#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	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
SPRR3	6707	broad.mit.edu	37	1	152975781	152975781	+	Silent	SNP	G	G	A			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr1:152975781G>A	ENST00000295367.4	+	2	327	c.285G>A	c.(283-285)gaG>gaA	p.E95E	SPRR3_ENST00000331860.3_Silent_p.E95E|SPRR3_ENST00000542696.1_Intron	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	95	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGGTCCCTGAGCCAGGTTGTA	0.592																																						ENST00000331860.3																			0				endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11						c.(283-285)gaG>gaA		small proline-rich protein 3							77.0	64.0	69.0					1																	152975781		2203	4300	6503	SO:0001819	synonymous_variant	6707				keratinization|peptide cross-linking|wound healing	cytoplasm	protein binding|structural molecule activity	g.chr1:152975781G>A	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.285G>A	1.37:g.152975781G>A			Somatic				SPRR3_ENST00000542696.1_Intron|SPRR3_ENST00000295367.4_Silent_p.E95E	p.E95E	NM_005416.2	NP_005407.1	WXS	Illumina GAIIx	Phase_I	Q9UBC9	SPRR3_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.171)		3	435	+	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		95			14 X 8 AA approximate tandem repeats.		A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	c.285G>A	CCDS1033.1																																																																																				0.592	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416		18	38	18	38	---	---	---	---
RPSA	3921	broad.mit.edu	37	3	39450137	39450137	+	Silent	SNP	T	T	G			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr3:39450137T>G	ENST00000301821.6	+	3	283	c.174T>G	c.(172-174)ctT>ctG	p.L58L	SNORA62_ENST00000365493.1_RNA|RPSA_ENST00000478027.1_3'UTR|RPSA_ENST00000443003.1_Silent_p.L58L|SNORA6_ENST00000384033.1_RNA	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2			ribosomal protein SA											endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7				KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)		GGGAGAAGCTTCTGCTGGCAG	0.458																																						ENST00000301821.6																			0				endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7						c.(172-174)ctT>ctG		ribosomal protein SA							71.0	72.0	72.0					3																	39450137		2203	4300	6503	SO:0001819	synonymous_variant	3921				cell adhesion|endocrine pancreas development|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA)|ribosomal small subunit assembly|rRNA export from nucleus|translational elongation|translational termination|viral transcription	90S preribosome|cytosolic small ribosomal subunit|nucleus|plasma membrane	protein binding|receptor activity|ribosome binding|structural constituent of ribosome	g.chr3:39450137T>G	S37431	CCDS2686.1	3p21.3	2014-09-17	2002-08-29	2005-02-11	ENSG00000168028	ENSG00000168028			6502	protein-coding gene	gene with protein product		150370	"""laminin receptor 1 (67kD, ribosomal protein SA)"""	LAMR1		1534510, 8760291	Standard	NM_001012321		Approved	LRP, 37LRP, p40, SA	uc003cjp.3	P08865	OTTHUMG00000131296	ENST00000301821.6:c.174T>G	3.37:g.39450137T>G			Somatic				RPSA_ENST00000478027.1_3'UTR|RPSA_ENST00000443003.1_Silent_p.L58L	p.L58L	NM_001012321.1|NM_002295.4	NP_001012321.1|NP_002286.2	WXS	Illumina GAIIx	Phase_I	P08865	RSSA_HUMAN		KIRC - Kidney renal clear cell carcinoma(284;0.0509)|Kidney(284;0.064)	3	283	+			58			Interaction with PPP1R16B.			Silent	SNP	ENST00000301821.6	37	c.174T>G	CCDS2686.1																																																																																				0.458	RPSA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254064.3	NM_002295		16	46	16	46	---	---	---	---
FOXP1	27086	broad.mit.edu	37	3	71037204	71037204	+	Nonsense_Mutation	SNP	G	G	A			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr3:71037204G>A	ENST00000318789.4	-	14	1612	c.1087C>T	c.(1087-1089)Caa>Taa	p.Q363*	FOXP1_ENST00000498215.1_Nonsense_Mutation_p.Q363*|FOXP1_ENST00000493089.1_Nonsense_Mutation_p.Q363*|FOXP1_ENST00000475937.1_Nonsense_Mutation_p.Q363*|FOXP1_ENST00000491238.1_Nonsense_Mutation_p.Q365*|FOXP1_ENST00000484350.1_Nonsense_Mutation_p.Q287*|FOXP1_ENST00000468577.1_Nonsense_Mutation_p.Q363*	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	363	Leucine-zipper.				negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		ATCATGGCTTGCAGGCGTTCT	0.428			T	PAX5	ALL																																	ENST00000318789.4				Dom	yes		3	3p14.1	27086	T	forkhead box P1			L	PAX5		ALL		0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31						c.(1087-1089)Caa>Taa		forkhead box P1							177.0	184.0	181.0					3																	71037204		2203	4300	6503	SO:0001587	stop_gained	27086				cardiac muscle cell differentiation|embryo development|immunoglobulin V(D)J recombination|pattern specification process|positive regulation of epithelial cell proliferation involved in lung morphogenesis|positive regulation of immunoglobulin production|positive regulation of mesenchymal cell proliferation|pre-B cell differentiation|regulation of sequence-specific DNA binding transcription factor activity|skeletal muscle tissue development|smooth muscle tissue development	cytoplasm|transcription factor complex	chromatin binding|DNA bending activity|double-stranded DNA binding|promoter binding|protein heterodimerization activity|protein homodimerization activity|sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding|zinc ion binding	g.chr3:71037204G>A	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.1087C>T	3.37:g.71037204G>A	ENSP00000318902:p.Gln363*		Somatic				FOXP1_ENST00000491238.1_Nonsense_Mutation_p.Q365*|FOXP1_ENST00000498215.1_Nonsense_Mutation_p.Q363*|FOXP1_ENST00000493089.1_Nonsense_Mutation_p.Q363*|FOXP1_ENST00000475937.1_Nonsense_Mutation_p.Q363*|FOXP1_ENST00000484350.1_Nonsense_Mutation_p.Q287*|FOXP1_ENST00000468577.1_Nonsense_Mutation_p.Q363*	p.Q363*	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	WXS	Illumina GAIIx	Phase_I	Q9H334	FOXP1_HUMAN		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)	14	1612	-		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)	363			Leucine-zipper.		A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Nonsense_Mutation	SNP	ENST00000318789.4	37	c.1087C>T	CCDS2914.1	.	.	.	.	.	.	.	.	.	.	G	39	7.432290	0.98279	.	.	ENSG00000114861	ENST00000318789;ENST00000358280;ENST00000318796;ENST00000475937;ENST00000339693;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577	.	.	.	5.84	5.84	0.93424	.	0.054481	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	20.1306	0.97998	0.0:0.0:1.0:0.0	.	.	.	.	X	363;175;263;363;363;259;365;363;363;287;363	.	ENSP00000318902:Q363X	Q	-	1	0	FOXP1	71119894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.476000	0.97823	2.751000	0.94390	0.655000	0.94253	CAA		0.428	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682		63	154	63	154	---	---	---	---
TLR1	7096	broad.mit.edu	37	4	38798749	38798749	+	Silent	SNP	C	C	T			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr4:38798749C>T	ENST00000502213.2	-	3	1933	c.1704G>A	c.(1702-1704)aaG>aaA	p.K568K	TLR1_ENST00000510552.1_5'Flank|TLR1_ENST00000308979.2_Silent_p.K568K			Q15399	TLR1_HUMAN	toll-like receptor 1	568	LRRCT.				cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						TGTGAAAGTCCTTTAGTAGGG	0.448																																					GBM(5;216 373 40795 46382)	ENST00000308979.2																			0				cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						c.(1702-1704)aaG>aaA		toll-like receptor 1							127.0	130.0	129.0					4																	38798749		2203	4300	6503	SO:0001819	synonymous_variant	7096				cellular response to triacyl bacterial lipopeptide|detection of triacyl bacterial lipopeptide|inflammatory response|innate immune response|macrophage activation|positive regulation of interleukin-6 biosynthetic process|positive regulation of tumor necrosis factor biosynthetic process	integral to plasma membrane|phagocytic vesicle membrane|Toll-like receptor 1-Toll-like receptor 2 protein complex	protein heterodimerization activity|transmembrane receptor activity	g.chr4:38798749C>T	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.1704G>A	4.37:g.38798749C>T			Somatic				TLR1_ENST00000502213.2_Silent_p.K568K	p.K568K	NM_003263.3	NP_003254.2	WXS	Illumina GAIIx	Phase_I	Q15399	TLR1_HUMAN			4	1977	-			568			LRRCT.		D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	c.1704G>A	CCDS33973.1																																																																																				0.448	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3			32	111	32	111	---	---	---	---
DCHS2	54798	broad.mit.edu	37	4	155158120	155158120	+	Missense_Mutation	SNP	C	C	A			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr4:155158120C>A	ENST00000357232.4	-	25	6318	c.6319G>T	c.(6319-6321)Gct>Tct	p.A2107S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2107	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCAACCAGAGCATCCTCACTT	0.398																																						ENST00000357232.4																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176						c.(6319-6321)Gct>Tct		dachsous cadherin-related 2							157.0	152.0	154.0					4																	155158120		2203	4300	6503	SO:0001583	missense	54798				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr4:155158120C>A	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6319G>T	4.37:g.155158120C>A	ENSP00000349768:p.Ala2107Ser		Somatic					p.A2107S	NM_017639.3	NP_060109.2	WXS	Illumina GAIIx	Phase_I	Q6V1P9	PCD23_HUMAN		LUSC - Lung squamous cell carcinoma(193;0.107)	25	6318	-	all_hematologic(180;0.208)	Renal(120;0.0854)				Cadherin 19.		B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	c.6319G>T	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	C	12.05	1.821832	0.32237	.	.	ENSG00000197410	ENST00000357232	T	0.54479	0.57	5.82	-6.9	0.01655	Cadherin (3);Cadherin-like (1);	0.824461	0.10855	N	0.626750	T	0.50377	0.1612	L	0.51422	1.61	0.36047	D	0.840488	P	0.48230	0.907	P	0.51297	0.665	T	0.65907	-0.6054	10	0.56958	D	0.05	.	9.9551	0.41661	0.0:0.3538:0.0923:0.5539	.	2107	Q6V1P9	PCD23_HUMAN	S	2107	ENSP00000349768:A2107S	ENSP00000349768:A2107S	A	-	1	0	DCHS2	155377570	0.261000	0.24063	0.000000	0.03702	0.107000	0.19398	-0.378000	0.07446	-2.269000	0.00684	-0.484000	0.04775	GCT		0.398	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552		5	207	5	207	---	---	---	---
NYAP1	222950	broad.mit.edu	37	7	100084560	100084560	+	Missense_Mutation	SNP	C	C	T			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr7:100084560C>T	ENST00000300179.2	+	3	344	c.185C>T	c.(184-186)aCg>aTg	p.T62M	NYAP1_ENST00000454988.1_Missense_Mutation_p.T5M|NYAP1_ENST00000423930.1_Missense_Mutation_p.T62M	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	62					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												GGTTTCATGACGATGCCCGCC	0.751																																						ENST00000423930.1																			0											c.(184-186)aCg>aTg		neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1							9.0	11.0	11.0					7																	100084560		2166	4254	6420	SO:0001583	missense	222950							g.chr7:100084560C>T	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"""chromosome 7 open reading frame 51"", ""KIAA1486-like"""	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.185C>T	7.37:g.100084560C>T	ENSP00000300179:p.Thr62Met		Somatic				NYAP1_ENST00000300179.2_Missense_Mutation_p.T62M|NYAP1_ENST00000454988.1_Missense_Mutation_p.T5M	p.T62M			WXS	Illumina GAIIx	Phase_I	Q6ZVC0	CG051_HUMAN			3	344	+			62					Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	c.185C>T	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	C	26.7	4.766953	0.90020	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.50813	0.73;0.73;0.73	5.03	5.03	0.67393	.	0.000000	0.52532	D	0.000069	T	0.65481	0.2695	L	0.57536	1.79	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.67891	-0.5553	10	0.87932	D	0	-14.223	15.8881	0.79269	0.0:1.0:0.0:0.0	.	62	Q6ZVC0	CG051_HUMAN	M	62;62;5	ENSP00000300179:T62M;ENSP00000411861:T62M;ENSP00000394424:T5M	ENSP00000300179:T62M	T	+	2	0	C7orf51	99922496	1.000000	0.71417	0.995000	0.50966	0.980000	0.70556	6.628000	0.74262	2.606000	0.88127	0.462000	0.41574	ACG		0.751	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564		4	11	4	11	---	---	---	---
KIFC2	90990	broad.mit.edu	37	8	145697577	145697577	+	Silent	SNP	G	G	A			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr8:145697577G>A	ENST00000301332.2	+	14	1919	c.1542G>A	c.(1540-1542)gaG>gaA	p.E514E	KIFC2_ENST00000531423.1_3'UTR|KIFC2_ENST00000301331.5_Silent_p.E262E|FOXH1_ENST00000525197.1_5'Flank	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	514	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			TGTTCCGGGAGATGGGGGCCG	0.652																																						ENST00000301332.2																			0				central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19						c.(1540-1542)gaG>gaA		kinesin family member C2							37.0	43.0	41.0					8																	145697577		2202	4300	6502	SO:0001819	synonymous_variant	90990				microtubule-based movement	cytoplasm|microtubule	ATP binding|microtubule motor activity|protein binding	g.chr8:145697577G>A	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"""Kinesins"""	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.1542G>A	8.37:g.145697577G>A			Somatic				KIFC2_ENST00000531423.1_3'UTR|KIFC2_ENST00000301331.5_Silent_p.E262E	p.E514E	NM_145754.2	NP_665697.1	WXS	Illumina GAIIx	Phase_I	Q96AC6	KIFC2_HUMAN	OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)		14	1919	+	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		514			Kinesin-motor.		E9PHB2|Q96NN6	Silent	SNP	ENST00000301332.2	37	c.1542G>A	CCDS6427.1	.	.	.	.	.	.	.	.	.	.	G	9.416	1.081772	0.20309	.	.	ENSG00000167702	ENST00000528415	.	.	.	5.07	1.27	0.21489	.	.	.	.	.	T	0.45776	0.1359	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23511	-1.0186	4	.	.	.	-26.8143	3.6966	0.08367	0.345:0.0:0.4918:0.1632	.	.	.	.	N	335	.	.	D	+	1	0	KIFC2	145668385	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	2.537000	0.45702	0.049000	0.15920	0.591000	0.81541	GAT		0.652	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754		3	74	3	74	---	---	---	---
ABL1	25	broad.mit.edu	37	9	133753877	133753877	+	Missense_Mutation	SNP	A	A	G			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr9:133753877A>G	ENST00000318560.5	+	8	1727	c.1346A>G	c.(1345-1347)tAt>tGt	p.Y449C		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	449	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TCCCAGGTGTATGAGCTGCTA	0.507			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""																																	ENST00000318560.5				Dom	yes		9	9q34.1	25	"""T, Mis"""	v-abl Abelson murine leukemia viral oncogene homolog 1			L	"""BCR, ETV6, NUP214"""		"""CML, ALL, T-ALL"""		0				breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195						c.(1345-1347)tAt>tGt		c-abl oncogene 1, non-receptor tyrosine kinase	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)						174.0	170.0	171.0					9																	133753877		2203	4300	6503	SO:0001583	missense	25				actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding	g.chr9:133753877A>G	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1346A>G	9.37:g.133753877A>G	ENSP00000323315:p.Tyr449Cys		Somatic					p.Y449C	NM_005157.4	NP_005148.2	WXS	Illumina GAIIx	Phase_I	P00519	ABL1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	8	1727	+		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)	449			Protein kinase.		A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	c.1346A>G	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	A	25.0	4.596272	0.86953	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.63096	-0.02;-0.02	5.16	5.16	0.70880	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.128125	0.53938	D	0.000041	T	0.70579	0.3240	L	0.37466	1.105	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.74348	0.971;0.983	T	0.74134	-0.3763	10	0.87932	D	0	.	14.4656	0.67482	1.0:0.0:0.0:0.0	.	449;486	P00519;Q59FK4	ABL1_HUMAN;.	C	264;468;449	ENSP00000361423:Y468C;ENSP00000323315:Y449C	ENSP00000323315:Y449C	Y	+	2	0	ABL1	132743698	1.000000	0.71417	0.991000	0.47740	0.946000	0.59487	9.287000	0.95975	2.073000	0.62155	0.533000	0.62120	TAT		0.507	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313		62	178	62	178	---	---	---	---
LDB3	11155	broad.mit.edu	37	10	88447004	88447004	+	Nonsense_Mutation	SNP	C	C	T			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr10:88447004C>T	ENST00000372066.3	+	5	602	c.523C>T	c.(523-525)Caa>Taa	p.Q175*	LDB3_ENST00000263066.6_Nonsense_Mutation_p.Q175*|LDB3_ENST00000361373.4_Intron|LDB3_ENST00000372056.4_Nonsense_Mutation_p.Q290*|LDB3_ENST00000429277.2_Nonsense_Mutation_p.Q290*|LDB3_ENST00000458213.2_Nonsense_Mutation_p.Q175*|LDB3_ENST00000310944.6_Intron|LDB3_ENST00000542786.1_3'UTR|LDB3_ENST00000352360.5_Intron	NM_001080116.1	NP_001073585.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						TGGGCAGGCCCAAGCCCAAGG	0.637																																						ENST00000429277.2																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						c.(868-870)Caa>Taa		LIM domain binding 3							89.0	104.0	99.0					10																	88447004		2168	4253	6421	SO:0001587	stop_gained	11155					cytoskeleton|perinuclear region of cytoplasm|pseudopodium	zinc ion binding	g.chr10:88447004C>T	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"""cypher"", ""oracle"", ""Z-band alternatively spliced PDZ motif protein"""	605906	"""cardiomyopathy, dilated 1C (autosomal dominant)"""	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000372066.3:c.523C>T	10.37:g.88447004C>T	ENSP00000361136:p.Gln175*		Somatic				LDB3_ENST00000542786.1_3'UTR|LDB3_ENST00000458213.2_Nonsense_Mutation_p.Q175*|LDB3_ENST00000372066.3_Nonsense_Mutation_p.Q175*|LDB3_ENST00000372056.4_Nonsense_Mutation_p.Q290*|LDB3_ENST00000361373.4_Intron|LDB3_ENST00000263066.6_Nonsense_Mutation_p.Q175*|LDB3_ENST00000310944.6_Intron|LDB3_ENST00000352360.5_Intron	p.Q290*	NM_001171610.1	NP_001165081.1	WXS	Illumina GAIIx	Phase_I	O75112	LDB3_HUMAN			6	1013	+			280						Nonsense_Mutation	SNP	ENST00000372066.3	37	c.868C>T	CCDS41545.1	.	.	.	.	.	.	.	.	.	.	C	37	6.246965	0.97408	.	.	ENSG00000122367	ENST00000429277;ENST00000458213;ENST00000372066;ENST00000263066;ENST00000372056	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	.	18.6007	0.91247	0.0:1.0:0.0:0.0	.	.	.	.	X	290;175;175;175;290	.	ENSP00000263066:Q175X	Q	+	1	0	LDB3	88436984	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.798000	0.85924	2.407000	0.81776	0.462000	0.41574	CAA		0.637	LDB3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049161.1			21	82	21	82	---	---	---	---
CHAMP1	283489	broad.mit.edu	37	13	115090966	115090966	+	Missense_Mutation	SNP	T	T	C			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr13:115090966T>C	ENST00000361283.1	+	3	1958	c.1649T>C	c.(1648-1650)cTt>cCt	p.L550P		NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	Q96JM3	CHAP1_HUMAN	chromosome alignment maintaining phosphoprotein 1	550	Mediates localization to the spindle and the kinetochore and is required for the attachment of spindle microtubules to the kinetochore.|Pro-rich.				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation (GO:0051315)|protein localization to kinetochore (GO:0034501)|protein localization to microtubule (GO:0035372)|sister chromatid biorientation (GO:0031134)	condensed chromosome (GO:0000793)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)										AAACGTGCCCTTTTTCCAGAG	0.517																																						ENST00000361283.1																			0											c.(1648-1650)cTt>cCt		chromosome alignment maintaining phosphoprotein 1							211.0	240.0	230.0					13																	115090966		2203	4300	6503	SO:0001583	missense	283489				attachment of spindle microtubules to kinetochore involved in mitotic sister chromatid segregation|protein localization to kinetochore|protein localization to microtubule|sister chromatid biorientation	condensed chromosome kinetochore|cytoplasm|nucleus|spindle	nucleic acid binding|protein binding|zinc ion binding	g.chr13:115090966T>C	AK074894	CCDS9545.1	13q34	2013-01-07	2011-10-07	2011-10-07	ENSG00000198824	ENSG00000198824		"""Zinc fingers, C2H2-type"""	20311	protein-coding gene	gene with protein product	"""chromosome alignment-maintaining phosphoprotein"""		"""chromosome 13 open reading frame 8"", ""zinc finger protein 828"""	C13orf8, ZNF828		21063390	Standard	NM_032436		Approved	CAMP, CHAMP	uc010ahb.3	Q96JM3	OTTHUMG00000017404	ENST00000361283.1:c.1649T>C	13.37:g.115090966T>C	ENSP00000354730:p.Leu550Pro		Somatic					p.L550P	NM_001164144.1|NM_001164145.1|NM_032436.2	NP_001157616.1|NP_001157617.1|NP_115812.1	WXS	Illumina GAIIx	Phase_I	Q96JM3	ZN828_HUMAN			3	1958	+			550			Mediates localization to the spindle and the kinetochore and is required for the attachment of spindle microtubules to the kinetochore.|Pro-rich.		B3KU06|Q6P181|Q8NC88|Q9BST0	Missense_Mutation	SNP	ENST00000361283.1	37	c.1649T>C	CCDS9545.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.020892	0.54576	.	.	ENSG00000198824	ENST00000361283	T	0.01902	4.57	5.59	5.59	0.84812	.	0.000000	0.51477	D	0.000081	T	0.07188	0.0182	M	0.65498	2.005	0.58432	D	0.999996	P	0.51537	0.946	P	0.51777	0.679	T	0.19257	-1.0311	9	.	.	.	-17.4144	14.3423	0.66636	0.0:0.0:0.0:1.0	.	550	Q96JM3	ZN828_HUMAN	P	550	ENSP00000354730:L550P	.	L	+	2	0	ZNF828	114109068	0.995000	0.38212	0.981000	0.43875	0.990000	0.78478	3.159000	0.50731	2.126000	0.65437	0.528000	0.53228	CTT		0.517	CHAMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045977.2	NM_032436		5	328	5	328	---	---	---	---
C14orf159	80017	broad.mit.edu	37	14	91655506	91655506	+	Missense_Mutation	SNP	T	T	G			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr14:91655506T>G	ENST00000523771.1	+	9	1775	c.1172T>G	c.(1171-1173)gTt>gGt	p.V391G	C14orf159_ENST00000520328.1_Missense_Mutation_p.V379G|C14orf159_ENST00000412671.2_Missense_Mutation_p.V396G|C14orf159_ENST00000518868.1_Missense_Mutation_p.V396G|C14orf159_ENST00000256324.10_Missense_Mutation_p.V396G|C14orf159_ENST00000523816.1_Missense_Mutation_p.V391G|C14orf159_ENST00000522322.1_Missense_Mutation_p.V391G|C14orf159_ENST00000525393.2_Missense_Mutation_p.V267G|C14orf159_ENST00000521077.2_Missense_Mutation_p.V396G|C14orf159_ENST00000428926.2_Missense_Mutation_p.V391G			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	391						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		GAAGATGCTGTTGAGCAAGGT	0.532																																						ENST00000518868.1																			0				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21						c.(1186-1188)gTt>gGt		chromosome 14 open reading frame 159							96.0	78.0	84.0					14																	91655506		2203	4300	6503	SO:0001583	missense	80017					mitochondrion		g.chr14:91655506T>G	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1172T>G	14.37:g.91655506T>G	ENSP00000429655:p.Val391Gly		Somatic				C14orf159_ENST00000523816.1_Missense_Mutation_p.V391G|C14orf159_ENST00000256324.10_Missense_Mutation_p.V396G|C14orf159_ENST00000521077.2_Missense_Mutation_p.V396G|C14orf159_ENST00000428926.2_Missense_Mutation_p.V391G|C14orf159_ENST00000525393.2_Missense_Mutation_p.V267G|C14orf159_ENST00000523771.1_Missense_Mutation_p.V391G|C14orf159_ENST00000412671.2_Missense_Mutation_p.V396G|C14orf159_ENST00000522322.1_Missense_Mutation_p.V391G|C14orf159_ENST00000520328.1_Missense_Mutation_p.V379G	p.V396G			WXS	Illumina GAIIx	Phase_I	Q7Z3D6	CN159_HUMAN		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)	12	1877	+		all_cancers(154;0.0191)|all_epithelial(191;0.241)	391					B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	c.1187T>G	CCDS32141.1	.	.	.	.	.	.	.	.	.	.	T	12.36	1.913778	0.33815	.	.	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000517518;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T;T	0.15139	2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45;2.45	4.82	3.67	0.42095	.	0.642001	0.15202	N	0.274969	T	0.36496	0.0969	M	0.69248	2.105	0.23346	N	0.997864	D;D;D;P;D;D	0.63880	0.984;0.993;0.991;0.95;0.98;0.98	P;D;P;P;P;P	0.65573	0.81;0.936;0.906;0.625;0.711;0.711	T	0.10683	-1.0619	10	0.87932	D	0	.	10.3142	0.43727	0.0:0.0787:0.0:0.9213	.	391;267;396;379;396;396	Q7Z3D6;Q8NB88;B3KVU6;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.;.	G	379;396;396;396;391;396;267;391;391;391;396	ENSP00000429453:V379G;ENSP00000256324:V396G;ENSP00000430137:V396G;ENSP00000428263:V396G;ENSP00000428974:V391G;ENSP00000428652:V396G;ENSP00000435459:V267G;ENSP00000404343:V391G;ENSP00000427953:V391G;ENSP00000429655:V391G;ENSP00000404196:V396G	ENSP00000256324:V396G	V	+	2	0	C14orf159	90725259	0.988000	0.35896	0.001000	0.08648	0.248000	0.25809	4.627000	0.61276	0.692000	0.31613	0.533000	0.62120	GTT		0.532	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952		19	87	19	87	---	---	---	---
KNOP1	400506	broad.mit.edu	37	16	19725711	19725711	+	Missense_Mutation	SNP	T	T	G			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr16:19725711T>G	ENST00000219837.7	-	2	725	c.647A>C	c.(646-648)aAa>aCa	p.K216T	AC002550.5_ENST00000565916.1_RNA|IQCK_ENST00000320394.6_5'Flank|KNOP1_ENST00000568230.1_5'Flank	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	216	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										GTGGATTTTTTTTTTCTTCTT	0.532																																						ENST00000219837.7																			0											c.(646-648)aAa>aCa		lysine-rich nucleolar protein 1							63.0	72.0	69.0					16																	19725711		2178	4297	6475	SO:0001583	missense	400506							g.chr16:19725711T>G	BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.647A>C	16.37:g.19725711T>G	ENSP00000219837:p.Lys216Thr		Somatic				AC002550.5_ENST00000565916.1_RNA	p.K216T	NM_001012991.2	NP_001013009.2	WXS	Illumina GAIIx	Phase_I					2	725	-								O43328|Q5FWF3	Missense_Mutation	SNP	ENST00000219837.7	37	c.647A>C	CCDS42127.1	.	.	.	.	.	.	.	.	.	.	T	8.331	0.826397	0.16749	.	.	ENSG00000103550	ENST00000219837	T	0.27402	1.67	4.71	3.61	0.41365	.	1.537720	0.04212	N	0.331973	T	0.40522	0.1120	L	0.34521	1.04	0.54753	D	0.999987	D	0.67145	0.996	P	0.62813	0.907	T	0.30909	-0.9962	9	.	.	.	-19.0976	4.1952	0.10440	0.1774:0.0954:0.0:0.7272	.	216	Q1ED39	CP088_HUMAN	T	216	ENSP00000219837:K216T	.	K	-	2	0	C16orf88	19633212	0.999000	0.42202	0.810000	0.32431	0.180000	0.23129	0.832000	0.27490	0.930000	0.37217	0.459000	0.35465	AAA		0.532	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991		3	59	3	59	---	---	---	---
KIAA1328	57536	broad.mit.edu	37	18	34802090	34802090	+	Missense_Mutation	SNP	G	G	T			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr18:34802090G>T	ENST00000280020.5	+	10	1656	c.1634G>T	c.(1633-1635)cGa>cTa	p.R545L	KIAA1328_ENST00000591619.1_Missense_Mutation_p.R541L|KIAA1328_ENST00000543923.1_Intron|KIAA1328_ENST00000586135.1_3'UTR	NM_020776.1	NP_065827.1	Q86T90	K1328_HUMAN	KIAA1328	545										central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14				COAD - Colon adenocarcinoma(74;0.195)		GGTACTTTCCGACTCAGTCCT	0.478																																						ENST00000591619.1																			0				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	14						c.(1621-1623)cGa>cTa		KIAA1328							45.0	42.0	43.0					18																	34802090		1864	4105	5969	SO:0001583	missense	57536							g.chr18:34802090G>T	AB037749	CCDS45855.1	18q12.2	2011-12-12			ENSG00000150477	ENSG00000150477			29248	protein-coding gene	gene with protein product						10718198	Standard	XM_005258317		Approved		uc002kzz.3	Q86T90		ENST00000280020.5:c.1634G>T	18.37:g.34802090G>T	ENSP00000280020:p.Arg545Leu		Somatic				KIAA1328_ENST00000280020.5_Missense_Mutation_p.R545L|KIAA1328_ENST00000543923.1_Intron|KIAA1328_ENST00000586135.1_3'UTR	p.R541L			WXS	Illumina GAIIx	Phase_I	Q86T90	K1328_HUMAN		COAD - Colon adenocarcinoma(74;0.195)	10	2408	+			545					Q05DL0|Q49AG6|Q9P2L8	Missense_Mutation	SNP	ENST00000280020.5	37	c.1622G>T	CCDS45855.1	.	.	.	.	.	.	.	.	.	.	G	5.945	0.358454	0.11239	.	.	ENSG00000150477	ENST00000280020;ENST00000383055	T	0.50277	0.75	5.93	-3.18	0.05186	.	0.790748	0.11311	N	0.577100	T	0.34483	0.0899	L	0.50333	1.59	0.09310	N	1	B;B	0.18013	0.002;0.025	B;B	0.17979	0.011;0.02	T	0.25882	-1.0119	10	0.31617	T	0.26	.	5.9963	0.19495	0.484:0.0:0.3084:0.2077	.	545;545	A8K8C3;Q86T90	.;K1328_HUMAN	L	545	ENSP00000280020:R545L	ENSP00000280020:R545L	R	+	2	0	KIAA1328	33056088	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-0.898000	0.04105	-0.552000	0.06167	-0.914000	0.02751	CGA		0.478	KIAA1328-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440455.1	NM_020776		4	15	4	15	---	---	---	---
YJEFN3	374887	broad.mit.edu	37	19	19645880	19645880	+	Missense_Mutation	SNP	C	C	T	rs545322147	byFrequency	TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr19:19645880C>T	ENST00000514277.4	+	4	394	c.356C>T	c.(355-357)aCg>aTg	p.T119M	CTC-260F20.3_ENST00000555938.1_Missense_Mutation_p.T118M|YJEFN3_ENST00000608404.1_Missense_Mutation_p.T118M|YJEFN3_ENST00000436027.5_Missense_Mutation_p.T69M	NM_198537.3	NP_940939.2	A6XGL0	YJEN3_HUMAN	YjeF N-terminal domain containing 3	119	YjeF N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00719}.									NS(1)|breast(1)|lung(3)	5						AAGCAGAGGACGGTGCTGGTC	0.642													C|||	2	0.000399361	0.0	0.0	5008	,	,		16304	0.0		0.001	False		,,,				2504	0.001					ENST00000555938.1																			0											c.(352-354)aCg>aTg									90.0	108.0	102.0					19																	19645880		2115	4230	6345	SO:0001583	missense	374887							g.chr19:19645880C>T		CCDS42530.1, CCDS54236.1	19p13.11	2014-09-11			ENSG00000250067	ENSG00000250067			24785	protein-coding gene	gene with protein product						17533573	Standard	NM_198537		Approved	hYjeF_N3-19p13.11, FLJ44968	uc002nmt.2	A6XGL0	OTTHUMG00000162251	ENST00000514277.4:c.356C>T	19.37:g.19645880C>T	ENSP00000426964:p.Thr119Met		Somatic				YJEFN3_ENST00000436027.5_Missense_Mutation_p.T69M|YJEFN3_ENST00000514277.4_Missense_Mutation_p.T119M|YJEFN3_ENST00000608404.1_Missense_Mutation_p.T118M	p.T118M			WXS	Illumina GAIIx	Phase_I					5	365	+								A6XGK9|Q4G1C0	Missense_Mutation	SNP	ENST00000514277.4	37	c.353C>T	CCDS42530.1	.	.	.	.	.	.	.	.	.	.	C	19.92	3.915845	0.73098	.	.	ENSG00000250067;ENSG00000250067;ENSG00000250067;ENSG00000250067;ENSG00000250067;ENSG00000258674	ENST00000553705;ENST00000397179;ENST00000436027;ENST00000514277;ENST00000510139;ENST00000555938	T;T;T	0.45276	0.9;0.9;0.9	4.53	3.49	0.39957	YjeF-related protein, N-terminal (5);	0.052888	0.85682	N	0.000000	T	0.52158	0.1717	M	0.72894	2.215	0.49299	D	0.999774	D;B;D	0.58620	0.983;0.308;0.98	P;B;P	0.53809	0.735;0.037;0.488	T	0.54866	-0.8229	10	0.52906	T	0.07	-24.1496	10.701	0.45926	0.0:0.9037:0.0:0.0963	.	118;69;119	E7ENQ6;A6XGL0-2;A6XGL0	.;.;YJEN3_HUMAN	M	118;119;69;119;69;118	ENSP00000398520:T69M;ENSP00000426964:T119M;ENSP00000452549:T118M	ENSP00000389732:T118M	T	+	2	0	YJEFN3;CTC-260F20.3	19506880	1.000000	0.71417	0.914000	0.36105	0.845000	0.48019	5.390000	0.66261	1.063000	0.40649	0.650000	0.86243	ACG		0.642	YJEFN3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368157.5	NM_198537		73	152	73	152	---	---	---	---
VPS16	64601	broad.mit.edu	37	20	2842496	2842496	+	Silent	SNP	G	G	A			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr20:2842496G>A	ENST00000380445.3	+	10	1017	c.945G>A	c.(943-945)ggG>ggA	p.G315G	VPS16_ENST00000380443.3_5'Flank|VPS16_ENST00000380469.3_Intron|PTPRA_ENST00000380393.3_5'Flank|VPS16_ENST00000481812.2_3'UTR	NM_022575.2	NP_072097.2	Q9H269	VPS16_HUMAN	vacuolar protein sorting 16 homolog (S. cerevisiae)	315					intracellular protein transport (GO:0006886)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|axon (GO:0030424)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|recycling endosome (GO:0055037)				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						AGCTCGATGGGGTCCGCATCT	0.592																																						ENST00000380445.3																			0				NS(3)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	37						c.(943-945)ggG>ggA		vacuolar protein sorting 16 homolog (S. cerevisiae)							82.0	72.0	76.0					20																	2842496		2203	4300	6503	SO:0001819	synonymous_variant	64601				intracellular protein transport	early endosome|HOPS complex|late endosome membrane|lysosomal membrane|recycling endosome		g.chr20:2842496G>A	AF308801	CCDS13036.1, CCDS13037.1	20p13	2009-07-07	2009-07-07	2009-07-07	ENSG00000215305	ENSG00000215305			14584	protein-coding gene	gene with protein product		608550					Standard	NM_022575		Approved		uc002whe.3	Q9H269	OTTHUMG00000031714	ENST00000380445.3:c.945G>A	20.37:g.2842496G>A			Somatic				VPS16_ENST00000380469.3_Intron|VPS16_ENST00000481812.2_3'UTR	p.G315G	NM_022575.2	NP_072097.2	WXS	Illumina GAIIx	Phase_I	Q9H269	VPS16_HUMAN			10	1017	+			315					Q5JUB1|Q8WU31|Q96EE7|Q96N92|Q9H1Q4|Q9H1Q5	Silent	SNP	ENST00000380445.3	37	c.945G>A	CCDS13036.1																																																																																				0.592	VPS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077658.2	NM_022575		7	24	7	24	---	---	---	---
IL3RA	3563	broad.mit.edu	37	X	1501315	1501315	+	Missense_Mutation	SNP	A	A	G			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chrX:1501315A>G	ENST00000331035.4	+	12	1443	c.1094A>G	c.(1093-1095)gAg>gGg	p.E365G	IL3RA_ENST00000381469.2_Missense_Mutation_p.E287G	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	365					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	GCCGGCCTGGAGGAGTGTCTG	0.637																																						ENST00000331035.4																			0				lung(1)|skin(2)	3						c.(1093-1095)gAg>gGg		interleukin 3 receptor, alpha (low affinity)	Sargramostim(DB00020)						186.0	197.0	193.0					X																	1501315		2203	4296	6499	SO:0001583	missense	3563					integral to membrane|plasma membrane	interleukin-3 receptor activity	g.chrX:1501315A>G	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"""Pseudoautosomal regions / PAR1"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.1094A>G	X.37:g.1501315A>G	ENSP00000327890:p.Glu365Gly		Somatic				IL3RA_ENST00000381469.2_Missense_Mutation_p.E287G	p.E365G	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	WXS	Illumina GAIIx	Phase_I	P26951	IL3RA_HUMAN			12	1443	+		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)	365					A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	c.1094A>G	CCDS14113.1	.	.	.	.	.	.	.	.	.	.	.	11.64	1.699891	0.30142	.	.	ENSG00000185291	ENST00000331035;ENST00000381469	T;T	0.50813	0.88;0.73	1.7	1.7	0.24286	.	0.450190	0.17438	U	0.174203	T	0.53498	0.1800	L	0.43152	1.355	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.994	T	0.30707	-0.9969	10	0.52906	T	0.07	.	5.2323	0.15428	1.0:0.0:0.0:0.0	.	286;365	P26951-2;P26951	.;IL3RA_HUMAN	G	365;287	ENSP00000327890:E365G;ENSP00000370878:E287G	ENSP00000327890:E365G	E	+	2	0	IL3RA	1461315	0.017000	0.18338	0.043000	0.18650	0.500000	0.33767	1.491000	0.35583	0.748000	0.32831	0.084000	0.15446	GAG		0.637	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3			32	161	32	161	---	---	---	---
RXFP1	59350	broad.mit.edu	37	4	159549858	159549858	+	Frame_Shift_Del	DEL	A	A	-			TCGA-HC-7209-01A-11D-2114-08	TCGA-HC-7209-10A-01D-2115-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	12dd9452-9a7b-4193-85c7-573b088b1979	77aa04fb-bbf6-4d20-b6c2-e9d4647bf6f6	g.chr4:159549858delA	ENST00000307765.5	+	11	1147	c.896delA	c.(895-897)gaafs	p.E299fs	RXFP1_ENST00000460056.2_Frame_Shift_Del_p.E218fs|RXFP1_ENST00000448688.2_Frame_Shift_Del_p.E194fs|RXFP1_ENST00000470033.1_Frame_Shift_Del_p.E266fs|RXFP1_ENST00000343542.5_Frame_Shift_Del_p.E299fs	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	Q9HBX9	RXFP1_HUMAN	relaxin/insulin-like family peptide receptor 1	299					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|lung connective tissue development (GO:0060427)|nipple morphogenesis (GO:0060658)|parturition (GO:0007567)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49	all_hematologic(180;0.24)	Renal(120;0.0854)		COAD - Colon adenocarcinoma(41;0.0219)		AAACTGGATGAATTGTAAGTA	0.264																																						ENST00000307765.5																			0				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|liver(2)|lung(22)|prostate(1)|skin(10)	49						c.(895-897)gaafs		relaxin/insulin-like family peptide receptor 1							40.0	39.0	39.0					4																	159549858		1795	4062	5857	SO:0001589	frameshift_variant	59350					integral to membrane|plasma membrane	G-protein coupled receptor activity|metal ion binding	g.chr4:159549858delA	AF190500	CCDS43276.1, CCDS58929.1, CCDS58930.1, CCDS75204.1, CCDS75205.1, CCDS75206.1	4q31.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000171509	ENSG00000171509		"""GPCR / Class A : Relaxin family peptide receptors"""	19718	protein-coding gene	gene with protein product		606654	"""leucine-rich repeat-containing G protein-coupled receptor 7"""	LGR7		15956688, 16507880	Standard	NM_021634		Approved	RXFPR1	uc003ipz.3	Q9HBX9	OTTHUMG00000149973	ENST00000307765.5:c.896delA	4.37:g.159549858delA	ENSP00000303248:p.Glu299fs		Somatic				RXFP1_ENST00000460056.2_Frame_Shift_Del_p.E218fs|RXFP1_ENST00000343542.5_Frame_Shift_Del_p.E299fs|RXFP1_ENST00000470033.1_Frame_Shift_Del_p.E266fs|RXFP1_ENST00000448688.2_Frame_Shift_Del_p.E194fs	p.E299fs	NM_001253727.1|NM_001253728.1|NM_001253730.1|NM_001253732.1|NM_001253733.1|NM_021634.3	NP_001240656.1|NP_001240657.1|NP_001240659.1|NP_001240661.1|NP_001240662.1|NP_067647.2	WXS	Illumina GAIIx	Phase_I	Q9HBX9	RXFP1_HUMAN		COAD - Colon adenocarcinoma(41;0.0219)	11	1147	+	all_hematologic(180;0.24)	Renal(120;0.0854)	299					B4DHD1|B4DTV2|Q2M215|Q3KU24|Q3KU25|Q3KU26	Frame_Shift_Del	DEL	ENST00000307765.5	37	c.896delA	CCDS43276.1																																																																																				0.264	RXFP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314865.1	NM_021634		11	31	11	31	---	---	---	---
