#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_BAM_File	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_EVS_AA	i_EVS_All	i_EVS_EA	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains_WU	i_amino_acid_change_WU	i_annotation_transcript	i_build	i_c_position_WU	i_ccds_id	i_chromosome_name_WU	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_default_gene_name_WU	i_deletion_substructures_WU	i_domain_WU	i_ensembl_gene_id	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_name_WU	i_gene_name_source_WU	i_gene_type	i_havana_transcript	i_normal_ref_reads	i_normal_vaf	i_normal_var_reads	i_reference_WU	i_refseq_mrna_id	i_secondary_variant_classification	i_start_WU	i_stop_WU	i_strand_WU	i_transcript_error_WU	i_transcript_name_WU	i_transcript_source_WU	i_transcript_species_WU	i_transcript_status_WU	i_transcript_version_WU	i_trv_type_WU	i_tumor_ref_reads	i_tumor_vaf	i_tumors_var_reads	i_type_WU	i_ucsc_cons_WU	i_variant_WU
ADAM9	8754	genome.wustl.edu	37	8	38871610	38871611	+	Intron	INS	-	-	C			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr8:38871610_38871611insC	ENST00000487273.2	+	4	411				ADAM9_ENST00000481513.1_Frame_Shift_Ins_p.I128fs|ADAM9_ENST00000466936.1_Intron	NM_003816.2	NP_003807.1	Q13443	ADAM9_HUMAN	ADAM metallopeptidase domain 9						activation of MAPKK activity (GO:0000186)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to lipopolysaccharide (GO:0071222)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|keratinocyte differentiation (GO:0030216)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte activation (GO:0042117)|PMA-inducible membrane protein ectodomain proteolysis (GO:0051088)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of macrophage fusion (GO:0034241)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of protein secretion (GO:0050714)|response to calcium ion (GO:0051592)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to laminar fluid shear stress (GO:0034616)|response to manganese ion (GO:0010042)|response to tumor necrosis factor (GO:0034612)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)	collagen binding (GO:0005518)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein kinase C binding (GO:0005080)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.0153)	LUSC - Lung squamous cell carcinoma(45;2.74e-07)			aaacaattataatttaaaaatG	0.342																																						dbGAP											0																																										-	-	-	SO:0001627	intron_variant	0			U41766	CCDS6112.1	8p11.23	2011-03-18	2010-06-24		ENSG00000168615	ENSG00000168615		"""ADAM metallopeptidase domain containing"""	216	protein-coding gene	gene with protein product	"""meltrin gamma"""	602713	"""a disintegrin and metalloproteinase domain 9 (meltrin gamma)"", ""cone rod dystrophy 9"""	CORD9		8647900, 11581183, 19409519	Standard	NR_027638		Approved	MDC9, KIAA0021, MCMP, Mltng	uc003xmr.3	Q13443	OTTHUMG00000159783	ENST00000487273.2:c.333+48->C	8.37:g.38871610_38871611insC			B7ZLN7|Q10718|Q8NFM6	Frame_Shift_Ins	INS	pfam_Peptidase_M12B_N	p.I127fs	ENST00000487273.2	37	c.381_382	CCDS6112.1	8																																																																																			ADAM9	-	NULL	ENSG00000168615		0.342	ADAM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ADAM9	HGNC	protein_coding	OTTHUMT00000357291.2	119	0.00	0	-			38871610	38871611	+1	no_errors	ENST00000481513	ensembl	human	putative	69_37n	frame_shift_ins	90	10.89	11	INS	0.000:0.000	C
ALK	238	genome.wustl.edu	37	2	29416321	29416321	+	Silent	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr2:29416321G>A	ENST00000389048.3	-	29	5538	c.4632C>T	c.(4630-4632)aaC>aaT	p.N1544N	ALK_ENST00000431873.1_Silent_p.N374N	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1544					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	CAGTTGCAACGTTAGGTGGGA	0.532			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																													dbGAP	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	0													187.0	197.0	194.0					2																	29416321		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4632C>T	2.37:g.29416321G>A			Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_MAM_dom,superfamily_Kinase-like_dom,superfamily_ConA-like_lec_gl,superfamily_LDrepeatLR_classA_rpt,smart_LDrepeatLR_classA_rpt,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pfscan_MAM_dom,pfscan_Prot_kinase_cat_dom,prints_Ser-Thr/Tyr_kinase_cat_dom	p.N1544	ENST00000389048.3	37	c.4632	CCDS33172.1	2																																																																																			ALK	-	NULL	ENSG00000171094		0.532	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ALK	HGNC	protein_coding	OTTHUMT00000324994.1	159	0.00	0	G	NM_004304		29416321	29416321	-1	no_errors	ENST00000389048	ensembl	human	known	69_37n	silent	121	18.12	27	SNP	0.000	A
ATRX	546	genome.wustl.edu	37	X	76939543	76939543	+	Missense_Mutation	SNP	A	A	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	A	A					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chrX:76939543A>T	ENST00000373344.5	-	9	1419	c.1205T>A	c.(1204-1206)aTt>aAt	p.I402N	ATRX_ENST00000480283.1_5'UTR|ATRX_ENST00000395603.3_Missense_Mutation_p.I364N	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	402					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						AGCCTTCTTAATATCAGCCAA	0.348			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															dbGAP		Rec	yes		X	Xq21.1	546	alpha thalassemia/mental retardation syndrome X-linked	yes	E	1	Unknown(1)	bone(1)											196.0	205.0	202.0					X																	76939543		2203	4296	6499	-	-	-	SO:0001583	missense	0			U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.1205T>A	X.37:g.76939543A>T	ENSP00000362441:p.Ile402Asn		D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Missense_Mutation	SNP	pfam_SNF2_N,pfam_Helicase_C,superfamily_Znf_FYVE_PHD,smart_Helicase_ATP-bd,smart_Helicase_C,pfscan_Helicase_ATP-bd,pfscan_Helicase_C	p.I402N	ENST00000373344.5	37	c.1205	CCDS14434.1	X	.	.	.	.	.	.	.	.	.	.	a	11.24	1.579848	0.28180	.	.	ENSG00000085224	ENST00000373344;ENST00000395603;ENST00000400862	D;D	0.93604	-3.25;-3.25	5.06	5.06	0.68205	.	0.099426	0.50627	D	0.000112	D	0.95472	0.8529	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.71674	0.989;0.998;0.993;0.989	P;D;P;P	0.66351	0.768;0.943;0.884;0.768	D	0.95839	0.8864	10	0.87932	D	0	-6.021	13.9857	0.64334	1.0:0.0:0.0:0.0	.	402;363;364;402	A4LAA3;P46100-6;P46100-4;P46100	.;.;.;ATRX_HUMAN	N	402;364;358	ENSP00000362441:I402N;ENSP00000378967:I364N	ENSP00000362441:I402N	I	-	2	0	ATRX	76826199	1.000000	0.71417	0.969000	0.41365	0.800000	0.45204	8.959000	0.93110	1.679000	0.50963	0.414000	0.27820	ATT	ATRX	-	NULL	ENSG00000085224		0.348	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ATRX	HGNC	protein_coding	OTTHUMT00000058860.2	152	0.00	0	A	NM_000489		76939543	76939543	-1	no_errors	ENST00000373344	ensembl	human	known	69_37n	missense	182	23.21	55	SNP	0.997	T
CYP4F2	8529	genome.wustl.edu	37	19	16003164	16003164	+	Silent	SNP	C	C	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr19:16003164C>A	ENST00000221700.6	-	5	575	c.480G>T	c.(478-480)ctG>ctT	p.L160L	CYP4F2_ENST00000011989.7_Silent_p.L11L	NM_001082.3	NP_001073.3			cytochrome P450, family 4, subfamily F, polypeptide 2											NS(2)|breast(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TATAGGGCTTCAGGATGTTGA	0.537																																						dbGAP											0													122.0	125.0	124.0					19																	16003164		2203	4298	6501	-	-	-	SO:0001819	synonymous_variant	0			U02388	CCDS12336.1	19p13.12	2013-11-11	2003-01-14		ENSG00000186115	ENSG00000186115		"""Cytochrome P450s"""	2645	protein-coding gene	gene with protein product		604426	"""cytochrome P450, subfamily IVF, polypeptide 2"""			8424651, 8026587	Standard	NM_001082		Approved		uc002nbs.1	P78329	OTTHUMG00000185995	ENST00000221700.6:c.480G>T	19.37:g.16003164C>A				Silent	SNP	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-I,prints_Cyt_P450_E_grp-IV,prints_Cyt_P450,prints_Cyt_P450_E_grp-II	p.L160	ENST00000221700.6	37	c.480	CCDS12336.1	19																																																																																			CYP4F2	-	pfam_Cyt_P450,superfamily_Cyt_P450,prints_Cyt_P450_E_grp-II	ENSG00000186115		0.537	CYP4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CYP4F2	HGNC	protein_coding	OTTHUMT00000460372.3	256	0.00	0	C	NM_001082		16003164	16003164	-1	no_errors	ENST00000221700	ensembl	human	known	69_37n	silent	696	30.24	303	SNP	1.000	A
DOC2A	8448	genome.wustl.edu	37	16	30020844	30020844	+	Silent	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr16:30020844G>A	ENST00000350119.4	-	3	487	c.297C>T	c.(295-297)taC>taT	p.Y99Y	DOC2A_ENST00000564979.1_Silent_p.Y99Y|DOC2A_ENST00000567824.1_5'Flank|DOC2A_ENST00000564944.1_Silent_p.Y99Y	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	99	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						AGGCCCGGTCGTAGAGAAGGT	0.652																																						dbGAP											0													49.0	41.0	43.0					16																	30020844		1904	3658	5562	-	-	-	SO:0001819	synonymous_variant	0			D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.297C>T	16.37:g.30020844G>A			B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Silent	SNP	pfam_C2_Ca-dep,superfamily_C2_Ca/lipid-bd_dom_CaLB,smart_C2_Ca-dep,pirsf_Doc2,pfscan_C2_membr_targeting,prints_Synaptotagmin,prints_C2_dom	p.Y99	ENST00000350119.4	37	c.297	CCDS10666.1	16																																																																																			DOC2A	-	superfamily_C2_Ca/lipid-bd_dom_CaLB,pirsf_Doc2	ENSG00000149927		0.652	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	DOC2A	HGNC	protein_coding	OTTHUMT00000255148.2	92	0.00	0	G	NM_003586		30020844	30020844	-1	no_errors	ENST00000350119	ensembl	human	known	69_37n	silent	108	11.48	14	SNP	0.987	A
GGT1	2678	genome.wustl.edu	37	22	25019807	25019807	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr22:25019807G>A	ENST00000400382.1	+	11	1699	c.944G>A	c.(943-945)cGc>cAc	p.R315H	GGT1_ENST00000466310.1_3'UTR|GGT1_ENST00000400383.1_Missense_Mutation_p.R315H|GGT1_ENST00000248923.4_Missense_Mutation_p.R315H|GGT1_ENST00000406383.2_Missense_Mutation_p.R315H|GGT1_ENST00000400380.1_Missense_Mutation_p.R315H			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	315					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|cysteine biosynthetic process (GO:0019344)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione catabolic process (GO:0006751)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|regulation of immune system process (GO:0002682)|regulation of inflammatory response (GO:0050727)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|xenobiotic metabolic process (GO:0006805)|zymogen activation (GO:0031638)	anchored component of external side of plasma membrane (GO:0031362)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(14)|large_intestine(2)|lung(6)|pancreas(1)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	40					Glutathione(DB00143)	ACGTACCACCGCATCGTAGAG	0.612																																						dbGAP											0													15.0	15.0	15.0					22																	25019807		1830	4055	5885	-	-	-	SO:0001583	missense	0			M24903	CCDS42992.1	22q11.23	2008-08-15			ENSG00000100031	ENSG00000100031	2.3.2.2	"""CD molecules"", ""Gamma-glutamyltransferases"""	4250	protein-coding gene	gene with protein product		612346		GGT		8104871, 18357469	Standard	NM_001288833		Approved	D22S672, D22S732, CD224	uc003aan.1	P19440	OTTHUMG00000030859	ENST00000400382.1:c.944G>A	22.37:g.25019807G>A	ENSP00000383232:p.Arg315His		Q08247|Q14404|Q8TBS1|Q9UMK1	Missense_Mutation	SNP	pfam_GGT_peptidase,prints_GGT_peptidase,tigrfam_GGT_peptidase	p.R315H	ENST00000400382.1	37	c.944	CCDS42992.1	22	.	.	.	.	.	.	.	.	.	.	.	16.16	3.043495	0.55003	.	.	ENSG00000100031	ENST00000248923;ENST00000412658;ENST00000400382;ENST00000400383;ENST00000400380;ENST00000406383	T;T;T;T;T;T	0.06933	3.24;3.24;3.24;3.24;3.24;3.24	3.53	2.51	0.30379	.	0.067228	0.64402	N	0.000010	T	0.15089	0.0364	M	0.78344	2.41	0.47778	D	0.999514	D	0.54047	0.964	P	0.46940	0.532	T	0.03249	-1.1056	10	0.51188	T	0.08	-3.3601	10.4875	0.44731	0.0977:0.0:0.9023:0.0	.	315	P19440	GGT1_HUMAN	H	315	ENSP00000248923:R315H;ENSP00000393537:R315H;ENSP00000383232:R315H;ENSP00000383233:R315H;ENSP00000383231:R315H;ENSP00000385975:R315H	ENSP00000248923:R315H	R	+	2	0	GGT1	23349807	1.000000	0.71417	0.997000	0.53966	0.215000	0.24574	7.251000	0.78297	0.832000	0.34804	-0.127000	0.14921	CGC	GGT1	-	pfam_GGT_peptidase,tigrfam_GGT_peptidase	ENSG00000100031		0.612	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	GGT1	HGNC	protein_coding	OTTHUMT00000250797.1	258	0.00	0	G	NM_013430		25019807	25019807	+1	no_errors	ENST00000248923	ensembl	human	known	69_37n	missense	195	18.75	45	SNP	1.000	A
GUSBP1	728411	genome.wustl.edu	37	5	21459801	21459801	+	RNA	SNP	G	G	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr5:21459801G>T	ENST00000607545.1	+	0	44					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1						carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)										AGGCTCAGACGCATCGGGACC	0.637											OREG0016459	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											0																																										-	-	-			0			BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666			13670	pseudogene	pseudogene						8565635	Standard	NR_027026		Approved		uc010iub.3	Q15486	OTTHUMG00000162474		5.37:g.21459801G>T		748	A6NLY8|A8K1B7|Q969T8|Q9BUH2	RNA	SNP	-	NULL	ENST00000607545.1	37	NULL		5																																																																																			RP11-823P9.1	-	-	ENSG00000183666		0.637	GUSBP1-006	KNOWN	basic	processed_transcript	GUSBP1	Clone_based_vega_gene	pseudogene	OTTHUMT00000470546.1	38	0.00	0	G	NG_008324		21459801	21459801	+1	no_errors	ENST00000508260	ensembl	human	known	69_37n	rna	40	24.53	13	SNP	0.029	T
MROH2B	133558	genome.wustl.edu	37	5	41005744	41005744	+	Silent	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr5:41005744G>A	ENST00000399564.4	-	35	4203	c.3753C>T	c.(3751-3753)agC>agT	p.S1251S	MROH2B_ENST00000506092.2_Silent_p.S806S	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	1251																	ACACTGCCATGCTCCTAGAAA	0.438																																						dbGAP											0													58.0	59.0	59.0					5																	41005744		2032	4208	6240	-	-	-	SO:0001819	synonymous_variant	0				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.3753C>T	5.37:g.41005744G>A			Q68DM1|Q7Z4U4|Q8N7X3	Silent	SNP	superfamily_ARM-type_fold	p.S1251	ENST00000399564.4	37	c.3753	CCDS47202.1	5																																																																																			HEATR7B2	-	superfamily_ARM-type_fold	ENSG00000171495		0.438	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HEATR7B2	HGNC	protein_coding	OTTHUMT00000367558.2	154	0.00	0	G	NM_173489		41005744	41005744	-1	no_errors	ENST00000399564	ensembl	human	known	69_37n	silent	165	22.33	48	SNP	0.999	A
MROH2B	133558	genome.wustl.edu	37	5	41015496	41015496	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr5:41015496G>A	ENST00000399564.4	-	29	3419	c.2969C>T	c.(2968-2970)tCt>tTt	p.S990F	MROH2B_ENST00000506092.2_Missense_Mutation_p.S545F	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	990																	AGCTATTTTAGAAGAAATCTT	0.413																																						dbGAP											0													78.0	79.0	79.0					5																	41015496		1864	4089	5953	-	-	-	SO:0001583	missense	0				CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.2969C>T	5.37:g.41015496G>A	ENSP00000382476:p.Ser990Phe		Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	superfamily_ARM-type_fold	p.S990F	ENST00000399564.4	37	c.2969	CCDS47202.1	5	.	.	.	.	.	.	.	.	.	.	G	16.79	3.219165	0.58560	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.04917	3.53;3.53	5.9	5.9	0.94986	Armadillo-like helical (1);Armadillo-type fold (1);	0.106373	0.43110	D	0.000610	T	0.17450	0.0419	L	0.56769	1.78	0.38377	D	0.945034	D	0.67145	0.996	P	0.61201	0.885	T	0.05582	-1.0876	10	0.16420	T	0.52	.	15.7823	0.78269	0.0:0.0:1.0:0.0	.	990	Q7Z745	HTRB2_HUMAN	F	545;695;990	ENSP00000441504:S545F;ENSP00000382476:S990F	ENSP00000296803:S695F	S	-	2	0	HEATR7B2	41051253	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	4.484000	0.60271	2.806000	0.96561	0.655000	0.94253	TCT	HEATR7B2	-	superfamily_ARM-type_fold	ENSG00000171495		0.413	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HEATR7B2	HGNC	protein_coding	OTTHUMT00000367558.2	212	0.00	0	G	NM_173489		41015496	41015496	-1	no_errors	ENST00000399564	ensembl	human	known	69_37n	missense	131	17.61	28	SNP	1.000	A
HIST1H1C	3006	genome.wustl.edu	37	6	26056019	26056021	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	TTC	TTC					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr6:26056019_26056021delTTC	ENST00000343677.2	-	1	678_680	c.636_638delGAA	c.(634-639)aagaaa>aaa	p.212_213KK>K		NM_005319.3	NP_005310.1	P16403	H12_HUMAN	histone cluster 1, H1c	212					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(4)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	34						GTTCGCCTATTTCTTCTTGGGCG	0.478																																						dbGAP											0																																										-	-	-	SO:0001651	inframe_deletion	0			X57129	CCDS4577.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000187837	ENSG00000187837		"""Histones / Replication-dependent"""	4716	protein-coding gene	gene with protein product		142710	"""H1 histone family, member 2"", ""histone 1, H1c"""	H1F2		2759094, 12408966	Standard	NM_005319		Approved	H1.2, H1s-1, H1c	uc003nfw.3	P16403	OTTHUMG00000016140	ENST00000343677.2:c.636_638delGAA	6.37:g.26056022_26056024delTTC	ENSP00000339566:p.Lys213del		A8K4I2	In_Frame_Del	DEL	pfam_Histone_H1/H5,smart_Histone_H1/H5,prints_Histone_H5	p.K213in_frame_del	ENST00000343677.2	37	c.638_636	CCDS4577.1	6																																																																																			HIST1H1C	-	NULL	ENSG00000187837		0.478	HIST1H1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HIST1H1C	HGNC	protein_coding	OTTHUMT00000043372.1	58	0.00	0	TTC	NM_005319		26056019	26056021	-1	no_errors	ENST00000343677	ensembl	human	known	69_37n	in_frame_del	42	25.00	14	DEL	1.000:1.000:1.000	-
HSPG2	3339	genome.wustl.edu	37	1	22211641	22211642	+	Frame_Shift_Ins	INS	-	-	G	rs546808961		TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr1:22211641_22211642insG	ENST00000374695.3	-	11	1298_1299	c.1219_1220insC	c.(1219-1221)cagfs	p.Q407fs		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	407	Ig-like C2-type 1.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGTCACCACCTGGGGGGGCACT	0.668																																						dbGAP											0																																										-	-	-	SO:0001589	frameshift_variant	0			M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.1220dupC	1.37:g.22211648_22211648dupG	ENSP00000363827:p.Gln407fs		Q16287|Q5SZI3|Q9H3V5	Frame_Shift_Ins	INS	pfam_Ig_I-set,pfam_Immunoglobulin,pfam_Laminin_G,pfam_Laminin_B_type_IV,pfam_EGF_laminin,pfam_LDrepeatLR_classA_rpt,pfam_EGF-like_dom,superfamily_ConA-like_lec_gl,superfamily_LDrepeatLR_classA_rpt,smart_SEA,smart_LDrepeatLR_classA_rpt,smart_EGF-like,smart_Ig_sub,smart_Ig_sub2,smart_Ig_V-set_subgr,smart_Laminin_B_subgr,smart_EGF_laminin,smart_EGF-like_Ca-bd,smart_Laminin_G,pfscan_EG-like_dom,pfscan_Laminin_B_type_IV,pfscan_EGF_laminin,pfscan_Laminin_G,pfscan_LDrepeatLR_classA_rpt,pfscan_SEA,pfscan_Ig-like	p.Q407fs	ENST00000374695.3	37	c.1220_1219	CCDS30625.1	1																																																																																			HSPG2	-	pfam_Ig_I-set,superfamily_LDrepeatLR_classA_rpt,pfscan_Ig-like	ENSG00000142798		0.668	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HSPG2	HGNC	protein_coding	OTTHUMT00000007598.1	16	0.00	0	-	NM_005529		22211641	22211642	-1	no_errors	ENST00000374695	ensembl	human	known	69_37n	frame_shift_ins	14	12.50	2	INS	1.000:0.999	G
IFFO1	25900	genome.wustl.edu	37	12	6657973	6657974	+	Frame_Shift_Ins	INS	-	-	C	rs371982613		TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr12:6657973_6657974insC	ENST00000396840.2	-	5	1130_1131	c.1089_1090insG	c.(1087-1092)gggcggfs	p.R364fs	IFFO1_ENST00000336604.4_Frame_Shift_Ins_p.R367fs|IFFO1_ENST00000436152.2_Frame_Shift_Ins_p.R60fs|IFFO1_ENST00000465801.1_Frame_Shift_Ins_p.R60fs|IFFO1_ENST00000356896.4_Frame_Shift_Ins_p.R367fs			Q0D2I5	IFFO1_HUMAN	intermediate filament family orphan 1	364						intermediate filament (GO:0005882)		p.R364fs*19(1)		central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	20						TCCCGCTTCCGCCCCCCCATGG	0.673																																						dbGAP											1	Insertion - Frameshift(1)	large_intestine(1)							,,	8,4256		0,8,2124					,,	3.7	1.0			20	15,8229		0,15,4107	no	frameshift,frameshift,frameshift	IFFO1	NM_080730.4,NM_001193457.1,NM_001039670.2	,,	0,23,6231	A1A1,A1R,RR		0.182,0.1876,0.1839	,,	,,		23,12485				-	-	-	SO:0001589	frameshift_variant	0			AF124432	CCDS8550.1, CCDS41741.1, CCDS8550.2, CCDS73425.1	12p13.31	2013-01-16	2008-09-11	2008-09-11	ENSG00000010295	ENSG00000010295		"""Intermediate filament family orphans"""	24970	protein-coding gene	gene with protein product		610495	"""intermediate filament family orphan"""	IFFO		8771189, 3052284	Standard	NM_001193457		Approved	HOM-TES-103	uc010sfe.2	Q0D2I5	OTTHUMG00000141264	ENST00000396840.2:c.1090dupG	12.37:g.6657980_6657980dupC	ENSP00000380052:p.Arg364fs		Q24JT6|Q7L5J9|Q7Z5X4|Q9BQ46	Frame_Shift_Ins	INS	NULL	p.R366fs	ENST00000396840.2	37	c.1099_1098		12																																																																																			IFFO1	-	NULL	ENSG00000010295		0.673	IFFO1-008	KNOWN	basic|appris_candidate	protein_coding	IFFO1	HGNC	protein_coding	OTTHUMT00000280428.1	29	0.00	0	-	NM_080730		6657973	6657974	-1	no_errors	ENST00000356896	ensembl	human	known	69_37n	frame_shift_ins	20	13.04	3	INS	1.000:1.000	C
KIT	3815	genome.wustl.edu	37	4	55569972	55569972	+	Missense_Mutation	SNP	C	C	T	rs386833402		TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr4:55569972C>T	ENST00000288135.5	+	5	936	c.839C>T	c.(838-840)gCg>gTg	p.A280V		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	280	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	ATCAGTTCAGCGAGAGTTAAT	0.388		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																													dbGAP	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	0													149.0	146.0	147.0					4																	55569972		2203	4300	6503	-	-	-	SO:0001583	missense	0	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.839C>T	4.37:g.55569972C>T	ENSP00000288135:p.Ala280Val		B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	pfam_Ser-Thr/Tyr_kinase_cat_dom,pfam_Prot_kinase_cat_dom,pfam_Ig_I-set,pfam_Immunoglobulin,superfamily_Kinase-like_dom,smart_Ig_sub,smart_Ig_sub2,smart_Ser/Thr_dual-sp_kinase_dom,smart_Tyr_kinase_cat_dom,pirsf_Tyr_kinase_CSF1/PDGF_rcpt,pfscan_Prot_kinase_cat_dom,pfscan_Ig-like	p.A280V	ENST00000288135.5	37	c.839	CCDS3496.1	4	.	.	.	.	.	.	.	.	.	.	C	0.776	-0.764153	0.02996	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	T;T	0.15256	2.44;2.44	6.01	1.4	0.22301	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.356685	0.25096	N	0.033165	T	0.07638	0.0192	N	0.19112	0.55	0.27756	N	0.943988	B;B	0.10296	0.001;0.003	B;B	0.04013	0.0;0.001	T	0.40701	-0.9549	10	0.02654	T	1	.	7.7013	0.28625	0.0:0.5021:0.0:0.4979	.	280;280	P10721-2;P10721	.;KIT_HUMAN	V	280	ENSP00000288135:A280V;ENSP00000390987:A280V	ENSP00000288135:A280V	A	+	2	0	KIT	55264729	0.998000	0.40836	0.607000	0.28956	0.564000	0.35744	0.829000	0.27449	0.455000	0.26910	-0.143000	0.13931	GCG	KIT	-	pfam_Ig_I-set,pfam_Immunoglobulin,smart_Ig_sub,smart_Ig_sub2,pirsf_Tyr_kinase_CSF1/PDGF_rcpt,pfscan_Ig-like	ENSG00000157404		0.388	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIT	HGNC	protein_coding	OTTHUMT00000250618.1	169	0.00	0	C			55569972	55569972	+1	no_errors	ENST00000288135	ensembl	human	known	69_37n	missense	91	38.51	57	SNP	0.800	T
ANK1	286	genome.wustl.edu	37	8	41518006	41518006	+	Intron	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr8:41518006G>A	ENST00000347528.4	-	41	5703				ANK1_ENST00000379758.2_Intron|ANK1_ENST00000522543.1_Intron|ANK1_ENST00000457297.1_Intron|ANK1_ENST00000396945.1_Intron|ANK1_ENST00000522231.1_Intron|RP11-930P14.1_ENST00000522388.1_RNA|MIR486_ENST00000408108.1_RNA|ANK1_ENST00000396942.1_Intron|RP11-930P14.1_ENST00000520418.1_RNA|ANK1_ENST00000265709.8_Intron|ANK1_ENST00000352337.4_Intron|RP11-930P14.1_ENST00000585088.1_RNA|ANK1_ENST00000314214.8_Intron|ANK1_ENST00000289734.7_Intron	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic						axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			AAGGGCCTCGGGGCAGCTCAG	0.662																																						dbGAP											0													17.0	21.0	20.0					8																	41518006		1186	2731	3917	-	-	-	SO:0001627	intron_variant	0			M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.5619+1312C>T	8.37:g.41518006G>A			A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	RNA	SNP	-	NULL	ENST00000347528.4	37	NULL	CCDS6119.1	8																																																																																			MIR486	-	-	ENSG00000221035		0.662	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	MIR486	HGNC	protein_coding	OTTHUMT00000317297.1	34	0.00	0	G	NM_020475		41518006	41518006	+1	no_errors	ENST00000408108	ensembl	human	known	69_37n	rna	10	44.44	8	SNP	1.000	A
MKL1	57591	genome.wustl.edu	37	22	40825739	40825739	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr22:40825739G>A	ENST00000355630.3	-	7	762	c.172C>T	c.(172-174)Cag>Tag	p.Q58*	MKL1_ENST00000407029.1_Nonsense_Mutation_p.Q58*|MKL1_ENST00000396617.3_Nonsense_Mutation_p.Q58*|MKL1_ENST00000402630.1_Nonsense_Mutation_p.Q58*|MKL1_ENST00000402042.1_Nonsense_Mutation_p.Q58*	NM_020831.3	NP_065882.1	Q969V6	MKL1_HUMAN	megakaryoblastic leukemia (translocation) 1	58	Mediates interaction with SCAI and ACTB. {ECO:0000250}.				negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription via serum response element binding (GO:0010735)|smooth muscle cell differentiation (GO:0051145)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	actin binding (GO:0003779)|actin monomer binding (GO:0003785)|leucine zipper domain binding (GO:0043522)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	30						AGCTTCAGCTGCTTGGCCTGG	0.572			T	RBM15	acute megakaryocytic leukemia																																	dbGAP		Dom	yes		22	22q13	57591	megakaryoblastic leukemia (translocation) 1		L	0													91.0	81.0	84.0					22																	40825739		2203	4300	6503	-	-	-	SO:0001587	stop_gained	0			AB037859	CCDS14003.1, CCDS74865.1, CCDS74866.1	22q13	2008-06-12			ENSG00000196588	ENSG00000196588			14334	protein-coding gene	gene with protein product	"""megakaryocytic acute leukemia"", ""myocardin-related transcription factor A"", ""basic, SAP and coiled-coil domain"""	606078				11431691, 12019265, 14970199	Standard	XM_005261692		Approved	KIAA1438, MAL, MRTF-A, BSAC	uc003ayw.1	Q969V6	OTTHUMG00000151146	ENST00000355630.3:c.172C>T	22.37:g.40825739G>A	ENSP00000347847:p.Gln58*		Q8TCL1|Q96SC5|Q96SC6|Q9P2B0	Nonsense_Mutation	SNP	pfam_RPEL_repeat,pfam_SAP_DNA-bd,smart_RPEL_repeat,smart_SAP_DNA-bd,pfscan_RPEL_repeat,pfscan_SAP_DNA-bd	p.Q58*	ENST00000355630.3	37	c.172	CCDS14003.1	22	.	.	.	.	.	.	.	.	.	.	G	40	8.346904	0.98769	.	.	ENSG00000196588	ENST00000355630;ENST00000396617;ENST00000402042;ENST00000407029;ENST00000402630	.	.	.	5.25	5.25	0.73442	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-21.0059	19.2381	0.93869	0.0:0.0:1.0:0.0	.	.	.	.	X	58	.	ENSP00000347847:Q58X	Q	-	1	0	MKL1	39155685	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.869000	0.99810	2.633000	0.89246	0.467000	0.42956	CAG	MKL1	-	NULL	ENSG00000196588		0.572	MKL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MKL1	HGNC	protein_coding	OTTHUMT00000321522.1	82	0.00	0	G	NM_020831		40825739	40825739	-1	no_errors	ENST00000355630	ensembl	human	known	69_37n	nonsense	73	37.07	43	SNP	1.000	A
MOV10L1	54456	genome.wustl.edu	37	22	50555645	50555645	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr22:50555645G>A	ENST00000262794.5	+	9	1402	c.1319G>A	c.(1318-1320)cGa>cAa	p.R440Q	MOV10L1_ENST00000545383.1_Missense_Mutation_p.R440Q|MOV10L1_ENST00000395858.3_Missense_Mutation_p.R440Q|MOV10L1_ENST00000540615.1_Missense_Mutation_p.R420Q|MOV10L1_ENST00000395843.1_5'UTR	NM_018995.2	NP_061868.1	Q9BXT6	M10L1_HUMAN	Mov10 RISC complex RNA helicase like 1	440					ATP catabolic process (GO:0006200)|germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|magnesium ion binding (GO:0000287)|RNA binding (GO:0003723)	p.R440Q(1)		breast(2)|endometrium(2)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|prostate(1)|skin(9)|stomach(4)|urinary_tract(3)	67		all_cancers(38;3.31e-11)|all_epithelial(38;5.69e-10)|all_lung(38;3.73e-05)|Breast(42;0.000525)|Lung NSC(38;0.000954)|Ovarian(80;0.0367)|Lung SC(80;0.114)		LUAD - Lung adenocarcinoma(64;0.0215)|BRCA - Breast invasive adenocarcinoma(115;0.24)		CTAATTGGGCGATACCTTGAA	0.388																																						dbGAP											1	Substitution - Missense(1)	large_intestine(1)											98.0	97.0	97.0					22																	50555645		2203	4300	6503	-	-	-	SO:0001583	missense	0			AF285604	CCDS14084.1, CCDS54541.1, CCDS54542.1, CCDS54543.1	22q13.33	2014-07-02	2014-07-02		ENSG00000073146	ENSG00000073146			7201	protein-coding gene	gene with protein product	"""cardiac helicase activated by MEF2C protein"""	605794	"""Mov10 (mouse)-like 1"", ""Mov10l1, Moloney leukemia virus 10-like 1, homolog (mouse)"""			11279525	Standard	NM_018995		Approved	DJ402G11.8, DKFZp434B0717, CHAMP	uc003bjj.3	Q9BXT6	OTTHUMG00000044648	ENST00000262794.5:c.1319G>A	22.37:g.50555645G>A	ENSP00000262794:p.Arg440Gln		A7E211|A8MXC6|B7WPP1|B7Z7R1|F5H403|Q5TGD5|Q8NBD4|Q9NXW3|Q9UFB3|Q9UGX9	Missense_Mutation	SNP	superfamily_NA-bd_OB-fold-like	p.R440Q	ENST00000262794.5	37	c.1319	CCDS14084.1	22	.	.	.	.	.	.	.	.	.	.	G	29.4	5.000256	0.93227	.	.	ENSG00000073146	ENST00000545383;ENST00000262794;ENST00000395858;ENST00000540615	D;D;D;D	0.89617	-2.36;-2.36;-1.96;-2.54	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	D	0.94899	0.8351	M	0.82323	2.585	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;0.999;0.999	D	0.94583	0.7781	10	0.51188	T	0.08	-20.499	18.4598	0.90735	0.0:0.0:1.0:0.0	.	201;420;440;440	B7Z893;F5H403;A8MXC6;Q9BXT6	.;.;.;M10L1_HUMAN	Q	440;440;440;420	ENSP00000438978:R440Q;ENSP00000262794:R440Q;ENSP00000379199:R440Q;ENSP00000438542:R420Q	ENSP00000262794:R440Q	R	+	2	0	MOV10L1	48897772	1.000000	0.71417	0.943000	0.38184	0.652000	0.38707	7.348000	0.79366	2.648000	0.89879	0.557000	0.71058	CGA	MOV10L1	-	NULL	ENSG00000073146		0.388	MOV10L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MOV10L1	HGNC	protein_coding	OTTHUMT00000075009.2	79	0.00	0	G	NM_018995		50555645	50555645	+1	no_errors	ENST00000262794	ensembl	human	known	69_37n	missense	62	18.42	14	SNP	0.997	A
MYH4	4622	genome.wustl.edu	37	17	10355578	10355578	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr17:10355578G>A	ENST00000255381.2	-	27	3528	c.3418C>T	c.(3418-3420)Cgc>Tgc	p.R1140C	RP11-799N11.1_ENST00000399342.2_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1140					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						AGGTCAGAGCGCTGCTTCTCT	0.582																																						dbGAP											0													60.0	66.0	64.0					17																	10355578		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3418C>T	17.37:g.10355578G>A	ENSP00000255381:p.Arg1140Cys			Missense_Mutation	SNP	pfam_Myosin_tail,pfam_Myosin_head_motor_dom,pfam_Myosin_N,superfamily_Prefoldin,superfamily_tRNA-bd_arm,smart_Myosin_head_motor_dom,pfscan_IQ_motif_EF-hand-BS,prints_Myosin_head_motor_dom	p.R1140C	ENST00000255381.2	37	c.3418	CCDS11154.1	17	.	.	.	.	.	.	.	.	.	.	G	19.62	3.861742	0.71949	.	.	ENSG00000141048	ENST00000255381	D	0.82893	-1.66	5.4	4.36	0.52297	Myosin tail (1);	0.000000	0.35291	U	0.003304	D	0.93446	0.7909	H	0.95712	3.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94902	0.8057	10	0.87932	D	0	.	15.2147	0.73254	0.0:0.0:0.8587:0.1413	.	1140	Q9Y623	MYH4_HUMAN	C	1140	ENSP00000255381:R1140C	ENSP00000255381:R1140C	R	-	1	0	MYH4	10296303	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	3.794000	0.55492	2.685000	0.91497	0.655000	0.94253	CGC	MYH4	-	pfam_Myosin_tail	ENSG00000264424		0.582	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	MYH4	HGNC	protein_coding	OTTHUMT00000252731.1	111	0.00	0	G	NM_017533		10355578	10355578	-1	no_errors	ENST00000255381	ensembl	human	known	69_37n	missense	39	72.73	104	SNP	1.000	A
NCOR2	9612	genome.wustl.edu	37	12	124841250	124841251	+	Frame_Shift_Ins	INS	-	-	G	rs372982176|rs199595579		TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	-	-					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr12:124841250_124841251insG	ENST00000405201.1	-	23	3178_3179	c.3178_3179insC	c.(3178-3180)cgtfs	p.R1060fs	NCOR2_ENST00000397355.1_Frame_Shift_Ins_p.R1051fs|NCOR2_ENST00000404621.1_Frame_Shift_Ins_p.R1050fs|NCOR2_ENST00000429285.2_Frame_Shift_Ins_p.R1050fs|NCOR2_ENST00000356219.3_Frame_Shift_Ins_p.R1067fs|NCOR2_ENST00000404121.2_Frame_Shift_Ins_p.R621fs			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1068					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GATCACCTCACGGGGGGGCACG	0.668																																						dbGAP											0									,,	19,3595		0,19,1788					,,	4.9	0.4			18	14,7804		0,14,3895	no	frameshift,frameshift,frameshift	NCOR2	NM_006312.5,NM_001206654.1,NM_001077261.3	,,	0,33,5683	A1A1,A1R,RR		0.1791,0.5257,0.2887	,,	,,		33,11399				-	-	-	SO:0001589	frameshift_variant	0			U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3179dupC	12.37:g.124841257_124841257dupG	ENSP00000384018:p.Arg1060fs		O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Frame_Shift_Ins	INS	pfam_SANT/Myb,superfamily_Homeodomain-like,smart_SANT/Myb,pfscan_Myb-like_dom	p.R1067fs	ENST00000405201.1	37	c.3200_3199	CCDS41858.2	12																																																																																			NCOR2	-	NULL	ENSG00000196498		0.668	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	NCOR2	HGNC	protein_coding	OTTHUMT00000318173.2	18	0.00	0	-	NM_006312		124841250	124841251	-1	no_errors	ENST00000356219	ensembl	human	known	69_37n	frame_shift_ins	15	11.76	2	INS	0.404:0.395	G
NDUFA1	4694	genome.wustl.edu	37	X	119005896	119005896	+	Missense_Mutation	SNP	G	G	A	rs104894884		TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chrX:119005896G>A	ENST00000371437.4	+	1	447	c.22G>A	c.(22-24)Gga>Aga	p.G8R	RNF113A_ENST00000371442.2_5'Flank	NM_004541.3	NP_004532.1	O15239	NDUA1_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1, 7.5kDa	8			G -> R (in MT-C1D). {ECO:0000269|PubMed:17262856}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|kidney(1)|large_intestine(2)|stomach(1)	5						GATTCTCCCCGGACTCTCCGT	0.582																																						dbGAP											0			GRCh37	CM070206	NDUFA1	M	rs104894884						184.0	149.0	161.0					X																	119005896		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS14590.1	Xq24	2011-07-04	2002-08-29		ENSG00000125356	ENSG00000125356		"""Mitochondrial respiratory chain complex / Complex I"""	7683	protein-coding gene	gene with protein product	"""NADH:ubiquinone oxidoreductase (complex 1)"", ""type I dehydrogenase"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1 (7.5kD, MWFE)"", ""complex I MWFE subunit"""	300078	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1 (7.5kD, MWFE)"""			8938439	Standard	NM_004541		Approved	MWFE, CI-MWFE	uc004esc.4	O15239	OTTHUMG00000022287	ENST00000371437.4:c.22G>A	X.37:g.119005896G>A	ENSP00000360492:p.Gly8Arg			Missense_Mutation	SNP	pirsf_NADH_Ub_cplx-1_asu_su-1	p.G8R	ENST00000371437.4	37	c.22	CCDS14590.1	X	.	.	.	.	.	.	.	.	.	.	G	14.10	2.436087	0.43224	.	.	ENSG00000125356	ENST00000371437	T	0.78481	-1.18	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.86810	0.6022	.	.	.	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.86588	0.1858	9	0.42905	T	0.14	-17.2435	13.6857	0.62515	0.0:0.0:1.0:0.0	.	8	O15239	NDUA1_HUMAN	R	8	ENSP00000360492:G8R	ENSP00000360492:G8R	G	+	1	0	NDUFA1	118889924	1.000000	0.71417	0.749000	0.31150	0.584000	0.36387	3.502000	0.53332	2.300000	0.77407	0.600000	0.82982	GGA	NDUFA1	-	pirsf_NADH_Ub_cplx-1_asu_su-1	ENSG00000125356		0.582	NDUFA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NDUFA1	HGNC	protein_coding	OTTHUMT00000058080.1	82	0.00	0	G	NM_004541		119005896	119005896	+1	no_errors	ENST00000371437	ensembl	human	known	69_37n	missense	107	26.21	38	SNP	0.789	A
NPTXR	23467	genome.wustl.edu	37	22	39219199	39219199	+	Silent	SNP	C	C	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr22:39219199C>T	ENST00000333039.2	-	4	1290	c.1167G>A	c.(1165-1167)agG>agA	p.R389R		NM_014293.3	NP_055108	O95502	NPTXR_HUMAN	neuronal pentraxin receptor	389	Pentaxin.					integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			central_nervous_system(2)|large_intestine(3)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	Melanoma(58;0.04)					ATAGGCCATCCCTTGTGGTCC	0.632																																					Pancreas(139;2521 3281 36965)	dbGAP											0													91.0	73.0	79.0					22																	39219199		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF052163	CCDS33647.1	22q13.1	2007-01-25			ENSG00000221890	ENSG00000221890			7954	protein-coding gene	gene with protein product		609474				16497176	Standard	NM_014293		Approved		uc003awk.3	O95502	OTTHUMG00000150458	ENST00000333039.2:c.1167G>A	22.37:g.39219199C>T				Silent	SNP	pfam_Pentaxin,superfamily_ConA-like_lec_gl,smart_Pentaxin,prints_Pentaxin	p.R389	ENST00000333039.2	37	c.1167	CCDS33647.1	22																																																																																			NPTXR	-	pfam_Pentaxin,superfamily_ConA-like_lec_gl,smart_Pentaxin,prints_Pentaxin	ENSG00000221890		0.632	NPTXR-001	KNOWN	non_ATG_start|basic|appris_principal|CCDS	protein_coding	NPTXR	HGNC	protein_coding	OTTHUMT00000318194.2	107	0.00	0	C	NM_014293		39219199	39219199	-1	no_errors	ENST00000333039	ensembl	human	known	69_37n	silent	51	46.32	44	SNP	1.000	T
OLFML3	56944	genome.wustl.edu	37	1	114523968	114523968	+	Silent	SNP	C	C	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr1:114523968C>T	ENST00000320334.4	+	3	872	c.798C>T	c.(796-798)taC>taT	p.Y266Y	OLFML3_ENST00000491700.1_3'UTR|OLFML3_ENST00000369551.1_Silent_p.Y246Y|OLFML3_ENST00000393300.2_Silent_p.Y246Y	NM_020190.2	NP_064575.1	Q9NRN5	OLFL3_HUMAN	olfactomedin-like 3	266	Olfactomedin-like. {ECO:0000255|PROSITE- ProRule:PRU00446}.				multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)|vesicle (GO:0031982)				breast(1)|endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|skin(2)|urinary_tract(1)	14	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TCCCCCCCTACGGCTTGACAG	0.557																																						dbGAP											0													74.0	67.0	69.0					1																	114523968		2203	4300	6503	-	-	-	SO:0001819	synonymous_variant	0			AF201945	CCDS870.1, CCDS65618.1, CCDS72839.1	1p13.1	2008-02-05			ENSG00000116774	ENSG00000116774			24956	protein-coding gene	gene with protein product		610088					Standard	NM_001286353		Approved	HNOEL-iso, OLF44	uc001eer.1	Q9NRN5	OTTHUMG00000011980	ENST00000320334.4:c.798C>T	1.37:g.114523968C>T			Q53FR1|Q53HV9|Q5SQL6|Q69AX9|Q8NBJ2	Silent	SNP	pfam_Olfac-like,smart_Olfac-like,pfscan_Olfac-like	p.Y266	ENST00000320334.4	37	c.798	CCDS870.1	1																																																																																			OLFML3	-	pfam_Olfac-like,smart_Olfac-like,pfscan_Olfac-like	ENSG00000116774		0.557	OLFML3-011	KNOWN	basic|appris_principal|CCDS	protein_coding	OLFML3	HGNC	protein_coding	OTTHUMT00000033119.1	100	0.00	0	C	NM_020190		114523968	114523968	+1	no_errors	ENST00000320334	ensembl	human	known	69_37n	silent	64	25.58	22	SNP	0.257	T
OR5R1	219479	genome.wustl.edu	37	11	56184810	56184810	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr11:56184810G>A	ENST00000312253.1	-	1	898	c.899C>T	c.(898-900)gCc>gTc	p.A300V		NM_001004744.1	NP_001004744.1	Q8NH85	OR5R1_HUMAN	olfactory receptor, family 5, subfamily R, member 1	300						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(17)|ovary(2)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(21;0.00448)					TTTCTTTGAGGCATCTTTCAC	0.333																																						dbGAP											0													98.0	97.0	97.0					11																	56184810		2201	4295	6496	-	-	-	SO:0001583	missense	0			AB065504	CCDS31530.1	11q11	2012-08-09		2004-03-10	ENSG00000174942	ENSG00000174942		"""GPCR / Class A : Olfactory receptors"""	14841	protein-coding gene	gene with protein product				OR5R1P			Standard	NM_001004744		Approved		uc010rji.2	Q8NH85	OTTHUMG00000154219	ENST00000312253.1:c.899C>T	11.37:g.56184810G>A	ENSP00000308595:p.Ala300Val			Missense_Mutation	SNP	pfam_7TM_GPCR_Rhodpsn,pfam_7TM_GPCR_olfarory/Srsx,pfscan_GPCR_Rhodpsn_supfam,prints_Olfact_rcpt,prints_7TM_GPCR_Rhodpsn	p.A300V	ENST00000312253.1	37	c.899	CCDS31530.1	11	.	.	.	.	.	.	.	.	.	.	G	13.30	2.194642	0.38806	.	.	ENSG00000174942	ENST00000312253	T	0.44881	0.91	5.79	5.79	0.91817	.	0.000000	0.31438	U	0.007655	T	0.59155	0.2173	L	0.41492	1.28	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	T	0.54397	-0.8300	10	0.72032	D	0.01	-10.1849	19.6278	0.95687	0.0:0.0:1.0:0.0	.	300	Q8NH85	OR5R1_HUMAN	V	300	ENSP00000308595:A300V	ENSP00000308595:A300V	A	-	2	0	OR5R1	55941386	1.000000	0.71417	0.043000	0.18650	0.026000	0.11368	4.943000	0.63554	2.736000	0.93811	0.643000	0.83706	GCC	OR5R1	-	NULL	ENSG00000174942		0.333	OR5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR5R1	HGNC	protein_coding	OTTHUMT00000334444.1	186	0.00	0	G	NM_001004744		56184810	56184810	-1	no_errors	ENST00000312253	ensembl	human	known	69_37n	missense	127	22.09	36	SNP	0.079	A
PIK3CB	5291	genome.wustl.edu	37	3	138403480	138403480	+	Missense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr3:138403480G>A	ENST00000477593.1	-	16	2375	c.2302C>T	c.(2302-2304)Ctc>Ttc	p.L768F	PIK3CB_ENST00000289153.2_Missense_Mutation_p.L768F|PIK3CB_ENST00000544716.1_Missense_Mutation_p.L214F			P42338	PK3CB_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit beta	768					activation of MAPK activity (GO:0000187)|autophagy (GO:0006914)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|cellular calcium ion homeostasis (GO:0006874)|chemotaxis (GO:0006935)|embryonic cleavage (GO:0040016)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|positive regulation of autophagy (GO:0010508)|regulation of cell-matrix adhesion (GO:0001952)|regulation of clathrin-mediated endocytosis (GO:2000369)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	41					Caffeine(DB00201)	AGTTCTGAGAGGATAACACAT	0.502																																						dbGAP											0													101.0	90.0	94.0					3																	138403480		2203	4300	6503	-	-	-	SO:0001583	missense	0				CCDS3104.1	3q22.3	2013-09-19	2012-07-13		ENSG00000051382	ENSG00000051382	2.7.1.153		8976	protein-coding gene	gene with protein product		602925	"""phosphoinositide-3-kinase, catalytic, beta polypeptide"""	PIK3C1		8246984	Standard	NM_006219		Approved		uc011bmq.3	P42338	OTTHUMG00000159893	ENST00000477593.1:c.2302C>T	3.37:g.138403480G>A	ENSP00000418143:p.Leu768Phe		D3DNF0|Q24JU2	Missense_Mutation	SNP	pfam_PInositide-3_kin_accessory_dom,pfam_PI3/4_kinase_cat_dom,pfam_PI3K_adapt-bd_dom,pfam_PI3K_Ras-bd_dom,pfam_PI3K_C2_dom,superfamily_Kinase-like_dom,superfamily_C2_Ca/lipid-bd_dom_CaLB,superfamily_ARM-type_fold,smart_PI3K_adapt-bd_dom,smart_PI3K_Ras-bd_dom,smart_PI3K_C2_dom,smart_PInositide-3_kin_accessory_dom,smart_PI3/4_kinase_cat_dom,pfscan_PI3/4_kinase_cat_dom	p.L768F	ENST00000477593.1	37	c.2302	CCDS3104.1	3	.	.	.	.	.	.	.	.	.	.	G	22.4	4.280505	0.80692	.	.	ENSG00000051382	ENST00000477593;ENST00000544716;ENST00000289153	D;D;D	0.81739	-1.53;-1.53;-1.53	5.78	3.93	0.45458	Protein kinase-like domain (1);	0.062472	0.64402	D	0.000003	T	0.79997	0.4543	M	0.75085	2.285	0.80722	D	1	P;P;P	0.46784	0.884;0.723;0.611	B;B;B	0.43155	0.41;0.274;0.242	T	0.80061	-0.1540	10	0.40728	T	0.16	-12.2076	11.7947	0.52093	0.0672:0.1223:0.8105:0.0	.	768;355;214	P42338;B4DZI3;Q68DL0	PK3CB_HUMAN;.;.	F	768;214;768	ENSP00000418143:L768F;ENSP00000438259:L214F;ENSP00000289153:L768F	ENSP00000289153:L768F	L	-	1	0	PIK3CB	139886170	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.690000	0.84178	1.411000	0.46957	0.591000	0.81541	CTC	PIK3CB	-	superfamily_Kinase-like_dom	ENSG00000051382		0.502	PIK3CB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PIK3CB	HGNC	protein_coding	OTTHUMT00000358019.1	104	0.00	0	G			138403480	138403480	-1	no_errors	ENST00000289153	ensembl	human	known	69_37n	missense	56	43.43	43	SNP	1.000	A
PRKRIR	5612	genome.wustl.edu	37	11	76062947	76062947	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr11:76062947C>T	ENST00000260045.3	-	5	1352	c.1247G>A	c.(1246-1248)gGt>gAt	p.G416D	PRKRIR_ENST00000531878.1_5'Flank	NM_004705.2	NP_004696.2	O43422	P52K_HUMAN	protein-kinase, interferon-inducible double stranded RNA dependent inhibitor, repressor of (P58 repressor)	416					negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)|signal transduction (GO:0007165)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(4)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	25						CAGTTCTTTACCCCTTTCTTT	0.373																																						dbGAP											0													21.0	23.0	22.0					11																	76062947		2171	4229	6400	-	-	-	SO:0001583	missense	0			AF007393	CCDS8243.1	11q13.5	2013-01-25			ENSG00000137492	ENSG00000137492		"""THAP (C2CH-type zinc finger) domain containing"""	9440	protein-coding gene	gene with protein product	"""THAP domain containing 12"""	607374				9447982	Standard	NM_004705		Approved	P52rIPK, DAP4, THAP12	uc001oxh.1	O43422	OTTHUMG00000165280	ENST00000260045.3:c.1247G>A	11.37:g.76062947C>T	ENSP00000260045:p.Gly416Asp		A8K728|Q17RY9|Q8WTW1|Q9Y3Z4	Missense_Mutation	SNP	pfam_Znf_C2CH,pfam_HATC,superfamily_RNaseH-like_dom,smart_Znf_C2CH,pfscan_Znf_C2CH	p.G416D	ENST00000260045.3	37	c.1247	CCDS8243.1	11	.	.	.	.	.	.	.	.	.	.	C	8.564	0.878530	0.17395	.	.	ENSG00000137492	ENST00000529901;ENST00000260045	.	.	.	4.78	2.84	0.33178	Ribonuclease H-like (1);	0.281111	0.41396	D	0.000890	T	0.41558	0.1164	N	0.22421	0.69	0.40835	D	0.983624	B	0.16166	0.016	B	0.09377	0.004	T	0.17137	-1.0379	9	0.18276	T	0.48	.	15.0128	0.71562	0.0:0.5936:0.4064:0.0	.	416	O43422	P52K_HUMAN	D	241;416	.	ENSP00000260045:G416D	G	-	2	0	PRKRIR	75740595	0.968000	0.33430	0.985000	0.45067	0.996000	0.88848	2.264000	0.43302	0.540000	0.28808	-0.190000	0.12839	GGT	PRKRIR	-	superfamily_RNaseH-like_dom	ENSG00000137492		0.373	PRKRIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PRKRIR	HGNC	protein_coding	OTTHUMT00000383188.1	73	0.00	0	C	NM_004705		76062947	76062947	-1	no_errors	ENST00000260045	ensembl	human	known	69_37n	missense	20	64.29	36	SNP	0.989	T
REG3G	130120	genome.wustl.edu	37	2	79255029	79255029	+	Missense_Mutation	SNP	G	G	T	rs149243674	byFrequency	TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr2:79255029G>T	ENST00000272324.5	+	5	614	c.430G>T	c.(430-432)Ggc>Tgc	p.G144C	REG3G_ENST00000409471.1_Missense_Mutation_p.G98C|REG3G_ENST00000393897.2_Missense_Mutation_p.G144C	NM_001008387.2	NP_001008388.1	Q6UW15	REG3G_HUMAN	regenerating islet-derived 3 gamma	144	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				acute-phase response (GO:0006953)|defense response to Gram-positive bacterium (GO:0050830)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of keratinocyte differentiation (GO:0045617)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of wound healing (GO:0090303)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(27)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTTAAACCCTGGCCACTGTGG	0.502																																						dbGAP											0													110.0	113.0	112.0					2																	79255029		2203	4300	6503	-	-	-	SO:0001583	missense	0			AY359047	CCDS1962.1, CCDS58714.1	2p12	2005-02-11			ENSG00000143954	ENSG00000143954			29595	protein-coding gene	gene with protein product		609933				12975309	Standard	NM_001008387		Approved	UNQ429, LPPM429, PAP1B	uc002snx.4	Q6UW15	OTTHUMG00000130018	ENST00000272324.5:c.430G>T	2.37:g.79255029G>T	ENSP00000272324:p.Gly144Cys		A8K980|D6W5J6|Q3SYE4|Q3SYE6|Q6FH18	Missense_Mutation	SNP	pfam_C-type_lectin,superfamily_C-type_lectin_fold,smart_C-type_lectin,pfscan_C-type_lectin,prints_Pancreatis_ac	p.G144C	ENST00000272324.5	37	c.430	CCDS1962.1	2	.	.	.	.	.	.	.	.	.	.	G	14.61	2.586190	0.46110	.	.	ENSG00000143954	ENST00000393897;ENST00000272324;ENST00000409471	T;T;T	0.20463	2.08;2.08;2.07	4.73	2.9	0.33743	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.122449	0.37348	N	0.002139	T	0.48150	0.1484	M	0.90977	3.165	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.994	T	0.35773	-0.9775	10	0.72032	D	0.01	.	5.9862	0.19436	0.2297:0.0:0.7703:0.0	.	98;144	Q3SYE6;Q6UW15	.;REG3G_HUMAN	C	144;144;98	ENSP00000377475:G144C;ENSP00000272324:G144C;ENSP00000387105:G98C	ENSP00000272324:G144C	G	+	1	0	REG3G	79108537	0.150000	0.22732	0.016000	0.15963	0.129000	0.20672	1.661000	0.37408	1.328000	0.45358	0.650000	0.86243	GGC	REG3G	-	pfam_C-type_lectin,superfamily_C-type_lectin_fold,smart_C-type_lectin,pfscan_C-type_lectin	ENSG00000143954		0.502	REG3G-002	KNOWN	basic|appris_principal|CCDS	protein_coding	REG3G	HGNC	protein_coding	OTTHUMT00000328247.1	132	0.00	0	G	NM_198448		79255029	79255029	+1	no_errors	ENST00000272324	ensembl	human	known	69_37n	missense	124	19.48	30	SNP	0.003	T
PSMD14	10213	genome.wustl.edu	37	2	162175351	162175351	+	Silent	SNP	T	T	G			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	T	T					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr2:162175351T>G	ENST00000409682.3	+	3	719	c.15T>G	c.(13-15)ctT>ctG	p.L5L		NM_005805.5	NP_005796.1	O00487	PSDE_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 14	5					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K63-linked deubiquitination (GO:0070536)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle, lid subcomplex (GO:0008541)	endopeptidase activator activity (GO:0061133)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|proteasome binding (GO:0070628)|ubiquitin thiolesterase activity (GO:0004221)			breast(1)|endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	12						ACAGACTTCTTAGACTTGGAG	0.368																																						dbGAP											0													128.0	127.0	127.0					2																	162175351		1821	4076	5897	-	-	-	SO:0001819	synonymous_variant	0			U86782	CCDS46437.1	2q14.3	2008-05-22			ENSG00000115233	ENSG00000115233		"""Proteasome (prosome, macropain) subunits"""	16889	protein-coding gene	gene with protein product		607173				9374539	Standard	NM_005805		Approved	POH1, pad1, Rpn11	uc002ubu.3	O00487	OTTHUMG00000153882	ENST00000409682.3:c.15T>G	2.37:g.162175351T>G			B3KNW2|O00176	Silent	SNP	pfam_JAB1_Mov34_MPN_PAD1,smart_JAB1_Mov34_MPN_PAD1	p.L5	ENST00000409682.3	37	c.15	CCDS46437.1	2																																																																																			PSMD14	-	NULL	ENSG00000115233		0.368	PSMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	PSMD14	HGNC	protein_coding	OTTHUMT00000332833.1	497	0.00	0	T	NM_005805		162175351	162175351	+1	no_errors	ENST00000409682	ensembl	human	known	69_37n	silent	244	21.04	65	SNP	1.000	G
SEMA5B	54437	genome.wustl.edu	37	3	122629793	122629793	+	Missense_Mutation	SNP	C	C	T	rs534828389		TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr3:122629793C>T	ENST00000357599.3	-	22	3577	c.3191G>A	c.(3190-3192)cGt>cAt	p.R1064H	SEMA5B_ENST00000451055.2_Missense_Mutation_p.R1118H|SEMA5B_ENST00000195173.4_3'UTR	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	1064					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		CTGGGACTGACGCTGGCAGTG	0.582													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15567	0.0		0.0	False		,,,				2504	0.0					dbGAP											0													102.0	92.0	95.0					3																	122629793		2203	4300	6503	-	-	-	SO:0001583	missense	0			AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.3191G>A	3.37:g.122629793C>T	ENSP00000350215:p.Arg1064His		A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	pfam_Semaphorin/CD100_Ag,pfam_Thrombospondin_1_rpt,superfamily_Semaphorin/CD100_Ag,superfamily_Thrombospondin_1_rpt,superfamily_Plexin-like_fold,smart_Semaphorin/CD100_Ag,smart_Plexin-like,smart_Thrombospondin_1_rpt,pfscan_Semaphorin/CD100_Ag,pfscan_Thrombospondin_1_rpt	p.R1118H	ENST00000357599.3	37	c.3353	CCDS35491.1	3	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.70|15.70	2.910812|2.910812	0.52439|0.52439	.|.	.|.	ENSG00000082684|ENSG00000082684	ENST00000357599;ENST00000418793;ENST00000451055;ENST00000393583|ENST00000451541	T;T;T|.	0.38887|.	1.11;1.15;1.23|.	4.86|4.86	3.93|3.93	0.45458|0.45458	.|.	0.307469|.	0.28653|.	N|.	0.014582|.	T|T	0.39145|0.39145	0.1067|0.1067	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	D|D	1|1	D;D|.	0.69078|.	0.997;0.995|.	P;P|.	0.62298|.	0.9;0.873|.	T|T	0.15665|0.15665	-1.0429|-1.0429	10|5	0.51188|.	T|.	0.08|.	.|.	11.1915|11.1915	0.48687|0.48687	0.0:0.9042:0.0:0.0958|0.0:0.9042:0.0:0.0958	.|.	970;1064|.	D3YTI7;Q9P283|.	.;SEM5B_HUMAN|.	H|I	1064;970;1118;1064|110	ENSP00000350215:R1064H;ENSP00000389588:R1118H;ENSP00000377208:R1064H|.	ENSP00000350215:R1064H|.	R|V	-|-	2|1	0|0	SEMA5B|SEMA5B	124112483|124112483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.989000|0.989000	0.77384|0.77384	2.193000|2.193000	0.42658|0.42658	1.162000|1.162000	0.42619|0.42619	0.655000|0.655000	0.94253|0.94253	CGT|GTC	SEMA5B	-	NULL	ENSG00000082684		0.582	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	SEMA5B	HGNC	protein_coding	OTTHUMT00000277165.1	105	0.00	0	C	NM_001031702		122629793	122629793	-1	no_errors	ENST00000451055	ensembl	human	known	69_37n	missense	59	22.37	17	SNP	1.000	T
SH3GL2	6456	genome.wustl.edu	37	9	17787384	17787384	+	Missense_Mutation	SNP	C	C	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr9:17787384C>T	ENST00000380607.4	+	5	458	c.338C>T	c.(337-339)gCa>gTa	p.A113V	SH3GL2_ENST00000537391.1_Missense_Mutation_p.A66V	NM_003026.2	NP_003017.1	Q99962	SH3G2_HUMAN	SH3-domain GRB2-like 2	113	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.|Binds and tubulates liposomes. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of receptor internalization (GO:0002090)|signal transduction (GO:0007165)|synaptic vesicle endocytosis (GO:0048488)	clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|skin(3)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(50;2.71e-10)|Lung(42;0.203)		CTAGGCCCAGCACTTGGTGAG	0.463																																						dbGAP											0													105.0	104.0	104.0					9																	17787384		2203	4300	6503	-	-	-	SO:0001583	missense	0			X99657	CCDS6483.1	9p22	2008-02-05			ENSG00000107295	ENSG00000107295			10831	protein-coding gene	gene with protein product		604465				9169142	Standard	XM_005251549		Approved	SH3P4, SH3D2A, CNSA2, EEN-B1	uc003zna.3	Q99962	OTTHUMG00000019601	ENST00000380607.4:c.338C>T	9.37:g.17787384C>T	ENSP00000369981:p.Ala113Val		B2R618|Q9NQK5	Missense_Mutation	SNP	pfam_BAR_dom,pfam_SH3_2,pfam_SH3_domain,pfam_BAR_dom-cont,superfamily_SH3_domain,smart_BAR_dom,smart_SH3_domain,pfscan_BAR_dom,pfscan_SH3_domain,prints_SH3_domain,prints_Spectrin_alpha_SH3	p.A113V	ENST00000380607.4	37	c.338	CCDS6483.1	9	.	.	.	.	.	.	.	.	.	.	C	36	5.637480	0.96693	.	.	ENSG00000107295	ENST00000397481;ENST00000380607;ENST00000537391	T;T	0.34667	1.35;1.35	5.85	5.85	0.93711	BAR (3);	0.000000	0.85682	D	0.000000	T	0.66915	0.2838	M	0.86028	2.79	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.98	T	0.70659	-0.4811	10	0.87932	D	0	.	20.1625	0.98139	0.0:1.0:0.0:0.0	.	78;113	B7Z7W3;Q99962	.;SH3G2_HUMAN	V	91;113;66	ENSP00000369981:A113V;ENSP00000443365:A66V	ENSP00000369981:A113V	A	+	2	0	SH3GL2	17777384	1.000000	0.71417	0.963000	0.40424	0.983000	0.72400	7.764000	0.85297	2.757000	0.94681	0.650000	0.86243	GCA	SH3GL2	-	pfam_BAR_dom,pfam_BAR_dom-cont,smart_BAR_dom,pfscan_BAR_dom	ENSG00000107295		0.463	SH3GL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SH3GL2	HGNC	protein_coding	OTTHUMT00000051796.1	136	0.00	0	C	NM_003026		17787384	17787384	+1	no_errors	ENST00000380607	ensembl	human	known	69_37n	missense	110	24.14	35	SNP	1.000	T
STARD9	57519	genome.wustl.edu	37	15	42984870	42984870	+	Silent	SNP	C	C	T			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	C	C					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr15:42984870C>T	ENST00000290607.7	+	23	11151	c.11094C>T	c.(11092-11094)ctC>ctT	p.L3698L		NM_020759.2	NP_065810.2	Q9P2P6	STAR9_HUMAN	StAR-related lipid transfer (START) domain containing 9	3698					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spindle assembly (GO:0051225)	centriole (GO:0005814)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|lipid binding (GO:0008289)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TTGGGAGTCTCTCCCAGCCAG	0.557																																						dbGAP											0													48.0	59.0	56.0					15																	42984870		692	1590	2282	-	-	-	SO:0001819	synonymous_variant	0			AB037721	CCDS53935.1	15q15.2	2013-10-16	2007-08-16		ENSG00000159433	ENSG00000159433		"""StAR-related lipid transfer (START) domain containing"""	19162	protein-coding gene	gene with protein product		614642	"""START domain containing 9"""			10718198	Standard	NM_020759		Approved	KIAA1300	uc010udj.2	Q9P2P6	OTTHUMG00000175799	ENST00000290607.7:c.11094C>T	15.37:g.42984870C>T			Q68DG2|Q6AI01|Q6ZWK0|Q9UF70	Silent	SNP	pfam_Kinesin_motor_dom,pfam_START_lipid-bd,pfam_FHA_dom,superfamily_SMAD_FHA_domain,smart_Kinesin_motor_dom,smart_FHA_dom,pfscan_START_lipid-bd,pfscan_Kinesin_motor_dom,prints_Kinesin_motor_dom	p.L3698	ENST00000290607.7	37	c.11094	CCDS53935.1	15																																																																																			STARD9	-	NULL	ENSG00000159433		0.557	STARD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	STARD9	HGNC	protein_coding	OTTHUMT00000431094.1	81	0.00	0	C			42984870	42984870	+1	no_errors	ENST00000290607	ensembl	human	known	69_37n	silent	27	34.15	14	SNP	0.999	T
TECPR1	25851	genome.wustl.edu	37	7	97847315	97847315	+	Frame_Shift_Del	DEL	G	G	-			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr7:97847315delG	ENST00000447648.2	-	24	3496	c.3197delC	c.(3196-3198)ccgfs	p.P1066fs	TECPR1_ENST00000379795.3_Frame_Shift_Del_p.P1068fs			Q7Z6L1	TCPR1_HUMAN	tectonin beta-propeller repeat containing 1	1066					autophagic vacuole fusion (GO:0000046)|autophagy (GO:0006914)	autophagic vacuole membrane (GO:0000421)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(2)|endometrium(8)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						GGAGCCCTGCGGGTAGCTGGG	0.662																																						dbGAP											0													21.0	25.0	23.0					7																	97847315		1935	4107	6042	-	-	-	SO:0001589	frameshift_variant	0				CCDS47648.1	7q21.3	2009-01-30			ENSG00000205356	ENSG00000205356			22214	protein-coding gene	gene with protein product		614781					Standard	NM_015395		Approved	DKFZP434B0335, FLJ23419, FLJ90593, KIAA1358	uc003upg.4	Q7Z6L1	OTTHUMG00000154273	ENST00000447648.2:c.3197delC	7.37:g.97847315delG	ENSP00000404923:p.Pro1066fs		A8KAD1|B3KPZ1|C9J024|F5GX57|Q96EB0|Q9P2I9|Q9UFR6	Frame_Shift_Del	DEL	pfam_Beta-propeller_rpt_TECPR,superfamily_Reg_csome_cond/b-lactamase_inh,smart_Beta-propeller_rpt_TECPR,smart_Peroxin/Ferlin	p.P1068fs	ENST00000447648.2	37	c.3203	CCDS47648.1	7																																																																																			TECPR1	-	pfam_Beta-propeller_rpt_TECPR	ENSG00000205356		0.662	TECPR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	TECPR1	HGNC	protein_coding	OTTHUMT00000334661.1	23	0.00	0	G	NM_015395		97847315	97847315	-1	no_errors	ENST00000379795	ensembl	human	known	69_37n	frame_shift_del	11	15.38	2	DEL	1.000	-
TRABD2A	129293	genome.wustl.edu	37	2	85097825	85097825	+	Nonsense_Mutation	SNP	G	G	A			TCGA-AN-A04A-01A-21W-A050-09	TCGA-AN-A04A-10A-01W-A055-09	G	G					Unknown	Untested	Somatic	Phase_IV	WXS	none	1		Illumina GAIIx	7e8f250c-6162-4049-8559-5bfdf054b021	2761c6e7-affc-4ffe-a72a-1d1203d574c4	g.chr2:85097825G>A	ENST00000409520.2	-	2	235	c.193C>T	c.(193-195)Cga>Tga	p.R65*	TRABD2A_ENST00000409133.1_Nonsense_Mutation_p.R65*|TRABD2A_ENST00000335459.5_Nonsense_Mutation_p.R65*	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	65					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										TCCCAAACTCGGGTGTACGGG	0.488																																						dbGAP											0													25.0	26.0	26.0					2																	85097825		1930	4125	6055	-	-	-	SO:0001587	stop_gained	0			BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.193C>T	2.37:g.85097825G>A	ENSP00000387075:p.Arg65*		B4DKK8|I6UMB9	Nonsense_Mutation	SNP	NULL	p.R65*	ENST00000409520.2	37	c.193		2	.	.	.	.	.	.	.	.	.	.	G	19.72	3.880760	0.72294	.	.	ENSG00000186854	ENST00000335459;ENST00000409520;ENST00000409133	.	.	.	3.66	2.73	0.32206	.	0.184388	0.34460	N	0.003943	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.537	0.39229	0.0:0.0:0.7787:0.2213	.	.	.	.	X	65	.	ENSP00000335004:R65X	R	-	1	2	C2orf89	84951336	1.000000	0.71417	0.217000	0.23759	0.468000	0.32798	4.261000	0.58841	0.681000	0.31386	0.455000	0.32223	CGA	TRABD2A	-	NULL	ENSG00000186854		0.488	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	TRABD2A	HGNC	protein_coding		36	0.00	0	G	NM_001080824		85097825	85097825	-1	no_errors	ENST00000409520	ensembl	human	known	69_37n	nonsense	35	27.08	13	SNP	0.978	A
