#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
PCNXL4	64430	broad.mit.edu	37	14	60581721	60581721	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr14:60581721G>C	ENST00000406854.1	+	4	1453	c.899G>C	c.(898-900)gGa>gCa	p.G300A	PCNXL4_ENST00000404681.2_Missense_Mutation_p.G300A|PCNXL4_ENST00000317623.4_Missense_Mutation_p.G66A|PCNXL4_ENST00000406949.1_Missense_Mutation_p.G66A			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	300						integral component of membrane (GO:0016021)											ATGTCTGCTGGAACAGCTATA	0.308																																						uc001xer.4																			0				endometrium(3)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)	18						c.(196-198)gGa>gCa		Homo sapiens chromosome 14 open reading frame 135 (C14orf135), mRNA.							78.0	64.0	68.0					14																	60581721		1830	4100	5930	SO:0001583	missense	64430					integral to membrane		g.chr14:60581721G>C	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.899G>C	14.37:g.60581721G>C	ENSP00000384801:p.Gly300Ala					C14orf135_uc001xeq.2_Missense_Mutation_p.G66A	p.G66A	NM_022495	NP_071940	Q63HM2	CN135_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.127)	2	719	+		Myeloproliferative disorder(585;0.163)	300					A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37	c.197G>C		.	.	.	.	.	.	.	.	.	.	G	1.293	-0.607078	0.03717	.	.	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.22743	1.96;1.97;1.94;1.97	5.08	4.17	0.49024	.	.	.	.	.	T	0.15825	0.0381	L	0.52011	1.625	0.80722	D	1	B;P	0.42409	0.386;0.779	B;B	0.35182	0.052;0.197	T	0.04481	-1.0948	9	0.05721	T	0.95	.	14.2012	0.65705	0.0:0.2853:0.7147:0.0	.	300;66	Q63HM2;B5MC47	CN135_HUMAN;.	A	66;300;66;300	ENSP00000317396:G66A;ENSP00000384801:G300A;ENSP00000385201:G66A;ENSP00000385713:G300A	ENSP00000317396:G66A	G	+	2	0	C14orf135	59651474	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.033000	0.57282	1.227000	0.43598	0.462000	0.41574	GGA		0.308	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495		11	33	0	0	0	1	0	11	33				
MT1E	4493	broad.mit.edu	37	16	56660717	56660717	+	Intron	SNP	G	G	A			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr16:56660717G>A	ENST00000306061.6	+	3	471				MT1E_ENST00000330439.6_Missense_Mutation_p.S123N|MT1E_ENST00000568293.1_Intron	NM_175617.3	NP_783316.2	P04732	MT1E_HUMAN	metallothionein 1E						cellular response to cadmium ion (GO:0071276)|cellular response to zinc ion (GO:0071294)|negative regulation of growth (GO:0045926)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)										CTGAGCTCGAGCCAGGCTTGC	0.582																																						uc002ejm.3																			0											c.(367-369)aGc>aAc		Homo sapiens metallothionein 1E (MT1E), mRNA.																																				SO:0001627	intron_variant	4493					cytoplasm	cadmium ion binding|copper ion binding|zinc ion binding	g.chr16:56660717G>A	BC009699	CCDS10764.2	16q13	2008-08-11	2007-03-02		ENSG00000169715	ENSG00000169715		"""Metallothioneins"""	7397	protein-coding gene	gene with protein product		156351		MT1		6089206, 2581970	Standard	XM_005255956		Approved	MTD	uc002ejl.3	P04732	OTTHUMG00000133014	ENST00000306061.6:c.95-75G>A	16.37:g.56660717G>A						MT1A_uc002eji.3_Intron|MT1M_uc010vhe.2_Intron|MT1E_uc002ejl.3_Intron	p.S123N			P04732	MT1E_HUMAN			1	547	+			30					A2RRF7|Q86YX4|Q8TD51	Missense_Mutation	SNP	ENST00000306061.6	37	c.368G>A	CCDS10764.2	.	.	.	.	.	.	.	.	.	.	G	12.02	1.811395	0.32053	.	.	ENSG00000169715	ENST00000330439	T	0.36878	1.23	1.17	1.17	0.20885	.	2746.690000	0.01273	U	0.009506	T	0.21145	0.0509	.	.	.	0.09310	N	1	P	0.46020	0.871	B	0.34931	0.192	T	0.24404	-1.0161	8	.	.	.	.	3.3352	0.07098	0.4474:0.0:0.5525:0.0	.	123	P04732-2	.	N	123	ENSP00000328137:S123N	.	S	+	2	0	MT1E	55218218	0.000000	0.05858	0.003000	0.11579	0.013000	0.08279	0.380000	0.20602	0.927000	0.37143	0.313000	0.20887	AGC		0.582	MT1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256600.1	NM_175617		4	72	0	0	0	1	0	4	72				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	uc003vwc.4	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(41204)|p.V600K(615)|p.V600?(377)|p.V600R(99)|p.V600D(40)|p.V600_K601>E(30)|p.V600L(28)|p.V600A(24)|p.V600G(22)|p.V600M(22)|p.A598_T599insV(7)|p.T599_V600insT(7)|p.T599I(5)|p.V600Q(4)|p.T599_R603>I(4)|p.T599_V600insTT(3)|p.T599_V600insDFGLAT(2)|p.T599_V600>IAL(2)|p.V600_S605>EK(2)|p.T599T(2)|p.V600_S605>DV(2)|p.V600_S605>D(2)|p.V600_W604del(1)|p.V600V(1)|p.T599_V600insV(1)|p.V600>DLAT(1)|p.D594_T599del(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		Homo sapiens v-raf murine sarcoma viral oncogene homolog B1 (BRAF), mRNA.	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333	NP_004324	P15056	BRAF_HUMAN			14	1860	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		37	84	0	0	0	1	0	37	84				
ARC	23237	broad.mit.edu	37	8	143695032	143695032	+	Missense_Mutation	SNP	C	C	T			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr8:143695032C>T	ENST00000356613.2	-	1	1801	c.601G>A	c.(601-603)Gag>Aag	p.E201K	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	0					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				TGCCCGTCCTCGCCGGGGACC	0.726																																						uc003ywn.1																			0				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13						c.(601-603)Gag>Aag		Homo sapiens activity-regulated cytoskeleton-associated protein (ARC), mRNA.							13.0	15.0	14.0					8																	143695032		2175	4266	6441	SO:0001583	missense	23237				endocytosis	acrosomal vesicle|cell junction|dendritic spine|endosome|postsynaptic density|postsynaptic membrane		g.chr8:143695032C>T	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.601G>A	8.37:g.143695032C>T	ENSP00000349022:p.Glu201Lys					ARC_uc022bca.1_Missense_Mutation_p.E201K	p.E201K	NM_015193	NP_056008	Q7LC44	ARC_HUMAN			0	802	-	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)	201			Required for binding DNM2 (By similarity).		B4DFL0|O60937	Missense_Mutation	SNP	ENST00000356613.2	37	c.601G>A	CCDS34950.1	.	.	.	.	.	.	.	.	.	.	C	13.03	2.114641	0.37339	.	.	ENSG00000198576	ENST00000356613	T	0.35605	1.3	4.56	4.56	0.56223	.	0.125935	0.35585	U	0.003117	T	0.20618	0.0496	N	0.19112	0.55	0.30131	N	0.804773	B	0.32071	0.355	B	0.19148	0.024	T	0.11227	-1.0596	10	0.29301	T	0.29	.	12.2406	0.54540	0.0:0.8282:0.1718:0.0	.	201	Q7LC44	ARC_HUMAN	K	201	ENSP00000349022:E201K	ENSP00000349022:E201K	E	-	1	0	ARC	143692034	0.878000	0.30173	0.900000	0.35374	0.141000	0.21300	2.313000	0.43735	2.075000	0.62263	0.462000	0.41574	GAG		0.726	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2			14	21	0	0	0	1	0	14	21				
SPTA1	6708	broad.mit.edu	37	1	158582606	158582606	+	Splice_Site	SNP	C	C	T			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr1:158582606C>T	ENST00000368147.4	-	51	7315		c.e51+1		SPTA1_ENST00000485680.1_5'Flank	NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1						actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAGAATCGGACCTGCTTCATG	0.458																																						uc001fst.1																			0				NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307						c.e51+1		Homo sapiens spectrin, alpha, erythrocytic 1 (elliptocytosis 2) (SPTA1), mRNA.							132.0	130.0	131.0					1																	158582606		1933	4128	6061	SO:0001630	splice_region_variant	6708				actin filament capping|actin filament organization|axon guidance|regulation of cell shape	cytosol|intrinsic to internal side of plasma membrane|spectrin|spectrin-associated cytoskeleton	actin filament binding|calcium ion binding|structural constituent of cytoskeleton	g.chr1:158582606C>T	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.7134+1G>A	1.37:g.158582606C>T							p.Q2378_splice	NM_003126	NP_003117	P02549	SPTA1_HUMAN			51	7333	-	all_hematologic(112;0.0378)		2378			EF-hand 3.		Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Splice_Site	SNP	ENST00000368147.4	37	c.7134_splice	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	19.10	3.761321	0.69763	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	.	.	.	5.09	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.6657	0.56842	0.0:0.9195:0.0:0.0805	.	.	.	.	.	-1	.	.	.	-	.	.	SPTA1	156849230	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	5.216000	0.65246	1.508000	0.48769	0.655000	0.94253	.		0.458	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	Intron	5	100	0	0	0	1	0	5	100				
DHX8	1659	broad.mit.edu	37	17	41577392	41577392	+	Silent	SNP	C	C	G			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr17:41577392C>G	ENST00000262415.3	+	11	1539	c.1467C>G	c.(1465-1467)ctC>ctG	p.L489L	DHX8_ENST00000540306.1_Silent_p.L489L	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	489					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		GGCGGGAACTCAAACAGGCCC	0.532																																					NSCLC(56;1548 1661 49258 49987)	uc002idu.1																			0				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42						c.(1465-1467)ctC>ctG		Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 8 (DHX8), mRNA.							174.0	182.0	179.0					17																	41577392		2203	4300	6503	SO:0001819	synonymous_variant	1659					catalytic step 2 spliceosome	ATP binding|ATP-dependent RNA helicase activity|RNA binding|protein binding	g.chr17:41577392C>G	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.1467C>G	17.37:g.41577392C>G						DHX8_uc010wif.1_Silent_p.L398L|DHX8_uc010wig.2_Silent_p.L489L	p.L489L	NM_004941	NP_004932	Q14562	DHX8_HUMAN		BRCA - Breast invasive adenocarcinoma(366;0.08)	10	1539	+		Breast(137;0.00908)	489						Silent	SNP	ENST00000262415.3	37	c.1467C>G	CCDS11464.1																																																																																				0.532	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1			116	194	0	0	0	1	0	116	194				
THPO	7066	broad.mit.edu	37	3	184093689	184093689	+	Missense_Mutation	SNP	A	A	C			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr3:184093689A>C	ENST00000204615.7	-	3	342	c.128T>G	c.(127-129)cTt>cGt	p.L43R	THPO_ENST00000445696.2_Missense_Mutation_p.L43R|THPO_ENST00000421442.2_Missense_Mutation_p.L43R|THPO_ENST00000477594.1_5'Flank|EIF2B5_ENST00000444495.1_Intron	NM_000460.2|NM_001177597.1|NM_001177598.1	NP_000451.1|NP_001171068.1|NP_001171069.1	P40225	TPO_HUMAN	thrombopoietin	43					blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|myeloid cell differentiation (GO:0030099)|platelet activation (GO:0030168)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|thrombopoietin-mediated signaling pathway (GO:0038163)	extracellular space (GO:0005615)	growth factor activity (GO:0008083)			NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCTGCTGTGAAGGACATGGGA	0.527																																						uc003fol.1																			0				NS(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)	16						c.(127-129)cTt>cGt		Homo sapiens thrombopoietin (THPO), transcript variant 1, mRNA.							119.0	115.0	116.0					3																	184093689		2203	4300	6503	SO:0001583	missense	7066				cell proliferation|platelet activation	extracellular space	cytokine activity|growth factor activity|hormone activity	g.chr3:184093689A>C		CCDS3265.1, CCDS54693.1	3q27	2014-01-30	2008-07-31		ENSG00000090534	ENSG00000090534		"""Endogenous ligands"""	11795	protein-coding gene	gene with protein product	"""prepro-thrombopoietin"", ""megakaryocyte stimulating factor"", ""myeloproliferative leukemia virus oncogene ligand"", ""megakaryocyte growth and development factor"", ""MPL ligand"", ""megakaryocyte colony-stimulating factor"", ""c-mpl ligand"", ""thrombopoietin nirs variant 1"""	600044		MGDF		8202154	Standard	XM_006713738		Approved	TPO, MPLLG	uc003fol.1	P40225	OTTHUMG00000156745	ENST00000204615.7:c.128T>G	3.37:g.184093689A>C	ENSP00000204615:p.Leu43Arg					THPO_uc003fom.2_Missense_Mutation_p.L43R|THPO_uc021xii.1_Missense_Mutation_p.L43R|THPO_uc003fon.3_Missense_Mutation_p.L43R|THPO_uc011bro.2_Missense_Mutation_p.L43R|THPO_uc003fop.3_Missense_Mutation_p.L43R|THPO_uc011brp.2_Missense_Mutation_p.L43R|THPO_uc011brq.2_Missense_Mutation_p.L43R|THPO_uc003for.1_5'Flank|THPO_uc003fos.1_5'Flank|THPO_uc003fot.1_Missense_Mutation_p.L43R|THPO_uc003fou.1_Missense_Mutation_p.L43R	p.L43R	NM_000460	NP_000451	P40225	TPO_HUMAN	Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		2	343	-	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		43					A1L3Y0|B7ZLR8|B9EGA8|Q13020|Q15790|Q15791|Q15792	Missense_Mutation	SNP	ENST00000204615.7	37	c.128T>G	CCDS3265.1	.	.	.	.	.	.	.	.	.	.	A	17.25	3.342173	0.61073	.	.	ENSG00000090534	ENST00000204615;ENST00000445696;ENST00000421442;ENST00000353488	T;T;T	0.51574	0.7;0.7;0.7	3.86	3.86	0.44501	Erythropoietin/thrombopoeitin, conserved site (1);Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.000000	0.36482	N	0.002577	T	0.52058	0.1711	L	0.27053	0.805	0.40202	D	0.977528	D;D;D;D;D;D	0.76494	0.999;0.999;0.998;0.997;0.999;0.999	D;D;D;D;D;D	0.91635	0.999;0.996;0.995;0.991;0.996;0.998	T	0.56353	-0.7993	10	0.72032	D	0.01	-27.0972	9.237	0.37473	1.0:0.0:0.0:0.0	.	43;43;43;43;43;43	Q5FBX4;P40225-3;Q5FBX8;F8W6L1;P40225-2;P40225	.;.;.;.;.;TPO_HUMAN	R	43	ENSP00000204615:L43R;ENSP00000410763:L43R;ENSP00000411704:L43R	ENSP00000204615:L43R	L	-	2	0	THPO	185576383	1.000000	0.71417	0.999000	0.59377	0.916000	0.54674	4.188000	0.58351	1.752000	0.51891	0.383000	0.25322	CTT		0.527	THPO-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345554.1	NM_000460		36	91	0	0	0	1	0	36	91				
CLCN3	1182	broad.mit.edu	37	4	170641066	170641066	+	Missense_Mutation	SNP	T	T	C			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr4:170641066T>C	ENST00000513761.1	+	13	2934	c.2375T>C	c.(2374-2376)cTt>cCt	p.L792P	CLCN3_ENST00000347613.4_Silent_p.P817P|CLCN3_ENST00000360642.3_Missense_Mutation_p.L765P|CLCN3_ENST00000504131.2_Missense_Mutation_p.L775P	NM_001829.3	NP_001820.2	P51790	CLCN3_HUMAN	chloride channel, voltage-sensitive 3	792	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				chloride transmembrane transport (GO:1902476)|endosomal lumen acidification (GO:0048388)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|voltage-gated chloride channel activity (GO:0005247)			breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)		AGGCGCCTCCTTGGCATTATA	0.398																																						uc003isi.3																			0				breast(5)|endometrium(3)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	29						c.(2374-2376)cTt>cCt		Homo sapiens chloride channel 3 (CLCN3), transcript variant b, mRNA.							42.0	45.0	44.0					4																	170641066		2196	4299	6495	SO:0001583	missense	1182				endosomal lumen acidification	Golgi membrane|cell surface|early endosome membrane|integral to membrane|late endosome membrane|transport vesicle membrane	ATP binding|PDZ domain binding|antiporter activity|protein heterodimerization activity|protein homodimerization activity|voltage-gated chloride channel activity	g.chr4:170641066T>C	X78520	CCDS34100.1, CCDS34101.1, CCDS58932.1, CCDS75208.1	4q	2012-09-26	2012-02-23		ENSG00000109572	ENSG00000109572		"""Ion channels / Chloride channels : Voltage-sensitive"""	2021	protein-coding gene	gene with protein product		600580	"""chloride channel 3"""				Standard	NM_001243374		Approved	CLC3, ClC-3	uc003ish.3	P51790	OTTHUMG00000160973	ENST00000513761.1:c.2375T>C	4.37:g.170641066T>C	ENSP00000424603:p.Leu792Pro					CLCN3_uc003ish.3_Silent_p.P817P|CLCN3_uc011cka.2_Missense_Mutation_p.L765P|CLCN3_uc011cjz.2_Missense_Mutation_p.L775P|CLCN3_uc003isj.2_Missense_Mutation_p.L765P	p.L792P	NM_001829	NP_001820	P51790	CLCN3_HUMAN		GBM - Glioblastoma multiforme(119;0.0233)|LUSC - Lung squamous cell carcinoma(193;0.131)	12	2934	+		Prostate(90;0.00601)|Renal(120;0.0183)	792			CBS 2.		B7Z932|B9EGJ9|D3DP34|E9PB97|O14918|Q86Z21	Missense_Mutation	SNP	ENST00000513761.1	37	c.2375T>C	CCDS34101.1	.	.	.	.	.	.	.	.	.	.	T	18.99	3.740737	0.69304	.	.	ENSG00000109572	ENST00000513761;ENST00000360642;ENST00000504131	D;D;D	0.94537	-3.45;-3.45;-3.45	5.52	5.52	0.82312	Cystathionine beta-synthase, core (3);	.	.	.	.	D	0.97087	0.9048	.	.	.	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.79784	0.988;0.993;0.991	D	0.97250	0.9897	7	.	.	.	-6.6465	15.6299	0.76899	0.0:0.0:0.0:1.0	.	765;775;792	B7Z932;B9EGJ9;P51790	.;.;CLCN3_HUMAN	P	792;765;775	ENSP00000424603:L792P;ENSP00000353857:L765P;ENSP00000424540:L775P	.	L	+	2	0	CLCN3	170877641	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.036000	0.88901	2.086000	0.62901	0.533000	0.62120	CTT		0.398	CLCN3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363210.2			5	59	0	0	0	1	0	5	59				
AASDHPPT	60496	broad.mit.edu	37	11	105961348	105961348	+	Silent	SNP	A	A	G			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr11:105961348A>G	ENST00000278618.4	+	3	696	c.474A>G	c.(472-474)gaA>gaG	p.E158E	RP11-677I18.3_ENST00000532422.1_RNA	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	158					macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		AAGAATGGGAAACAATCAGAA	0.303																																						uc001pjc.1																			0		p.W157L(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17						c.(472-474)gaA>gaG		Homo sapiens aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase (AASDHPPT), mRNA.							103.0	118.0	113.0					11																	105961348		2201	4297	6498	SO:0001819	synonymous_variant	60496				macromolecule biosynthetic process|pantothenate metabolic process	cytosol	holo-[acyl-carrier-protein] synthase activity|magnesium ion binding|protein binding	g.chr11:105961348A>G	AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.474A>G	11.37:g.105961348A>G						AASDHPPT_uc010rvn.1_Intron|AASDHPPT_uc001pjd.1_Silent_p.E11E	p.E158E	NM_015423	NP_056238	Q9NRN7	ADPPT_HUMAN		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)	2	620	+		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)	158					B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Silent	SNP	ENST00000278618.4	37	c.474A>G	CCDS31664.1																																																																																				0.303	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423		3	116	0	0	0	1	0	3	116				
NUDT12	83594	broad.mit.edu	37	5	102895751	102895751	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr5:102895751C>G	ENST00000230792.2	-	2	295	c.199G>C	c.(199-201)Gag>Cag	p.E67Q	NUDT12_ENST00000507423.1_Intron	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	67					NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TACCCTTTCTCAAGCAGAAAT	0.363																																						uc003koi.3																			0				endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12						c.(199-201)Gag>Cag		Homo sapiens nudix (nucleoside diphosphate linked moiety X)-type motif 12 (NUDT12), mRNA.							108.0	103.0	104.0					5																	102895751		2202	4300	6502	SO:0001583	missense	83594					nucleus|peroxisome	NAD+ diphosphatase activity|metal ion binding	g.chr5:102895751C>G	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.199G>C	5.37:g.102895751C>G	ENSP00000230792:p.Glu67Gln					NUDT12_uc011cvb.2_Intron|NUDT12_uc010jbq.1_Missense_Mutation_p.E67Q	p.E67Q	NM_031438	NP_113626	Q9BQG2	NUD12_HUMAN		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)	1	292	-		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)	67					B3KUW2|Q8TAL7	Missense_Mutation	SNP	ENST00000230792.2	37	c.199G>C	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	14.91	2.676933	0.47886	.	.	ENSG00000112874	ENST00000230792	T	0.67345	-0.26	5.9	5.9	0.94986	Ankyrin repeat-containing domain (4);	0.278431	0.39210	N	0.001440	T	0.54062	0.1835	N	0.16368	0.405	0.80722	D	1	B	0.24920	0.114	B	0.26416	0.069	T	0.49753	-0.8906	10	0.38643	T	0.18	-4.2576	17.1924	0.86883	0.0:0.8744:0.1256:0.0	.	67	Q9BQG2	NUD12_HUMAN	Q	67	ENSP00000230792:E67Q	ENSP00000230792:E67Q	E	-	1	0	NUDT12	102923650	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.749000	0.55150	2.788000	0.95919	0.650000	0.86243	GAG		0.363	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438		45	94	0	0	0	1	0	45	94				
ANKRD19P	138649	broad.mit.edu	37	9	95599903	95599903	+	RNA	SNP	G	G	A			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr9:95599903G>A	ENST00000473204.1	+	0	1984							Q9H560	ANR19_HUMAN	ankyrin repeat domain 19, pseudogene							extracellular vesicular exosome (GO:0070062)											CGTCATATTTGAACTTGTCGA	0.552																																						uc004ass.2																			0													Homo sapiens ankyrin repeat domain 19, pseudogene (ANKRD19P), non-coding RNA.																																						138649							g.chr9:95599903G>A	BC038951		9q22.32	2011-04-27	2011-04-27	2011-04-27	ENSG00000187984	ENSG00000187984			22567	pseudogene	pseudogene			"""ankyrin repeat domain 19"", ""ankyrin repeat domain 19 pseudogene"""	ANKRD19			Standard	NR_026868		Approved	FLJ36178	uc011lua.1	Q9H560	OTTHUMG00000020237		9.37:g.95599903G>A						ANKRD19P_uc004asr.4_Non-coding_Transcript								8		+								A8K853|Q17RD3	RNA	SNP	ENST00000473204.1	37	c.1987G>A																																																																																					0.552	ANKRD19P-004	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000053116.3	NR_026868		21	39	0	0	0	1	0	21	39				
PRPS1	5631	broad.mit.edu	37	X	106885605	106885605	+	Missense_Mutation	SNP	G	G	C			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chrX:106885605G>C	ENST00000372435.4	+	4	537	c.415G>C	c.(415-417)Gat>Cat	p.D139H	PRPS1_ENST00000543248.1_Missense_Mutation_p.D139H|PRPS1_ENST00000372418.1_Missense_Mutation_p.D39H|PRPS1_ENST00000372428.4_Missense_Mutation_p.D72H	NM_002764.3	NP_002755.1	P60891	PRPS1_HUMAN	phosphoribosyl pyrophosphate synthetase 1	139					5-phosphoribose 1-diphosphate biosynthetic process (GO:0006015)|carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|hypoxanthine biosynthetic process (GO:0046101)|nervous system development (GO:0007399)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide biosynthetic process (GO:0006164)|pyrimidine nucleotide biosynthetic process (GO:0006221)|ribonucleoside monophosphate biosynthetic process (GO:0009156)|small molecule metabolic process (GO:0044281)|urate biosynthetic process (GO:0034418)	cytosol (GO:0005829)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)|ribose phosphate diphosphokinase activity (GO:0004749)			breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						GGGCTTTTTTGATATCCCAGT	0.418																																						uc004ene.4																			0				breast(3)|endometrium(2)|kidney(3)|large_intestine(3)|lung(11)|upper_aerodigestive_tract(1)	23						c.(415-417)Gat>Cat		Homo sapiens phosphoribosyl pyrophosphate synthetase 1 (PRPS1), transcript variant 1, mRNA.							101.0	92.0	95.0					X																	106885605		2203	4300	6503	SO:0001583	missense	5631				5-phosphoribose 1-diphosphate biosynthetic process|hypoxanthine biosynthetic process|nervous system development|nucleoside metabolic process|purine nucleotide biosynthetic process|pyrimidine nucleotide biosynthetic process|ribonucleoside monophosphate biosynthetic process|urate biosynthetic process	cytosol	ATP binding|kinase activity|magnesium ion binding|protein homodimerization activity|ribose phosphate diphosphokinase activity	g.chrX:106885605G>C	X15331	CCDS14529.1, CCDS76007.1	Xq22.3	2014-09-17			ENSG00000147224	ENSG00000147224	2.7.6.1		9462	protein-coding gene	gene with protein product	"""PRS I"", ""ribose-phosphate diphosphokinase 1"""	311850	"""deafness, X-linked 2, perceptive, congenital"""	DFN2		1962753, 20021999	Standard	NM_002764		Approved	CMTX5, DFNX1	uc004ene.4	P60891	OTTHUMG00000022167	ENST00000372435.4:c.415G>C	X.37:g.106885605G>C	ENSP00000361512:p.Asp139His					PRPS1_uc011msj.2_Intron|PRPS1_uc010npg.3_Missense_Mutation_p.D106H	p.D139H	NM_002764	NP_002755	P60891	PRPS1_HUMAN			3	620	+			139					B1ALA8|B2R6T7|B4DNL6|D3DUX6|P09329	Missense_Mutation	SNP	ENST00000372435.4	37	c.415G>C	CCDS14529.1	.	.	.	.	.	.	.	.	.	.	G	15.24	2.774331	0.49786	.	.	ENSG00000147224	ENST00000372435;ENST00000372428;ENST00000543248;ENST00000372418	D;D;D;D	0.92249	-3.0;-3.0;-3.0;-2.74	4.5	4.5	0.54988	Phosphoribosyl pyrophosphate synthetase, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.95730	0.8611	M	0.89353	3.025	0.80722	D	1	D;D	0.69078	0.997;0.997	P;P	0.58130	0.833;0.833	D	0.96368	0.9271	10	0.59425	D	0.04	.	16.0021	0.80301	0.0:0.0:1.0:0.0	.	139;139	Q53FW2;P60891	.;PRPS1_HUMAN	H	139;72;139;39	ENSP00000361512:D139H;ENSP00000361505:D72H;ENSP00000443185:D139H;ENSP00000361495:D39H	ENSP00000361495:D39H	D	+	1	0	PRPS1	106772261	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.357000	0.97099	2.170000	0.68504	0.538000	0.68166	GAT		0.418	PRPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057840.1			32	79	0	0	0	1	0	32	79				
STAG1	10274	broad.mit.edu	37	3	136162169	136162169	+	Missense_Mutation	SNP	C	C	G			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chr3:136162169C>G	ENST00000383202.2	-	15	1762	c.1506G>C	c.(1504-1506)atG>atC	p.M502I	STAG1_ENST00000434713.2_Missense_Mutation_p.M276I|STAG1_ENST00000236698.5_Missense_Mutation_p.M502I|STAG1_ENST00000536929.1_Missense_Mutation_p.M86I	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	502					chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GCAACTCTGTCATACATTCCC	0.358																																						uc003era.1																			0				NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						c.(1504-1506)atG>atC		Homo sapiens stromal antigen 1 (STAG1), mRNA.							140.0	133.0	135.0					3																	136162169		2203	4300	6503	SO:0001583	missense	10274				cell division|chromosome segregation|mitotic metaphase/anaphase transition|mitotic prometaphase	cell junction|chromatin|chromosome, centromeric region|nucleoplasm	protein binding	g.chr3:136162169C>G	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.1506G>C	3.37:g.136162169C>G	ENSP00000372689:p.Met502Ile					STAG1_uc003erb.1_Missense_Mutation_p.M502I|STAG1_uc003erc.1_Missense_Mutation_p.M276I|STAG1_uc010hua.1_Missense_Mutation_p.M365I	p.M502I	NM_005862	NP_005853	Q8WVM7	STAG1_HUMAN			14	1798	-			502					O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	c.1506G>C	CCDS3090.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.1|24.1	4.488922|4.488922	0.84962|0.84962	.|.	.|.	ENSG00000118007|ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929|ENST00000492318	T;T;T;T|.	0.38077|.	1.7;1.72;1.83;1.16|.	5.83|5.83	5.83|5.83	0.93111|0.93111	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|.	0.82866|.	0.5130|.	M|M	0.83312|0.83312	2.635|2.635	0.80722|0.80722	D|D	1|1	P;B;P|.	0.48089|.	0.905;0.382;0.843|.	P;B;P|.	0.52598|.	0.703;0.146;0.613|.	T|.	0.82916|.	-0.0220|.	10|.	0.30078|.	T|.	0.28|.	.|.	20.1133|20.1133	0.97917|0.97917	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	519;502;502|.	Q4LE48;Q6P275;Q8WVM7|.	.;.;STAG1_HUMAN|.	I|S	502;502;276;86|113	ENSP00000372689:M502I;ENSP00000236698:M502I;ENSP00000404396:M276I;ENSP00000445787:M86I|.	ENSP00000236698:M502I|.	M|X	-|-	3|2	0|2	STAG1|STAG1	137644859|137644859	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.818000|7.818000	0.86416|0.86416	2.762000|2.762000	0.94881|0.94881	0.591000|0.591000	0.81541|0.81541	ATG|TGA		0.358	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862		7	95	0	0	0	1	0	7	95				
ATP7A	538	broad.mit.edu	37	X	77302017	77302020	+	Frame_Shift_Del	DEL	CACT	CACT	-			TCGA-EL-A3GR-01A-21D-A202-08	TCGA-EL-A3GR-10A-01D-A202-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	eb029001-2260-47d5-aec9-3cdd61540fc1	57ec11e4-f353-45b8-9896-fa92f4e2d563	g.chrX:77302017_77302020delCACT	ENST00000341514.6	+	23	4608_4611	c.4453_4456delCACT	c.(4453-4458)cactcafs	p.HS1485fs	ATP7A_ENST00000350425.4_Frame_Shift_Del_p.HS488fs|ATP7A_ENST00000343533.5_Frame_Shift_Del_p.HS1407fs	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	1485					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACCTGACAAGCACTCACTCCTGGT	0.451																																						uc004ecx.4																			0				breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53						c.(4453-4458)cactcafs		Homo sapiens ATPase, Cu++ transporting, alpha polypeptide (ATP7A), mRNA.																																				SO:0001589	frameshift_variant	538				ATP biosynthetic process|T-helper cell differentiation|blood vessel development|blood vessel remodeling|cartilage development|cellular copper ion homeostasis|cerebellar Purkinje cell differentiation|collagen fibril organization|copper ion import|detoxification of copper ion|dopamine metabolic process|elastic fiber assembly|elastin biosynthetic process|epinephrine metabolic process|hair follicle morphogenesis|locomotory behavior|lung alveolus development|negative regulation of metalloenzyme activity|neuroprotection|peptidyl-lysine modification|pigmentation|positive regulation of metalloenzyme activity|positive regulation of oxidoreductase activity|pyramidal neuron development|regulation of oxidative phosphorylation|removal of superoxide radicals|serotonin metabolic process|skin development|tryptophan metabolic process	basolateral plasma membrane|cytosol|endoplasmic reticulum|integral to membrane|late endosome|neuron projection|neuronal cell body|perinuclear region of cytoplasm|trans-Golgi network|trans-Golgi network transport vesicle	ATP binding|copper-dependent protein binding|copper-exporting ATPase activity|superoxide dismutase copper chaperone activity	g.chrX:77302017_77302020delCACT	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.4453_4456delCACT	X.37:g.77302021_77302024delCACT	ENSP00000345728:p.His1485fs						p.H1485fs	NM_000052	NP_000043	Q04656	ATP7A_HUMAN			22	4613_4616	+			1485					B1AT72|O00227|O00745|Q9BYY8	Frame_Shift_Del	DEL	ENST00000341514.6	37	c.4453_4456delCACT	CCDS35339.1																																																																																				0.451	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052		123	272						123	272	---	---	---	---
