#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	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_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	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
HSPG2	3339	hgsc.bcm.edu	37	1	22176680	22176680	+	Missense_Mutation	SNP	C	C	T	rs372361312		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:22176680C>T	ENST00000374695.3	-	57	7379	c.7300G>A	c.(7300-7302)Ggg>Agg	p.G2434R	HSPG2_ENST00000430507.1_3'UTR	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2434	Ig-like C2-type 9.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GGGGTGACCCCAAGTGCTGGG	0.637																																					p.G2434R		Atlas-SNP	.											.	HSPG2	311	.	0			c.G7300A						PASS	.						37.0	42.0	40.0					1																	22176680		2203	4300	6503	SO:0001583	missense	3339	exon57			TGACCCCAAGTGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.7300G>A	chr1.hg19:g.22176680C>T	ENSP00000363827:p.Gly2434Arg	146.0	0.0	.		89.0	11.0	.	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	hg19	CCDS30625.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.075228	0.36662	.	.	ENSG00000142798	ENST00000374695	T	0.75938	-0.98	5.29	3.33	0.38152	.	0.000000	0.39083	N	0.001469	T	0.67268	0.2875	M	0.63843	1.955	0.22330	N	0.999195	B;B	0.16802	0.01;0.019	B;B	0.20577	0.03;0.025	T	0.54918	-0.8221	10	0.29301	T	0.29	.	7.5389	0.27727	0.0:0.7341:0.1656:0.1003	.	374;2434	Q59EG0;P98160	.;PGBM_HUMAN	R	2434	ENSP00000363827:G2434R	ENSP00000363827:G2434R	G	-	1	0	HSPG2	22049267	0.006000	0.16342	0.483000	0.27378	0.979000	0.70002	0.634000	0.24614	0.522000	0.28464	0.561000	0.74099	GGG	.	.	.	none		0.637	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
TAF12	6883	hgsc.bcm.edu	37	1	28948461	28948461	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:28948461C>T	ENST00000263974.4	-	2	567	c.133G>A	c.(133-135)Ggg>Agg	p.G45R	TAF12_ENST00000373824.4_Missense_Mutation_p.G45R	NM_001135218.1	NP_001128690.1	Q16514	TAF12_HUMAN	TAF12 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 20kDa	45					chromatin organization (GO:0006325)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone H3 acetylation (GO:0043966)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of RNA biosynthetic process (GO:2001141)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			ovary(1)|upper_aerodigestive_tract(1)	2		Colorectal(325;3.46e-05)|Lung NSC(340;0.000451)|all_lung(284;0.00063)|Renal(390;0.00121)|Breast(348;0.00502)|all_neural(195;0.0227)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)		Colorectal(126;3.21e-08)|COAD - Colon adenocarcinoma(152;1.74e-06)|STAD - Stomach adenocarcinoma(196;0.00303)|KIRC - Kidney renal clear cell carcinoma(1967;0.0109)|BRCA - Breast invasive adenocarcinoma(304;0.0228)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCCTGCCCCAGGAGTGCCT	0.468																																					p.G45R		Atlas-SNP	.											.	TAF12	17	.	0			c.G133A						PASS	.						157.0	149.0	151.0					1																	28948461		2203	4300	6503	SO:0001583	missense	6883	exon2			CTGCCCCAGGAGT	BC011986	CCDS326.1	1p35	2008-02-05	2002-08-29	2001-12-07	ENSG00000120656	ENSG00000120656			11545	protein-coding gene	gene with protein product		600773	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, J, 20kD"""	TAF2J		7729427	Standard	NM_005644		Approved	TAFII20	uc001bqy.3	Q16514	OTTHUMG00000003655	ENST00000263974.4:c.133G>A	chr1.hg19:g.28948461C>T	ENSP00000263974:p.Gly45Arg	132.0	0.0	.		112.0	5.0	.	NM_001135218	D3DPM5|Q15775|Q5T077	Missense_Mutation	SNP	ENST00000263974.4	hg19	CCDS326.1	.	.	.	.	.	.	.	.	.	.	C	9.352	1.065712	0.20067	.	.	ENSG00000120656	ENST00000373824;ENST00000263974	.	.	.	5.17	5.17	0.71159	.	0.101675	0.64402	D	0.000002	T	0.45955	0.1368	L	0.32530	0.975	0.43724	D	0.996205	B;B	0.26512	0.126;0.151	B;B	0.32533	0.147;0.095	T	0.32666	-0.9898	9	0.13470	T	0.59	-5.9182	11.6763	0.51432	0.0:0.913:0.0:0.087	.	15;45	Q16514-2;Q16514	.;TAF12_HUMAN	R	45	.	ENSP00000263974:G45R	G	-	1	0	TAF12	28821048	1.000000	0.71417	1.000000	0.80357	0.011000	0.07611	3.514000	0.53422	2.405000	0.81733	0.591000	0.81541	GGG	.	.	.	none		0.468	TAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010367.1	NM_005644	
FPGT	8790	hgsc.bcm.edu	37	1	74671342	74671342	+	Silent	SNP	A	A	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:74671342A>G	ENST00000609362.1	+	4	1648	c.1611A>G	c.(1609-1611)tcA>tcG	p.S537S	FPGT_ENST00000370894.5_3'UTR|FPGT_ENST00000524915.1_Intron|FPGT_ENST00000534056.1_Silent_p.S283S|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370898.3_Silent_p.S550S|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|TNNI3K_ENST00000370891.2_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	537					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)			breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						TGAGTGACTCAGTTATAACAT	0.383																																					p.S537S		Atlas-SNP	.											.	FPGT	77	.	0			c.A1611G						PASS	.						136.0	124.0	128.0					1																	74671342		2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TGACTCAGTTATA	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.1611A>G	chr1.hg19:g.74671342A>G		74.0	0.0	.		90.0	31.0	.	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	hg19	CCDS663.1																																																																																			.	.	.	none		0.383	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CA14	23632	hgsc.bcm.edu	37	1	150235713	150235713	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:150235713G>C	ENST00000369111.4	+	8	1706	c.736G>C	c.(736-738)Ggg>Cgg	p.G246R	snoU13_ENST00000458929.1_RNA	NM_012113.1	NP_036245.1	Q9ULX7	CAH14_HUMAN	carbonic anhydrase XIV	246					bicarbonate transport (GO:0015701)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	18	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)		Acetazolamide(DB00819)|Zonisamide(DB00909)	AAAGCTTCAGGGGACATTGTT	0.517																																					p.G246R		Atlas-SNP	.											.	CA14	37	.	0			c.G736C						PASS	.						92.0	97.0	95.0					1																	150235713		2203	4300	6503	SO:0001583	missense	23632	exon8			CTTCAGGGGACAT	AB025904	CCDS947.1	1q21	2008-02-05			ENSG00000118298	ENSG00000118298		"""Carbonic anhydrases"""	1372	protein-coding gene	gene with protein product		604832				10512682	Standard	XM_005245059		Approved		uc001etx.3	Q9ULX7	OTTHUMG00000012549	ENST00000369111.4:c.736G>C	chr1.hg19:g.150235713G>C	ENSP00000358107:p.Gly246Arg	149.0	0.0	.		178.0	77.0	.	NM_012113	Q5TB24|Q8NCF4	Missense_Mutation	SNP	ENST00000369111.4	hg19	CCDS947.1	.	.	.	.	.	.	.	.	.	.	G	13.89	2.372423	0.42003	.	.	ENSG00000118298	ENST00000369111	T	0.65549	-0.16	5.46	3.56	0.40772	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.341654	0.31279	N	0.007932	T	0.13970	0.0338	N	0.01817	-0.705	0.24121	N	0.995806	B	0.18610	0.029	B	0.24701	0.055	T	0.22208	-1.0223	10	0.29301	T	0.29	.	7.2635	0.26217	0.089:0.1705:0.7405:0.0	.	246	Q9ULX7	CAH14_HUMAN	R	246	ENSP00000358107:G246R	ENSP00000358107:G246R	G	+	1	0	CA14	148502337	0.976000	0.34144	0.954000	0.39281	0.918000	0.54935	1.973000	0.40550	0.834000	0.34852	0.655000	0.94253	GGG	.	.	.	none		0.517	CA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035064.2	NM_012113	
RPRD2	23248	hgsc.bcm.edu	37	1	150437078	150437078	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:150437078C>A	ENST00000369068.4	+	10	1491	c.1487C>A	c.(1486-1488)cCt>cAt	p.P496H	RPRD2_ENST00000492220.1_3'UTR|RPRD2_ENST00000401000.4_Missense_Mutation_p.P470H|RPRD2_ENST00000539519.1_Missense_Mutation_p.P470H	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	496	Ser-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						CTGAAAACACCTGCACCTGCC	0.547											OREG0013786	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P496H		Atlas-SNP	.											.	RPRD2	189	.	0			c.C1487A						PASS	.						73.0	92.0	86.0					1																	150437078		2064	4183	6247	SO:0001583	missense	23248	exon10			AAACACCTGCACC	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.1487C>A	chr1.hg19:g.150437078C>A	ENSP00000358064:p.Pro496His	72.0	0.0	.	1732	92.0	39.0	.	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	hg19	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.080155	0.76528	.	.	ENSG00000163125	ENST00000401000;ENST00000539519;ENST00000369068	T;T;T	0.68479	-0.33;0.06;-0.24	5.34	4.42	0.53409	.	0.188129	0.45361	N	0.000370	T	0.53142	0.1778	M	0.61703	1.905	0.52099	D	0.999945	B;B;B	0.24368	0.005;0.062;0.102	B;B;B	0.24155	0.003;0.023;0.051	T	0.61535	-0.7043	10	0.87932	D	0	-12.2819	15.5276	0.75923	0.1392:0.8608:0.0:0.0	.	470;496;470	B4E2Q6;Q5VT52;Q5VT52-3	.;RPRD2_HUMAN;.	H	470;470;496	ENSP00000383785:P470H;ENSP00000445482:P470H;ENSP00000358064:P496H	ENSP00000358064:P496H	P	+	2	0	RPRD2	148703702	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	7.060000	0.76692	1.472000	0.48140	-0.182000	0.12963	CCT	.	.	.	none		0.547	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
KDM5B	10765	hgsc.bcm.edu	37	1	202724423	202724423	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr1:202724423C>T	ENST00000367265.3	-	11	2678	c.1514G>A	c.(1513-1515)aGc>aAc	p.S505N	KDM5B_ENST00000367264.2_Missense_Mutation_p.S541N|KDM5B_ENST00000456180.1_5'UTR	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	505	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						AATTGAATAGCTCCAGTGGTC	0.403																																					p.S505N		Atlas-SNP	.											.	KDM5B	166	.	0			c.G1514A						PASS	.						113.0	113.0	113.0					1																	202724423		2203	4300	6503	SO:0001583	missense	10765	exon11			GAATAGCTCCAGT	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.1514G>A	chr1.hg19:g.202724423C>T	ENSP00000356234:p.Ser505Asn	78.0	0.0	.		77.0	25.0	.	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	hg19	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	C	36	5.653576	0.96724	.	.	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790	T;T;T	0.73152	-0.72;-0.72;-0.72	5.73	5.73	0.89815	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.000000	0.85682	D	0.000000	D	0.83367	0.5239	M	0.69358	2.11	0.80722	D	1	D;D	0.63046	0.992;0.989	P;D	0.68039	0.798;0.955	D	0.84199	0.0449	10	0.87932	D	0	-17.7337	19.9036	0.96999	0.0:1.0:0.0:0.0	.	541;505	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	N	505;347;541;347	ENSP00000356234:S505N;ENSP00000356233:S541N;ENSP00000235790:S347N	ENSP00000235790:S347N	S	-	2	0	KDM5B	200991046	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.814000	0.86154	2.706000	0.92434	0.655000	0.94253	AGC	.	.	.	none		0.403	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
CGREF1	10669	hgsc.bcm.edu	37	2	27324436	27324436	+	Silent	SNP	G	G	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:27324436G>T	ENST00000260595.5	-	6	955	c.663C>A	c.(661-663)ccC>ccA	p.P221P	CGREF1_ENST00000452318.2_Intron|CGREF1_ENST00000402550.1_Intron|CGREF1_ENST00000402394.1_Silent_p.P221P|CGREF1_ENST00000312734.4_Silent_p.P221P|CGREF1_ENST00000405600.1_Silent_p.P221P|CGREF1_ENST00000404694.3_Silent_p.P343P			Q99674	CGRE1_HUMAN	cell growth regulator with EF-hand domain 1	221					cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|response to stress (GO:0006950)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			kidney(1)|lung(4)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CTTCCCCTCTGGGCCCTGGAA	0.652																																					p.P221P		Atlas-SNP	.											.	CGREF1	31	.	0			c.C663A						PASS	.						113.0	133.0	126.0					2																	27324436		2203	4300	6503	SO:0001819	synonymous_variant	10669	exon6			CCCTCTGGGCCCT	BC034764	CCDS33162.1, CCDS33162.2, CCDS54339.1	2p23.3	2013-01-10			ENSG00000138028	ENSG00000138028		"""EF-hand domain containing"""	16962	protein-coding gene	gene with protein product		606137				8968090	Standard	NM_006569		Approved	CGR11	uc002riq.3	Q99674	OTTHUMG00000152009	ENST00000260595.5:c.663C>A	chr2.hg19:g.27324436G>T		47.0	0.0	.		50.0	15.0	.	NM_001166239	A6NHV7|B4DXY8|B5MCB7|B5MCC9|B5MCP5|E7EU99|Q8N4B7	Silent	SNP	ENST00000260595.5	hg19																																																																																				.	.	.	none		0.652	CGREF1-201	KNOWN	basic	protein_coding	protein_coding		NM_006569	
C2orf78	388960	hgsc.bcm.edu	37	2	74043789	74043789	+	Silent	SNP	A	A	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:74043789A>T	ENST00000409561.1	+	3	2560	c.2439A>T	c.(2437-2439)tcA>tcT	p.S813S		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	813										cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						CTAGGCCATCAGCCTACAAAA	0.522																																					p.S813S		Atlas-SNP	.											.	C2orf78	150	.	0			c.A2439T						PASS	.						71.0	69.0	70.0					2																	74043789		2020	4178	6198	SO:0001819	synonymous_variant	388960	exon3			GCCATCAGCCTAC	AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.2439A>T	chr2.hg19:g.74043789A>T		70.0	0.0	.		83.0	34.0	.	NM_001080474		Silent	SNP	ENST00000409561.1	hg19	CCDS46338.1																																																																																			.	.	.	none		0.522	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474	
PKP4	8502	hgsc.bcm.edu	37	2	159477605	159477605	+	Silent	SNP	A	A	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:159477605A>G	ENST00000389759.3	+	5	496	c.384A>G	c.(382-384)ccA>ccG	p.P128P	PKP4_ENST00000389757.3_Silent_p.P128P	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	128					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TCTATTCACCAGAACAGACAT	0.423										HNSCC(62;0.18)																											p.P128P		Atlas-SNP	.											.	PKP4	133	.	0			c.A384G						PASS	.						110.0	98.0	102.0					2																	159477605		2203	4300	6503	SO:0001819	synonymous_variant	8502	exon5			TTCACCAGAACAG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.384A>G	chr2.hg19:g.159477605A>G		241.0	0.0	.		253.0	83.0	.	NM_001005476	Q86W91	Silent	SNP	ENST00000389759.3	hg19	CCDS33305.1																																																																																			.	.	.	none		0.423	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
HSPE1	3336	hgsc.bcm.edu	37	2	198367837	198367837	+	Silent	SNP	A	A	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:198367837A>G	ENST00000233893.5	+	3	686	c.243A>G	c.(241-243)gtA>gtG	p.V81V	HSPE1_ENST00000465573.1_3'UTR|HSPE1-MOB4_ENST00000604458.1_Intron|HSPE1_ENST00000409468.1_Silent_p.V81V|HSPE1_ENST00000409729.1_Silent_p.V26V|HSPD1_ENST00000345042.2_5'Flank	NM_002157.2	NP_002148.1	P61604	CH10_HUMAN	heat shock 10kDa protein 1	81					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|osteoblast differentiation (GO:0001649)|protein folding (GO:0006457)|response to unfolded protein (GO:0006986)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			lung(1)	1			Epithelial(96;0.225)			GCACCAAAGTAGTTCTAGATG	0.343																																					p.V81V		Atlas-SNP	.											.	HSPE1	2	.	0			c.A243G						PASS	.						148.0	159.0	155.0					2																	198367837		2203	4300	6503	SO:0001819	synonymous_variant	3336	exon3			CAAAGTAGTTCTA	AF109872	CCDS2320.1	2q33.1	2013-10-17	2013-10-17		ENSG00000115541	ENSG00000115541		"""Heat Shock Proteins / Chaperonins"""	5269	protein-coding gene	gene with protein product	"""chaperonin 10"""	600141	"""heat shock 10kD protein 1 (chaperonin 10)"""			7914093, 7698325	Standard	NM_002157		Approved	CPN10, GROES		P61604	OTTHUMG00000132749	ENST00000233893.5:c.243A>G	chr2.hg19:g.198367837A>G		69.0	0.0	.		31.0	13.0	.	NM_002157	O95421|Q04984|Q53X54|Q9UDH0	Silent	SNP	ENST00000233893.5	hg19	CCDS2320.1																																																																																			.	.	.	none		0.343	HSPE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256112.1	NM_002157	
CD200R1	131450	hgsc.bcm.edu	37	3	112648333	112648333	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:112648333T>G	ENST00000471858.1	-	3	387	c.155A>C	c.(154-156)aAg>aCg	p.K52T	CD200R1_ENST00000440122.2_Missense_Mutation_p.K75T|CD200R1_ENST00000490004.1_Missense_Mutation_p.K52T|CD200R1_ENST00000295863.4_Missense_Mutation_p.K30T|CD200R1_ENST00000308611.3_Missense_Mutation_p.K75T	NM_170780.2	NP_740750.1	Q8TD46	MO2R1_HUMAN	CD200 receptor 1	52					regulation of immune response (GO:0050776)|viral process (GO:0016032)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	26						TGTAGCCATCTTTACAGGCCA	0.373																																					p.K75T		Atlas-SNP	.											.	CD200R1	91	.	0			c.A224C						PASS	.						76.0	73.0	74.0					3																	112648333		2203	4300	6503	SO:0001583	missense	131450	exon4			GCCATCTTTACAG	AK126349	CCDS2969.1, CCDS2970.1, CCDS46889.1, CCDS54623.1	3q13	2014-05-15	2004-08-31	2004-09-01	ENSG00000163606	ENSG00000163606		"""Immunoglobulin superfamily / C2-set domain containing"""	24235	protein-coding gene	gene with protein product		607546	"""MOX2 receptor"""	MOX2R		10981966, 11133863	Standard	NM_138806		Approved	OX2R, HCRTR2, CD200R	uc003dzj.1	Q8TD46	OTTHUMG00000159298	ENST00000471858.1:c.155A>C	chr3.hg19:g.112648333T>G	ENSP00000418928:p.Lys52Thr	30.0	0.0	.		50.0	14.0	.	NM_138806	B3KWZ9|E9PCM9|Q52LJ7|Q6IS95|Q6UW94|Q6WHB8|Q8TD44|Q8TD45|Q8TD52	Missense_Mutation	SNP	ENST00000471858.1	hg19	CCDS2970.1	.	.	.	.	.	.	.	.	.	.	T	6.153	0.396370	0.11638	.	.	ENSG00000163606	ENST00000471858;ENST00000308611;ENST00000295863;ENST00000440122;ENST00000490004	T;T;T;T;T	0.09255	3.0;3.0;3.0;3.0;3.0	5.5	-11.0	0.00169	Immunoglobulin subtype (1);	2.986180	0.00757	N	0.001111	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.0;0.0;0.0	T	0.21484	-1.0244	10	0.25751	T	0.34	.	6.6183	0.22788	0.2992:0.0:0.3016:0.3992	.	30;52;75;52;75	B4E2U2;Q8TD46-3;Q8TD46-2;Q8TD46;Q8TD46-4	.;.;.;MO2R1_HUMAN;.	T	52;75;30;75;52	ENSP00000418928:K52T;ENSP00000311035:K75T;ENSP00000295863:K30T;ENSP00000405733:K75T;ENSP00000418801:K52T	ENSP00000295863:K30T	K	-	2	0	CD200R1	114131023	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.518000	0.02246	-2.599000	0.00452	-2.119000	0.00349	AAG	.	.	.	none		0.373	CD200R1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354467.1	NM_138806	
IGSF10	285313	hgsc.bcm.edu	37	3	151155418	151155418	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:151155418A>T	ENST00000282466.3	-	6	6930	c.6931T>A	c.(6931-6933)Ttt>Att	p.F2311I	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2311	Ig-like C2-type 9.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACACAGATAAAGTCGGCTGAA	0.418																																					p.F2311I		Atlas-SNP	.											.	IGSF10	279	.	0			c.T6931A						PASS	.						138.0	133.0	135.0					3																	151155418		2203	4300	6503	SO:0001583	missense	285313	exon6			AGATAAAGTCGGC	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.6931T>A	chr3.hg19:g.151155418A>T	ENSP00000282466:p.Phe2311Ile	104.0	0.0	.		139.0	22.0	.	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	hg19	CCDS3160.1	.	.	.	.	.	.	.	.	.	.	A	23.9	4.468341	0.84533	.	.	ENSG00000152580	ENST00000282466	T	0.28454	1.61	5.77	5.77	0.91146	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.48767	D	0.000161	T	0.53061	0.1773	M	0.64676	1.99	0.80722	D	1	D;D	0.69078	0.997;0.964	D;P	0.69654	0.965;0.841	T	0.55604	-0.8115	10	0.87932	D	0	.	16.084	0.81025	1.0:0.0:0.0:0.0	.	2311;338	Q6WRI0;Q6WRI0-2	IGS10_HUMAN;.	I	2311	ENSP00000282466:F2311I	ENSP00000282466:F2311I	F	-	1	0	IGSF10	152638108	1.000000	0.71417	0.040000	0.18447	0.970000	0.65996	8.904000	0.92590	2.202000	0.70862	0.482000	0.46254	TTT	.	.	.	none		0.418	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
PHC3	80012	hgsc.bcm.edu	37	3	169896600	169896600	+	Missense_Mutation	SNP	C	C	A	rs375674359		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:169896600C>A	ENST00000494943.1	-	2	173	c.105G>T	c.(103-105)caG>caT	p.Q35H	PHC3_ENST00000467570.1_Missense_Mutation_p.Q47H|PHC3_ENST00000474275.1_Missense_Mutation_p.Q35H|PHC3_ENST00000495893.2_Missense_Mutation_p.Q47H|PHC3_ENST00000481639.1_Missense_Mutation_p.Q47H|PHC3_ENST00000497658.1_Missense_Mutation_p.Q47H			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	35					multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			AGACAGAGATCTGTGGCTGCT	0.458																																					p.Q47H		Atlas-SNP	.											.	PHC3	113	.	0			c.G141T						PASS	.	C	HIS/GLN	1,4131		0,1,2065	247.0	248.0	248.0		141	5.2	1.0	3		248	0,8456		0,0,4228	no	missense	PHC3	NM_024947.3	24	0,1,6293	AA,AC,CC		0.0,0.0242,0.0079	benign	47/996	169896600	1,12587	2066	4228	6294	SO:0001583	missense	80012	exon2			AGAGATCTGTGGC		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"""Sterile alpha motif (SAM) domain containing"""	15682	protein-coding gene	gene with protein product	"""early development regulator 3"", ""polyhomeotic like 3"""		"""polyhomeotic like 3 (Drosophila)"""			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.105G>T	chr3.hg19:g.169896600C>A	ENSP00000420271:p.Gln35His	84.0	0.0	.		72.0	14.0	.	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Missense_Mutation	SNP	ENST00000494943.1	hg19		.	.	.	.	.	.	.	.	.	.	C	23.0	4.364917	0.82463	2.42E-4	0.0	ENSG00000173889	ENST00000494943;ENST00000495893;ENST00000467570;ENST00000484931;ENST00000466189;ENST00000475729;ENST00000474275;ENST00000465896;ENST00000497658;ENST00000481639	T;T	0.39592	1.07;1.08	6.03	5.15	0.70609	.	0.098560	0.46145	D	0.000311	T	0.58032	0.2094	L	0.54323	1.7	0.40012	D	0.975309	D;D;D;D;D;D;D;D	0.64830	0.994;0.994;0.98;0.994;0.994;0.994;0.994;0.988	D;D;D;D;D;P;D;D	0.78314	0.986;0.991;0.965;0.986;0.991;0.805;0.986;0.984	T	0.54200	-0.8329	9	.	.	.	-6.4983	13.908	0.63848	0.0:0.9291:0.0:0.0709	.	47;47;35;47;47;35;47;47	B4E2T1;E7EX82;Q8NDX5;Q8NDX5-5;G5E9U7;Q8NDX5-4;Q8NDX5-3;Q8NDX5-7	.;.;PHC3_HUMAN;.;.;.;.;.	H	35;47;47;47;47;47;35;47;47;47	ENSP00000420271:Q35H;ENSP00000420294:Q47H	.	Q	-	3	2	PHC3	171379294	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.462000	0.35266	2.861000	0.98227	0.655000	0.94253	CAG	.	.	.	weak		0.458	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947	
SLC6A19	340024	hgsc.bcm.edu	37	5	1221280	1221280	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr5:1221280T>C	ENST00000304460.10	+	11	1609	c.1553T>C	c.(1552-1554)aTc>aCc	p.I518T		NM_001003841.2	NP_001003841.1	Q695T7	S6A19_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 19	518					amino acid transport (GO:0006865)|ion transport (GO:0006811)|response to nutrient (GO:0007584)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|neutral amino acid transmembrane transporter activity (GO:0015175)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(25)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	44	all_cancers(3;3.55e-15)|Lung NSC(6;2.89e-14)|all_lung(6;2.2e-13)|all_epithelial(6;3.75e-10)		Epithelial(17;0.000356)|all cancers(22;0.00137)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)			AATAAGGACATCGAGTTCATG	0.542																																					p.I518T		Atlas-SNP	.											.	SLC6A19	99	.	0			c.T1553C						PASS	.						124.0	92.0	103.0					5																	1221280		2203	4300	6503	SO:0001583	missense	340024	exon11			AGGACATCGAGTT	AK096054	CCDS34130.1	5p15	2013-07-19			ENSG00000174358	ENSG00000174358		"""Solute carriers"""	27960	protein-coding gene	gene with protein product	"""Hartnup disease"""	608893					Standard	NM_001003841		Approved		uc003jbw.4	Q695T7	OTTHUMG00000161636	ENST00000304460.10:c.1553T>C	chr5.hg19:g.1221280T>C	ENSP00000305302:p.Ile518Thr	89.0	0.0	.		60.0	28.0	.	NM_001003841	A8K446	Missense_Mutation	SNP	ENST00000304460.10	hg19	CCDS34130.1	.	.	.	.	.	.	.	.	.	.	T	18.98	3.737729	0.69304	.	.	ENSG00000174358	ENST00000304460	T	0.79033	-1.23	4.81	4.81	0.61882	.	0.107611	0.64402	D	0.000006	D	0.87916	0.6298	M	0.92367	3.3	0.51012	D	0.9999	P	0.50528	0.936	P	0.54174	0.744	D	0.90994	0.4837	10	0.87932	D	0	.	14.3786	0.66897	0.0:0.0:0.0:1.0	.	518	Q695T7	S6A19_HUMAN	T	518	ENSP00000305302:I518T	ENSP00000305302:I518T	I	+	2	0	SLC6A19	1274280	1.000000	0.71417	0.978000	0.43139	0.517000	0.34286	7.825000	0.86693	1.808000	0.52836	0.402000	0.26972	ATC	.	.	.	none		0.542	SLC6A19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365557.1	XM_291120	
ADAMTS6	11174	hgsc.bcm.edu	37	5	64755996	64755996	+	Splice_Site	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr5:64755996C>T	ENST00000536360.1	-	4	1445		c.e4+1					Q9UKP5	ATS6_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 6							proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|pancreas(1)|prostate(1)|skin(3)	18		Lung NSC(167;2.44e-06)|Prostate(74;0.014)|Ovarian(174;0.0549)|Breast(144;0.111)|Colorectal(97;0.235)		Lung(70;0.00942)		CACTCACTCACCCGAAACCCC	0.398																																					.		Atlas-SNP	.											.	ADAMTS6	174	.	0			c.631+1G>A						PASS	.						136.0	131.0	132.0					5																	64755996		2203	4300	6503	SO:0001630	splice_region_variant	11174	exon5			CACTCACCCGAAA	AF140674	CCDS3983.2	5q13	2008-07-18	2005-08-19		ENSG00000049192	ENSG00000049192		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	222	protein-coding gene	gene with protein product	"""a disintegrin and metalloproteinase with thrombospondin motifs 6"""	605008	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 6"""			10464288	Standard	NM_197941		Approved	ADAM-TS6	uc003jtp.3	Q9UKP5	OTTHUMG00000074079	ENST00000536360.1:c.631+1G>A	chr5.hg19:g.64755996C>T		49.0	0.0	.		59.0	4.0	.	NM_197941	Q59EX6|Q5IR87|Q5IR88|Q5IR89|Q68DL1	Splice_Site	SNP	ENST00000536360.1	hg19		.	.	.	.	.	.	.	.	.	.	C	17.65	3.442004	0.63067	.	.	ENSG00000049192	ENST00000381055;ENST00000261306;ENST00000464680;ENST00000536360	.	.	.	6.06	6.06	0.98353	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.6397	0.99537	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	ADAMTS6	64791752	1.000000	0.71417	1.000000	0.80357	0.424000	0.31475	7.353000	0.79414	2.880000	0.98712	0.650000	0.86243	.	.	.	.	none		0.398	ADAMTS6-201	KNOWN	basic	protein_coding	protein_coding		NM_197941	Intron
ELFN1	392617	hgsc.bcm.edu	37	7	1784273	1784273	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:1784273C>A	ENST00000424383.2	+	3	528	c.41C>A	c.(40-42)gCg>gAg	p.A14E	ELFN1_ENST00000541472.1_Missense_Mutation_p.A14E|AC074389.9_ENST00000453348.1_lincRNA|ELFN1_ENST00000561626.1_Missense_Mutation_p.A14E			P0C7U0	ELFN1_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 1	14					negative regulation of phosphatase activity (GO:0010923)|synapse organization (GO:0050808)	dendrite (GO:0030425)|excitatory synapse (GO:0060076)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)			endometrium(1)	1						GTGTGCGTGGCGGCCGCCACC	0.736																																					p.A14E		Atlas-SNP	.											.	ELFN1	22	.	0			c.C41A						PASS	.						21.0	30.0	27.0					7																	1784273		692	1590	2282	SO:0001583	missense	392617	exon2			GCGTGGCGGCCGC		CCDS59046.1	7p22.3	2013-02-11	2011-10-27	2011-10-27	ENSG00000225968	ENSG00000225968		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	33154	protein-coding gene	gene with protein product		614964	"""extracellular leucine-rich repeat and fibronectin type III containing 1"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 1"", ""protein phosphatase 1, regulatory subunit 28"""	PPP1R28		17868438	Standard	NM_001128636		Approved		uc010ksg.2	P0C7U0	OTTHUMG00000151495	ENST00000424383.2:c.41C>A	chr7.hg19:g.1784273C>A	ENSP00000456548:p.Ala14Glu	189.0	0.0	.		151.0	34.0	.	NM_001128636	H3BS57	Missense_Mutation	SNP	ENST00000424383.2	hg19	CCDS59046.1																																																																																			.	.	.	none		0.736	ELFN1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322893.2	NM_001128636	
PIP	5304	hgsc.bcm.edu	37	7	142832288	142832288	+	Splice_Site	SNP	C	C	T	rs376369577		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:142832288C>T	ENST00000291009.3	+	2	137	c.97C>T	c.(97-99)Cgg>Tgg	p.R33W		NM_002652.2	NP_002643.1	P12273	PIP_HUMAN	prolactin-induced protein	33					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of T cell apoptotic process (GO:0070233)|positive regulation of gene expression (GO:0010628)|proteolysis (GO:0006508)|regulation of immune system process (GO:0002682)|retina homeostasis (GO:0001895)	apical plasma membrane (GO:0016324)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	actin binding (GO:0003779)|aspartic-type endopeptidase activity (GO:0004190)|glycoprotein binding (GO:0001948)|IgG binding (GO:0019864)|protein dimerization activity (GO:0046983)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)	18	Melanoma(164;0.059)	Ovarian(593;2.82e-05)|Breast(660;0.012)		BRCA - Breast invasive adenocarcinoma(188;0.0026)|LUSC - Lung squamous cell carcinoma(290;0.0733)|Lung(243;0.08)		CACAATCAGTCGGAAGATCAT	0.463																																					p.R33W		Atlas-SNP	.											.	PIP	34	.	0			c.C97T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	52.0	47.0	49.0		97	0.0	0.0	7		49	1,8597	1.2+/-3.3	0,1,4298	no	missense-near-splice	PIP	NM_002652.2	101	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	33/147	142832288	1,13003	2203	4299	6502	SO:0001630	splice_region_variant	5304	exon2			ATCAGTCGGAAGA		CCDS34768.1	7q34	2013-09-19			ENSG00000159763	ENSG00000159763			8993	protein-coding gene	gene with protein product	"""prolactin-inducible protein"""	176720				2727805, 1955075	Standard	NM_002652		Approved	GCDFP-15, GCDFP15, GPIP4	uc003wcf.1	P12273	OTTHUMG00000152635	ENST00000291009.3:c.96-1C>T	chr7.hg19:g.142832288C>T		68.0	0.0	.		103.0	63.0	.	NM_002652	A0A963|A0A9C3|A0A9F3|A4D2I1	Missense_Mutation	SNP	ENST00000291009.3	hg19	CCDS34768.1	.	.	.	.	.	.	.	.	.	.	C	8.675	0.903680	0.17760	0.0	1.16E-4	ENSG00000159763	ENST00000291009	T	0.14640	2.49	4.2	0.0331	0.14178	.	0.625933	0.12805	N	0.437679	T	0.08980	0.0222	L	0.39397	1.21	0.09310	N	1	B	0.21452	0.056	B	0.15052	0.012	T	0.32877	-0.9890	10	0.51188	T	0.08	.	1.421	0.02312	0.172:0.4618:0.1673:0.1989	.	33	P12273	PIP_HUMAN	W	33	ENSP00000291009:R33W	ENSP00000291009:R33W	R	+	1	2	PIP	142542410	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.057000	0.14279	-0.096000	0.12329	-0.535000	0.04281	CGG	.	.	.	weak		0.463	PIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327089.1	NM_002652	Missense_Mutation
GSTK1	373156	hgsc.bcm.edu	37	7	142961758	142961758	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:142961758T>A	ENST00000358406.5	+	3	343	c.272T>A	c.(271-273)aTg>aAg	p.M91K	GSTK1_ENST00000443571.2_Intron|AC073342.12_ENST00000427392.1_RNA|GSTK1_ENST00000494735.1_3'UTR|GSTK1_ENST00000479303.1_Missense_Mutation_p.M91K|GSTK1_ENST00000409500.3_Missense_Mutation_p.M91K	NM_015917.2	NP_057001.1	Q9Y2Q3	GSTK1_HUMAN	glutathione S-transferase kappa 1	91					epithelial cell differentiation (GO:0030855)|glutathione metabolic process (GO:0006749)|oxidation-reduction process (GO:0055114)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|peroxisome (GO:0005777)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|protein disulfide oxidoreductase activity (GO:0015035)|receptor binding (GO:0005102)			lung(4)	4	Melanoma(164;0.059)				Glutathione(DB00143)	TTGTCTGTGATGCTTGAAAAA	0.488																																					p.M91K		Atlas-SNP	.											.	GSTK1	36	.	0			c.T272A						PASS	.						171.0	176.0	175.0					7																	142961758		2203	4300	6503	SO:0001583	missense	373156	exon3			CTGTGATGCTTGA		CCDS5877.1, CCDS47730.1, CCDS47731.1, CCDS47732.1	7q34	2012-06-21			ENSG00000197448	ENSG00000197448	2.5.1.18	"""Glutathione S-transferases / Mitochondrial (kappa)"""	16906	protein-coding gene	gene with protein product		602321				12720545, 14742434	Standard	NM_015917		Approved	GST13	uc003wcj.3	Q9Y2Q3	OTTHUMG00000152637	ENST00000358406.5:c.272T>A	chr7.hg19:g.142961758T>A	ENSP00000351181:p.Met91Lys	49.0	0.0	.		65.0	30.0	.	NM_015917	B4DIH1|B4DSY2|Q6P4H0|Q7Z520|Q9P1S4	Missense_Mutation	SNP	ENST00000358406.5	hg19	CCDS5877.1	.	.	.	.	.	.	.	.	.	.	T	13.43	2.234674	0.39498	.	.	ENSG00000197448	ENST00000436038;ENST00000409500;ENST00000358406;ENST00000479303	.	.	.	5.76	3.38	0.38709	DSBA-like thioredoxin domain (1);Thioredoxin-like fold (1);	0.436900	0.29383	N	0.012301	T	0.31295	0.0792	L	0.42245	1.32	0.09310	N	1	B;B;B	0.33583	0.003;0.418;0.151	B;B;B	0.40134	0.014;0.32;0.155	T	0.27673	-1.0067	9	0.05833	T	0.94	-6.0991	6.2182	0.20667	0.1428:0.0781:0.0:0.7791	.	91;91;91	Q9Y2Q3-3;Q9Y2Q3-2;Q9Y2Q3	.;.;GSTK1_HUMAN	K	81;91;91;91	.	ENSP00000351181:M91K	M	+	2	0	GSTK1	142671880	0.012000	0.17670	0.000000	0.03702	0.043000	0.13939	2.071000	0.41500	0.449000	0.26747	0.529000	0.55759	ATG	.	.	.	none		0.488	GSTK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327091.1	NM_015917	
CHD7	55636	hgsc.bcm.edu	37	8	61707584	61707584	+	Silent	SNP	A	A	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr8:61707584A>G	ENST00000423902.2	+	4	2615	c.2136A>G	c.(2134-2136)aaA>aaG	p.K712K	CHD7_ENST00000524602.1_Intron|CHD7_ENST00000525508.1_Silent_p.K712K	NM_017780.3	NP_060250.2	Q9P2D1	CHD7_HUMAN	chromodomain helicase DNA binding protein 7	712	Lys-rich.				adult heart development (GO:0007512)|adult walking behavior (GO:0007628)|artery morphogenesis (GO:0048844)|blood circulation (GO:0008015)|central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|cognition (GO:0050890)|cranial nerve development (GO:0021545)|embryonic hindlimb morphogenesis (GO:0035116)|epithelium development (GO:0060429)|face development (GO:0060324)|female genitalia development (GO:0030540)|genitalia development (GO:0048806)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|limb development (GO:0060173)|nose development (GO:0043584)|olfactory behavior (GO:0042048)|olfactory bulb development (GO:0021772)|olfactory nerve development (GO:0021553)|palate development (GO:0060021)|positive regulation of multicellular organism growth (GO:0040018)|regulation of growth hormone secretion (GO:0060123)|regulation of neurogenesis (GO:0050767)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|rRNA processing (GO:0006364)|semicircular canal morphogenesis (GO:0048752)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|T cell differentiation (GO:0030217)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)	p.556_871dup(1)		NS(1)|breast(6)|central_nervous_system(8)|cervix(2)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(16)|lung(49)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(3)	123		all_cancers(86;0.2)|all_lung(136;0.0402)|Lung NSC(129;0.0459)|all_epithelial(80;0.0477)	BRCA - Breast invasive adenocarcinoma(89;0.143)			CTTTGAAGAAAAAGGTCAACA	0.403																																					p.K712K		Atlas-SNP	.											.	CHD7	534	.	1	Insertion - In frame(1)	lung(1)	c.A2136G						PASS	.						78.0	79.0	78.0					8																	61707584		1823	4071	5894	SO:0001819	synonymous_variant	55636	exon4			GAAGAAAAAGGTC	AB037837	CCDS47865.1	8q12.2	2014-09-17				ENSG00000171316			20626	protein-coding gene	gene with protein product		608892	"""CHARGE association"""	CRG		15300250, 18834967	Standard	NM_017780		Approved	KIAA1416, FLJ20357, FLJ20361	uc003xue.3	Q9P2D1		ENST00000423902.2:c.2136A>G	chr8.hg19:g.61707584A>G		104.0	0.0	.		100.0	7.0	.	NM_017780	D0VBA5|E9PNZ2|Q05DI5|Q2TAN4|Q66K35|Q7Z6C0|Q7Z7Q2|Q9NXA0|Q9NXA3	Silent	SNP	ENST00000423902.2	hg19	CCDS47865.1																																																																																			.	.	.	none		0.403	CHD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383468.2	XM_098762	
VCPIP1	80124	hgsc.bcm.edu	37	8	67576667	67576667	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr8:67576667C>A	ENST00000310421.4	-	1	2785	c.2527G>T	c.(2527-2529)Ggc>Tgc	p.G843C		NM_025054.4	NP_079330.2	Q96JH7	VCIP1_HUMAN	valosin containing protein (p97)/p47 complex interacting protein 1	843					endoplasmic reticulum membrane fusion (GO:0016320)|Golgi reassembly (GO:0090168)|mitotic nuclear division (GO:0007067)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	ubiquitin-specific protease activity (GO:0004843)			breast(7)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(6)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		Lung NSC(129;0.142)|all_lung(136;0.227)	Epithelial(68;0.000771)|OV - Ovarian serous cystadenocarcinoma(28;0.00248)|all cancers(69;0.00296)|BRCA - Breast invasive adenocarcinoma(89;0.149)			ATTCTGTCGCCATGCTGTAAA	0.428																																					p.G843C	NSCLC(179;265 2915 6144 43644)	Atlas-SNP	.											.	VCPIP1	110	.	0			c.G2527T						PASS	.						108.0	111.0	110.0					8																	67576667		2203	4300	6503	SO:0001583	missense	80124	exon1			TGTCGCCATGCTG	AB058753	CCDS6192.1	8q13	2014-02-24			ENSG00000175073	ENSG00000175073		"""OTU domain containing"""	30897	protein-coding gene	gene with protein product		611745				11347906, 12509440	Standard	NM_025054		Approved	VCIP135, KIAA1850, FLJ23132, DUBA3	uc003xwn.3	Q96JH7	OTTHUMG00000164560	ENST00000310421.4:c.2527G>T	chr8.hg19:g.67576667C>A	ENSP00000309031:p.Gly843Cys	108.0	0.0	.		143.0	46.0	.	NM_025054	Q504T4|Q86T93|Q86W01|Q8N3A9|Q9H5R8	Missense_Mutation	SNP	ENST00000310421.4	hg19	CCDS6192.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.576700	0.86645	.	.	ENSG00000175073	ENST00000310421	T	0.69806	-0.43	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	D	0.83142	0.5190	M	0.78637	2.42	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84857	0.0817	10	0.87932	D	0	-12.7363	19.4386	0.94807	0.0:1.0:0.0:0.0	.	843	Q96JH7	VCIP1_HUMAN	C	843	ENSP00000309031:G843C	ENSP00000309031:G843C	G	-	1	0	VCPIP1	67739221	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.456000	0.80751	2.578000	0.87016	0.655000	0.94253	GGC	.	.	.	none		0.428	VCPIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379227.1		
USP20	10868	hgsc.bcm.edu	37	9	132625464	132625464	+	Splice_Site	SNP	G	G	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr9:132625464G>T	ENST00000315480.4	+	9	655		c.e9-1		USP20_ENST00000358355.1_Splice_Site|USP20_ENST00000372429.3_Splice_Site			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20						endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CCTGCACCCAGCCCGCCGCTG	0.607																																					.		Atlas-SNP	.											.	USP20	186	.	0			c.498-1G>T						PASS	.						13.0	15.0	15.0					9																	132625464		1952	3941	5893	SO:0001630	splice_region_variant	10868	exon9			CACCCAGCCCGCC	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.498-1G>T	chr9.hg19:g.132625464G>T		91.0	0.0	.		125.0	41.0	.	NM_001110303	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Splice_Site	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	G	14.01	2.408788	0.42715	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	.	.	.	5.65	5.65	0.86999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7287	0.91726	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	USP20	131665285	1.000000	0.71417	1.000000	0.80357	0.044000	0.14063	9.781000	0.99029	2.655000	0.90218	0.655000	0.94253	.	.	.	.	none		0.607	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		Intron
CUBN	8029	hgsc.bcm.edu	37	10	17164868	17164868	+	Silent	SNP	T	T	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr10:17164868T>C	ENST00000377833.4	-	6	584	c.519A>G	c.(517-519)gaA>gaG	p.E173E		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	173	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AAATCTCACATTCGTTAACAT	0.413																																					p.E173E		Atlas-SNP	.											.	CUBN	515	.	0			c.A519G						PASS	.						85.0	73.0	77.0					10																	17164868		2203	4300	6503	SO:0001819	synonymous_variant	8029	exon6			CTCACATTCGTTA	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.519A>G	chr10.hg19:g.17164868T>C		146.0	0.0	.		153.0	62.0	.	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Silent	SNP	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.413	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
CTBP2	1488	hgsc.bcm.edu	37	10	126715159	126715159	+	Intron	SNP	A	A	G	rs529129641|rs372118432	byFrequency	TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr10:126715159A>G	ENST00000337195.5	-	3	458				CTBP2_ENST00000411419.2_Intron|CTBP2_ENST00000309035.6_Silent_p.A390A|CTBP2_ENST00000494626.2_Intron|CTBP2_ENST00000531469.1_Intron	NM_001329.2	NP_001320.1	P56545	CTBP2_HUMAN	C-terminal binding protein 2						negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)|white fat cell differentiation (GO:0050872)	cell junction (GO:0030054)|nucleus (GO:0005634)|synapse (GO:0045202)|transcriptional repressor complex (GO:0017053)	NAD binding (GO:0051287)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		all_lung(145;0.0132)|Lung NSC(174;0.0193)|all_neural(114;0.116)|Colorectal(57;0.173)		Colorectal(40;0.00572)|COAD - Colon adenocarcinoma(40;0.0127)|GBM - Glioblastoma multiforme(135;0.147)		TCTGCAGAGGAGCCGCAGCGC	0.701																																					p.A390A		Atlas-SNP	.											.,1	CTBP2	100	.	0			c.T1170C						PASS	.						9.0	7.0	8.0					10																	126715159		2126	4169	6295	SO:0001627	intron_variant	1488	exon1			CAGAGGAGCCGCA	AF016507	CCDS7643.1, CCDS7644.1	10q26.13	2008-08-01			ENSG00000175029	ENSG00000175029			2495	protein-coding gene	gene with protein product		602619				9479502, 11864595	Standard	NM_022802		Approved	ribeye	uc001lie.4	P56545	OTTHUMG00000019224	ENST00000337195.5:c.58+12406T>C	chr10.hg19:g.126715159A>G		80.0	0.0	.		49.0	5.0	.	NM_022802	A8K2X5|D3DRF5|O43449|Q5SQP7|Q69YI3|Q86SV0|Q9H2T8	Silent	SNP	ENST00000337195.5	hg19	CCDS7643.1																																																																																			.	.	.	none		0.701	CTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050900.3	NM_001083914	
METTL15	196074	hgsc.bcm.edu	37	11	28311807	28311807	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:28311807G>T	ENST00000407364.3	+	5	814	c.462G>T	c.(460-462)atG>atT	p.M154I	METTL15_ENST00000342303.5_Missense_Mutation_p.M154I|METTL15_ENST00000303459.6_Missense_Mutation_p.M154I|METTL15_ENST00000406787.3_Missense_Mutation_p.M154I			A6NJ78	MET15_HUMAN	methyltransferase like 15	154							methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						CCTTATTAATGAAAGCTGGAG	0.448																																					p.M154I		Atlas-SNP	.											.	METTL15	63	.	0			c.G462T						PASS	.						49.0	50.0	49.0					11																	28311807		2202	4296	6498	SO:0001583	missense	196074	exon5			ATTAATGAAAGCT	AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"""methyltransferase 5 domain containing 1"""	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.462G>T	chr11.hg19:g.28311807G>T	ENSP00000384369:p.Met154Ile	42.0	0.0	.		73.0	23.0	.	NM_152636	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	hg19	CCDS44559.1	.	.	.	.	.	.	.	.	.	.	G	6.896	0.534856	0.13188	.	.	ENSG00000169519	ENST00000406787;ENST00000342303;ENST00000407364;ENST00000303459	T;T;T;T	0.28255	1.62;1.62;1.62;1.62	5.88	1.95	0.26073	.	0.738697	0.14439	N	0.319525	T	0.19046	0.0457	L	0.31926	0.97	0.09310	N	0.999999	B;B;B	0.19331	0.0;0.001;0.035	B;B;B	0.15484	0.0;0.001;0.013	T	0.24404	-1.0161	9	.	.	.	.	5.2287	0.15410	0.2941:0.279:0.4269:0.0	.	154;154;154	A6NJ78;A6NJ78-2;A6NJ78-4	MET15_HUMAN;.;.	I	154	ENSP00000385507:M154I;ENSP00000342259:M154I;ENSP00000384369:M154I;ENSP00000307251:M154I	.	M	+	3	0	METTL15	28268383	0.001000	0.12720	0.988000	0.46212	0.444000	0.32077	-0.076000	0.11412	0.115000	0.18071	0.655000	0.94253	ATG	.	.	.	none		0.448	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636	
CDC42BPG	55561	hgsc.bcm.edu	37	11	64594522	64594522	+	Splice_Site	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:64594522C>T	ENST00000342711.5	-	34	4388	c.4389G>A	c.(4387-4389)ccG>ccA	p.P1463P		NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						GAGGACTAACCGGGGACTTGT	0.597																																					p.P1463P		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.G4389A						PASS	.						43.0	46.0	45.0					11																	64594522		2201	4297	6498	SO:0001630	splice_region_variant	55561	exon34			ACTAACCGGGGAC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.4389+1G>A	chr11.hg19:g.64594522C>T		93.0	0.0	.		92.0	39.0	.	NM_017525		Silent	SNP	ENST00000342711.5	hg19	CCDS31601.1																																																																																			.	.	.	none		0.597	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	Silent
TM7SF2	7108	hgsc.bcm.edu	37	11	64882278	64882278	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:64882278T>A	ENST00000279263.7	+	6	859	c.697T>A	c.(697-699)Tac>Aac	p.Y233N	AP003068.12_ENST00000527789.1_RNA|TM7SF2_ENST00000540748.1_Missense_Mutation_p.Y117N|TM7SF2_ENST00000531029.1_3'UTR|TM7SF2_ENST00000345348.5_Missense_Mutation_p.Y233N	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	233					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCAGTTGCTCTACGTGGGTGA	0.607																																					p.Y233N		Atlas-SNP	.											.	TM7SF2	30	.	0			c.T697A						PASS	.						96.0	113.0	108.0					11																	64882278		2162	4249	6411	SO:0001583	missense	7108	exon6			TTGCTCTACGTGG	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"""delta(14)-sterol reductase"""	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.697T>A	chr11.hg19:g.64882278T>A	ENSP00000279263:p.Tyr233Asn	112.0	0.0	.		98.0	34.0	.	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Missense_Mutation	SNP	ENST00000279263.7	hg19	CCDS41669.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.647237	0.87958	.	.	ENSG00000149809	ENST00000526809;ENST00000279263;ENST00000524986;ENST00000534371;ENST00000540748;ENST00000525385;ENST00000345348;ENST00000531321;ENST00000526085;ENST00000527968	D;D;D;D;D;D;D;D;D;D	0.99270	-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66;-5.66	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.99638	0.9867	H	0.98155	4.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.997;0.998;0.999	D	0.97633	1.0143	10	0.87932	D	0	-4.6127	13.1215	0.59329	0.0:0.0:0.0:1.0	.	117;233;233	F5GYV3;O76062-2;O76062	.;.;ERG24_HUMAN	N	115;233;204;165;117;204;233;139;84;65	ENSP00000432171:Y115N;ENSP00000279263:Y233N;ENSP00000435972:Y204N;ENSP00000432187:Y165N;ENSP00000441215:Y117N;ENSP00000433325:Y204N;ENSP00000329520:Y233N;ENSP00000431300:Y139N;ENSP00000434447:Y84N;ENSP00000431685:Y65N	ENSP00000279263:Y233N	Y	+	1	0	TM7SF2	64638854	1.000000	0.71417	0.982000	0.44146	0.983000	0.72400	7.466000	0.80914	2.200000	0.70718	0.459000	0.35465	TAC	.	.	.	none		0.607	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273	
C11orf30	56946	hgsc.bcm.edu	37	11	76255546	76255546	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr11:76255546G>A	ENST00000529032.1	+	18	2953	c.2953G>A	c.(2953-2955)Gac>Aac	p.D985N	C11orf30_ENST00000334736.3_Missense_Mutation_p.D985N|C11orf30_ENST00000343878.3_Missense_Mutation_p.D985N|C11orf30_ENST00000524490.1_Missense_Mutation_p.D887N|C11orf30_ENST00000533248.1_Missense_Mutation_p.D894N|C11orf30_ENST00000524767.1_Missense_Mutation_p.D1000N|C11orf30_ENST00000525919.1_Missense_Mutation_p.D986N|C11orf30_ENST00000525038.1_Missense_Mutation_p.D986N			Q7Z589	EMSY_HUMAN	chromosome 11 open reading frame 30	985	Gln-rich.				chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(10)|liver(1)|lung(23)|ovary(5)|prostate(2)|skin(4)|stomach(1)|urinary_tract(2)	60						CCTGCAGGCAGACCAGCTCCA	0.542																																					p.D985N		Atlas-SNP	.											.	C11orf30	123	.	0			c.G2953A						PASS	.						106.0	107.0	107.0					11																	76255546		2200	4292	6492	SO:0001583	missense	56946	exon19			CAGGCAGACCAGC	AF226047	CCDS8244.1, CCDS73349.1, CCDS73350.1, CCDS73351.1	11q13.5	2010-07-01			ENSG00000158636	ENSG00000158636			18071	protein-coding gene	gene with protein product		608574					Standard	XM_005274106		Approved	EMSY	uc001oxl.3	Q7Z589	OTTHUMG00000165282	ENST00000529032.1:c.2953G>A	chr11.hg19:g.76255546G>A	ENSP00000432327:p.Asp985Asn	42.0	0.0	.		77.0	22.0	.	NM_020193	B7ZKT8|B7ZKU0|B7ZKU2|Q17RM7|Q4G109|Q8NBU6|Q8TE50|Q9H8I9|Q9NRH0	Missense_Mutation	SNP	ENST00000529032.1	hg19	CCDS8244.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.829846	0.50845	.	.	ENSG00000158636	ENST00000524490;ENST00000334736;ENST00000343878;ENST00000393457;ENST00000524767;ENST00000533248;ENST00000525919;ENST00000525038;ENST00000529032;ENST00000532719	.	.	.	5.92	5.92	0.95590	.	0.269805	0.41938	D	0.000786	T	0.58163	0.2103	N	0.19112	0.55	0.38630	D	0.951348	D;B;B;B;B;B;B	0.59357	0.985;0.148;0.148;0.144;0.023;0.148;0.023	P;B;B;B;B;B;B	0.55508	0.777;0.056;0.056;0.056;0.01;0.056;0.01	T	0.53781	-0.8390	9	0.20519	T	0.43	-1.593	20.3081	0.98638	0.0:0.0:1.0:0.0	.	894;986;1000;339;986;887;985	B7ZKT8;B7ZKU2;B7ZKU0;B3KWW8;Q17RM7;E9PMC9;Q7Z589	.;.;.;.;.;.;EMSY_HUMAN	N	887;985;985;667;1000;894;986;986;985;125	.	ENSP00000334130:D985N	D	+	1	0	C11orf30	75933194	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.155000	0.71833	2.795000	0.96236	0.655000	0.94253	GAC	.	.	.	none		0.542	C11orf30-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000383288.2	NM_020193	
HDAC7	51564	hgsc.bcm.edu	37	12	48179627	48179627	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr12:48179627C>T	ENST00000427332.2	-	23	2653	c.2497G>A	c.(2497-2499)Ggc>Agc	p.G833S	AC004466.1_ENST00000599515.1_3'UTR|HDAC7_ENST00000354334.3_Missense_Mutation_p.G835S|HDAC7_ENST00000080059.7_Missense_Mutation_p.G872S|HDAC7_ENST00000488927.1_5'Flank|HDAC7_ENST00000552960.1_Missense_Mutation_p.G855S|HDAC7_ENST00000380610.4_Missense_Mutation_p.G889S			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	833	Histone deacetylase.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		ACCACTGCGCCTCCTGCCAGG	0.602																																					p.G872S		Atlas-SNP	.											.	HDAC7	71	.	0			c.G2614A						PASS	.						49.0	40.0	43.0					12																	48179627		2203	4300	6503	SO:0001583	missense	51564	exon23			CTGCGCCTCCTGC	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.2497G>A	chr12.hg19:g.48179627C>T	ENSP00000404394:p.Gly833Ser	176.0	0.0	.		203.0	62.0	.	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	hg19		.	.	.	.	.	.	.	.	.	.	C	32	5.175569	0.94807	.	.	ENSG00000061273	ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46	4.78	4.78	0.61160	Histone deacetylase domain (2);	0.000000	0.85682	D	0.000000	T	0.81356	0.4805	M	0.78916	2.43	0.80722	D	1	P;P;B;D	0.71674	0.489;0.784;0.433;0.998	B;P;B;D	0.67900	0.368;0.84;0.353;0.954	D	0.84350	0.0532	10	0.87932	D	0	.	16.8244	0.85927	0.0:1.0:0.0:0.0	.	833;872;855;835	Q8WUI4;Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	HDAC7_HUMAN;.;.;.	S	872;835;855;889;833	ENSP00000080059:G872S;ENSP00000351326:G835S;ENSP00000448532:G855S;ENSP00000369984:G889S;ENSP00000404394:G833S	ENSP00000080059:G872S	G	-	1	0	HDAC7	46465894	1.000000	0.71417	0.995000	0.50966	0.971000	0.66376	7.742000	0.85008	2.407000	0.81776	0.543000	0.68304	GGC	.	.	.	none		0.602	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
ZNF219	51222	hgsc.bcm.edu	37	14	21560330	21560330	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr14:21560330G>A	ENST00000360947.3	-	3	1537	c.1126C>T	c.(1126-1128)Ccg>Tcg	p.P376S	RP11-998D10.7_ENST00000554733.2_lincRNA|ZNF219_ENST00000451119.2_Missense_Mutation_p.P376S|ZNF219_ENST00000421093.2_Missense_Mutation_p.P376S|ZNF219_ENST00000556101.1_5'Flank	NM_016423.2	NP_057507.2	Q9P2Y4	ZN219_HUMAN	zinc finger protein 219	376					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of neurotransmitter levels (GO:0001505)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histamine receptor activity (GO:0004969)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(1)|ovary(1)|prostate(2)	8	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;9.86e-11)|Epithelial(56;1.27e-08)|all cancers(55;6.06e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AAGAGGCTCGGGGGCTCACGG	0.761																																					p.P376S		Atlas-SNP	.											.	ZNF219	28	.	0			c.C1126T						PASS	.						1.0	1.0	1.0					14																	21560330		1016	2266	3282	SO:0001583	missense	51222	exon3			GGCTCGGGGGCTC	AB015427	CCDS9568.1	14q11	2013-01-08			ENSG00000165804	ENSG00000165804		"""Zinc fingers, C2H2-type"""	13011	protein-coding gene	gene with protein product		605036				10819330	Standard	NM_016423		Approved		uc001vzs.2	Q9P2Y4	OTTHUMG00000029647	ENST00000360947.3:c.1126C>T	chr14.hg19:g.21560330G>A	ENSP00000354206:p.Pro376Ser	99.0	0.0	.		34.0	14.0	.	NM_001102454	D3DS16|Q53Y57|Q8IYC1|Q9BW28	Missense_Mutation	SNP	ENST00000360947.3	hg19	CCDS9568.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.445264	0.25987	.	.	ENSG00000165804	ENST00000360947;ENST00000451119;ENST00000421093	T;T;T	0.06294	3.32;3.32;3.32	4.67	3.77	0.43336	.	0.153084	0.43110	D	0.000614	T	0.04543	0.0124	N	0.24115	0.695	0.35849	D	0.826595	B	0.24186	0.099	B	0.19391	0.025	T	0.40572	-0.9556	10	0.20046	T	0.44	-14.7276	10.523	0.44931	0.0:0.2258:0.7742:0.0	.	376	Q9P2Y4	ZN219_HUMAN	S	376	ENSP00000354206:P376S;ENSP00000388558:P376S;ENSP00000392401:P376S	ENSP00000354206:P376S	P	-	1	0	ZNF219	20630170	.	.	0.977000	0.42913	0.987000	0.75469	.	.	1.152000	0.42452	0.563000	0.77884	CCG	.	.	.	none		0.761	ZNF219-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073931.2		
UBE3A	7337	hgsc.bcm.edu	37	15	25616263	25616263	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr15:25616263A>T	ENST00000397954.2	-	4	1066	c.1067T>A	c.(1066-1068)tTt>tAt	p.F356Y	UBE3A_ENST00000566215.1_Missense_Mutation_p.F333Y|SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000232165.3_Missense_Mutation_p.F353Y|UBE3A_ENST00000428984.2_Missense_Mutation_p.F333Y|UBE3A_ENST00000438097.1_Missense_Mutation_p.F333Y			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	356					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TCGACTGTTAAATTCATTGCT	0.383																																					p.F356Y		Atlas-SNP	.											UBE3A,colon,carcinoma,0,1	UBE3A	109	.	0			c.T1067A						PASS	.						108.0	104.0	105.0					15																	25616263		2203	4300	6503	SO:0001583	missense	7337	exon7			CTGTTAAATTCAT	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"""Angelman syndrome"""	601623	"""human papilloma virus E6-associated protein"""	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.1067T>A	chr15.hg19:g.25616263A>T	ENSP00000381045:p.Phe356Tyr	60.0	0.0	.		59.0	23.0	.	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Missense_Mutation	SNP	ENST00000397954.2	hg19	CCDS45192.1	.	.	.	.	.	.	.	.	.	.	A	9.469	1.095036	0.20471	.	.	ENSG00000114062	ENST00000232165;ENST00000356465;ENST00000397954;ENST00000438097;ENST00000428984	T;T;T;T	0.17854	2.25;2.25;2.25;2.25	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.09202	0.0227	N	0.11560	0.145	0.58432	D	0.999999	B;B	0.15141	0.012;0.004	B;B	0.15484	0.013;0.009	T	0.08911	-1.0699	10	0.02654	T	1	.	16.0417	0.80687	1.0:0.0:0.0:0.0	.	353;356	Q05086-3;Q05086	.;UBE3A_HUMAN	Y	353;353;356;333;333	ENSP00000232165:F353Y;ENSP00000381045:F356Y;ENSP00000411258:F333Y;ENSP00000401265:F333Y	ENSP00000232165:F353Y	F	-	2	0	UBE3A	23167356	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.135000	0.77276	2.198000	0.70561	0.482000	0.46254	TTT	.	.	.	none		0.383	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462	
LTK	4058	hgsc.bcm.edu	37	15	41797613	41797613	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr15:41797613T>C	ENST00000263800.6	-	14	1909	c.1813A>G	c.(1813-1815)Agt>Ggt	p.S605G	LTK_ENST00000355166.5_Missense_Mutation_p.S544G|LTK_ENST00000561619.1_Missense_Mutation_p.S303G|LTK_ENST00000453182.2_Missense_Mutation_p.S475G	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	605	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		TGTGGCCGACTGTGCCTCAGG	0.597										TSP Lung(18;0.14)																											p.S605G		Atlas-SNP	.											.	LTK	117	.	0			c.A1813G						PASS	.						56.0	62.0	60.0					15																	41797613		2203	4300	6503	SO:0001583	missense	4058	exon14			GCCGACTGTGCCT	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.1813A>G	chr15.hg19:g.41797613T>C	ENSP00000263800:p.Ser605Gly	240.0	0.0	.		172.0	60.0	.	NM_002344	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	hg19	CCDS10077.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.017279	0.35606	.	.	ENSG00000062524	ENST00000355166;ENST00000263800;ENST00000453182	D;D;D	0.83075	-1.68;-1.68;-1.68	4.2	4.2	0.49525	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	D	0.84320	0.5446	L	0.45422	1.42	0.09310	N	0.999995	P;B;P;P	0.50272	0.933;0.012;0.846;0.872	P;B;P;P	0.56343	0.796;0.011;0.467;0.674	T	0.74231	-0.3732	9	0.30078	T	0.28	.	12.4104	0.55464	0.0:0.0:0.0:1.0	.	475;475;544;605	E9PFX4;B4DL89;P29376-4;P29376	.;.;.;LTK_HUMAN	G	544;605;475	ENSP00000347293:S544G;ENSP00000263800:S605G;ENSP00000392196:S475G	ENSP00000263800:S605G	S	-	1	0	LTK	39584905	0.590000	0.26815	0.008000	0.14137	0.354000	0.29330	2.992000	0.49417	1.768000	0.52137	0.402000	0.26972	AGT	.	.	.	none		0.597	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
CREBBP	1387	hgsc.bcm.edu	37	16	3779274	3779274	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr16:3779274G>C	ENST00000262367.5	-	31	6583	c.5774C>G	c.(5773-5775)gCc>gGc	p.A1925G	CREBBP_ENST00000382070.3_Missense_Mutation_p.A1887G	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1925					cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		CTGAGTCCGGGCCACGCTGGG	0.736			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.A1925G		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	.	CREBBP	546	.	0			c.C5774G						PASS	.						7.0	8.0	8.0					16																	3779274		2041	4026	6067	SO:0001583	missense	1387	exon31			GTCCGGGCCACGC	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.5774C>G	chr16.hg19:g.3779274G>C	ENSP00000262367:p.Ala1925Gly	54.0	0.0	.		57.0	12.0	.	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	hg19	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	8.148	0.786786	0.16189	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.83591	-1.74;-1.68	5.16	4.2	0.49525	.	0.484348	0.20989	N	0.082069	T	0.70334	0.3212	L	0.29908	0.895	0.33812	D	0.628027	B;B	0.17038	0.02;0.02	B;B	0.14578	0.011;0.011	T	0.67341	-0.5695	10	0.19147	T	0.46	-4.3631	7.9121	0.29798	0.0813:0.0:0.76:0.1587	.	1955;1925	Q4LE28;Q92793	.;CBP_HUMAN	G	1925;1955;1887;460	ENSP00000262367:A1925G;ENSP00000371502:A1887G	ENSP00000262367:A1925G	A	-	2	0	CREBBP	3719275	0.952000	0.32445	1.000000	0.80357	0.997000	0.91878	3.424000	0.52764	1.184000	0.42957	0.655000	0.94253	GCC	.	.	.	none		0.736	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
GRIN2A	2903	hgsc.bcm.edu	37	16	10032281	10032281	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr16:10032281C>A	ENST00000396573.2	-	4	851	c.542G>T	c.(541-543)aGg>aTg	p.R181M	GRIN2A_ENST00000330684.3_Missense_Mutation_p.R181M|GRIN2A_ENST00000562109.1_Missense_Mutation_p.R181M|GRIN2A_ENST00000566670.1_5'UTR|GRIN2A_ENST00000404927.2_Missense_Mutation_p.R181M|GRIN2A_ENST00000535259.1_Missense_Mutation_p.R24M|GRIN2A_ENST00000396575.2_Missense_Mutation_p.R181M	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	181					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	GATGAATTCCCTGTAGCCAGG	0.517																																					p.R181M		Atlas-SNP	.											.	GRIN2A	366	.	0			c.G542T						PASS	.						108.0	96.0	100.0					16																	10032281		2197	4300	6497	SO:0001583	missense	2903	exon4			AATTCCCTGTAGC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.542G>T	chr16.hg19:g.10032281C>A	ENSP00000379818:p.Arg181Met	29.0	0.0	.		104.0	28.0	.	NM_000833	O00669|Q17RZ6	Missense_Mutation	SNP	ENST00000396573.2	hg19	CCDS10539.1	.	.	.	.	.	.	.	.	.	.	c	22.6	4.306611	0.81247	.	.	ENSG00000183454	ENST00000396573;ENST00000404927;ENST00000535259;ENST00000330684;ENST00000396575	D;D;D;D;D	0.92752	-3.1;-3.1;-3.1;-3.1;-3.1	5.47	5.47	0.80525	Extracellular ligand-binding receptor (1);	0.051432	0.85682	D	0.000000	D	0.94879	0.8345	M	0.61703	1.905	0.41884	D	0.990333	D;D;D	0.61697	0.964;0.99;0.989	P;D;P	0.63033	0.844;0.91;0.87	D	0.94078	0.7341	9	.	.	.	.	18.6894	0.91577	0.0:1.0:0.0:0.0	.	24;181;181	F5GZ52;Q17RZ6;Q12879	.;.;NMDE1_HUMAN	M	181;181;24;181;181	ENSP00000379818:R181M;ENSP00000385872:R181M;ENSP00000441572:R24M;ENSP00000332549:R181M;ENSP00000379820:R181M	.	R	-	2	0	GRIN2A	9939782	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	4.792000	0.62467	2.724000	0.93272	0.561000	0.74099	AGG	.	.	.	none		0.517	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
ABCC6	368	hgsc.bcm.edu	37	16	16244436	16244436	+	Splice_Site	SNP	G	G	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr16:16244436G>C	ENST00000205557.7	-	30	4431	c.4402C>G	c.(4402-4404)Cgg>Ggg	p.R1468G		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1468	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	GAGCCTTACCGGGCACAGTCC	0.672																																					p.R1468G		Atlas-SNP	.											.	ABCC6	110	.	0			c.C4402G						PASS	.						32.0	27.0	29.0					16																	16244436		2197	4298	6495	SO:0001630	splice_region_variant	368	exon30			CTTACCGGGCACA	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.4403+1C>G	chr16.hg19:g.16244436G>C		121.0	0.0	.		141.0	71.0	.	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	G	13.40	2.225530	0.39300	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	T	0.76316	-1.01	4.38	3.3	0.37823	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.000000	0.45361	U	0.000380	D	0.89508	0.6735	M	0.93328	3.405	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	D	0.90091	0.4177	10	0.87932	D	0	.	10.7299	0.46089	0.0:0.0:0.3466:0.6534	.	1468;1468	O95255;A8Y988	MRP6_HUMAN;.	G	1468;406	ENSP00000205557:R1468G	ENSP00000205557:R1468G	R	-	1	2	ABCC6	16151937	1.000000	0.71417	0.987000	0.45799	0.152000	0.21847	2.582000	0.46085	0.699000	0.31761	0.561000	0.74099	CGG	.	.	.	none		0.672	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		Missense_Mutation
RAI1	10743	hgsc.bcm.edu	37	17	17698698	17698698	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:17698698G>T	ENST00000353383.1	+	3	2905	c.2436G>T	c.(2434-2436)caG>caT	p.Q812H	RAI1_ENST00000261641.6_Missense_Mutation_p.Q812H	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	812					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		ACTTCAAGCAGGAGGAGGTGG	0.677																																					p.Q812H		Atlas-SNP	.											.	RAI1	121	.	0			c.G2436T						PASS	.						29.0	37.0	34.0					17																	17698698		2203	4300	6503	SO:0001583	missense	10743	exon3			CAAGCAGGAGGAG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.2436G>T	chr17.hg19:g.17698698G>T	ENSP00000323074:p.Gln812His	109.0	0.0	.		111.0	30.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.204428	0.38905	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.69806	-0.43;2.31;0.17	5.37	4.39	0.52855	.	0.247497	0.35495	N	0.003161	T	0.61211	0.2329	L	0.60455	1.87	0.30237	N	0.795346	B	0.25441	0.126	B	0.22753	0.041	T	0.62987	-0.6737	10	0.54805	T	0.06	.	11.0862	0.48089	0.1501:0.0:0.8499:0.0	.	812	Q7Z5J4	RAI1_HUMAN	H	812;812;812;812;812;764	ENSP00000323074:Q812H;ENSP00000379120:Q812H;ENSP00000261641:Q812H	ENSP00000261641:Q812H	Q	+	3	2	RAI1	17639423	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	2.004000	0.40854	1.256000	0.44068	0.561000	0.74099	CAG	.	.	.	none		0.677	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
RAI1	10743	hgsc.bcm.edu	37	17	17698712	17698712	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:17698712G>T	ENST00000353383.1	+	3	2919	c.2450G>T	c.(2449-2451)gGg>gTg	p.G817V	RAI1_ENST00000261641.6_Missense_Mutation_p.G817V	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	817					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		GAGGTGGGTGGGGTGAAGGAG	0.687																																					p.G817V		Atlas-SNP	.											.	RAI1	121	.	0			c.G2450T						PASS	.						27.0	35.0	32.0					17																	17698712		2201	4299	6500	SO:0001583	missense	10743	exon3			TGGGTGGGGTGAA	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.2450G>T	chr17.hg19:g.17698712G>T	ENSP00000323074:p.Gly817Val	100.0	0.0	.		115.0	30.0	.	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Missense_Mutation	SNP	ENST00000353383.1	hg19	CCDS11188.1	.	.	.	.	.	.	.	.	.	.	G	18.45	3.625786	0.66901	.	.	ENSG00000108557	ENST00000353383;ENST00000395774;ENST00000395776;ENST00000355970;ENST00000261641;ENST00000315321	T;T;T	0.66460	-0.21;2.51;0.39	5.37	4.31	0.51392	.	0.157090	0.43260	D	0.000600	T	0.56352	0.1979	L	0.44542	1.39	0.80722	D	1	D	0.54397	0.966	P	0.47299	0.543	T	0.55835	-0.8078	10	0.31617	T	0.26	.	3.5178	0.07731	0.3696:0.0:0.6304:0.0	.	817	Q7Z5J4	RAI1_HUMAN	V	817;817;817;817;817;769	ENSP00000323074:G817V;ENSP00000379120:G817V;ENSP00000261641:G817V	ENSP00000261641:G817V	G	+	2	0	RAI1	17639437	1.000000	0.71417	0.992000	0.48379	0.764000	0.43329	2.141000	0.42168	2.519000	0.84933	0.561000	0.74099	GGG	.	.	.	none		0.687	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
SLC5A10	125206	hgsc.bcm.edu	37	17	18922878	18922878	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:18922878G>A	ENST00000395645.3	+	12	1402	c.1384G>A	c.(1384-1386)Gtc>Atc	p.V462I	SLC5A10_ENST00000395647.2_Missense_Mutation_p.V478I|SLC5A10_ENST00000417251.2_Missense_Mutation_p.V426I|SLC5A10_ENST00000395643.2_Missense_Mutation_p.V435I|SLC5A10_ENST00000395642.1_Missense_Mutation_p.V432I|SLC5A10_ENST00000317977.6_Missense_Mutation_p.V432I	NM_001042450.2	NP_001035915.1	A0PJK1	SC5AA_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 10	462					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(3)|ovary(3)|prostate(3)|skin(3)	24						TGTCCTGGGCGTCTTCTGGCG	0.637																																					p.V478I		Atlas-SNP	.											.	SLC5A10	55	.	0			c.G1432A						PASS	.						69.0	61.0	64.0					17																	18922878		2203	4300	6503	SO:0001583	missense	125206	exon12			CTGGGCGTCTTCT		CCDS11201.2, CCDS42275.1, CCDS59277.1, CCDS59278.1, CCDS74008.1	17p11.2	2013-07-19	2013-07-19		ENSG00000154025	ENSG00000154025		"""Solute carriers"""	23155	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 10"""				Standard	NM_152351		Approved	SGLT5	uc002gut.2	A0PJK1	OTTHUMG00000178143	ENST00000395645.3:c.1384G>A	chr17.hg19:g.18922878G>A	ENSP00000379007:p.Val462Ile	37.0	0.0	.		68.0	18.0	.	NM_152351	A8MUC9|B4DPI0|B7WPR4|Q6P5X0|Q8IXM4|Q96LQ1	Missense_Mutation	SNP	ENST00000395645.3	hg19	CCDS42275.1	.	.	.	.	.	.	.	.	.	.	G	0.941	-0.709631	0.03230	.	.	ENSG00000154025	ENST00000317977;ENST00000395647;ENST00000395642;ENST00000417251;ENST00000395645;ENST00000395643	D;D;D;D;D;D	0.86956	-2.19;-2.19;-2.19;-2.09;-2.19;-2.19	4.49	0.944	0.19537	Sodium/solute symporter, conserved site (1);	0.231384	0.43579	N	0.000551	T	0.59905	0.2228	N	0.01454	-0.855	0.31052	N	0.715133	B;B;B;B;B	0.09022	0.001;0.0;0.001;0.001;0.002	B;B;B;B;B	0.12156	0.007;0.003;0.007;0.002;0.005	T	0.57493	-0.7802	10	0.02654	T	1	.	7.4201	0.27067	0.6057:0.0:0.3942:0.0	.	426;435;462;478;432	B4DPI0;A0PJK1-2;A0PJK1;A0PJK1-4;A0PJK1-3	.;.;SC5AA_HUMAN;.;.	I	432;478;432;426;462;435	ENSP00000324346:V432I;ENSP00000379008:V478I;ENSP00000379004:V432I;ENSP00000401875:V426I;ENSP00000379007:V462I;ENSP00000379005:V435I	ENSP00000324346:V432I	V	+	1	0	SLC5A10	18863603	0.322000	0.24634	1.000000	0.80357	0.531000	0.34715	0.814000	0.27239	0.213000	0.20722	-0.340000	0.08031	GTC	.	.	.	none		0.637	SLC5A10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132129.2	NM_152351	
SPAG9	9043	hgsc.bcm.edu	37	17	49157055	49157055	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:49157055T>A	ENST00000262013.7	-	2	522	c.314A>T	c.(313-315)gAa>gTa	p.E105V	SPAG9_ENST00000357122.4_Missense_Mutation_p.E105V|SPAG9_ENST00000505279.1_Missense_Mutation_p.E105V|RP11-481C4.1_ENST00000509833.1_RNA	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	105					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)				NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GTCTTCAAATTCAATGAATTT	0.294																																					p.E105V		Atlas-SNP	.											.	SPAG9	151	.	0			c.A314T						PASS	.						82.0	83.0	83.0					17																	49157055		2203	4300	6503	SO:0001583	missense	9043	exon2			TCAAATTCAATGA	AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.314A>T	chr17.hg19:g.49157055T>A	ENSP00000262013:p.Glu105Val	49.0	0.0	.		94.0	22.0	.	NM_001130528	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	hg19	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	T	15.09	2.731306	0.48939	.	.	ENSG00000008294	ENST00000262013;ENST00000505279;ENST00000357122;ENST00000546269	T;T;T	0.48201	0.82;0.82;0.82	5.19	5.19	0.71726	JNK/Rab-associated protein-1, N-terminal (1);	0.317983	0.29752	N	0.011294	T	0.67674	0.2918	M	0.81341	2.54	0.50632	D	0.999886	P;P;B	0.50369	0.523;0.934;0.348	P;P;B	0.59643	0.543;0.861;0.22	T	0.73110	-0.4086	10	0.87932	D	0	-16.6007	15.3432	0.74314	0.0:0.0:0.0:1.0	.	105;105;105	O60271-2;O60271;O60271-4	.;JIP4_HUMAN;.	V	105	ENSP00000262013:E105V;ENSP00000426900:E105V;ENSP00000349636:E105V	ENSP00000262013:E105V	E	-	2	0	SPAG9	46512054	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.896000	0.56266	2.088000	0.63022	0.528000	0.53228	GAA	.	.	.	none		0.294	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2	NM_003971	
BAIAP2	10458	hgsc.bcm.edu	37	17	79031740	79031740	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:79031740A>G	ENST00000321300.6	+	3	283	c.190A>G	c.(190-192)Agc>Ggc	p.S64G	BAIAP2_ENST00000435091.3_Missense_Mutation_p.S64G|BAIAP2_ENST00000575712.1_Missense_Mutation_p.S64G|BAIAP2_ENST00000573894.1_3'UTR|BAIAP2_ENST00000428708.2_Missense_Mutation_p.S64G|BAIAP2_ENST00000392411.3_Intron|BAIAP2_ENST00000575245.1_Missense_Mutation_p.S97G|BAIAP2_ENST00000321280.7_Missense_Mutation_p.S64G	NM_001144888.1|NM_017451.2	NP_001138360.1|NP_059345.1	Q9UQB8	BAIP2_HUMAN	BAI1-associated protein 2	64	IMD. {ECO:0000255|PROSITE- ProRule:PRU00668}.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axonogenesis (GO:0007409)|dendrite development (GO:0016358)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|filopodium assembly (GO:0046847)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of synaptic plasticity (GO:0048167)|response to bacterium (GO:0009617)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	cytoskeletal adaptor activity (GO:0008093)|identical protein binding (GO:0042802)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(6)|skin(1)	18	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			GGAGCTGGCCAGCGAGAGCCA	0.622																																					p.S64G		Atlas-SNP	.											.	BAIAP2	74	.	0			c.A190G						PASS	.						41.0	39.0	40.0					17																	79031740		2203	4300	6503	SO:0001583	missense	10458	exon3			CTGGCCAGCGAGA	AB015019	CCDS11775.1, CCDS11776.1, CCDS11777.1, CCDS45806.1	17q25.3	2014-09-11			ENSG00000175866				947	protein-coding gene	gene with protein product		605475				10343108	Standard	NM_017451		Approved	BAP2	uc002jzg.2	Q9UQB8	OTTHUMG00000177698	ENST00000321300.6:c.190A>G	chr17.hg19:g.79031740A>G	ENSP00000316338:p.Ser64Gly	40.0	0.0	.		56.0	25.0	.	NM_001144888	O43858|Q53HB1|Q86WC1|Q8N5C0|Q96CR7|Q9UBR3|Q9UQ43	Missense_Mutation	SNP	ENST00000321300.6	hg19	CCDS11775.1	.	.	.	.	.	.	.	.	.	.	A	22.2	4.264088	0.80358	.	.	ENSG00000175866	ENST00000321300;ENST00000428708;ENST00000435091;ENST00000321280	T;T;T;T	0.38077	1.16;1.16;1.16;1.16	4.99	3.83	0.44106	IRSp53/MIM homology domain (IMD) (3);	0.043292	0.85682	D	0.000000	T	0.53222	0.1783	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.85130	0.997;0.969;0.952;0.995;0.995;0.977	T	0.49744	-0.8907	10	0.30078	T	0.28	-13.536	10.5453	0.45056	0.8379:0.1621:0.0:0.0	.	64;64;64;64;64;64	Q9UQB8;Q9UQB8-2;Q9UQB8-3;Q9UQB8-5;Q9UQB8-6;Q9UQB8-4	BAIP2_HUMAN;.;.;.;.;.	G	64	ENSP00000316338:S64G;ENSP00000401022:S64G;ENSP00000413069:S64G;ENSP00000315685:S64G	ENSP00000315685:S64G	S	+	1	0	BAIAP2	76646335	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.338000	0.72963	1.875000	0.54330	0.459000	0.35465	AGC	.	.	.	none		0.622	BAIAP2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438553.1		
LAMA3	3909	hgsc.bcm.edu	37	18	21418824	21418824	+	Missense_Mutation	SNP	G	G	T	rs546055094		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr18:21418824G>T	ENST00000313654.9	+	26	3414	c.3173G>T	c.(3172-3174)gGg>gTg	p.G1058V	LAMA3_ENST00000399516.3_Missense_Mutation_p.G1058V	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	1058	Domain IV 1 (domain IV B).				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					GCCAGTTATGGGCGATTTGTC	0.418																																					p.G1058V		Atlas-SNP	.											.	LAMA3	397	.	0			c.G3173T						PASS	.						188.0	186.0	187.0					18																	21418824		1957	4143	6100	SO:0001583	missense	3909	exon26			GTTATGGGCGATT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.3173G>T	chr18.hg19:g.21418824G>T	ENSP00000324532:p.Gly1058Val	64.0	0.0	.		79.0	24.0	.	NM_001127717	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	G	15.43	2.831649	0.50845	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000416669	T;T	0.26373	1.76;1.74	5.52	4.65	0.58169	.	.	.	.	.	T	0.47600	0.1454	M	0.67953	2.075	0.80722	D	1	D;D	0.76494	0.999;0.993	D;P	0.66602	0.945;0.843	T	0.50988	-0.8762	9	0.66056	D	0.02	.	14.7529	0.69540	0.0697:0.0:0.9303:0.0	.	1058;1058	Q6VU67;Q16787	.;LAMA3_HUMAN	V	1058;1058;1056	ENSP00000324532:G1058V;ENSP00000382432:G1058V	ENSP00000324532:G1058V	G	+	2	0	LAMA3	19672822	0.990000	0.36364	0.012000	0.15200	0.220000	0.24768	4.035000	0.57297	1.476000	0.48215	0.655000	0.94253	GGG	.	.	.	none		0.418	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
SMAD2	4087	hgsc.bcm.edu	37	18	45395677	45395677	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr18:45395677A>C	ENST00000402690.2	-	4	851	c.457T>G	c.(457-459)Ttt>Gtt	p.F153V	SMAD2_ENST00000587353.1_5'UTR|SMAD2_ENST00000591214.1_Missense_Mutation_p.F123V|SMAD2_ENST00000586040.1_Missense_Mutation_p.F123V|SMAD2_ENST00000356825.4_Missense_Mutation_p.F123V|SMAD2_ENST00000262160.6_Missense_Mutation_p.F153V	NM_001003652.3	NP_001003652.1	Q15796	SMAD2_HUMAN	SMAD family member 2	153	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|cell fate commitment (GO:0045165)|common-partner SMAD protein phosphorylation (GO:0007182)|developmental growth (GO:0048589)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic foregut morphogenesis (GO:0048617)|endoderm formation (GO:0001706)|gastrulation (GO:0007369)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|insulin secretion (GO:0030073)|intracellular signal transduction (GO:0035556)|lung development (GO:0030324)|mesoderm formation (GO:0001707)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|nodal signaling pathway (GO:0038092)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|paraxial mesoderm morphogenesis (GO:0048340)|pericardium development (GO:0060039)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry (GO:1900224)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primary miRNA processing (GO:0031053)|regulation of binding (GO:0051098)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|response to cholesterol (GO:0070723)|response to glucose (GO:0009749)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein complex assembly (GO:0007183)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	activin responsive factor complex (GO:0032444)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMAD protein complex (GO:0071141)|SMAD2-SMAD3 protein complex (GO:0071144)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|double-stranded DNA binding (GO:0003690)|enhancer binding (GO:0035326)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|phosphatase binding (GO:0019902)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)|transforming growth factor beta receptor binding (GO:0005160)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(21)|liver(1)|lung(8)|prostate(2)|urinary_tract(1)	43						TTAAGATTAAAAGCATATTCG	0.373																																					p.F153V		Atlas-SNP	.											.	SMAD2	85	.	0			c.T457G						PASS	.						106.0	106.0	106.0					18																	45395677		2203	4300	6503	SO:0001583	missense	4087	exon4			GATTAAAAGCATA	U65019	CCDS11934.1	18q21	2006-11-06	2006-11-06	2004-05-26	ENSG00000175387	ENSG00000175387		"""SMADs"""	6768	protein-coding gene	gene with protein product		601366	"""MAD, mothers against decapentaplegic homolog 2 (Drosophila)"", ""SMAD, mothers against DPP homolog 2 (Drosophila)"""	MADH2		8752209, 8673135	Standard	NM_001003652		Approved	MADR2, JV18-1	uc002lcz.4	Q15796	OTTHUMG00000132652	ENST00000402690.2:c.457T>G	chr18.hg19:g.45395677A>C	ENSP00000384449:p.Phe153Val	90.0	0.0	.		124.0	9.0	.	NM_005901		Missense_Mutation	SNP	ENST00000402690.2	hg19	CCDS11934.1	.	.	.	.	.	.	.	.	.	.	A	19.89	3.911800	0.72983	.	.	ENSG00000175387	ENST00000262160;ENST00000356825;ENST00000402690	T;T;T	0.77358	-1.09;-1.09;-1.09	5.17	5.17	0.71159	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.000000	0.85682	D	0.000000	D	0.85999	0.5828	M	0.70595	2.14	0.80722	D	1	D;D;D	0.63046	0.992;0.989;0.992	D;P;D	0.62955	0.909;0.897;0.909	D	0.87886	0.2681	10	0.87932	D	0	.	15.2967	0.73913	1.0:0.0:0.0:0.0	.	123;123;153	B7Z5N5;Q15796-2;Q15796	.;.;SMAD2_HUMAN	V	153;123;153	ENSP00000262160:F153V;ENSP00000349282:F123V;ENSP00000384449:F153V	ENSP00000262160:F153V	F	-	1	0	SMAD2	43649675	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.287000	0.95975	2.074000	0.62210	0.482000	0.46254	TTT	.	.	.	none		0.373	SMAD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450571.1	NM_005901	
OR7G1	125962	hgsc.bcm.edu	37	19	9226308	9226308	+	Silent	SNP	G	G	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:9226308G>A	ENST00000541538.1	-	1	131	c.132C>T	c.(130-132)ctC>ctT	p.L44L	OR7G1_ENST00000293614.1_Silent_p.L44L	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						CCAGGAGAATGAGCAGGTTCC	0.478																																					p.L44L		Atlas-SNP	.											.	OR7G1	53	.	0			c.C132T						PASS	.						147.0	138.0	141.0					19																	9226308		2203	4300	6503	SO:0001819	synonymous_variant	125962	exon1			GAGAATGAGCAGG		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"""GPCR / Class A : Olfactory receptors"""	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.132C>T	chr19.hg19:g.9226308G>A		82.0	0.0	.		63.0	20.0	.	NM_001005192	Q6IFJ5|Q96RA1	Silent	SNP	ENST00000541538.1	hg19	CCDS32898.2																																																																																			.	.	.	none		0.478	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1		
QTRT1	81890	hgsc.bcm.edu	37	19	10823829	10823829	+	Silent	SNP	G	G	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:10823829G>A	ENST00000250237.5	+	10	1105	c.1095G>A	c.(1093-1095)gtG>gtA	p.V365V		NM_031209.2	NP_112486.1	Q9BXR0	TGT_HUMAN	queuine tRNA-ribosyltransferase 1	365					queuosine biosynthetic process (GO:0008616)|tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|queuine tRNA-ribosyltransferase activity (GO:0008479)			large_intestine(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	12			Epithelial(33;1.55e-05)|all cancers(31;3.42e-05)			CCAGCATCGTGGAGAAGCGCT	0.687																																					p.V365V		Atlas-SNP	.											.	QTRT1	25	.	0			c.G1095A						PASS	.						62.0	60.0	60.0					19																	10823829		2203	4300	6503	SO:0001819	synonymous_variant	81890	exon10			CATCGTGGAGAAG	AF302783	CCDS12248.1	19p13.3	2014-06-11	2008-07-31		ENSG00000213339	ENSG00000213339	2.4.2.29		23797	protein-coding gene	gene with protein product	"""tRNA-guanine transglycosylase"""	609615				20354154	Standard	NM_031209		Approved	TGT	uc002mpr.3	Q9BXR0		ENST00000250237.5:c.1095G>A	chr19.hg19:g.10823829G>A		57.0	0.0	.		41.0	13.0	.	NM_031209	B4DFM7|Q96BQ4|Q9BXQ9	Silent	SNP	ENST00000250237.5	hg19	CCDS12248.1																																																																																			.	.	.	none		0.687	QTRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452086.1	NM_031209	
ETHE1	23474	hgsc.bcm.edu	37	19	44012185	44012185	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:44012185T>A	ENST00000292147.2	-	6	689	c.623A>T	c.(622-624)gAg>gTg	p.E208V	ETHE1_ENST00000600651.1_Missense_Mutation_p.E208V	NM_014297.3	NP_055112.2	O95571	ETHE1_HUMAN	ethylmalonic encephalopathy 1	208					cellular nitrogen compound metabolic process (GO:0034641)|glutathione metabolic process (GO:0006749)|hydrogen sulfide metabolic process (GO:0070813)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|sulfur dioxygenase activity (GO:0050313)			central_nervous_system(1)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	5		Prostate(69;0.0153)				CAGAGTCCTCTCCTCCTCCAC	0.557																																					p.E208V		Atlas-SNP	.											.	ETHE1	7	.	0			c.A623T						PASS	.						74.0	59.0	64.0					19																	44012185		2203	4300	6503	SO:0001583	missense	23474	exon6			GTCCTCTCCTCCT		CCDS12622.1	19q13.32	2014-06-20				ENSG00000105755	1.13.11.18		23287	protein-coding gene	gene with protein product		608451				19136963	Standard	NM_014297		Approved	YF13H12, HSCO	uc002owp.3	O95571		ENST00000292147.2:c.623A>T	chr19.hg19:g.44012185T>A	ENSP00000292147:p.Glu208Val	49.0	0.0	.		52.0	24.0	.	NM_014297	Q96HR0|Q9H001	Missense_Mutation	SNP	ENST00000292147.2	hg19	CCDS12622.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.543602	0.86022	.	.	ENSG00000105755	ENST00000292147	D	0.96856	-4.15	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	D	0.98557	0.9518	H	0.95365	3.66	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.979;0.995	D	0.99433	1.0936	10	0.87932	D	0	-8.9073	13.0221	0.58794	0.0:0.0:0.0:1.0	.	181;208	B2RCZ7;O95571	.;ETHE1_HUMAN	V	208	ENSP00000292147:E208V	ENSP00000292147:E208V	E	-	2	0	ETHE1	48704025	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.780000	0.68956	2.232000	0.73038	0.524000	0.50904	GAG	.	.	.	none		0.557	ETHE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463184.1	NM_014297	
ZNF180	7733	hgsc.bcm.edu	37	19	44980632	44980632	+	Missense_Mutation	SNP	T	T	C	rs141416252		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr19:44980632T>C	ENST00000221327.4	-	5	2347	c.2066A>G	c.(2065-2067)tAt>tGt	p.Y689C	ZNF180_ENST00000585514.1_5'Flank|ZNF180_ENST00000391956.4_Missense_Mutation_p.Y664C|AC069278.4_ENST00000591684.1_lincRNA|ZNF180_ENST00000592529.1_Missense_Mutation_p.Y662C	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	689					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)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				GTTACATTCATAGAGTTTCTC	0.313																																					p.Y689C	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.A2066G						PASS	.	T	CYS/TYR	2,4402	4.2+/-10.8	0,2,2200	70.0	76.0	74.0		2066	2.1	0.0	19	dbSNP_134	74	0,8598		0,0,4299	no	missense	ZNF180	NM_013256.3	194	0,2,6499	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging	689/693	44980632	2,13000	2202	4299	6501	SO:0001583	missense	7733	exon5			CATTCATAGAGTT	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.2066A>G	chr19.hg19:g.44980632T>C	ENSP00000221327:p.Tyr689Cys	75.0	0.0	.		77.0	25.0	.	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Missense_Mutation	SNP	ENST00000221327.4	hg19	CCDS12639.1	.	.	.	.	.	.	.	.	.	.	T	11.70	1.716111	0.30413	4.54E-4	0.0	ENSG00000167384	ENST00000221327;ENST00000391956	T;T	0.03065	4.06;4.06	5.39	2.09	0.27110	.	0.920664	0.08851	N	0.884394	T	0.07458	0.0188	M	0.83953	2.67	0.19300	N	0.999979	B;B;B	0.22746	0.074;0.044;0.044	B;B;B	0.18561	0.022;0.01;0.01	T	0.32877	-0.9890	10	0.87932	D	0	-3.506	5.3213	0.15883	0.0:0.1527:0.2806:0.5667	.	664;688;689	G5E9B8;Q58F03;Q9UJW8	.;.;ZN180_HUMAN	C	689;664	ENSP00000221327:Y689C;ENSP00000375818:Y664C	ENSP00000221327:Y689C	Y	-	2	0	ZNF180	49672472	0.001000	0.12720	0.000000	0.03702	0.939000	0.58152	0.680000	0.25306	0.088000	0.17205	0.482000	0.46254	TAT	.	T|1.000;C|0.000	0.000	weak		0.313	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
PROKR2	128674	hgsc.bcm.edu	37	20	5294901	5294901	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr20:5294901C>T	ENST00000217270.3	-	1	114	c.115G>A	c.(115-117)Gag>Aag	p.E39K	PROKR2_ENST00000546004.1_Missense_Mutation_p.E39K	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	39					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						TCCTCATCCTCATCCATAGGG	0.507										HNSCC(71;0.22)																											p.E39K		Atlas-SNP	.											.	PROKR2	90	.	0			c.G115A						PASS	.						139.0	121.0	127.0					20																	5294901		2203	4300	6503	SO:0001583	missense	128674	exon1			CATCCTCATCCAT	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"""GPCR / Class A : Prokineticin receptors"""	15836	protein-coding gene	gene with protein product		607123	"""G protein-coupled receptor 73-like 1"", ""Kallmann syndrome 3 (autosomal dominant)"""	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.115G>A	chr20.hg19:g.5294901C>T	ENSP00000217270:p.Glu39Lys	111.0	0.0	.		114.0	33.0	.	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	hg19	CCDS13089.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.007135	0.75046	.	.	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.71103	-0.54;-0.54	4.6	4.6	0.57074	.	0.259050	0.40640	N	0.001056	T	0.67552	0.2905	M	0.68593	2.085	0.58432	D	0.999999	B	0.30146	0.27	B	0.32724	0.151	T	0.63902	-0.6532	10	0.11485	T	0.65	.	15.2898	0.73857	0.0:1.0:0.0:0.0	.	39	Q8NFJ6	PKR2_HUMAN	K	39	ENSP00000440790:E39K;ENSP00000217270:E39K	ENSP00000217270:E39K	E	-	1	0	PROKR2	5242901	0.998000	0.40836	0.996000	0.52242	0.934000	0.57294	3.102000	0.50291	2.269000	0.75478	0.655000	0.94253	GAG	.	.	.	none		0.507	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773	
SLC13A3	64849	hgsc.bcm.edu	37	20	45239165	45239165	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr20:45239165A>T	ENST00000279027.4	-	3	479	c.461T>A	c.(460-462)aTt>aAt	p.I154N	SLC13A3_ENST00000413164.2_Missense_Mutation_p.I154N|SLC13A3_ENST00000396360.1_Missense_Mutation_p.I107N|SLC13A3_ENST00000417157.2_Missense_Mutation_p.I107N|SLC13A3_ENST00000372121.1_Missense_Mutation_p.I154N|SLC13A3_ENST00000472148.1_Missense_Mutation_p.I107N|SLC13A3_ENST00000495082.1_Missense_Mutation_p.I107N|SLC13A3_ENST00000339636.3_Missense_Mutation_p.I154N|SLC13A3_ENST00000435032.1_De_novo_Start_InFrame|SLC13A3_ENST00000290317.5_Missense_Mutation_p.I107N	NM_001193342.1|NM_022829.5	NP_001180271.1|NP_073740.2	Q8WWT9	S13A3_HUMAN	solute carrier family 13 (sodium-dependent dicarboxylate transporter), member 3	154					transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-affinity sodium:dicarboxylate symporter activity (GO:0015362)			breast(2)|endometrium(2)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(115;0.0122)			Succinic acid(DB00139)	GGCATTGGCAATGGGAAGCAT	0.552																																					p.I154N		Atlas-SNP	.											.	SLC13A3	88	.	0			c.T461A						PASS	.						210.0	192.0	198.0					20																	45239165		2203	4300	6503	SO:0001583	missense	64849	exon3			TTGGCAATGGGAA	AF154121	CCDS13400.1, CCDS42886.1, CCDS54469.1, CCDS54470.1	20q13.12	2013-05-22			ENSG00000158296	ENSG00000158296		"""Solute carriers"""	14430	protein-coding gene	gene with protein product		606411				10794676, 10992006	Standard	NM_001011554		Approved	NADC3, SDCT2	uc002xsf.2	Q8WWT9	OTTHUMG00000033042	ENST00000279027.4:c.461T>A	chr20.hg19:g.45239165A>T	ENSP00000279027:p.Ile154Asn	56.0	0.0	.		53.0	19.0	.	NM_022829	B4DIR8|E1P5U4|F6WI18|Q5JYC9|Q5JYD0|Q5JYD1|Q5TCQ2|Q8IVB1|Q8N8K4|Q96MM5|Q9BR25|Q9H1G1|Q9H3W4|Q9NQN5|Q9NS04	Missense_Mutation	SNP	ENST00000279027.4	hg19	CCDS13400.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.993818	0.74703	.	.	ENSG00000158296	ENST00000290317;ENST00000396360;ENST00000279027;ENST00000472148;ENST00000413164;ENST00000495082;ENST00000468915;ENST00000420568;ENST00000372121;ENST00000417157;ENST00000339636	T;T;T;T;T;T;T;T;T;T;T	0.05925	3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37;3.37	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.31918	0.0812	M	0.89163	3.01	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;0.999;1.0	T	0.19224	-1.0312	10	0.87932	D	0	-25.0823	16.1297	0.81418	1.0:0.0:0.0:0.0	.	154;107;107;107;154	B4DIR8;Q8WWT9-3;F6WI18;C9J4A3;Q8WWT9	.;.;.;.;S13A3_HUMAN	N	107;107;154;107;154;107;107;117;154;107;154	ENSP00000290317:I107N;ENSP00000379648:I107N;ENSP00000279027:I154N;ENSP00000420177:I107N;ENSP00000415852:I154N;ENSP00000419621:I107N;ENSP00000417784:I107N;ENSP00000395095:I117N;ENSP00000361193:I154N;ENSP00000397955:I107N;ENSP00000344912:I154N	ENSP00000279027:I154N	I	-	2	0	SLC13A3	44672572	1.000000	0.71417	0.974000	0.42286	0.386000	0.30323	9.287000	0.95975	2.270000	0.75569	0.460000	0.39030	ATT	.	.	.	none		0.552	SLC13A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080329.2		
TTC3	7267	hgsc.bcm.edu	37	21	38494164	38494164	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr21:38494164C>G	ENST00000399017.2	+	12	3695	c.948C>G	c.(946-948)gaC>gaG	p.D316E	TTC3_ENST00000354749.2_Missense_Mutation_p.D316E|TTC3_ENST00000355666.1_Missense_Mutation_p.D316E|TTC3_ENST00000540756.1_Missense_Mutation_p.D6E|TTC3_ENST00000479930.1_3'UTR	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	316					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GGGAATATGACTGGGCCCTGC	0.343																																					p.D316E	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.C948G						PASS	.						62.0	63.0	63.0					21																	38494164		2203	4300	6503	SO:0001583	missense	7267	exon12			ATATGACTGGGCC	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.948C>G	chr21.hg19:g.38494164C>G	ENSP00000381981:p.Asp316Glu	217.0	0.0	.		181.0	24.0	.	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	hg19	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	C	5.051	0.195106	0.09599	.	.	ENSG00000182670	ENST00000418766;ENST00000450533;ENST00000438055;ENST00000355666;ENST00000540756;ENST00000399017;ENST00000354749	T;T;T;T;T;T;T	0.39406	1.34;1.34;1.34;3.27;1.08;3.27;3.27	5.55	2.52	0.30459	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.196102	0.35525	N	0.003151	T	0.15782	0.0380	N	0.02539	-0.55	0.24581	N	0.993876	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.21042	-1.0257	10	0.20046	T	0.44	-8.2624	8.1826	0.31319	0.4198:0.4365:0.1436:0.0	.	6;316	B4DSZ9;P53804	.;TTC3_HUMAN	E	316;316;298;316;6;316;316	ENSP00000403943:D316E;ENSP00000408456:D316E;ENSP00000391891:D298E;ENSP00000347889:D316E;ENSP00000442875:D6E;ENSP00000381981:D316E;ENSP00000346791:D316E	ENSP00000346791:D316E	D	+	3	2	TTC3	37416034	0.996000	0.38824	1.000000	0.80357	0.999000	0.98932	0.383000	0.20651	0.679000	0.31345	0.650000	0.86243	GAC	.	.	.	none		0.343	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26164198	26164198	+	Silent	SNP	G	G	C			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr22:26164198G>C	ENST00000407587.2	+	4	484	c.315G>C	c.(313-315)ctG>ctC	p.L105L	MYO18B_ENST00000536101.1_Silent_p.L105L|MYO18B_ENST00000335473.7_Silent_p.L105L			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	105	Ser-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CAGACATTCTGGGCAAGGAGA	0.602																																					p.L105L		Atlas-SNP	.											.	MYO18B	322	.	0			c.G315C						PASS	.						76.0	82.0	80.0					22																	26164198		1969	4152	6121	SO:0001819	synonymous_variant	84700	exon4			CATTCTGGGCAAG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.315G>C	chr22.hg19:g.26164198G>C		157.0	0.0	.		186.0	10.0	.	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	hg19																																																																																				.	.	.	none		0.602	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
ITIH6	347365	hgsc.bcm.edu	37	X	54777684	54777684	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chrX:54777684C>T	ENST00000218436.6	-	12	3511	c.3482G>A	c.(3481-3483)cGc>cAc	p.R1161H		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	1161					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										TATAGAACTGCGGCTGATGGT	0.587													C|||	1	0.000264901	0.0008	0.0	3775	,	,		14301	0.0		0.0	False		,,,				2504	0.0				p.R1161H		Atlas-SNP	.											.	.	.	.	0			c.G3482A						PASS	.						80.0	66.0	71.0					X																	54777684		2203	4300	6503	SO:0001583	missense	347365	exon12			GAACTGCGGCTGA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.3482G>A	chrX.hg19:g.54777684C>T	ENSP00000218436:p.Arg1161His	123.0	0.0	.		153.0	106.0	.	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	hg19	CCDS14361.1	.	.	.	.	.	.	.	.	.	.	C	2.230	-0.376357	0.05000	.	.	ENSG00000102313	ENST00000218436	T	0.11495	2.77	3.58	-4.03	0.04021	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	2.392490	0.02752	N	0.117600	T	0.06690	0.0171	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.32613	-0.9900	10	0.38643	T	0.18	.	2.5439	0.04732	0.1157:0.3461:0.1136:0.4246	.	1161	Q6UXX5	ITH5L_HUMAN	H	1161	ENSP00000218436:R1161H	ENSP00000218436:R1161H	R	-	2	0	ITIH5L	54794409	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.458000	0.02372	-0.749000	0.04747	-0.742000	0.03525	CGC	.	.	.	none		0.587	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
CCDC64	92558	hgsc.bcm.edu	37	12	120427989	120427991	+	In_Frame_Del	DEL	AGG	AGG	-	rs560592174		TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr12:120427989_120427991delAGG	ENST00000397558.2	+	1	317_319	c.317_319delAGG	c.(316-321)aaggag>aag	p.E107del		NM_207311.2	NP_997194.2	Q6ZP65	BICR1_HUMAN	coiled-coil domain containing 64	107					Golgi to secretory granule transport (GO:0055107)|neuron projection development (GO:0031175)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	dynactin binding (GO:0034452)|Rab GTPase binding (GO:0017137)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(2)|lung(4)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					ATCCGACAGAAGGAGAAGGATCT	0.67																																					p.106_106del		Atlas-Indel,Pindel	.											.	CCDC64	40	.	0			c.316_318del						PASS	.																																			SO:0001651	inframe_deletion	92558	exon1			.	U88834, AK129960	CCDS41845.1	12q24.23	2006-01-24				ENSG00000135127			28095	protein-coding gene	gene with protein product							Standard	NM_207311		Approved	FLJ26450	uc001txl.1	Q6ZP65	OTTHUMG00000169311	ENST00000397558.2:c.317_319delAGG	chr12.hg19:g.120427989_120427991delAGG	ENSP00000380690:p.Glu107del	157.0	0.0	0		168.0	42.0	0.25	NM_207311	A8MUC8|B4DWL0|B5MDJ0|O95000	In_Frame_Del	DEL	ENST00000397558.2	hg19	CCDS41845.1																																																																																			.	.	.	none		0.670	CCDC64-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000403390.2	NM_207311	
ST7	7982	hgsc.bcm.edu	37	7	116770588	116770588	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr7:116770588delA	ENST00000393446.2	+	5	796	c.493delA	c.(493-495)atgfs	p.M165fs	ST7_ENST00000393451.3_Frame_Shift_Del_p.M165fs|ST7_ENST00000487459.1_3'UTR|ST7_ENST00000393449.1_Frame_Shift_Del_p.M165fs|ST7-AS2_ENST00000432541.1_RNA|ST7_ENST00000323984.3_Frame_Shift_Del_p.M165fs|ST7_ENST00000465133.1_Frame_Shift_Del_p.M122fs|ST7_ENST00000393444.3_Frame_Shift_Del_p.M122fs|ST7-AS2_ENST00000442719.1_RNA|ST7-AS2_ENST00000434993.1_RNA|ST7_ENST00000432298.1_Frame_Shift_Del_p.M119fs|ST7_ENST00000265437.5_Frame_Shift_Del_p.M165fs|ST7_ENST00000393443.1_Frame_Shift_Del_p.M115fs|ST7_ENST00000422922.1_Frame_Shift_Del_p.M119fs|ST7_ENST00000393447.4_Frame_Shift_Del_p.M122fs			Q9Y561	LRP12_HUMAN	suppression of tumorigenicity 7	0	LDL-receptor class A 1. {ECO:0000255|PROSITE-ProRule:PRU00124}.				endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(1)	21	all_cancers(3;3.88e-07)|all_epithelial(6;3.42e-07)|Lung NSC(10;0.00072)|all_lung(10;0.000847)		STAD - Stomach adenocarcinoma(10;0.000512)	LUSC - Lung squamous cell carcinoma(290;0.133)		TTACTATGACATGAATCTCTC	0.428																																					p.D164fs		Atlas-Indel,Pindel	.											.	ST7	64	.	0			c.492delC						PASS	.						171.0	168.0	169.0					7																	116770588		2203	4299	6502	SO:0001589	frameshift_variant	7982	exon5			.	AJ277291	CCDS5769.1, CCDS5770.1	7q31.2	2008-06-06			ENSG00000004866	ENSG00000004866			11351	protein-coding gene	gene with protein product		600833		FAM4A1		8105370, 8938430	Standard	NM_021908		Approved	TSG7, SEN4, ETS7q, HELG, RAY1, FAM4A	uc003vin.3	Q9NRC1	OTTHUMG00000023888	ENST00000393446.2:c.493delA	chr7.hg19:g.116770588delA	ENSP00000377092:p.Met165fs	39.0	0.0	0		116.0	33.0	0.284483	NM_018412	A8K137|B4DRQ2	Frame_Shift_Del	DEL	ENST00000393446.2	hg19																																																																																				.	.	.	none		0.428	ST7-013	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000319687.1	NM_021908	
TGOLN2	10618	hgsc.bcm.edu	37	2	85553951	85553951	+	Frame_Shift_Del	DEL	T	T	-			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr2:85553951delT	ENST00000409232.3	-	2	965	c.904delA	c.(904-906)actfs	p.T302fs	TGOLN2_ENST00000409015.1_Frame_Shift_Del_p.T302fs|TGOLN2_ENST00000282120.2_Intron|TGOLN2_ENST00000398263.2_Intron|TGOLN2_ENST00000377386.3_Frame_Shift_Del_p.T302fs|TGOLN2_ENST00000444342.2_Frame_Shift_Del_p.T302fs			O43493	TGON2_HUMAN	trans-golgi network protein 2	302						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)											ATGAGGTCAGTTTCCTCCCCA	0.512																																					p.T302fs		Atlas-Indel,Pindel	.											.	TGOLN2	32	.	0			c.905delC						PASS	.						56.0	52.0	53.0					2																	85553951		1901	4128	6029	SO:0001589	frameshift_variant	10618	exon2			.	AF027515	CCDS46351.1, CCDS56126.1, CCDS56127.1	2p11.2	2012-06-25			ENSG00000152291	ENSG00000152291			15450	protein-coding gene	gene with protein product	"""trans-Golgi network protein (46, 48, 51kD isoforms)"""	603062				9422759, 21994457	Standard	NM_001206840		Approved	TGN51, TGN46, TGN48, TGN38, TTGN2	uc021vjw.1	O43493	OTTHUMG00000153017	ENST00000409232.3:c.904delA	chr2.hg19:g.85553951delT	ENSP00000386443:p.Thr302fs	117.0	0.0	0		130.0	41.0	0.315385	NM_001206841	B2R686|B8ZZ88|D6W5K3|F8WBK2|O15282|O43492|O43499|O43500|O43501|Q53G68|Q53GV2|Q6MZV1|Q6ZTM7|Q8N6T8|Q92760|Q96QL2	Frame_Shift_Del	DEL	ENST00000409232.3	hg19	CCDS56126.1																																																																																			.	.	.	none		0.512	TGOLN2-006	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000329045.2	NM_006464	
MYH4	4622	hgsc.bcm.edu	37	17	10352186	10352187	+	Frame_Shift_Ins	INS	-	-	A			TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr17:10352186_10352187insA	ENST00000255381.2	-	31	4469_4470	c.4359_4360insT	c.(4357-4362)tttgacfs	p.D1454fs	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1454					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)			NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						ACCACCTTGTCAAAGTTTCTTT	0.446																																					p.D1454_K1455delinsX		Atlas-Indel,Pindel	.											.	MYH4	349	.	0			c.4360_4361insT						PASS	.																																			SO:0001589	frameshift_variant	4622	exon31			.		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.4360dupT	chr17.hg19:g.10352189_10352189dupA	ENSP00000255381:p.Asp1454fs	76.0	0.0	0		138.0	38.0	0.275362	NM_017533		Frame_Shift_Ins	INS	ENST00000255381.2	hg19	CCDS11154.1																																																																																			.	.	.	none		0.446	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
MUC4	4585	hgsc.bcm.edu	37	3	195506007	195506102	+	In_Frame_Del	DEL	GGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTC	GGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTC	-	rs568017375|rs199748333|rs529273490|rs191235959|rs547812110|rs559770239|rs531891299|rs574341510|rs544126797|rs564750842|rs545980189|rs553395016|rs367572598|rs566138201|rs562257952|rs555863624|rs566197584|rs376661673|rs200152370|rs74941663|rs577053797|rs538185950|rs71634712|rs533505851|rs570653011|rs2432527|rs571820970|rs535044025|rs533926243	byFrequency	TCGA-2Z-A9J6-01A-11D-A382-10	TCGA-2Z-A9J6-10A-01D-A385-10	GGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTC	GGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b4d9f71f-1f39-480d-bb51-01ec0e2b06dd	6b322937-8164-4794-b588-a7711b2e8a48	g.chr3:195506007_195506102delGGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTC	ENST00000463781.3	-	2	12808_12903	c.12349_12444delGACACTTCCTCTGCATCCACAGGTCAGGCCACCCCTCTTCCTGTCACCAGCCTTTCCTCAGTATCCACAGGTGACACCACGCCTCTTCCTGTCACC	c.(12349-12444)gacacttcctctgcatccacaggtcaggccacccctcttcctgtcaccagcctttcctcagtatccacaggtgacaccacgcctcttcctgtcaccdel	p.DTSSASTGQATPLPVTSLSSVSTGDTTPLPVT4117del	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.DTSSASTGQATPLPVTSLSSVSTGDTTPLPVT4117del|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T4148T(2)|p.T4118A(2)|p.D4117N(1)|p.D4117V(1)|p.Q4125H(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGGAAGGGATGGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTCGGTGACAGGA	0.591																																					p.4117_4149del		Pindel	.											.	MUC4	1505	.	7	Substitution - Missense(5)|Substitution - coding silent(2)	endometrium(4)|kidney(2)|central_nervous_system(1)	c.12350_12445del						PASS	.																																			SO:0001651	inframe_deletion	4585	exon2			.	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.12349_12444delGACACTTCCTCTGCATCCACAGGTCAGGCCACCCCTCTTCCTGTCACCAGCCTTTCCTCAGTATCCACAGGTGACACCACGCCTCTTCCTGTCACC	chr3.hg19:g.195506007_195506102delGGTGACAGGAAGAGGCGTGGTGTCACCTGTGGATACTGAGGAAAGGCTGGTGACAGGAAGAGGGGTGGCCTGACCTGTGGATGCAGAGGAAGTGTC	ENSP00000417498:p.Asp4117_Thr4148del	73.0	0.0	.		145.0	14.0	0.097	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	hg19	CCDS54700.1																																																																																			.	.	.	none		0.591	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
