#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
BMP6	654	broad.mit.edu	37	6	7862663	7862663	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr6:7862663G>A	ENST00000283147.6	+	4	1295	c.1136G>A	c.(1135-1137)cGg>cAg	p.R379Q		NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN	bone morphogenetic protein 6	379					BMP signaling pathway (GO:0030509)|cartilage development (GO:0051216)|cellular response to mechanical stimulus (GO:0071260)|endochondral ossification (GO:0001958)|eye development (GO:0001654)|growth (GO:0040007)|immune response (GO:0006955)|inflammatory response (GO:0006954)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|osteoblast differentiation (GO:0001649)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of aldosterone secretion (GO:2000860)|positive regulation of bone mineralization (GO:0030501)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to activity (GO:0014823)|response to glucocorticoid (GO:0051384)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to retinoic acid (GO:0032526)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|type B pancreatic cell development (GO:0003323)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	BMP receptor binding (GO:0070700)|protein heterodimerization activity (GO:0046982)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23	Ovarian(93;0.0721)					GCCTCCAGCCGGCGCCGACAA	0.607																																						ENST00000283147.6																			0				breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(6)|ovary(1)|prostate(1)	23						c.(1135-1137)cGg>cAg		bone morphogenetic protein 6							65.0	65.0	65.0					6																	7862663		2203	4300	6503	SO:0001583	missense	654				BMP signaling pathway|cartilage development|growth|immune response|positive regulation of aldosterone biosynthetic process|positive regulation of bone mineralization|positive regulation of osteoblast differentiation|positive regulation of pathway-restricted SMAD protein phosphorylation|positive regulation of transcription from RNA polymerase II promoter|SMAD protein signal transduction	extracellular space	BMP receptor binding|cytokine activity|growth factor activity|protein heterodimerization activity	g.chr6:7862663G>A	AF083030	CCDS4503.1	6p24-p23	2014-01-30	2003-10-06		ENSG00000153162	ENSG00000153162		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1073	protein-coding gene	gene with protein product		112266	"""vegetal related growth factor (TGFB-related)"""	VGR		1427904, 1453478	Standard	NM_001718		Approved	VGR1	uc003mxu.4	P22004	OTTHUMG00000014217	ENST00000283147.6:c.1136G>A	6.37:g.7862663G>A	ENSP00000283147:p.Arg379Gln						p.R379Q	NM_001718.4	NP_001709.1	P22004	BMP6_HUMAN			4	1295	+	Ovarian(93;0.0721)		379					Q5TCP3	Missense_Mutation	SNP	ENST00000283147.6	37	c.1136G>A	CCDS4503.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.862836	0.91511	.	.	ENSG00000153162	ENST00000537240;ENST00000283147;ENST00000540959	T	0.74209	-0.82	5.8	5.8	0.92144	.	0.058336	0.64402	D	0.000002	T	0.56659	0.2000	M	0.63428	1.95	0.46564	D	0.999107	P	0.34462	0.454	B	0.20384	0.029	T	0.62144	-0.6916	10	0.40728	T	0.16	.	13.2791	0.60205	0.0719:0.0:0.928:0.0	.	379	P22004	BMP6_HUMAN	Q	301;379;342	ENSP00000283147:R379Q	ENSP00000283147:R379Q	R	+	2	0	BMP6	7807662	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	5.387000	0.66243	2.735000	0.93741	0.655000	0.94253	CGG		0.607	BMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039794.1	NM_001718		8	136	0	0	0	1	0	8	136				
DHX36	170506	broad.mit.edu	37	3	154033843	154033843	+	Missense_Mutation	SNP	G	G	C			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr3:154033843G>C	ENST00000496811.1	-	2	433	c.353C>G	c.(352-354)gCt>gGt	p.A118G	DHX36_ENST00000308361.6_Missense_Mutation_p.A118G|DHX36_ENST00000544526.1_Missense_Mutation_p.A118G|DHX36_ENST00000329463.5_Missense_Mutation_p.A118G	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	118					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			ATCCTCAGGAGCAAACCAGGA	0.333																																						ENST00000496811.1																			0				endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35						c.(352-354)gCt>gGt		DEAH (Asp-Glu-Ala-His) box polypeptide 36							121.0	109.0	113.0					3																	154033843		2203	4300	6503	SO:0001583	missense	170506					cytoplasm|nucleus	ATP binding|ATP-dependent helicase activity|nucleic acid binding|protein binding	g.chr3:154033843G>C	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.353C>G	3.37:g.154033843G>C	ENSP00000417078:p.Ala118Gly					DHX36_ENST00000308361.6_Missense_Mutation_p.A118G|DHX36_ENST00000544526.1_Missense_Mutation_p.A118G|DHX36_ENST00000329463.5_Missense_Mutation_p.A118G	p.A118G	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)		2	433	-			118					B2RB00|Q70JU3|Q8IYE5|Q9P240	Missense_Mutation	SNP	ENST00000496811.1	37	c.353C>G	CCDS3171.1	.	.	.	.	.	.	.	.	.	.	G	9.784	1.176202	0.21704	.	.	ENSG00000174953	ENST00000496811;ENST00000308361;ENST00000544526;ENST00000329463;ENST00000481941	D;D;D;D;T	0.91124	-2.79;-2.79;-2.79;-2.79;4.06	5.58	4.68	0.58851	.	0.566392	0.19635	N	0.109582	T	0.80686	0.4670	N	0.08118	0	0.31553	N	0.658563	B;B;B	0.27068	0.082;0.167;0.049	B;B;B	0.28011	0.058;0.085;0.026	T	0.77000	-0.2750	10	0.24483	T	0.36	.	12.8514	0.57860	0.0:0.0:0.7042:0.2958	.	118;118;118	Q9H2U1-2;Q9H2U1-3;Q9H2U1	.;.;DHX36_HUMAN	G	118;118;118;118;32	ENSP00000417078:A118G;ENSP00000309296:A118G;ENSP00000444247:A118G;ENSP00000330113:A118G;ENSP00000419862:A32G	ENSP00000309296:A118G	A	-	2	0	DHX36	155516537	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	5.009000	0.63998	1.294000	0.44707	0.637000	0.83480	GCT		0.333	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865		12	53	0	0	0	1	0	12	53				
GZF1	64412	broad.mit.edu	37	20	23349552	23349552	+	Missense_Mutation	SNP	T	T	C			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr20:23349552T>C	ENST00000338121.5	+	4	1690	c.1613T>C	c.(1612-1614)aTt>aCt	p.I538T	GZF1_ENST00000542987.1_Missense_Mutation_p.I47T|GZF1_ENST00000544236.1_Missense_Mutation_p.I62T|GZF1_ENST00000377051.2_Missense_Mutation_p.I538T			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	538					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					TACCAGCATATTAAAGTCCAC	0.378																																						ENST00000338121.5																			0				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24						c.(1612-1614)aTt>aCt		GDNF-inducible zinc finger protein 1							106.0	105.0	105.0					20																	23349552		2203	4300	6503	SO:0001583	missense	64412				transcription, DNA-dependent	nucleolus|nucleoplasm	sequence-specific DNA binding|zinc ion binding	g.chr20:23349552T>C	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.1613T>C	20.37:g.23349552T>C	ENSP00000338290:p.Ile538Thr					GZF1_ENST00000377051.2_Missense_Mutation_p.I538T|GZF1_ENST00000542987.1_Missense_Mutation_p.I47T|GZF1_ENST00000544236.1_Missense_Mutation_p.I62T	p.I538T			Q9H116	GZF1_HUMAN			4	1690	+	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)		538					A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	c.1613T>C	CCDS13151.1	.	.	.	.	.	.	.	.	.	.	T	11.44	1.638414	0.29157	.	.	ENSG00000125812	ENST00000544236;ENST00000338121;ENST00000542987;ENST00000377051	T;T;T;T	0.19938	2.11;2.11;2.11;2.11	5.87	4.76	0.60689	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.201336	0.32120	N	0.006543	T	0.14830	0.0358	N	0.20610	0.595	0.35766	D	0.820556	P	0.43938	0.822	B	0.40825	0.341	T	0.16129	-1.0413	10	0.40728	T	0.16	.	11.6634	0.51361	0.1328:0.0:0.0:0.8671	.	538	Q9H116	GZF1_HUMAN	T	62;538;47;538	ENSP00000445458:I62T;ENSP00000338290:I538T;ENSP00000445118:I47T;ENSP00000366250:I538T	ENSP00000338290:I538T	I	+	2	0	GZF1	23297552	0.872000	0.30054	0.878000	0.34440	0.371000	0.29859	4.196000	0.58407	1.020000	0.39573	0.528000	0.53228	ATT		0.378	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482		24	158	0	0	0	1	0	24	158				
AC002472.1	0	broad.mit.edu	37	22	21363306	21363306	+	5'Flank	SNP	G	G	A	rs2075274	byFrequency	TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr22:21363306G>A	ENST00000547793.2	-	0	0				TUBA3FP_ENST00000422086.1_RNA|THAP7-AS1_ENST00000452284.1_RNA|THAP7-AS1_ENST00000436079.1_RNA																							GATGACCAGGGCGTAGGTGGC	0.582													G|||	939	0.1875	0.0968	0.3746	5008	,	,		20123	0.0536		0.3648	False		,,,				2504	0.1329					ENST00000452284.1																			0																																																	SO:0001631	upstream_gene_variant	0							g.chr22:21363306G>A																													22.37:g.21363306G>A	Exception_encountered					TUBA3FP_ENST00000422086.1_RNA|THAP7-AS1_ENST00000436079.1_RNA		NR_027051.1						0	973	+									RNA	SNP	ENST00000547793.2	37																																																																																						0.582	AC002472.1-201	NOVEL	basic|appris_principal	protein_coding	protein_coding				5	107	0	0	0	1	0	5	107				
PSAP	5660	broad.mit.edu	37	10	73587777	73587777	+	Silent	SNP	G	G	A	rs141199649	byFrequency	TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr10:73587777G>A	ENST00000394936.3	-	6	861	c.714C>T	c.(712-714)gcC>gcT	p.A238A	PSAP_ENST00000394934.1_Silent_p.A238A			P07602	SAP_HUMAN	prosaposin	238	Saposin B-type 2. {ECO:0000255|PROSITE- ProRule:PRU00415}.				blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TCACTATGTCGGCCATGCCAG	0.572																																						ENST00000394936.3																			0				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						c.(712-714)gcC>gcT		prosaposin							104.0	77.0	86.0					10																	73587777		2203	4300	6503	SO:0001819	synonymous_variant	5660				glycosphingolipid metabolic process|lipid transport|platelet activation|platelet degranulation	extracellular space|Golgi apparatus|integral to membrane|lysosomal lumen	enzyme activator activity|lipid binding	g.chr10:73587777G>A	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429	ENST00000394936.3:c.714C>T	10.37:g.73587777G>A						PSAP_ENST00000394934.1_Silent_p.A238A	p.A238A			P07602	SAP_HUMAN			6	861	-			238			Saposin B-type 2.		P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Silent	SNP	ENST00000394936.3	37	c.714C>T	CCDS7311.1																																																																																				0.572	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778		6	79	0	0	0	1	0	6	79				
NCOR2	9612	broad.mit.edu	37	12	124887093	124887093	+	Silent	SNP	C	C	T			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr12:124887093C>T	ENST00000405201.1	-	14	1497	c.1497G>A	c.(1495-1497)caG>caA	p.Q499Q	NCOR2_ENST00000404121.2_Silent_p.Q69Q|NCOR2_ENST00000404621.1_Silent_p.Q498Q|NCOR2_ENST00000356219.3_Silent_p.Q499Q|NCOR2_ENST00000429285.2_Silent_p.Q498Q|NCOR2_ENST00000397355.1_Silent_p.Q499Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	499	Poly-Gln.				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)	p.Q499Q(9)		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)		gctgctgctgctgttgttgct	0.617																																						ENST00000356219.3																			9	Substitution - coding silent(9)	p.Q499Q(9)	endometrium(4)|large_intestine(3)|kidney(2)	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						c.(1495-1497)caG>caA		nuclear receptor corepressor 2							9.0	10.0	10.0					12																	124887093		2051	4183	6234	SO:0001819	synonymous_variant	9612				cellular lipid metabolic process|negative regulation of transcription from RNA polymerase II promoter|regulation of cellular ketone metabolic process by negative regulation of transcription from an RNA polymerase II promoter|transcription, DNA-dependent	nuclear body|nucleus|transcriptional repressor complex	DNA binding|histone deacetylase binding|Notch binding|protein N-terminus binding|transcription corepressor activity	g.chr12:124887093C>T	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.1497G>A	12.37:g.124887093C>T						NCOR2_ENST00000429285.2_Silent_p.Q498Q|NCOR2_ENST00000405201.1_Silent_p.Q499Q|NCOR2_ENST00000404621.1_Silent_p.Q498Q|NCOR2_ENST00000404121.2_Silent_p.Q69Q|NCOR2_ENST00000397355.1_Silent_p.Q499Q	p.Q499Q	NM_006312.5	NP_006303.4	Q9Y618	NCOR2_HUMAN		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)	15	1652	-	all_neural(191;0.0804)|Medulloblastoma(191;0.163)		499			Poly-Gln.		O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	c.1497G>A	CCDS41858.2																																																																																				0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312		3	13	0	0	0	1	0	3	13				
LINC00969	440993	broad.mit.edu	37	3	195400728	195400728	+	lincRNA	SNP	A	A	G	rs12107841	byFrequency	TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr3:195400728A>G	ENST00000445430.1	+	0	1324									long intergenic non-protein coding RNA 969																		GATTGTGCCCAGCCTGTACGC	0.587																																						ENST00000445430.1																			0																																																			0							g.chr3:195400728A>G	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195400728A>G														0	1324	+									RNA	SNP	ENST00000445430.1	37																																																																																						0.587	LINC00969-038	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000341951.1			5	43	0	0	0	1	0	5	43				
OR4S1	256148	broad.mit.edu	37	11	48328468	48328468	+	Missense_Mutation	SNP	C	C	T			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr11:48328468C>T	ENST00000319988.1	+	1	694	c.694C>T	c.(694-696)Cgt>Tgt	p.R232C		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	232						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						TGAGGACCGGCGTAAGGCTGT	0.478																																						ENST00000319988.1																			0				endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						c.(694-696)Cgt>Tgt		olfactory receptor, family 4, subfamily S, member 1							211.0	191.0	198.0					11																	48328468		2201	4298	6499	SO:0001583	missense	256148				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:48328468C>T	AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"""GPCR / Class A : Olfactory receptors"""	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.694C>T	11.37:g.48328468C>T	ENSP00000321447:p.Arg232Cys						p.R232C	NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN			1	694	+			232					Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	c.694C>T	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	C	5.337	0.247435	0.10130	.	.	ENSG00000176555	ENST00000319988	T	0.00164	8.64	5.02	1.91	0.25777	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00144	0.0004	L	0.48362	1.52	0.09310	N	1	B	0.22276	0.067	B	0.27170	0.077	T	0.33343	-0.9872	9	0.59425	D	0.04	.	3.1116	0.06360	0.1932:0.5271:0.0:0.2797	.	232	Q8NGB4	OR4S1_HUMAN	C	232	ENSP00000321447:R232C	ENSP00000321447:R232C	R	+	1	0	OR4S1	48285044	0.000000	0.05858	0.007000	0.13788	0.004000	0.04260	-0.093000	0.11111	1.248000	0.43934	0.655000	0.94253	CGT		0.478	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725		9	269	0	0	0	1	0	9	269				
NBPF10	100132406	broad.mit.edu	37	1	145324377	145324377	+	Missense_Mutation	SNP	C	C	A	rs77113202		TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr1:145324377C>A	ENST00000342960.5	+	28	3607	c.3572C>A	c.(3571-3573)gCg>gAg	p.A1191E	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	778						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAGGTAGTAGCGCCTGAAGTC	0.483																																						ENST00000342960.5																			0				NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73						c.(3571-3573)gCg>gAg		neuroblastoma breakpoint family, member 10																																				SO:0001583	missense	100132406							g.chr1:145324377C>A	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.3572C>A	1.37:g.145324377C>A	ENSP00000345684:p.Ala1191Glu					NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.2_Intron	p.A1191E	NM_001039703.4	NP_001034792.4	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	28	3607	+	all_hematologic(923;0.032)		1191					Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	c.3572C>A	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.756002	0.00085	.	.	ENSG00000163386	ENST00000342960	T	0.02552	4.25	.	.	.	.	.	.	.	.	T	0.00144	0.0004	N	0.00162	-1.95	0.09310	N	1	.	.	.	.	.	.	T	0.40534	-0.9558	5	0.02654	T	1	.	.	.	.	.	.	.	.	E	1191	ENSP00000345684:A1191E	ENSP00000345684:A1191E	A	+	2	0	NBPF10	144035734	0.004000	0.15560	0.001000	0.08648	0.000000	0.00434	0.161000	0.16481	-1.406000	0.02045	0.000000	0.15137	GCG		0.483	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703		3	4	1	0	6.4e-05	1	6.4e-05	3	4				
PRR12	57479	broad.mit.edu	37	19	50100109	50100109	+	Silent	SNP	A	A	C			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr19:50100109A>C	ENST00000418929.2	+	4	2529	c.2517A>C	c.(2515-2517)ccA>ccC	p.P839P		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	0							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		CTCCACCGCCACCCCCGCCTC	0.741																																						ENST00000418929.2																			0				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11						c.(2515-2517)ccA>ccC		proline rich 12							4.0	5.0	4.0					19																	50100109		1573	3497	5070	SO:0001819	synonymous_variant	57479						DNA binding	g.chr19:50100109A>C	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.2517A>C	19.37:g.50100109A>C							p.P839P	NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)	4	2529	+		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)	18					E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	c.2517A>C	CCDS46143.1																																																																																				0.741	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719		4	10	0	0	0	1	0	4	10				
GGT3P	2679	broad.mit.edu	37	22	18778612	18778612	+	RNA	SNP	C	C	T	rs1055042	byFrequency	TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr22:18778612C>T	ENST00000412448.1	-	0	793							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene						glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)										GCGGCCACGGCAGCCCTGGTG	0.637																																						ENST00000412448.1																			0																																																			0							g.chr22:18778612C>T			22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421		"""Gamma-glutamyltransferases"""	4252	pseudogene	pseudogene			"""gamma-glutamyltransferase 3"""	GGT3		8104871, 18357469	Standard	NR_003267		Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161		22.37:g.18778612C>T														0	793	-									RNA	SNP	ENST00000412448.1	37																																																																																						0.637	GGT3P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000341281.1	NR_003267		3	18	0	0	0	1	0	3	18				
DERL1	79139	broad.mit.edu	37	8	124034940	124034940	+	Missense_Mutation	SNP	A	A	G			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr8:124034940A>G	ENST00000259512.4	-	5	737	c.437T>C	c.(436-438)tTt>tCt	p.F146S	DERL1_ENST00000523036.1_Missense_Mutation_p.F46S|DERL1_ENST00000419562.2_Intron|DERL1_ENST00000405944.3_Missense_Mutation_p.F146S|DERL1_ENST00000519018.1_Missense_Mutation_p.F46S|RP11-557C18.3_ENST00000521258.1_RNA	NM_001134671.2|NM_024295.5	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	derlin 1	146					endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|establishment of protein localization (GO:0045184)|intracellular transport of viral protein in host cell (GO:0019060)|response to unfolded protein (GO:0006986)|retrograde protein transport, ER to cytosol (GO:0030970)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Hrd1p ubiquitin ligase complex (GO:0000836)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)	MHC class I protein binding (GO:0042288)|receptor activity (GO:0004872)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		STAD - Stomach adenocarcinoma(47;0.00527)			TCGTGTTCCAAACCAAAATGA	0.413											OREG0018957	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										ENST00000259512.4																			0				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	8						c.(436-438)tTt>tCt		derlin 1							215.0	191.0	199.0					8																	124034940		2203	4300	6503	SO:0001583	missense	79139				endoplasmic reticulum unfolded protein response|ER-associated protein catabolic process|intracellular transport of viral proteins in host cell|retrograde protein transport, ER to cytosol	integral to endoplasmic reticulum membrane	MHC class I protein binding|receptor activity	g.chr8:124034940A>G	BC002457	CCDS6337.1, CCDS47915.1	8q24.13	2012-02-01	2012-02-01		ENSG00000136986	ENSG00000136986			28454	protein-coding gene	gene with protein product		608813	"""Der1-like domain family, member 1"""			12975309, 15215855	Standard	NM_024295		Approved	MGC3067, PRO2577, FLJ13784, DER1, DER-1, derlin-1	uc003ypl.3	Q9BUN8	OTTHUMG00000165080	ENST00000259512.4:c.437T>C	8.37:g.124034940A>G	ENSP00000259512:p.Phe146Ser		OREG0018957	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1531	DERL1_ENST00000419562.2_Intron|DERL1_ENST00000405944.3_Missense_Mutation_p.F146S|DERL1_ENST00000523036.1_Missense_Mutation_p.F46S|RP11-557C18.3_ENST00000521258.1_RNA|DERL1_ENST00000519018.1_Missense_Mutation_p.F46S	p.F146S	NM_001134671.1|NM_024295.4	NP_001128143.1|NP_077271.1	Q9BUN8	DERL1_HUMAN	STAD - Stomach adenocarcinoma(47;0.00527)		5	737	-	Lung NSC(37;1.06e-09)|Ovarian(258;0.0205)		146					B3KW41|E9PH19	Missense_Mutation	SNP	ENST00000259512.4	37	c.437T>C	CCDS6337.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.334388	0.81801	.	.	ENSG00000136986	ENST00000259512;ENST00000405944;ENST00000519018;ENST00000523036	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.68	5.68	0.88126	.	0.089656	0.85682	D	0.000000	T	0.60818	0.2298	M	0.91196	3.185	0.80722	D	1	D;D	0.60160	0.958;0.987	D;D	0.72338	0.913;0.977	T	0.65545	-0.6142	10	0.11794	T	0.64	.	15.9239	0.79597	1.0:0.0:0.0:0.0	.	146;146	Q9BUN8-2;Q9BUN8	.;DERL1_HUMAN	S	146;146;46;46	ENSP00000259512:F146S;ENSP00000384289:F146S;ENSP00000430086:F46S;ENSP00000429199:F46S	ENSP00000259512:F146S	F	-	2	0	DERL1	124104121	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	8.938000	0.92943	2.170000	0.68504	0.533000	0.62120	TTT		0.413	DERL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381714.2	NM_024295		82	164	0	0	0	1	0	82	164				
TMEM246	84302	broad.mit.edu	37	9	104238214	104238214	+	Silent	SNP	G	G	A			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr9:104238214G>A	ENST00000374851.1	-	4	2308	c.1161C>T	c.(1159-1161)caC>caT	p.H387H	RP11-490D19.6_ENST00000431507.1_RNA|RP11-490D19.6_ENST00000424154.1_RNA|RP11-490D19.6_ENST00000425734.1_RNA|TMEM246_ENST00000374848.3_Silent_p.H387H|RP11-490D19.6_ENST00000450109.1_RNA|TMEM246_ENST00000374847.1_Silent_p.H387H			Q9BRR3	TM246_HUMAN	transmembrane protein 246	387						integral component of membrane (GO:0016021)											AGAGCCCGATGTGTTTCACGA	0.527																																						ENST00000374851.1																			0											c.(1159-1161)caC>caT		transmembrane protein 246							103.0	100.0	101.0					9																	104238214		2203	4300	6503	SO:0001819	synonymous_variant	84302					integral to membrane		g.chr9:104238214G>A	BC006115	CCDS6757.1	9q31.1	2012-04-02	2012-04-02	2012-04-02	ENSG00000165152	ENSG00000165152			28180	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 125"""	C9orf125		12477932	Standard	NM_032342		Approved	MGC12992	uc004bbm.3	Q9BRR3	OTTHUMG00000020381	ENST00000374851.1:c.1161C>T	9.37:g.104238214G>A						TMEM246_ENST00000374848.3_Silent_p.H387H|RP11-490D19.6_ENST00000425734.1_RNA|RP11-490D19.6_ENST00000424154.1_RNA|RP11-490D19.6_ENST00000450109.1_RNA|RP11-490D19.6_ENST00000431507.1_RNA|TMEM246_ENST00000374847.1_Silent_p.H387H	p.H387H			Q9BRR3	CI125_HUMAN			4	2308	-			387					Q49AQ4	Silent	SNP	ENST00000374851.1	37	c.1161C>T	CCDS6757.1																																																																																				0.527	TMEM246-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053444.1	NM_032342		24	130	0	0	0	1	0	24	130				
STXBP1	6812	broad.mit.edu	37	9	130374691	130374691	+	Silent	SNP	C	C	G			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr9:130374691C>G	ENST00000373299.1	+	1	124	c.9C>G	c.(7-9)ccC>ccG	p.P3P	STXBP1_ENST00000373302.3_Silent_p.P3P	NM_001032221.3	NP_001027392.1	P61764	STXB1_HUMAN	syntaxin binding protein 1	3					axon target recognition (GO:0007412)|energy reserve metabolic process (GO:0006112)|glutamate secretion (GO:0014047)|long term synaptic depression (GO:0060292)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter secretion (GO:0007269)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|protein stabilization (GO:0050821)|protein transport (GO:0015031)|regulation of insulin secretion (GO:0050796)|regulation of SNARE complex assembly (GO:0035542)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|regulation of synaptic vesicle priming (GO:0010807)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|synaptic vesicle maturation (GO:0016188)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)|protein complex (GO:0043234)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|SNARE binding (GO:0000149)|syntaxin binding (GO:0019905)|syntaxin-1 binding (GO:0017075)			breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						CCATGGCCCCCATTGGCCTCA	0.741																																						ENST00000373302.3																			0				breast(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(7)|skin(2)	23						c.(7-9)ccC>ccG		syntaxin binding protein 1							28.0	21.0	23.0					9																	130374691		2198	4289	6487	SO:0001819	synonymous_variant	6812				axon target recognition|energy reserve metabolic process|glutamate secretion|negative regulation of synaptic transmission, GABAergic|neurotransmitter secretion|platelet aggregation|platelet degranulation|protein transport|regulation of insulin secretion|regulation of synaptic vesicle priming|synaptic vesicle maturation|vesicle docking involved in exocytosis	cytosol|mitochondrion|plasma membrane|platelet alpha granule|protein complex	identical protein binding|syntaxin-1 binding|syntaxin-2 binding	g.chr9:130374691C>G	AF004563	CCDS6874.1, CCDS35146.1	9q34.1	2008-07-21			ENSG00000136854	ENSG00000136854			11444	protein-coding gene	gene with protein product	"""syntaxin-binding protein 1"""	602926				9545644	Standard	NM_001032221		Approved	hUNC18, MUNC18-1, UNC18, rbSec1	uc004brk.2	P61764	OTTHUMG00000020713	ENST00000373299.1:c.9C>G	9.37:g.130374691C>G						STXBP1_ENST00000373299.1_Silent_p.P3P	p.P3P	NM_003165.3	NP_003156.1	P61764	STXB1_HUMAN			1	148	+			3					B1AM97|Q28208|Q62759|Q64320|Q96TG8	Silent	SNP	ENST00000373299.1	37	c.9C>G	CCDS35146.1																																																																																				0.741	STXBP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054229.1	NM_003165		2	14	0	0	0	1	0	2	14				
ANKRD36BP2	645784	broad.mit.edu	37	2	89084114	89084114	+	RNA	SNP	G	G	A			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr2:89084114G>A	ENST00000393525.3	+	0	576									ankyrin repeat domain 36B pseudogene 2																		TTGCTTTTCAGTGTCTTCTCA	0.313																																						ENST00000393525.3																			0																																																			0							g.chr2:89084114G>A			2q11.2	2010-09-30			ENSG00000230006	ENSG00000230006			33607	pseudogene	pseudogene							Standard	NR_015424		Approved		uc010fhg.4		OTTHUMG00000151690		2.37:g.89084114G>A														0	576	+									RNA	SNP	ENST00000393525.3	37																																																																																						0.313	ANKRD36BP2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000323523.1			5	121	0	0	0	1	0	5	121				
APOL2	23780	broad.mit.edu	37	22	36623751	36623751	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr22:36623751G>A	ENST00000249066.6	-	6	1189	c.713C>T	c.(712-714)gCg>gTg	p.A238V	APOL2_ENST00000358502.5_Missense_Mutation_p.A238V|APOL2_ENST00000451256.2_Missense_Mutation_p.A350V	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN	apolipoprotein L, 2	238					acute-phase response (GO:0006953)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|maternal process involved in female pregnancy (GO:0060135)|multicellular organismal development (GO:0007275)	endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|membrane (GO:0016020)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						TGGGGCATACGCTCCTAACTG	0.542																																						ENST00000249066.6																			0				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)|urinary_tract(2)	9						c.(712-714)gCg>gTg		apolipoprotein L, 2							123.0	126.0	125.0					22																	36623751		2173	4292	6465	SO:0001583	missense	23780				acute-phase response|cholesterol metabolic process|lipid transport|lipoprotein metabolic process|maternal process involved in female pregnancy|multicellular organismal development	endoplasmic reticulum membrane|extracellular region	high-density lipoprotein particle binding|lipid binding|receptor binding	g.chr22:36623751G>A	AF324224	CCDS43014.1	22q12.3	2013-09-20			ENSG00000128335	ENSG00000128335		"""Apolipoproteins"""	619	protein-coding gene	gene with protein product	"""apolipoprotein L-II"""	607252				10591208, 11374903	Standard	NM_145637		Approved	APOL-II	uc003apa.3	Q9BQE5	OTTHUMG00000150634	ENST00000249066.6:c.713C>T	22.37:g.36623751G>A	ENSP00000249066:p.Ala238Val					APOL2_ENST00000451256.2_Missense_Mutation_p.A350V|APOL2_ENST00000358502.5_Missense_Mutation_p.A238V	p.A238V	NM_145637.1	NP_663612.1	Q9BQE5	APOL2_HUMAN			6	1189	-			238					B0QYK7|O95915|Q59GW9|Q5TH96|Q969T6|Q9BT28|Q9UGT1|Q9UH10	Missense_Mutation	SNP	ENST00000249066.6	37	c.713C>T	CCDS43014.1	.	.	.	.	.	.	.	.	.	.	G	11.72	1.724214	0.30593	.	.	ENSG00000128335	ENST00000358502;ENST00000249066;ENST00000451256	T;T;T	0.03982	3.74;3.74;3.74	3.71	-7.41	0.01392	.	1.441560	0.04508	N	0.382331	T	0.04770	0.0129	L	0.34521	1.04	0.09310	N	1	P;P	0.51653	0.904;0.947	B;B	0.44278	0.445;0.411	T	0.32929	-0.9888	10	0.46703	T	0.11	.	8.781	0.34792	0.0:0.4675:0.1765:0.3561	.	350;238	B4E1T5;Q9BQE5	.;APOL2_HUMAN	V	238;238;350	ENSP00000351292:A238V;ENSP00000249066:A238V;ENSP00000403153:A350V	ENSP00000249066:A238V	A	-	2	0	APOL2	34953697	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.970000	0.03810	-1.278000	0.02408	0.411000	0.27672	GCG		0.542	APOL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000319279.1	NM_145637		100	135	0	0	0	1	0	100	135				
VPS4B	9525	broad.mit.edu	37	18	61077535	61077535	+	Missense_Mutation	SNP	G	G	A			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr18:61077535G>A	ENST00000238497.5	-	3	487	c.284C>T	c.(283-285)gCa>gTa	p.A95V	VPS4B_ENST00000591519.1_Missense_Mutation_p.A95V	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN	vacuolar protein sorting 4 homolog B (S. cerevisiae)	95					ATP catabolic process (GO:0006200)|cell cycle (GO:0007049)|cell division (GO:0051301)|endosomal transport (GO:0016197)|endosome organization (GO:0007032)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|intracellular cholesterol transport (GO:0032367)|membrane organization (GO:0061024)|positive regulation of viral release from host cell (GO:1902188)|potassium ion transport (GO:0006813)|protein transport (GO:0015031)|regulation of viral process (GO:0050792)|response to lipid (GO:0033993)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|nucleus (GO:0005634)|vacuolar membrane (GO:0005774)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)			breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						CTTCTCATCTGCTGGACTCGG	0.358																																						ENST00000238497.5																			0				breast(1)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	13						c.(283-285)gCa>gTa		vacuolar protein sorting 4 homolog B (S. cerevisiae)							217.0	202.0	207.0					18																	61077535		2203	4300	6503	SO:0001583	missense	9525				cell cycle|cell division|cellular membrane organization|endosome to lysosome transport via multivesicular body sorting pathway|intracellular cholesterol transport|protein transport|response to lipid	cytosol|early endosome|late endosome membrane|lysosome|nucleus|vacuolar membrane	ATP binding|ATPase activity, coupled|protein C-terminus binding	g.chr18:61077535G>A	AF038960	CCDS11983.1	18q21.33	2010-04-21	2006-04-04	2002-06-14	ENSG00000119541	ENSG00000119541		"""ATPases / AAA-type"""	10895	protein-coding gene	gene with protein product		609983	"""suppressor of K+ transport defect 1"", ""vacuolar protein sorting 4B (yeast)"""	SKD1		11563910	Standard	XM_006722582		Approved	VPS4-2, SKD1B	uc002lix.3	O75351	OTTHUMG00000132790	ENST00000238497.5:c.284C>T	18.37:g.61077535G>A	ENSP00000238497:p.Ala95Val					VPS4B_ENST00000591519.1_Missense_Mutation_p.A95V	p.A95V	NM_004869.3	NP_004860.2	O75351	VPS4B_HUMAN			3	487	-			95					Q69HW4|Q9GZS7	Missense_Mutation	SNP	ENST00000238497.5	37	c.284C>T	CCDS11983.1	.	.	.	.	.	.	.	.	.	.	G	10.99	1.506797	0.26949	.	.	ENSG00000119541	ENST00000238497	D	0.93906	-3.31	5.63	3.76	0.43208	.	0.446123	0.25458	N	0.030535	D	0.87216	0.6122	N	0.25647	0.755	0.34374	D	0.692331	B;B	0.11235	0.004;0.001	B;B	0.10450	0.005;0.005	D	0.85892	0.1429	10	0.36615	T	0.2	-9.0418	10.4142	0.44311	0.0748:0.1347:0.7905:0.0	.	95;95	A8K4G7;O75351	.;VPS4B_HUMAN	V	95	ENSP00000238497:A95V	ENSP00000238497:A95V	A	-	2	0	VPS4B	59228515	0.990000	0.36364	0.923000	0.36655	0.522000	0.34438	2.463000	0.45058	1.363000	0.46019	0.655000	0.94253	GCA		0.358	VPS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256198.2	NM_004869		110	187	0	0	0	1	0	110	187				
BRAF	673	broad.mit.edu	37	7	140453136	140453136	+	Missense_Mutation	SNP	A	A	T	rs121913377|rs113488022|rs121913227|rs397516897		TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr7:140453136A>T	ENST00000288602.6	-	15	1859	c.1799T>A	c.(1798-1800)gTg>gAg	p.V600E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	600	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions). {ECO:0000269|PubMed:12068308}.|V -> E (in CRC; also found in sarcoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis; loss of regulation by PMRT5). {ECO:0000269|PubMed:12068308, ECO:0000269|PubMed:12198537, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:23263490, ECO:0000269|PubMed:24455489}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	TCGAGATTTCACTGTAGCTAG	0.368	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												Colon(40;35 892 2973 5743 27438)	ENST00000288602.6	V600D(K029AX_SKIN)|V600D(WM115_SKIN)|V600D(WM2664_SKIN)|V600E(8505C_THYROID)|V600E(A101D_SKIN)|V600E(A2058_SKIN)|V600E(A375_SKIN)|V600E(A673_BONE)|V600E(AM38_CENTRAL_NERVOUS_SYSTEM)|V600E(BCPAP_THYROID)|V600E(BHT101_THYROID)|V600E(BT474_BREAST)|V600E(C32_SKIN)|V600E(CL34_LARGE_INTESTINE)|V600E(COLO205_LARGE_INTESTINE)|V600E(COLO679_SKIN)|V600E(COLO741_SKIN)|V600E(COLO783_SKIN)|V600E(COLO800_SKIN)|V600E(COLO818_SKIN)|V600E(COLO829_SKIN)|V600E(COLO849_SKIN)|V600E(DBTRG05MG_CENTRAL_NERVOUS_SYSTEM)|V600E(DU4475_BREAST)|V600E(ES2_OVARY)|V600E(G361_SKIN)|V600E(GCT_SOFT_TISSUE)|V600E(HS294T_SKIN)|V600E(HS695T_SKIN)|V600E(HS939T_SKIN)|V600E(IGR1_SKIN)|V600E(IGR37_SKIN)|V600E(IGR39_SKIN)|V600E(K029AX_SKIN)|V600E(KG1C_CENTRAL_NERVOUS_SYSTEM)|V600E(LOXIMVI_SKIN)|V600E(MALME3M_SKIN)|V600E(MELHO_SKIN)|V600E(OUMS23_LARGE_INTESTINE)|V600E(RKO_LARGE_INTESTINE)|V600E(RPMI7951_SKIN)|V600E(RVH421_SKIN)|V600E(SH4_SKIN)|V600E(SIGM5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|V600E(SKHEP1_LIVER)|V600E(SKMEL24_SKIN)|V600E(SKMEL28_SKIN)|V600E(SKMEL5_SKIN)|V600E(SW1417_LARGE_INTESTINE)|V600E(UACC257_SKIN)|V600E(UACC62_SKIN)|V600E(WM793_SKIN)|V600E(WM88_SKIN)|V600E(WM983B_SKIN)	61		Dom	yes		7	7q34	673	"""Mis, T, O"""	v-raf murine sarcoma viral oncogene homolog B1	yes	Cardio-facio-cutaneous syndrome	E	"""AKAP9, KIAA1549"""		"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	15808	Substitution - Missense(15790)|Complex - deletion inframe(17)|Insertion - In frame(1)	p.V600E(15453)|p.V600K(252)|p.V600R(44)|p.V600D(16)|p.V600A(12)|p.V600_K601>E(12)|p.V600G(11)|p.T599_R603>I(2)|p.V600Q(2)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)|p.T599_V600insDFGLAT(1)	thyroid(7476)|skin(3822)|large_intestine(3288)|NS(360)|haematopoietic_and_lymphoid_tissue(336)|ovary(211)|lung(58)|eye(57)|central_nervous_system(53)|soft_tissue(30)|biliary_tract(18)|liver(17)|prostate(13)|breast(10)|upper_aerodigestive_tract(9)|endometrium(8)|pancreas(8)|testis(7)|small_intestine(7)|genital_tract(4)|stomach(4)|bone(3)|autonomic_ganglia(2)|oesophagus(2)|urinary_tract(2)|adrenal_gland(2)|pituitary(1)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380						c.(1798-1800)gTg>gAg		v-raf murine sarcoma viral oncogene homolog B	Sorafenib(DB00398)						112.0	104.0	107.0					7																	140453136		2203	4300	6503	SO:0001583	missense	673	Cardiofaciocutaneous syndrome	Familial Cancer Database	CFC, CFCS	activation of MAPKK activity|anti-apoptosis|nerve growth factor receptor signaling pathway|organ morphogenesis|positive regulation of peptidyl-serine phosphorylation|small GTPase mediated signal transduction|synaptic transmission	cytosol|nucleus|plasma membrane	ATP binding|metal ion binding	g.chr7:140453136A>T	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1799T>A	7.37:g.140453136A>T	ENSP00000288602:p.Val600Glu						p.V600E	NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN			15	1859	-	Melanoma(164;0.00956)		600		V -> D (in a melanoma cell line; requires 2 nucleotide substitutions).|V -> E (in sarcoma, colorectal adenocarcinoma, metastatic melanoma, ovarian serous carcinoma, pilocytic astrocytoma; somatic mutation; most common mutation; constitutive and elevated kinase activity; efficiently induces cell transformation; suppression of mutation in melanoma causes growth arrest and promotes apoptosis).	Protein kinase.		A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	c.1799T>A	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	24.0|24.0	4.486113|4.486113	0.84854|0.84854	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.81739|.	-1.53|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.61565|.	0.2357|.	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	D|.	0.55385|.	0.971|.	D|.	0.66351|.	0.943|.	T|.	0.58160|.	-0.7685|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	600|.	P15056|.	BRAF_HUMAN|.	E|R	600|208	ENSP00000288602:V600E|.	ENSP00000288602:V600E|.	V|X	-|-	2|1	0|0	BRAF|BRAF	140099605|140099605	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	9.197000|9.197000	0.94985|0.94985	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	GTG|TGA		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333		39	91	0	0	0	1	0	39	91				
CACNA1B	774	broad.mit.edu	37	9	140777318	140777318	+	Silent	SNP	C	C	T	rs200076426		TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr9:140777318C>T	ENST00000371372.1	+	3	658	c.513C>T	c.(511-513)ttC>ttT	p.F171F	CACNA1B_ENST00000277551.2_Silent_p.F171F|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Silent_p.F171F|CACNA1B_ENST00000371355.4_Silent_p.F171F|CACNA1B_ENST00000371357.1_Silent_p.F171F|CACNA1B_ENST00000277549.5_5'UTR	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	171					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TCATGGACTTCGTGGTCGTCC	0.607																																						ENST00000371372.1																			0				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80						c.(511-513)ttC>ttT		calcium channel, voltage-dependent, N type, alpha 1B subunit	Amlodipine(DB00381)|Gabapentin(DB00996)						173.0	187.0	183.0					9																	140777318		2126	4253	6379	SO:0001819	synonymous_variant	774				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity	g.chr9:140777318C>T	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.513C>T	9.37:g.140777318C>T						CACNA1B_ENST00000371355.4_Silent_p.F171F|CACNA1B_ENST00000371357.1_Silent_p.F171F|CACNA1B_ENST00000371363.1_Silent_p.F171F|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000277551.2_Silent_p.F171F|CACNA1B_ENST00000277549.5_5'UTR	p.F171F	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	3	658	+	all_cancers(76;0.166)		171					B1AQK5	Silent	SNP	ENST00000371372.1	37	c.513C>T	CCDS59522.1																																																																																				0.607	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		25	350	0	0	0	1	0	25	350				
WASH3P	374666	broad.mit.edu	37	15	102516473	102516473	+	RNA	SNP	G	G	A			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr15:102516473G>A	ENST00000557932.1	+	0	1421				DDX11L9_ENST00000562189.1_RNA			C4AMC7	WASH3_HUMAN	WAS protein family homolog 3 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)			central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25						ATCCTAGGGGGCTCCATGACA	0.642																																						ENST00000557932.1																			0				central_nervous_system(1)|endometrium(6)|kidney(11)|prostate(5)|stomach(1)|urinary_tract(1)	25																																														0							g.chr15:102516473G>A			15q26.3	2014-03-20	2008-01-16	2008-01-16	ENSG00000185596	ENSG00000185596		"""WAS protein homologs"""	24362	pseudogene	pseudogene			"""family with sequence similarity 39, member D pseudogene"""	FAM39DP		11701968, 18159949	Standard	NR_003659		Approved	FLJ25222	uc002cdi.3	C4AMC7	OTTHUMG00000172275		15.37:g.102516473G>A														0	1421	+									RNA	SNP	ENST00000557932.1	37																																																																																						0.642	WASH3P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000417608.1	NM_199163		6	88	0	0	0	1	0	6	88				
COL12A1	1303	broad.mit.edu	37	6	75884986	75884986	+	Silent	SNP	C	C	T			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr6:75884986C>T	ENST00000322507.8	-	13	2787	c.2478G>A	c.(2476-2478)acG>acA	p.T826T	COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Silent_p.T826T|COL12A1_ENST00000416123.2_Silent_p.T826T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	826	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						TAGTAGACGTCGTAGGGTCAG	0.393																																						ENST00000322507.8																			0				breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						c.(2476-2478)acG>acA		collagen, type XII, alpha 1							107.0	101.0	103.0					6																	75884986		1857	4085	5942	SO:0001819	synonymous_variant	1303				cell adhesion|collagen fibril organization|skeletal system development	collagen type XII|extracellular space	extracellular matrix structural constituent conferring tensile strength	g.chr6:75884986C>T	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.2478G>A	6.37:g.75884986C>T						COL12A1_ENST00000416123.2_Silent_p.T826T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000483888.2_Silent_p.T826T	p.T826T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN			13	2787	-			826			Fibronectin type-III 5.		O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Silent	SNP	ENST00000322507.8	37	c.2478G>A	CCDS43482.1																																																																																				0.393	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370		15	122	0	0	0	1	0	15	122				
DLG2	1740	broad.mit.edu	37	11	83173135	83173135	+	Splice_Site	DEL	C	C	-			TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr11:83173135delC	ENST00000532653.1	-	22	2664	c.2362delG	c.(2362-2364)gag>ag	p.E788fs	DLG2_ENST00000426717.2_Splice_Site_p.E270fs|DLG2_ENST00000524982.1_Splice_Site_p.E802fs|DLG2_ENST00000376106.3_Splice_Site_p.E270fs|DLG2_ENST00000330014.6_Splice_Site_p.E727fs|DLG2_ENST00000280241.8_Splice_Site_p.E845fs|DLG2_ENST00000398309.2_Splice_Site_p.E806fs|DLG2_ENST00000543673.1_Splice_Site_p.E911fs|DLG2_ENST00000418306.2_Splice_Site_p.E685fs|DLG2_ENST00000376104.2_Splice_Site_p.E911fs|DLG2_ENST00000537455.1_Splice_Site_p.E556fs|DLG2_ENST00000404783.3_Splice_Site_p.E284fs|DLG2_ENST00000531015.1_Splice_Site_p.E773fs			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	502					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TTATTCATCTCCCTGGGAAAA	0.333																																						ENST00000398309.2																			0				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71						c.e22-1		discs, large homolog 2 (Drosophila)							126.0	117.0	120.0					11																	83173135		1874	4136	6010	SO:0001630	splice_region_variant	1740					cell junction|postsynaptic density|postsynaptic membrane	guanylate kinase activity|protein binding	g.chr11:83173135delC	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.2361-1G>-	11.37:g.83173135delC						DLG2_ENST00000543673.1_Splice_Site_p.E911_splice|DLG2_ENST00000418306.2_Splice_Site_p.E685_splice|DLG2_ENST00000531015.1_Splice_Site_p.E773_splice|DLG2_ENST00000426717.2_Splice_Site_p.E270_splice|DLG2_ENST00000376104.2_Splice_Site_p.E911_splice|DLG2_ENST00000376106.3_Splice_Site_p.E270_splice|DLG2_ENST00000537455.1_Splice_Site_p.E556_splice|DLG2_ENST00000330014.6_Splice_Site_p.E727_splice|DLG2_ENST00000280241.8_Splice_Site_p.E845_splice|DLG2_ENST00000404783.3_Splice_Site_p.E284_splice|DLG2_ENST00000524982.1_Splice_Site_p.E802_splice|DLG2_ENST00000532653.1_Splice_Site_p.E788_splice	p.E806_splice	NM_001364.3	NP_001355.2	Q15700	DLG2_HUMAN			22	2886	-		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)	806			Guanylate kinase-like.		B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Splice_Site	DEL	ENST00000532653.1	37	c.2414_splice																																																																																					0.333	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	Frame_Shift_Del	7	142						7	142	---	---	---	---
RP11-252A24.2	0	broad.mit.edu	37	16	74394379	74394380	+	RNA	INS	-	-	A	rs142790741	byFrequency	TCGA-DJ-A3VE-01A-11D-A23M-08	TCGA-DJ-A3VE-10A-01D-A23K-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	749bbead-26b4-4262-9bcf-f9c209a45bfb	1178e2e9-37c4-4111-80ac-e57b675025bb	g.chr16:74394379_74394380insA	ENST00000429810.2	-	0	435																											TAGTCATCCTTAAACAAAATTC	0.347													|||unknown(NO_COVERAGE)	1085	0.216653	0.2474	0.1888	5008	,	,		27432	0.1379		0.2604	False		,,,				2504	0.2311					ENST00000429810.2																			0																																																			0							g.chr16:74394379_74394380insA																													16.37:g.74394382_74394382dupA														0	435	-									RNA	INS	ENST00000429810.2	37																																																																																						0.347	RP11-252A24.2-003	KNOWN	basic	retained_intron	pseudogene	OTTHUMT00000434683.1			4	5						4	5	---	---	---	---
