#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_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
E2F1	1869	hgsc.bcm.edu	37	20	32267687	32267690	+	Frame_Shift_Del	DEL	CCGT	CCGT	-			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	CCGT	CCGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr20:32267687_32267690delCCGT	ENST00000343380.5	-	3	582_585	c.443_446delACGG	c.(442-447)gacggtfs	p.DG148fs		NM_005225.2	NP_005216.1	Q01094	E2F1_HUMAN	E2F transcription factor 1	148	Interaction with BIRC2/c-IAP1.				anoikis (GO:0043276)|apoptotic process (GO:0006915)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|DNA damage checkpoint (GO:0000077)|forebrain development (GO:0030900)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lens fiber cell apoptotic process (GO:1990086)|mitotic cell cycle (GO:0000278)|mRNA stabilization (GO:0048255)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(2)|breast(1)|endometrium(3)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	16						GTCGACGACACCGTCAGCCGAGTG	0.593																																					p.148_149del		Atlas-Indel	.											.	E2F1	41	.	0			c.444_447del						PASS	.																																			SO:0001589	frameshift_variant	1869	exon3			.		CCDS13224.1	20q11	2008-05-14			ENSG00000101412	ENSG00000101412			3113	protein-coding gene	gene with protein product		189971		RBBP3		8964493	Standard	NM_005225		Approved	RBP3	uc002wzu.4	Q01094	OTTHUMG00000032265	ENST00000343380.5:c.443_446delACGG	20.37:g.32267687_32267690delCCGT	ENSP00000345571:p.Asp148fs	125.0	0.0	0		91.0	12.0	0.131868	NM_005225	Q13143|Q92768	Frame_Shift_Del	DEL	ENST00000343380.5	37	CCDS13224.1																																																																																			.	.	none		0.593	E2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078731.2		
TNFAIP3	7128	hgsc.bcm.edu	37	6	138198239	138198240	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:138198239_138198240delAG	ENST00000237289.4	+	6	898_899	c.832_833delAG	c.(832-834)agafs	p.R278fs	TNFAIP3_ENST00000485192.1_3'UTR	NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	278	TRAF-binding.				apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		ACTTGTTAACAGAGACCGGGGA	0.342			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""																																p.277_278del	GBM(130;153 1739 22295 28918 47987)	Atlas-Indel	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	.	TNFAIP3	340	.	25	Whole gene deletion(25)	haematopoietic_and_lymphoid_tissue(25)	c.831_832del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon6			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.832_833delAG	6.37:g.138198241_138198242delAG	ENSP00000237289:p.Arg278fs	286.0	0.0	0		165.0	12.0	0.0727273	NM_001270508	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.342	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
SCN9A	6335	hgsc.bcm.edu	37	2	167055184	167055185	+	Stop_Codon_Ins	INS	-	-	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr2:167055184_167055185insT	ENST00000409435.1	-	0	5963_5964				SCN9A_ENST00000409672.1_Stop_Codon_Ins|SCN9A_ENST00000375387.4_Stop_Codon_Ins|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Stop_Codon_Ins			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit						behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGAAGCTCTATTTTTTGCTTT	0.327																																					p.X1978delinsI		Atlas-Indel	.											.	SCN9A	296	.	0			c.5932_5933insA						PASS	.																																			SO:0001567	stop_retained_variant	6335	exon27			.	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.5965dupA	2.37:g.167055190_167055190dupT	ENSP00000386330:p.*1989Ileext*?	372.0	0.0	0		243.0	22.0	0.090535	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Frame_Shift_Ins	INS	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.327	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
ARID1A	8289	hgsc.bcm.edu	37	1	27101417	27101417	+	Frame_Shift_Del	DEL	C	C	-			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:27101417delC	ENST00000324856.7	+	18	5070	c.4699delC	c.(4699-4701)cccfs	p.P1569fs	ARID1A_ENST00000540690.1_Intron|ARID1A_ENST00000457599.2_Intron|ARID1A_ENST00000374152.2_Frame_Shift_Del_p.P1186fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1569					androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		CATGACAAGGCCCCCTCCATC	0.632			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.R1566fs		Atlas-Indel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.4698delG						PASS	.						51.0	50.0	51.0					1																	27101417		2203	4300	6503	SO:0001589	frameshift_variant	8289	exon18			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.4699delC	1.37:g.27101417delC	ENSP00000320485:p.Pro1569fs	124.0	0.0	0		119.0	28.0	0.235294	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																			.	.	none		0.632	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
KMT2D	8085	hgsc.bcm.edu	37	12	49436376	49436377	+	Frame_Shift_Ins	INS	-	-	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:49436376_49436377insG	ENST00000301067.7	-	27	5833_5834	c.5834_5835insC	c.(5833-5835)ccafs	p.P1945fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1945					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GGCAGAGGCCTGGGTAGGAGTC	0.559																																					p.P1945fs		Atlas-Indel	.											.	MLL2	1173	.	0			c.5835_5836insC						PASS	.																																			SO:0001589	frameshift_variant	8085	exon27			.	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.5835dupC	12.37:g.49436379_49436379dupG	ENSP00000301067:p.Pro1945fs	87.0	0.0	0		66.0	11.0	0.166667	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.559	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
CTSH	1512	hgsc.bcm.edu	37	15	79221796	79221797	+	Frame_Shift_Ins	INS	-	-	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr15:79221796_79221797insT	ENST00000220166.5	-	8	696_697	c.587_588insA	c.(586-588)aacfs	p.N196fs	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	196					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						TGATCCCCTTGTTGTACAGGAT	0.579																																					p.N196fs		Atlas-Indel	.											.	CTSH	23	.	0			c.588_589insA						PASS	.																																			SO:0001589	frameshift_variant	1512	exon8			.	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.588dupA	15.37:g.79221798_79221798dupT	ENSP00000220166:p.Asn196fs	226.0	0.0	0		129.0	12.0	0.0930233	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Frame_Shift_Ins	INS	ENST00000220166.5	37	CCDS10308.1																																																																																			.	.	none		0.579	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
OR2T34	127068	hgsc.bcm.edu	37	1	248737510	248737511	+	Frame_Shift_Ins	INS	-	-	A	rs150608839	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:248737510_248737511insA	ENST00000328782.2	-	1	569_570	c.548_549insT	c.(547-549)ttcfs	p.F183fs		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	183						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F183S(1)		breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GAGTCTCACAGAAAAAACTCAG	0.515																																					p.F183fs		Atlas-Indel	.											OR2T34,NS,haematopoietic_neoplasm,-1,2	OR2T34	72	2	1	Substitution - Missense(1)	stomach(1)	c.549_550insT						PASS	.																																			SO:0001589	frameshift_variant	127068	exon1			.	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.549dupT	1.37:g.248737516_248737516dupA	ENSP00000330904:p.Phe183fs	333.0	0.0	0		230.0	39.0	0.169565	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Frame_Shift_Ins	INS	ENST00000328782.2	37	CCDS31120.1																																																																																			.	.	none		0.515	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
RIMS1	22999	hgsc.bcm.edu	37	6	73023228	73023228	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:73023228A>G	ENST00000521978.1	+	28	3983	c.3983A>G	c.(3982-3984)cAg>cGg	p.Q1328R	RIMS1_ENST00000491071.2_Missense_Mutation_p.Q1151R|RIMS1_ENST00000538414.1_Missense_Mutation_p.Q134R|RIMS1_ENST00000348717.5_Missense_Mutation_p.Q1120R|RIMS1_ENST00000517960.1_Missense_Mutation_p.Q1120R|RIMS1_ENST00000264839.7_Missense_Mutation_p.Q1177R|RIMS1_ENST00000518273.1_Intron|RIMS1_ENST00000425662.2_Intron|RIMS1_ENST00000520567.1_Intron|RIMS1_ENST00000517827.1_Intron|RIMS1_ENST00000401910.3_Missense_Mutation_p.Q648R|RIMS1_ENST00000522291.1_Intron|RIMS1_ENST00000523963.1_Intron	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	1328					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				CATAAAGATCAGTACAGAAGC	0.403																																					p.Q1328R		Atlas-SNP	.											.	RIMS1	278	.	0			c.A3983G						PASS	.						57.0	60.0	59.0					6																	73023228		1962	4152	6114	SO:0001583	missense	22999	exon28			AAGATCAGTACAG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.3983A>G	6.37:g.73023228A>G	ENSP00000428417:p.Gln1328Arg	93.0	0.0	0		78.0	19.0	0.24359	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.95|11.95	1.792225|1.792225	0.31685|0.31685	.|.	.|.	ENSG00000079841|ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000264839;ENST00000517960;ENST00000521978;ENST00000401910;ENST00000453976;ENST00000370420;ENST00000538414|ENST00000522211	T;T;T;T;T;T;T;T;T|.	0.18338|.	2.55;2.68;2.6;2.68;2.58;2.67;2.55;2.28;2.22|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.64402|.	D|.	0.000007|.	T|T	0.59266|0.59266	0.2181|0.2181	L|L	0.50333|0.50333	1.59|1.59	0.47308|0.47308	D|D	0.999389|0.999389	B;P;P;B;D;B;P|.	0.56035|.	0.017;0.949;0.885;0.003;0.974;0.016;0.936|.	B;D;P;B;P;B;P|.	0.64042|.	0.016;0.921;0.549;0.003;0.521;0.01;0.885|.	T|T	0.58869|0.58869	-0.7560|-0.7560	10|5	0.07990|.	T|.	0.79|.	-18.4387|-18.4387	16.0343|16.0343	0.80612|0.80612	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	134;1177;648;1120;404;1151;1328|.	B7Z7W2;E9PHR1;E9PF48;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.;.;.;.;.;.;RIMS1_HUMAN|.	R|G	1151;1177;1151;1120;1177;1120;1328;648;493;376;134|246	ENSP00000430101:Q1151R;ENSP00000275037:Q1120R;ENSP00000264839:Q1177R;ENSP00000429959:Q1120R;ENSP00000428417:Q1328R;ENSP00000385649:Q648R;ENSP00000389503:Q493R;ENSP00000359448:Q376R;ENSP00000439730:Q134R|.	ENSP00000264839:Q1177R|.	Q|S	+|+	2|1	0|0	RIMS1|RIMS1	73079949|73079949	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.914000|6.914000	0.75764|0.75764	2.198000|2.198000	0.70561|0.70561	0.533000|0.533000	0.62120|0.62120	CAG|AGT	.	.	none		0.403	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
SMAD9	4093	hgsc.bcm.edu	37	13	37453460	37453460	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:37453460C>T	ENST00000399275.2	-	1	506	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	SMAD9_ENST00000350148.5_Missense_Mutation_p.E123K|SMAD9_ENST00000483941.1_5'Flank|SMAD9_ENST00000379826.4_Missense_Mutation_p.E123K			O15198	SMAD9_HUMAN	SMAD family member 9	123	MH1. {ECO:0000255|PROSITE- ProRule:PRU00438}.				BMP signaling pathway (GO:0030509)|bone development (GO:0060348)|cartilage development (GO:0051216)|cellular response to organic cyclic compound (GO:0071407)|hindbrain development (GO:0030902)|intracellular signal transduction (GO:0035556)|midbrain development (GO:0030901)|Mullerian duct regression (GO:0001880)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity (GO:0030618)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)	18		Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.184)		all cancers(112;3.38e-07)|Epithelial(112;1.93e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00804)|BRCA - Breast invasive adenocarcinoma(63;0.0129)|GBM - Glioblastoma multiforme(144;0.026)		ATGCACACTTCTTTCTGCTTG	0.557																																					p.E123K		Atlas-SNP	.											.	SMAD9	91	.	0			c.G367A						PASS	.						38.0	41.0	40.0					13																	37453460		2202	4300	6502	SO:0001583	missense	4093	exon2			ACACTTCTTTCTG		CCDS9360.1, CCDS45032.1	13q12-q14	2014-09-17	2006-11-06	2004-05-26	ENSG00000120693	ENSG00000120693		"""SMADs"""	6774	protein-coding gene	gene with protein product		603295	"""MAD, mothers against decapentaplegic homolog 9 (Drosophila)"", ""SMAD, mothers against DPP homolog 9 (Drosophila)"""	MADH6, MADH9		9205116	Standard	NM_001127217		Approved		uc001uvw.3	O15198	OTTHUMG00000016740	ENST00000399275.2:c.367G>A	13.37:g.37453460C>T	ENSP00000382216:p.Glu123Lys	81.0	0.0	0		52.0	6.0	0.115385	NM_005905	A2A2Y6|O14989|Q5TBA1	Missense_Mutation	SNP	ENST00000399275.2	37	CCDS45032.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.715825	0.89112	.	.	ENSG00000120693	ENST00000399275;ENST00000350148;ENST00000379826	T;T;T	0.77098	-1.07;-1.07;-1.07	5.47	5.47	0.80525	MAD homology, MH1 (3);MAD homology 1, Dwarfin-type (2);	0.092522	0.64402	D	0.000001	D	0.87481	0.6188	M	0.85859	2.78	0.80722	D	1	B;D	0.53745	0.408;0.962	B;P	0.56216	0.138;0.794	D	0.89288	0.3617	10	0.72032	D	0.01	.	18.3033	0.90171	0.0:1.0:0.0:0.0	.	123;123	O15198-2;O15198	.;SMAD9_HUMAN	K	123	ENSP00000382216:E123K;ENSP00000239885:E123K;ENSP00000369154:E123K	ENSP00000239885:E123K	E	-	1	0	SMAD9	36351460	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	7.762000	0.85270	2.565000	0.86533	0.514000	0.50259	GAA	.	.	none		0.557	SMAD9-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044525.2	NM_005905	
KCNN4	3783	hgsc.bcm.edu	37	19	44278489	44278489	+	Missense_Mutation	SNP	G	G	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:44278489G>C	ENST00000262888.3	-	3	933	c.538C>G	c.(538-540)Cgc>Ggc	p.R180G		NM_002250.2	NP_002241.1	O15554	KCNN4_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4	180					calcium ion transport (GO:0006816)|cell volume homeostasis (GO:0006884)|defense response (GO:0006952)|immune system process (GO:0002376)|phospholipid translocation (GO:0045332)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell receptor signaling pathway (GO:0050862)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|saliva secretion (GO:0046541)|stabilization of membrane potential (GO:0030322)|synaptic transmission (GO:0007268)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|Intermediate conductance calcium-activated potassium channel activity (GO:0022894)|protein phosphatase binding (GO:0019903)			biliary_tract(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0352)			Clotrimazole(DB00257)|Enflurane(DB00228)|Halothane(DB01159)|Miconazole(DB01110)|Procaine(DB00721)|Quinine(DB00468)	CCGATGCTGCGGTAGGAAGCG	0.662											OREG0025535	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R180G		Atlas-SNP	.											.	KCNN4	37	.	0			c.C538G						PASS	.						27.0	25.0	26.0					19																	44278489		2196	4300	6496	SO:0001583	missense	3783	exon3			TGCTGCGGTAGGA	AF022797	CCDS12630.1	19q13.2	2012-07-05				ENSG00000104783		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6293	protein-coding gene	gene with protein product		602754				9380751, 9407042, 16382103	Standard	NM_002250		Approved	KCa3.1, hSK4, hKCa4, hIKCa1	uc002oxl.3	O15554		ENST00000262888.3:c.538C>G	19.37:g.44278489G>C	ENSP00000262888:p.Arg180Gly	119.0	0.0	0	922	98.0	11.0	0.112245	NM_002250	Q53XR4	Missense_Mutation	SNP	ENST00000262888.3	37	CCDS12630.1	.	.	.	.	.	.	.	.	.	.	G	18.46	3.628785	0.67015	.	.	ENSG00000104783	ENST00000262888;ENST00000407385	D	0.99896	-7.6	4.38	3.33	0.38152	.	0.053759	0.64402	D	0.000002	D	0.99789	0.9911	M	0.74467	2.265	0.50039	D	0.999843	D;D	0.89917	0.98;1.0	P;D	0.87578	0.67;0.998	D	0.98041	1.0382	10	0.87932	D	0	-21.927	5.9886	0.19448	0.1001:0.0:0.7138:0.1861	.	74;180	D1MQ10;O15554	.;KCNN4_HUMAN	G	180;48	ENSP00000262888:R180G	ENSP00000262888:R180G	R	-	1	0	KCNN4	48970329	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.516000	0.45520	0.972000	0.38314	-0.300000	0.09419	CGC	.	.	none		0.662	KCNN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463598.1	NM_002250	
IRF4	3662	hgsc.bcm.edu	37	6	394899	394899	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:394899T>C	ENST00000380956.4	+	3	421	c.295T>C	c.(295-297)Tgc>Cgc	p.C99R	IRF4_ENST00000495137.1_3'UTR	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	99					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		GCGCCTGCGGTGCGCTTTGAA	0.542			T	IGH@	MM																																p.C99R		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	IRF4_ENST00000380956,NS,carcinoma,-1,1	IRF4	65	1	0			c.T295C						PASS	.						89.0	94.0	92.0					6																	394899		2203	4300	6503	SO:0001583	missense	3662	exon3			CTGCGGTGCGCTT	U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.295T>C	6.37:g.394899T>C	ENSP00000370343:p.Cys99Arg	55.0	0.0	0		46.0	8.0	0.173913	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.011366	0.54468	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.99418	-5.87	5.81	5.81	0.92471	Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.000000	0.85682	D	0.000000	D	0.99664	0.9875	M	0.94063	3.49	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.97583	1.0112	10	0.87932	D	0	-17.4096	16.1535	0.81640	0.0:0.0:0.0:1.0	.	99;99;99	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	R	99;129	ENSP00000370343:C99R	ENSP00000370343:C99R	C	+	1	0	IRF4	339899	1.000000	0.71417	0.108000	0.21378	0.035000	0.12851	7.586000	0.82596	2.217000	0.71921	0.528000	0.53228	TGC	.	.	none		0.542	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1		
KCTD3	51133	hgsc.bcm.edu	37	1	215751396	215751396	+	Silent	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:215751396C>T	ENST00000259154.4	+	6	663	c.369C>T	c.(367-369)gtC>gtT	p.V123V		NM_016121.3	NP_057205.2	Q9Y597	KCTD3_HUMAN	potassium channel tetramerization domain containing 3	123					protein homooligomerization (GO:0051260)					breast(4)|endometrium(2)|kidney(1)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)	33				all cancers(67;0.0164)|OV - Ovarian serous cystadenocarcinoma(81;0.019)|GBM - Glioblastoma multiforme(131;0.0862)|Epithelial(68;0.13)		GTGGCAGTGTCCTTTTTCATG	0.348																																					p.V123V		Atlas-SNP	.											.	KCTD3	101	.	0			c.C369T						PASS	.						187.0	180.0	182.0					1																	215751396		2203	4300	6503	SO:0001819	synonymous_variant	51133	exon6			CAGTGTCCTTTTT	AK024547	CCDS1515.1	1q41	2013-06-20	2013-06-20		ENSG00000136636	ENSG00000136636			21305	protein-coding gene	gene with protein product		613272	"""potassium channel tetramerisation domain containing 3"""			10508479	Standard	NM_016121		Approved	NY-REN-45	uc001hks.3	Q9Y597	OTTHUMG00000037019	ENST00000259154.4:c.369C>T	1.37:g.215751396C>T		297.0	0.0	0		184.0	23.0	0.125	NM_016121	A0AV15|D3DTA6|Q49AG7|Q504Q9|Q6PJN6|Q8ND58|Q8NDJ0|Q8WX16	Silent	SNP	ENST00000259154.4	37	CCDS1515.1	.	.	.	.	.	.	.	.	.	.	C	9.424	1.083728	0.20309	.	.	ENSG00000136636	ENST00000448333	.	.	.	5.8	0.154	0.14901	.	.	.	.	.	T	0.60818	0.2298	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57596	-0.7784	4	.	.	.	-26.6937	12.4313	0.55575	0.0:0.4808:0.4559:0.0632	.	.	.	.	S	96	.	.	P	+	1	0	KCTD3	213818019	0.883000	0.30277	0.984000	0.44739	0.988000	0.76386	-0.075000	0.11431	0.050000	0.15949	-0.479000	0.04858	CCT	.	.	none		0.348	KCTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089871.2	NM_016121	
FAT1	2195	hgsc.bcm.edu	37	4	187539303	187539303	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:187539303G>T	ENST00000441802.2	-	10	8646	c.8437C>A	c.(8437-8439)Cca>Aca	p.P2813T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	2813	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GCCTCATATGGACTAGATTCA	0.463										HNSCC(5;0.00058)																											p.P2813T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C8437A						PASS	.						125.0	120.0	122.0					4																	187539303		1879	4121	6000	SO:0001583	missense	2195	exon10			CATATGGACTAGA	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.8437C>A	4.37:g.187539303G>T	ENSP00000406229:p.Pro2813Thr	151.0	0.0	0		103.0	14.0	0.135922	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	G	12.30	1.897051	0.33535	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.37411	1.2	5.0	5.0	0.66597	Cadherin (2);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.42653	0.1212	N	0.16862	0.45	0.80722	D	1	D	0.76494	0.999	D	0.69142	0.962	T	0.16512	-1.0400	10	0.17832	T	0.49	.	18.8402	0.92180	0.0:0.0:1.0:0.0	.	2813	Q14517	FAT1_HUMAN	T	2813;2815	ENSP00000406229:P2813T	ENSP00000260147:P2815T	P	-	1	0	FAT1	187776297	1.000000	0.71417	0.268000	0.24571	0.914000	0.54420	7.674000	0.83992	2.757000	0.94681	0.655000	0.94253	CCA	.	.	none		0.463	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
GPC1	2817	hgsc.bcm.edu	37	2	241401695	241401695	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr2:241401695C>T	ENST00000264039.2	+	3	661	c.413C>T	c.(412-414)gCg>gTg	p.A138V		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	138					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		ACGCAGAACGCGAGGGCCTTC	0.672																																					p.A138V		Atlas-SNP	.											.	GPC1	32	.	0			c.C413T						PASS	.						21.0	23.0	22.0					2																	241401695		2190	4296	6486	SO:0001583	missense	2817	exon3			AGAACGCGAGGGC	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.413C>T	2.37:g.241401695C>T	ENSP00000264039:p.Ala138Val	147.0	0.0	0		111.0	11.0	0.0990991	NM_002081	B3KTD1|Q53QM4	Missense_Mutation	SNP	ENST00000264039.2	37	CCDS2534.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	12.09|12.09	1.832212|1.832212	0.32421|0.32421	.|.	.|.	ENSG00000063660|ENSG00000063660	ENST00000264039;ENST00000426280|ENST00000427506;ENST00000425056	T;T|.	0.52057|.	0.68;0.68|.	3.1|3.1	1.2|1.2	0.21068|0.21068	.|.	1.004560|.	0.08007|.	N|.	0.989674|.	T|.	0.36331|.	0.0963|.	L|L	0.53617|0.53617	1.68|1.68	0.09310|0.09310	N|N	1|1	B|.	0.30193|.	0.272|.	B|.	0.39617|.	0.305|.	T|.	0.31641|.	-0.9936|.	10|.	0.52906|.	T|.	0.07|.	-13.7881|-13.7881	1.889|1.889	0.03243|0.03243	0.2067:0.4686:0.2019:0.1227|0.2067:0.4686:0.2019:0.1227	.|.	138|.	P35052|.	GPC1_HUMAN|.	V|X	138;88|95;134	ENSP00000264039:A138V;ENSP00000410251:A88V|.	ENSP00000264039:A138V|.	A|R	+|+	2|1	0|2	GPC1|GPC1	241050368|241050368	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.583000|0.583000	0.36354|0.36354	-0.002000|-0.002000	0.12924|0.12924	0.161000|0.161000	0.19458|0.19458	0.586000|0.586000	0.80456|0.80456	GCG|CGA	.	.	none		0.672	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
XRCC2	7516	hgsc.bcm.edu	37	7	152346254	152346254	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:152346254C>A	ENST00000359321.1	-	3	401	c.316G>T	c.(316-318)Gaa>Taa	p.E106*	XRCC2_ENST00000495707.1_5'UTR	NM_005431.1	NP_005422.1	O43543	XRCC2_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 2	106					centrosome organization (GO:0051297)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|in utero embryonic development (GO:0001701)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of neurogenesis (GO:0050769)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|strand invasion (GO:0042148)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)			NS(1)|breast(1)|large_intestine(5)|liver(1)|lung(1)|prostate(2)	11		all_hematologic(28;0.0592)|Prostate(32;0.081)	OV - Ovarian serous cystadenocarcinoma(82;0.0423)	UCEC - Uterine corpus endometrioid carcinoma (81;0.0429)		TTGATTATTTCTTCAGAGCTT	0.378								Homologous recombination																													p.E106X		Atlas-SNP	.											.	XRCC2	30	.	0			c.G316T						PASS	.						81.0	83.0	82.0					7																	152346254		2203	4300	6503	SO:0001587	stop_gained	7516	exon3			TTATTTCTTCAGA	Y08837	CCDS5933.1	7q36	2006-05-04			ENSG00000196584	ENSG00000196584			12829	protein-coding gene	gene with protein product	"""RAD51-like"""	600375				7607692, 10422536	Standard	NM_005431		Approved		uc003wld.3	O43543	OTTHUMG00000151470	ENST00000359321.1:c.316G>T	7.37:g.152346254C>A	ENSP00000352271:p.Glu106*	59.0	0.0	0		35.0	5.0	0.142857	NM_005431	B2R925	Nonsense_Mutation	SNP	ENST00000359321.1	37	CCDS5933.1	.	.	.	.	.	.	.	.	.	.	C	15.70	2.911472	0.52439	.	.	ENSG00000196584	ENST00000359321	.	.	.	5.11	5.11	0.69529	.	0.363029	0.29522	N	0.011904	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.48119	T	0.1	-13.1414	17.5401	0.87845	0.0:1.0:0.0:0.0	.	.	.	.	X	106	.	ENSP00000352271:E106X	E	-	1	0	XRCC2	151977187	1.000000	0.71417	0.763000	0.31416	0.118000	0.20060	4.693000	0.61753	2.367000	0.80283	0.591000	0.81541	GAA	.	.	none		0.378	XRCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322783.1	NM_005431	
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158776	26158776	+	Nonstop_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:26158776T>C	ENST00000289316.2	+	1	403	c.379T>C	c.(379-381)Taa>Caa	p.*127Q	HIST1H2BD_ENST00000377777.4_Nonstop_Mutation_p.*127Q	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	0					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						CAGTTCCAAGTAACTTTGCCA	0.512																																					p.X127Q		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.T379C						PASS	.						61.0	66.0	64.0					6																	26158776		2203	4300	6503	SO:0001578	stop_lost	3017	exon1			TCCAAGTAACTTT	M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"""Histones / Replication-dependent"""	4747	protein-coding gene	gene with protein product		602799	"""H2B histone family, member B"", ""histone 1, H2bd"""	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.379T>C	6.37:g.26158776T>C	ENSP00000289316:p.*127Glnext*13	163.0	0.0	0		105.0	14.0	0.133333	NM_021063		Missense_Mutation	SNP	ENST00000289316.2	37	CCDS4587.1	.	.	.	.	.	.	.	.	.	.	.	8.266	0.812203	0.16537	.	.	ENSG00000158373	ENST00000377777;ENST00000289316	.	.	.	5.1	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.6541	0.17633	0.155:0.0888:0.0:0.7563	.	.	.	.	Q	127	.	.	X	+	1	0	HIST1H2BD	26266755	1.000000	0.71417	0.599000	0.28851	0.305000	0.27757	4.678000	0.61641	0.988000	0.38734	0.529000	0.55759	TAA	.	.	none		0.512	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063	
NBEA	26960	hgsc.bcm.edu	37	13	35729913	35729913	+	Silent	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:35729913C>A	ENST00000400445.3	+	19	2982	c.2448C>A	c.(2446-2448)atC>atA	p.I816I	NBEA_ENST00000379939.2_Silent_p.I816I|NBEA_ENST00000310336.4_Silent_p.I816I|NBEA_ENST00000540320.1_Silent_p.I816I	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	816					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		TTTTTCAGATCTTGACAGAAC	0.323																																					p.I816I		Atlas-SNP	.											.	NBEA	340	.	0			c.C2448A						PASS	.						92.0	86.0	88.0					13																	35729913		1846	4092	5938	SO:0001819	synonymous_variant	26960	exon19			TCAGATCTTGACA	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.2448C>A	13.37:g.35729913C>A		118.0	0.0	0		64.0	9.0	0.140625	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Silent	SNP	ENST00000400445.3	37	CCDS45026.1																																																																																			.	.	none		0.323	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
PTBP1	5725	hgsc.bcm.edu	37	19	804886	804886	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:804886T>C	ENST00000349038.4	+	7	737	c.664T>C	c.(664-666)Ttc>Ctc	p.F222L	PTBP1_ENST00000350092.4_Intron|PTBP1_ENST00000394601.4_Missense_Mutation_p.F222L|PTBP1_ENST00000356948.6_Missense_Mutation_p.F222L|MIR4745_ENST00000577608.1_RNA	NM_031991.3	NP_114368.1	P26599	PTBP1_HUMAN	polypyrimidine tract binding protein 1	222	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				alternative mRNA splicing, via spliceosome (GO:0000380)|gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of muscle cell differentiation (GO:0051148)|negative regulation of RNA splicing (GO:0033119)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|poly-pyrimidine tract binding (GO:0008187)|pre-mRNA binding (GO:0036002)|RNA binding (GO:0003723)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)|upper_aerodigestive_tract(4)	19		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GAACAACCAGTTCCAGGCCCT	0.662																																					p.F222L		Atlas-SNP	.											PTBP1,larynx,carcinoma,-2,1	PTBP1	43	1	0			c.T664C						scavenged	.						100.0	90.0	94.0					19																	804886		2203	4300	6503	SO:0001583	missense	5725	exon7			AACCAGTTCCAGG	X60648	CCDS32859.1, CCDS42456.1, CCDS45892.1	19p13.3	2013-07-16	2002-01-25	2002-01-25	ENSG00000011304	ENSG00000011304		"""RNA binding motif (RRM) containing"""	9583	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein I"""	600693	"""polypyrimidine tract binding protein (heterogeneous nuclear ribonucleoprotein I)"""	PTB		1906036, 11024286	Standard	NM_002819		Approved	HNRPI, HNRNP-I, PTB2, PTB3, PTB-1, PTB4, pPTB	uc002lpp.2	P26599		ENST00000349038.4:c.664T>C	19.37:g.804886T>C	ENSP00000014112:p.Phe222Leu	60.0	0.0	0		63.0	3.0	0.047619	NM_031990	Q9BUQ0	Missense_Mutation	SNP	ENST00000349038.4	37	CCDS32859.1	.	.	.	.	.	.	.	.	.	.	T	27.7	4.851512	0.91355	.	.	ENSG00000011304	ENST00000356948;ENST00000394601;ENST00000349038	T;T;T	0.50548	0.74;0.77;1.06	5.09	5.09	0.68999	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.207707	0.51477	D	0.000096	T	0.63838	0.2545	L	0.53561	1.675	0.80722	D	1	D;D;P	0.89917	1.0;0.964;0.923	D;P;P	0.83275	0.996;0.884;0.856	T	0.67241	-0.5720	10	0.87932	D	0	-30.2985	14.045	0.64700	0.0:0.0:0.0:1.0	.	222;222;222	P26599;P26599-2;Q9BUQ0	PTBP1_HUMAN;.;.	L	222	ENSP00000349428:F222L;ENSP00000408096:F222L;ENSP00000014112:F222L	ENSP00000014112:F222L	F	+	1	0	PTBP1	755886	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	7.904000	0.87408	1.915000	0.55452	0.460000	0.39030	TTC	.	.	none		0.662	PTBP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457605.1		
ZNF880	400713	hgsc.bcm.edu	37	19	52877609	52877609	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:52877609G>A	ENST00000422689.2	+	3	212	c.197G>A	c.(196-198)cGg>cAg	p.R66Q	ZNF880_ENST00000597976.1_Missense_Mutation_p.R66Q|ZNF880_ENST00000344085.5_Missense_Mutation_p.R66Q|ZNF880_ENST00000424032.2_Missense_Mutation_p.R66Q|ZNF880_ENST00000600321.1_Missense_Mutation_p.R66Q	NM_001145434.1	NP_001138906.1	Q6PDB4	ZN880_HUMAN	zinc finger protein 880	66	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)	10						AGAGATCCCCGGAATCTGCAG	0.458																																					p.R66Q		Atlas-SNP	.											.	ZNF880	45	.	0			c.G197A						PASS	.						79.0	71.0	73.0					19																	52877609		692	1591	2283	SO:0001583	missense	400713	exon3			ATCCCCGGAATCT	BC058819	CCDS46164.1	19q13.41	2013-01-08			ENSG00000221923	ENSG00000221923		"""Zinc fingers, C2H2-type"", ""-"""	37249	protein-coding gene	gene with protein product							Standard	NM_001145434		Approved		uc002pzc.3	Q6PDB4	OTTHUMG00000167972	ENST00000422689.2:c.197G>A	19.37:g.52877609G>A	ENSP00000406318:p.Arg66Gln	118.0	0.0	0		138.0	13.0	0.0942029	NM_001145434	B4DNA6	Missense_Mutation	SNP	ENST00000422689.2	37	CCDS46164.1	.	.	.	.	.	.	.	.	.	.	G	4.337	0.061871	0.08339	.	.	ENSG00000221923	ENST00000424032;ENST00000344085;ENST00000422689	T;T;T	0.06294	5.42;5.46;3.32	1.13	0.00405	0.14057	Krueppel-associated box (2);	.	.	.	.	T	0.03305	0.0096	N	0.12527	0.23	0.09310	N	1	B	0.16603	0.018	B	0.01281	0.0	T	0.42015	-0.9476	9	0.54805	T	0.06	.	3.5828	0.07959	0.2752:0.0:0.7248:0.0	.	66	Q6PDB4	ZN880_HUMAN	Q	66	ENSP00000414470:R66Q;ENSP00000343625:R66Q;ENSP00000406318:R66Q	ENSP00000343625:R66Q	R	+	2	0	ZNF880	57569421	0.002000	0.14202	0.002000	0.10522	0.006000	0.05464	0.073000	0.14640	0.044000	0.15775	0.448000	0.29417	CGG	.	.	none		0.458	ZNF880-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397374.1	NM_001145434	
PTPRQ	374462	hgsc.bcm.edu	37	12	81046571	81046571	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:81046571C>G	ENST00000266688.5	+	43	6061	c.6061C>G	c.(6061-6063)Cct>Gct	p.P2021A				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	2058					regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						TGCTGATCTGCCTTGGAATAG	0.328																																					p.P1853A		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C5557G						PASS	.						114.0	97.0	103.0					12																	81046571		692	1590	2282	SO:0001583	missense	374462	exon35			GATCTGCCTTGGA	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.6061C>G	12.37:g.81046571C>G	ENSP00000266688:p.Pro2021Ala	145.0	0.0	0		117.0	5.0	0.042735	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	26.4|26.4	4.737635|4.737635	0.89573|0.89573	.|.	.|.	ENSG00000139304|ENSG00000139304	ENST00000532722;ENST00000547881|ENST00000266688	.|T	.|0.12465	.|2.68	5.78|5.78	5.78|5.78	0.91487|0.91487	.|Protein-tyrosine phosphatase, receptor/non-receptor type (2);	.|.	.|.	.|.	.|.	T|T	0.39627|0.39627	0.1085|0.1085	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.83275	.|0.996	T|T	0.01748|0.01748	-1.1282|-1.1282	4|8	.|0.37606	.|T	.|0.19	.|.	19.9918|19.9918	0.97368|0.97368	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|2058	.|Q9UMZ3	.|PTPRQ_HUMAN	W|A	1721;110|2021	.|ENSP00000266688:P2021A	.|ENSP00000266688:P2021A	C|P	+|+	3|1	2|0	PTPRQ|PTPRQ	79570702|79570702	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	6.826000|6.826000	0.75298|0.75298	2.728000|2.728000	0.93425|0.93425	0.585000|0.585000	0.79938|0.79938	TGC|CCT	.	.	none		0.328	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
MYOM1	8736	hgsc.bcm.edu	37	18	3089200	3089200	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr18:3089200C>A	ENST00000356443.4	-	29	4442	c.4109G>T	c.(4108-4110)gGt>gTt	p.G1370V	MYOM1_ENST00000261606.7_Missense_Mutation_p.G1274V|MYOM1_ENST00000400569.3_Missense_Mutation_p.G1370V	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1370	Ig-like C2-type 4.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						ATTACATTCACCAGTCACTTC	0.308																																					p.G1370V		Atlas-SNP	.											.	MYOM1	192	.	0			c.G4109T						PASS	.						80.0	74.0	76.0					18																	3089200		1820	4083	5903	SO:0001583	missense	8736	exon29			CATTCACCAGTCA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.4109G>T	18.37:g.3089200C>A	ENSP00000348821:p.Gly1370Val	492.0	0.0	0		316.0	52.0	0.164557	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	12.58	1.980320	0.34942	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.70399	-0.48;-0.48;-0.48	5.98	4.19	0.49359	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.528555	0.22207	N	0.063145	T	0.48187	0.1486	N	0.08118	0	0.53688	D	0.999972	B;B	0.25235	0.099;0.121	B;B	0.31191	0.076;0.125	T	0.33777	-0.9855	10	0.33141	T	0.24	.	5.6992	0.17873	0.0:0.5235:0.2513:0.2252	.	1274;1370	P52179-2;P52179	.;MYOM1_HUMAN	V	1370;1370;1274	ENSP00000348821:G1370V;ENSP00000383413:G1370V;ENSP00000261606:G1274V	ENSP00000261606:G1274V	G	-	2	0	MYOM1	3079200	0.943000	0.32029	0.999000	0.59377	0.996000	0.88848	1.552000	0.36244	0.851000	0.35264	0.591000	0.81541	GGT	.	.	none		0.308	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
NKTR	4820	hgsc.bcm.edu	37	3	42674280	42674280	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr3:42674280A>C	ENST00000232978.8	+	9	926	c.738A>C	c.(736-738)gaA>gaC	p.E246D	RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA|RP4-613B23.1_ENST00000438017.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	246					protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		GCAGTTCAGAAGAGCCAAGGA	0.393																																					p.E246D		Atlas-SNP	.											.	NKTR	116	.	0			c.A738C						PASS	.						91.0	96.0	94.0					3																	42674280		2203	4300	6503	SO:0001583	missense	4820	exon9			TTCAGAAGAGCCA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.738A>C	3.37:g.42674280A>C	ENSP00000232978:p.Glu246Asp	214.0	0.0	0		127.0	18.0	0.141732	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	37	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.317054	0.81469	.	.	ENSG00000114857	ENST00000232978	T	0.13196	2.61	5.83	-1.96	0.07525	.	0.387908	0.30142	N	0.010302	T	0.22166	0.0534	M	0.63428	1.95	0.80722	D	1	P;D	0.62365	0.935;0.991	B;P	0.53689	0.315;0.732	T	0.03818	-1.1001	10	0.62326	D	0.03	-10.0199	12.9061	0.58154	0.3415:0.0:0.6585:0.0	.	126;246	Q59EC3;P30414	.;NKTR_HUMAN	D	246	ENSP00000232978:E246D	ENSP00000232978:E246D	E	+	3	2	NKTR	42649284	1.000000	0.71417	0.990000	0.47175	0.899000	0.52679	0.525000	0.22956	-0.326000	0.08564	0.533000	0.62120	GAA	.	.	none		0.393	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
PCDH15	65217	hgsc.bcm.edu	37	10	55626476	55626476	+	Silent	SNP	T	T	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:55626476T>G	ENST00000320301.6	-	27	4037	c.3643A>C	c.(3643-3645)Aga>Cga	p.R1215R	PCDH15_ENST00000414778.1_Silent_p.R1220R|PCDH15_ENST00000395433.1_Silent_p.R1193R|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000437009.1_Silent_p.R1144R|PCDH15_ENST00000395432.2_Silent_p.R1178R|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000409834.1_Silent_p.R826R|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Silent_p.R1222R|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000373965.2_Silent_p.R1222R|PCDH15_ENST00000395438.1_Silent_p.R1215R|PCDH15_ENST00000361849.3_Silent_p.R1215R|PCDH15_ENST00000395430.1_Silent_p.R1215R	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1215	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				AAGTAGGATCTCCTCATATTA	0.403										HNSCC(58;0.16)																											p.R1220R		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A3658C						PASS	.						145.0	127.0	133.0					10																	55626476		2203	4300	6503	SO:0001819	synonymous_variant	65217	exon28			AGGATCTCCTCAT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.3643A>C	10.37:g.55626476T>G		214.0	0.0	0		145.0	6.0	0.0413793	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Silent	SNP	ENST00000320301.6	37	CCDS7248.1																																																																																			.	.	none		0.403	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
CTNNA3	29119	hgsc.bcm.edu	37	10	67829199	67829199	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:67829199G>T	ENST00000433211.2	-	15	2200	c.2026C>A	c.(2026-2028)Caa>Aaa	p.Q676K	CTNNA3_ENST00000373744.4_Missense_Mutation_p.Q676K|CTNNA3_ENST00000373735.1_5'UTR	NM_013266.2	NP_037398.2			catenin (cadherin-associated protein), alpha 3											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(1)|lung(50)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|stomach(1)|urinary_tract(1)	95						TCAGCAACTTGCTCAGCAATC	0.378																																					p.Q676K		Atlas-SNP	.											.	CTNNA3	401	.	0			c.C2026A						PASS	.						207.0	178.0	188.0					10																	67829199		2203	4300	6503	SO:0001583	missense	29119	exon15			CAACTTGCTCAGC	AF091606	CCDS7269.1	10q21	2006-11-24			ENSG00000183230	ENSG00000183230			2511	protein-coding gene	gene with protein product		607667				12596047, 11590244	Standard	XM_005269717		Approved	VR22, MGC26194	uc001jmw.2	Q9UI47	OTTHUMG00000018334	ENST00000433211.2:c.2026C>A	10.37:g.67829199G>T	ENSP00000389714:p.Gln676Lys	260.0	0.0	0		150.0	16.0	0.106667	NM_013266		Missense_Mutation	SNP	ENST00000433211.2	37	CCDS7269.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.815033	0.90790	.	.	ENSG00000183230	ENST00000433211;ENST00000373744;ENST00000373735	T;T;T	0.39787	1.06;1.06;1.06	5.29	5.29	0.74685	.	0.000000	0.49916	D	0.000129	T	0.69223	0.3087	M	0.88105	2.93	0.80722	D	1	D	0.53885	0.963	D	0.71414	0.973	T	0.71494	-0.4576	10	0.37606	T	0.19	-13.4866	16.4194	0.83753	0.0:0.0:1.0:0.0	.	676	Q9UI47	CTNA3_HUMAN	K	676;676;15	ENSP00000389714:Q676K;ENSP00000362849:Q676K;ENSP00000362840:Q15K	ENSP00000362840:Q15K	Q	-	1	0	CTNNA3	67499205	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.492000	0.97957	2.483000	0.83821	0.591000	0.81541	CAA	.	.	none		0.378	CTNNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048282.2	NM_013266	
DLX4	1748	hgsc.bcm.edu	37	17	48051195	48051195	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr17:48051195T>C	ENST00000240306.3	+	3	906	c.611T>C	c.(610-612)cTc>cCc	p.L204P	DLX4_ENST00000411890.2_Missense_Mutation_p.L132P	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	204					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CTCCCCTCCCTCTGGGATCTA	0.592																																					p.L204P		Atlas-SNP	.											.	DLX4	25	.	0			c.T611C						PASS	.						57.0	61.0	60.0					17																	48051195		2203	4300	6503	SO:0001583	missense	1748	exon3			CCTCCCTCTGGGA		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"""Homeoboxes / ANTP class : NKL subclass"""	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	ENST00000240306.3:c.611T>C	17.37:g.48051195T>C	ENSP00000240306:p.Leu204Pro	92.0	0.0	0		70.0	11.0	0.157143	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Missense_Mutation	SNP	ENST00000240306.3	37	CCDS11555.1	.	.	.	.	.	.	.	.	.	.	T	11.42	1.633462	0.29068	.	.	ENSG00000108813	ENST00000240306;ENST00000411890	D;D	0.93189	-2.97;-3.18	5.14	2.91	0.33838	.	.	.	.	.	D	0.94318	0.8174	L	0.60455	1.87	0.32491	N	0.540234	D;B	0.60160	0.987;0.001	P;B	0.62649	0.905;0.0	D	0.92773	0.6234	9	0.54805	T	0.06	-12.0893	8.3009	0.32014	0.0:0.1652:0.0:0.8348	.	132;204	Q92988-2;Q92988	.;DLX4_HUMAN	P	204;132	ENSP00000240306:L204P;ENSP00000410622:L132P	ENSP00000240306:L204P	L	+	2	0	DLX4	45406194	0.443000	0.25641	0.650000	0.29550	0.931000	0.56810	3.111000	0.50360	0.406000	0.25560	-0.411000	0.06167	CTC	.	.	none		0.592	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1		
NAA25	80018	hgsc.bcm.edu	37	12	112516526	112516526	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:112516526T>C	ENST00000261745.4	-	6	745	c.497A>G	c.(496-498)gAa>gGa	p.E166G		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	166						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						TGAGAGGTTTTCATCCTGTGC	0.373																																					p.E166G		Atlas-SNP	.											.	NAA25	105	.	0			c.A497G						PASS	.						150.0	136.0	141.0					12																	112516526		2203	4300	6503	SO:0001583	missense	80018	exon6			AGGTTTTCATCCT	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.497A>G	12.37:g.112516526T>C	ENSP00000261745:p.Glu166Gly	219.0	0.0	0		153.0	10.0	0.0653595	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	25.7|25.7	4.661054|4.661054	0.88154|0.88154	.|.	.|.	ENSG00000111300|ENSG00000111300	ENST00000261745|ENST00000547133	T|.	0.26223|.	1.75|.	6.05|6.05	6.05|6.05	0.98169|0.98169	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.55609|.	0.1931|.	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.69307|.	0.963;0.963|.	T|.	0.51694|.	-0.8673|.	10|.	0.44086|.	T|.	0.13|.	-17.6823|-17.6823	16.5932|16.5932	0.84781|0.84781	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	166;166|.	A8K8X0;Q14CX7|.	.;NAA25_HUMAN|.	G|W	166|127	ENSP00000261745:E166G|.	ENSP00000261745:E166G|.	E|X	-|-	2|3	0|0	NAA25|NAA25	111000909|111000909	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.454000|7.454000	0.80714|0.80714	2.320000|2.320000	0.78422|0.78422	0.528000|0.528000	0.53228|0.53228	GAA|TGA	.	.	none		0.373	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
LRRC4	64101	hgsc.bcm.edu	37	7	127669744	127669744	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:127669744T>C	ENST00000249363.3	-	2	1207	c.950A>G	c.(949-951)gAg>gGg	p.E317G	SND1_ENST00000354725.3_Intron	NM_022143.4	NP_071426.1	Q9HBW1	LRRC4_HUMAN	leucine rich repeat containing 4	317	LRRCT.				postsynaptic density protein 95 clustering (GO:0097119)|regulation of synapse organization (GO:0050807)|synapse organization (GO:0050808)	cell junction (GO:0030054)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(6)|lung(4)|pancreas(1)|skin(2)	26				Lung(243;0.124)		GGGTATATACTCTCGAAGCCA	0.572																																					p.E317G		Atlas-SNP	.											.	LRRC4	72	.	0			c.A950G						PASS	.						44.0	38.0	40.0					7																	127669744		2203	4300	6503	SO:0001583	missense	64101	exon2			ATATACTCTCGAA	AF196976	CCDS5799.1	7q31	2013-01-14	2003-11-19		ENSG00000128594	ENSG00000128594		"""Immunoglobulin superfamily / I-set domain containing"""	15586	protein-coding gene	gene with protein product		610486	"""leucine-rich repeat-containing 4"""			12969517	Standard	NM_022143		Approved	NAG14	uc003vmk.3	Q9HBW1	OTTHUMG00000157563	ENST00000249363.3:c.950A>G	7.37:g.127669744T>C	ENSP00000249363:p.Glu317Gly	135.0	0.0	0		110.0	17.0	0.154545	NM_022143	A4D0Y9|Q14DU9|Q6ZMI8|Q96A85	Missense_Mutation	SNP	ENST00000249363.3	37	CCDS5799.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.016570	0.35606	.	.	ENSG00000128594	ENST00000249363	T	0.02656	4.21	4.46	4.46	0.54185	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.02767	0.0083	L	0.45137	1.4	0.80722	D	1	P	0.40515	0.719	B	0.29524	0.103	T	0.58567	-0.7614	10	0.39692	T	0.17	.	11.7482	0.51832	0.0:0.0:0.0:1.0	.	317	Q9HBW1	LRRC4_HUMAN	G	317	ENSP00000249363:E317G	ENSP00000249363:E317G	E	-	2	0	LRRC4	127456980	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.854000	0.86942	1.858000	0.53909	0.533000	0.62120	GAG	.	.	none		0.572	LRRC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349170.1	NM_022143	
AGTR2	186	hgsc.bcm.edu	37	X	115304549	115304549	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:115304549G>T	ENST00000371906.4	+	3	1206	c.1016G>T	c.(1015-1017)tGg>tTg	p.W339L		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	339					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	CCAATTACTTGGCTCCAAGGG	0.433																																					p.W339L		Atlas-SNP	.											.	AGTR2	62	.	0			c.G1016T						PASS	.						121.0	112.0	115.0					X																	115304549		2203	4300	6503	SO:0001583	missense	186	exon3			TTACTTGGCTCCA	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"""GPCR / Class A : Angiotensin receptors"""	338	protein-coding gene	gene with protein product		300034	"""angiotensin receptor 2"""			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.1016G>T	X.37:g.115304549G>T	ENSP00000360973:p.Trp339Leu	334.0	0.0	0		215.0	12.0	0.055814	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	G	3.385	-0.125487	0.06795	.	.	ENSG00000180772	ENST00000371906	T	0.35421	1.31	4.63	3.68	0.42216	.	0.416542	0.24431	N	0.038588	T	0.13841	0.0335	N	0.08118	0	0.27245	N	0.959054	B	0.09022	0.002	B	0.01281	0.0	T	0.22138	-1.0225	10	0.09843	T	0.71	-0.0597	4.2132	0.10521	0.1367:0.237:0.6263:0.0	.	339	P50052	AGTR2_HUMAN	L	339	ENSP00000360973:W339L	ENSP00000360973:W339L	W	+	2	0	AGTR2	115218577	0.999000	0.42202	1.000000	0.80357	0.917000	0.54804	2.382000	0.44345	2.129000	0.65627	0.506000	0.49869	TGG	.	.	none		0.433	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686	
HIST2H2BE	8349	hgsc.bcm.edu	37	1	149857825	149857825	+	Silent	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:149857825G>A	ENST00000369155.2	-	1	407	c.366C>T	c.(364-366)taC>taT	p.Y122Y	HIST2H2AC_ENST00000331380.2_5'Flank|BOLA1_ENST00000369153.2_5'Flank	NM_003528.2	NP_003519.1	Q16778	H2B2E_HUMAN	histone cluster 2, H2be	122					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	14	Breast(34;0.0124)|all_hematologic(923;0.127)		STAD - Stomach adenocarcinoma(528;0.133)|LUSC - Lung squamous cell carcinoma(543;0.221)			TGGAGCTGGTGTACTTGGTGA	0.657																																					p.Y122Y		Atlas-SNP	.											.	HIST2H2BE	33	.	0			c.C366T						PASS	.						30.0	35.0	33.0					1																	149857825		2202	4299	6501	SO:0001819	synonymous_variant	8349	exon1			GCTGGTGTACTTG	AY131979	CCDS936.1	1q21.2	2011-01-27	2006-10-11	2003-03-07	ENSG00000184678	ENSG00000184678		"""Histones / Replication-dependent"""	4760	protein-coding gene	gene with protein product		601831	"""H2B histone family, member Q"", ""histone 2, H2be"""	H2B, H2BFQ		1469070, 12408966	Standard	NM_003528		Approved	H2B/q, H2B.1	uc001etc.3	Q16778	OTTHUMG00000012095	ENST00000369155.2:c.366C>T	1.37:g.149857825G>A		160.0	0.0	0		166.0	9.0	0.0542169	NM_003528	A3KMC7|A8K110|Q4KMY1|Q5QNX0|Q9UE88	Silent	SNP	ENST00000369155.2	37	CCDS936.1																																																																																			.	.	none		0.657	HIST2H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033455.1	NM_003528	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18491371	18491371	+	Silent	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:18491371T>C	ENST00000266497.5	+	8	1322	c.1284T>C	c.(1282-1284)taT>taC	p.Y428Y	PIK3C2G_ENST00000433979.1_Silent_p.Y428Y|PIK3C2G_ENST00000538779.1_Silent_p.Y428Y|PIK3C2G_ENST00000535651.1_Silent_p.Y428Y			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	428					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				AAAACGTGTATAATATTATTG	0.308																																					p.Y428Y		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.T1284C						PASS	.						81.0	83.0	82.0					12																	18491371		1824	4063	5887	SO:0001819	synonymous_variant	5288	exon9			CGTGTATAATATT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1284T>C	12.37:g.18491371T>C		171.0	0.0	0		124.0	7.0	0.0564516	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			.	.	none		0.308	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
ABCB5	340273	hgsc.bcm.edu	37	7	20683092	20683092	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:20683092A>G	ENST00000404938.2	+	7	1167	c.515A>G	c.(514-516)gAc>gGc	p.D172G		NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	172	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AGTGACATTGACAAAATCAGT	0.368																																					p.D172G		Atlas-SNP	.											.	ABCB5	357	.	0			c.A515G						PASS	.						224.0	197.0	205.0					7																	20683092		1568	3582	5150	SO:0001583	missense	340273	exon7			ACATTGACAAAAT	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.515A>G	7.37:g.20683092A>G	ENSP00000384881:p.Asp172Gly	214.0	0.0	0		149.0	17.0	0.114094	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	.	.	.	.	.	.	.	.	.	.	A	9.693	1.152310	0.21371	.	.	ENSG00000004846	ENST00000404938	D	0.90261	-2.64	3.85	-0.101	0.13618	.	.	.	.	.	D	0.82472	0.5044	L	0.41492	1.28	0.80722	D	1	B	0.18013	0.025	B	0.23275	0.045	T	0.67480	-0.5660	9	0.25106	T	0.35	.	4.5733	0.12221	0.6388:0.1667:0.1946:0.0	.	172	A7BKA4	.	G	172	ENSP00000384881:D172G	ENSP00000384881:D172G	D	+	2	0	ABCB5	20649617	1.000000	0.71417	0.999000	0.59377	0.371000	0.29859	2.424000	0.44714	-0.012000	0.14223	0.460000	0.39030	GAC	.	.	none		0.368	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
PCSK5	5125	hgsc.bcm.edu	37	9	78923585	78923585	+	Missense_Mutation	SNP	G	G	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr9:78923585G>C	ENST00000545128.1	+	28	4086	c.3548G>C	c.(3547-3549)tGt>tCt	p.C1183S		NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	1183	CRM (Cys-rich motif).				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						CTCCAGCCTTGTCATTCTTCT	0.428																																					p.C1183S		Atlas-SNP	.											.	PCSK5	329	.	0			c.G3548C						PASS	.						47.0	46.0	46.0					9																	78923585		876	1991	2867	SO:0001583	missense	5125	exon28			AGCCTTGTCATTC		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.3548G>C	9.37:g.78923585G>C	ENSP00000446280:p.Cys1183Ser	163.0	0.0	0		105.0	5.0	0.047619	NM_001190482	F5H2G7|Q13527|Q96EP4	Missense_Mutation	SNP	ENST00000545128.1	37	CCDS55320.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981331	0.34942	.	.	ENSG00000099139	ENST00000545128;ENST00000376754;ENST00000424854	T;T	0.68181	0.56;-0.31	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	D	0.89996	0.6877	H	0.99475	4.585	0.52501	D	0.999954	.	.	.	.	.	.	D	0.93690	0.7006	8	0.87932	D	0	-12.5672	15.7567	0.78037	0.0:0.0:1.0:0.0	.	.	.	.	S	1183;913;883	ENSP00000446280:C1183S;ENSP00000411654:C883S	ENSP00000365945:C913S	C	+	2	0	PCSK5	78113405	1.000000	0.71417	0.678000	0.29963	0.410000	0.31052	5.660000	0.68018	2.793000	0.96121	0.561000	0.74099	TGT	.	.	none		0.428	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPEN	23013	hgsc.bcm.edu	37	1	16255388	16255388	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:16255388G>T	ENST00000375759.3	+	11	2857	c.2653G>T	c.(2653-2655)Gag>Tag	p.E885*		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	885					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|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)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TCGAGTGAAAGAGAAAGAGGG	0.453																																					p.E885X		Atlas-SNP	.											.	SPEN	374	.	0			c.G2653T						PASS	.						104.0	110.0	108.0					1																	16255388		2203	4300	6503	SO:0001587	stop_gained	23013	exon11			GTGAAAGAGAAAG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.2653G>T	1.37:g.16255388G>T	ENSP00000364912:p.Glu885*	92.0	0.0	0		66.0	6.0	0.0909091	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Nonsense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	G	40	8.364123	0.98779	.	.	ENSG00000065526	ENST00000375759	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	-13.6494	18.3094	0.90194	0.0:0.0:1.0:0.0	.	.	.	.	X	885	.	ENSP00000364912:E885X	E	+	1	0	SPEN	16127975	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	8.792000	0.91856	2.548000	0.85928	0.591000	0.81541	GAG	.	.	none		0.453	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
NPAS3	64067	hgsc.bcm.edu	37	14	34270175	34270175	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr14:34270175G>A	ENST00000356141.4	+	12	2662	c.2662G>A	c.(2662-2664)Gca>Aca	p.A888T	NPAS3_ENST00000551492.1_Missense_Mutation_p.A893T|NPAS3_ENST00000357798.5_Missense_Mutation_p.A875T|NPAS3_ENST00000548645.1_Missense_Mutation_p.A858T|NPAS3_ENST00000346562.2_Missense_Mutation_p.A856T			Q8IXF0	NPAS3_HUMAN	neuronal PAS domain protein 3	888					locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|positive regulation of transcription, DNA-templated (GO:0045893)|startle response (GO:0001964)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(4)|endometrium(3)|kidney(1)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	40	Breast(36;0.0102)|Hepatocellular(127;0.133)		LUAD - Lung adenocarcinoma(48;0.00169)|Lung(238;0.00968)	GBM - Glioblastoma multiforme(1;1.31e-09)|all cancers(1;0.000112)|OV - Ovarian serous cystadenocarcinoma(311;0.115)		GTTCGGCGGCGCAGTGAGCGC	0.652																																					p.A888T		Atlas-SNP	.											.	NPAS3	266	.	0			c.G2662A						PASS	.						31.0	20.0	24.0					14																	34270175		2201	4289	6490	SO:0001583	missense	64067	exon12			GGCGGCGCAGTGA	AF164438	CCDS9645.1, CCDS53891.1, CCDS53892.1, CCDS55912.1	14q13.1	2013-08-23			ENSG00000151322	ENSG00000151322		"""Basic helix-loop-helix proteins"""	19311	protein-coding gene	gene with protein product		609430					Standard	NM_022123		Approved	MOP6, PASD6, bHLHe12	uc001wru.3	Q8IXF0	OTTHUMG00000140215	ENST00000356141.4:c.2662G>A	14.37:g.34270175G>A	ENSP00000348460:p.Ala888Thr	65.0	0.0	0		55.0	7.0	0.127273	NM_001164749	Q86US6|Q86US7|Q8IXF2|Q9BY81|Q9H323|Q9Y4L8	Missense_Mutation	SNP	ENST00000356141.4	37	CCDS53891.1	.	.	.	.	.	.	.	.	.	.	G	6.253	0.414758	0.11870	.	.	ENSG00000151322	ENST00000551634;ENST00000551492;ENST00000346562;ENST00000548645;ENST00000356141;ENST00000357798	T;T;T;T;T;T	0.08458	3.35;3.22;3.23;3.23;3.22;3.09	5.68	3.85	0.44370	.	0.169134	0.52532	N	0.000071	T	0.06508	0.0167	N	0.19112	0.55	0.80722	D	1	B;B;B;B	0.15719	0.014;0.008;0.014;0.014	B;B;B;B	0.11329	0.006;0.003;0.006;0.006	T	0.23119	-1.0197	10	0.59425	D	0.04	.	11.8985	0.52669	0.1404:0.0:0.8595:0.0	.	858;888;856;875	Q8IXF0-2;Q8IXF0;Q8IXF0-4;Q8IXF0-3	.;NPAS3_HUMAN;.;.	T	862;893;856;858;888;875	ENSP00000448373:A862T;ENSP00000450392:A893T;ENSP00000319610:A856T;ENSP00000448916:A858T;ENSP00000348460:A888T;ENSP00000350446:A875T	ENSP00000319610:A856T	A	+	1	0	NPAS3	33339926	1.000000	0.71417	0.869000	0.34112	0.006000	0.05464	5.397000	0.66302	1.398000	0.46701	-0.300000	0.09419	GCA	.	.	none		0.652	NPAS3-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276645.1		
SLC5A9	200010	hgsc.bcm.edu	37	1	48688529	48688529	+	Missense_Mutation	SNP	G	G	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:48688529G>C	ENST00000438567.2	+	1	173	c.121G>C	c.(121-123)Gtg>Ctg	p.V41L	SLC5A9_ENST00000420136.2_Missense_Mutation_p.V34L|SLC5A9_ENST00000533824.1_Missense_Mutation_p.V41L|SLC5A9_ENST00000236495.5_Missense_Mutation_p.V41L	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	41					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)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						CATCAGCGTGGTGGTCATCTA	0.587																																					p.V41L		Atlas-SNP	.											.	SLC5A9	82	.	0			c.G121C						PASS	.						147.0	100.0	116.0					1																	48688529		2203	4300	6503	SO:0001583	missense	200010	exon1			AGCGTGGTGGTCA	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.121G>C	1.37:g.48688529G>C	ENSP00000401730:p.Val41Leu	163.0	0.0	0		135.0	9.0	0.0666667	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	.	.	.	.	.	.	.	.	.	.	G	11.22	1.575087	0.28092	.	.	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495;ENST00000420136	D;D;D;D	0.87412	-2.14;-2.15;-2.25;-1.56	4.83	3.92	0.45320	.	0.132348	0.49916	N	0.000137	T	0.76205	0.3955	N	0.16656	0.425	0.48830	D	0.999719	B;B;B	0.09022	0.002;0.001;0.002	B;B;B	0.08055	0.001;0.003;0.001	T	0.69034	-0.5252	10	0.19590	T	0.45	.	13.2689	0.60150	0.0:0.2305:0.7695:0.0	.	41;41;41	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	L	41;41;41;34	ENSP00000431900:V41L;ENSP00000401730:V41L;ENSP00000236495:V41L;ENSP00000408881:V34L	ENSP00000236495:V41L	V	+	1	0	SLC5A9	48461116	0.971000	0.33674	0.977000	0.42913	0.648000	0.38561	1.581000	0.36558	1.365000	0.46057	0.557000	0.71058	GTG	.	.	none		0.587	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
ANKRD30A	91074	hgsc.bcm.edu	37	10	37508026	37508026	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:37508026A>T	ENST00000602533.1	+	34	3317	c.3218A>T	c.(3217-3219)gAa>gTa	p.E1073V	ANKRD30A_ENST00000374660.1_Missense_Mutation_p.E1192V|ANKRD30A_ENST00000361713.1_Missense_Mutation_p.E1073V			Q9BXX3	AN30A_HUMAN	ankyrin repeat domain 30A	1129					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(8)|endometrium(14)|kidney(21)|large_intestine(13)|lung(70)|ovary(8)|pancreas(1)|prostate(3)|skin(15)|stomach(1)|urinary_tract(3)	158						CAGGAAAAGGAAAATAAATAC	0.318																																					p.E1073V		Atlas-SNP	.											.	ANKRD30A	448	.	0			c.A3218T						PASS	.						77.0	77.0	77.0					10																	37508026		1813	4064	5877	SO:0001583	missense	91074	exon34			AAAAGGAAAATAA	AF269087	CCDS7193.1	10p11.21	2013-01-10			ENSG00000148513	ENSG00000148513		"""Ankyrin repeat domain containing"""	17234	protein-coding gene	gene with protein product	"""breast cancer antigen NY-BR-1"""	610856				11280766	Standard	NM_052997		Approved	NY-BR-1	uc001iza.1	Q9BXX3	OTTHUMG00000017968	ENST00000602533.1:c.3218A>T	10.37:g.37508026A>T	ENSP00000473551:p.Glu1073Val	216.0	0.0	0		160.0	12.0	0.075	NM_052997	Q5W025	Missense_Mutation	SNP	ENST00000602533.1	37		.	.	.	.	.	.	.	.	.	.	a	9.278	1.047446	0.19827	.	.	ENSG00000148513	ENST00000361713;ENST00000374660	T;T	0.28454	1.61;1.61	2.81	2.81	0.32909	.	.	.	.	.	T	0.52533	0.1740	M	0.81112	2.525	0.32056	N	0.596317	D	0.69078	0.997	D	0.68483	0.958	T	0.61481	-0.7054	9	0.87932	D	0	.	8.8066	0.34941	1.0:0.0:0.0:0.0	.	1129	Q9BXX3	AN30A_HUMAN	V	1073;1192	ENSP00000354432:E1073V;ENSP00000363792:E1192V	ENSP00000354432:E1073V	E	+	2	0	ANKRD30A	37548032	1.000000	0.71417	0.063000	0.19743	0.004000	0.04260	3.826000	0.55738	1.151000	0.42436	0.381000	0.24937	GAA	.	.	none		0.318	ANKRD30A-001	KNOWN	NMD_exception|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047588.2	NM_052997	
EFNB1	1947	hgsc.bcm.edu	37	X	68058642	68058642	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:68058642C>A	ENST00000204961.4	+	2	1091	c.311C>A	c.(310-312)cCa>cAa	p.P104Q		NM_004429.4	NP_004420.1	P98172	EFNB1_HUMAN	ephrin-B1	104	Ephrin RBD. {ECO:0000255|PROSITE- ProRule:PRU00884}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|embryonic pattern specification (GO:0009880)|ephrin receptor signaling pathway (GO:0048013)|neural crest cell migration (GO:0001755)|positive regulation of T cell proliferation (GO:0042102)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ephrin receptor binding (GO:0046875)			breast(1)|endometrium(7)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)	22						TGCAATAGGCCAGAGCAGGAA	0.532																																					p.P104Q		Atlas-SNP	.											.	EFNB1	37	.	0			c.C311A						PASS	.						110.0	62.0	78.0					X																	68058642		2203	4300	6503	SO:0001583	missense	1947	exon2			ATAGGCCAGAGCA	U09303	CCDS14391.1	Xq12	2011-03-09			ENSG00000090776	ENSG00000090776		"""Ephrins"""	3226	protein-coding gene	gene with protein product		300035	"""craniofrontonasal syndrome (craniofrontonasal dysplasia)"""	EPLG2, CFNS		7774950, 16526919	Standard	NM_004429		Approved	LERK2, Elk-L	uc004dxd.4	P98172	OTTHUMG00000021751	ENST00000204961.4:c.311C>A	X.37:g.68058642C>A	ENSP00000204961:p.Pro104Gln	389.0	0.0	0		195.0	9.0	0.0461538	NM_004429	D3DVU0	Missense_Mutation	SNP	ENST00000204961.4	37	CCDS14391.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.519345	0.85495	.	.	ENSG00000090776	ENST00000204961	D	0.97303	-4.33	5.13	5.13	0.70059	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.98419	0.9474	M	0.86268	2.805	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99218	1.0878	10	0.66056	D	0.02	-10.4548	14.8667	0.70422	0.0:1.0:0.0:0.0	.	104	P98172	EFNB1_HUMAN	Q	104	ENSP00000204961:P104Q	ENSP00000204961:P104Q	P	+	2	0	EFNB1	67975367	1.000000	0.71417	0.996000	0.52242	0.871000	0.50021	7.320000	0.79064	2.390000	0.81377	0.436000	0.28706	CCA	.	.	none		0.532	EFNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057029.1	NM_004429	
UHRF1BP1	54887	hgsc.bcm.edu	37	6	34825160	34825160	+	Missense_Mutation	SNP	C	C	T	rs201864059		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:34825160C>T	ENST00000192788.5	+	12	1657	c.1486C>T	c.(1486-1488)Cgg>Tgg	p.R496W	UHRF1BP1_ENST00000452449.2_Missense_Mutation_p.R496W	NM_017754.3	NP_060224.3	Q6BDS2	URFB1_HUMAN	UHRF1 binding protein 1	496							histone deacetylase binding (GO:0042826)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(24)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	54						TTCCTGCAGTCGGAAACTTCA	0.433																																					p.R496W		Atlas-SNP	.											.	UHRF1BP1	102	.	0			c.C1486T						PASS	.						124.0	118.0	120.0					6																	34825160		1875	4119	5994	SO:0001583	missense	54887	exon12			TGCAGTCGGAAAC	AB126777	CCDS43455.1	6p21.31	2008-10-28	2008-08-15	2007-11-27	ENSG00000065060	ENSG00000065060			21216	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 107"""	C6orf107			Standard	NM_017754		Approved	FLJ20302, dJ349A12.1, ICBP90	uc003oju.4	Q6BDS2	OTTHUMG00000014557	ENST00000192788.5:c.1486C>T	6.37:g.34825160C>T	ENSP00000192788:p.Arg496Trp	152.0	0.0	0		105.0	9.0	0.0857143	NM_017754	Q9NXE0	Missense_Mutation	SNP	ENST00000192788.5	37	CCDS43455.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.014324	0.75161	.	.	ENSG00000065060	ENST00000192788;ENST00000452449	T;T	0.12879	2.64;2.64	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.21718	0.0523	L	0.50333	1.59	0.58432	D	0.999999	D	0.89917	1.0	D	0.87578	0.998	T	0.00196	-1.1931	10	0.87932	D	0	-22.6533	11.8255	0.52265	0.2922:0.7078:0.0:0.0	.	496	Q6BDS2	URFB1_HUMAN	W	496	ENSP00000192788:R496W;ENSP00000400628:R496W	ENSP00000192788:R496W	R	+	1	2	UHRF1BP1	34933138	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	2.939000	0.48995	2.758000	0.94735	0.563000	0.77884	CGG	.	.	weak		0.433	UHRF1BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040260.1	NM_017754	
SYNE1	23345	hgsc.bcm.edu	37	6	152768599	152768599	+	Silent	SNP	C	C	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:152768599C>G	ENST00000367255.5	-	29	4264	c.3663G>C	c.(3661-3663)ctG>ctC	p.L1221L	SYNE1_ENST00000413186.2_Silent_p.L1221L|SYNE1_ENST00000341594.5_Silent_p.L1287L|SYNE1_ENST00000448038.1_Silent_p.L1228L|SYNE1_ENST00000367248.3_Silent_p.L1211L|SYNE1_ENST00000265368.4_Silent_p.L1221L|SYNE1_ENST00000367253.4_Silent_p.L1221L|SYNE1_ENST00000423061.1_Silent_p.L1228L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	1221					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		GTACCTCTGACAGCAGCGTCA	0.413										HNSCC(10;0.0054)																											p.L1228L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G3684C						PASS	.						55.0	55.0	55.0					6																	152768599		2203	4300	6503	SO:0001819	synonymous_variant	23345	exon29			CTCTGACAGCAGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.3663G>C	6.37:g.152768599C>G		105.0	0.0	0		69.0	7.0	0.101449	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			.	.	none		0.413	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
PYY	5697	hgsc.bcm.edu	37	17	42030694	42030694	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr17:42030694C>T	ENST00000360085.2	-	5	698	c.158G>A	c.(157-159)cGc>cAc	p.R53H	PYY_ENST00000592796.1_Missense_Mutation_p.R53H	NM_004160.4	NP_004151	P10082	PYY_HUMAN	peptide YY	53					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|digestion (GO:0007586)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|G-protein coupled receptor signaling pathway (GO:0007186)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	hormone activity (GO:0005179)			endometrium(1)|ovary(1)	2		Breast(137;0.00314)|Prostate(33;0.0724)		BRCA - Breast invasive adenocarcinoma(366;0.12)		GAGGTAGTGGCGCAGGGAGGC	0.726																																					p.R53H		Atlas-SNP	.											.	PYY	11	.	0			c.G158A						PASS	.						17.0	19.0	19.0					17																	42030694		2200	4297	6497	SO:0001583	missense	5697	exon5			TAGTGGCGCAGGG		CCDS32662.1	17q21.1	2013-02-28				ENSG00000131096		"""Endogenous ligands"""	9748	protein-coding gene	gene with protein product	"""prepro-PYY"""	600781				7782089	Standard	NM_004160		Approved	PYY1	uc002ieq.3	P10082		ENST00000360085.2:c.158G>A	17.37:g.42030694C>T	ENSP00000353198:p.Arg53His	188.0	0.0	0		178.0	13.0	0.0730337	NM_004160	Q5U5Q6|Q6FGH8	Missense_Mutation	SNP	ENST00000360085.2	37	CCDS32662.1	.	.	.	.	.	.	.	.	.	.	.	35	5.542943	0.96474	.	.	ENSG00000131096	ENST00000360085	T	0.52983	0.64	4.64	4.64	0.57946	Pancreatic hormone-like, conserved site (1);	.	.	.	.	T	0.67804	0.2932	.	.	.	0.58432	D	0.999999	D	0.89917	1.0	D	0.81914	0.995	T	0.72673	-0.4222	8	0.87932	D	0	-1.6458	12.9887	0.58606	0.0:1.0:0.0:0.0	.	53	P10082	PYY_HUMAN	H	53	ENSP00000353198:R53H	ENSP00000353198:R53H	R	-	2	0	PYY	39386220	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.097000	0.64542	2.109000	0.64355	0.549000	0.68633	CGC	.	.	none		0.726	PYY-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000457658.1	NM_004160	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230409	23230409	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr22:23230409G>A	ENST00000526893.1	+	1	450	c.176G>A	c.(175-177)aGc>aAc	p.S59N	IGLL5_ENST00000531372.1_Missense_Mutation_p.S59N|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000532223.2_Missense_Mutation_p.S59N	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	59						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GTTGGAAGCAGCCGATCCAGC	0.657																																					p.S59N		Atlas-SNP	.											.	IGLL5	26	.	0			c.G176A						PASS	.																																			SO:0001583	missense	100423062	exon1			GAAGCAGCCGATC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.176G>A	22.37:g.23230409G>A	ENSP00000431254:p.Ser59Asn	117.0	0.0	0		102.0	14.0	0.137255	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.14	1.267343	0.23136	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00583	6.41;6.41	3.92	-0.797	0.10909	.	.	.	.	.	T	0.00440	0.0014	N	0.19112	0.55	0.09310	N	1	B	0.21821	0.061	B	0.17098	0.017	T	0.45056	-0.9287	9	0.59425	D	0.04	.	3.0635	0.06207	0.2132:0.0:0.4153:0.3715	.	59	B9A064	IGLL5_HUMAN	N	59	ENSP00000436353:S59N;ENSP00000431254:S59N	ENSP00000431254:S59N	S	+	2	0	IGLL5	21560409	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.100000	0.10990	-0.036000	0.13669	-0.196000	0.12772	AGC	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
OR4S1	256148	hgsc.bcm.edu	37	11	48328231	48328231	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:48328231C>T	ENST00000319988.1	+	1	457	c.457C>T	c.(457-459)Cat>Tat	p.H153Y		NM_001004725.1	NP_001004725.1	Q8NGB4	OR4S1_HUMAN	olfactory receptor, family 4, subfamily S, member 1	153						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|skin(3)	21						TGGCTTCCTGCATTCCATCCT	0.567																																					p.H153Y		Atlas-SNP	.											.	OR4S1	52	.	0			c.C457T						PASS	.						119.0	102.0	108.0					11																	48328231		2201	4298	6499	SO:0001583	missense	256148	exon1			TTCCTGCATTCCA	AB065908	CCDS31488.1	11p11.2	2012-08-09			ENSG00000176555	ENSG00000176555		"""GPCR / Class A : Olfactory receptors"""	14705	protein-coding gene	gene with protein product							Standard	NM_001004725		Approved		uc010rhu.2	Q8NGB4	OTTHUMG00000166578	ENST00000319988.1:c.457C>T	11.37:g.48328231C>T	ENSP00000321447:p.His153Tyr	191.0	0.0	0		113.0	10.0	0.0884956	NM_001004725	Q6IFB4	Missense_Mutation	SNP	ENST00000319988.1	37	CCDS31488.1	.	.	.	.	.	.	.	.	.	.	C	18.14	3.558614	0.65538	.	.	ENSG00000176555	ENST00000319988	T	0.36699	1.24	5.02	5.02	0.67125	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.60090	0.2242	M	0.66506	2.035	0.09310	N	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.53781	-0.8390	9	0.87932	D	0	.	16.186	0.81950	0.0:1.0:0.0:0.0	.	153	Q8NGB4	OR4S1_HUMAN	Y	153	ENSP00000321447:H153Y	ENSP00000321447:H153Y	H	+	1	0	OR4S1	48284807	0.000000	0.05858	0.759000	0.31340	0.986000	0.74619	-0.017000	0.12590	2.497000	0.84241	0.655000	0.94253	CAT	.	.	none		0.567	OR4S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390556.1	NM_001004725	
KCNH1	3756	hgsc.bcm.edu	37	1	210856924	210856924	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:210856924C>T	ENST00000271751.4	-	11	2696	c.2669G>A	c.(2668-2670)cGc>cAc	p.R890H	KCNH1_ENST00000367007.4_Missense_Mutation_p.R863H			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	890					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		GTTGTCCAGGCGCAAGTCGCT	0.592																																					p.R890H		Atlas-SNP	.											.	KCNH1	199	.	0			c.G2669A						PASS	.						73.0	67.0	69.0					1																	210856924		2203	4300	6503	SO:0001583	missense	3756	exon11			TCCAGGCGCAAGT	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2669G>A	1.37:g.210856924C>T	ENSP00000271751:p.Arg890His	166.0	0.0	0		136.0	6.0	0.0441176	NM_172362	B1AQ26|O76035|Q14CL3	Missense_Mutation	SNP	ENST00000271751.4	37	CCDS1496.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.870929	0.72065	.	.	ENSG00000143473	ENST00000271751;ENST00000367007	D;D	0.99537	-6.03;-6.11	4.93	4.93	0.64822	.	0.000000	0.85682	D	0.000000	D	0.99444	0.9803	L	0.58101	1.795	0.80722	D	1	D;D	0.89917	0.998;1.0	P;D	0.71184	0.858;0.972	D	0.98847	1.0757	10	0.56958	D	0.05	.	18.1618	0.89710	0.0:1.0:0.0:0.0	.	863;890	Q14CL3;O95259	.;KCNH1_HUMAN	H	890;863	ENSP00000271751:R890H;ENSP00000355974:R863H	ENSP00000271751:R890H	R	-	2	0	KCNH1	208923547	1.000000	0.71417	0.907000	0.35723	0.337000	0.28794	7.538000	0.82048	2.290000	0.77057	0.561000	0.74099	CGC	.	.	none		0.592	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
HNF4G	3174	hgsc.bcm.edu	37	8	76471075	76471075	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr8:76471075T>C	ENST00000354370.1	+	9	1055	c.785T>C	c.(784-786)aTg>aCg	p.M262T	HNF4G_ENST00000396423.2_Missense_Mutation_p.M299T			Q14541	HNF4G_HUMAN	hepatocyte nuclear factor 4, gamma	262					endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	37	Breast(64;0.0448)		BRCA - Breast invasive adenocarcinoma(89;0.161)			ATTAAGAACATGAGGTTCCAA	0.448																																					p.M299T		Atlas-SNP	.											.	HNF4G	111	.	0			c.T896C						PASS	.						81.0	75.0	77.0					8																	76471075		2203	4300	6503	SO:0001583	missense	3174	exon8			AGAACATGAGGTT		CCDS6220.2	8q21-q22	2013-01-16			ENSG00000164749	ENSG00000164749		"""Nuclear hormone receptors"""	5026	protein-coding gene	gene with protein product		605966				8622695, 12220494	Standard	NM_004133		Approved	NR2A2	uc003yar.3	Q14541	OTTHUMG00000149920	ENST00000354370.1:c.785T>C	8.37:g.76471075T>C	ENSP00000346339:p.Met262Thr	117.0	0.0	0		89.0	9.0	0.101124	NM_004133	Q7Z2V9|Q9UH81|Q9UIS6	Missense_Mutation	SNP	ENST00000354370.1	37		.	.	.	.	.	.	.	.	.	.	T	21.4	4.150652	0.78001	.	.	ENSG00000164749	ENST00000354370;ENST00000396423	D;D	0.96427	-4.01;-4.01	5.62	5.62	0.85841	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.033448	0.85682	D	0.000000	D	0.96728	0.8932	L	0.42245	1.32	0.80722	D	1	B;P	0.42409	0.121;0.779	B;P	0.57620	0.234;0.824	D	0.97499	1.0059	10	0.87932	D	0	.	15.8221	0.78662	0.0:0.0:0.0:1.0	.	299;262	F1D8Q4;Q14541	.;HNF4G_HUMAN	T	262;299	ENSP00000346339:M262T;ENSP00000379701:M299T	ENSP00000346339:M262T	M	+	2	0	HNF4G	76633630	1.000000	0.71417	1.000000	0.80357	0.849000	0.48306	7.991000	0.88244	2.139000	0.66308	0.533000	0.62120	ATG	.	.	none		0.448	HNF4G-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000313914.2	NM_004133	
F7	2155	hgsc.bcm.edu	37	13	113773002	113773002	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:113773002A>G	ENST00000375581.3	+	9	1116	c.1081A>G	c.(1081-1083)Aac>Gac	p.N361D	F7_ENST00000346342.3_Missense_Mutation_p.N339D|F7_ENST00000541084.1_Missense_Mutation_p.N292D	NM_000131.4	NP_000122.1	P08709	FA7_HUMAN	coagulation factor VII (serum prothrombin conversion accelerator)	361	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|cellular protein metabolic process (GO:0044267)|circadian rhythm (GO:0007623)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of blood coagulation (GO:0030194)|positive regulation of cell migration (GO:0030335)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of platelet-derived growth factor receptor signaling pathway (GO:0010641)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)|response to estrogen (GO:0043627)|response to growth hormone (GO:0060416)|response to vitamin K (GO:0032571)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|glycoprotein binding (GO:0001948)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(4)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0364)|all_epithelial(44;0.0393)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0737)|Epithelial(84;0.213)|BRCA - Breast invasive adenocarcinoma(86;0.218)		Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Menadione(DB00170)	CATGGTCCTCAACGTGCCCCG	0.632																																					p.N361D		Atlas-SNP	.											.	F7	49	.	0			c.A1081G						PASS	.						33.0	32.0	32.0					13																	113773002		2202	4298	6500	SO:0001583	missense	2155	exon9			GTCCTCAACGTGC		CCDS9528.1, CCDS9529.1, CCDS73602.1	13q34	2014-02-03			ENSG00000057593	ENSG00000057593	3.4.21.21		3544	protein-coding gene	gene with protein product	"""eptacog alfa"", ""FVII coagulation protein"", ""factor VII"""	613878				3264725, 2511201	Standard	NM_000131		Approved		uc001vsv.4	P08709	OTTHUMG00000017373	ENST00000375581.3:c.1081A>G	13.37:g.113773002A>G	ENSP00000364731:p.Asn361Asp	122.0	0.0	0		100.0	22.0	0.22	NM_000131	B0YJC8|Q14339|Q5JVF1|Q5JVF2|Q9UD52|Q9UD53|Q9UD54	Missense_Mutation	SNP	ENST00000375581.3	37	CCDS9528.1	.	.	.	.	.	.	.	.	.	.	A	0.753	-0.772186	0.02951	.	.	ENSG00000057593	ENST00000346342;ENST00000541084;ENST00000375581	D;D;D	0.88741	-2.42;-2.42;-2.42	4.17	-1.31	0.09230	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.595590	0.03454	N	0.211073	T	0.76521	0.3999	N	0.04820	-0.15	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.63305	-0.6667	10	0.24483	T	0.36	.	8.5642	0.33530	0.2473:0.4789:0.2738:0.0	.	292;339;361	F5H8B0;P08709-2;P08709	.;.;FA7_HUMAN	D	339;292;361	ENSP00000329546:N339D;ENSP00000442051:N292D;ENSP00000364731:N361D	ENSP00000329546:N339D	N	+	1	0	F7	112821003	0.003000	0.15002	0.001000	0.08648	0.008000	0.06430	0.407000	0.21049	-0.234000	0.09782	0.383000	0.25322	AAC	.	.	none		0.632	F7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045838.4	NM_000131	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768074	31768074	+	Silent	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:31768074G>A	ENST00000240587.4	-	2	2952	c.2625C>T	c.(2623-2625)gaC>gaT	p.D875D		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	875					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GAGTGGCCCCGTCAATGTCAG	0.572																																					p.D875D		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2625T						PASS	.						70.0	65.0	66.0					19																	31768074		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			GGCCCCGTCAATG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2625C>T	19.37:g.31768074G>A		125.0	0.0	0		90.0	19.0	0.211111	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			.	.	none		0.572	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
MPEG1	219972	hgsc.bcm.edu	37	11	58979509	58979509	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:58979509C>T	ENST00000361050.3	-	1	915	c.830G>A	c.(829-831)aGc>aAc	p.S277N	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	277	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				CCCTCCAATGCTCTGCACCCT	0.542																																					p.S277N		Atlas-SNP	.											.	MPEG1	72	.	0			c.G830A						PASS	.						29.0	26.0	27.0					11																	58979509		1851	4082	5933	SO:0001583	missense	219972	exon1			CCAATGCTCTGCA	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.830G>A	11.37:g.58979509C>T	ENSP00000354335:p.Ser277Asn	119.0	0.0	0		117.0	11.0	0.0940171	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930767	0.73327	.	.	ENSG00000197629	ENST00000361050	D	0.84589	-1.87	5.38	5.38	0.77491	Membrane attack complex component/perforin (MACPF) domain (3);	0.000000	0.85682	D	0.000000	D	0.91297	0.7256	M	0.67953	2.075	0.50313	D	0.999864	D	0.89917	1.0	D	0.91635	0.999	D	0.91418	0.5156	10	0.54805	T	0.06	-33.9117	16.1079	0.81237	0.0:1.0:0.0:0.0	.	277	Q2M385	MPEG1_HUMAN	N	277	ENSP00000354335:S277N	ENSP00000354335:S277N	S	-	2	0	MPEG1	58736085	1.000000	0.71417	0.677000	0.29947	0.973000	0.67179	7.032000	0.76498	2.541000	0.85698	0.650000	0.86243	AGC	.	.	none		0.542	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
TRAM1L1	133022	hgsc.bcm.edu	37	4	118005633	118005633	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:118005633G>A	ENST00000310754.4	-	1	1103	c.917C>T	c.(916-918)aCg>aTg	p.T306M		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	306	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						GGCTTGGATCGTGCAACTGGA	0.453																																					p.T306M		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.C917T						PASS	.						129.0	120.0	123.0					4																	118005633		2203	4300	6503	SO:0001583	missense	133022	exon1			TGGATCGTGCAAC	AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.917C>T	4.37:g.118005633G>A	ENSP00000309402:p.Thr306Met	225.0	0.0	0		179.0	18.0	0.100559	NM_152402	Q8N2L7	Missense_Mutation	SNP	ENST00000310754.4	37	CCDS3707.1	.	.	.	.	.	.	.	.	.	.	G	7.466	0.645766	0.14451	.	.	ENSG00000174599	ENST00000310754	D	0.85258	-1.96	3.74	2.87	0.33458	TRAM/LAG1/CLN8 homology domain (3);	0.890367	0.09839	N	0.749176	T	0.79936	0.4532	L	0.29908	0.895	0.09310	N	1	P	0.48089	0.905	P	0.45946	0.498	T	0.67837	-0.5567	10	0.45353	T	0.12	-6.284	9.0284	0.36243	0.0:0.2389:0.7611:0.0	.	306	Q8N609	TR1L1_HUMAN	M	306	ENSP00000309402:T306M	ENSP00000309402:T306M	T	-	2	0	TRAM1L1	118225081	0.009000	0.17119	0.428000	0.26697	0.038000	0.13279	1.409000	0.34680	1.113000	0.41760	0.650000	0.86243	ACG	.	.	none		0.453	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402	
BMP1	649	hgsc.bcm.edu	37	8	22052356	22052356	+	Silent	SNP	G	G	A	rs11552824		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr8:22052356G>A	ENST00000306385.5	+	12	2233	c.1563G>A	c.(1561-1563)acG>acA	p.T521T	BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000306349.8_Silent_p.T521T|BMP1_ENST00000397816.3_Silent_p.T521T|BMP1_ENST00000397814.3_Silent_p.T521T	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	521	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		TCAAGAGCACGTCCAGCCGCC	0.567																																					p.T521T		Atlas-SNP	.											.	BMP1	131	.	0			c.G1563A						PASS	.						84.0	83.0	83.0					8																	22052356		2203	4300	6503	SO:0001819	synonymous_variant	649	exon12			GAGCACGTCCAGC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1563G>A	8.37:g.22052356G>A		84.0	0.0	0		70.0	10.0	0.142857	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			.	.	alt		0.567	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
NPAT	4863	hgsc.bcm.edu	37	11	108044437	108044437	+	Missense_Mutation	SNP	T	T	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:108044437T>A	ENST00000278612.8	-	13	1379	c.1274A>T	c.(1273-1275)aAa>aTa	p.K425I	NPAT_ENST00000610253.1_5'UTR	NM_002519.2	NP_002510.2	Q14207	NPAT_HUMAN	nuclear protein, ataxia-telangiectasia locus	425					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(21)|ovary(2)|prostate(2)|skin(5)	46		all_cancers(61;2.31e-10)|all_epithelial(67;1.11e-06)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;1.05e-05)|Epithelial(105;3.01e-05)|all cancers(92;0.000816)|Colorectal(284;0.116)		AAAGGCCTTTTTCTGTATGCT	0.378																																					p.K425I		Atlas-SNP	.											.	NPAT	124	.	0			c.A1274T						PASS	.						151.0	141.0	144.0					11																	108044437		1861	4089	5950	SO:0001583	missense	4863	exon13			GCCTTTTTCTGTA	X97186	CCDS41710.1	11q22-q23	2008-02-01			ENSG00000149308	ENSG00000149308			7896	protein-coding gene	gene with protein product		601448				9205109	Standard	NM_002519		Approved	E14	uc001pjz.4	Q14207	OTTHUMG00000166385	ENST00000278612.8:c.1274A>T	11.37:g.108044437T>A	ENSP00000278612:p.Lys425Ile	543.0	0.0	0		391.0	34.0	0.0869565	NM_002519	A8K1V5|A8K6M2|Q13632|Q14967|Q16580|Q86W55|Q8IWE9	Missense_Mutation	SNP	ENST00000278612.8	37	CCDS41710.1	.	.	.	.	.	.	.	.	.	.	T	14.14	2.447588	0.43429	.	.	ENSG00000149308	ENST00000278612	T	0.05925	3.37	5.54	5.54	0.83059	.	0.119077	0.56097	D	0.000025	T	0.23688	0.0573	M	0.69823	2.125	0.42227	D	0.991876	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00386	-1.1772	10	0.56958	D	0.05	-24.8189	13.7058	0.62639	0.0:0.0:0.0:1.0	.	425;425	B9EG70;Q14207	.;NPAT_HUMAN	I	425	ENSP00000278612:K425I	ENSP00000278612:K425I	K	-	2	0	NPAT	107549647	1.000000	0.71417	1.000000	0.80357	0.089000	0.18198	2.613000	0.46351	2.231000	0.72958	0.455000	0.32223	AAA	.	.	none		0.378	NPAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389506.2	NM_002519	
CDH3	1001	hgsc.bcm.edu	37	16	68716273	68716273	+	Silent	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:68716273C>T	ENST00000264012.4	+	9	1609	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D	CDH3_ENST00000581171.1_Silent_p.D300D|CDH3_ENST00000429102.2_Silent_p.D355D	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	355	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		CTGATCTGGACGCCCCCAACT	0.592																																					p.D355D		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.C1065T						PASS	.						102.0	73.0	83.0					16																	68716273		2198	4300	6498	SO:0001819	synonymous_variant	1001	exon9			TCTGGACGCCCCC	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1065C>T	16.37:g.68716273C>T		76.0	0.0	0		63.0	8.0	0.126984	NM_001793	B2R6F4|Q05DI6	Silent	SNP	ENST00000264012.4	37	CCDS10868.1																																																																																			.	.	none		0.592	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
CD36	948	hgsc.bcm.edu	37	7	80285936	80285936	+	Silent	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:80285936C>A	ENST00000435819.1	+	7	885	c.201C>A	c.(199-201)atC>atA	p.I67I	CD36_ENST00000309881.7_Silent_p.I67I|CD36_ENST00000432207.1_Silent_p.I67I|CD36_ENST00000394788.3_Silent_p.I67I|CD36_ENST00000441109.2_3'UTR|CD36_ENST00000538969.1_Silent_p.I67I|CD36_ENST00000447544.2_Silent_p.I67I|CD36_ENST00000534394.1_5'UTR|CD36_ENST00000433696.2_Silent_p.I67I|CD36_ENST00000544133.1_Silent_p.I67I			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	67					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						AGTTTTGGATCTTTGATGTGC	0.378																																					p.I67I		Atlas-SNP	.											.	CD36	185	.	0			c.C201A						PASS	.						92.0	88.0	90.0					7																	80285936		2203	4300	6503	SO:0001819	synonymous_variant	948	exon2			TTGGATCTTTGAT	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"""CD molecules"""	1663	protein-coding gene	gene with protein product		173510	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)"""			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.201C>A	7.37:g.80285936C>A		156.0	0.0	0		126.0	22.0	0.174603	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Silent	SNP	ENST00000435819.1	37	CCDS34673.1																																																																																			.	.	none		0.378	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547	
UTS2B	257313	hgsc.bcm.edu	37	3	190999976	190999976	+	Start_Codon_SNP	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr3:190999976C>A	ENST00000340524.5	-	5	789	c.3G>T	c.(1-3)atG>atT	p.M1I	UTS2B_ENST00000427544.2_Start_Codon_SNP_p.M1I	NM_198152.3	NP_937795.2	Q765I0	UTS2B_HUMAN	urotensin 2B	1					regulation of blood pressure (GO:0008217)|regulation of vasodilation (GO:0042312)	extracellular region (GO:0005576)											GGATCTTGTTCATGTTAAAAA	0.383																																					p.M1I		Atlas-SNP	.											.	.	.	.	0			c.G3T						PASS	.						70.0	65.0	66.0					3																	190999976		2203	4300	6503	SO:0001582	initiator_codon_variant	257313	exon5			CTTGTTCATGTTA	AB116021	CCDS3300.1	3q28	2013-02-28	2013-02-28	2013-02-28	ENSG00000188958	ENSG00000188958		"""Endogenous ligands"""	30894	protein-coding gene	gene with protein product	"""prepro-URP"""		"""urotensin 2 domain containing"""	UTS2D		14550283	Standard	NM_198152		Approved	URP, U2B	uc003fsu.3	Q765I0	OTTHUMG00000156192	ENST00000340524.5:c.3G>T	3.37:g.190999976C>A	ENSP00000340526:p.Met1Ile	145.0	0.0	0		120.0	5.0	0.0416667	NM_198152	B3KQY8|D3DNW1|Q2M1Z2	Missense_Mutation	SNP	ENST00000340524.5	37	CCDS3300.1	.	.	.	.	.	.	.	.	.	.	C	12.33	1.904784	0.33628	.	.	ENSG00000188958	ENST00000340524;ENST00000427544;ENST00000432514	T;T;T	0.60548	0.68;0.68;0.18	4.9	4.03	0.46877	.	0.451571	0.18931	N	0.127207	T	0.62319	0.2418	.	.	.	0.80722	D	1	D	0.57571	0.98	P	0.52598	0.703	T	0.62539	-0.6833	9	0.45353	T	0.12	-11.1179	9.5763	0.39459	0.0:0.9049:0.0:0.0951	.	1	Q765I0	UTS2B_HUMAN	I	1	ENSP00000340526:M1I;ENSP00000398761:M1I;ENSP00000401028:M1I	ENSP00000340526:M1I	M	-	3	0	UTS2D	192482670	0.996000	0.38824	0.656000	0.29637	0.046000	0.14306	1.515000	0.35845	1.447000	0.47661	-0.133000	0.14855	ATG	.	.	none		0.383	UTS2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343353.1	NM_198152	Missense_Mutation
FRAS1	80144	hgsc.bcm.edu	37	4	79328899	79328899	+	Silent	SNP	C	C	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:79328899C>G	ENST00000325942.6	+	31	4652	c.4212C>G	c.(4210-4212)acC>acG	p.T1404T	FRAS1_ENST00000264895.6_Silent_p.T1404T	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1404					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						GGACAGCTACCCCCACCAGCA	0.597																																					p.T1404T		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4212G						PASS	.						80.0	87.0	85.0					4																	79328899		2124	4233	6357	SO:0001819	synonymous_variant	80144	exon31			AGCTACCCCCACC	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4212C>G	4.37:g.79328899C>G		121.0	0.0	0		98.0	8.0	0.0816327	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000325942.6	37	CCDS54772.1																																																																																			.	.	none		0.597	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
DDC	1644	hgsc.bcm.edu	37	7	50531011	50531011	+	Missense_Mutation	SNP	G	G	A	rs147562019		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:50531011G>A	ENST00000444124.2	-	14	1561	c.1361C>T	c.(1360-1362)aCg>aTg	p.T454M	DDC_ENST00000426377.1_Missense_Mutation_p.T376M|DDC_ENST00000431062.1_Missense_Mutation_p.T361M|DDC_ENST00000357936.5_Missense_Mutation_p.T454M	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	454					catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	AGATTCCACCGTGCGAGAACA	0.547																																					p.T454M		Atlas-SNP	.											.	DDC	100	.	0			c.C1361T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	1,4405		0,1,2202	120.0	104.0	110.0		1361,1361,1247,1217,1127,1082	2.6	0.0	7	dbSNP_134	110	0,8600		0,0,4300	no	missense,missense,missense,missense,missense,missense	DDC	NM_000790.3,NM_001082971.1,NM_001242886.1,NM_001242887.1,NM_001242888.1,NM_001242889.1	81,81,81,81,81,81	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	454/481,454/481,416/443,406/433,376/403,361/388	50531011	1,13005	2203	4300	6503	SO:0001583	missense	1644	exon14			TCCACCGTGCGAG		CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.1361C>T	7.37:g.50531011G>A	ENSP00000403644:p.Thr454Met	218.0	0.0	0		165.0	14.0	0.0848485	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Missense_Mutation	SNP	ENST00000444124.2	37	CCDS5511.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.557|7.557	0.663813|0.663813	0.14710|0.14710	2.27E-4|2.27E-4	0.0|0.0	ENSG00000132437|ENSG00000132437	ENST00000430300|ENST00000357936;ENST00000431062;ENST00000426377;ENST00000444124	.|T;T;T;T	.|0.38077	.|1.16;1.16;1.16;1.16	5.44|5.44	2.61|2.61	0.31194|0.31194	.|Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	.|0.388045	.|0.31102	.|N	.|0.008259	T|T	0.35451|0.35451	0.0932|0.0932	M|M	0.73962|0.73962	2.25|2.25	0.27720|0.27720	N|N	0.945142|0.945142	.|B;B	.|0.21147	.|0.052;0.052	.|B;B	.|0.12156	.|0.007;0.007	T|T	0.33548|0.33548	-0.9864|-0.9864	5|10	.|0.59425	.|D	.|0.04	-7.455|-7.455	7.8343|7.8343	0.29362|0.29362	0.1397:0.0:0.728:0.1323|0.1397:0.0:0.728:0.1323	.|.	.|454;454	.|Q53Y41;P20711	.|.;DDC_HUMAN	W|M	335|454;361;376;454	.|ENSP00000350616:T454M;ENSP00000399184:T361M;ENSP00000395069:T376M;ENSP00000403644:T454M	.|ENSP00000350616:T454M	R|T	-|-	1|2	2|0	DDC|DDC	50498505|50498505	0.021000|0.021000	0.18746|0.18746	0.002000|0.002000	0.10522|0.10522	0.066000|0.066000	0.16364|0.16364	0.704000|0.704000	0.25661|0.25661	0.245000|0.245000	0.21373|0.21373	0.655000|0.655000	0.94253|0.94253	CGG|ACG	G|1.000;A|0.000	0.000	weak		0.547	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
TLX1	3195	hgsc.bcm.edu	37	10	102896618	102896618	+	Missense_Mutation	SNP	A	A	G	rs567197994	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:102896618A>G	ENST00000370196.6	+	3	2983	c.941A>G	c.(940-942)gAc>gGc	p.D314G	RP11-31L23.3_ENST00000411459.1_RNA|TLX1_ENST00000467928.2_3'UTR			P31314	TLX1_HUMAN	T-cell leukemia homeobox 1	314					cell fate commitment (GO:0045165)|central nervous system development (GO:0007417)|neuron differentiation (GO:0030182)|organ formation (GO:0048645)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spleen development (GO:0048536)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|upper_aerodigestive_tract(1)	2				Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CCGTGGTCTGACGACTCGACC	0.647			T	"""TRB@, TRD@"""	T-ALL																																p.D314G		Atlas-SNP	.		Dom	yes		10	10q24	3195	""" T-cell leukemia, homeobox 1 (HOX11)"""		L	TLX1,NS,carcinoma,-1,1	TLX1	20	1	0			c.A941G						PASS	.						87.0	71.0	76.0					10																	102896618		2203	4300	6503	SO:0001583	missense	3195	exon3			GGTCTGACGACTC	M62626	CCDS7510.1, CCDS55725.1	10q24.32	2011-06-20	2005-12-22	2002-05-31	ENSG00000107807	ENSG00000107807		"""Homeoboxes / ANTP class : NKL subclass"""	5056	protein-coding gene	gene with protein product	"""Homeo box-11 (T-cell leukemia-3 associated breakpoint, homologous to Drosophila Notch)"", ""homeo box 11 (T-cell lymphoma 3-associated breakpoint)"""	186770	"""homeo box 11 (T-cell lymphoma 3-associated breakpoint)"", ""T-cell leukemia, homeobox 1"""	TCL3, HOX11		1676542, 1973146	Standard	NM_005521		Approved		uc001ksw.3	P31314	OTTHUMG00000019341	ENST00000370196.6:c.941A>G	10.37:g.102896618A>G	ENSP00000359215:p.Asp314Gly	144.0	0.0	0		124.0	18.0	0.145161	NM_005521	A1L4G3|O75699|Q5VXP2|Q9HCA0|Q9UD59	Missense_Mutation	SNP	ENST00000370196.6	37	CCDS7510.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.333134	0.81801	.	.	ENSG00000107807	ENST00000370196	D	0.90069	-2.61	4.39	4.39	0.52855	.	0.048467	0.85682	D	0.000000	D	0.82458	0.5041	L	0.31664	0.95	0.80722	D	1	P	0.37864	0.61	B	0.34873	0.191	D	0.84604	0.0674	10	0.72032	D	0.01	.	13.8955	0.63768	1.0:0.0:0.0:0.0	.	314	P31314	TLX1_HUMAN	G	314	ENSP00000359215:D314G	ENSP00000359215:D314G	D	+	2	0	TLX1	102886608	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	8.774000	0.91767	1.750000	0.51863	0.379000	0.24179	GAC	.	.	none		0.647	TLX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051193.3	NM_005521	
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126812	19126812	+	Silent	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:19126812G>A	ENST00000381440.3	+	1	1559	c.1029G>A	c.(1027-1029)gcG>gcA	p.A343A	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	343						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GCCTGCGTGCGGAGGCACTGT	0.667																																					p.A343A		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.G1029A						PASS	.						32.0	36.0	35.0					16																	19126812		2197	4300	6497	SO:0001819	synonymous_variant	162073	exon1			GCGTGCGGAGGCA		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.1029G>A	16.37:g.19126812G>A		54.0	0.0	0		44.0	4.0	0.0909091	NM_001034841		Silent	SNP	ENST00000381440.3	37	CCDS32395.1																																																																																			.	.	none		0.667	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841	
BICC1	80114	hgsc.bcm.edu	37	10	60549152	60549152	+	Missense_Mutation	SNP	G	G	A	rs192860241	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:60549152G>A	ENST00000373886.3	+	7	735	c.731G>A	c.(730-732)cGt>cAt	p.R244H		NM_001080512.1	NP_001073981.1	Q9H694	BICC1_HUMAN	BicC family RNA binding protein 1	244					multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)	cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	44						TTTAAACAGCGTTCCCGAATG	0.388													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18107	0.0		0.0	False		,,,				2504	0.001				p.R244H		Atlas-SNP	.											BICC1,colon,carcinoma,+1,1	BICC1	121	1	0			c.G731A						PASS	.						138.0	132.0	134.0					10																	60549152		2203	4300	6503	SO:0001583	missense	80114	exon7			AACAGCGTTCCCG	AK026129	CCDS31206.1	10q21.3	2014-09-17	2014-02-03		ENSG00000122870	ENSG00000122870		"""Sterile alpha motif (SAM) domain containing"""	19351	protein-coding gene	gene with protein product		614295	"""bicaudal C homolog 1 (Drosophila)"""				Standard	XM_005270166		Approved		uc001jki.1	Q9H694	OTTHUMG00000018271	ENST00000373886.3:c.731G>A	10.37:g.60549152G>A	ENSP00000362993:p.Arg244His	221.0	0.0	0		155.0	10.0	0.0645161	NM_001080512		Missense_Mutation	SNP	ENST00000373886.3	37	CCDS31206.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	26.2	4.712381	0.89112	.	.	ENSG00000122870	ENST00000373886	T	0.32023	1.47	5.66	5.66	0.87406	.	0.048305	0.85682	D	0.000000	T	0.51075	0.1653	L	0.60455	1.87	0.80722	D	1	D	0.76494	0.999	P	0.60117	0.869	T	0.46871	-0.9160	10	0.56958	D	0.05	-7.8917	19.756	0.96291	0.0:0.0:1.0:0.0	.	244	Q9H694	BICC1_HUMAN	H	244	ENSP00000362993:R244H	ENSP00000362993:R244H	R	+	2	0	BICC1	60219158	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.939000	0.70179	2.665000	0.90641	0.655000	0.94253	CGT	G|1.000;A|0.000	0.000	strong		0.388	BICC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048150.2	NM_025044	
SLC6A14	11254	hgsc.bcm.edu	37	X	115588850	115588850	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:115588850G>A	ENST00000371900.4	+	13	1778	c.1690G>A	c.(1690-1692)Gct>Act	p.A564T	SLC6A14_ENST00000463626.1_Intron	NM_007231.3	NP_009162.1	Q9UN76	S6A14_HUMAN	solute carrier family 6 (amino acid transporter), member 14	564					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	amino acid transmembrane transporter activity (GO:0015171)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	23					L-Proline(DB00172)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	CTGGGGAGTTGCTTTAGGCTG	0.368																																					p.A564T		Atlas-SNP	.											.	SLC6A14	56	.	0			c.G1690A						PASS	.						205.0	184.0	191.0					X																	115588850		2203	4300	6503	SO:0001583	missense	11254	exon13			GGAGTTGCTTTAG	AF151978	CCDS14570.1	Xq23	2013-05-22			ENSG00000087916	ENSG00000268104		"""Solute carriers"""	11047	protein-coding gene	gene with protein product		300444	"""solute carrier family 6 (neurotransmitter transporter), member 14"""			10446133	Standard	NM_007231		Approved		uc004eqi.3	Q9UN76	OTTHUMG00000022245	ENST00000371900.4:c.1690G>A	X.37:g.115588850G>A	ENSP00000360967:p.Ala564Thr	252.0	0.0	0		136.0	8.0	0.0588235	NM_007231	Q5H942	Missense_Mutation	SNP	ENST00000371900.4	37	CCDS14570.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.516113	0.44763	.	.	ENSG00000087916	ENST00000371900	T	0.74947	-0.89	5.17	4.31	0.51392	.	0.169081	0.51477	D	0.000091	T	0.69477	0.3115	L	0.51914	1.62	0.39830	D	0.972966	B	0.32604	0.377	B	0.37047	0.24	T	0.68243	-0.5460	10	0.44086	T	0.13	.	10.5295	0.44969	0.0965:0.0:0.9035:0.0	.	564	Q9UN76	S6A14_HUMAN	T	564	ENSP00000360967:A564T	ENSP00000360967:A564T	A	+	1	0	SLC6A14	115502878	0.998000	0.40836	0.991000	0.47740	0.970000	0.65996	3.357000	0.52277	0.974000	0.38366	0.538000	0.68166	GCT	.	.	none		0.368	SLC6A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057986.1		
ATN1	1822	hgsc.bcm.edu	37	12	7045906	7045906	+	Silent	SNP	G	G	A	rs377147612		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:7045906G>A	ENST00000356654.4	+	5	1713	c.1476G>A	c.(1474-1476)caG>caA	p.Q492Q	ATN1_ENST00000396684.2_Silent_p.Q492Q	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	492	Poly-Gln.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						agcagcagcagcagcagcagc	0.647																																					p.Q492Q		Atlas-SNP	.											.	ATN1	95	.	0			c.G1476A						PASS	.						43.0	53.0	49.0					12																	7045906		2188	4263	6451	SO:0001819	synonymous_variant	1822	exon5			GCAGCAGCAGCAG	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1476G>A	12.37:g.7045906G>A		58.0	0.0	0		46.0	5.0	0.108696	NM_001007026	Q99495|Q99621|Q9UEK7	Silent	SNP	ENST00000356654.4	37	CCDS31734.1																																																																																			.	.	none		0.647	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401948.2	NM_001940	
MPEG1	219972	hgsc.bcm.edu	37	11	58978519	58978519	+	Missense_Mutation	SNP	G	G	A	rs376216311		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:58978519G>A	ENST00000361050.3	-	1	1905	c.1820C>T	c.(1819-1821)aCc>aTc	p.T607I		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	607						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				GACAGTATTGGTGGCAGCCTG	0.582																																					p.T607I		Atlas-SNP	.											.	MPEG1	72	.	0			c.C1820T						PASS	.						108.0	114.0	112.0					11																	58978519		1948	4124	6072	SO:0001583	missense	219972	exon1			GTATTGGTGGCAG	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1820C>T	11.37:g.58978519G>A	ENSP00000354335:p.Thr607Ile	119.0	0.0	0		126.0	15.0	0.119048	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	37	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	G	11.17	1.559489	0.27827	.	.	ENSG00000197629	ENST00000361050	T	0.25085	1.82	5.69	5.69	0.88448	.	0.113776	0.64402	D	0.000019	T	0.47619	0.1455	M	0.72894	2.215	0.43300	D	0.995291	D	0.65815	0.995	P	0.59424	0.857	T	0.40608	-0.9554	10	0.54805	T	0.06	-19.9386	16.7224	0.85413	0.0:0.0:1.0:0.0	.	607	Q2M385	MPEG1_HUMAN	I	607	ENSP00000354335:T607I	ENSP00000354335:T607I	T	-	2	0	MPEG1	58735095	1.000000	0.71417	1.000000	0.80357	0.398000	0.30690	3.083000	0.50136	2.682000	0.91365	0.655000	0.94253	ACC	.	.	alt		0.582	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
PADI1	29943	hgsc.bcm.edu	37	1	17566209	17566209	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:17566209C>G	ENST00000375471.4	+	14	1655	c.1563C>G	c.(1561-1563)caC>caG	p.H521Q	PADI1_ENST00000460293.1_3'UTR|PADI1_ENST00000413717.2_Missense_Mutation_p.H78Q|PADI1_ENST00000536552.1_5'UTR|PADI1_ENST00000537499.1_Missense_Mutation_p.H78Q	NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	521					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	GGTTAAAACACCAGGCAAAAA	0.517																																					p.H521Q	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.C1563G						PASS	.						63.0	61.0	62.0					1																	17566209		2203	4300	6503	SO:0001583	missense	29943	exon14			AAAACACCAGGCA	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.1563C>G	1.37:g.17566209C>G	ENSP00000364620:p.His521Gln	203.0	0.0	0		128.0	14.0	0.109375	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	37	CCDS178.1	.	.	.	.	.	.	.	.	.	.	C	3.748	-0.052131	0.07362	.	.	ENSG00000142623	ENST00000375471;ENST00000537499;ENST00000413717	T;T;T	0.21361	2.01;2.01;2.01	5.0	-3.5	0.04710	Protein-arginine deiminase, C-terminal (1);	1.843040	0.02096	N	0.053523	T	0.14141	0.0342	L	0.39898	1.24	0.18873	N	0.999982	B;B	0.13594	0.008;0.002	B;B	0.14578	0.011;0.005	T	0.15549	-1.0433	10	0.23302	T	0.38	-5.7269	0.9834	0.01441	0.1784:0.3415:0.1289:0.3512	.	78;521	B4DPX6;Q9ULC6	.;PADI1_HUMAN	Q	521;78;78	ENSP00000364620:H521Q;ENSP00000444032:H78Q;ENSP00000396697:H78Q	ENSP00000364620:H521Q	H	+	3	2	PADI1	17438796	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.834000	0.01693	-0.305000	0.08831	0.563000	0.77884	CAC	.	.	none		0.517	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
VIPR2	7434	hgsc.bcm.edu	37	7	158935181	158935181	+	Silent	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr7:158935181T>C	ENST00000262178.2	-	2	293	c.108A>G	c.(106-108)acA>acG	p.T36T	VIPR2_ENST00000402066.1_Silent_p.T177T|VIPR2_ENST00000421760.2_Silent_p.T36T	NM_003382.4	NP_003373.2	P41587	VIPR2_HUMAN	vasoactive intestinal peptide receptor 2	36					activation of adenylate cyclase activity (GO:0007190)|cell-cell signaling (GO:0007267)|negative regulation of smooth muscle cell proliferation (GO:0048662)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|vasoactive intestinal polypeptide receptor activity (GO:0004999)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22	Ovarian(565;0.152)	all_cancers(7;1.13e-11)|all_epithelial(9;0.000545)|all_hematologic(28;0.00603)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.2)|STAD - Stomach adenocarcinoma(7;0.18)		CTGCACATTTTGTTTCTTCCT	0.423																																					p.T36T	Pancreas(154;1876 1931 2329 17914 20079)	Atlas-SNP	.											.	VIPR2	53	.	0			c.A108G						PASS	.						217.0	202.0	207.0					7																	158935181		2203	4298	6501	SO:0001819	synonymous_variant	7434	exon2			ACATTTTGTTTCT	CA449700, X95097	CCDS5950.1	7q36.3	2012-08-10			ENSG00000106018	ENSG00000106018		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12695	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 2"""	601970				7811244	Standard	NM_003382		Approved	VPAC2, VPAC2R	uc003woh.3	P41587	OTTHUMG00000151446	ENST00000262178.2:c.108A>G	7.37:g.158935181T>C		264.0	0.0	0		190.0	21.0	0.110526	NM_003382	Q13053|Q15870|Q53Y09|Q6ZN22|Q9UCW0	Silent	SNP	ENST00000262178.2	37	CCDS5950.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.671893	0.47781	.	.	ENSG00000106018	ENST00000418475	.	.	.	5.09	-3.04	0.05412	.	.	.	.	.	T	0.49012	0.1532	.	.	.	0.53688	D	0.999975	.	.	.	.	.	.	T	0.45234	-0.9275	4	.	.	.	.	6.3447	0.21343	0.0:0.1642:0.4153:0.4205	.	.	.	.	R	31	.	.	Q	-	2	0	VIPR2	158627942	0.850000	0.29656	0.923000	0.36655	0.980000	0.70556	-0.238000	0.08977	-0.256000	0.09473	0.482000	0.46254	CAA	.	.	none		0.423	VIPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322675.1	NM_003382	
MPEG1	219972	hgsc.bcm.edu	37	11	58979544	58979544	+	Silent	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:58979544G>A	ENST00000361050.3	-	1	880	c.795C>T	c.(793-795)agC>agT	p.S265S	RN7SL42P_ENST00000579786.1_RNA	NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	265	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.					integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				TTGAGAGGTAGCTCTTGGTGA	0.532																																					p.S265S		Atlas-SNP	.											.	MPEG1	72	.	0			c.C795T						PASS	.						38.0	36.0	37.0					11																	58979544		1901	4108	6009	SO:0001819	synonymous_variant	219972	exon1			GAGGTAGCTCTTG	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.795C>T	11.37:g.58979544G>A		128.0	0.0	0		133.0	12.0	0.0902256	NM_001039396	Q2M1T6|Q8TEF8	Silent	SNP	ENST00000361050.3	37	CCDS41650.1																																																																																			.	.	none		0.532	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117576	46117576	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr21:46117576C>T	ENST00000400365.3	+	1	490	c.460C>T	c.(460-462)Ccc>Tcc	p.P154S	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	154	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						CTGCTGTGTGCCCGTCTGCTG	0.617																																					p.P154S		Atlas-SNP	.											KRTAP10-12,rectum,carcinoma,0,2	KRTAP10-12	21	2	0			c.C460T						scavenged	.						177.0	182.0	180.0					21																	46117576		2203	4300	6503	SO:0001583	missense	386685	exon1			TGTGTGCCCGTCT	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.460C>T	21.37:g.46117576C>T	ENSP00000383216:p.Pro154Ser	88.0	0.0	0		64.0	4.0	0.0625	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	37	CCDS42967.1	.	.	.	.	.	.	.	.	.	.	c	2.310	-0.358108	0.05138	.	.	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.00648	5.99	3.7	1.73	0.24493	.	.	.	.	.	T	0.00815	0.0027	L	0.49778	1.585	0.09310	N	1	B	0.24963	0.115	B	0.25884	0.064	T	0.44360	-0.9333	9	0.15952	T	0.53	.	10.0177	0.42024	0.3626:0.6374:0.0:0.0	.	154	P60413	KR10C_HUMAN	S	154;62	ENSP00000383216:P154S	ENSP00000383216:P154S	P	+	1	0	KRTAP10-12	44942004	0.001000	0.12720	0.001000	0.08648	0.016000	0.09150	0.087000	0.14958	0.117000	0.18138	0.305000	0.20034	CCC	.	.	none		0.617	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
HS6ST2	90161	hgsc.bcm.edu	37	X	132091067	132091067	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:132091067C>A	ENST00000370836.2	-	3	1131	c.716G>T	c.(715-717)gGc>gTc	p.G239V	HS6ST2_ENST00000370833.2_Missense_Mutation_p.G93V|HS6ST2_ENST00000521489.1_Missense_Mutation_p.G239V	NM_147175.3	NP_671704.3	Q96MM7	H6ST2_HUMAN	heparan sulfate 6-O-sulfotransferase 2	239	5'-phosphosulfate-binding. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(2)	9	Acute lymphoblastic leukemia(192;0.000127)					GAAAGTGGTGCCCCCGGTCTT	0.617																																					p.G239V		Atlas-SNP	.											.	HS6ST2	89	.	0			c.G716T						PASS	.						28.0	34.0	32.0					X																	132091067		2186	4279	6465	SO:0001583	missense	90161	exon3			GTGGTGCCCCCGG	AB067776	CCDS48169.1, CCDS48170.1	Xq26.2	2008-02-05			ENSG00000171004	ENSG00000171004		"""Sulfotransferases, membrane-bound"""	19133	protein-coding gene	gene with protein product		300545				10644753	Standard	NM_147175		Approved		uc011mvd.1	Q96MM7	OTTHUMG00000022430	ENST00000370836.2:c.716G>T	X.37:g.132091067C>A	ENSP00000359873:p.Gly239Val	134.0	0.0	0		100.0	8.0	0.08	NM_001077188	B9WRT4|B9WRT5|E9PDY5|Q2TB13|Q4VC07|Q6PIC4|Q86SM9|Q8N3T4|Q8NBN4|Q96SJ4	Missense_Mutation	SNP	ENST00000370836.2	37	CCDS48169.1	.	.	.	.	.	.	.	.	.	.	C	19.88	3.909561	0.72868	.	.	ENSG00000171004	ENST00000370837;ENST00000370836;ENST00000521489;ENST00000370833;ENST00000319809	T;T;T;T	0.45276	0.9;0.9;0.9;0.9	4.78	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.70613	0.3244	M	0.89601	3.045	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.78375	-0.2228	10	0.87932	D	0	-18.7584	15.4915	0.75607	0.0:1.0:0.0:0.0	.	239;239	Q96MM7;E9PDY5	H6ST2_HUMAN;.	V	93;239;239;93;80	ENSP00000359874:G93V;ENSP00000359873:G239V;ENSP00000429473:G239V;ENSP00000359870:G93V	ENSP00000324617:G80V	G	-	2	0	HS6ST2	131918749	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.244000	0.78228	2.212000	0.71576	0.529000	0.55759	GGC	.	.	none		0.617	HS6ST2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058332.3	NM_147174	
BTG1	694	hgsc.bcm.edu	37	12	92539203	92539203	+	Silent	SNP	G	G	A	rs369374957		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:92539203G>A	ENST00000256015.3	-	1	470	c.109C>T	c.(109-111)Ctg>Ttg	p.L37L	C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000501008.2_RNA|C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	37					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)	p.L37L(1)		haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				AAGGTCTGCAGCTGTCGCTCG	0.677			T	MYC	BCLL																																p.L37L		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	BTG1,NS,lymphoid_neoplasm,0,3	BTG1	30	3	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.C109T						PASS	.						38.0	41.0	40.0					12																	92539203		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			TCTGCAGCTGTCG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.109C>T	12.37:g.92539203G>A		187.0	0.0	0		181.0	8.0	0.0441989	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	alt		0.677	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
KIF25	3834	hgsc.bcm.edu	37	6	168443315	168443315	+	Missense_Mutation	SNP	G	G	A	rs146787013	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr6:168443315G>A	ENST00000443060.2	+	9	1295	c.904G>A	c.(904-906)Gtc>Atc	p.V302I	KIF25_ENST00000351261.3_Intron|KIF25_ENST00000354419.2_Missense_Mutation_p.V302I			Q9UIL4	KIF25_HUMAN	kinesin family member 25	302	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CCTGGCAGGCGTCCTGGGGGC	0.647													G|||	46	0.0091853	0.0318	0.0058	5008	,	,		16877	0.0		0.0	False		,,,				2504	0.0				p.V302I		Atlas-SNP	.											KIF25,NS,carcinoma,-2,1	KIF25	75	1	0			c.G904A						PASS	.	G	,ILE/VAL	88,4318	73.6+/-111.7	0,88,2115	98.0	95.0	96.0		,904	3.2	0.3	6	dbSNP_134	96	0,8600		0,0,4300	yes	intron,missense	KIF25	NM_005355.3,NM_030615.2	,29	0,88,6415	AA,AG,GG		0.0,1.9973,0.6766	,probably-damaging	,302/385	168443315	88,12918	2203	4300	6503	SO:0001583	missense	3834	exon8			GCAGGCGTCCTGG	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.904G>A	6.37:g.168443315G>A	ENSP00000388878:p.Val302Ile	91.0	0.0	0		62.0	12.0	0.193548	NM_030615	O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	CCDS5305.1	14	0.00641025641025641	11	0.022357723577235773	3	0.008287292817679558	0	0.0	0	0.0	G	14.81	2.647615	0.47258	0.019973	0.0	ENSG00000125337	ENST00000443060;ENST00000354419	T;T	0.79454	-1.27;-1.27	4.13	3.24	0.37175	Kinesin, motor domain (3);	0.000000	0.64402	D	0.000002	D	0.84433	0.5471	M	0.87900	2.915	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.86005	0.1497	10	0.87932	D	0	-20.8353	9.7087	0.40231	0.1042:0.0:0.8958:0.0	.	302	Q9UIL4	KIF25_HUMAN	I	302	ENSP00000388878:V302I;ENSP00000346401:V302I	ENSP00000346401:V302I	V	+	1	0	KIF25	168186164	1.000000	0.71417	0.297000	0.24988	0.082000	0.17680	4.083000	0.57643	0.839000	0.34971	0.543000	0.68304	GTC	G|0.993;A|0.007	0.007	strong		0.647	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1		
PCDH17	27253	hgsc.bcm.edu	37	13	58209024	58209024	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr13:58209024G>A	ENST00000377918.3	+	1	2370	c.2344G>A	c.(2344-2346)Gtc>Atc	p.V782I		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	782					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CGCCATGAACGTCATGAACGT	0.597																																					p.V782I	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G2344A						PASS	.						106.0	99.0	102.0					13																	58209024		2203	4300	6503	SO:0001583	missense	27253	exon1			ATGAACGTCATGA	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.2344G>A	13.37:g.58209024G>A	ENSP00000367151:p.Val782Ile	58.0	0.0	0		41.0	5.0	0.121951	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.976644	0.34848	.	.	ENSG00000118946	ENST00000377918	T	0.53640	0.61	5.21	5.21	0.72293	.	0.055010	0.64402	D	0.000001	T	0.40272	0.1110	L	0.36672	1.1	0.46131	D	0.998881	B;B	0.23442	0.085;0.051	B;B	0.18263	0.021;0.011	T	0.15292	-1.0442	9	.	.	.	.	18.9482	0.92630	0.0:0.0:1.0:0.0	.	782;782	O14917-2;O14917	.;PCD17_HUMAN	I	782	ENSP00000367151:V782I	.	V	+	1	0	PCDH17	57107025	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.375000	0.79646	2.708000	0.92522	0.467000	0.42956	GTC	.	.	none		0.597	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
ITCH	83737	hgsc.bcm.edu	37	20	32996580	32996580	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr20:32996580G>A	ENST00000262650.6	+	4	330	c.194G>A	c.(193-195)tGg>tAg	p.W65*	ITCH_ENST00000535650.1_Intron|ITCH_ENST00000374864.4_Nonsense_Mutation_p.W65*			Q96J02	ITCH_HUMAN	itchy E3 ubiquitin protein ligase	65	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|defense response to virus (GO:0051607)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of defense response to virus (GO:0050687)|negative regulation of JNK cascade (GO:0046329)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of cell growth (GO:0001558)|regulation of protein deubiquitination (GO:0090085)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	CXCR chemokine receptor binding (GO:0045236)|ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(9)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(13)|skin(1)|upper_aerodigestive_tract(1)	36						AGTCCCAAGTGGAAGCAACCC	0.353																																					p.W65X		Atlas-SNP	.											.	ITCH	73	.	0			c.G194A						PASS	.						127.0	117.0	120.0					20																	32996580		2203	4300	6503	SO:0001587	stop_gained	83737	exon4			CCAAGTGGAAGCA	AF095745	CCDS13234.1, CCDS58768.1, CCDS58769.1	20q11.22	2014-09-17	2012-02-23		ENSG00000078747	ENSG00000078747			13890	protein-coding gene	gene with protein product		606409	"""itchy (mouse homolog) E3 ubiquitin protein ligase"", ""itchy E3 ubiquitin protein ligase homolog (mouse)"""			11318614	Standard	NM_001257137		Approved	AIP4	uc010geu.2	Q96J02	OTTHUMG00000032300	ENST00000262650.6:c.194G>A	20.37:g.32996580G>A	ENSP00000262650:p.Trp65*	151.0	0.0	0		105.0	10.0	0.0952381	NM_001257137	A6NEW4|B4E234|E1P5P3|F5H217|O43584|Q5QP37|Q5TEL0|Q96F66|Q9BY75|Q9H451|Q9H4U5	Nonsense_Mutation	SNP	ENST00000262650.6	37	CCDS58768.1	.	.	.	.	.	.	.	.	.	.	G	36	5.743412	0.96873	.	.	ENSG00000078747	ENST00000374864;ENST00000262650	.	.	.	5.24	5.24	0.73138	.	0.177655	0.53938	D	0.000057	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.4283	0.90617	0.0:0.0:1.0:0.0	.	.	.	.	X	65	.	ENSP00000262650:W65X	W	+	2	0	ITCH	32460241	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.385000	0.97223	2.464000	0.83262	0.655000	0.94253	TGG	.	.	none		0.353	ITCH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078783.2		
SFR1	119392	hgsc.bcm.edu	37	10	105883796	105883796	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:105883796G>A	ENST00000369727.3	+	3	479	c.460G>A	c.(460-462)Gct>Act	p.A154T	SFR1_ENST00000336358.5_Missense_Mutation_p.A216T|SFR1_ENST00000369729.3_Missense_Mutation_p.A141T	NM_001002759.1	NP_001002759.1	Q86XK3	SFR1_HUMAN	SWI5-dependent recombination repair 1	154					double-strand break repair via homologous recombination (GO:0000724)	nucleus (GO:0005634)|Swi5-Sfr1 complex (GO:0032798)											AAGATTAAACGCTGAAAAAGC	0.393																																					p.A154T		Atlas-SNP	.											MEIR5,NS,carcinoma,-2,1	.	.	1	0			c.G460A						PASS	.						44.0	46.0	45.0					10																	105883796		2203	4300	6503	SO:0001583	missense	119392	exon3			TTAAACGCTGAAA	BC020892	CCDS31279.1, CCDS31280.1	10q25.1	2013-10-11	2011-08-01	2011-08-01	ENSG00000156384	ENSG00000156384			29574	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 78"", ""MEI5 recombination repair protein homolog (S. cerevisiae)"""	C10orf78, MEIR5		21252223, 21779174, 20976249	Standard	NM_145247		Approved	MEI5, bA373N18.1, FLJ41960	uc001kxu.3	Q86XK3	OTTHUMG00000019000	ENST00000369727.3:c.460G>A	10.37:g.105883796G>A	ENSP00000358742:p.Ala154Thr	297.0	0.0	0		203.0	24.0	0.118227	NM_001002759	A8K569|B2RTV8|Q5JT39|Q5JT40|Q8WW47	Missense_Mutation	SNP	ENST00000369727.3	37	CCDS31279.1	.	.	.	.	.	.	.	.	.	.	G	14.40	2.524280	0.44866	.	.	ENSG00000156384	ENST00000369729;ENST00000369727;ENST00000336358	T;T;T	0.45276	0.95;0.94;0.9	5.72	2.67	0.31697	.	0.329743	0.32190	N	0.006447	T	0.18759	0.0450	N	0.08118	0	0.09310	N	0.999995	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.20739	-1.0266	10	0.17369	T	0.5	-5.8542	7.0584	0.25111	0.1524:0.2566:0.591:0.0	.	216;154	Q86XK3-2;Q86XK3	.;SFR1_HUMAN	T	141;154;216	ENSP00000358744:A141T;ENSP00000358742:A154T;ENSP00000338089:A216T	ENSP00000338089:A216T	A	+	1	0	SFR1	105873786	1.000000	0.71417	0.879000	0.34478	0.681000	0.39784	2.676000	0.46883	0.350000	0.24002	0.655000	0.94253	GCT	.	.	none		0.393	SFR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050191.1	NM_145247	
TAB3	257397	hgsc.bcm.edu	37	X	30873153	30873153	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:30873153G>T	ENST00000378933.1	-	3	806	c.629C>A	c.(628-630)cCa>cAa	p.P210Q	TAB3_ENST00000378928.1_5'Flank|TAB3-AS2_ENST00000445240.1_RNA|TAB3_ENST00000378932.2_Missense_Mutation_p.P210Q|TAB3_ENST00000288422.2_Missense_Mutation_p.P210Q|TAB3_ENST00000378930.3_Missense_Mutation_p.P210Q	NM_152787.3	NP_690000.2	Q8N5C8	TAB3_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 3	210	Pro-rich.				activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|skin(1)	27						TAAAGCTCTTGGTACAGTCTG	0.428																																					p.P210Q	Pancreas(164;1598 1985 29022 43301 49529)	Atlas-SNP	.											.	TAB3	82	.	0			c.C629A						PASS	.						74.0	67.0	69.0					X																	30873153		2202	4300	6502	SO:0001583	missense	257397	exon6			GCTCTTGGTACAG	AY331591	CCDS14226.1	Xp21.2	2010-02-05	2010-02-05	2010-02-05	ENSG00000157625	ENSG00000157625			30681	protein-coding gene	gene with protein product	"""TAK1 binding protein 3"""	300480	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 3"""	MAP3K7IP3		14633987, 14670075	Standard	XM_005274482		Approved		uc004dcj.3	Q8N5C8	OTTHUMG00000021329	ENST00000378933.1:c.629C>A	X.37:g.30873153G>T	ENSP00000368215:p.Pro210Gln	243.0	0.0	0		170.0	22.0	0.129412	NM_152787	A6NDD9|Q6VQR0	Missense_Mutation	SNP	ENST00000378933.1	37	CCDS14226.1	.	.	.	.	.	.	.	.	.	.	G	15.34	2.805702	0.50315	.	.	ENSG00000157625	ENST00000378933;ENST00000378930;ENST00000288422;ENST00000378932	D;D;D;D	0.91464	-2.85;-2.85;-2.85;-2.84	5.31	4.42	0.53409	.	0.000000	0.85682	D	0.000000	D	0.87625	0.6224	L	0.54323	1.7	0.58432	D	0.999996	B;B	0.33318	0.408;0.286	B;B	0.31101	0.124;0.058	D	0.87804	0.2627	10	0.51188	T	0.08	-3.3679	14.5534	0.68084	0.0:0.0:0.8535:0.1465	.	210;210	Q8N5C8-2;Q8N5C8	.;TAB3_HUMAN	Q	210	ENSP00000368215:P210Q;ENSP00000368212:P210Q;ENSP00000288422:P210Q;ENSP00000368214:P210Q	ENSP00000288422:P210Q	P	-	2	0	TAB3	30783074	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.915000	0.69973	2.219000	0.72066	0.600000	0.82982	CCA	.	.	none		0.428	TAB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056173.1	NM_152787	
ELOVL6	79071	hgsc.bcm.edu	37	4	111119485	111119485	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr4:111119485T>G	ENST00000394607.3	-	2	170	c.7A>C	c.(7-9)Atg>Ctg	p.M3L	ELOVL6_ENST00000506461.1_5'UTR|ELOVL6_ENST00000302274.3_Missense_Mutation_p.M3L			Q9H5J4	ELOV6_HUMAN	ELOVL fatty acid elongase 6	3					cellular lipid metabolic process (GO:0044255)|fatty acid elongation, saturated fatty acid (GO:0019367)|long-chain fatty acid biosynthetic process (GO:0042759)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	8				OV - Ovarian serous cystadenocarcinoma(123;0.00462)		AACACTGACATGTTCATTGGG	0.428																																					p.M3L		Atlas-SNP	.											.	ELOVL6	27	.	0			c.A7C						PASS	.						200.0	174.0	183.0					4																	111119485		2203	4300	6503	SO:0001583	missense	79071	exon2			CTGACATGTTCAT	AK027031	CCDS3690.1	4q25	2011-05-25	2011-05-25		ENSG00000170522	ENSG00000170522			15829	protein-coding gene	gene with protein product		611546	"""ELOVL family member 6, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"""			11567032	Standard	NM_024090		Approved	FLJ23378, MGC5487, LCE	uc003hzz.3	Q9H5J4	OTTHUMG00000132547	ENST00000394607.3:c.7A>C	4.37:g.111119485T>G	ENSP00000378105:p.Met3Leu	126.0	0.0	0		102.0	7.0	0.0686275	NM_001130721	Q4W5L0|Q8NCD1	Missense_Mutation	SNP	ENST00000394607.3	37	CCDS3690.1	.	.	.	.	.	.	.	.	.	.	T	16.99	3.274309	0.59649	.	.	ENSG00000170522	ENST00000394607;ENST00000302274;ENST00000506625;ENST00000503885	T;T	0.20200	2.09;2.09	5.68	5.68	0.88126	.	0.150731	0.64402	D	0.000016	T	0.14399	0.0348	N	0.19112	0.55	0.47511	D	0.999443	B	0.02656	0.0	B	0.01281	0.0	T	0.11131	-1.0600	10	0.16420	T	0.52	-11.0653	14.9246	0.70866	0.0:0.0:0.0:1.0	.	3	Q9H5J4	ELOV6_HUMAN	L	3	ENSP00000378105:M3L;ENSP00000304736:M3L	ENSP00000304736:M3L	M	-	1	0	ELOVL6	111338934	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.985000	0.76193	2.168000	0.68352	0.533000	0.62120	ATG	.	.	none		0.428	ELOVL6-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255748.1	NM_024090	
CDH11	1009	hgsc.bcm.edu	37	16	64981740	64981740	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:64981740G>T	ENST00000268603.4	-	13	2772	c.2157C>A	c.(2155-2157)gaC>gaA	p.D719E	CDH11_ENST00000394156.3_3'UTR|CDH11_ENST00000566827.1_Missense_Mutation_p.D593E	NM_001797.2	NP_001788.2	P55287	CAD11_HUMAN	cadherin 11, type 2, OB-cadherin (osteoblast)	719					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|corticospinal tract morphogenesis (GO:0021957)|homophilic cell adhesion (GO:0007156)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(19)|lung(40)|ovary(3)|prostate(3)|skin(2)|urinary_tract(2)	88		Ovarian(137;0.0973)		OV - Ovarian serous cystadenocarcinoma(108;0.205)		TGTTGATGAAGTCATCGACAT	0.527			T	USP6	aneurysmal bone cysts					TSP Lung(24;0.17)																											p.D719E		Atlas-SNP	.		Dom	yes		16	16q22.1	1009	"""cadherin 11, type 2, OB-cadherin (osteoblast)"""		M	.	CDH11	260	.	0			c.C2157A						PASS	.						120.0	110.0	114.0					16																	64981740		2203	4300	6503	SO:0001583	missense	1009	exon13			GATGAAGTCATCG	D21255	CCDS10803.1	16q21	2010-01-26			ENSG00000140937	ENSG00000140937		"""Cadherins / Major cadherins"""	1750	protein-coding gene	gene with protein product	"""OB-Cadherin"""	600023				9615235	Standard	NM_001797		Approved	OB, CAD11	uc002eoi.3	P55287	OTTHUMG00000137494	ENST00000268603.4:c.2157C>A	16.37:g.64981740G>T	ENSP00000268603:p.Asp719Glu	190.0	0.0	0		162.0	15.0	0.0925926	NM_001797	A8K5D6|A8MZC8|B7WP28|Q15065|Q15066|Q9UQ93|Q9UQ94	Missense_Mutation	SNP	ENST00000268603.4	37	CCDS10803.1	.	.	.	.	.	.	.	.	.	.	G	7.665	0.685808	0.14973	.	.	ENSG00000140937	ENST00000268603;ENST00000538390	T	0.76709	-1.04	6.02	2.6	0.31112	Cadherin, cytoplasmic domain (1);	0.000000	0.85682	D	0.000000	T	0.54679	0.1873	N	0.05012	-0.13	0.48135	D	0.999594	B	0.13594	0.008	B	0.24006	0.05	T	0.39961	-0.9588	10	0.18276	T	0.48	.	9.6097	0.39654	0.3055:0.0:0.6945:0.0	.	719	P55287	CAD11_HUMAN	E	719;702	ENSP00000268603:D719E	ENSP00000268603:D719E	D	-	3	2	CDH11	63539241	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.451000	0.52964	0.890000	0.36211	0.655000	0.94253	GAC	.	.	none		0.527	CDH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268755.1	NM_033664	
ITLN1	55600	hgsc.bcm.edu	37	1	160850422	160850422	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:160850422C>T	ENST00000326245.3	-	6	756	c.641G>A	c.(640-642)gGc>gAc	p.G214D	ITLN1_ENST00000487531.1_5'UTR	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	214	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			CTGGGCGTCGCCAAAATCATA	0.438																																					p.G214D		Atlas-SNP	.											ITLN1,caecum,carcinoma,+1,1	ITLN1	45	1	0			c.G641A						PASS	.						181.0	181.0	181.0					1																	160850422		2203	4300	6503	SO:0001583	missense	55600	exon6			GCGTCGCCAAAAT	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.641G>A	1.37:g.160850422C>T	ENSP00000323587:p.Gly214Asp	132.0	0.0	0		91.0	22.0	0.241758	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Missense_Mutation	SNP	ENST00000326245.3	37	CCDS1211.1	.	.	.	.	.	.	.	.	.	.	C	14.31	2.496243	0.44352	.	.	ENSG00000179914	ENST00000326245	T	0.20200	2.09	4.17	3.25	0.37280	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (1);	0.000000	0.64402	D	0.000005	T	0.41282	0.1152	M	0.91510	3.215	0.45194	D	0.998203	D	0.89917	1.0	D	0.97110	1.0	T	0.50866	-0.8777	10	0.87932	D	0	-11.3367	9.6915	0.40131	0.0:0.8959:0.0:0.1041	.	214	Q8WWA0	ITLN1_HUMAN	D	214	ENSP00000323587:G214D	ENSP00000323587:G214D	G	-	2	0	ITLN1	159117046	0.856000	0.29760	0.825000	0.32803	0.184000	0.23303	4.577000	0.60922	0.942000	0.37525	0.655000	0.94253	GGC	.	.	none		0.438	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
KLHDC4	54758	hgsc.bcm.edu	37	16	87748161	87748161	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr16:87748161C>T	ENST00000270583.5	-	8	836	c.778G>A	c.(778-780)Gac>Aac	p.D260N	KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Missense_Mutation_p.D203N|KLHDC4_ENST00000347925.5_Missense_Mutation_p.D229N	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	260										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		GTGCCCTTGTCCACGTCTTTC	0.567																																					p.D260N		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G778A						PASS	.						231.0	191.0	204.0					16																	87748161		2198	4300	6498	SO:0001583	missense	54758	exon8			CCTTGTCCACGTC	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.778G>A	16.37:g.87748161C>T	ENSP00000270583:p.Asp260Asn	169.0	0.0	0		138.0	7.0	0.0507246	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	.	.	.	.	.	.	.	.	.	.	C	19.36	3.812535	0.70912	.	.	ENSG00000104731	ENST00000270583;ENST00000316853;ENST00000347925;ENST00000353170	T;T;T	0.67698	-0.28;-0.28;-0.28	5.21	5.21	0.72293	Kelch-type beta propeller (1);	0.093608	0.64402	D	0.000001	D	0.84293	0.5440	M	0.89095	3.005	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.992	D;D;D;D	0.78314	0.991;0.991;0.971;0.925	D	0.85106	0.0960	10	0.38643	T	0.18	-18.2028	17.7521	0.88438	0.0:1.0:0.0:0.0	.	79;203;229;260	Q9UF94;Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;.;KLDC4_HUMAN	N	260;79;229;203	ENSP00000270583:D260N;ENSP00000325717:D229N;ENSP00000262530:D203N	ENSP00000270583:D260N	D	-	1	0	KLHDC4	86305662	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	7.012000	0.76366	2.427000	0.82271	0.561000	0.74099	GAC	.	.	none		0.567	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566	
INPP5B	3633	hgsc.bcm.edu	37	1	38355355	38355355	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:38355355G>A	ENST00000373026.1	-	8	911	c.911C>T	c.(910-912)tCc>tTc	p.S304F	INPP5B_ENST00000373024.3_Missense_Mutation_p.S224F|INPP5B_ENST00000373023.2_Missense_Mutation_p.S304F|INPP5B_ENST00000467066.1_5'Flank|INPP5B_ENST00000373027.1_Missense_Mutation_p.S60F|INPP5B_ENST00000458109.2_5'Flank			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	304					in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GATAGTGGAGGAGCGAACCAT	0.393																																					p.S224F		Atlas-SNP	.											.	INPP5B	76	.	0			c.C671T						PASS	.						157.0	146.0	149.0					1																	38355355		1845	4092	5937	SO:0001583	missense	3633	exon9			GTGGAGGAGCGAA	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.911C>T	1.37:g.38355355G>A	ENSP00000362117:p.Ser304Phe	177.0	0.0	0		122.0	6.0	0.0491803	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		.	.	.	.	.	.	.	.	.	.	G	18.95	3.732267	0.69189	.	.	ENSG00000204084	ENST00000373027;ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024	D;D;D;D	0.93488	-3.23;-3.11;-3.11;-3.07	5.85	5.85	0.93711	.	0.446945	0.25549	N	0.029904	D	0.96722	0.8930	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76071	0.987;0.983	D	0.96665	0.9492	10	0.87932	D	0	.	20.1731	0.98165	0.0:0.0:1.0:0.0	.	304;224	P32019;P32019-2	I5P2_HUMAN;.	F	60;304;304;304;224	ENSP00000362118:S60F;ENSP00000362114:S304F;ENSP00000362117:S304F;ENSP00000362115:S224F	ENSP00000362114:S304F	S	-	2	0	INPP5B	38127942	1.000000	0.71417	0.998000	0.56505	0.482000	0.33219	4.276000	0.58933	2.768000	0.95171	0.655000	0.94253	TCC	.	.	none		0.393	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
PRPF31	26121	hgsc.bcm.edu	37	19	54632434	54632434	+	Silent	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr19:54632434C>A	ENST00000321030.4	+	12	1498	c.1149C>A	c.(1147-1149)atC>atA	p.I383I	PRPF31_ENST00000391755.1_Silent_p.I377I|PRPF31_ENST00000419967.1_Silent_p.I383I	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	383					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)			breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCCCCTAGATCGAGGAGGACG	0.682																																					p.I383I		Atlas-SNP	.											.	PRPF31	48	.	0			c.C1149A						PASS	.						21.0	20.0	21.0					19																	54632434		2176	4259	6435	SO:0001819	synonymous_variant	26121	exon12			CTAGATCGAGGAG	AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"""PRP31 pre-mRNA processing factor 31 homolog (yeast)"", ""PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"""	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.1149C>A	19.37:g.54632434C>A		53.0	0.0	0		51.0	8.0	0.156863	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Silent	SNP	ENST00000321030.4	37	CCDS12879.1																																																																																			.	.	none		0.682	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2		
CYBB	1536	hgsc.bcm.edu	37	X	37663373	37663373	+	Nonsense_Mutation	SNP	A	A	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:37663373A>T	ENST00000378588.4	+	9	1208	c.1141A>T	c.(1141-1143)Aaa>Taa	p.K381*	CYBB_ENST00000536160.1_Nonsense_Mutation_p.K114*|CYBB_ENST00000545017.1_Nonsense_Mutation_p.K349*|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	381	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	AGATGCGTGGAAACTACCTAA	0.428																																					p.K381X		Atlas-SNP	.											.	CYBB	62	.	0			c.A1141T						PASS	.						66.0	61.0	63.0					X																	37663373		2202	4300	6502	SO:0001587	stop_gained	1536	exon9			GCGTGGAAACTAC	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"""Cytochrome b genes"""	2578	protein-coding gene	gene with protein product		300481	"""chronic granulomatous disease"""	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1141A>T	X.37:g.37663373A>T	ENSP00000367851:p.Lys381*	324.0	0.0	0		196.0	24.0	0.122449	NM_000397	A8K138|Q2PP16	Nonsense_Mutation	SNP	ENST00000378588.4	37	CCDS14242.1	.	.	.	.	.	.	.	.	.	.	A	39	7.610350	0.98387	.	.	ENSG00000165168	ENST00000378588;ENST00000545017;ENST00000536160	.	.	.	5.77	5.77	0.91146	.	0.042364	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.0692	0.72021	1.0:0.0:0.0:0.0	.	.	.	.	X	381;349;114	.	ENSP00000367851:K381X	K	+	1	0	CYBB	37548317	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	5.161000	0.64935	1.941000	0.56285	0.441000	0.28932	AAA	.	.	none		0.428	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1		
LYRM5	144363	hgsc.bcm.edu	37	12	25357062	25357062	+	Missense_Mutation	SNP	A	A	C	rs534127550	byFrequency	TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr12:25357062A>C	ENST00000381356.4	+	3	248	c.89A>C	c.(88-90)gAc>gCc	p.D30A	LYRM5_ENST00000556402.1_3'UTR|LYRM5_ENST00000556351.1_Missense_Mutation_p.D28A|LYRM5_ENST00000555711.1_Missense_Mutation_p.R36S|LYRM5_ENST00000557540.2_Missense_Mutation_p.D28A|LYRM5_ENST00000556885.1_Missense_Mutation_p.D28A|LYRM5_ENST00000554266.1_3'UTR|LYRM5_ENST00000553788.1_Intron|LYRM5_ENST00000556927.1_Missense_Mutation_p.D28A	NM_001001660.2	NP_001001660.2	Q6IPR1	LYRM5_HUMAN	LYR motif containing 5	30						mitochondrion (GO:0005739)				large_intestine(3)	3	all_cancers(2;4.75e-35)|all_epithelial(2;1.91e-37)|all_lung(3;1.07e-23)|Lung NSC(3;5.49e-23)|Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.0016)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;2.21e-21)|Epithelial(3;8.04e-19)|all cancers(3;2.26e-16)|STAD - Stomach adenocarcinoma(2;0.00138)			AAAGGAGCAGACTATTTTAAA	0.303																																					p.D30A		Atlas-SNP	.											.	LYRM5	10	.	0			c.A89C						PASS	.						28.0	25.0	26.0					12																	25357062		1786	4064	5850	SO:0001583	missense	144363	exon3			GAGCAGACTATTT	AK057730	CCDS53764.1	12p12.1	2006-09-19				ENSG00000205707		"""LYR motif containing"""	27052	protein-coding gene	gene with protein product							Standard	NM_001001660		Approved		uc001rgn.3	Q6IPR1		ENST00000381356.4:c.89A>C	12.37:g.25357062A>C	ENSP00000370761:p.Asp30Ala	260.0	0.0	0		194.0	26.0	0.134021	NM_001001660	J3KPI7	Missense_Mutation	SNP	ENST00000381356.4	37	CCDS53764.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.182|8.182	0.794003|0.794003	0.16327|0.16327	.|.	.|.	ENSG00000205707|ENSG00000205707	ENST00000557540;ENST00000381356;ENST00000556885;ENST00000556351;ENST00000556927;ENST00000556198|ENST00000555711	T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	0.179966|.	0.64402|.	D|.	0.000015|.	T|T	0.61451|0.61451	0.2348|0.2348	.|.	.|.	.|.	0.48135|0.48135	D|D	0.999595|0.999595	B;B|.	0.17268|.	0.001;0.021|.	B;B|.	0.18561|.	0.009;0.022|.	T|T	0.60954|0.60954	-0.7160|-0.7160	9|4	0.19590|.	T|.	0.45|.	.|.	9.8919|9.8919	0.41296|0.41296	0.9246:0.0:0.0753:0.0|0.9246:0.0:0.0753:0.0	.|.	28;28|.	Q6IPR1;G3V521|.	LYRM5_HUMAN;.|.	A|S	28;30;28;28;28;28|36	ENSP00000450584:D28A;ENSP00000370761:D30A;ENSP00000451494:D28A;ENSP00000452146:D28A;ENSP00000450443:D28A|.	ENSP00000370761:D30A|.	D|R	+|+	2|3	0|2	LYRM5|LYRM5	25248329|25248329	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	4.399000|4.399000	0.59703|0.59703	2.239000|2.239000	0.73571|0.73571	0.533000|0.533000	0.62120|0.62120	GAC|AGA	.	.	none		0.303	LYRM5-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001001660	
AMBRA1	55626	hgsc.bcm.edu	37	11	46419037	46419037	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr11:46419037T>C	ENST00000458649.2	-	18	4278	c.3860A>G	c.(3859-3861)gAc>gGc	p.D1287G	AMBRA1_ENST00000528950.1_Missense_Mutation_p.D1258G|AMBRA1_ENST00000298834.3_Missense_Mutation_p.D1227G|AMBRA1_ENST00000534300.1_Missense_Mutation_p.D1227G|AMBRA1_ENST00000533727.1_Missense_Mutation_p.D1168G|AMBRA1_ENST00000314845.3_Missense_Mutation_p.D1197G|AMBRA1_ENST00000426438.1_Missense_Mutation_p.D1258G			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1287					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		GCCTGCAGCGTCCCCCCTGCT	0.602																																					p.D1290G		Atlas-SNP	.											AMBRA1_ENST00000458649,bladder,carcinoma,0,2	AMBRA1	201	2	0			c.A3869G						scavenged	.						99.0	92.0	94.0					11																	46419037		2202	4299	6501	SO:0001583	missense	55626	exon20			GCAGCGTCCCCCC	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.3860A>G	11.37:g.46419037T>C	ENSP00000415327:p.Asp1287Gly	64.0	1.0	0.015625		50.0	6.0	0.12	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	T	3.583	-0.085189	0.07097	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000526545;ENST00000528950	T;T;T;T;T;T;T	0.71103	-0.39;-0.54;-0.13;-0.25;-0.13;-0.25;-0.25	4.22	4.22	0.49857	.	0.672381	0.14331	N	0.326324	T	0.49304	0.1549	N	0.08118	0	0.20196	N	0.999929	B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0	T	0.41680	-0.9495	10	0.66056	D	0.02	.	8.3457	0.32272	0.0:0.0907:0.0:0.9093	.	1287;1258;1227;1168;1290;1197	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	G	1197;1168;1227;1258;1227;1287;245;1258	ENSP00000318313:D1197G;ENSP00000433372:D1168G;ENSP00000431926:D1227G;ENSP00000410899:D1258G;ENSP00000298834:D1227G;ENSP00000415327:D1287G;ENSP00000433945:D1258G	ENSP00000298834:D1227G	D	-	2	0	AMBRA1	46375613	0.641000	0.27251	0.867000	0.34043	0.009000	0.06853	1.775000	0.38584	2.135000	0.66039	0.459000	0.35465	GAC	.	.	none		0.602	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
SORCS3	22986	hgsc.bcm.edu	37	10	106959775	106959775	+	Silent	SNP	C	C	T			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr10:106959775C>T	ENST00000369701.3	+	15	2255	c.2028C>T	c.(2026-2028)agC>agT	p.S676S	SORCS3_ENST00000369699.4_5'UTR	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	676					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		GCCACTTCAGCCTCCGCTCCG	0.502																																					p.S676S	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C2028T						PASS	.						112.0	100.0	104.0					10																	106959775		2203	4300	6503	SO:0001819	synonymous_variant	22986	exon15			CTTCAGCCTCCGC	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2028C>T	10.37:g.106959775C>T		91.0	0.0	0		81.0	9.0	0.111111	NM_014978	Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	CCDS7558.1																																																																																			.	.	none		0.502	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
ZNF496	84838	hgsc.bcm.edu	37	1	247492064	247492064	+	Silent	SNP	G	G	A	rs146066456		TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr1:247492064G>A	ENST00000294753.4	-	4	959	c.495C>T	c.(493-495)aaC>aaT	p.N165N	ZNF496_ENST00000366498.2_Silent_p.N165N	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	165					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			GGGCATCCTGGTTCTTTGCAA	0.627																																					p.N165N		Atlas-SNP	.											.	ZNF496	80	.	0			c.C495T						PASS	.						131.0	133.0	133.0					1																	247492064		2203	4300	6503	SO:0001819	synonymous_variant	84838	exon4			ATCCTGGTTCTTT	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.495C>T	1.37:g.247492064G>A		102.0	0.0	0		93.0	5.0	0.0537634	NM_032752	Q8TBS2	Silent	SNP	ENST00000294753.4	37	CCDS1631.1																																																																																			G|1.000;T|0.000	.	alt		0.627	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
IRS4	8471	hgsc.bcm.edu	37	X	107977810	107977810	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chrX:107977810C>A	ENST00000372129.2	-	1	1841	c.1765G>T	c.(1765-1767)Ggg>Tgg	p.G589W	RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA|RP6-24A23.6_ENST00000563887.1_5'Flank	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	589					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TTGCCCCCCCCAGAGTTCTTG	0.552																																					p.G589W		Atlas-SNP	.											.	IRS4	253	.	0			c.G1765T						PASS	.						165.0	171.0	169.0					X																	107977810		2203	4300	6503	SO:0001583	missense	8471	exon1			CCCCCCCAGAGTT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1765G>T	X.37:g.107977810C>A	ENSP00000361202:p.Gly589Trp	103.0	0.0	0		76.0	7.0	0.0921053	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	37	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	C	4.030	0.003029	0.07866	.	.	ENSG00000133124	ENST00000372129	T	0.36340	1.26	4.9	4.02	0.46733	.	0.343723	0.21762	N	0.069500	T	0.48677	0.1513	M	0.66939	2.045	0.09310	N	1	D	0.69078	0.997	P	0.58577	0.841	T	0.38286	-0.9668	10	0.62326	D	0.03	-4.4135	8.2031	0.31436	0.0:0.8871:0.0:0.1129	.	589	O14654	IRS4_HUMAN	W	589	ENSP00000361202:G589W	ENSP00000361202:G589W	G	-	1	0	IRS4	107864466	0.147000	0.22687	0.968000	0.41197	0.287000	0.27160	1.500000	0.35682	2.257000	0.74773	0.600000	0.82982	GGG	.	.	none		0.552	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
MYBL1	4603	hgsc.bcm.edu	37	8	67492515	67492515	+	Silent	SNP	A	A	G			TCGA-FA-A86F-01A-11D-A382-10	TCGA-FA-A86F-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	b8a8bb7b-4ae4-40f5-8d6e-e942b0288c71	c6136d19-d490-4585-bc8a-f8ee1c7d7906	g.chr8:67492515A>G	ENST00000522677.3	-	9	1364	c.954T>C	c.(952-954)acT>acC	p.T318T	MYBL1_ENST00000517885.1_Intron|MYBL1_ENST00000524176.2_Silent_p.T318T	NM_001080416.2|NM_001144755.1	NP_001073885.1|NP_001138227.1	P10243	MYBA_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 1	318	Negative regulatory domain. {ECO:0000250}.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|skin(1)	25			Epithelial(68;0.00211)|all cancers(69;0.00726)|OV - Ovarian serous cystadenocarcinoma(28;0.00989)|BRCA - Breast invasive adenocarcinoma(89;0.0938)			AAAACTCACTAGTGTGCTCGT	0.438																																					p.T318T		Atlas-SNP	.											.	MYBL1	73	.	0			c.T954C						PASS	.						72.0	71.0	71.0					8																	67492515		1917	4134	6051	SO:0001819	synonymous_variant	4603	exon9			CTCACTAGTGTGC	X13294	CCDS47867.1, CCDS55241.1	8q22	2013-07-09	2013-07-09		ENSG00000185697	ENSG00000185697			7547	protein-coding gene	gene with protein product		159405					Standard	XM_005251251		Approved	AMYB, A-myb	uc003xwj.3	P10243	OTTHUMG00000164559	ENST00000522677.3:c.954T>C	8.37:g.67492515A>G		116.0	0.0	0		87.0	6.0	0.0689655	NM_001080416	E7EW29|Q495F9	Silent	SNP	ENST00000522677.3	37	CCDS47867.1																																																																																			.	.	none		0.438	MYBL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379221.3	XM_034274	
