.edu	37	2	206869669	206869669	+	Missense_Mutation	SNP	G	G	T			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr2:206869669G>T	ENST00000403263.1	-	11	2911	c.2507C>A	c.(2506-2508)cCg>cAg	p.P836Q	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	836					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						GTAGGGAGACGGCACATGCTC	0.507																																						uc002vaz.4																			0				NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						c.(2506-2508)cCg>cAg		Homo sapiens INO80 complex subunit D (INO80D), mRNA.							254.0	241.0	245.0					2																	206869669		2150	4259	6409	SO:0001583	missense	54891				DNA recombination|DNA repair|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus		g.chr2:206869669G>T		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.2507C>A	2.37:g.206869669G>T	ENSP00000384198:p.Pro836Gln		Somatic					p.P836Q	NM_017759	NP_060229	WXS	Illumina GAIIx	Phase_I	Q53TQ3	IN80D_HUMAN			10	2912	-			836					B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Missense_Mutation	SNP	ENST00000403263.1	37	c.2507C>A	CCDS46500.1	.	.	.	.	.	.	.	.	.	.	G	17.39	3.376665	0.61735	.	.	ENSG00000114933	ENST00000403263;ENST00000233270	T	0.38560	1.13	5.91	5.02	0.67125	.	0.166320	0.53938	D	0.000043	T	0.43211	0.1237	L	0.27053	0.805	0.58432	D	0.99999	D	0.60575	0.988	P	0.51101	0.659	T	0.43393	-0.9394	10	0.56958	D	0.05	.	17.0934	0.86627	0.0:0.1268:0.8732:0.0	.	836	Q53TQ3-2	.	Q	836	ENSP00000384198:P836Q	ENSP00000233270:P836Q	P	-	2	0	INO80D	206577914	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.230000	0.95299	1.482000	0.48325	-0.175000	0.13238	CCG		0.507	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759		4	127	0	0	0	1	0	4	127				
AXIN1	8312	broad.mit.edu	37	16	341240	341240	+	Silent	SNP	C	C	T			TCGA-ET-A39N-01A-11D-A19J-08	TCGA-ET-A39N-10A-01D-A19M-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	5904b857-04c7-404e-83b5-0d000ae43a35	5ab942e6-6a35-4b33-a4fa-8061207d8ec4	g.chr16:341240C>T	ENST00000262320.3	-	9	2615	c.2244G>A	c.(2242-2244)ccG>ccA	p.P748P	AXIN1_ENST00000354866.3_Intron	NM_003502.3	NP_003493.1	O15169	AXIN1_HUMAN	axin 1	748	Interaction with HIPK2. {ECO:0000250}.|Interaction with PPP2CA.|Interaction with RNF111.				activation of JUN kinase activity (GO:0007257)|activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|axial mesoderm formation (GO:0048320)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in neural plate anterior/posterior pattern formation (GO:0060823)|cell death (GO:0008219)|cellular protein complex assembly (GO:0043623)|cellular response to organic cyclic compound (GO:0071407)|cytoplasmic microtubule organization (GO:0031122)|determination of left/right symmetry (GO:0007368)|dorsal/ventral axis specification (GO:0009950)|embryonic eye morphogenesis (GO:0048048)|embryonic skeletal joint morphogenesis (GO:0060272)|forebrain anterior/posterior pattern specification (GO:0021797)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein metabolic process (GO:0051248)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of Wnt signaling pathway (GO:0030178)|nucleocytoplasmic transport (GO:0006913)|olfactory placode formation (GO:0030910)|optic placode formation (GO:0001743)|positive regulation of GTPase activity (GO:0043547)|positive regulation of JNK cascade (GO:0046330)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|post-anal tail morphogenesis (GO:0036342)|protein catabolic process (GO:0030163)|protein homooligomerization (GO:0051260)|protein polyubiquitination (GO:0000209)|regulation of catenin import into nucleus (GO:0035412)|sensory perception of sound (GO:0007605)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)|Wnt-activated signaling pathway involved in forebrain neuron fate commitment (GO:0021881)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|I-SMAD binding (GO:0070411)|identical protein binding (GO:0042802)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|ubiquitin protein ligase binding (GO:0031625)			biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)				CGTGCAGCACCGGCGCGCACG	0.692																																						uc002cgp.2																			0				biliary_tract(27)|breast(4)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(20)|liver(81)|lung(5)|ovary(2)|prostate(3)|salivary_gland(7)|skin(5)|stomach(4)|thyroid(41)|upper_aerodigestive_tract(4)|urinary_tract(2)	221						c.(2242-2244)ccG>ccA		Homo sapiens axin 1 (AXIN1), transcript variant 1, mRNA.							50.0	35.0	40.0					16																	341240		2166	4271	6437	SO:0001819	synonymous_variant	8312				Wnt receptor signaling pathway involved in forebrain neuron fate commitment|Wnt receptor signaling pathway involved in somitogenesis|activation of JUN kinase activity|activation of protein kinase activity|apoptosis|axial mesoderm formation|canonical Wnt receptor signaling pathway involved in neural plate anterior/posterior pattern formation|cellular protein complex assembly|cellular response to organic cyclic compound|cytoplasmic microtubule organization|determination of left/right symmetry|dorsal/ventral axis specification|embryonic eye morphogenesis|embryonic skeletal joint morphogenesis|forebrain anterior/posterior pattern formation|muscle cell development|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of fat cell differentiation|olfactory placode formation|optic placode formation|positive regulation of JNK cascade|positive regulation of peptidyl-serine phosphorylation|positive regulation of peptidyl-threonine phosphorylation|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of transcription, DNA-dependent|positive regulation of ubiquitin-protein ligase activity|regulation of catenin import into nucleus|tail morphogenesis	APC-Axin-1-beta-catenin complex|Axin-APC-beta-catenin-GSK3B complex|beta-catenin destruction complex|cell cortex|cytoplasmic membrane-bounded vesicle|cytoplasmic microtubule|cytosol|lateral plasma membrane|nucleus|perinuclear region of cytoplasm|postsynaptic density	GTPase activator activity|I-SMAD binding|armadillo repeat domain binding|beta-catenin binding|p53 binding|protein complex scaffold|protein homodimerization activity|protein kinase binding|signal transducer activity|ubiquitin protein ligase binding	g.chr16:341240C>T	AF009674	CCDS10405.1, CCDS10406.1	16p13.3	2012-04-17			ENSG00000103126	ENSG00000103126		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	903	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 49"""	603816				9230313	Standard	NM_003502		Approved	PPP1R49	uc002cgp.2	O15169	OTTHUMG00000064930	ENST00000262320.3:c.2244G>A	16.37:g.341240C>T			Somatic				LUC7L_uc021szo.1_Intron|AXIN1_uc002cgq.2_Intron	p.P748P	NM_003502	NP_003493	WXS	Illumina GAIIx	Phase_I	O15169	AXIN1_HUMAN			8	2633	-		all_cancers(16;2.75e-07)|all_epithelial(16;1.6e-06)|Hepatocellular(16;0.000105)|Lung NSC(18;0.00774)|all_lung(18;0.0187)	748			Interaction with HIPK2 (By similarity).|Interaction with PPP2CA.|Interaction with RNF111.		Q4TT26|Q4TT27|Q86YA7|Q8WVW6|Q96S28	Silent	SNP	ENST00000262320.3	37	c.2244G>A	CCDS10405.1																																																																																				0.692	AXIN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139441.3			3	7	0	0	0	1	0	3	7				
