#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
PI3	5266	broad.mit.edu	37	20	43804501	43804501	+	Splice_Site	SNP	G	G	A			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr20:43804501G>A	ENST00000243924.3	+	2	126		c.e2-1			NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN	peptidase inhibitor 3, skin-derived						copulation (GO:0007620)|negative regulation of endopeptidase activity (GO:0010951)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			large_intestine(1)|lung(5)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TCTTTTAACAGTTCCTGTTAA	0.448																																						ENST00000243924.3																			0				large_intestine(1)|lung(5)|skin(1)	7						c.e2-1		peptidase inhibitor 3, skin-derived							84.0	81.0	82.0					20																	43804501		2203	4300	6503	SO:0001630	splice_region_variant	5266				copulation	proteinaceous extracellular matrix	serine-type endopeptidase inhibitor activity	g.chr20:43804501G>A	D13156	CCDS13344.1	20q13.12	2013-01-21	2008-10-03		ENSG00000124102	ENSG00000124102		"""WAP four-disulfide core domain containing"""	8947	protein-coding gene	gene with protein product	"""skin-derived antileukoproteinase"", ""trappin-2"""	182257	"""protease inhibitor 3, skin-derived (SKALP)"""			8287685, 12206714	Standard	NM_002638		Approved	ESI, SKALP, ELAFIN, WAP3, WFDC14, cementoin	uc002xng.3	P19957	OTTHUMG00000032567	ENST00000243924.3:c.80-1G>A	20.37:g.43804501G>A								NM_002638.3	NP_002629.1	P19957	ELAF_HUMAN			2	126	+		Myeloproliferative disorder(115;0.0122)						E1P618|Q6FG74	Splice_Site	SNP	ENST00000243924.3	37		CCDS13344.1	.	.	.	.	.	.	.	.	.	.	G	11.02	1.517264	0.27123	.	.	ENSG00000124102	ENST00000243924	.	.	.	3.78	2.81	0.32909	.	.	.	.	.	.	.	.	.	.	.	0.24368	N	0.994842	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.4187	0.38536	0.0:0.2169:0.7831:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PI3	43237915	0.011000	0.17503	0.030000	0.17652	0.318000	0.28184	0.785000	0.26830	1.153000	0.42468	0.655000	0.94253	.		0.448	PI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079418.3	NM_002638	Intron	5	75	0	0	0	1	0	5	75				
IFITM3	10410	broad.mit.edu	37	11	320606	320606	+	Missense_Mutation	SNP	G	G	T	rs199749095	byFrequency	TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr11:320606G>T	ENST00000399808.4	-	1	444	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	RP11-326C3.14_ENST00000602809.1_lincRNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.P49T|IFITM3_ENST00000602735.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.11_ENST00000602756.1_RNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	70	Interaction with SPP1.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)		p.P70T(3)		central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGCAGCAGGGGTTCATGAAG	0.632																																						ENST00000399808.4																			3	Substitution - Missense(3)	p.P70T(3)	endometrium(2)|central_nervous_system(1)	central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18						c.(208-210)Ccc>Acc		interferon induced transmembrane protein 3							89.0	95.0	93.0					11																	320606		2101	4210	6311	SO:0001583	missense	10410				response to virus|type I interferon-mediated signaling pathway	integral to membrane|plasma membrane		g.chr11:320606G>T	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.208C>A	11.37:g.320606G>T	ENSP00000382707:p.Pro70Thr					IFITM3_ENST00000602735.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000602756.1_RNA|RP11-326C3.11_ENST00000602429.1_RNA|IFITM3_ENST00000526811.1_Missense_Mutation_p.P49T	p.P70T	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)	1	444	-		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)	70			Interaction with SPP1.		Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	c.208C>A	CCDS41585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|G	0.076|0.076	-1.193620|-1.193620	0.01594|0.01594	.|.	.|.	ENSG00000142089|ENSG00000142089	ENST00000270031|ENST00000399808;ENST00000526811	.|T;T	.|0.78595	.|-0.94;-1.19	4.65|4.65	-9.3|-9.3	0.00649|0.00649	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54447	.|0.1859	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.32375	.|-0.9909	.|9	.|0.22109	.|T	.|0.4	.|.	2.5632|2.5632	0.04777|0.04777	0.1587:0.0951:0.2785:0.4676|0.1587:0.0951:0.2785:0.4676	.|.	.|70	.|Q01628	.|IFM3_HUMAN	.|T	-1|70;49	.|ENSP00000382707:P70T;ENSP00000432108:P49T	.|ENSP00000382707:P70T	.|P	-|-	.|1	.|0	IFITM3|IFITM3	310606|310606	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.022000|0.022000	0.10575|0.10575	-1.460000|-1.460000	0.02368|0.02368	-3.272000|-3.272000	0.00199|0.00199	-2.532000|-2.532000	0.00182|0.00182	.|CCC		0.632	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034		6	73	1	0	0.000442599	1	0.000442599	6	73				
HRAS	3265	broad.mit.edu	37	11	533874	533874	+	Missense_Mutation	SNP	T	T	C	rs121913233		TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr11:533874T>C	ENST00000451590.1	-	3	369	c.182A>G	c.(181-183)cAg>cGg	p.Q61R	HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000397594.1_Missense_Mutation_p.Q61R|HRAS_ENST00000417302.1_Missense_Mutation_p.Q61R|HRAS_ENST00000311189.7_Missense_Mutation_p.Q61R|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61R	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	61			Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406). {ECO:0000269|PubMed:12727991}.|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.Q61R(136)|p.Q61L(117)|p.Q61P(3)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GTACTCCTCCTGGCCGGCGGT	0.597	Q61L(KNS62_LUNG)|Q61L(KYSE30_OESOPHAGUS)|Q61L(NCIH1915_LUNG)	6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)																												ENST00000417302.1	Q61L(KNS62_LUNG)|Q61L(KYSE30_OESOPHAGUS)|Q61L(NCIH1915_LUNG)	6	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	Mis	v-Ha-ras Harvey rat sarcoma viral oncogene homolog			"""E, L, M"""		"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""	"""infrequent sarcomas, rare other types"""		256	Substitution - Missense(256)	p.Q61R(136)|p.Q61L(117)|p.Q61P(3)	skin(70)|thyroid(58)|urinary_tract(53)|prostate(23)|upper_aerodigestive_tract(22)|lung(11)|salivary_gland(6)|haematopoietic_and_lymphoid_tissue(5)|testis(3)|liver(2)|cervix(1)|penis(1)|oesophagus(1)	adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901						c.(181-183)cAg>cGg		Harvey rat sarcoma viral oncogene homolog	Sulindac(DB00605)						117.0	102.0	107.0					11																	533874		2203	4300	6503	SO:0001583	missense	3265	Costello syndrome	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	activation of MAPKK activity|axon guidance|blood coagulation|cell cycle arrest|cellular senescence|epidermal growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|mitotic cell cycle G1/S transition checkpoint|negative regulation of cell proliferation|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of DNA replication|positive regulation of epithelial cell proliferation|Ras protein signal transduction|synaptic transmission	cytosol|Golgi membrane|plasma membrane	GTP binding|GTPase activity|protein C-terminus binding	g.chr11:533874T>C	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.182A>G	11.37:g.533874T>C	ENSP00000407586:p.Gln61Arg	HNSCC(11;0.0054)				HRAS_ENST00000397594.1_Missense_Mutation_p.Q61R|HRAS_ENST00000397596.2_Missense_Mutation_p.Q61R|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000451590.1_Missense_Mutation_p.Q61R|HRAS_ENST00000311189.7_Missense_Mutation_p.Q61R	p.Q61R	NM_176795.3	NP_789765.1	P01112	RASH_HUMAN		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)	3	369	-		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)	61		Q -> K (in follicular thyroid carcinoma samples; somatic mutation; increases transformation of cultured cell lines; dbSNP:rs28933406).|Q -> L (in melanoma; strongly reduced GTP hydrolysis in the presence of RAF1; increases transformation of cultured cell lines).			B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Missense_Mutation	SNP	ENST00000451590.1	37	c.182A>G	CCDS7698.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.546606	0.45383	.	.	ENSG00000174775	ENST00000397594;ENST00000397596;ENST00000451590;ENST00000417302;ENST00000311189	D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75	3.64	3.64	0.41730	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85613	0.5737	M	0.90870	3.155	0.80722	D	1	B;B	0.21071	0.051;0.008	B;B	0.22152	0.022;0.038	D	0.85970	0.1476	10	0.66056	D	0.02	.	11.8872	0.52608	0.0:0.0:0.0:1.0	.	61;61	P01112-2;P01112	.;RASH_HUMAN	R	61	ENSP00000380722:Q61R;ENSP00000380723:Q61R;ENSP00000407586:Q61R;ENSP00000388246:Q61R;ENSP00000309845:Q61R	ENSP00000309845:Q61R	Q	-	2	0	HRAS	523874	1.000000	0.71417	0.985000	0.45067	0.482000	0.33219	7.727000	0.84838	1.662000	0.50781	0.459000	0.35465	CAG		0.597	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795		18	34	0	0	0	1	0	18	34				
PLEKHG4B	153478	broad.mit.edu	37	5	162009	162009	+	Missense_Mutation	SNP	A	A	G			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr5:162009A>G	ENST00000283426.6	+	10	1581	c.1531A>G	c.(1531-1533)Agg>Ggg	p.R511G		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	511							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GGCTGAGTGCAGGGAGGGAGA	0.632																																						ENST00000283426.6																			0				endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11						c.(1531-1533)Agg>Ggg		pleckstrin homology domain containing, family G (with RhoGef domain) member 4B							82.0	70.0	74.0					5																	162009		2203	4300	6503	SO:0001583	missense	153478				regulation of Rho protein signal transduction	intracellular	Rho guanyl-nucleotide exchange factor activity	g.chr5:162009A>G	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1531A>G	5.37:g.162009A>G	ENSP00000283426:p.Arg511Gly						p.R511G	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)	10	1581	+			511						Missense_Mutation	SNP	ENST00000283426.6	37	c.1531A>G	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	A	8.792	0.930784	0.18131	.	.	ENSG00000153404	ENST00000283426	D	0.92446	-3.04	2.59	-0.344	0.12628	.	.	.	.	.	D	0.86083	0.5848	L	0.58101	1.795	0.09310	N	1	P	0.43477	0.808	B	0.39027	0.288	T	0.74497	-0.3646	9	0.21540	T	0.41	.	3.0878	0.06284	0.5972:0.249:0.1538:0.0	.	511	Q96PX9	PKH4B_HUMAN	G	511	ENSP00000283426:R511G	ENSP00000283426:R511G	R	+	1	2	PLEKHG4B	215009	0.115000	0.22152	0.000000	0.03702	0.002000	0.02628	0.295000	0.19065	-0.340000	0.08388	-0.556000	0.04195	AGG		0.632	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909		7	25	0	0	0	1	0	7	25				
PLEKHM1P	440456	broad.mit.edu	37	17	62818136	62818136	+	RNA	SNP	G	G	C	rs200037995		TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr17:62818136G>C	ENST00000582986.1	-	0	362					NR_024386.1		Q69YJ1	PKHMP_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1 pseudogene						intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)										CTGAAGAATGGGAAATGGAAT	0.572																																						ENST00000582986.1																			0																																																			440456							g.chr17:62818136G>C			17q24.1	2012-10-03			ENSG00000214176	ENSG00000214176			35411	pseudogene	pseudogene							Standard	NR_024386		Approved	LOC440456	uc002jew.4	Q69YJ1	OTTHUMG00000179296		17.37:g.62818136G>C								NR_024386.1						0	362	-									RNA	SNP	ENST00000582986.1	37																																																																																						0.572	PLEKHM1P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000445598.1	NR_024386		4	39	0	0	0	1	0	4	39				
PTCHD4	442213	broad.mit.edu	37	6	48036151	48036151	+	Missense_Mutation	SNP	C	C	T			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr6:48036151C>T	ENST00000339488.4	-	1	274	c.241G>A	c.(241-243)Gcc>Acc	p.A81T	PTCHD4_ENST00000543600.1_Missense_Mutation_p.A64T	NM_001013732.3	NP_001013754.3	Q6ZW05	PTHD4_HUMAN	patched domain containing 4	81						integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)										TCGATCTTGGCCAGGCTGTGG	0.652																																						ENST00000543600.1																			0											c.(190-192)Gcc>Acc		patched domain containing 4							47.0	53.0	51.0					6																	48036151		1972	4150	6122	SO:0001583	missense	442213					integral to membrane	hedgehog receptor activity	g.chr6:48036151C>T		CCDS34473.2	6p12.3	2012-02-06	2012-02-06	2012-02-06	ENSG00000244694	ENSG00000244694			21345	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 138"""	C6orf138			Standard	NM_001013732		Approved	dJ402H5.2, FLJ41841	uc011dwm.2	Q6ZW05	OTTHUMG00000150404	ENST00000339488.4:c.241G>A	6.37:g.48036151C>T	ENSP00000341914:p.Ala81Thr					PTCHD4_ENST00000339488.4_Missense_Mutation_p.A81T	p.A64T			Q6ZW05	CF138_HUMAN			1	229	-			81					B0QZ29|B4DRK3|Q5T884	Missense_Mutation	SNP	ENST00000339488.4	37	c.190G>A	CCDS34473.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.70|18.70	3.679259|3.679259	0.68042|0.68042	.|.	.|.	ENSG00000244694|ENSG00000244694	ENST00000339488;ENST00000543600|ENST00000398738	D;T|.	0.94280|.	-3.39;0.19|.	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	0.060335|.	0.64402|.	D|.	0.000005|.	T|T	0.68897|0.68897	0.3051|0.3051	M|M	0.71036|0.71036	2.16|2.16	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;0.993|.	D;D|.	0.80764|.	0.994;0.984|.	T|T	0.69503|0.69503	-0.5128|-0.5128	10|5	0.62326|.	D|.	0.03|.	.|.	18.0082|18.0082	0.89215|0.89215	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	81;64|.	Q6ZW05;B0QZ29|.	CF138_HUMAN;.|.	T|D	81;64|80	ENSP00000341914:A81T;ENSP00000439864:A64T|.	ENSP00000341914:A81T|.	A|G	-|-	1|2	0|0	C6orf138|C6orf138	48144110|48144110	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.394000|7.394000	0.79862|0.79862	2.237000|2.237000	0.73441|0.73441	0.563000|0.563000	0.77884|0.77884	GCC|GGC		0.652	PTCHD4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317987.2	NM_001013732		3	44	0	0	0	1	0	3	44				
LOC101927209	101927209	broad.mit.edu	37	1	142713944	142713944	+	lincRNA	SNP	C	C	T	rs199960649		TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr1:142713944C>T	ENST00000610091.1	-	0	1714																											TGATTACCTCCGAAGTTAAAG	0.308																																						ENST00000369381.2																			0																																																			101927209							g.chr1:142713944C>T																													1.37:g.142713944C>T														0	661	-									RNA	SNP	ENST00000610091.1	37																																																																																						0.308	RP11-417J8.6-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000037265.2			3	30	0	0	0	1	0	3	30				
SAG	6295	broad.mit.edu	37	2	234243689	234243689	+	Silent	SNP	C	C	T			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr2:234243689C>T	ENST00000409110.1	+	11	1118	c.888C>T	c.(886-888)ggC>ggT	p.G296G	SAG_ENST00000449594.2_Silent_p.G162G	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN	S-antigen; retina and pineal gland (arrestin)	296					cell surface receptor signaling pathway (GO:0007166)|negative regulation of catalytic activity (GO:0043086)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cytosol (GO:0005829)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)		AAAGGAGAGGCATTGCCCTGG	0.542																																						ENST00000409110.1																			0				cervix(1)|kidney(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9						c.(886-888)ggC>ggT		S-antigen; retina and pineal gland (arrestin)							79.0	85.0	83.0					2																	234243689		2173	4284	6457	SO:0001819	synonymous_variant	6295				rhodopsin mediated phototransduction|rhodopsin mediated signaling pathway		protein phosphatase inhibitor activity	g.chr2:234243689C>T		CCDS46545.1	2q37.1	2013-02-14			ENSG00000130561	ENSG00000130561			10521	protein-coding gene	gene with protein product	"""arrestin 1"""	181031				2249983	Standard	NM_000541		Approved	ARRESTIN, RP47	uc002vuh.2	P10523	OTTHUMG00000153213	ENST00000409110.1:c.888C>T	2.37:g.234243689C>T						SAG_ENST00000449594.2_Silent_p.G162G	p.G296G	NM_000541.4	NP_000532.2	P10523	ARRS_HUMAN		Epithelial(121;2.86e-17)|BRCA - Breast invasive adenocarcinoma(100;0.00037)|LUSC - Lung squamous cell carcinoma(224;0.00608)|Lung(119;0.00714)|GBM - Glioblastoma multiforme(43;0.207)	11	1118	+		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.018)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.054)	296					A0FDN6|Q53SV3|Q99858	Silent	SNP	ENST00000409110.1	37	c.888C>T	CCDS46545.1																																																																																				0.542	SAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330126.1	NM_000541		22	30	0	0	0	1	0	22	30				
NBPF15	284565	broad.mit.edu	37	1	148594434	148594434	+	Missense_Mutation	SNP	G	G	A			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr1:148594434G>A	ENST00000369187.3	+	19	2296	c.1807G>A	c.(1807-1809)Gtc>Atc	p.V603I	NBPF15_ENST00000442702.2_Missense_Mutation_p.V603I	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	603	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					AGAGCCTGAAGTCTTACAGGA	0.458																																						ENST00000442702.2																			0				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12						c.(1807-1809)Gtc>Atc		neuroblastoma breakpoint family, member 15																																				SO:0001583	missense	284565					cytoplasm		g.chr1:148594434G>A	BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1807G>A	1.37:g.148594434G>A	ENSP00000358188:p.Val603Ile					NBPF15_ENST00000369187.3_Missense_Mutation_p.V603I	p.V603I	NM_001170755.1	NP_001164226.1	Q8N660	NBPFF_HUMAN			21	2874	+	all_hematologic(923;0.032)		603			NBPF 6.		Q3BBV9|Q8IX77	Missense_Mutation	SNP	ENST00000369187.3	37	c.1807G>A	CCDS932.1	.	.	.	.	.	.	.	.	.	.	.	10.11	1.259285	0.23051	.	.	ENSG00000243452	ENST00000442702;ENST00000369187	T;T	0.15372	2.43;2.43	0.502	0.502	0.16932	DUF1220 (2);	.	.	.	.	T	0.27098	0.0664	M	0.84683	2.71	0.09310	N	1	D	0.57257	0.979	D	0.75484	0.986	T	0.02539	-1.1144	8	0.56958	D	0.05	.	.	.	.	.	603	Q8N660	NBPFF_HUMAN	I	603	ENSP00000416864:V603I;ENSP00000358188:V603I	ENSP00000358188:V603I	V	+	1	0	NBPF15	146861058	0.951000	0.32395	0.009000	0.14445	0.006000	0.05464	0.894000	0.28350	0.557000	0.29117	0.377000	0.23210	GTC		0.458	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638		7	258	0	0	0	1	0	7	258				
NBPF15	284565	broad.mit.edu	37	1	148594439	148594439	+	Silent	SNP	A	A	G			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr1:148594439A>G	ENST00000369187.3	+	19	2301	c.1812A>G	c.(1810-1812)ttA>ttG	p.L604L	NBPF15_ENST00000442702.2_Silent_p.L604L	NM_173638.3	NP_775909.2	Q8N660	NBPFF_HUMAN	neuroblastoma breakpoint family, member 15	604	NBPF 6. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12	all_hematologic(923;0.032)					CTGAAGTCTTACAGGACTCAC	0.463																																						ENST00000442702.2																			0				NS(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)	12						c.(1810-1812)ttA>ttG		neuroblastoma breakpoint family, member 15																																				SO:0001819	synonymous_variant	284565					cytoplasm		g.chr1:148594439A>G	BC023087	CCDS72852.1	1q21.1	2014-01-16			ENSG00000243452	ENSG00000266338		"""neuroblastoma breakpoint family"""	28791	protein-coding gene	gene with protein product		610414, 614005	"""neuroblastoma breakpoint family, member 16"""	NBPF16		16079250	Standard	NM_173638		Approved	MGC8902	uc001esc.2	Q8N660	OTTHUMG00000013634	ENST00000369187.3:c.1812A>G	1.37:g.148594439A>G						NBPF15_ENST00000369187.3_Silent_p.L604L	p.L604L	NM_001170755.1	NP_001164226.1	Q8N660	NBPFF_HUMAN			21	2879	+	all_hematologic(923;0.032)		604			NBPF 6.		Q3BBV9|Q8IX77	Silent	SNP	ENST00000369187.3	37	c.1812A>G	CCDS932.1																																																																																				0.463	NBPF15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038609.3	NM_173638		7	262	0	0	0	1	0	7	262				
PTPN18	26469	broad.mit.edu	37	2	131129929	131129934	+	In_Frame_Del	DEL	GACGGG	GACGGG	-	rs112040677	byFrequency	TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr2:131129929_131129934delGACGGG	ENST00000175756.5	+	13	1214_1219	c.1113_1118delGACGGG	c.(1111-1119)cagacgggg>cag	p.TG378del	PTPN18_ENST00000347849.3_In_Frame_Del_p.TG271del	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	378				Missing (in Ref. 1; CAA56105). {ECO:0000305}.	peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.T378_G379delTG(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					gtgggacgcagacggggacggggacg	0.777														1724	0.344249	0.6324	0.2349	5008	,	,		12983	0.3214		0.2008	False		,,,				2504	0.2035					ENST00000175756.5																			1	Deletion - In frame(1)	p.T378_G379delTG(1)	prostate(1)	endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15						c.(1111-1119)cag>ca		protein tyrosine phosphatase, non-receptor type 18 (brain-derived)			,	1068,966		446,176,395					,	-3.8	0.0		dbSNP_132	3	951,4205		280,391,1907	no	coding,coding	PTPN18	NM_014369.3,NM_001142370.1	,	726,567,2302	A1A1,A1R,RR		18.4445,47.4926,28.0807	,	,		2019,5171				SO:0001651	inframe_deletion	26469					cytoplasm|nucleus	non-membrane spanning protein tyrosine phosphatase activity	g.chr2:131129929_131129934delGACGGG	X79568	CCDS2161.1, CCDS46410.1	2q21	2011-06-09			ENSG00000072135	ENSG00000072135		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9649	protein-coding gene	gene with protein product		606587				8950995	Standard	NM_014369		Approved	BDP1	uc002trc.3	Q99952	OTTHUMG00000131630	ENST00000175756.5:c.1113_1118delGACGGG	2.37:g.131129935_131129940delGACGGG	ENSP00000175756:p.Thr378_Gly379del					PTPN18_ENST00000347849.3_In_Frame_Del_p.QTG264del	p.QTG371del	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN			13	1214_1219	+	Colorectal(110;0.1)		371					B4E1E6|Q53P42	In_Frame_Del	DEL	ENST00000175756.5	37	c.1113_1118delGACGGG	CCDS2161.1																																																																																				0.777	PTPN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254523.2			2	4						2	4	---	---	---	---
THAP4	51078	broad.mit.edu	37	2	242545840	242545840	+	Frame_Shift_Del	DEL	C	C	-			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr2:242545840delC	ENST00000407315.1	-	3	1720	c.1289delG	c.(1288-1290)ggcfs	p.G430fs	THAP4_ENST00000402545.1_Frame_Shift_Del_p.G18fs|THAP4_ENST00000402136.1_Frame_Shift_Del_p.G18fs	NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	430							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		CAGCCAGGTGCCCAGCATCCA	0.617																																						ENST00000407315.1																			0				kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9						c.(1288-1290)gcfs		THAP domain containing 4							40.0	32.0	35.0					2																	242545840		2203	4296	6499	SO:0001589	frameshift_variant	51078						DNA binding|metal ion binding	g.chr2:242545840delC	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.1289delG	2.37:g.242545840delC	ENSP00000385006:p.Gly430fs					THAP4_ENST00000402136.1_Frame_Shift_Del_p.G18fs|THAP4_ENST00000402545.1_Frame_Shift_Del_p.G18fs	p.G430fs	NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)	3	1720	-		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)	430					Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Frame_Shift_Del	DEL	ENST00000407315.1	37	c.1289delG	CCDS2551.1																																																																																				0.617	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963		2	4						2	4	---	---	---	---
RBPJ	3516	broad.mit.edu	37	4	26417145	26417146	+	Frame_Shift_Ins	INS	-	-	A			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr4:26417145_26417146insA	ENST00000361572.6	+	4	437_438	c.243_244insA	c.(244-246)aaafs	p.K82fs	RBPJ_ENST00000511401.1_3'UTR|RBPJ_ENST00000342320.4_Frame_Shift_Ins_p.K68fs|RBPJ_ENST00000355476.3_Frame_Shift_Ins_p.K68fs|RBPJ_ENST00000342295.1_Frame_Shift_Ins_p.K82fs|RBPJ_ENST00000348160.4_Frame_Shift_Ins_p.K69fs|RBPJ_ENST00000507561.1_Frame_Shift_Ins_p.K47fs|RBPJ_ENST00000504907.1_Frame_Shift_Ins_p.K68fs|RBPJ_ENST00000345843.3_Frame_Shift_Ins_p.K67fs			Q06330	SUH_HUMAN	recombination signal binding protein for immunoglobulin kappa J region	82					angiogenesis (GO:0001525)|arterial endothelial cell fate commitment (GO:0060844)|atrioventricular canal development (GO:0036302)|auditory receptor cell fate commitment (GO:0009912)|B cell differentiation (GO:0030183)|blood vessel endothelial cell fate specification (GO:0097101)|blood vessel lumenization (GO:0072554)|blood vessel remodeling (GO:0001974)|cardiac left ventricle morphogenesis (GO:0003214)|Clara cell differentiation (GO:0060486)|defense response to bacterium (GO:0042742)|DNA recombination (GO:0006310)|dorsal aorta morphogenesis (GO:0035912)|endocardium morphogenesis (GO:0003160)|epidermal cell fate specification (GO:0009957)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|gene expression (GO:0010467)|hair follicle maturation (GO:0048820)|humoral immune response (GO:0006959)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|labyrinthine layer blood vessel development (GO:0060716)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ossification (GO:0030279)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|outflow tract morphogenesis (GO:0003151)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:1901297)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of ephrin receptor signaling pathway (GO:1901189)|positive regulation of ERBB signaling pathway (GO:1901186)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription of Notch receptor target (GO:0007221)|regulation of timing of cell differentiation (GO:0048505)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|sebaceous gland development (GO:0048733)|secondary heart field specification (GO:0003139)|somatic stem cell maintenance (GO:0035019)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|recombinase activity (GO:0000150)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15		Breast(46;0.0503)				GTGGATGGAAGAAAAAAAAAGA	0.371																																						ENST00000342320.4																			0				central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)	15						c.(199-204)aaaaaafs		recombination signal binding protein for immunoglobulin kappa J region																																				SO:0001589	frameshift_variant	3516				DNA recombination|negative regulation of transcription, DNA-dependent|positive regulation of transcription of Notch receptor target	cytoplasm|nucleolus|nucleoplasm	DNA binding|protein binding|recombinase activity|sequence-specific DNA binding transcription factor activity	g.chr4:26417145_26417146insA	L07872	CCDS3436.1, CCDS3437.1, CCDS33969.1, CCDS43219.1	4p15.2	2013-10-18	2007-02-26	2007-02-26	ENSG00000168214	ENSG00000168214			5724	protein-coding gene	gene with protein product	"""suppressor of hairless homolog (Drosophila)"""	147183	"""recombining binding protein suppressor of hairless (Drosophila)"""	IGKJRB1, RBPSUH		8406481, 9290259	Standard	NM_005349		Approved	SUH, IGKJRB, RBPJK, KBF2, RBP-J, CBF1	uc003gsb.2	Q06330	OTTHUMG00000097793	ENST00000361572.6:c.252dupA	4.37:g.26417154_26417154dupA	ENSP00000354528:p.Lys82fs					RBPJ_ENST00000348160.4_Frame_Shift_Ins_p.KK68fs|RBPJ_ENST00000504907.1_Frame_Shift_Ins_p.KK67fs|RBPJ_ENST00000507561.1_Frame_Shift_Ins_p.KK46fs|RBPJ_ENST00000361572.6_Frame_Shift_Ins_p.KK81fs|RBPJ_ENST00000511401.1_3'UTR|RBPJ_ENST00000355476.3_Frame_Shift_Ins_p.KK67fs|RBPJ_ENST00000342295.1_Frame_Shift_Ins_p.KK81fs|RBPJ_ENST00000345843.3_Frame_Shift_Ins_p.KK66fs	p.KK67fs			Q06330	SUH_HUMAN			4	377_378	+		Breast(46;0.0503)	81					B4DY22|Q5XKH9|Q6P1N3	Frame_Shift_Ins	INS	ENST00000361572.6	37	c.201_202insA	CCDS3437.1																																																																																				0.371	RBPJ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215046.2	NM_015874		9	111						9	111	---	---	---	---
KIAA1958	158405	broad.mit.edu	37	9	115421618	115421627	+	Frame_Shift_Del	DEL	CTGGCCACCT	CTGGCCACCT	-			TCGA-QR-A70W-01A-12D-A35D-08	TCGA-QR-A70W-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	6c255364-521b-4bba-b407-7d148b987883	21630a1c-4fd2-400a-ba3d-63ecedc1d4cc	g.chr9:115421618_115421627delCTGGCCACCT	ENST00000337530.6	+	4	1716_1725	c.1420_1429delCTGGCCACCT	c.(1420-1431)ctggccacctcgfs	p.LATS474fs	KIAA1958_ENST00000536272.1_Frame_Shift_Del_p.LATS502fs	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	474										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						CTCGGACTTCCTGGCCACCTCGCTCCATGC	0.543																																						ENST00000337530.6																			0				endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						c.(1420-1431)cgfs		KIAA1958																																				SO:0001589	frameshift_variant	158405							g.chr9:115421618_115421627delCTGGCCACCT	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.1420_1429delCTGGCCACCT	9.37:g.115421618_115421627delCTGGCCACCT	ENSP00000336940:p.Leu474fs					KIAA1958_ENST00000536272.1_Frame_Shift_Del_p.LATS502fs	p.LATS474fs	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN			4	1716_1725	+			474					B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Frame_Shift_Del	DEL	ENST00000337530.6	37	c.1420_1429delCTGGCCACCT	CCDS35108.1																																																																																				0.543	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465		23	55						23	55	---	---	---	---
