#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
TAB3	257397	broad.mit.edu	37	X	30877655	30877655	+	Silent	SNP	T	T	C			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chrX:30877655T>C	ENST00000378933.1	-	2	228	c.51A>G	c.(49-51)cgA>cgG	p.R17R	TAB3_ENST00000288422.2_Silent_p.R17R|TAB3_ENST00000378930.3_Silent_p.R17R|TAB3_ENST00000378932.2_Silent_p.R17R	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	17	CUE. {ECO:0000255|PROSITE- ProRule:PRU00468}.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						GGAAACGTTGTCGAAGATCAT	0.448																																					Pancreas(164;1598 1985 29022 43301 49529)	ENST00000378933.1																			0				NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						c.(49-51)cgA>cgG		TGF-beta activated kinase 1/MAP3K7 binding protein 3							99.0	78.0	85.0					X																	30877655		2202	4300	6502	SO:0001819	synonymous_variant	257397				activation of MAPK activity|I-kappaB kinase/NF-kappaB cascade|innate immune response|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|positive regulation of NF-kappaB transcription factor activity|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytosol|endosome membrane|plasma membrane	protein binding|zinc ion binding	g.chrX:30877655T>C	AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"""TAK1 binding protein 3"""	300480	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 3"""	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.51A>G	X.37:g.30877655T>C						TAB3_ENST00000378932.2_Silent_p.R17R|TAB3_ENST00000378930.3_Silent_p.R17R|TAB3_ENST00000288422.2_Silent_p.R17R	p.R17R	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN			2	228	-			17			CUE.		A6NDD9|Q6VQR0	Silent	SNP	ENST00000378933.1	37	c.51A>G	CCDS14226.1																																																																																				0.448	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787		4	22	0	0	0	1	0	4	22				
TDRD9	122402	broad.mit.edu	37	14	104473169	104473169	+	Missense_Mutation	SNP	T	T	C			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr14:104473169T>C	ENST00000409874.4	+	18	2042	c.1994T>C	c.(1993-1995)gTt>gCt	p.V665A	TDRD9_ENST00000339063.5_Missense_Mutation_p.V665A	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN	tudor domain containing 9	665					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|fertilization (GO:0009566)|gene silencing by RNA (GO:0031047)|male meiosis (GO:0007140)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|piP-body (GO:0071547)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)				ATTGCACTTGTTGAGGCATTT	0.358																																						ENST00000409874.4																			0				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	33						c.(1993-1995)gTt>gCt		tudor domain containing 9							73.0	64.0	67.0					14																	104473169		2203	4300	6503	SO:0001583	missense	122402				cell differentiation|DNA methylation involved in gamete generation|fertilization|gene silencing by RNA|male meiosis|multicellular organismal development|piRNA metabolic process|spermatogenesis	nucleus|piP-body	ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr14:104473169T>C	AK093483	CCDS9987.2	14q32.33	2013-01-23	2004-04-01	2004-04-02	ENSG00000156414	ENSG00000156414		"""Tudor domain containing"""	20122	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 75"""	C14orf75			Standard	NM_153046		Approved	DKFZp434N0820, FLJ36164, NET54	uc001yom.4	Q8NDG6	OTTHUMG00000152876	ENST00000409874.4:c.1994T>C	14.37:g.104473169T>C	ENSP00000387303:p.Val665Ala					TDRD9_ENST00000339063.5_Missense_Mutation_p.V665A	p.V665A	NM_153046.2	NP_694591.2	Q8NDG6	TDRD9_HUMAN			18	2042	+		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0768)	665					A1A4S7|Q6ZU54|Q8N7T3|Q8N827|Q8N9V5|Q96AS9	Missense_Mutation	SNP	ENST00000409874.4	37	c.1994T>C	CCDS9987.2	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826620	0.71143	.	.	ENSG00000156414	ENST00000409874;ENST00000339063	T;T	0.02656	4.21;4.21	5.37	5.37	0.77165	Helicase-associated domain (1);	0.089497	0.46758	D	0.000264	T	0.08447	0.0210	M	0.62723	1.935	0.58432	D	0.999999	P;B	0.52061	0.95;0.16	P;B	0.49999	0.628;0.314	T	0.01748	-1.1282	10	0.87932	D	0	.	15.3623	0.74487	0.0:0.0:0.0:1.0	.	665;665	Q8NDG6-2;Q8NDG6	.;TDRD9_HUMAN	A	665	ENSP00000387303:V665A;ENSP00000343545:V665A	ENSP00000343545:V665A	V	+	2	0	TDRD9	103542922	0.997000	0.39634	0.225000	0.23894	0.854000	0.48673	3.957000	0.56730	2.023000	0.59567	0.455000	0.32223	GTT		0.358	TDRD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328325.3	NM_153046		4	10	0	0	0	1	0	4	10				
ARHGAP30	257106	broad.mit.edu	37	1	161039405	161039405	+	Missense_Mutation	SNP	G	G	A	rs149081252		TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr1:161039405G>A	ENST00000368013.3	-	1	330	c.10C>T	c.(10-12)Cgg>Tgg	p.R4W	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R4W|ARHGAP30_ENST00000368015.1_Intron|PVRL4_ENST00000486694.1_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	4					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CCTTTCTGCCGAGACTTCATG	0.637																																						ENST00000368013.3																			0				breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						c.(10-12)Cgg>Tgg		Rho GTPase activating protein 30		G	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	90.0	83.0	85.0		10,10	4.6	1.0	1	dbSNP_134	85	0,8600		0,0,4300	no	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	101,101	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	probably-damaging,probably-damaging	4/1102,4/891	161039405	2,13004	2203	4300	6503	SO:0001583	missense	257106				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity	g.chr1:161039405G>A	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.10C>T	1.37:g.161039405G>A	ENSP00000356992:p.Arg4Trp					ARHGAP30_ENST00000368015.1_Intron|ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R4W	p.R4W	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.00122)		1	330	-	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		4					Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	c.10C>T	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	G	19.65	3.866667	0.72065	4.54E-4	0.0	ENSG00000186517	ENST00000368016;ENST00000368013	T;T	0.15139	2.6;2.45	4.64	4.64	0.57946	Rho GTPase-activating protein domain (1);	0.069143	0.56097	D	0.000040	T	0.26629	0.0651	L	0.54323	1.7	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.991;0.995	T	0.01242	-1.1408	10	0.87932	D	0	.	12.876	0.57989	0.0:0.0:1.0:0.0	.	4;4	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	W	4	ENSP00000356995:R4W;ENSP00000356992:R4W	ENSP00000356992:R4W	R	-	1	2	ARHGAP30	159306029	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.535000	0.53575	2.376000	0.81061	0.655000	0.94253	CGG		0.637	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720		6	66	0	0	0	1	0	6	66				
ATXN2	6311	broad.mit.edu	37	12	111894043	111894043	+	Silent	SNP	G	G	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr12:111894043G>A	ENST00000377617.3	-	23	3695	c.3534C>T	c.(3532-3534)gcC>gcT	p.A1178A	ATXN2_ENST00000389153.4_Silent_p.A915A|ATXN2_ENST00000542287.2_Silent_p.A913A|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000535949.1_Silent_p.A871A|ATXN2_ENST00000608853.1_Silent_p.A1018A	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN	ataxin 2	1178					cell death (GO:0008219)|cerebellar Purkinje cell differentiation (GO:0021702)|cytoplasmic mRNA processing body assembly (GO:0033962)|homeostasis of number of cells (GO:0048872)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of receptor internalization (GO:0002091)|neuromuscular process (GO:0050905)|neuron projection morphogenesis (GO:0048812)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA transport (GO:0050658)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)|trans-Golgi network (GO:0005802)	epidermal growth factor receptor binding (GO:0005154)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						GAGCCTGGGCGGCCTGGTGCT	0.552																																						ENST00000377617.3																			0				NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(8)|lung(6)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	37						c.(3532-3534)gcC>gcT		ataxin 2							135.0	126.0	129.0					12																	111894043		2203	4300	6503	SO:0001819	synonymous_variant	6311				cell death|cytoplasmic mRNA processing body assembly|regulation of translation|RNA metabolic process|RNA transport|stress granule assembly	nucleus|perinuclear region of cytoplasm|polysome|stress granule|trans-Golgi network	protein C-terminus binding|RNA binding	g.chr12:111894043G>A	U80749	CCDS31902.1	12q23-q24.1	2014-09-17	2004-08-12	2004-08-13	ENSG00000204842	ENSG00000204842		"""Ataxins"""	10555	protein-coding gene	gene with protein product	"""trinucleotide repeat containing 13"""	601517	"""spinocerebellar ataxia 2 (olivopontocerebellar ataxia 2, autosomal dominant, ataxin 2)"""	SCA2, TNRC13		8358438, 9225980	Standard	NM_002973		Approved	ATX2	uc001tsj.3	Q99700	OTTHUMG00000133475	ENST00000377617.3:c.3534C>T	12.37:g.111894043G>A						ATXN2_ENST00000535949.1_Silent_p.A871A|ATXN2_ENST00000389153.4_Silent_p.A915A|ATXN2_ENST00000550104.1_3'UTR|ATXN2_ENST00000542287.2_Silent_p.A913A	p.A1178A	NM_002973.3	NP_002964.3	Q99700	ATX2_HUMAN			23	3695	-			1178					A6NLD4|Q6ZQZ7|Q99493	Silent	SNP	ENST00000377617.3	37	c.3534C>T	CCDS31902.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143230	0.37825	.	.	ENSG00000204842	ENST00000550889	.	.	.	5.95	-5.31	0.02730	.	.	.	.	.	T	0.50582	0.1624	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57625	-0.7779	5	0.87932	D	0	-9.3575	1.933	0.03331	0.473:0.1142:0.1187:0.2941	.	.	.	.	L	63	.	ENSP00000449162:P63L	P	-	2	0	ATXN2	110378426	0.018000	0.18449	0.932000	0.37286	0.981000	0.71138	-0.906000	0.04071	-0.853000	0.04136	-1.149000	0.01842	CCG		0.552	ATXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257351.3	NM_002973		10	103	0	0	0	1	0	10	103				
IRF9	10379	broad.mit.edu	37	14	24633826	24633826	+	Missense_Mutation	SNP	A	A	G	rs569115226		TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr14:24633826A>G	ENST00000396864.3	+	7	940	c.653A>G	c.(652-654)tAc>tGc	p.Y218C	RP11-468E2.4_ENST00000558468.1_3'UTR|IRF9_ENST00000557894.1_Missense_Mutation_p.Y116C	NM_006084.4	NP_006075.3	Q00978	IRF9_HUMAN	interferon regulatory factor 9	218					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16				GBM - Glioblastoma multiforme(265;0.00853)		TCCCCAGACTACTCACTGCTG	0.642													A|||	1	0.000199681	0.0008	0.0	5008	,	,		18512	0.0		0.0	False		,,,				2504	0.0					ENST00000396864.3																			0				NS(1)|breast(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(2)	16						c.(652-654)tAc>tGc		interferon regulatory factor 9							83.0	83.0	83.0					14																	24633826		2202	4295	6497	SO:0001583	missense	10379				interferon-gamma-mediated signaling pathway|response to virus|transcription from RNA polymerase II promoter|type I interferon-mediated signaling pathway	cytosol|nucleoplasm	DNA binding|identical protein binding|sequence-specific DNA binding transcription factor activity	g.chr14:24633826A>G	M87503	CCDS9615.1	14q11.2	2007-07-06	2007-07-06	2007-07-06	ENSG00000213928	ENSG00000213928			6131	protein-coding gene	gene with protein product		147574	"""interferon-stimulated transcription factor 3, gamma (48kD)"", ""interferon-stimulated transcription factor 3, gamma 48kDa"""	ISGF3G		1630447, 10199920	Standard	NM_006084		Approved		uc001wmq.3	Q00978	OTTHUMG00000028799	ENST00000396864.3:c.653A>G	14.37:g.24633826A>G	ENSP00000380073:p.Tyr218Cys					RP11-468E2.4_ENST00000558468.1_3'UTR|IRF9_ENST00000557894.1_Missense_Mutation_p.Y116C	p.Y218C	NM_006084.4	NP_006075.3	Q00978	IRF9_HUMAN		GBM - Glioblastoma multiforme(265;0.00853)	7	940	+			218					D3DS61	Missense_Mutation	SNP	ENST00000396864.3	37	c.653A>G	CCDS9615.1	.	.	.	.	.	.	.	.	.	.	A	14.79	2.639555	0.47153	.	.	ENSG00000213928	ENST00000396864	D	0.94897	-3.55	5.32	1.39	0.22231	SMAD domain-like (1);SMAD/FHA domain (1);Interferon regulatory factor-3 (1);	0.177258	0.37530	U	0.002055	D	0.92388	0.7584	L	0.37850	1.14	0.34445	D	0.700012	D	0.65815	0.995	P	0.60236	0.871	D	0.89878	0.4028	10	0.33141	T	0.24	-16.9105	4.0443	0.09766	0.5917:0.0:0.089:0.3193	.	218	Q00978	IRF9_HUMAN	C	218	ENSP00000380073:Y218C	ENSP00000380073:Y218C	Y	+	2	0	IRF9	23703666	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.681000	0.25320	0.404000	0.25506	0.460000	0.39030	TAC		0.642	IRF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071927.2			16	100	0	0	0	1	0	16	100				
LCT	3938	broad.mit.edu	37	2	136564823	136564823	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr2:136564823C>T	ENST00000264162.2	-	9	4058	c.4048G>A	c.(4048-4050)Gcc>Acc	p.A1350T	Y_RNA_ENST00000363794.1_RNA	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN	lactase	1350	4 X approximate repeats.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glycosylceramidase activity (GO:0017042)|lactase activity (GO:0000016)			breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124				BRCA - Breast invasive adenocarcinoma(221;0.169)	Vitamin C(DB00126)	CTGGCGGAGGCTCTTGCTGTG	0.517																																						ENST00000264162.2																			0				breast(6)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(26)|lung(57)|ovary(7)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(4)	124						c.(4048-4050)Gcc>Acc		lactase							218.0	169.0	185.0					2																	136564823		2203	4300	6503	SO:0001583	missense	3938				carbohydrate metabolic process|polysaccharide digestion	apical plasma membrane|integral to plasma membrane|membrane fraction	cation binding|glycosylceramidase activity|lactase activity	g.chr2:136564823C>T	X07994	CCDS2178.1	2q21	2014-09-17			ENSG00000115850	ENSG00000115850	3.2.1.108, 3.2.1.62		6530	protein-coding gene	gene with protein product		603202					Standard	NM_002299		Approved		uc002tuu.1	P09848	OTTHUMG00000131738	ENST00000264162.2:c.4048G>A	2.37:g.136564823C>T	ENSP00000264162:p.Ala1350Thr						p.A1350T	NM_002299.2	NP_002290.2	P09848	LPH_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.169)	9	4058	-			1350			4 X approximate repeats.		Q4ZG58	Missense_Mutation	SNP	ENST00000264162.2	37	c.4048G>A	CCDS2178.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.330312	0.24167	.	.	ENSG00000115850	ENST00000264162;ENST00000455227	T	0.32753	1.44	5.87	-0.469	0.12142	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.849281	0.11193	N	0.589663	T	0.17831	0.0428	L	0.31926	0.97	0.19575	N	0.999963	B	0.06786	0.001	B	0.11329	0.006	T	0.37220	-0.9715	10	0.07644	T	0.81	-7.0941	7.39	0.26905	0.0:0.3094:0.188:0.5026	.	1350	P09848	LPH_HUMAN	T	1350;782	ENSP00000264162:A1350T	ENSP00000264162:A1350T	A	-	1	0	LCT	136281293	0.990000	0.36364	0.990000	0.47175	0.922000	0.55478	0.558000	0.23469	-0.187000	0.10516	-0.797000	0.03246	GCC		0.517	LCT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254657.1	NM_002299		7	61	0	0	0	1	0	7	61				
COLGALT2	23127	broad.mit.edu	37	1	183914685	183914685	+	Missense_Mutation	SNP	T	T	G			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr1:183914685T>G	ENST00000361927.4	-	9	1521	c.1150A>C	c.(1150-1152)Agc>Cgc	p.S384R	COLGALT2_ENST00000546159.1_Missense_Mutation_p.S384R|COLGALT2_ENST00000367521.1_5'UTR|COLGALT2_ENST00000367520.3_Missense_Mutation_p.S121R	NM_015101.2	NP_055916.1	Q8IYK4	GT252_HUMAN	collagen beta(1-O)galactosyltransferase 2	384					extracellular matrix organization (GO:0030198)|lipopolysaccharide biosynthetic process (GO:0009103)	endoplasmic reticulum lumen (GO:0005788)	procollagen galactosyltransferase activity (GO:0050211)										TTCAGCTGGCTTGTGTTGAGT	0.488																																						ENST00000361927.4																			0											c.(1150-1152)Agc>Cgc		collagen beta(1-O)galactosyltransferase 2							131.0	128.0	129.0					1																	183914685		2203	4300	6503	SO:0001583	missense	23127							g.chr1:183914685T>G	AF288389	CCDS1360.1	1q25	2013-02-27	2013-02-27	2013-02-27	ENSG00000198756	ENSG00000198756			16790	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 17"", ""glycosyltransferase 25 domain containing 2"""	C1orf17, GLT25D2		19075007	Standard	XM_005245008		Approved	KIAA0584	uc001gqr.3	Q8IYK4	OTTHUMG00000035460	ENST00000361927.4:c.1150A>C	1.37:g.183914685T>G	ENSP00000354960:p.Ser384Arg					COLGALT2_ENST00000546159.1_Missense_Mutation_p.S384R|COLGALT2_ENST00000367520.3_Missense_Mutation_p.S121R|COLGALT2_ENST00000367521.1_5'UTR	p.S384R	NM_015101.2	NP_055916.1					9	1521	-								O60327|Q9BZR0	Missense_Mutation	SNP	ENST00000361927.4	37	c.1150A>C	CCDS1360.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.029135	0.75504	.	.	ENSG00000198756	ENST00000546159;ENST00000361927;ENST00000367520	T;T	0.78924	-1.21;-1.22	5.39	5.39	0.77823	.	0.147534	0.64402	D	0.000010	D	0.87661	0.6233	M	0.77712	2.385	0.53688	D	0.999975	D;D;D	0.76494	0.999;0.996;0.998	D;D;D	0.75020	0.967;0.985;0.985	D	0.88868	0.3331	10	0.59425	D	0.04	-16.0238	15.3979	0.74812	0.0:0.0:0.0:1.0	.	384;384;121	F5H3T5;Q8IYK4;Q5SXQ3	.;GT252_HUMAN;.	R	384;384;121	ENSP00000439112:S384R;ENSP00000354960:S384R	ENSP00000354960:S384R	S	-	1	0	GLT25D2	182181308	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	4.788000	0.62439	2.042000	0.60477	0.455000	0.32223	AGC		0.488	COLGALT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086128.1	NM_015101		41	56	0	0	0	1	0	41	56				
TBP	6908	broad.mit.edu	37	6	170871058	170871058	+	Silent	SNP	G	G	A	rs113440919		TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr6:170871058G>A	ENST00000392092.2	+	3	513	c.234G>A	c.(232-234)caG>caA	p.Q78Q	TBP_ENST00000230354.6_Silent_p.Q78Q|TBP_ENST00000540980.1_Silent_p.Q58Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	78	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagc	0.577																																						ENST00000392092.2																			0				breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26						c.(232-234)caG>caA		TATA box binding protein							13.0	18.0	16.0					6																	170871058		1927	3786	5713	SO:0001819	synonymous_variant	6908				cell death|interspecies interaction between organisms|transcription elongation from RNA polymerase II promoter|transcription from RNA polymerase III promoter|viral reproduction	transcription factor TFIIA complex|transcription factor TFIID complex	repressing transcription factor binding|transcription regulatory region DNA binding	g.chr6:170871058G>A	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.234G>A	6.37:g.170871058G>A						TBP_ENST00000230354.6_Silent_p.Q78Q|TBP_ENST00000540980.1_Silent_p.Q58Q	p.Q78Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)	3	513	+		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)	78			Poly-Gln.		B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	c.234G>A	CCDS5315.1																																																																																				0.577	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194		3	28	0	0	0	1	0	3	28				
SLC12A8	84561	broad.mit.edu	37	3	124854521	124854521	+	Missense_Mutation	SNP	G	G	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr3:124854521G>A	ENST00000393469.4	-	5	777	c.728C>T	c.(727-729)gCg>gTg	p.A243V	SLC12A8_ENST00000314584.7_5'UTR|SLC12A8_ENST00000423114.2_Missense_Mutation_p.A272V|SLC12A8_ENST00000469902.1_Missense_Mutation_p.A243V	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	243					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						ACCTGTAGCCGCTGGGAAGAA	0.448																																						ENST00000423114.2																			0				endometrium(2)|kidney(2)|lung(12)	16						c.(814-816)gCg>gTg		solute carrier family 12, member 8							52.0	52.0	52.0					3																	124854521		1842	4089	5931	SO:0001583	missense	84561				potassium ion transport	integral to membrane	symporter activity	g.chr3:124854521G>A		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.728C>T	3.37:g.124854521G>A	ENSP00000377112:p.Ala243Val					SLC12A8_ENST00000393469.4_Missense_Mutation_p.A243V|SLC12A8_ENST00000469902.1_Missense_Mutation_p.A243V|SLC12A8_ENST00000314584.7_5'UTR	p.A272V			A0AV02	S12A8_HUMAN			6	814	-			243					C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Missense_Mutation	SNP	ENST00000393469.4	37	c.815C>T	CCDS43143.1	.	.	.	.	.	.	.	.	.	.	g	25.9	4.689803	0.88735	.	.	ENSG00000221955	ENST00000393469;ENST00000423114;ENST00000469902;ENST00000479826	D;D;D;D	0.99143	-5.48;-5.48;-5.48;-5.48	5.14	5.14	0.70334	Amino acid permease domain (1);	.	.	.	.	D	0.99330	0.9765	M	0.90650	3.135	0.80722	D	1	D;P;D	0.89917	1.0;0.899;0.995	D;P;P	0.67382	0.951;0.559;0.892	D	0.98832	1.0751	9	0.87932	D	0	.	15.6479	0.77068	0.0:0.0:1.0:0.0	.	135;272;243	B5MDT1;A0AV02-2;A0AV02	.;.;S12A8_HUMAN	V	243;272;243;125	ENSP00000377112:A243V;ENSP00000404243:A272V;ENSP00000418783:A243V;ENSP00000420197:A125V	ENSP00000377112:A243V	A	-	2	0	SLC12A8	126337211	1.000000	0.71417	0.807000	0.32361	0.920000	0.55202	6.401000	0.73256	2.664000	0.90586	0.550000	0.68814	GCG		0.448	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628		4	12	0	0	0	1	0	4	12				
KBTBD2	25948	broad.mit.edu	37	7	32910344	32910344	+	Missense_Mutation	SNP	G	G	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr7:32910344G>A	ENST00000304056.4	-	4	1184	c.485C>T	c.(484-486)gCt>gTt	p.A162V	AVL9_ENST00000404479.1_Intron|KBTBD2_ENST00000485611.1_5'Flank	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	kelch repeat and BTB (POZ) domain containing 2	162										endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17			GBM - Glioblastoma multiforme(11;0.0499)			ATGATACACAGCAGTGAACTT	0.398																																						ENST00000304056.4																			0				endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|urinary_tract(1)	17						c.(484-486)gCt>gTt		kelch repeat and BTB (POZ) domain containing 2							123.0	113.0	116.0					7																	32910344		2203	4300	6503	SO:0001583	missense	25948							g.chr7:32910344G>A	AB040922	CCDS34614.1	7p14.3	2013-01-08	2003-12-12	2003-12-12	ENSG00000170852	ENSG00000170852		"""BTB/POZ domain containing"""	21751	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 1"""	BKLHD1		10819331	Standard	NM_015483		Approved	DKFZP566C134	uc003tdb.2	Q8IY47	OTTHUMG00000152984	ENST00000304056.4:c.485C>T	7.37:g.32910344G>A	ENSP00000302586:p.Ala162Val					AVL9_ENST00000404479.1_Intron	p.A162V	NM_015483.2	NP_056298.2	Q8IY47	KBTB2_HUMAN	GBM - Glioblastoma multiforme(11;0.0499)		4	1184	-			162					A8K9T7|Q86Y62|Q9P239|Q9UFM7|Q9Y382	Missense_Mutation	SNP	ENST00000304056.4	37	c.485C>T	CCDS34614.1	.	.	.	.	.	.	.	.	.	.	G	6.697	0.497327	0.12762	.	.	ENSG00000170852	ENST00000304056	T	0.69685	-0.42	5.72	3.93	0.45458	BTB/Kelch-associated (2);	0.195495	0.53938	N	0.000042	T	0.50888	0.1642	N	0.17764	0.52	0.33491	D	0.588663	B	0.06786	0.001	B	0.04013	0.001	T	0.56571	-0.7957	10	0.44086	T	0.13	.	12.6831	0.56932	0.1336:0.0:0.8664:0.0	.	162	Q8IY47	KBTB2_HUMAN	V	162	ENSP00000302586:A162V	ENSP00000302586:A162V	A	-	2	0	KBTBD2	32876869	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.864000	0.48404	0.897000	0.36392	0.655000	0.94253	GCT		0.398	KBTBD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328890.1	XM_291224		9	73	0	0	0	1	0	9	73				
FGD6	55785	broad.mit.edu	37	12	95604019	95604019	+	Missense_Mutation	SNP	G	G	C			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr12:95604019G>C	ENST00000343958.4	-	2	1264	c.1041C>G	c.(1039-1041)agC>agG	p.S347R	FGD6_ENST00000546711.1_Missense_Mutation_p.S347R|FGD6_ENST00000550368.1_5'Flank|FGD6_ENST00000549499.1_Missense_Mutation_p.S347R	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN	FYVE, RhoGEF and PH domain containing 6	347	Poly-Ser.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						GACAGGAAGAGCTACTGTCTG	0.418																																						ENST00000343958.4																			0				breast(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(14)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56						c.(1039-1041)agC>agG		FYVE, RhoGEF and PH domain containing 6							105.0	107.0	106.0					12																	95604019		2203	4300	6503	SO:0001583	missense	55785				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding	g.chr12:95604019G>C	AB037783	CCDS31878.1	12q23.1	2013-01-10				ENSG00000180263		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	21740	protein-coding gene	gene with protein product		613520					Standard	NM_018351		Approved	ZFYVE24, FLJ11183	uc001tdp.4	Q6ZV73	OTTHUMG00000170133	ENST00000343958.4:c.1041C>G	12.37:g.95604019G>C	ENSP00000344446:p.Ser347Arg					FGD6_ENST00000546711.1_Missense_Mutation_p.S347R|FGD6_ENST00000549499.1_Missense_Mutation_p.S347R	p.S347R	NM_018351.3	NP_060821.3	Q6ZV73	FGD6_HUMAN			2	1264	-			347			Poly-Ser.		Q6ZR53|Q7Z2Z7|Q96D44|Q9NUR8|Q9P2I5	Missense_Mutation	SNP	ENST00000343958.4	37	c.1041C>G	CCDS31878.1	.	.	.	.	.	.	.	.	.	.	G	9.305	1.054051	0.19907	.	.	ENSG00000180263	ENST00000343958;ENST00000546711;ENST00000549499	T;T;T	0.67345	-0.16;-0.26;-0.18	5.71	5.71	0.89125	.	0.947990	0.08799	N	0.892073	T	0.55970	0.1954	N	0.22421	0.69	0.09310	N	1	B	0.28128	0.201	B	0.26969	0.075	T	0.49808	-0.8900	10	0.66056	D	0.02	0.0064	11.7743	0.51977	0.0869:0.0:0.9131:0.0	.	347	Q6ZV73	FGD6_HUMAN	R	347	ENSP00000344446:S347R;ENSP00000450342:S347R;ENSP00000449005:S347R	ENSP00000344446:S347R	S	-	3	2	FGD6	94128150	0.976000	0.34144	0.107000	0.21349	0.595000	0.36748	2.837000	0.48191	2.684000	0.91462	0.561000	0.74099	AGC		0.418	FGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407600.1	NM_018351		35	46	0	0	0	1	0	35	46				
RYR1	6261	broad.mit.edu	37	19	38976754	38976754	+	Missense_Mutation	SNP	G	G	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr19:38976754G>A	ENST00000359596.3	+	34	5459	c.5459G>A	c.(5458-5460)cGc>cAc	p.R1820H	RYR1_ENST00000360985.3_Missense_Mutation_p.R1820H|RYR1_ENST00000355481.4_Missense_Mutation_p.R1820H			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1820	6 X approximate repeats.				calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GAGGCGGTGCGCGACGGTGGG	0.706																																						ENST00000355481.4																			0				NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285						c.(5458-5460)cGc>cAc		ryanodine receptor 1 (skeletal)	Dantrolene(DB01219)						59.0	58.0	59.0					19																	38976754		2203	4292	6495	SO:0001583	missense	6261				muscle contraction|release of sequestered calcium ion into cytosol|response to caffeine|response to hypoxia	cell cortex|cytosol|I band|integral to plasma membrane|junctional sarcoplasmic reticulum membrane|smooth endoplasmic reticulum|terminal cisterna	calcium ion binding|calmodulin binding|receptor activity|ryanodine-sensitive calcium-release channel activity	g.chr19:38976754G>A	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.5459G>A	19.37:g.38976754G>A	ENSP00000352608:p.Arg1820His					RYR1_ENST00000359596.3_Missense_Mutation_p.R1820H|RYR1_ENST00000360985.3_Missense_Mutation_p.R1820H	p.R1820H	NM_000540.2|NM_001042723.1	NP_000531.2|NP_001036188.1	P21817	RYR1_HUMAN	Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		34	5590	+	all_cancers(60;7.91e-06)		1820			6 X approximate repeats.		Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	c.5459G>A	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	G	9.869	1.198354	0.22037	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	T;T;T	0.73152	-0.72;-0.72;-0.72	3.7	2.65	0.31530	.	0.568502	0.14066	U	0.343739	T	0.59702	0.2213	N	0.22421	0.69	0.23735	N	0.996982	D;D	0.65815	0.995;0.99	P;P	0.52309	0.648;0.695	T	0.48269	-0.9050	10	0.36615	T	0.2	.	2.8544	0.05568	0.2771:0.0:0.5137:0.2092	.	1820;1820	P21817-2;P21817	.;RYR1_HUMAN	H	1820	ENSP00000352608:R1820H;ENSP00000347667:R1820H;ENSP00000354254:R1820H	ENSP00000347667:R1820H	R	+	2	0	RYR1	43668594	0.015000	0.18098	0.610000	0.28997	0.810000	0.45777	0.929000	0.28844	0.746000	0.32786	0.585000	0.79938	CGC		0.706	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1			10	77	0	0	0	1	0	10	77				
MYO5C	55930	broad.mit.edu	37	15	52488561	52488561	+	Missense_Mutation	SNP	G	G	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr15:52488561G>A	ENST00000261839.7	-	39	5101	c.4940C>T	c.(4939-4941)aCa>aTa	p.T1647I	RP11-430B1.2_ENST00000560518.1_lincRNA	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	1647	Dilute. {ECO:0000255|PROSITE- ProRule:PRU00503}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		ATCACTGTCTGTGGTCTTCTT	0.512																																						ENST00000261839.7																			0				breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66						c.(4939-4941)aCa>aTa		myosin VC							110.0	114.0	113.0					15																	52488561		2007	4168	6175	SO:0001583	missense	55930					myosin complex	actin binding|ATP binding|calmodulin binding|motor activity	g.chr15:52488561G>A	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.4940C>T	15.37:g.52488561G>A	ENSP00000261839:p.Thr1647Ile					RP11-430B1.2_ENST00000560518.1_lincRNA	p.T1647I	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN		all cancers(107;0.0137)	39	5101	-			1647			Dilute.		Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	c.4940C>T	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.724473	0.89298	.	.	ENSG00000128833	ENST00000261839	D	0.89746	-2.56	4.83	4.83	0.62350	Dilute (1);Dil domain (1);	0.000000	0.85682	D	0.000000	D	0.94637	0.8271	M	0.80746	2.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.95163	0.8283	10	0.72032	D	0.01	.	18.1264	0.89587	0.0:0.0:1.0:0.0	.	1647	Q9NQX4	MYO5C_HUMAN	I	1647	ENSP00000261839:T1647I	ENSP00000261839:T1647I	T	-	2	0	MYO5C	50275853	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	9.657000	0.98554	2.522000	0.85027	0.462000	0.41574	ACA		0.512	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728		7	42	0	0	0	1	0	7	42				
SEC14L5	9717	broad.mit.edu	37	16	5057420	5057420	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr16:5057420C>T	ENST00000251170.7	+	13	1685	c.1505C>T	c.(1504-1506)aCg>aTg	p.T502M		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	502						integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						CAGGAGCACACGGACCAGCTG	0.647																																						ENST00000251170.7																			0				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						c.(1504-1506)aCg>aTg		SEC14-like 5 (S. cerevisiae)							44.0	47.0	46.0					16																	5057420		2080	4203	6283	SO:0001583	missense	9717					integral to membrane|intracellular	transporter activity	g.chr16:5057420C>T	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1505C>T	16.37:g.5057420C>T	ENSP00000251170:p.Thr502Met						p.T502M	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN			13	1685	+			502						Missense_Mutation	SNP	ENST00000251170.7	37	c.1505C>T	CCDS45403.1	.	.	.	.	.	.	.	.	.	.	C	8.411	0.844213	0.16963	.	.	ENSG00000103184	ENST00000251170	T	0.70631	-0.5	4.82	3.86	0.44501	Cellular retinaldehyde-binding/triple function, C-terminal (1);	0.410645	0.22883	N	0.054496	T	0.57021	0.2025	N	0.22421	0.69	0.09310	N	1	P	0.38473	0.633	B	0.36378	0.223	T	0.53244	-0.8466	10	0.49607	T	0.09	-25.3283	14.263	0.66097	0.1566:0.8434:0.0:0.0	.	502	O43304	S14L5_HUMAN	M	502	ENSP00000251170:T502M	ENSP00000251170:T502M	T	+	2	0	SEC14L5	4997421	0.007000	0.16637	0.001000	0.08648	0.049000	0.14656	2.221000	0.42917	1.234000	0.43709	0.555000	0.69702	ACG		0.647	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1			12	14	0	0	0	1	0	12	14				
ASTL	431705	broad.mit.edu	37	2	96789863	96789863	+	Missense_Mutation	SNP	T	T	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr2:96789863T>A	ENST00000342380.2	-	9	1021	c.1022A>T	c.(1021-1023)gAg>gTg	p.E341V		NM_001002036.3	NP_001002036.3			astacin-like metallo-endopeptidase (M12 family)											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						ATGTGGGCTCTCCCCAGGCCC	0.652																																						ENST00000342380.2																			0				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|prostate(1)|skin(2)	30						c.(1021-1023)gAg>gTg		astacin-like metallo-endopeptidase (M12 family)							42.0	47.0	45.0					2																	96789863		2203	4299	6502	SO:0001583	missense	431705				proteolysis		metalloendopeptidase activity|zinc ion binding	g.chr2:96789863T>A	AJ537600	CCDS33249.1	2q11.1	2014-07-23	2006-10-10		ENSG00000188886	ENSG00000188886	3.4.24.21		31704	protein-coding gene	gene with protein product	"""sperm acrosomal SLLP1 binding"""	608860	"""astacin-like metalloendopeptidase (M12 family)"""			15087446	Standard	NM_001002036		Approved	ovastacin, SAS1B	uc010yui.2	Q6HA08	OTTHUMG00000155212	ENST00000342380.2:c.1022A>T	2.37:g.96789863T>A	ENSP00000343674:p.Glu341Val						p.E341V	NM_001002036.3	NP_001002036.3	Q6HA08	ASTL_HUMAN			9	1021	-			341						Missense_Mutation	SNP	ENST00000342380.2	37	c.1022A>T	CCDS33249.1	.	.	.	.	.	.	.	.	.	.	T	13.73	2.324970	0.41197	.	.	ENSG00000188886	ENST00000342380	T	0.68765	-0.35	4.77	3.61	0.41365	.	1.101640	0.07105	N	0.841237	T	0.53802	0.1819	L	0.27053	0.805	0.09310	N	1	B	0.32693	0.38	B	0.32533	0.147	T	0.50533	-0.8817	10	0.87932	D	0	-8.975	6.5764	0.22569	0.0:0.1081:0.0:0.8919	.	341	Q6HA08	ASTL_HUMAN	V	341	ENSP00000343674:E341V	ENSP00000343674:E341V	E	-	2	0	ASTL	96153590	0.044000	0.20184	0.173000	0.22940	0.030000	0.12068	0.526000	0.22971	1.919000	0.55581	0.454000	0.30748	GAG		0.652	ASTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338801.1			4	75	0	0	0	1	0	4	75				
FBXL20	84961	broad.mit.edu	37	17	37420555	37420555	+	Missense_Mutation	SNP	A	A	G			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr17:37420555A>G	ENST00000264658.6	-	14	1336	c.1076T>C	c.(1075-1077)aTt>aCt	p.I359T	FBXL20_ENST00000583610.1_Missense_Mutation_p.I359T|FBXL20_ENST00000577399.1_Missense_Mutation_p.I361T|FBXL20_ENST00000394294.3_Missense_Mutation_p.I327T	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	F-box and leucine-rich repeat protein 20	359					behavioral fear response (GO:0001662)	cytoplasm (GO:0005737)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22			LUAD - Lung adenocarcinoma(14;0.146)			GTCCAGCTCAATCACCTCCAG	0.522																																						ENST00000264658.6																			0				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22						c.(1075-1077)aTt>aCt		F-box and leucine-rich repeat protein 20							114.0	95.0	102.0					17																	37420555		2203	4300	6503	SO:0001583	missense	84961					cytoplasm		g.chr17:37420555A>G	BC007557	CCDS32640.1, CCDS54116.1	17q21.2	2011-06-09				ENSG00000108306		"""F-boxes / Leucine-rich repeats"""	24679	protein-coding gene	gene with protein product		609086				12477932	Standard	NM_032875		Approved	MGC15482, Fbl2, Fbl20	uc002hrt.3	Q96IG2		ENST00000264658.6:c.1076T>C	17.37:g.37420555A>G	ENSP00000264658:p.Ile359Thr					FBXL20_ENST00000577399.1_Missense_Mutation_p.I361T|FBXL20_ENST00000394294.3_Missense_Mutation_p.I327T|FBXL20_ENST00000583610.1_Missense_Mutation_p.I359T	p.I359T	NM_032875.2	NP_116264.2	Q96IG2	FXL20_HUMAN	LUAD - Lung adenocarcinoma(14;0.146)		14	1336	-			359					A8K729|Q38J52	Missense_Mutation	SNP	ENST00000264658.6	37	c.1076T>C	CCDS32640.1	.	.	.	.	.	.	.	.	.	.	A	24.2	4.504822	0.85176	.	.	ENSG00000108306	ENST00000264658;ENST00000394294	T;T	0.56103	0.48;0.48	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	L	0.46157	1.445	0.80722	D	1	P;P	0.39862	0.692;0.57	B;B	0.33620	0.167;0.071	T	0.53697	-0.8402	10	0.87932	D	0	.	15.7399	0.77887	1.0:0.0:0.0:0.0	.	327;359	Q96IG2-2;Q96IG2	.;FXL20_HUMAN	T	359;327	ENSP00000264658:I359T;ENSP00000377832:I327T	ENSP00000264658:I359T	I	-	2	0	FBXL20	34674081	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.287000	0.95975	2.254000	0.74563	0.460000	0.39030	ATT		0.522	FBXL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444315.2	NM_032875		7	36	0	0	0	1	0	7	36				
RLTPR	146206	broad.mit.edu	37	16	67680391	67680391	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr16:67680391C>T	ENST00000334583.6	+	6	765	c.437C>T	c.(436-438)tCg>tTg	p.S146L	RLTPR_ENST00000545661.1_Missense_Mutation_p.S146L	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN	RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing	146					cell migration (GO:0016477)|establishment of protein localization (GO:0045184)|homeostasis of number of cells (GO:0048872)|maintenance of cell polarity (GO:0030011)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma secretion (GO:1902715)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|T cell receptor signaling pathway (GO:0050852)|thymus development (GO:0048538)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|F-actin capping protein complex (GO:0008290)|immunological synapse (GO:0001772)|membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)		AGCAGCCCCTCGGAGTCCACT	0.652																																						ENST00000334583.6																			0				breast(1)|cervix(1)|endometrium(4)|kidney(1)|lung(9)|urinary_tract(2)	18						c.(436-438)tCg>tTg		RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing							43.0	49.0	47.0					16																	67680391		1949	4158	6107	SO:0001583	missense	146206							g.chr16:67680391C>T	AB113647	CCDS45513.1	16q22.1	2010-09-10				ENSG00000159753			27089	protein-coding gene	gene with protein product	"""RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein"", ""leucine rich repeat containing 16C"""	610859				15588584, 19846667	Standard	XM_005255807		Approved	LRRC16C, CARMIL2	uc002etn.3	Q6F5E8		ENST00000334583.6:c.437C>T	16.37:g.67680391C>T	ENSP00000334958:p.Ser146Leu					RLTPR_ENST00000545661.1_Missense_Mutation_p.S146L	p.S146L	NM_001013838.1	NP_001013860.1	Q6F5E8	LR16C_HUMAN		OV - Ovarian serous cystadenocarcinoma(108;0.0146)|Epithelial(162;0.0481)|all cancers(182;0.232)	6	765	+		Acute lymphoblastic leukemia(13;3.23e-05)|all_hematologic(13;0.00251)|Ovarian(137;0.192)	146					B8X2Z3	Missense_Mutation	SNP	ENST00000334583.6	37	c.437C>T	CCDS45513.1	.	.	.	.	.	.	.	.	.	.	C	4.560	0.104001	0.08731	.	.	ENSG00000159753	ENST00000334583;ENST00000545661	T;T	0.14766	2.54;2.48	4.87	-0.84	0.10755	.	3.336290	0.02247	N	0.066329	T	0.12220	0.0297	L	0.32530	0.975	0.09310	N	1	B;B	0.16396	0.0;0.017	B;B	0.10450	0.0;0.005	T	0.33979	-0.9847	10	0.23302	T	0.38	-7.4372	10.0101	0.41981	0.0:0.5638:0.0:0.4362	.	146;146	B8X2Z3;Q6F5E8	.;LR16C_HUMAN	L	146	ENSP00000334958:S146L;ENSP00000441481:S146L	ENSP00000334958:S146L	S	+	2	0	RLTPR	66237892	0.000000	0.05858	0.272000	0.24630	0.002000	0.02628	-0.546000	0.06062	0.008000	0.14787	-1.149000	0.01842	TCG		0.652	RLTPR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467858.1	NM_001013838		4	63	0	0	0	1	0	4	63				
FOXM1	2305	broad.mit.edu	37	12	2970493	2970493	+	Intron	SNP	A	A	G			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr12:2970493A>G	ENST00000359843.3	-	9	1335				FOXM1_ENST00000342628.2_Missense_Mutation_p.L451S|FOXM1_ENST00000361953.3_Intron|Y_RNA_ENST00000410561.1_RNA	NM_021953.3	NP_068772.2	Q08050	FOXM1_HUMAN	forkhead box M1						cell cycle (GO:0007049)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|G2/M transition of mitotic cell cycle (GO:0000086)|liver development (GO:0001889)|mitotic cell cycle (GO:0000278)|negative regulation of cell aging (GO:0090344)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell cycle (GO:0051726)|regulation of cell cycle arrest (GO:0071156)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of Ras protein signal transduction (GO:0046578)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24			OV - Ovarian serous cystadenocarcinoma(31;0.000622)			aaaattaaacaagctggtgat	0.363																																						ENST00000342628.2																			0				breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(3)	24						c.(1351-1353)tTg>tCg		forkhead box M1							71.0	66.0	68.0					12																	2970493		2203	4300	6503	SO:0001627	intron_variant	2305				cell cycle|embryo development|liver development|negative regulation of cell aging|negative regulation of stress-activated MAPK cascade|negative regulation of transcription from RNA polymerase II promoter|pattern specification process|positive regulation of cell proliferation|positive regulation of transcription from RNA polymerase II promoter|regulation of cell cycle arrest|regulation of cell growth|regulation of cell proliferation|regulation of oxygen and reactive oxygen species metabolic process|regulation of Ras protein signal transduction|regulation of reactive oxygen species metabolic process|regulation of sequence-specific DNA binding transcription factor activity|tissue development|transcription from RNA polymerase II promoter|vasculogenesis	cytoplasm|transcription factor complex	DNA bending activity|DNA binding|double-stranded DNA binding|promoter binding|protein binding|protein domain specific binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|transcription factor binding	g.chr12:2970493A>G	Y12773	CCDS8515.1, CCDS8516.1, CCDS8517.1	12p13	2007-09-18			ENSG00000111206	ENSG00000111206		"""Forkhead boxes"""	3818	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 2"""	602341		FKHL16		9032290, 9441747	Standard	NM_202002		Approved	HFH-11, trident, HNF-3, INS-1, MPP2, MPHOSPH2, TGT3	uc001qlf.3	Q08050	OTTHUMG00000168118	ENST00000359843.3:c.1267-1664T>C	12.37:g.2970493A>G						FOXM1_ENST00000361953.3_Intron|FOXM1_ENST00000359843.3_Intron	p.L451S	NM_202002.2	NP_973731.1	Q08050	FOXM1_HUMAN	OV - Ovarian serous cystadenocarcinoma(31;0.000622)		9	1465	-			422					O43258|O43259|O43260|Q4ZGG7|Q9BRL2	Missense_Mutation	SNP	ENST00000359843.3	37	c.1352T>C	CCDS8515.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.296105	0.23650	.	.	ENSG00000111206	ENST00000342628	D	0.94184	-3.37	0.865	0.865	0.19074	.	.	.	.	.	D	0.92116	0.7501	.	.	.	0.33007	D	0.527072	D	0.62365	0.991	D	0.65323	0.934	D	0.87995	0.2752	8	0.13470	T	0.59	.	3.9806	0.09493	1.0:0.0:0.0:0.0	.	451	Q08050-3	.	S	451	ENSP00000342307:L451S	ENSP00000342307:L451S	L	-	2	0	FOXM1	2840754	0.006000	0.16342	0.494000	0.27515	0.036000	0.12997	-0.007000	0.12810	0.637000	0.30526	0.164000	0.16699	TTG		0.363	FOXM1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398272.1	NM_021953		6	24	0	0	0	1	0	6	24				
NPHS1	4868	broad.mit.edu	37	19	36333388	36333388	+	Missense_Mutation	SNP	C	C	T	rs146400394		TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr19:36333388C>T	ENST00000378910.5	-	18	2398	c.2399G>A	c.(2398-2400)cGc>cAc	p.R800H	NPHS1_ENST00000353632.6_Missense_Mutation_p.R800H	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	800	Ig-like C2-type 7.				cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)	p.R800H(1)		NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			AATCCGCAGGCGCCCCGTTGG	0.607													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17530	0.0		0.0	False		,,,				2504	0.0					ENST00000378910.5																			1	Substitution - Missense(1)	p.R800H(1)	ovary(1)	NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74						c.(2398-2400)cGc>cAc		nephrosis 1, congenital, Finnish type (nephrin)		C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	94.0	90.0	92.0		2399	3.4	0.2	19	dbSNP_134	92	0,8600		0,0,4300	no	missense	NPHS1	NM_004646.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	800/1242	36333388	1,13005	2203	4300	6503	SO:0001583	missense	4868				cell adhesion|excretion|muscle organ development	integral to plasma membrane		g.chr19:36333388C>T		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.2399G>A	19.37:g.36333388C>T	ENSP00000368190:p.Arg800His					NPHS1_ENST00000353632.6_Missense_Mutation_p.R800H	p.R800H	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	LUSC - Lung squamous cell carcinoma(66;0.0515)		18	2398	-	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		800			Ig-like C2-type 7.		A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	c.2399G>A	CCDS32996.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.629	-0.818010	0.02776	2.27E-4	0.0	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.78707	-1.2;-1.2	4.46	3.43	0.39272	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.340502	0.29791	N	0.011187	T	0.76912	0.4054	M	0.65498	2.005	0.09310	N	0.999992	D	0.55385	0.971	P	0.49597	0.616	T	0.65990	-0.6034	10	0.25751	T	0.34	-1.0032	8.212	0.31488	0.0:0.8912:0.0:0.1088	.	800	O60500	NPHN_HUMAN	H	800	ENSP00000368190:R800H;ENSP00000343634:R800H	ENSP00000343634:R800H	R	-	2	0	NPHS1	41025228	0.000000	0.05858	0.179000	0.23059	0.016000	0.09150	0.127000	0.15790	1.117000	0.41842	0.558000	0.71614	CGC		0.607	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1			6	105	0	0	0	1	0	6	105				
HSD17B7P2	158160	broad.mit.edu	37	10	38654432	38654432	+	RNA	SNP	A	A	G	rs2257765		TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr10:38654432A>G	ENST00000494540.1	+	0	599					NR_003086.1				hydroxysteroid (17-beta) dehydrogenase 7 pseudogene 2																		TCATCTCGCAATGCAAGGAAA	0.453																																						ENST00000494540.1																			0																																																			158160							g.chr10:38654432A>G			10p11.1	2011-06-29			ENSG00000099251	ENSG00000099251			28120	pseudogene	pseudogene						10544267	Standard	NR_003086		Approved	HSD17B7, bA291L22.1	uc010qex.1		OTTHUMG00000017993		10.37:g.38654432A>G								NR_003086.1						0	599	+									RNA	SNP	ENST00000494540.1	37																																																																																						0.453	HSD17B7P2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000047631.2	NR_003086		3	45	0	0	0	1	0	3	45				
DGAT2	84649	broad.mit.edu	37	11	75509417	75509417	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr11:75509417C>T	ENST00000228027.7	+	7	1215	c.955C>T	c.(955-957)Ctc>Ttc	p.L319F	RP11-535A19.1_ENST00000534354.1_RNA|DGAT2_ENST00000376262.3_Missense_Mutation_p.L276F	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN	diacylglycerol O-acyltransferase 2	319					acylglycerol acyl-chain remodeling (GO:0036155)|cellular lipid metabolic process (GO:0044255)|cellular response to oleic acid (GO:0071400)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|diacylglycerol metabolic process (GO:0046339)|fat pad development (GO:0060613)|fatty acid homeostasis (GO:0055089)|glycerol metabolic process (GO:0006071)|glycerophospholipid biosynthetic process (GO:0046474)|lipid storage (GO:0019915)|long-chain fatty-acyl-CoA metabolic process (GO:0035336)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid metabolic process (GO:0006644)|regulation of plasma lipoprotein particle levels (GO:0097006)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)|protein homodimerization activity (GO:0042803)|retinol O-fatty-acyltransferase activity (GO:0050252)			endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17	Ovarian(111;0.103)					TGGTCGAGGCCTCTTCTCCTC	0.587																																					Melanoma(35;811 1096 8354 24009 39363)	ENST00000228027.7																			0				endometrium(3)|large_intestine(5)|lung(5)|prostate(2)|skin(2)	17						c.(955-957)Ctc>Ttc		diacylglycerol O-acyltransferase 2							82.0	70.0	74.0					11																	75509417		2200	4293	6493	SO:0001583	missense	84649				glycerol metabolic process|triglyceride biosynthetic process	endoplasmic reticulum membrane|integral to membrane	diacylglycerol O-acyltransferase activity	g.chr11:75509417C>T		CCDS31642.1, CCDS58162.1	11q13.3	2010-06-24	2010-06-24		ENSG00000062282	ENSG00000062282			16940	protein-coding gene	gene with protein product		606983	"""diacylglycerol O-acyltransferase homolog 2 (mouse)"""			11481335, 14970677	Standard	NM_032564		Approved		uc001oxa.3	Q96PD7	OTTHUMG00000165338	ENST00000228027.7:c.955C>T	11.37:g.75509417C>T	ENSP00000228027:p.Leu319Phe					DGAT2_ENST00000376262.3_Missense_Mutation_p.L276F	p.L319F	NM_032564.4	NP_115953.2	Q96PD7	DGAT2_HUMAN			7	1215	+	Ovarian(111;0.103)		319					A6ND76|Q5U810|Q68CL3|Q68DJ0|Q8NDB7|Q96BS0|Q9BYE5	Missense_Mutation	SNP	ENST00000228027.7	37	c.955C>T	CCDS31642.1	.	.	.	.	.	.	.	.	.	.	C	14.05	2.420812	0.42918	.	.	ENSG00000062282	ENST00000228027;ENST00000376262;ENST00000525612	T;T	0.15952	2.38;2.38	5.59	-2.85	0.05734	.	0.374334	0.30686	N	0.009086	T	0.03827	0.0108	N	0.01297	-0.9	0.47905	D	0.999543	B;B	0.19935	0.04;0.004	B;B	0.21546	0.035;0.007	T	0.35076	-0.9803	10	0.29301	T	0.29	-9.7641	2.8998	0.05701	0.1109:0.3521:0.1091:0.428	.	276;319	Q96PD7-2;Q96PD7	.;DGAT2_HUMAN	F	319;276;273	ENSP00000228027:L319F;ENSP00000365438:L276F	ENSP00000228027:L319F	L	+	1	0	DGAT2	75187065	0.997000	0.39634	0.974000	0.42286	0.991000	0.79684	0.718000	0.25866	-0.441000	0.07201	-0.150000	0.13652	CTC		0.587	DGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383506.1	NM_032564		6	28	0	0	0	1	0	6	28				
ARID2	196528	broad.mit.edu	37	12	46246107	46246107	+	Missense_Mutation	SNP	A	A	C			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr12:46246107A>C	ENST00000334344.6	+	15	4373	c.4201A>C	c.(4201-4203)Atc>Ctc	p.I1401L	ARID2_ENST00000444670.1_Missense_Mutation_p.I1011L|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000422737.1_Missense_Mutation_p.I1252L|ARID2_ENST00000457135.1_Missense_Mutation_p.I9L	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1401					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		GACTTTAGATATCACTCAGCA	0.383			"""N, S, F"""		hepatocellular carcinoma																																	ENST00000334344.6				Rec	yes		12	12q12	196528	"""N, S, F"""	AT rich interactive domain 2			E			hepatocellular carcinoma		0				NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116						c.(4201-4203)Atc>Ctc		AT rich interactive domain 2 (ARID, RFX-like)							70.0	69.0	69.0					12																	46246107		2203	4300	6503	SO:0001583	missense	196528				chromatin modification|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|protein binding|zinc ion binding	g.chr12:46246107A>C		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.4201A>C	12.37:g.46246107A>C	ENSP00000335044:p.Ile1401Leu					ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000457135.1_Missense_Mutation_p.I9L|ARID2_ENST00000422737.1_Missense_Mutation_p.I1252L|ARID2_ENST00000444670.1_Missense_Mutation_p.I1011L	p.I1401L	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)	15	4373	+	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	1401					Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Missense_Mutation	SNP	ENST00000334344.6	37	c.4201A>C	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	A	1.337	-0.595237	0.03771	.	.	ENSG00000189079	ENST00000334344;ENST00000549153;ENST00000338636;ENST00000422737;ENST00000444670;ENST00000457135	T	0.27557	1.66	6.07	3.19	0.36642	.	0.456013	0.26891	N	0.021979	T	0.12305	0.0299	N	0.03608	-0.345	0.21147	N	0.999775	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.0;0.005;0.0	T	0.19745	-1.0296	10	0.34782	T	0.22	0.0677	6.1414	0.20261	0.2036:0.0:0.6652:0.1312	.	1401;1011;1401	Q68CP9-3;F8W108;Q68CP9	.;.;ARID2_HUMAN	L	1401;518;518;1252;1011;9	ENSP00000335044:I1401L	ENSP00000335044:I1401L	I	+	1	0	ARID2	44532374	1.000000	0.71417	0.999000	0.59377	0.933000	0.57130	1.618000	0.36954	0.451000	0.26802	-0.177000	0.13119	ATC		0.383	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875		7	50	0	0	0	1	0	7	50				
PADI2	11240	broad.mit.edu	37	1	17395638	17395638	+	Silent	SNP	G	G	A	rs61731909	byFrequency	TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr1:17395638G>A	ENST00000375486.4	-	16	1962	c.1899C>T	c.(1897-1899)gaC>gaT	p.D633D	PADI2_ENST00000466151.1_5'UTR|PADI2_ENST00000444885.2_Silent_p.D517D	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	633					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	CAGAAATGTCGTCGATGAAGG	0.597													G|||	2	0.000399361	0.0	0.0	5008	,	,		21555	0.001		0.0	False		,,,				2504	0.001					ENST00000375486.4																			0				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29						c.(1897-1899)gaC>gaT		peptidyl arginine deiminase, type II	L-Citrulline(DB00155)	G		2,4404	4.2+/-10.8	0,2,2201	115.0	105.0	108.0		1899	-8.4	0.4	1	dbSNP_129	108	0,8600		0,0,4300	no	coding-synonymous	PADI2	NM_007365.2		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		633/666	17395638	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11240				peptidyl-citrulline biosynthetic process from peptidyl-arginine	cytoplasm	calcium ion binding|protein-arginine deiminase activity	g.chr1:17395638G>A	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1899C>T	1.37:g.17395638G>A						PADI2_ENST00000444885.2_Silent_p.D517D|PADI2_ENST00000466151.1_5'UTR	p.D633D	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	16	1962	-		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)	633					Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	c.1899C>T	CCDS177.1																																																																																				0.597	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1			16	53	0	0	0	1	0	16	53				
FOXA2	3170	broad.mit.edu	37	20	22563313	22563313	+	Missense_Mutation	SNP	G	G	C			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr20:22563313G>C	ENST00000377115.4	-	3	730	c.549C>G	c.(547-549)agC>agG	p.S183R	FOXA2_ENST00000419308.2_Missense_Mutation_p.S189R	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	183					adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					GGTAGATCTCGCTCAGCGTCA	0.587																																						ENST00000419308.2																			0				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22						c.(547-549)agC>agG		forkhead box A2							135.0	117.0	123.0					20																	22563313		2203	4300	6503	SO:0001583	missense	3170				cell differentiation in hindbrain|central nervous system myelin formation|chromatin modification|dorsal/ventral neural tube patterning|ectoderm formation|endocrine pancreas development|endoderm development|epithelial tube branching involved in lung morphogenesis|in utero embryonic development|lung epithelial cell differentiation|negative regulation of neuron differentiation|neuron fate specification|oligodendrocyte cell fate commitment|positive regulation of embryonic development|positive regulation of gastrulation|positive regulation of neuron differentiation|primitive streak formation|regulation of blood coagulation|regulation of sequence-specific DNA binding transcription factor activity|response to interleukin-6	cytoplasm|transcription factor complex	DNA bending activity|double-stranded DNA binding|protein domain specific binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding|sequence-specific enhancer binding RNA polymerase II transcription factor activity|specific RNA polymerase II transcription factor activity|specific transcriptional repressor activity|transcription activator activity|transcription factor binding	g.chr20:22563313G>C	AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"""Forkhead boxes"""	5022	protein-coding gene	gene with protein product		600288	"""hepatocyte nuclear factor 3, beta"""	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.549C>G	20.37:g.22563313G>C	ENSP00000366319:p.Ser183Arg					FOXA2_ENST00000377115.4_Missense_Mutation_p.S183R|FOXA2_ENST00000319993.4_Missense_Mutation_p.S189R	p.S183R	NM_021784.4	NP_068556.2	Q9Y261	FOXA2_HUMAN			2	751	-	Lung NSC(19;0.188)		183					Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	c.549C>G	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.230300	0.58777	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.95853	-3.83;-3.83;-3.83	4.98	3.81	0.43845	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (4);	0.183985	0.32273	U	0.006324	D	0.96756	0.8941	M	0.63169	1.94	0.58432	D	0.999999	D;D	0.76494	0.981;0.999	P;D	0.74348	0.64;0.983	D	0.96995	0.9725	10	0.87932	D	0	.	13.9539	0.64135	0.0897:0.0:0.9103:0.0	.	183;189	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	R	183;183;189;69	ENSP00000366319:S183R;ENSP00000400341:S183R;ENSP00000315955:S189R	ENSP00000315955:S189R	S	-	3	2	FOXA2	22511313	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	0.865000	0.27940	2.304000	0.77564	0.574000	0.79327	AGC		0.587	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1			61	58	0	0	0	1	0	61	58				
NF1	4763	broad.mit.edu	37	17	29556992	29556992	+	Splice_Site	SNP	G	G	C			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr17:29556992G>C	ENST00000358273.4	+	22	3373	c.2990G>C	c.(2989-2991)aGg>aCg	p.R997T	NF1_ENST00000356175.3_Splice_Site_p.R997T	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	997					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(4)|p.R997K(1)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AATCTGGTCAGGTAAGCATTC	0.353			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												ENST00000358273.4			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	"""D, Mis, N, F, S, O"""	neurofibromatosis type 1 gene			O		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""	NF1/ACCN1(2)	13	Whole gene deletion(8)|Unknown(4)|Substitution - Missense(1)	p.0?(8)|p.?(4)|p.R997K(1)	soft_tissue(7)|central_nervous_system(3)|autonomic_ganglia(2)|lung(1)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599						c.e22+1		neurofibromin 1							86.0	86.0	86.0					17																	29556992		2201	4298	6499	SO:0001630	splice_region_variant	4763	Neurofibromatosis, type 1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29556992G>C		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.2990+1G>C	17.37:g.29556992G>C		TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_ENST00000356175.3_Splice_Site_p.R997_splice	p.R997_splice	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	22	3373	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	997					O00662|Q14284|Q14930|Q14931|Q9UMK3	Splice_Site	SNP	ENST00000358273.4	37	c.2990_splice	CCDS42292.1	.	.	.	.	.	.	.	.	.	.	.	32	5.138451	0.94560	.	.	ENSG00000196712	ENST00000358273;ENST00000356175;ENST00000456735	T;T;T	0.10382	3.05;3.19;2.88	5.46	5.46	0.80206	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.36248	0.0960	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	1.0;0.998;0.981;0.983	D;D;D;P	0.91635	0.999;0.94;0.962;0.908	T	0.05146	-1.0903	10	0.56958	D	0.05	.	19.3015	0.94145	0.0:0.0:1.0:0.0	.	997;47;997;997	E1P657;Q59FX3;P21359-2;P21359	.;.;.;NF1_HUMAN	T	997;997;663	ENSP00000351015:R997T;ENSP00000348498:R997T;ENSP00000389907:R663T	ENSP00000348498:R997T	R	+	2	0	NF1	26581118	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	9.434000	0.97515	2.550000	0.86006	0.455000	0.32223	AGG		0.353	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	Missense_Mutation	37	11	0	0	0	1	0	37	11				
MAGEC1	9947	broad.mit.edu	37	X	140994473	140994473	+	Missense_Mutation	SNP	C	C	T			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chrX:140994473C>T	ENST00000285879.4	+	4	1569	c.1283C>T	c.(1282-1284)cCt>cTt	p.P428L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	428										breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					CAGAGTTCTCCTGAGAGTGCT	0.448										HNSCC(15;0.026)																												ENST00000285879.4																			0				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127						c.(1282-1284)cCt>cTt		melanoma antigen family C, 1							102.0	111.0	108.0					X																	140994473		2194	4290	6484	SO:0001583	missense	9947						protein binding	g.chrX:140994473C>T	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.1283C>T	X.37:g.140994473C>T	ENSP00000285879:p.Pro428Leu	HNSCC(15;0.026)				MAGEC1_ENST00000406005.2_Intron	p.P428L	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN			4	1569	+	Acute lymphoblastic leukemia(192;6.56e-05)		428					A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	c.1283C>T	CCDS35417.1	.	.	.	.	.	.	.	.	.	.	c	5.018	0.189098	0.09547	.	.	ENSG00000155495	ENST00000285879	T	0.06768	3.26	.	.	.	.	.	.	.	.	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	P	0.38110	0.618	B	0.28638	0.092	T	0.39881	-0.9592	8	0.87932	D	0	.	5.9409	0.19192	0.0:0.9994:0.0:6.0E-4	.	428	O60732	MAGC1_HUMAN	L	428	ENSP00000285879:P428L	ENSP00000285879:P428L	P	+	2	0	MAGEC1	140822139	0.002000	0.14202	0.005000	0.12908	0.005000	0.04900	0.619000	0.24388	0.148000	0.19059	0.150000	0.16122	CCT		0.448	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462		7	184	0	0	0	1	0	7	184				
LOC100288069	100288069	broad.mit.edu	37	1	700514	700514	+	lincRNA	DEL	A	A	-			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr1:700514delA	ENST00000428504.1	-	0	1039				RP11-206L10.5_ENST00000417659.1_lincRNA	NR_033908.1																						actccatctcaaaaaaaaaaa	0.453																																						ENST00000428504.1																			0																																																			100288069							g.chr1:700514delA																													1.37:g.700514delA								NR_033908.1						0	1039	-									RNA	DEL	ENST00000428504.1	37																																																																																						0.453	RP11-206L10.2-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000006889.1			2	4						2	4	---	---	---	---
CSMD1	64478	broad.mit.edu	37	8	2815310	2815310	+	Frame_Shift_Del	DEL	A	A	-			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr8:2815310delA	ENST00000520002.1	-	64	10280	c.9725delT	c.(9724-9726)ttcfs	p.F3242fs	CSMD1_ENST00000537824.1_Frame_Shift_Del_p.F3241fs|CSMD1_ENST00000602723.1_Frame_Shift_Del_p.F3065fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.F3065fs|CSMD1_ENST00000542608.1_Frame_Shift_Del_p.F3064fs|CSMD1_ENST00000602557.1_Frame_Shift_Del_p.F3242fs			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	3242	Sushi 27. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TCTGCACCTGAAAAAAACCGT	0.453																																						ENST00000602557.1																			0				breast(20)|large_intestine(5)	25						c.(9724-9726)tcfs		CUB and Sushi multiple domains 1							84.0	76.0	78.0					8																	2815310		1899	4120	6019	SO:0001589	frameshift_variant	64478					integral to membrane		g.chr8:2815310delA			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.9725delT	8.37:g.2815310delA	ENSP00000430733:p.Phe3242fs					CSMD1_ENST00000602723.1_Frame_Shift_Del_p.F3065fs|CSMD1_ENST00000537824.1_Frame_Shift_Del_p.F3241fs|CSMD1_ENST00000520002.1_Frame_Shift_Del_p.F3242fs|CSMD1_ENST00000542608.1_Frame_Shift_Del_p.F3064fs|CSMD1_ENST00000400186.3_Frame_Shift_Del_p.F3065fs	p.F3242fs			Q96PZ7	CSMD1_HUMAN		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)	64	10280	-		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)	3242			Sushi 27.		Q0H0J5|Q96QU9|Q96RM4	Frame_Shift_Del	DEL	ENST00000520002.1	37	c.9725delT																																																																																					0.453	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225		2	4						2	4	---	---	---	---
GPSM1	26086	broad.mit.edu	37	9	139235482	139235482	+	Intron	DEL	C	C	-	rs374298038|rs145729152	byFrequency	TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr9:139235482delC	ENST00000440944.1	+	9	1427				GPSM1_ENST00000392945.3_Frame_Shift_Del_p.L413fs	NM_001145638.1	NP_001139110	Q86YR5	GPSM1_HUMAN	G-protein signaling modulator 1						cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	GDP-dissociation inhibitor activity (GO:0005092)			biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)		GGGTCTTGCTCCCCACAGGCA	0.687													?|CCCC|CCC|unsure	747	0.149161	0.0961	0.0793	5008	,	,		14952	0.252		0.1372	False		,,,				2504	0.1769					ENST00000392945.3																			0				biliary_tract(1)|endometrium(1)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9						c.(1237-1239)ctfs		G-protein signaling modulator 1			,	494,3628		54,386,1621	12.0	14.0	14.0		,	0.3	0.0	9	dbSNP_134	15	1203,6943		136,931,3006	no	frameshift,intron	GPSM1	NM_015597.4,NM_001145638.1	,	190,1317,4627	A1A1,A1R,RR		14.768,11.9845,13.8327	,	,	139235482	1697,10571	2116	4195	6311	SO:0001627	intron_variant	26086				cell differentiation|nervous system development|signal transduction	cytosol|endoplasmic reticulum membrane|Golgi membrane|plasma membrane	binding|GTPase activator activity	g.chr9:139235482delC	AI272212	CCDS6996.2, CCDS48055.1, CCDS48056.1	9q34.3	2013-01-10	2010-06-24		ENSG00000160360	ENSG00000160360		"""Tetratricopeptide (TTC) repeat domain containing"""	17858	protein-coding gene	gene with protein product	"""AGS3 homolog (C. elegans)"""	609491	"""G-protein signalling modulator 1 (AGS3-like, C. elegans)"""			11278352, 10969064	Standard	NM_001145639		Approved	AGS3, DKFZP727I051	uc004chd.2	Q86YR5	OTTHUMG00000020930	ENST00000440944.1:c.1207+32C>-	9.37:g.139235482delC						GPSM1_ENST00000440944.1_Intron	p.L413fs	NM_015597.4	NP_056412.4	Q86YR5	GPSM1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;2.39e-06)|Epithelial(140;3.24e-06)	9	1459	+		Myeloproliferative disorder(178;0.0821)	0			Interaction with STK11/LKB1 (By similarity).|Mediates association with membranes (By similarity).		A9Z1X4|B1B0W3|Q86SR5|Q969T1|Q9UFS8	Frame_Shift_Del	DEL	ENST00000440944.1	37	c.1239delC	CCDS48055.1																																																																																				0.687	GPSM1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015597		7	2						7	2	---	---	---	---
RP11-19N8.4	0	broad.mit.edu	37	16	33070154	33070154	+	lincRNA	DEL	C	C	-			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr16:33070154delC	ENST00000561541.1	-	0	291																											CCTATCACATCCCATTCCAGC	0.488																																						ENST00000561541.1																			0																																																			0							g.chr16:33070154delC																													16.37:g.33070154delC														0	291	-									RNA	DEL	ENST00000561541.1	37																																																																																						0.488	RP11-19N8.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000432096.1			3	6						3	6	---	---	---	---
BCAS3	54828	broad.mit.edu	37	17	59465991	59465992	+	Frame_Shift_Ins	INS	-	-	A			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr17:59465991_59465992insA	ENST00000589222.1	+	25	2740_2741	c.2672_2673insA	c.(2671-2676)ggaaaafs	p.GK891fs	BCAS3_ENST00000390652.5_Intron|RP11-332H18.5_ENST00000585765.1_RNA|BCAS3_ENST00000588874.1_Intron|BCAS3_ENST00000408905.3_Intron|BCAS3_ENST00000585744.1_Intron|BCAS3_ENST00000588462.1_Intron|BCAS3_ENST00000407086.3_Intron|BCAS3_ENST00000585812.1_Intron					breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			AAAAAAAAAGGAAAAAAAAAAC	0.431																																						ENST00000589222.1																			0				NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						c.(2671-2673)gaafs		breast carcinoma amplified sequence 3																																				SO:0001589	frameshift_variant	54828					nucleus		g.chr17:59465991_59465992insA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000589222.1:c.2682dupA	17.37:g.59466001_59466001dupA	ENSP00000466078:p.Gly891fs					BCAS3_ENST00000588462.1_Intron|BCAS3_ENST00000390652.5_Intron|RP11-332H18.5_ENST00000585765.1_RNA|BCAS3_ENST00000585812.1_Intron|BCAS3_ENST00000407086.3_Intron|BCAS3_ENST00000408905.3_Intron|BCAS3_ENST00000585744.1_Intron|BCAS3_ENST00000588874.1_Intron	p.E891fs			Q9H6U6	BCAS3_HUMAN	BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)		25	2740_2741	+			0						Frame_Shift_Ins	INS	ENST00000589222.1	37	c.2672_2673insA																																																																																					0.431	BCAS3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000449571.1	NM_017679		3	4						3	4	---	---	---	---
KCTD1	284252	broad.mit.edu	37	18	24128262	24128264	+	Intron	DEL	TCC	TCC	-			TCGA-RT-A6YA-01A-12D-A35D-08	TCGA-RT-A6YA-10B-01D-A35B-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	05227ee7-4ecf-4dd2-bbff-9e457664f858	5d7caf6d-3e44-48f0-96f4-0838b3c38d98	g.chr18:24128262_24128264delTCC	ENST00000408011.3	-	1	545				KCTD1_ENST00000417602.1_In_Frame_Del_p.E79del|KCTD1_ENST00000580059.1_5'Flank|KCTD1_ENST00000317932.7_Intron|KCTD1_ENST00000579973.1_Intron	NM_001136205.2	NP_001129677.1	Q719H9	KCTD1_HUMAN	potassium channel tetramerization domain containing 1						negative regulation of transcription, DNA-templated (GO:0045892)|protein homooligomerization (GO:0051260)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)			cccacctccgtcctcctcctcct	0.69																																						ENST00000417602.1																			0				endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(3)	12						c.(235-240)gac>ga		potassium channel tetramerization domain containing 1			,,	34,7,3315		2,0,30,2,3,1641					,,	3.5	1.0			3	107,4,6623		7,0,93,0,4,3263	no	intron,codingComplex,intron	KCTD1	NM_198991.2,NM_001142730.1,NM_001136205.1	,,	9,0,123,2,7,4904	A1A1,A1A2,A1R,A2A2,A2R,RR		1.6484,1.2217,1.5064	,,	,,		141,11,9938				SO:0001627	intron_variant	284252				negative regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|voltage-gated potassium channel complex	transcription corepressor activity|transcription factor binding|voltage-gated potassium channel activity	g.chr18:24128262_24128264delTCC	AF542549	CCDS11888.1	18q11.2	2013-09-20	2013-06-20		ENSG00000134504	ENSG00000134504			18249	protein-coding gene	gene with protein product		613420	"""potassium channel tetramerisation domain containing 1"""	C18orf5			Standard	NM_001142730		Approved		uc010xbj.3	Q719H9	OTTHUMG00000131947	ENST00000408011.3:c.14+590GGA>-	18.37:g.24128271_24128273delTCC						KCTD1_ENST00000317932.7_Intron|KCTD1_ENST00000408011.3_Intron|KCTD1_ENST00000579973.1_Intron	p.ED79del	NM_001142730.2	NP_001136202.1	Q719H9	KCTD1_HUMAN	Epithelial(2;7.8e-06)|OV - Ovarian serous cystadenocarcinoma(3;9.02e-06)|all cancers(3;3.37e-05)		1	236_238	-	all_cancers(21;0.00191)|Lung NSC(5;0.000698)|all_lung(6;0.0019)|Ovarian(20;0.0848)		0			BTB.		A8K1F5	In_Frame_Del	DEL	ENST00000408011.3	37	c.237_239delGGA	CCDS11888.1																																																																																				0.690	KCTD1-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000446265.1	XM_209091		3	3						3	3	---	---	---	---
