#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
ROBO3	64221	broad.mit.edu	37	11	124739959	124739959	+	Missense_Mutation	SNP	T	T	C			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr11:124739959T>C	ENST00000397801.1	+	4	953	c.761T>C	c.(760-762)gTa>gCa	p.V254A	ROBO3_ENST00000538940.1_Missense_Mutation_p.V232A	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN	roundabout, axon guidance receptor, homolog 3 (Drosophila)	254					axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|neuron migration (GO:0001764)	axon (GO:0030424)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)		GAAGTCATGGTACTGGGTAGG	0.522																																						ENST00000397801.1																			0				breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	35						c.(760-762)gTa>gCa		roundabout, axon guidance receptor, homolog 3 (Drosophila)							101.0	117.0	112.0					11																	124739959		2049	4199	6248	SO:0001583	missense	64221				axon midline choice point recognition	integral to membrane	receptor activity	g.chr11:124739959T>C	AK024697	CCDS44755.1	11q24	2013-02-11	2001-11-28		ENSG00000154134	ENSG00000154134		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13433	protein-coding gene	gene with protein product		608630	"""roundabout (axon guidance receptor, Drosophila) homolog 3"", ""horizontal gaze palsy with progressive scoliosis"""	HGPPS		15105459	Standard	NM_022370		Approved	RBIG1, FLJ21044, HGPS	uc001qbc.3	Q96MS0	OTTHUMG00000165934	ENST00000397801.1:c.761T>C	11.37:g.124739959T>C	ENSP00000380903:p.Val254Ala					ROBO3_ENST00000538940.1_Missense_Mutation_p.V232A	p.V254A	NM_022370.3	NP_071765.2	Q96MS0	ROBO3_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0296)	4	953	+	all_hematologic(175;0.215)	Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|Breast(109;0.0481)|all_neural(223;0.112)	254						Missense_Mutation	SNP	ENST00000397801.1	37	c.761T>C	CCDS44755.1	.	.	.	.	.	.	.	.	.	.	T	17.22	3.334680	0.60853	.	.	ENSG00000154134	ENST00000397801;ENST00000538940	T;T	0.62364	0.03;0.03	4.72	4.72	0.59763	Immunoglobulin-like fold (1);	0.000000	0.30639	U	0.009188	D	0.84534	0.5493	H	0.95079	3.62	0.80722	D	1	D	0.69078	0.997	D	0.83275	0.996	D	0.89281	0.3612	10	0.87932	D	0	.	14.1511	0.65384	0.0:0.0:0.0:1.0	.	254	Q96MS0	ROBO3_HUMAN	A	254;232	ENSP00000380903:V254A;ENSP00000441797:V232A	ENSP00000380903:V254A	V	+	2	0	ROBO3	124245169	1.000000	0.71417	0.459000	0.27081	0.126000	0.20510	7.902000	0.87389	1.895000	0.54865	0.379000	0.24179	GTA		0.522	ROBO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387091.1	XM_370663		19	18	0	0	0	1	0	19	18				
KIT	3815	broad.mit.edu	37	4	55575675	55575675	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr4:55575675G>A	ENST00000288135.5	+	7	1298	c.1201G>A	c.(1201-1203)Gct>Act	p.A401T		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	401	Ig-like C2-type 4.				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)	TGACGTCAATGCTGCCATAGC	0.368		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																													ENST00000288135.5		1	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	"""Mis, O"""	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	Piebald trait	"""L, M, O, E"""		"""GIST, epithelioma"""	"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""		0				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						c.(1201-1203)Gct>Act		v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	Dasatinib(DB01254)|Imatinib(DB00619)|Sorafenib(DB00398)|Sunitinib(DB01268)						110.0	103.0	106.0					4																	55575675		2203	4300	6503	SO:0001583	missense	3815	Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	male gonad development|transmembrane receptor protein tyrosine kinase signaling pathway	extracellular space|integral to membrane	ATP binding|protein binding|receptor signaling protein tyrosine kinase activity	g.chr4:55575675G>A	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.1201G>A	4.37:g.55575675G>A	ENSP00000288135:p.Ala401Thr						p.A401T	NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	7	1298	+	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)		401			Ig-like C2-type 4.		B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Missense_Mutation	SNP	ENST00000288135.5	37	c.1201G>A	CCDS3496.1	.	.	.	.	.	.	.	.	.	.	G	5.307	0.242044	0.10077	.	.	ENSG00000157404	ENST00000288135;ENST00000412167;ENST00000536403	T;T	0.56275	0.47;0.47	5.89	0.14	0.14804	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.445683	0.21355	N	0.075914	T	0.39279	0.1072	L	0.39898	1.24	0.26038	N	0.981645	B;B	0.11235	0.003;0.004	B;B	0.10450	0.005;0.004	T	0.29671	-1.0004	10	0.34782	T	0.22	.	10.0776	0.42370	0.0818:0.0:0.4179:0.5003	.	401;401	P10721-2;P10721	.;KIT_HUMAN	T	401	ENSP00000288135:A401T;ENSP00000390987:A401T	ENSP00000288135:A401T	A	+	1	0	KIT	55270432	0.807000	0.29009	0.296000	0.24974	0.009000	0.06853	0.954000	0.29175	0.229000	0.21039	-0.270000	0.10280	GCT		0.368	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1			4	84	0	0	0	1	0	4	84				
ARID3A	1820	broad.mit.edu	37	19	964334	964334	+	Missense_Mutation	SNP	C	C	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr19:964334C>A	ENST00000263620.3	+	5	1180	c.853C>A	c.(853-855)Ctc>Atc	p.L285I		NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	285	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.					cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAGGGCGGCCTCGTGGAGGT	0.612																																					Pancreas(29;54 1022 32760 50921)	ENST00000263620.3																			0				breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10						c.(853-855)Ctc>Atc		AT rich interactive domain 3A (BRIGHT-like)							163.0	121.0	135.0					19																	964334		2203	4299	6502	SO:0001583	missense	1820					cytoplasm|nucleus	DNA binding|sequence-specific DNA binding transcription factor activity	g.chr19:964334C>A	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.853C>A	19.37:g.964334C>A	ENSP00000263620:p.Leu285Ile						p.L285I	NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)	5	1180	+		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)	285			ARID.		Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Missense_Mutation	SNP	ENST00000263620.3	37	c.853C>A	CCDS12050.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076111	0.76415	.	.	ENSG00000116017	ENST00000263620	T	0.64438	-0.1	4.5	4.5	0.54988	ARID/BRIGHT DNA-binding domain (5);	0.072721	0.56097	D	0.000026	T	0.73544	0.3600	M	0.66939	2.045	0.80722	D	1	P	0.47302	0.893	D	0.65773	0.938	T	0.75428	-0.3321	10	0.72032	D	0.01	-1.5464	8.525	0.33300	0.0:0.8916:0.0:0.1084	.	285	Q99856	ARI3A_HUMAN	I	285	ENSP00000263620:L285I	ENSP00000263620:L285I	L	+	1	0	ARID3A	915334	0.998000	0.40836	1.000000	0.80357	0.981000	0.71138	3.727000	0.54984	2.061000	0.61500	0.561000	0.74099	CTC		0.612	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224		3	24	1	0	0.150653	1	0.150653	3	24				
TUBBP5	643224	broad.mit.edu	37	9	141070173	141070173	+	RNA	SNP	G	G	A	rs181671405		TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr9:141070173G>A	ENST00000503395.1	+	0	1253									tubulin, beta pseudogene 5																		GGTGAGCTGCGGGCGAGGACT	0.647																																						ENST00000503395.1																			0																																																			643224							g.chr9:141070173G>A	AF355123		9q34.3	2012-03-06	2005-11-15		ENSG00000159247	ENSG00000159247			23674	pseudogene	pseudogene			"""tubulin, beta polypeptide pseudogene 5"""			11731935	Standard	NR_027156		Approved		uc010ncq.3		OTTHUMG00000021001		9.37:g.141070173G>A														0	1253	+									RNA	SNP	ENST00000503395.1	37																																																																																						0.647	TUBBP5-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000373087.1	NR_027156		3	32	0	0	0	1	0	3	32				
PAOX	196743	broad.mit.edu	37	10	135193918	135193918	+	Missense_Mutation	SNP	C	C	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr10:135193918C>A	ENST00000278060.5	+	2	680	c.597C>A	c.(595-597)agC>agA	p.S199R	PAOX_ENST00000357296.3_Missense_Mutation_p.S199R|PAOX_ENST00000480071.2_Missense_Mutation_p.S199R|AL360181.1_ENST00000597657.1_5'Flank|PAOX_ENST00000368539.4_Intron|PAOX_ENST00000368535.2_3'UTR	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN	polyamine oxidase (exo-N4-amino)	337					cellular nitrogen compound metabolic process (GO:0034641)|oxidation-reduction process (GO:0055114)|polyamine biosynthetic process (GO:0006596)|polyamine catabolic process (GO:0006598)|polyamine metabolic process (GO:0006595)|positive regulation of spermidine biosynthetic process (GO:1901307)|putrescine biosynthetic process (GO:0009446)|putrescine catabolic process (GO:0009447)|small molecule metabolic process (GO:0044281)|spermidine catabolic process (GO:0046203)|spermine catabolic process (GO:0046208)|xenobiotic metabolic process (GO:0006805)	peroxisomal matrix (GO:0005782)	N(1),N(12)-diacetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052899)|N1-acetylspermidine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052904)|N1-acetylspermine:oxygen oxidoreductase (3-acetamidopropanal-forming) activity (GO:0052903)|polyamine oxidase activity (GO:0046592)|receptor binding (GO:0005102)|spermidine:oxygen oxidoreductase (3-aminopropanal-forming) activity (GO:0052902)|spermine:oxygen oxidoreductase (spermidine-forming) activity (GO:0052901)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)		GCACCCACAGCATGGACCTGG	0.627																																						ENST00000278060.5																			0				cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(13)|ovary(1)|urinary_tract(2)	23						c.(595-597)agC>agA		polyamine oxidase (exo-N4-amino)							32.0	36.0	34.0					10																	135193918		2202	4300	6502	SO:0001583	missense	196743				polyamine biosynthetic process|xenobiotic metabolic process	peroxisomal matrix	polyamine oxidase activity	g.chr10:135193918C>A	BC032778	CCDS7682.1, CCDS7683.1, CCDS7684.1	10q26.3	2003-11-13			ENSG00000148832	ENSG00000148832			20837	protein-coding gene	gene with protein product		615853				12660232	Standard	NM_207127		Approved	PAO	uc001lmv.3	Q6QHF9	OTTHUMG00000019318	ENST00000278060.5:c.597C>A	10.37:g.135193918C>A	ENSP00000278060:p.Ser199Arg					PAOX_ENST00000357296.3_Missense_Mutation_p.S199R|PAOX_ENST00000480071.2_Missense_Mutation_p.S199R|PAOX_ENST00000368535.2_3'UTR|PAOX_ENST00000368539.4_Intron	p.S199R	NM_152911.2	NP_690875.1	Q6QHF9	PAOX_HUMAN		all cancers(32;4.39e-07)|OV - Ovarian serous cystadenocarcinoma(35;1.21e-06)|Epithelial(32;1.94e-06)	2	680	+		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)	337					D3DXI6|Q5VWY0|Q6QHF5|Q6QHF6|Q6QHF7|Q6QHF8|Q6QHG0|Q6QHG1|Q6QHG2|Q6QHG3|Q6QHG4|Q6QHG5|Q6QHG6|Q86WP9|Q8N555|Q8NCX3	Missense_Mutation	SNP	ENST00000278060.5	37	c.597C>A	CCDS7683.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.71|19.71	3.878960|3.878960	0.72294|0.72294	.|.	.|.	ENSG00000148832|ENSG00000148832	ENST00000368534|ENST00000368542;ENST00000278060;ENST00000357296;ENST00000480071	.|D;D;D	.|0.92545	.|-3.06;-3.06;-3.06	4.74|4.74	1.3|1.3	0.21679|0.21679	.|.	.|0.079629	.|0.85682	.|D	.|0.000000	.|D	.|0.94837	.|0.8332	M|M	0.83603|0.83603	2.65|2.65	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;0.997;0.996	.|D;D;D	.|0.75484	.|0.986;0.968;0.943	.|D	.|0.93085	.|0.6495	.|10	.|0.87932	.|D	.|0	.|-33.3414	7.2886|7.2886	0.26354|0.26354	0.0:0.5827:0.0:0.4173|0.0:0.5827:0.0:0.4173	.|.	.|199;199;199	.|Q6QHF9-5;Q6QHF9-4;Q6QHF9-2	.|.;.;.	.|R	-1|199	.|ENSP00000278060:S199R;ENSP00000349847:S199R;ENSP00000435514:S199R	.|ENSP00000278060:S199R	.|S	+|+	.|3	.|2	PAOX|PAOX	135043908|135043908	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.781000|2.781000	0.47750|0.47750	0.422000|0.422000	0.26005|0.26005	0.563000|0.563000	0.77884|0.77884	.|AGC		0.627	PAOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051146.2	NM_152911		3	34	1	0	0.004672	1	0.00486667	3	34				
LRRN2	10446	broad.mit.edu	37	1	204587794	204587794	+	Silent	SNP	G	G	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:204587794G>A	ENST00000367175.1	-	1	3539	c.1327C>T	c.(1327-1329)Ctg>Ttg	p.L443L	LRRN2_ENST00000367177.3_Silent_p.L443L|RP11-430C7.4_ENST00000453895.1_RNA|LRRN2_ENST00000367176.3_Silent_p.L443L|LRRN2_ENST00000496057.1_5'Flank			O75325	LRRN2_HUMAN	leucine rich repeat neuronal 2	443	Ig-like C2-type.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)			CGGCAATGCAGCACCATGCTC	0.632																																						ENST00000367175.1																			0				central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|liver(1)|lung(22)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	38						c.(1327-1329)Ctg>Ttg		leucine rich repeat neuronal 2							53.0	44.0	47.0					1																	204587794		2203	4300	6503	SO:0001819	synonymous_variant	10446				cell adhesion	integral to membrane	receptor activity	g.chr1:204587794G>A	AF030435	CCDS1448.1	1q32.1	2013-01-11	2007-01-31	2007-01-31	ENSG00000170382	ENSG00000170382		"""Immunoglobulin superfamily / I-set domain containing"""	16914	protein-coding gene	gene with protein product	"""leucine rich and ankyrin repeats 1"", ""fibronectin type III, immunoglobulin and leucine rich repeat domain 7"""	605492	"""leucine rich repeat neuronal 5"""	LRRN5		9662332	Standard	NM_006338		Approved	GAC1, LRANK1, FIGLER7	uc001hbf.1	O75325	OTTHUMG00000035989	ENST00000367175.1:c.1327C>T	1.37:g.204587794G>A						LRRN2_ENST00000367176.3_Silent_p.L443L|LRRN2_ENST00000367177.3_Silent_p.L443L	p.L443L			O75325	LRRN2_HUMAN	KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)		1	3539	-	all_cancers(21;0.0519)|Breast(84;0.112)|Prostate(682;0.19)		443			Ig-like C2-type.		B2R624|Q5T0Y0|Q6UXM0|Q8N182	Silent	SNP	ENST00000367175.1	37	c.1327C>T	CCDS1448.1																																																																																				0.632	LRRN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089894.1	NM_006338		3	30	0	0	0	1	0	3	30				
SYTL4	94121	broad.mit.edu	37	X	99945087	99945087	+	Missense_Mutation	SNP	T	T	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chrX:99945087T>A	ENST00000372989.1	-	10	1124	c.793A>T	c.(793-795)Atc>Ttc	p.I265F	SYTL4_ENST00000455616.1_Missense_Mutation_p.I265F|SYTL4_ENST00000263033.5_Missense_Mutation_p.I265F|SYTL4_ENST00000454200.2_Missense_Mutation_p.I266F|SYTL4_ENST00000276141.6_Missense_Mutation_p.I265F|SYTL4_ENST00000372981.1_Missense_Mutation_p.I265F	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	265					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GGCCTGAGGATTTTTCTGGTG	0.443																																						ENST00000372981.1																			0				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27						c.(793-795)Atc>Ttc		synaptotagmin-like 4	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)						85.0	74.0	77.0					X																	99945087		2203	4300	6503	SO:0001583	missense	94121				exocytosis|intracellular protein transport	extrinsic to membrane|plasma membrane|synaptic vesicle|transport vesicle membrane	neurexin binding|phospholipid binding|Rab GTPase binding|transporter activity|zinc ion binding	g.chrX:99945087T>A		CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.793A>T	X.37:g.99945087T>A	ENSP00000362080:p.Ile265Phe					SYTL4_ENST00000454200.2_Missense_Mutation_p.I266F|SYTL4_ENST00000263033.5_Missense_Mutation_p.I265F|SYTL4_ENST00000372989.1_Missense_Mutation_p.I265F|SYTL4_ENST00000276141.6_Missense_Mutation_p.I265F|SYTL4_ENST00000455616.1_Missense_Mutation_p.I265F	p.I265F			Q96C24	SYTL4_HUMAN			8	979	-			265					Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Missense_Mutation	SNP	ENST00000372989.1	37	c.793A>T	CCDS14472.1	.	.	.	.	.	.	.	.	.	.	t	6.098	0.386359	0.11524	.	.	ENSG00000102362	ENST00000372989;ENST00000455616;ENST00000454200;ENST00000276141;ENST00000263033;ENST00000372981	T;T;T;T;T;T	0.64991	2.01;2.01;2.0;2.01;2.01;-0.13	5.7	1.65	0.23941	.	0.798927	0.12227	N	0.487785	T	0.46190	0.1380	L	0.40543	1.245	0.19300	N	0.999974	B;B	0.22909	0.077;0.001	B;B	0.15052	0.012;0.002	T	0.26538	-1.0100	9	.	.	.	-6.0553	4.81	0.13339	0.0:0.4154:0.1704:0.4141	.	265;265	Q96C24-2;Q96C24	.;SYTL4_HUMAN	F	265;265;266;265;265;265	ENSP00000362080:I265F;ENSP00000390252:I265F;ENSP00000403556:I266F;ENSP00000276141:I265F;ENSP00000263033:I265F;ENSP00000362072:I265F	.	I	-	1	0	SYTL4	99831743	0.394000	0.25246	0.983000	0.44433	0.987000	0.75469	-0.131000	0.10482	0.299000	0.22661	0.478000	0.44815	ATC		0.443	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1	NM_080737		8	40	0	0	0	1	0	8	40				
PIF1	80119	broad.mit.edu	37	15	65108897	65108897	+	Missense_Mutation	SNP	G	G	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr15:65108897G>A	ENST00000268043.4	-	12	1836	c.1742C>T	c.(1741-1743)gCc>gTc	p.A581V	PIF1_ENST00000559239.1_Missense_Mutation_p.A581V|PIF1_ENST00000333425.6_Missense_Mutation_p.A581V					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						CCGAGAAAGGGCCACATAGGC	0.622																																						ENST00000268043.4																			0				kidney(1)|lung(1)	2						c.(1741-1743)gCc>gTc		PIF1 5'-to-3' DNA helicase							49.0	49.0	49.0					15																	65108897		2202	4299	6501	SO:0001583	missense	80119				negative regulation of telomerase activity|regulation of telomere maintenance|viral genome replication	nuclear chromosome, telomeric region	ATP binding|ATP-dependent 5'-3' DNA helicase activity|ATP-dependent 5'-3' DNA/RNA helicase activity|magnesium ion binding|single-stranded DNA-dependent ATP-dependent DNA helicase activity|telomeric DNA binding	g.chr15:65108897G>A	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1742C>T	15.37:g.65108897G>A	ENSP00000268043:p.Ala581Val					PIF1_ENST00000559239.1_Missense_Mutation_p.A581V|PIF1_ENST00000333425.6_Missense_Mutation_p.A581V	p.A581V			Q9H611	PIF1_HUMAN			12	1836	-			581			Hydrolyzes ATP in the presence of both magnesium and single-stranded DNA; weak activity in the presence of RNA or double-stranded DNA; No unwinding activity.			Missense_Mutation	SNP	ENST00000268043.4	37	c.1742C>T	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	G	36	5.740822	0.96873	.	.	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.38560	1.13;1.13	5.73	5.73	0.89815	.	0.000000	0.85682	D	0.000000	T	0.74275	0.3695	M	0.93462	3.42	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80999	-0.1131	10	0.87932	D	0	-23.7146	17.3974	0.87450	0.0:0.0:1.0:0.0	.	581	Q9H611	PIF1_HUMAN	V	581	ENSP00000268043:A581V;ENSP00000328174:A581V	ENSP00000268043:A581V	A	-	2	0	PIF1	62895950	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.797000	0.99108	2.706000	0.92434	0.655000	0.94253	GCC		0.622	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049		8	60	0	0	0	1	0	8	60				
SALL4	57167	broad.mit.edu	37	20	50407310	50407310	+	Missense_Mutation	SNP	C	C	T			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr20:50407310C>T	ENST00000217086.4	-	2	1823	c.1712G>A	c.(1711-1713)tGc>tAc	p.C571Y	SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron|SALL4_ENST00000483130.1_5'Flank	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	571					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GACTCGGTGGCAAATGAGACA	0.547																																						ENST00000217086.4																			0				endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						c.(1711-1713)tGc>tAc		spalt-like transcription factor 4							130.0	111.0	117.0					20																	50407310		2203	4300	6503	SO:0001583	missense	57167				transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr20:50407310C>T	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.1712G>A	20.37:g.50407310C>T	ENSP00000217086:p.Cys571Tyr					SALL4_ENST00000395997.3_Intron|SALL4_ENST00000371539.3_Intron	p.C571Y	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN			2	1823	-			571					A2A2D8|Q540H3|Q6Y8G6	Missense_Mutation	SNP	ENST00000217086.4	37	c.1712G>A	CCDS13438.1	.	.	.	.	.	.	.	.	.	.	C	21.1	4.100425	0.76983	.	.	ENSG00000101115	ENST00000217086	T	0.57752	0.38	5.59	5.59	0.84812	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.49916	D	0.000133	T	0.78685	0.4322	M	0.88842	2.985	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.82402	-0.0475	10	0.87932	D	0	-20.1912	19.5703	0.95409	0.0:1.0:0.0:0.0	.	571	Q9UJQ4	SALL4_HUMAN	Y	571	ENSP00000217086:C571Y	ENSP00000217086:C571Y	C	-	2	0	SALL4	49840717	1.000000	0.71417	0.998000	0.56505	0.970000	0.65996	7.813000	0.86123	2.620000	0.88729	0.650000	0.86243	TGC		0.547	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3			50	58	0	0	0	1	0	50	58				
MAGEA12	4111	broad.mit.edu	37	X	151896589	151896589	+	IGR	SNP	C	C	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chrX:151896589C>A	ENST00000357916.4	-	0	1664				CSAG4_ENST00000361201.4_RNA	NM_005367.5	NP_005358.2	P43365	MAGAC_HUMAN	melanoma antigen family A, 12									p.L11F(1)		breast(5)|large_intestine(5)|liver(1)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					GGTTGTTGGACAATGGGCTGG	0.557																																						ENST00000361201.4																			1	Substitution - Missense(1)	p.L11F(1)	kidney(1)	endometrium(2)|kidney(2)|lung(1)	5																																												SO:0001628	intergenic_variant	100130935							g.chrX:151896589C>A		CCDS76048.1	Xq28	2009-03-13			ENSG00000213401	ENSG00000213401			6799	protein-coding gene	gene with protein product	"""cancer/testis antigen family 1, member 12"""	300177		MAGE12		8575766	Standard	NM_001166386		Approved	CT1.12	uc004fgc.3	P43365	OTTHUMG00000022650		X.37:g.151896589C>A								NR_073432.1						0	351	-								Q9NSD3	RNA	SNP	ENST00000357916.4	37		CCDS14710.1																																																																																				0.557	MAGEA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058764.1	NM_005367		4	122	1	0	0.000602214	1	0.000716922	4	122				
KBTBD8	84541	broad.mit.edu	37	3	67054375	67054375	+	Silent	SNP	G	G	T			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr3:67054375G>T	ENST00000417314.2	+	3	1033	c.984G>T	c.(982-984)ggG>ggT	p.G328G	KBTBD8_ENST00000295568.4_Silent_p.G302G|KBTBD8_ENST00000460576.1_Intron			Q8NFY9	KBTB8_HUMAN	kelch repeat and BTB (POZ) domain containing 8	328						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20		Lung NSC(201;0.0765)		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)		GAGAAGTTGGGATTCTTGTAT	0.433																																						ENST00000295568.4																			0				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)	20						c.(904-906)ggG>ggT		kelch repeat and BTB (POZ) domain containing 8							141.0	135.0	137.0					3																	67054375		2203	4300	6503	SO:0001819	synonymous_variant	84541							g.chr3:67054375G>T	AF385438	CCDS2906.1, CCDS2906.2	3p14	2013-01-08			ENSG00000163376	ENSG00000163376		"""BTB/POZ domain containing"""	30691	protein-coding gene	gene with protein product	"""T-cell activation kelch repeat protein"""					11347906	Standard	NM_032505		Approved	TA-KRP, KIAA1842	uc003dmy.3	Q8NFY9	OTTHUMG00000158779	ENST00000417314.2:c.984G>T	3.37:g.67054375G>T						KBTBD8_ENST00000460576.1_Intron|KBTBD8_ENST00000417314.2_Silent_p.G328G	p.G302G	NM_032505.2	NP_115894.2	Q8NFY9	KBTB8_HUMAN		BRCA - Breast invasive adenocarcinoma(55;6.02e-06)|KIRC - Kidney renal clear cell carcinoma(39;0.105)|Kidney(39;0.125)	3	1037	+		Lung NSC(201;0.0765)	328					B4DTW6|Q96JI5	Silent	SNP	ENST00000417314.2	37	c.906G>T	CCDS2906.2																																																																																				0.433	KBTBD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352189.1	NM_032505		11	103	1	0	0.000978159	1	0.00111154	11	103				
EHD2	30846	broad.mit.edu	37	19	48239781	48239781	+	Silent	SNP	G	G	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr19:48239781G>A	ENST00000263277.3	+	5	1322	c.1071G>A	c.(1069-1071)caG>caA	p.Q357Q	EHD2_ENST00000538399.1_Silent_p.Q221Q|EHD2_ENST00000540884.1_3'UTR	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN	EH-domain containing 2	357					blood coagulation (GO:0007596)|cortical actin cytoskeleton organization (GO:0030866)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein localization to plasma membrane (GO:0072659)	caveola (GO:0005901)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|nucleic acid binding (GO:0003676)			endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)		CTGATTGCCAGAAAATGCAGG	0.532																																						ENST00000263277.3																			0				endometrium(3)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	19						c.(1069-1071)caG>caA		EH-domain containing 2							76.0	72.0	73.0					19																	48239781		2203	4300	6503	SO:0001819	synonymous_variant	30846				blood coagulation|endocytic recycling	nucleus|plasma membrane|recycling endosome membrane	ATP binding|calcium ion binding|GTP binding|GTPase activity|nucleic acid binding	g.chr19:48239781G>A	AF181263	CCDS12704.1	19q13.3	2014-08-12			ENSG00000024422	ENSG00000024422		"""EF-hand domain containing"""	3243	protein-coding gene	gene with protein product		605890		PAST2		10673336	Standard	NM_014601		Approved		uc002phj.4	Q9NZN4	OTTHUMG00000183266	ENST00000263277.3:c.1071G>A	19.37:g.48239781G>A						EHD2_ENST00000540884.1_3'UTR|EHD2_ENST00000538399.1_Silent_p.Q221Q	p.Q357Q	NM_014601.3	NP_055416.2	Q9NZN4	EHD2_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.000336)|all cancers(93;0.000415)|Epithelial(262;0.0132)|GBM - Glioblastoma multiforme(486;0.0537)	5	1322	+		all_cancers(25;6.74e-07)|all_lung(116;2.02e-05)|Lung NSC(112;3.77e-05)|all_epithelial(76;4.89e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)	357					B2RDH9|B4DNU6|Q96CB6	Silent	SNP	ENST00000263277.3	37	c.1071G>A	CCDS12704.1																																																																																				0.532	EHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465851.1			16	20	0	0	0	1	0	16	20				
CROCCP3	114819	broad.mit.edu	37	1	16812092	16812092	+	RNA	SNP	G	G	A	rs3895546		TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:16812092G>A	ENST00000263511.4	-	0	1459					NR_023386.1		Q8IVE0	CROL2_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 3						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											AGTGAGGTCCGTGTTGACCTG	0.597																																						ENST00000263511.4																			0																																																			114819							g.chr1:16812092G>A	AB067509		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000080947	ENSG00000080947			29405	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 2"""	CROCCL2		11572484	Standard	NR_023386		Approved	KIAA1922	uc001ayt.2	Q8IVE0	OTTHUMG00000037885		1.37:g.16812092G>A								NR_023386.1						0	1459	-								Q96PW6	RNA	SNP	ENST00000263511.4	37																																																																																						0.597	CROCCP3-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000458172.1	XM_057040		11	7	0	0	0	1	0	11	7				
PANX3	116337	broad.mit.edu	37	11	124489205	124489205	+	Silent	SNP	C	C	A	rs575063752		TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr11:124489205C>A	ENST00000284288.2	+	4	620	c.553C>A	c.(553-555)Cga>Aga	p.R185R		NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN	pannexin 3	185					cell-cell signaling (GO:0007267)|ion transport (GO:0006811)|protein hexamerization (GO:0034214)|transmembrane transport (GO:0055085)	gap junction (GO:0005921)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gap junction hemi-channel activity (GO:0055077)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)		TCGGAAAGAACGATACTTTGA	0.488																																						ENST00000284288.2																			0				NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|urinary_tract(1)	26						c.(553-555)Cga>Aga		pannexin 3							123.0	101.0	108.0					11																	124489205		2201	4299	6500	SO:0001819	synonymous_variant	116337				protein hexamerization	gap junction|integral to membrane	gap junction hemi-channel activity|ion channel activity	g.chr11:124489205C>A	AF406650	CCDS8447.1	11q24.2	2011-12-02			ENSG00000154143	ENSG00000154143		"""Ion channels / Pannexins"""	20573	protein-coding gene	gene with protein product		608422					Standard	NM_052959		Approved	Px3	uc001qah.3	Q96QZ0	OTTHUMG00000165925	ENST00000284288.2:c.553C>A	11.37:g.124489205C>A							p.R185R	NM_052959.2	NP_443191.1	Q96QZ0	PANX3_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0219)	4	620	+	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	185						Silent	SNP	ENST00000284288.2	37	c.553C>A	CCDS8447.1																																																																																				0.488	PANX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387064.1			21	28	1	0	3.5997e-14	1	4.49962e-14	21	28				
MTR	4548	broad.mit.edu	37	1	237024423	237024423	+	Splice_Site	SNP	A	A	T			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:237024423A>T	ENST00000366577.5	+	20	2437		c.e20-1		MTR_ENST00000535889.1_Intron	NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase						cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|methylation (GO:0032259)|nervous system development (GO:0007399)|pteridine-containing compound metabolic process (GO:0042558)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	cobalamin binding (GO:0031419)|methionine synthase activity (GO:0008705)|S-adenosylmethionine-homocysteine S-methyltransferase activity (GO:0008898)|zinc ion binding (GO:0008270)	p.?(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)	tgtcttttttAGGGCATTGAA	0.323																																						ENST00000366577.5																			1	Unknown(1)	p.?(1)	lung(1)	breast(4)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	67						c.e20-1		5-methyltetrahydrofolate-homocysteine methyltransferase	Hydroxocobalamin(DB00200)|L-Methionine(DB00134)|Tetrahydrofolic acid(DB00116)						28.0	28.0	28.0					1																	237024423		2190	4294	6484	SO:0001630	splice_region_variant	4548				nervous system development|xenobiotic metabolic process	cytosol	cobalamin binding|homocysteine S-methyltransferase activity|methionine synthase activity|protein binding|zinc ion binding	g.chr1:237024423A>T	U73338	CCDS1614.1, CCDS73054.1	1q43	2011-05-12			ENSG00000116984	ENSG00000116984	2.1.1.13		7468	protein-coding gene	gene with protein product		156570				8968735	Standard	NM_000254		Approved	cblG	uc001hyi.4	Q99707	OTTHUMG00000040060	ENST00000366577.5:c.2044-1A>T	1.37:g.237024423A>T						MTR_ENST00000535889.1_Intron		NM_000254.2	NP_000245.2	Q99707	METH_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0106)	KIRC - Kidney renal clear cell carcinoma(1967;0.248)	20	2437	+	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;2.79e-22)|all_epithelial(177;4.84e-14)|Breast(1374;0.00123)|Prostate(94;0.0181)|Lung SC(1967;0.0262)|Acute lymphoblastic leukemia(190;0.117)						A1L4N8|A9Z1W4|B9EGF7|Q99713|Q99723	Splice_Site	SNP	ENST00000366577.5	37		CCDS1614.1	.	.	.	.	.	.	.	.	.	.	A	19.94	3.919996	0.73098	.	.	ENSG00000116984	ENST00000417743;ENST00000366577;ENST00000366576	.	.	.	5.43	5.43	0.79202	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6414	0.77006	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MTR	235091046	1.000000	0.71417	0.990000	0.47175	0.822000	0.46500	9.300000	0.96151	2.279000	0.76181	0.533000	0.62120	.		0.323	MTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096632.2	NM_000254	Intron	6	17	0	0	0	1	0	6	17				
PRX	57716	broad.mit.edu	37	19	40900182	40900182	+	Silent	SNP	C	C	T	rs139624657|rs142743305		TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr19:40900182C>T	ENST00000324001.7	-	7	4347	c.4077G>A	c.(4075-4077)gaG>gaA	p.E1359E	PRX_ENST00000291825.7_3'UTR	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	periaxin	1359	Poly-Glu.		Missing. {ECO:0000269|PubMed:11133365}.		axon ensheathment (GO:0008366)|cell death (GO:0008219)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47			Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)			TGCcctcttcctcctcctcct	0.697																																						ENST00000324001.7																			0				breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|urinary_tract(9)	47						c.(4075-4077)gaG>gaA		periaxin							16.0	16.0	16.0					19																	40900182		2198	4297	6495	SO:0001819	synonymous_variant	57716				axon ensheathment	cytoplasm|nucleus|plasma membrane	protein binding	g.chr19:40900182C>T	AB046840	CCDS12556.1, CCDS33028.1	19q13.2	2014-09-17				ENSG00000105227			13797	protein-coding gene	gene with protein product		605725				10839370, 9143514	Standard	NM_181882		Approved	KIAA1620	uc002onr.3	Q9BXM0		ENST00000324001.7:c.4077G>A	19.37:g.40900182C>T						PRX_ENST00000291825.7_3'UTR	p.E1359E	NM_181882.2	NP_870998.2	Q9BXM0	PRAX_HUMAN	Lung(22;6.24e-05)|LUSC - Lung squamous cell carcinoma(20;0.000384)		7	4347	-			1359		Missing.	Poly-Glu.		Q9BXL9|Q9HCF2	Silent	SNP	ENST00000324001.7	37	c.4077G>A	CCDS33028.1																																																																																				0.697	PRX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462582.1	NM_020956		3	19	0	0	0	1	0	3	19				
RBM17	84991	broad.mit.edu	37	10	6154185	6154185	+	Silent	SNP	G	G	A	rs148263630	byFrequency	TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr10:6154185G>A	ENST00000446108.1	+	8	1361	c.717G>A	c.(715-717)gcG>gcA	p.A239A	RBM17_ENST00000379888.4_Silent_p.A239A	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN	RNA binding motif protein 17	239	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				alternative mRNA splicing, via spliceosome (GO:0000380)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						GCACGGTGGCGCACAAGATCA	0.557													G|||	7	0.00139776	0.0	0.0	5008	,	,		19150	0.0		0.001	False		,,,				2504	0.0061					ENST00000446108.1																			0				NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(2)	19						c.(715-717)gcG>gcA		RNA binding motif protein 17		G	,	1,4405	2.1+/-5.4	0,1,2202	61.0	57.0	58.0		717,717	-10.8	0.7	10	dbSNP_134	58	17,8583	11.9+/-42.8	1,15,4284	no	coding-synonymous,coding-synonymous	RBM17	NM_001145547.1,NM_032905.4	,	1,16,6486	AA,AG,GG		0.1977,0.0227,0.1384	,	239/402,239/402	6154185	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	84991				mRNA processing|RNA splicing	spliceosomal complex	nucleotide binding|protein binding|RNA binding	g.chr10:6154185G>A	AF083384	CCDS7077.1	10p15.1	2013-01-28			ENSG00000134453	ENSG00000134453		"""RNA binding motif (RRM) containing"", ""G patch domain containing"""	16944	protein-coding gene	gene with protein product	"""splicing factor 45kDa"""	606935				9731529	Standard	NM_032905		Approved	SPF45, MGC14439	uc001ijb.3	Q96I25	OTTHUMG00000017618	ENST00000446108.1:c.717G>A	10.37:g.6154185G>A						RBM17_ENST00000379888.4_Silent_p.A239A	p.A239A	NM_001145547.1	NP_001139019.1	Q96I25	SPF45_HUMAN			8	1361	+			239			G-patch.		Q96GY6	Silent	SNP	ENST00000446108.1	37	c.717G>A	CCDS7077.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	1.056	-0.674345	0.03378	2.27E-4	0.001977	ENSG00000134453	ENST00000447032	.	.	.	5.41	-10.8	0.00216	.	.	.	.	.	T	0.30541	0.0768	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42224	-0.9464	4	.	.	.	-21.2661	0.4896	0.00562	0.2071:0.2128:0.2105:0.3696	.	.	.	.	H	146	.	.	R	+	2	0	RBM17	6194191	0.117000	0.22190	0.737000	0.30932	0.018000	0.09664	-0.492000	0.06467	-1.543000	0.01723	-0.253000	0.11424	CGC		0.557	RBM17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046635.1	NM_032905		3	36	0	0	0	1	0	3	36				
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	G	A			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr9:20414340G>A	ENST00000380338.4	-	5	790	c.504C>T	c.(502-504)agC>agT	p.S168S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	168	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S168S(5)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctgctactgctgc	0.537			T	MLL	ALL																																	ENST00000380338.4				Dom	yes		9	9p22	4300	T	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""			L	MLL		ALL		5	Substitution - coding silent(5)	p.S168S(5)	lung(2)|urinary_tract(1)|endometrium(1)|kidney(1)	central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66						c.(502-504)agC>agT		myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3							9.0	16.0	13.0					9																	20414340		1646	3412	5058	SO:0001819	synonymous_variant	4300				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr9:20414340G>A	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.504C>T	9.37:g.20414340G>A						MLLT3_ENST00000475957.1_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000355930.6_5'UTR	p.S168S	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN		GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)	5	790	-			168			Poly-Ser.		B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	c.504C>T	CCDS6494.1																																																																																				0.537	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529		4	44	0	0	0	1	0	4	44				
MAP7D1	55700	broad.mit.edu	37	1	36643701	36643703	+	In_Frame_Del	DEL	AGA	AGA	-	rs3045695|rs141305015|rs200892098	byFrequency	TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:36643701_36643703delAGA	ENST00000373151.2	+	9	1823_1825	c.1607_1609delAGA	c.(1606-1611)gagaag>gag	p.K537del	MAP7D1_ENST00000373148.4_In_Frame_Del_p.K83del|MAP7D1_ENST00000373150.4_In_Frame_Del_p.K505del|MAP7D1_ENST00000316156.4_In_Frame_Del_p.K500del	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	537	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				GCCAGTAACGAGAAGGAGTCAGC	0.719														323	0.0644968	0.003	0.0836	5008	,	,		9186	0.1964		0.0497	False		,,,				2504	0.0133					ENST00000316156.4																			0				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19						c.(1495-1500)gag>g		MAP7 domain containing 1				72,4170		17,38,2066						4.1	0.8		dbSNP_102	30	425,7795		48,329,3733	no	coding	MAP7D1	NM_018067.3		65,367,5799	A1A1,A1R,RR		5.1703,1.6973,3.9881				497,11965				SO:0001651	inframe_deletion	55700					cytoplasm|spindle		g.chr1:36643701_36643703delAGA	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.1607_1609delAGA	1.37:g.36643701_36643703delAGA	ENSP00000362244:p.Lys537del					MAP7D1_ENST00000373151.2_In_Frame_Del_p.EK536del|MAP7D1_ENST00000373150.4_In_Frame_Del_p.EK504del|MAP7D1_ENST00000373148.4_In_Frame_Del_p.EK82del	p.EK499del			Q3KQU3	MA7D1_HUMAN			8	1949_1951	+		Myeloproliferative disorder(586;0.0393)	536			Pro-rich.		D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	In_Frame_Del	DEL	ENST00000373151.2	37	c.1496_1498delAGA	CCDS30673.1																																																																																				0.719	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067		5	2						5	2	---	---	---	---
FAF1	11124	broad.mit.edu	37	1	51121170	51121170	+	Missense_Mutation	SNP	T	T	C			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:51121170T>C	ENST00000396153.2	-	8	1139	c.688A>G	c.(688-690)Atc>Gtc	p.I230V	FAF1_ENST00000371778.4_Missense_Mutation_p.I230V	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN	Fas (TNFRSF6) associated factor 1	230					apoptotic process (GO:0006915)|cell death (GO:0008219)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of protein complex assembly (GO:0031334)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of cell adhesion (GO:0030155)|regulation of protein catabolic process (GO:0042176)|regulation of protein kinase activity (GO:0045859)	CD95 death-inducing signaling complex (GO:0031265)|Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	heat shock protein binding (GO:0031072)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)	p.0?(1)		breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)		CGAACGGGGATACTTGTAAGG	0.368																																						ENST00000396153.2																			1	Whole gene deletion(1)	p.0?(1)	thyroid(1)	breast(2)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|pancreas(2)|upper_aerodigestive_tract(1)	24						c.(688-690)Atc>Gtc		Fas (TNFRSF6) associated factor 1							125.0	118.0	121.0					1																	51121170		2203	4300	6503	SO:0001583	missense	11124				apoptosis|cytoplasmic sequestering of NF-kappaB|positive regulation of apoptosis|positive regulation of protein complex assembly|proteasomal ubiquitin-dependent protein catabolic process|regulation of protein catabolic process	CD95 death-inducing signaling complex|cytosol|perinuclear region of cytoplasm	heat shock protein binding|NF-kappaB binding|protein kinase binding|protein kinase regulator activity	g.chr1:51121170T>C	AF132938	CCDS554.1	1p32.3	2012-09-20			ENSG00000185104	ENSG00000185104		"""UBX domain containing"""	3578	protein-coding gene	gene with protein product	"""TNFRSF6-associated factor 1"", ""UBX domain protein 3A"""	604460				10462485	Standard	NM_007051		Approved	CGI-03, hFAF1, HFAF1s, UBXD12, UBXN3A	uc001cse.1	Q9UNN5	OTTHUMG00000007930	ENST00000396153.2:c.688A>G	1.37:g.51121170T>C	ENSP00000379457:p.Ile230Val					FAF1_ENST00000371778.4_Missense_Mutation_p.I230V	p.I230V	NM_007051.2	NP_008982.1	Q9UNN5	FAF1_HUMAN		GBM - Glioblastoma multiforme(3;3.18e-11)|all cancers(3;0.00526)	8	1139	-			230					Q549F0|Q9UF34|Q9UNT3|Q9Y2Z3	Missense_Mutation	SNP	ENST00000396153.2	37	c.688A>G	CCDS554.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.119323	0.77323	.	.	ENSG00000185104	ENST00000396153;ENST00000371778	T;T	0.28895	1.59;1.59	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.51363	0.1670	L	0.55481	1.735	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	T	0.39820	-0.9595	10	0.37606	T	0.19	-11.8054	16.8222	0.85835	0.0:0.0:0.0:1.0	.	230	Q9UNN5	FAF1_HUMAN	V	230	ENSP00000379457:I230V;ENSP00000360843:I230V	ENSP00000360843:I230V	I	-	1	0	FAF1	50893758	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	6.615000	0.74201	2.371000	0.80710	0.533000	0.62120	ATC		0.368	FAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021807.1	NM_007051		25	5	0	0	0	1	0	25	5				
LINC01562	104054213	broad.mit.edu	37	1	51662882	51662882	+	lincRNA	DEL	A	A	-			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:51662882delA	ENST00000366181.2	-	0	250																		p.0?(2)									aaataaaaataaaaaaaaaTT	0.502																																						ENST00000366181.2																			2	Whole gene deletion(2)	p.0?(2)	thyroid(1)|central_nervous_system(1)																																																104054213							g.chr1:51662882delA																													1.37:g.51662882delA														0	250	-									RNA	DEL	ENST00000366181.2	37																																																																																						0.502	RP11-296A18.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000022441.1			2	4						2	4	---	---	---	---
CSDE1	7812	broad.mit.edu	37	1	115272911	115272912	+	Frame_Shift_Ins	INS	-	-	C			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr1:115272911_115272912insC	ENST00000358528.4	-	12	1749_1750	c.1323_1324insG	c.(1321-1326)cctaaafs	p.K442fs	CSDE1_ENST00000530886.1_Frame_Shift_Ins_p.K312fs|CSDE1_ENST00000369530.1_Frame_Shift_Ins_p.K457fs|CSDE1_ENST00000534699.1_Frame_Shift_Ins_p.K442fs|CSDE1_ENST00000339438.6_Frame_Shift_Ins_p.K411fs|CSDE1_ENST00000261443.5_Frame_Shift_Ins_p.K411fs|Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000438362.2_Frame_Shift_Ins_p.K488fs	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	442					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTAGTGGTTTTAGGATTGGAAA	0.381																																						ENST00000438362.2																			0				NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51						c.(1459-1464)ccaaacfs		cold shock domain containing E1, RNA-binding																																				SO:0001589	frameshift_variant	7812				male gonad development|regulation of transcription, DNA-dependent	cytoplasm	DNA binding|protein binding|RNA binding	g.chr1:115272911_115272912insC		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1323_1324insG	1.37:g.115272911_115272912insC	ENSP00000351329:p.Lys442fs					CSDE1_ENST00000358528.4_Frame_Shift_Ins_p.N442fs|CSDE1_ENST00000534699.1_Frame_Shift_Ins_p.N442fs|CSDE1_ENST00000339438.6_Frame_Shift_Ins_p.N411fs|CSDE1_ENST00000530886.1_Frame_Shift_Ins_p.N312fs|CSDE1_ENST00000261443.5_Frame_Shift_Ins_p.N411fs|CSDE1_ENST00000369530.1_Frame_Shift_Ins_p.N457fs	p.N488fs	NM_001242891.1	NP_001229820.1	O75534	CSDE1_HUMAN		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)	12	1839_1840	-	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)	442			CSD 6.		A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Frame_Shift_Ins	INS	ENST00000358528.4	37	c.1461_1462insG	CCDS30812.1																																																																																				0.381	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158		36	8						36	8	---	---	---	---
SPEG	10290	broad.mit.edu	37	2	220348359	220348359	+	Frame_Shift_Del	DEL	G	G	-			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr2:220348359delG	ENST00000312358.7	+	30	6306	c.6174delG	c.(6172-6174)ctgfs	p.L2058fs	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2058					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GGGGAGGCCTGGGTGAGGGCG	0.776																																						ENST00000312358.7																			0				breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100						c.(6172-6174)ctfs		SPEG complex locus							2.0	2.0	2.0					2																	220348359		936	2190	3126	SO:0001589	frameshift_variant	10290				muscle organ development|negative regulation of cell proliferation	nucleus	ATP binding|protein serine/threonine kinase activity	g.chr2:220348359delG	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.6174delG	2.37:g.220348359delG	ENSP00000311684:p.Leu2058fs					AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	p.L2058fs	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)	30	6306	+		Renal(207;0.0183)	2058					A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Frame_Shift_Del	DEL	ENST00000312358.7	37	c.6174delG	CCDS42824.1																																																																																				0.776	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876		2	4						2	4	---	---	---	---
POT1-AS1	401398	broad.mit.edu	37	7	124675408	124675408	+	RNA	DEL	G	G	-			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr7:124675408delG	ENST00000453342.1	+	0	614				RP11-3B12.1_ENST00000429134.1_RNA|RP11-3B12.1_ENST00000435452.2_RNA|RP11-3B12.1_ENST00000449642.1_RNA|RP11-3B12.1_ENST00000415715.1_RNA																							TCAGGGAGACGGGGGTCATTa	0.488																																						ENST00000453342.1																			0																																																			401398							g.chr7:124675408delG																													7.37:g.124675408delG														0	614	+									RNA	DEL	ENST00000453342.1	37																																																																																						0.488	RP11-3B12.1-002	KNOWN	basic	antisense	antisense	OTTHUMT00000347736.1			2	4						2	4	---	---	---	---
MUC2	4583	broad.mit.edu	37	11	1090951	1090951	+	Frame_Shift_Del	DEL	T	T	-	rs72655327|rs72655328		TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr11:1090951delT	ENST00000441003.2	+	28	3873	c.3846delT	c.(3844-3846)actfs	p.T1288fs	MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1289fs|MUC2_ENST00000361558.6_5'Flank|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	1288					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccttcaccactaccaccacca	0.617																																						ENST00000441003.2																			0				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102						c.(3844-3846)acfs		mucin 2, oligomeric mucus/gel-forming	Pranlukast(DB01411)						44.0	46.0	45.0					11																	1090951		2016	4147	6163	SO:0001589	frameshift_variant	4583					inner mucus layer|outer mucus layer	protein binding	g.chr11:1090951delT	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.3846delT	11.37:g.1090951delT	ENSP00000415183:p.Thr1288fs					MUC2_ENST00000359061.5_Frame_Shift_Del_p.T1289fs	p.T1288fs	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	28	3873	+		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)	1288					Q14878	Frame_Shift_Del	DEL	ENST00000441003.2	37	c.3846delT																																																																																					0.617	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457		2	4						2	4	---	---	---	---
MESP2	145873	broad.mit.edu	37	15	90320121	90320144	+	In_Frame_Del	DEL	AGGGGCAGGGGCAAGGGCAGGGGC	AGGGGCAGGGGCAAGGGCAGGGGC	-	rs56192595|rs200021459|rs199821487	byFrequency	TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr15:90320121_90320144delAGGGGCAGGGGCAAGGGCAGGGGC	ENST00000341735.3	+	1	533_556	c.533_556delAGGGGCAGGGGCAAGGGCAGGGGC	c.(532-558)gaggggcaggggcaagggcaggggcag>gag	p.GQGQGQGQ195del	MESP2_ENST00000560219.1_Intron|MESP2_ENST00000558723.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	195	13 X 2 AA tandem repeats of G-Q.				mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.Q198_G205delQGQGQGQG(1)		kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			ACGCaggcggaggggcaggggcaagggcaggggcaggggcaggg	0.777														3487	0.696286	0.4168	0.7824	5008	,	,		13432	0.8879		0.7654	False		,,,				2504	0.7444					ENST00000341735.3																			1	Deletion - In frame(1)	p.Q198_G205delQGQGQGQG(1)	upper_aerodigestive_tract(1)	kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						c.(532-558)gag>g		mesoderm posterior 2 homolog (mouse)				995,777		385,225,276						0.1	0.0		dbSNP_129	3	3389,1453		1404,581,436	no	coding	MESP2	NM_001039958.1		1789,806,712	A1A1,A1R,RR		30.0083,43.8488,33.7164				4384,2230				SO:0001651	inframe_deletion	145873				Notch signaling pathway	nucleus	DNA binding	g.chr15:90320121_90320144delAGGGGCAGGGGCAAGGGCAGGGGC		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.533_556delAGGGGCAGGGGCAAGGGCAGGGGC	15.37:g.90320121_90320144delAGGGGCAGGGGCAAGGGCAGGGGC	ENSP00000342392:p.Gly195_Gln202del					MESP2_ENST00000558723.1_Intron|MESP2_ENST00000560219.1_Intron	p.EGQGQGQGQ178del	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)		1	533_556	+	Lung NSC(78;0.0221)|all_lung(78;0.0448)		178					Q7RTU2	In_Frame_Del	DEL	ENST00000341735.3	37	c.533_556delAGGGGCAGGGGCAAGGGCAGGGGC	CCDS42078.1																																																																																				0.777	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261		6	2						6	2	---	---	---	---
UBALD1	124402	broad.mit.edu	37	16	4660590	4660591	+	Intron	INS	-	-	C			TCGA-WB-A81M-01A-11D-A35I-08	TCGA-WB-A81M-10A-01D-A35G-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	befe16ec-3f43-439f-83f8-026df4c06e29	da047bf6-64c5-4fbd-aa9e-7f963c8ee970	g.chr16:4660590_4660591insC	ENST00000283474.7	-	2	249				UBALD1_ENST00000587649.1_Intron|UBALD1_ENST00000591897.1_Intron|UBALD1_ENST00000590965.1_Frame_Shift_Ins_p.A63fs|UBALD1_ENST00000590891.1_5'UTR|UBALD1_ENST00000591401.1_Intron|UBALD1_ENST00000587615.1_Intron	NM_145253.2	NP_660296.1	Q8TB05	UBAD1_HUMAN	UBA-like domain containing 1																		CACCCTCCAGGCCCCCGCCGGC	0.649																																						ENST00000590965.1																			0											c.(187-189)ctgfs		UBA-like domain containing 1				43,4153		3,37,2058						-4.9	0.0			36	87,8077		3,81,3998	no	intron	FAM100A	NM_145253.2		6,118,6056	A1A1,A1R,RR		1.0657,1.0248,1.0518				130,12230				SO:0001627	intron_variant	124402							g.chr16:4660590_4660591insC	BC025327	CCDS10518.1	16p13.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000153443	ENSG00000153443			29576	protein-coding gene	gene with protein product			"""family with sequence similarity 100, member A"""	FAM100A			Standard	NM_145253		Approved		uc002cwx.2	Q8TB05	OTTHUMG00000129472	ENST00000283474.7:c.121-34->G	16.37:g.4660595_4660595dupC						UBALD1_ENST00000283474.7_Intron|UBALD1_ENST00000590891.1_5'UTR|UBALD1_ENST00000587615.1_Intron|UBALD1_ENST00000591401.1_Intron|UBALD1_ENST00000587649.1_Intron|UBALD1_ENST00000591897.1_Intron	p.L63fs							2	263_264	-								Q71MF6	Frame_Shift_Ins	INS	ENST00000283474.7	37	c.187_188insG	CCDS10518.1																																																																																				0.649	UBALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251635.2	NM_145253		2	4						2	4	---	---	---	---
