#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_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_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_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
CD1E	913	hgsc.bcm.edu	37	1	158325802	158325802	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr1:158325802G>A	ENST00000368167.3	+	4	1050	c.811G>A	c.(811-813)Gca>Aca	p.A271T	CD1E_ENST00000368154.1_Intron|CD1E_ENST00000452291.2_Missense_Mutation_p.A82T|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000368161.3_Intron|CD1E_ENST00000368166.3_Missense_Mutation_p.A82T|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368156.1_Missense_Mutation_p.A181T|CD1E_ENST00000444681.2_Missense_Mutation_p.A172T|CD1E_ENST00000434258.1_Missense_Mutation_p.A269T|CD1E_ENST00000368160.3_Missense_Mutation_p.A271T|CD1E_ENST00000368165.3_Missense_Mutation_p.A181T|CD1E_ENST00000368163.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	271	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					GTATCTCCGAGCAACCCTGGA	0.607																																					p.A271T		Atlas-SNP	.											.	CD1E	129	.	0			c.G811A						.						100.0	99.0	99.0					1																	158325802		2203	4300	6503	SO:0001583	missense	913	exon4			CTCCGAGCAACCC	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.811G>A	chr1.hg19:g.158325802G>A	ENSP00000357149:p.Ala271Thr	92.0	0.0		128.0	41.0	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	hg19	CCDS41417.1	.	.	.	.	.	.	.	.	.	.	G	16.79	3.220546	0.58560	.	.	ENSG00000158488	ENST00000434258;ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368160;ENST00000368156	T;T;T;T;T;T;T;T	0.02863	4.13;4.13;4.13;4.13;4.13;4.13;4.13;4.13	4.38	4.38	0.52667	Immunoglobulin-like (1);MHC class I-like antigen recognition (1);Immunoglobulin C1-set (2);	0.588914	0.14197	N	0.334970	T	0.05364	0.0142	L	0.60012	1.86	0.09310	N	1	P;D;D;P;P;D;P;P;P;B;D	0.61697	0.917;0.985;0.985;0.91;0.657;0.981;0.89;0.798;0.91;0.405;0.99	P;P;P;P;P;P;P;P;P;B;P	0.62885	0.908;0.841;0.841;0.688;0.688;0.851;0.456;0.561;0.688;0.357;0.851	T	0.15009	-1.0452	10	0.72032	D	0.01	-5.0189	12.3045	0.54893	0.0:0.0:1.0:0.0	.	82;172;269;271;172;181;82;271;271;82;181	B4E057;B4E042;E7ET31;A2RRL5;E7EP01;P15812-5;P15812-9;P15812-2;P15812;P15812-8;P15812-6	.;.;.;.;.;.;.;.;CD1E_HUMAN;.;.	T	269;172;271;82;181;82;271;181	ENSP00000401957:A269T;ENSP00000402906:A172T;ENSP00000357149:A271T;ENSP00000416228:A82T;ENSP00000357147:A181T;ENSP00000357148:A82T;ENSP00000357142:A271T;ENSP00000357138:A181T	ENSP00000357138:A181T	A	+	1	0	CD1E	156592426	0.045000	0.20229	0.006000	0.13384	0.565000	0.35776	2.831000	0.48144	2.277000	0.76020	0.563000	0.77884	GCA	.	.		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
NPHP1	4867	hgsc.bcm.edu	37	2	110959033	110959033	+	Silent	SNP	A	A	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr2:110959033A>G	ENST00000393272.3	-	2	205	c.108T>C	c.(106-108)gcT>gcC	p.A36A	NPHP1_ENST00000355301.4_Silent_p.A36A|NPHP1_ENST00000417665.1_Silent_p.A36A|NPHP1_ENST00000316534.4_Silent_p.A36A|NPHP1_ENST00000418527.1_Silent_p.A36A|NPHP1_ENST00000445609.2_Silent_p.A36A	NM_000272.3|NM_207181.2	NP_000263.2|NP_997064.2	O15259	NPHP1_HUMAN	nephronophthisis 1 (juvenile)	36					actin cytoskeleton organization (GO:0030036)|cell projection organization (GO:0030030)|cellular protein localization (GO:0034613)|excretion (GO:0007588)|photoreceptor cell outer segment organization (GO:0035845)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|spermatid differentiation (GO:0048515)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|motile cilium (GO:0031514)|photoreceptor connecting cilium (GO:0032391)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(10)|ovary(2)	24						TGGGTTCTAGAGCTTCTTTCA	0.313																																					p.A36A		Atlas-SNP	.											.	NPHP1	68	.	0			c.T108C						.						123.0	114.0	117.0					2																	110959033		2203	4300	6503	SO:0001819	synonymous_variant	4867	exon2			TTCTAGAGCTTCT	AF023674	CCDS2086.1, CCDS46384.1, CCDS46385.1, CCDS46386.1	2q13	2014-01-28			ENSG00000144061	ENSG00000144061			7905	protein-coding gene	gene with protein product	"""nephrocystin-1"""	607100		NPH1			Standard	NM_000272		Approved	JBTS4, SLSN1	uc002tfm.4	O15259	OTTHUMG00000131195	ENST00000393272.3:c.108T>C	chr2.hg19:g.110959033A>G		68.0	0.0		93.0	42.0	NM_207181	O14837	Silent	SNP	ENST00000393272.3	hg19	CCDS46385.1																																																																																			.	.		0.313	NPHP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253919.3	NM_000272	
ERBB4	2066	hgsc.bcm.edu	37	2	212615384	212615384	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr2:212615384G>T	ENST00000342788.4	-	5	912	c.602C>A	c.(601-603)aCa>aAa	p.T201K	ERBB4_ENST00000436443.1_Missense_Mutation_p.T201K|ERBB4_ENST00000402597.1_Missense_Mutation_p.T201K|ERBB4_ENST00000484474.1_5'UTR	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	201	Cys-rich.				cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.T201K(1)		NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	ATGATTTTCTGTGGGTCCCCA	0.458										TSP Lung(8;0.080)																											p.T201K		Atlas-SNP	.											ERBB4,NS,carcinoma,0,1	ERBB4	480	.	1	Substitution - Missense(1)	endometrium(1)	c.C602A						.						136.0	113.0	121.0					2																	212615384		2203	4300	6503	SO:0001583	missense	2066	exon5			TTTTCTGTGGGTC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.602C>A	chr2.hg19:g.212615384G>T	ENSP00000342235:p.Thr201Lys	32.0	0.0		51.0	24.0	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Missense_Mutation	SNP	ENST00000342788.4	hg19	CCDS2394.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.73|17.73	3.462532|3.462532	0.63513|0.63513	.|.	.|.	ENSG00000178568|ENSG00000178568	ENST00000260943|ENST00000342788;ENST00000436443;ENST00000402597	.|D;D;D	.|0.82081	.|-1.57;-1.57;-1.57	5.58|5.58	5.58|5.58	0.84498|0.84498	.|Growth factor, receptor (1);Furin-like cysteine-rich domain (1);	.|0.211367	.|0.49916	.|D	.|0.000132	T|T	0.69557|0.69557	0.3124|0.3124	N|N	0.08118|0.08118	0|0	0.43559|0.43559	D|D	0.995878|0.995878	.|B;B;B;B;B	.|0.06786	.|0.0;0.001;0.0;0.0;0.0	.|B;B;B;B;B	.|0.09377	.|0.001;0.004;0.001;0.001;0.0	T|T	0.64041|0.64041	-0.6500|-0.6500	5|9	.|.	.|.	.|.	.|.	19.6257|19.6257	0.95677|0.95677	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|201;201;60;201;201	.|Q15303-4;Q15303-2;Q53QS8;Q15303-3;Q15303	.|.;.;.;.;ERBB4_HUMAN	K|K	201|201	.|ENSP00000342235:T201K;ENSP00000403204:T201K;ENSP00000385565:T201K	.|.	Q|T	-|-	1|2	0|0	ERBB4|ERBB4	212323629|212323629	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.980000|0.980000	0.70556|0.70556	5.303000|5.303000	0.65738|0.65738	2.625000|2.625000	0.88918|0.88918	0.650000|0.650000	0.86243|0.86243	CAG|ACA	.	.		0.458	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
SATB1	6304	hgsc.bcm.edu	37	3	18456693	18456693	+	Silent	SNP	T	T	C	rs61733671		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:18456693T>C	ENST00000338745.6	-	5	2283	c.549A>G	c.(547-549)caA>caG	p.Q183Q	TBC1D5_ENST00000414318.2_Intron|SATB1_ENST00000454909.2_Silent_p.Q183Q|SATB1_ENST00000475083.1_5'UTR|SATB1_ENST00000417717.2_Silent_p.Q183Q	NM_002971.4	NP_002962.1	Q01826	SATB1_HUMAN	SATB homeobox 1	183	PDZ-like dimerization domain.				activated T cell proliferation (GO:0050798)|apoptotic process (GO:0006915)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|epidermis development (GO:0008544)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|reflex (GO:0060004)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(2)|endometrium(6)|large_intestine(4)|lung(10)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	32						TGTGCGACCATTGTTCGGGAG	0.448																																					p.Q183Q		Atlas-SNP	.											.	SATB1	96	.	0			c.A549G						.						114.0	103.0	107.0					3																	18456693		2203	4300	6503	SO:0001819	synonymous_variant	6304	exon5			CGACCATTGTTCG		CCDS2631.1, CCDS56242.1	3p24.3	2011-07-19	2007-02-15		ENSG00000182568	ENSG00000182568		"""Homeoboxes / CUT class"""	10541	protein-coding gene	gene with protein product		602075	"""special AT-rich sequence binding protein 1 (binds to nuclear matrix/scaffold-associating DNA)"""			1505028	Standard	NM_002971		Approved		uc003cbj.3	Q01826	OTTHUMG00000129890	ENST00000338745.6:c.549A>G	chr3.hg19:g.18456693T>C		104.0	0.0		105.0	41.0	NM_002971	B3KXF1|C9JTR6|Q59EQ0	Silent	SNP	ENST00000338745.6	hg19	CCDS2631.1																																																																																			.	T|0.987;C|0.013		0.448	SATB1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252138.4	NM_001131010	
NISCH	11188	hgsc.bcm.edu	37	3	52513791	52513791	+	Silent	SNP	A	A	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:52513791A>G	ENST00000479054.1	+	13	1401	c.1329A>G	c.(1327-1329)acA>acG	p.T443T	NISCH_ENST00000488380.1_Silent_p.T443T|NISCH_ENST00000345716.4_Silent_p.T443T|NISCH_ENST00000420808.2_Silent_p.T443T			Q9Y2I1	NISCH_HUMAN	nischarin	443	Interaction with PAK1. {ECO:0000250}.|Necessary for homooligomerization and targeting to endosomes.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	CAGTGACCACAGAGAAGGAGC	0.512																																					p.T443T		Atlas-SNP	.											.	NISCH	97	.	0			c.A1329G						.						84.0	66.0	72.0					3																	52513791		2203	4300	6503	SO:0001819	synonymous_variant	11188	exon12			GACCACAGAGAAG	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"""imidazoline receptor candidate"", ""I-1 receptor candidate protein"", ""imidazoline receptor antisera selected"""	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.1329A>G	chr3.hg19:g.52513791A>G		74.0	0.0		91.0	42.0	NM_001276293	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Silent	SNP	ENST00000479054.1	hg19	CCDS33767.1																																																																																			.	.		0.512	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184	
PTPRG	5793	hgsc.bcm.edu	37	3	61975392	61975392	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:61975392T>C	ENST00000474889.1	+	3	661	c.284T>C	c.(283-285)gTt>gCt	p.V95A	PTPRG_ENST00000295874.10_Missense_Mutation_p.V95A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	95	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		TATGCGCGTGTTGGGGAAGAA	0.493																																					p.V95A		Atlas-SNP	.											.	PTPRG	153	.	0			c.T284C						.						119.0	109.0	112.0					3																	61975392		2203	4300	6503	SO:0001583	missense	5793	exon3			CGCGTGTTGGGGA	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.284T>C	chr3.hg19:g.61975392T>C	ENSP00000418112:p.Val95Ala	81.0	0.0		88.0	37.0	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Missense_Mutation	SNP	ENST00000474889.1	hg19	CCDS2895.1	.	.	.	.	.	.	.	.	.	.	T	18.83	3.707702	0.68615	.	.	ENSG00000144724	ENST00000474889;ENST00000295874	T;T	0.67171	-0.25;-0.25	5.92	5.92	0.95590	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.359047	0.29300	N	0.012560	T	0.66934	0.2840	L	0.52011	1.625	0.52501	D	0.999954	P;P	0.44429	0.835;0.517	B;B	0.43889	0.435;0.226	T	0.71237	-0.4652	10	0.87932	D	0	.	16.3413	0.83082	0.0:0.0:0.0:1.0	.	95;95	P23470-2;P23470	.;PTPRG_HUMAN	A	95	ENSP00000418112:V95A;ENSP00000295874:V95A	ENSP00000295874:V95A	V	+	2	0	PTPRG	61950432	1.000000	0.71417	0.107000	0.21349	0.943000	0.58893	7.642000	0.83385	2.257000	0.74773	0.533000	0.62120	GTT	.	.		0.493	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
CEP70	80321	hgsc.bcm.edu	37	3	138219253	138219253	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:138219253G>A	ENST00000264982.3	-	15	1791	c.1525C>T	c.(1525-1527)Ctc>Ttc	p.L509F	CEP70_ENST00000542237.1_Missense_Mutation_p.L489F|CEP70_ENST00000489254.1_Missense_Mutation_p.L357F|CEP70_ENST00000481834.1_Missense_Mutation_p.L509F|CEP70_ENST00000484888.1_Missense_Mutation_p.L509F	NM_024491.2	NP_077817.2	Q8NHQ1	CEP70_HUMAN	centrosomal protein 70kDa	509					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(6)|skin(3)	24						AATTCTAAGAGTTCTTGGAGG	0.318																																					p.L509F		Atlas-SNP	.											.	CEP70	51	.	0			c.C1525T						.						100.0	112.0	108.0					3																	138219253		2203	4300	6503	SO:0001583	missense	80321	exon15			CTAAGAGTTCTTG	AF202146	CCDS3102.1, CCDS75022.1, CCDS75023.1, CCDS75024.1	3q22.3	2014-02-20			ENSG00000114107	ENSG00000114107			29972	protein-coding gene	gene with protein product		614310				14654843	Standard	XM_005247802		Approved	BITE, FLJ13036	uc003esl.3	Q8NHQ1	OTTHUMG00000159891	ENST00000264982.3:c.1525C>T	chr3.hg19:g.138219253G>A	ENSP00000264982:p.Leu509Phe	120.0	0.0		196.0	76.0	NM_024491	B7Z5I8|B7Z7E8|D3DNE9|F5GZX8|Q96B31|Q9H2C3|Q9H2Z1|Q9H940	Missense_Mutation	SNP	ENST00000264982.3	hg19	CCDS3102.1	.	.	.	.	.	.	.	.	.	.	G	16.36	3.100107	0.56183	.	.	ENSG00000114107	ENST00000264982;ENST00000542237;ENST00000489254;ENST00000484888;ENST00000474781;ENST00000481834	T;T;T;T;T;T	0.28255	1.62;1.62;1.62;1.62;1.62;1.62	4.88	3.93	0.45458	Tetratricopeptide repeat-containing (1);	0.326421	0.29838	N	0.011079	T	0.50103	0.1596	M	0.66939	2.045	0.42564	D	0.993153	D;P;D;P	0.69078	0.96;0.904;0.997;0.904	P;P;D;P	0.68192	0.663;0.625;0.956;0.625	T	0.52866	-0.8518	10	0.72032	D	0.01	-0.9042	12.1533	0.54062	0.0:0.0:0.8187:0.1813	.	357;489;509;509	B7Z2D2;F5GZX8;Q8NHQ1-2;Q8NHQ1	.;.;.;CEP70_HUMAN	F	509;489;357;509;491;509	ENSP00000264982:L509F;ENSP00000444128:L489F;ENSP00000417821:L357F;ENSP00000419231:L509F;ENSP00000419833:L491F;ENSP00000417465:L509F	ENSP00000264982:L509F	L	-	1	0	CEP70	139701943	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.310000	0.43708	2.552000	0.86080	0.655000	0.94253	CTC	.	.		0.318	CEP70-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000358001.1	NM_024491	
TFDP2	7029	hgsc.bcm.edu	37	3	141678612	141678613	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:141678612_141678613CC>AA	ENST00000489671.1	-	11	1384_1385	c.954_955GG>TT	c.(952-957)atGGga>atTTga	p.318_319MG>I*	TFDP2_ENST00000310282.6_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000397991.4_Nonsense_Mutation_p.290_291MG>I*|TFDP2_ENST00000479040.1_Nonsense_Mutation_p.257_258MG>I*|TFDP2_ENST00000499676.2_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000495310.1_Nonsense_Mutation_p.221_222MG>I*|TFDP2_ENST00000317104.7_Nonsense_Mutation_p.242_243MG>I*|TFDP2_ENST00000486111.1_Nonsense_Mutation_p.258_259MG>I*|TFDP2_ENST00000477292.1_Nonsense_Mutation_p.182_183MG>I*|TFDP2_ENST00000467072.1_Nonsense_Mutation_p.258_259MG>I*			Q14188	TFDP2_HUMAN	transcription factor Dp-2 (E2F dimerization partner 2)	318	DCB2.				gene expression (GO:0010467)|heart development (GO:0007507)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			kidney(1)|upper_aerodigestive_tract(2)	3						AACGACATTCCCATCCGCTTTA	0.421																																					p.G319X|p.M318I		Atlas-SNP	.											.	TFDP2	44	.	0			c.G955T|c.G954T						.																																			SO:0001587	stop_gained	7029	exon11			ACATTCCCATCCG|CATTCCCATCCGC	U18422	CCDS43159.1, CCDS54647.1, CCDS54648.1, CCDS54649.1, CCDS54650.1	3q23	2011-05-24			ENSG00000114126	ENSG00000114126			11751	protein-coding gene	gene with protein product		602160				7784053, 9027491	Standard	NM_001178138		Approved	Dp-2	uc003eun.4	Q14188	OTTHUMG00000164975	ENST00000489671.1:c.954_955delinsAA	chr3.hg19:g.141678612_141678613delinsAA	ENSP00000420616:p.M318_G319delinsI*	68.0|71.0	0.0		60.0	26.0|28.0	NM_001178139	B7Z8C8|B7Z8L5|D3DNG1|E9PFC3|F8WAI2|Q13331|Q14187|Q6R754|Q8WU88|Q9UG28	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000489671.1	hg19	CCDS54650.1																																																																																			.	.		0.421	TFDP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000353294.4	NM_006286	
SUCNR1	56670	hgsc.bcm.edu	37	3	151598552	151598552	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:151598552G>T	ENST00000362032.5	+	3	326	c.221G>T	c.(220-222)tGc>tTc	p.C74F	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	74						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	GCTTTTCTGTGCACCCTCCCC	0.423																																					p.C74F		Atlas-SNP	.											.	SUCNR1	31	.	0			c.G221T						.						152.0	149.0	150.0					3																	151598552		2203	4300	6503	SO:0001583	missense	56670	exon3			TTCTGTGCACCCT	AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"""GPCR / Class A : Orphans"""	4542	protein-coding gene	gene with protein product		606381	"""G protein-coupled receptor 91"""	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.221G>T	chr3.hg19:g.151598552G>T	ENSP00000355156:p.Cys74Phe	142.0	0.0		162.0	59.0	NM_033050	A8K305|Q8TDQ8	Missense_Mutation	SNP	ENST00000362032.5	hg19	CCDS3162.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.603049	0.28534	.	.	ENSG00000198829	ENST00000362032	T	0.35789	1.29	5.26	5.26	0.73747	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.50548	0.1622	L	0.33624	1.015	0.47441	D	0.999423	D	0.76494	0.999	D	0.79784	0.993	T	0.39603	-0.9606	10	0.34782	T	0.22	.	19.2413	0.93886	0.0:0.0:1.0:0.0	.	74	Q9BXA5	SUCR1_HUMAN	F	74	ENSP00000355156:C74F	ENSP00000355156:C74F	C	+	2	0	SUCNR1	153081242	1.000000	0.71417	0.999000	0.59377	0.058000	0.15608	4.301000	0.59086	2.625000	0.88918	0.655000	0.94253	TGC	.	.		0.423	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050	
PIK3CA	5290	hgsc.bcm.edu	37	3	178916692	178916692	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr3:178916692C>A	ENST00000263967.3	+	2	236	c.79C>A	c.(79-81)Cca>Aca	p.P27T		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	27	PI3K-ABD. {ECO:0000255|PROSITE- ProRule:PRU00877}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|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)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)			NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGTTTACTACCAAATGGAAT	0.413		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.P27T	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	.	PIK3CA	8460	.	0			c.C79A						.						67.0	66.0	66.0					3																	178916692		1853	4089	5942	SO:0001583	missense	5290	exon2			TTACTACCAAATG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.79C>A	chr3.hg19:g.178916692C>A	ENSP00000263967:p.Pro27Thr	74.0	0.0		80.0	38.0	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	hg19	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.364380	0.82463	.	.	ENSG00000121879	ENST00000263967;ENST00000468036	D;D	0.91740	-1.97;-2.9	5.28	5.28	0.74379	.	0.000000	0.85682	D	0.000000	D	0.96516	0.8863	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96326	0.9240	9	.	.	.	-18.5061	19.267	0.93990	0.0:1.0:0.0:0.0	.	27	P42336	PK3CA_HUMAN	T	27	ENSP00000263967:P27T;ENSP00000417479:P27T	.	P	+	1	0	PIK3CA	180399386	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.394000	0.79862	2.616000	0.88540	0.650000	0.86243	CCA	.	.		0.413	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
SHROOM3	57619	hgsc.bcm.edu	37	4	77357245	77357245	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr4:77357245A>G	ENST00000296043.6	+	1	993	c.40A>G	c.(40-42)Aca>Gca	p.T14A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	14					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			GCCTAGTGCCACATTAAACTC	0.483																																					p.T14A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.A40G						.						174.0	167.0	170.0					4																	77357245		2203	4300	6503	SO:0001583	missense	57619	exon1			AGTGCCACATTAA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.40A>G	chr4.hg19:g.77357245A>G	ENSP00000296043:p.Thr14Ala	109.0	0.0		88.0	42.0	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Missense_Mutation	SNP	ENST00000296043.6	hg19	CCDS3579.2	.	.	.	.	.	.	.	.	.	.	A	15.25	2.778445	0.49786	.	.	ENSG00000138771	ENST00000296043	T	0.19532	2.14	5.12	-1.69	0.08186	.	1.822020	0.02688	N	0.110299	T	0.11239	0.0274	N	0.16478	0.41	0.09310	N	1	B	0.21452	0.056	B	0.12156	0.007	T	0.21449	-1.0245	10	0.41790	T	0.15	-1.3602	0.3518	0.00350	0.307:0.1287:0.2417:0.3227	.	14	Q8TF72	SHRM3_HUMAN	A	14	ENSP00000296043:T14A	ENSP00000296043:T14A	T	+	1	0	SHROOM3	77576269	0.009000	0.17119	0.182000	0.23118	0.004000	0.04260	-0.211000	0.09332	-0.122000	0.11766	-0.334000	0.08254	ACA	.	.		0.483	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
SDHA	6389	hgsc.bcm.edu	37	5	240575	240575	+	Missense_Mutation	SNP	G	G	T	rs192818312		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr5:240575G>T	ENST00000264932.6	+	11	1650	c.1535G>T	c.(1534-1536)cGa>cTa	p.R512L	SDHA_ENST00000510361.1_Missense_Mutation_p.R464L|SDHA_ENST00000504309.1_Missense_Mutation_p.R512L	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	512					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	TCGGAACTGCGACTCAGCATG	0.458									Familial Paragangliomas																												p.R512L		Atlas-SNP	.											.	SDHA	80	.	0			c.G1535T						.						46.0	51.0	50.0					5																	240575		2202	4299	6501	SO:0001583	missense	6389	exon11	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	AACTGCGACTCAG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1535G>T	chr5.hg19:g.240575G>T	ENSP00000264932:p.Arg512Leu	176.0	0.0		157.0	67.0	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Missense_Mutation	SNP	ENST00000264932.6	hg19	CCDS3853.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	N|N	18.62|18.62	3.662639|3.662639	0.67700|0.67700	.|.	.|.	ENSG00000073578|ENSG00000073578	ENST00000515815|ENST00000264932;ENST00000327872;ENST00000504309;ENST00000510361	.|D;T;D	.|0.83250	.|-1.7;-0.15;-1.7	4.95|4.95	4.95|4.95	0.65309|0.65309	.|Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal (2);Fumarate reductase/succinate dehydrogenase flavoprotein, C-terminal (1);	.|0.000000	.|0.85682	.|U	.|0.000000	D|D	0.93903|0.93903	0.8049|0.8049	H|H	0.96048|0.96048	3.76|3.76	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.89917	.|1.0;0.998;1.0;1.0;1.0	.|D;D;D;D;D	.|0.97110	.|0.998;0.97;1.0;0.985;0.991	D|D	0.95671|0.95671	0.8723|0.8723	5|10	.|0.87932	.|D	.|0	.|.	16.0271|16.0271	0.80551|0.80551	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|464;512;106;512;512	.|E9PBJ5;B4DYN5;B3KYA5;D6RFM5;P31040	.|.;.;.;.;DHSA_HUMAN	Y|L	64|512;367;512;464	.|ENSP00000264932:R512L;ENSP00000426514:R512L;ENSP00000427703:R464L	.|ENSP00000264932:R512L	D|R	+|+	1|2	0|0	SDHA|SDHA	293575|293575	1.000000|1.000000	0.71417|0.71417	0.446000|0.446000	0.26920|0.26920	0.521000|0.521000	0.34408|0.34408	9.240000|9.240000	0.95396|0.95396	2.442000|2.442000	0.82660|0.82660	0.650000|0.650000	0.86243|0.86243	GAC|CGA	.	G|0.999;A|0.001		0.458	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
GABRB2	2561	hgsc.bcm.edu	37	5	160972296	160972296	+	Silent	SNP	G	G	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr5:160972296G>A	ENST00000393959.1	-	3	173	c.174C>T	c.(172-174)ccC>ccT	p.P58P	GABRB2_ENST00000517901.1_5'UTR|GABRB2_ENST00000517547.1_5'UTR|GABRB2_ENST00000523730.1_5'Flank|GABRB2_ENST00000353437.6_Silent_p.P58P|GABRB2_ENST00000274547.2_Silent_p.P58P|GABRB2_ENST00000520240.1_Silent_p.P58P			P47870	GBRB2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 2	58					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|GABA-A receptor activity (GO:0004890)|inhibitory extracellular ligand-gated ion channel activity (GO:0005237)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	26	Renal(175;0.00259)	Medulloblastoma(196;0.021)|all_neural(177;0.0463)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	CAGCCACGGGGGGACCTGCAA	0.453																																					p.P58P		Atlas-SNP	.											.	GABRB2	161	.	0			c.C174T						.						55.0	49.0	51.0					5																	160972296		2203	4300	6503	SO:0001819	synonymous_variant	2561	exon4			CACGGGGGGACCT		CCDS4354.1, CCDS4355.1	5q34	2012-06-22			ENSG00000145864	ENSG00000145864		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4082	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 2"""	600232				7851879	Standard	NM_000813		Approved		uc003lys.1	P47870	OTTHUMG00000130349	ENST00000393959.1:c.174C>T	chr5.hg19:g.160972296G>A		53.0	0.0		60.0	26.0	NM_021911	A8K115|A8K1A0|D1LYT0|D1LYT1|Q16323|Q4FZB2	Silent	SNP	ENST00000393959.1	hg19	CCDS4355.1																																																																																			.	.		0.453	GABRB2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252704.1		
CAP2	10486	hgsc.bcm.edu	37	6	17463259	17463259	+	Silent	SNP	G	G	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr6:17463259G>A	ENST00000229922.2	+	4	787	c.255G>A	c.(253-255)caG>caA	p.Q85Q	CAP2_ENST00000489374.1_Silent_p.Q85Q|CAP2_ENST00000493172.1_Intron|CAP2_ENST00000465994.1_Silent_p.Q85Q|CAP2_ENST00000378990.2_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	85					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TCCAGGCCCAGCGGGCTTTCC	0.502																																					p.Q85Q		Atlas-SNP	.											.	CAP2	61	.	0			c.G255A						.						90.0	82.0	84.0					6																	17463259		2203	4300	6503	SO:0001819	synonymous_variant	10486	exon4			GGCCCAGCGGGCT	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.255G>A	chr6.hg19:g.17463259G>A		49.0	0.0		64.0	34.0	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	hg19	CCDS4539.1																																																																																			.	.		0.502	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
ZNF804B	219578	hgsc.bcm.edu	37	7	88963115	88963115	+	Silent	SNP	A	A	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr7:88963115A>G	ENST00000333190.4	+	4	1428	c.819A>G	c.(817-819)acA>acG	p.T273T		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	273							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATAAAGATACACACCTTACCA	0.358										HNSCC(36;0.09)																											p.T273T		Atlas-SNP	.											.	ZNF804B	322	.	0			c.A819G						.						73.0	69.0	70.0					7																	88963115		2202	4300	6502	SO:0001819	synonymous_variant	219578	exon4			AGATACACACCTT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.819A>G	chr7.hg19:g.88963115A>G		119.0	0.0		109.0	54.0	NM_181646	B2RTV2|Q7Z714|Q96MN7	Silent	SNP	ENST00000333190.4	hg19	CCDS5613.1																																																																																			.	.		0.358	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
ARHGEF39	84904	hgsc.bcm.edu	37	9	35662720	35662720	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr9:35662720T>A	ENST00000378387.3	-	7	809	c.692A>T	c.(691-693)cAg>cTg	p.Q231L	ARHGEF39_ENST00000490970.1_5'UTR|ARHGEF39_ENST00000378395.2_Missense_Mutation_p.Q195L|ARHGEF39_ENST00000343259.3_Intron	NM_032818.2	NP_116207.2	Q8N4T4	ARG39_HUMAN	Rho guanine nucleotide exchange factor (GEF) 39	231	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of cell migration (GO:0030335)	plasma membrane (GO:0005886)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)										CAGCCAGCCCTGGCGTAGGAA	0.592																																					p.Q231L		Atlas-SNP	.											.	.	.	.	0			c.A692T						.						13.0	14.0	13.0					9																	35662720		2183	4256	6439	SO:0001583	missense	84904	exon7			CAGCCCTGGCGTA	AK001187	CCDS6584.2	9p13.3	2012-08-08	2012-08-08	2012-08-08	ENSG00000137135	ENSG00000137135			25909	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 100"""	C9orf100		22327280	Standard	XR_242516		Approved	FLJ14642	uc003zxm.1	Q8N4T4	OTTHUMG00000019869	ENST00000378387.3:c.692A>T	chr9.hg19:g.35662720T>A	ENSP00000367638:p.Gln231Leu	57.0	0.0		94.0	34.0	NM_032818	Q49AG0|Q6TPQ2|Q96ST6	Missense_Mutation	SNP	ENST00000378387.3	hg19	CCDS6584.2	.	.	.	.	.	.	.	.	.	.	T	24.1	4.498025	0.85069	.	.	ENSG00000137135	ENST00000378387;ENST00000378395	T;T	0.44881	0.91;0.91	5.94	5.94	0.96194	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.050478	0.85682	D	0.000000	T	0.41903	0.1179	L	0.44542	1.39	0.80722	D	1	D	0.54207	0.965	P	0.46758	0.526	T	0.29671	-1.0004	10	0.45353	T	0.12	-26.927	12.7916	0.57537	0.0:0.0:0.0:1.0	.	231	Q8N4T4	CI100_HUMAN	L	231;195	ENSP00000367638:Q231L;ENSP00000367648:Q195L	ENSP00000367638:Q231L	Q	-	2	0	C9orf100	35652720	1.000000	0.71417	0.998000	0.56505	0.923000	0.55619	5.581000	0.67471	2.275000	0.75901	0.528000	0.53228	CAG	.	.		0.592	ARHGEF39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052330.1	NM_032818	
COL15A1	1306	hgsc.bcm.edu	37	9	101778304	101778304	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr9:101778304C>T	ENST00000375001.3	+	11	1973	c.1550C>T	c.(1549-1551)cCc>cTc	p.P517L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	517	4 X tandem repeats.|Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				ACAGAGGAGCCCCTCATCACA	0.592																																					p.P517L		Atlas-SNP	.											.	COL15A1	211	.	0			c.C1550T						.						44.0	45.0	45.0					9																	101778304		2203	4300	6503	SO:0001583	missense	1306	exon11			AGGAGCCCCTCAT	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.1550C>T	chr9.hg19:g.101778304C>T	ENSP00000364140:p.Pro517Leu	34.0	0.0		51.0	30.0	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	hg19	CCDS35081.1	.	.	.	.	.	.	.	.	.	.	C	11.19	1.567139	0.28003	.	.	ENSG00000204291	ENST00000375001;ENST00000536083	D	0.90955	-2.76	3.1	3.1	0.35709	.	.	.	.	.	D	0.84356	0.5454	L	0.46157	1.445	0.18873	N	0.999984	P	0.37781	0.608	B	0.29862	0.108	T	0.74902	-0.3506	9	0.34782	T	0.22	-0.6635	9.8268	0.40916	0.0:1.0:0.0:0.0	.	517	P39059	COFA1_HUMAN	L	517;487	ENSP00000364140:P517L	ENSP00000364140:P517L	P	+	2	0	COL15A1	100818125	0.000000	0.05858	0.005000	0.12908	0.024000	0.10985	0.321000	0.19558	1.736000	0.51660	0.650000	0.86243	CCC	.	.		0.592	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
HK1	3098	hgsc.bcm.edu	37	10	71148962	71148962	+	Silent	SNP	C	C	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr10:71148962C>T	ENST00000359426.6	+	14	2049	c.1945C>T	c.(1945-1947)Ctg>Ttg	p.L649L	HK1_ENST00000298649.3_Silent_p.L648L|HK1_ENST00000404387.2_Silent_p.L653L|HK1_ENST00000360289.2_Silent_p.L637L|HK1_ENST00000448642.2_Silent_p.L684L	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	649	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						GGAATTTGACCTGGACGTGGT	0.517																																					p.L653L		Atlas-SNP	.											.	HK1	170	.	0			c.C1957T						.						169.0	129.0	143.0					10																	71148962		2203	4300	6503	SO:0001819	synonymous_variant	3098	exon17			TTTGACCTGGACG	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1945C>T	chr10.hg19:g.71148962C>T		162.0	0.0		57.0	46.0	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	hg19	CCDS7292.1																																																																																			.	.		0.517	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
HIPK3	10114	hgsc.bcm.edu	37	11	33358704	33358704	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:33358704A>T	ENST00000303296.4	+	4	1610	c.1305A>T	c.(1303-1305)aaA>aaT	p.K435N	HIPK3_ENST00000525975.1_Missense_Mutation_p.K435N|HIPK3_ENST00000379016.3_Missense_Mutation_p.K435N|HIPK3_ENST00000534262.1_3'UTR|HIPK3_ENST00000456517.1_Missense_Mutation_p.K435N	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	435	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TTTTTTGCAAAGAAACAGATA	0.313																																					p.K435N		Atlas-SNP	.											.	HIPK3	92	.	0			c.A1305T						.						66.0	67.0	67.0					11																	33358704		2201	4295	6496	SO:0001583	missense	10114	exon4			TTGCAAAGAAACA	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"""homeodomain-interacting protein kinase 3"""			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1305A>T	chr11.hg19:g.33358704A>T	ENSP00000304226:p.Lys435Asn	57.0	0.0		72.0	33.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.552904	0.45487	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.20332	2.08;2.08;2.08;2.08	4.88	2.53	0.30540	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.090432	0.48286	D	0.000187	T	0.12475	0.0303	N	0.20845	0.615	0.38943	D	0.958193	B;B	0.15141	0.008;0.012	B;B	0.22152	0.022;0.038	T	0.09143	-1.0688	10	0.87932	D	0	.	5.5243	0.16949	0.7032:0.1447:0.1521:0.0	.	435;435	Q9H422-2;Q9H422	.;HIPK3_HUMAN	N	435	ENSP00000431710:K435N;ENSP00000304226:K435N;ENSP00000368301:K435N;ENSP00000398241:K435N	ENSP00000304226:K435N	K	+	3	2	HIPK3	33315280	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.372000	0.52387	0.302000	0.22762	-0.371000	0.07208	AAA	.	.		0.313	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734	
HIPK3	10114	hgsc.bcm.edu	37	11	33358706	33358706	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:33358706A>C	ENST00000303296.4	+	4	1612	c.1307A>C	c.(1306-1308)gAa>gCa	p.E436A	HIPK3_ENST00000525975.1_Missense_Mutation_p.E436A|HIPK3_ENST00000379016.3_Missense_Mutation_p.E436A|HIPK3_ENST00000534262.1_3'UTR|HIPK3_ENST00000456517.1_Missense_Mutation_p.E436A	NM_005734.3	NP_005725.3	Q9H422	HIPK3_HUMAN	homeodomain interacting protein kinase 3	436	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|mRNA transcription (GO:0009299)|negative regulation of apoptotic process (GO:0043066)|negative regulation of JUN kinase activity (GO:0043508)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(3)|kidney(3)|large_intestine(9)|liver(4)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	39						TTTTGCAAAGAAACAGATATG	0.308																																					p.E436A		Atlas-SNP	.											.	HIPK3	92	.	0			c.A1307C						.						65.0	66.0	65.0					11																	33358706		2201	4295	6496	SO:0001583	missense	10114	exon4			GCAAAGAAACAGA	AF004849	CCDS7884.1, CCDS41634.1	11p13	2008-07-18	2001-11-29		ENSG00000110422	ENSG00000110422			4915	protein-coding gene	gene with protein product		604424	"""homeodomain-interacting protein kinase 3"""			9373137, 9748262	Standard	NM_005734		Approved	PKY, DYRK6, YAK1, FIST3	uc031pzm.1	Q9H422	OTTHUMG00000132269	ENST00000303296.4:c.1307A>C	chr11.hg19:g.33358706A>C	ENSP00000304226:p.Glu436Ala	56.0	0.0		71.0	32.0	NM_001048200	O14632|Q2PBG4|Q2PBG5|Q92632|Q9HAS2	Missense_Mutation	SNP	ENST00000303296.4	hg19	CCDS7884.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.782867	0.70222	.	.	ENSG00000110422	ENST00000525975;ENST00000303296;ENST00000379016;ENST00000456517	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	4.88	4.88	0.63580	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000013	T	0.16342	0.0393	N	0.20986	0.625	0.80722	D	1	B;P	0.35527	0.198;0.507	B;B	0.34346	0.171;0.18	T	0.05767	-1.0865	10	0.72032	D	0.01	.	14.7855	0.69800	1.0:0.0:0.0:0.0	.	436;436	Q9H422-2;Q9H422	.;HIPK3_HUMAN	A	436	ENSP00000431710:E436A;ENSP00000304226:E436A;ENSP00000368301:E436A;ENSP00000398241:E436A	ENSP00000304226:E436A	E	+	2	0	HIPK3	33315282	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.426000	0.80270	1.952000	0.56665	0.460000	0.39030	GAA	.	.		0.308	HIPK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255358.1	NM_005734	
AHNAK	79026	hgsc.bcm.edu	37	11	62290411	62290411	+	Silent	SNP	C	C	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:62290411C>A	ENST00000378024.4	-	5	11752	c.11478G>T	c.(11476-11478)gtG>gtT	p.V3826V	AHNAK_ENST00000257247.7_Intron|AHNAK_ENST00000530124.1_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3826					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TGGGCAGGTTCACATCCACAT	0.522																																					p.V3826V		Atlas-SNP	.											.	AHNAK	532	.	0			c.G11478T						.						196.0	204.0	201.0					11																	62290411		2202	4296	6498	SO:0001819	synonymous_variant	79026	exon5			CAGGTTCACATCC	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.11478G>T	chr11.hg19:g.62290411C>A		71.0	0.0		81.0	34.0	NM_001620	A1A586	Silent	SNP	ENST00000378024.4	hg19	CCDS31584.1																																																																																			.	.		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
VPS51	738	hgsc.bcm.edu	37	11	64878964	64878964	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:64878964C>G	ENST00000279281.3	+	10	2346	c.2254C>G	c.(2254-2256)Ctg>Gtg	p.L752V	VPS51_ENST00000527646.1_3'UTR|AP003068.9_ENST00000528887.1_RNA|TM7SF2_ENST00000279263.7_5'Flank|TM7SF2_ENST00000345348.5_5'Flank|TM7SF2_ENST00000540748.1_5'Flank	NM_013265.2	NP_037397.2	Q9UID3	VPS51_HUMAN	vacuolar protein sorting 51 homolog (S. cerevisiae)	752					autophagy (GO:0006914)|lipid transport (GO:0006869)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											CGTGCACTTGCTGCTGGACGA	0.632																																					p.L752V		Atlas-SNP	.											.	.	.	.	0			c.C2254G						.						115.0	85.0	95.0					11																	64878964		2201	4297	6498	SO:0001583	missense	738	exon10			CACTTGCTGCTGG	AF024631	CCDS8093.1	11q13.1	2012-07-19	2012-07-19	2012-07-19	ENSG00000149823	ENSG00000149823			1172	protein-coding gene	gene with protein product	"""fat-free homolog (zebrafish)"""	615738	"""chromosome 11 open reading frame 3"", ""chromosome 11 open reading frame 2"""	C11orf3, C11orf2		9286704, 20685960	Standard	NM_013265		Approved	ANG2, ANG3, FFR	uc001ocr.2	Q9UID3	OTTHUMG00000165600	ENST00000279281.3:c.2254C>G	chr11.hg19:g.64878964C>G	ENSP00000279281:p.Leu752Val	83.0	0.0		73.0	28.0	NM_013265	Q6PJV5|Q7L8A6|Q8WZ35|Q96DF4|Q96GR3	Missense_Mutation	SNP	ENST00000279281.3	hg19	CCDS8093.1	.	.	.	.	.	.	.	.	.	.	C	17.45	3.393038	0.62066	.	.	ENSG00000149823	ENST00000279281	.	.	.	5.05	5.05	0.67936	.	0.000000	0.64402	D	0.000001	T	0.80423	0.4620	M	0.83692	2.655	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.81959	-0.0694	9	0.52906	T	0.07	-13.1403	16.005	0.80357	0.0:1.0:0.0:0.0	.	752	Q9UID3	FFR_HUMAN	V	752	.	ENSP00000279281:L752V	L	+	1	2	C11orf2	64635540	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	2.909000	0.48758	2.647000	0.89833	0.555000	0.69702	CTG	.	.		0.632	VPS51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385217.1	NM_013265	
TMEM218	219854	hgsc.bcm.edu	37	11	124972140	124972140	+	5'UTR	SNP	C	C	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr11:124972140C>T	ENST00000279968.4	-	0	321				TMEM218_ENST00000527766.1_5'UTR|TMEM218_ENST00000532407.1_5'UTR|TMEM218_ENST00000529609.1_5'UTR|TMEM218_ENST00000532156.1_5'UTR|TMEM218_ENST00000528724.1_5'UTR|TMEM218_ENST00000455225.1_5'UTR|TMEM218_ENST00000526175.1_5'UTR|TMEM218_ENST00000529583.1_5'UTR|TMEM218_ENST00000531262.1_Intron|TMEM218_ENST00000527271.1_5'UTR|TMEM218_ENST00000531909.1_5'UTR			A2RU14	TM218_HUMAN	transmembrane protein 218							integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						CCAGCCATCCCGCGGGGAGGC	0.652																																					p.G35R		Atlas-SNP	.											.	TMEM218	14	.	0			c.G103A						.						30.0	32.0	31.0					11																	124972140		2197	4292	6489	SO:0001623	5_prime_UTR_variant	219854	exon4			CCATCCCGCGGGG		CCDS31715.1	11q24.2	2008-08-08			ENSG00000150433	ENSG00000150433			27344	protein-coding gene	gene with protein product							Standard	NM_001258238		Approved		uc031qeu.1	A2RU14		ENST00000279968.4:c.-3G>A	chr11.hg19:g.124972140C>T		25.0	0.0		11.0	11.0	NM_001258243	B7ZM48	Missense_Mutation	SNP	ENST00000279968.4	hg19	CCDS31715.1																																																																																			.	.		0.652	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386849.1	NM_001080546	
TULP3	7289	hgsc.bcm.edu	37	12	3048495	3048495	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr12:3048495A>T	ENST00000448120.2	+	11	1265	c.1214A>T	c.(1213-1215)cAg>cTg	p.Q405L	TULP3_ENST00000397132.2_Missense_Mutation_p.Q405L	NM_003324.4	NP_003315.2	O75386	TULP3_HUMAN	tubby like protein 3	405					anterior/posterior pattern specification (GO:0009952)|bone development (GO:0060348)|brain development (GO:0007420)|bronchus morphogenesis (GO:0060434)|central nervous system neuron differentiation (GO:0021953)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic neurocranium morphogenesis (GO:0048702)|G-protein coupled receptor signaling pathway (GO:0007186)|ganglion development (GO:0061548)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of transcription, DNA-templated (GO:0006355)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	axoneme (GO:0005930)|ciliary base (GO:0097546)|cilium (GO:0005929)|extracellular region (GO:0005576)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	enzyme binding (GO:0019899)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein complex binding (GO:0032403)			endometrium(1)|large_intestine(4)|lung(13)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			ATAGTCATGCAGTTTGGACGT	0.393																																					p.Q405L		Atlas-SNP	.											.	TULP3	45	.	0			c.A1214T						.						301.0	255.0	270.0					12																	3048495		2203	4300	6503	SO:0001583	missense	7289	exon11			TCATGCAGTTTGG	AF045583	CCDS8519.1, CCDS53737.1	12p13	2014-02-21			ENSG00000078246	ENSG00000078246		"""Intraflagellar transport homologs"""	12425	protein-coding gene	gene with protein product		604730				9828123	Standard	NM_003324		Approved	TUBL3	uc001qlj.2	O75386	OTTHUMG00000168152	ENST00000448120.2:c.1214A>T	chr12.hg19:g.3048495A>T	ENSP00000410051:p.Gln405Leu	150.0	0.0		124.0	51.0	NM_003324	B3KNB7|B7Z6A2|D3DUQ4|F8WBZ9|Q8N5B0	Missense_Mutation	SNP	ENST00000448120.2	hg19	CCDS8519.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.099136	0.76983	.	.	ENSG00000078246	ENST00000228245;ENST00000544943;ENST00000542730;ENST00000448120;ENST00000397132	D;D;D	0.97870	-4.58;-4.58;-4.58	5.64	5.64	0.86602	Tubby, C-terminal (4);	0.000000	0.85682	D	0.000000	D	0.98833	0.9606	M	0.88450	2.955	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;0.999	D	0.99793	1.1032	10	0.87932	D	0	-10.6884	15.0316	0.71710	1.0:0.0:0.0:0.0	.	229;405;405	B7Z1E7;O75386;F8WBZ9	.;TULP3_HUMAN;.	L	405;132;229;405;405	ENSP00000442631:Q132L;ENSP00000410051:Q405L;ENSP00000380321:Q405L	ENSP00000228245:Q405L	Q	+	2	0	TULP3	2918756	1.000000	0.71417	1.000000	0.80357	0.523000	0.34469	9.339000	0.96797	2.150000	0.67090	0.402000	0.26972	CAG	.	.		0.393	TULP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398468.1	NM_003324	
APAF1	317	hgsc.bcm.edu	37	12	99117014	99117014	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr12:99117014A>G	ENST00000551964.1	+	23	3864	c.3128A>G	c.(3127-3129)cAt>cGt	p.H1043R	APAF1_ENST00000549007.1_Missense_Mutation_p.H1000R|APAF1_ENST00000550527.1_Missense_Mutation_p.H1032R|APAF1_ENST00000357310.1_Missense_Mutation_p.H1000R|APAF1_ENST00000547045.1_Missense_Mutation_p.H1000R|APAF1_ENST00000359972.2_Missense_Mutation_p.H989R|APAF1_ENST00000333991.1_Intron|APAF1_ENST00000339433.3_Missense_Mutation_p.H1000R|APAF1_ENST00000552268.1_Intron	NM_181861.1	NP_863651.1	O14727	APAF_HUMAN	apoptotic peptidase activating factor 1	1043					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|forebrain development (GO:0030900)|intrinsic apoptotic signaling pathway (GO:0097193)|nervous system development (GO:0007399)|neural tube closure (GO:0001843)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|regulation of apoptotic DNA fragmentation (GO:1902510)|regulation of apoptotic process (GO:0042981)|response to G1 DNA damage checkpoint signaling (GO:0072432)	apoptosome (GO:0043293)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(13)|liver(1)|lung(15)|ovary(2)|prostate(2)|skin(1)	42					Adenosine triphosphate(DB00171)	CTACGAGGCCATCAGGAAACA	0.353																																					p.H1043R		Atlas-SNP	.											.	APAF1	111	.	0			c.A3128G						.						129.0	133.0	132.0					12																	99117014		2203	4300	6503	SO:0001583	missense	317	exon23			GAGGCCATCAGGA	AF013263	CCDS9069.1, CCDS9070.1, CCDS9071.1, CCDS55862.1, CCDS55863.1	12q23	2013-01-10	2006-10-23			ENSG00000120868		"""WD repeat domain containing"""	576	protein-coding gene	gene with protein product		602233	"""apoptotic protease activating factor"", ""apoptotic peptidase activating factor"""			9267021, 10702682	Standard	NM_181861		Approved	CED4, APAF-1	uc001tfz.3	O14727	OTTHUMG00000170214	ENST00000551964.1:c.3128A>G	chr12.hg19:g.99117014A>G	ENSP00000448165:p.His1043Arg	113.0	0.0		123.0	48.0	NM_181861	B2RMX8|O43297|Q7Z438|Q9BXZ6|Q9UBZ5|Q9UGN8|Q9UGN9|Q9UGP0|Q9UJ58|Q9UJ59|Q9UJ60|Q9UJ61|Q9UJ62|Q9UJ63|Q9UJ64|Q9UJ65|Q9UJ66|Q9UJ67|Q9UNC9	Missense_Mutation	SNP	ENST00000551964.1	hg19	CCDS9069.1	.	.	.	.	.	.	.	.	.	.	A	15.42	2.829789	0.50845	.	.	ENSG00000120868	ENST00000551964;ENST00000359972;ENST00000357310;ENST00000339433;ENST00000550527;ENST00000547045;ENST00000549007	T;T;T;T;T;T;T	0.81163	-1.46;-1.46;-1.46;-1.46;-1.46;-1.46;-1.46	5.76	5.76	0.90799	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.091058	0.85682	D	0.000000	D	0.94315	0.8173	H	0.99379	4.54	0.80722	D	1	D;D;D;D;P	0.89917	1.0;0.999;1.0;0.999;0.925	D;D;D;D;P	0.91635	0.998;0.999;0.996;0.975;0.793	D	0.96041	0.9024	10	0.51188	T	0.08	-3.8213	14.6627	0.68885	1.0:0.0:0.0:0.0	.	1000;1000;989;1043;1032	C9JLV4;O14727-4;O14727-3;O14727;O14727-2	.;.;.;APAF_HUMAN;.	R	1043;989;1000;1000;1032;1000;1000	ENSP00000448165:H1043R;ENSP00000353059:H989R;ENSP00000349862:H1000R;ENSP00000341830:H1000R;ENSP00000448449:H1032R;ENSP00000449791:H1000R;ENSP00000448161:H1000R	ENSP00000341830:H1000R	H	+	2	0	APAF1	97641145	1.000000	0.71417	0.999000	0.59377	0.161000	0.22273	7.094000	0.76944	2.186000	0.69663	0.533000	0.62120	CAT	.	.		0.353	APAF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408006.1	NM_181861.1	
NBEA	26960	hgsc.bcm.edu	37	13	35731313	35731313	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr13:35731313A>G	ENST00000400445.3	+	21	3284	c.2750A>G	c.(2749-2751)tAc>tGc	p.Y917C	NBEA_ENST00000310336.4_Missense_Mutation_p.Y917C|NBEA_ENST00000379939.2_Missense_Mutation_p.Y917C|NBEA_ENST00000540320.1_Missense_Mutation_p.Y917C	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	917					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)		GAAATGGTCTACAATATCTTC	0.408																																					p.Y917C		Atlas-SNP	.											.	NBEA	340	.	0			c.A2750G						.						115.0	113.0	114.0					13																	35731313		1826	4081	5907	SO:0001583	missense	26960	exon21			TGGTCTACAATAT	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.2750A>G	chr13.hg19:g.35731313A>G	ENSP00000383295:p.Tyr917Cys	111.0	1.0		116.0	109.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	A	19.82	3.898496	0.72639	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.77280	0.4107	M	0.69248	2.105	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.79022	-0.1973	10	0.56958	D	0.05	.	15.6702	0.77267	1.0:0.0:0.0:0.0	.	917	Q5T321	.	C	917	ENSP00000440951:Y917C;ENSP00000383295:Y917C;ENSP00000369271:Y917C;ENSP00000308534:Y917C	ENSP00000308534:Y917C	Y	+	2	0	NBEA	34629313	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.171000	0.68590	0.528000	0.53228	TAC	.	.		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
PPP2R5C	5527	hgsc.bcm.edu	37	14	102391540	102391540	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr14:102391540C>A	ENST00000334743.5	+	14	1554	c.1506C>A	c.(1504-1506)gaC>gaA	p.D502E	PPP2R5C_ENST00000350249.3_Missense_Mutation_p.D463E|PPP2R5C_ENST00000422945.2_Missense_Mutation_p.D533E|PPP2R5C_ENST00000328724.5_Missense_Mutation_p.D518E	NM_002719.3	NP_002710.2	Q13362	2A5G_HUMAN	protein phosphatase 2, regulatory subunit B', gamma	502					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell proliferation (GO:0008285)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20						TGCCTCAGGACCCCCACACCA	0.632																																					p.D533E		Atlas-SNP	.											.	PPP2R5C	74	.	0			c.C1599A						.						93.0	102.0	99.0					14																	102391540		2203	4300	6503	SO:0001583	missense	5527	exon16			TCAGGACCCCCAC	L42375	CCDS9964.1, CCDS9965.1, CCDS45163.1, CCDS53911.1, CCDS53912.1	14q32.31	2010-06-18	2010-04-14		ENSG00000078304	ENSG00000078304		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9311	protein-coding gene	gene with protein product		601645	"""protein phosphatase 2, regulatory subunit B (B56), gamma isoform"", ""protein phosphatase 2, regulatory subunit B', gamma isoform"""			7592815	Standard	NM_002719		Approved	B56G, PR61G	uc001ykk.3	Q13362		ENST00000334743.5:c.1506C>A	chr14.hg19:g.102391540C>A	ENSP00000333905:p.Asp502Glu	61.0	0.0		80.0	36.0	NM_001161725	B4DYJ8|B5BUA5|F5GWP3|Q14391|Q15060|Q15174|Q6ZN33	Missense_Mutation	SNP	ENST00000334743.5	hg19	CCDS9964.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.586613	0.86851	.	.	ENSG00000078304	ENST00000422945;ENST00000328724;ENST00000557268;ENST00000350249;ENST00000334743	T;T;T;T;T	0.61510	0.1;0.53;0.1;0.51;0.1	6.17	0.338	0.15974	.	0.000000	0.85682	D	0.000000	T	0.70465	0.3227	M	0.85630	2.765	0.50171	D	0.999854	D;D;D;D	0.71674	0.994;0.966;0.998;0.994	D;D;D;D	0.66847	0.947;0.921;0.931;0.938	T	0.68176	-0.5478	10	0.59425	D	0.04	-9.0671	5.6504	0.17612	0.0:0.5105:0.1548:0.3347	.	533;463;502;518	F5GWP3;Q13362-3;Q13362;Q6ZN33	.;.;2A5G_HUMAN;.	E	533;518;531;463;502	ENSP00000412324:D533E;ENSP00000329009:D518E;ENSP00000450931:D531E;ENSP00000262239:D463E;ENSP00000333905:D502E	ENSP00000329009:D518E	D	+	3	2	PPP2R5C	101461293	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	1.080000	0.30779	0.284000	0.22305	-0.290000	0.09829	GAC	.	.		0.632	PPP2R5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414373.2	NM_002719	
IL16	3603	hgsc.bcm.edu	37	15	81589305	81589305	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr15:81589305G>A	ENST00000302987.4	+	12	1939	c.1939G>A	c.(1939-1941)Gaa>Aaa	p.E647K	IL16_ENST00000394652.2_5'UTR|IL16_ENST00000394660.2_Missense_Mutation_p.E647K			Q14005	IL16_HUMAN	interleukin 16	647					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GCTACCACAGGAAGACACAGC	0.602																																					p.E647K		Atlas-SNP	.											.	IL16	254	.	0			c.G1939A						.						35.0	39.0	38.0					15																	81589305		1963	4158	6121	SO:0001583	missense	3603	exon13			CCACAGGAAGACA	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1939G>A	chr15.hg19:g.81589305G>A	ENSP00000302935:p.Glu647Lys	65.0	0.0		46.0	22.0	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460644	0.43736	.	.	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653	T;T	0.11063	2.81;2.81	4.7	4.7	0.59300	.	0.582759	0.14620	N	0.308470	T	0.15912	0.0383	M	0.65975	2.015	0.80722	D	1	B;B;B;B;B	0.26635	0.089;0.155;0.155;0.016;0.027	B;B;B;B;B	0.32864	0.034;0.043;0.154;0.021;0.047	T	0.07083	-1.0791	10	0.10636	T	0.68	.	15.7839	0.78286	0.0:0.0:1.0:0.0	.	141;184;37;647;647	Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;IL16_HUMAN;.	K	647;479;647;184;37	ENSP00000378155:E647K;ENSP00000302935:E647K	ENSP00000302935:E647K	E	+	1	0	IL16	79376360	1.000000	0.71417	0.985000	0.45067	0.317000	0.28152	2.648000	0.46647	2.305000	0.77605	0.655000	0.94253	GAA	.	.		0.602	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
STARD5	80765	hgsc.bcm.edu	37	15	81615246	81615246	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr15:81615246C>A	ENST00000302824.6	-	2	168	c.143G>T	c.(142-144)gGg>gTg	p.G48V	RP11-761I4.3_ENST00000560973.1_RNA|STARD5_ENST00000559913.1_5'UTR|RP11-761I4.3_ENST00000559781.1_RNA	NM_181900.2	NP_871629.1	Q9NSY2	STAR5_HUMAN	StAR-related lipid transfer (START) domain containing 5	48	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				C21-steroid hormone biosynthetic process (GO:0006700)|lipid transport (GO:0006869)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytosol (GO:0005829)	lipid binding (GO:0008289)			large_intestine(3)|ovary(1)|skin(1)|stomach(1)	6						TTACAGGTTCCCTGGAAACTC	0.483																																					p.G48V		Atlas-SNP	.											.	STARD5	20	.	0			c.G143T						.						76.0	76.0	76.0					15																	81615246		2203	4300	6503	SO:0001583	missense	80765	exon2			AGGTTCCCTGGAA	AF480304	CCDS10318.1	15q26	2011-09-12	2007-08-16		ENSG00000172345	ENSG00000172345		"""StAR-related lipid transfer (START) domain containing"""	18065	protein-coding gene	gene with protein product		607050	"""START domain containing 5"""			12011452	Standard	NM_181900		Approved	MGC10327	uc002bgm.3	Q9NSY2	OTTHUMG00000147342	ENST00000302824.6:c.143G>T	chr15.hg19:g.81615246C>A	ENSP00000304032:p.Gly48Val	69.0	0.0		74.0	43.0	NM_181900	P59094	Missense_Mutation	SNP	ENST00000302824.6	hg19	CCDS10318.1	.	.	.	.	.	.	.	.	.	.	C	27.8	4.868363	0.91587	.	.	ENSG00000172345	ENST00000302824	T	0.79247	-1.25	5.4	5.4	0.78164	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	D	0.88987	0.6587	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86928	0.2071	10	0.25106	T	0.35	-11.9245	18.7698	0.91887	0.0:1.0:0.0:0.0	.	48	Q9NSY2	STAR5_HUMAN	V	48	ENSP00000304032:G48V	ENSP00000304032:G48V	G	-	2	0	STARD5	79402301	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.520000	0.73773	2.542000	0.85734	0.655000	0.94253	GGG	.	.		0.483	STARD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303950.2		
TP53	7157	hgsc.bcm.edu	37	17	7577534	7577534	+	Missense_Mutation	SNP	C	C	A	rs28934571		TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr17:7577534C>A	ENST00000269305.4	-	7	936	c.747G>T	c.(745-747)agG>agT	p.R249S	TP53_ENST00000455263.2_Missense_Mutation_p.R249S|TP53_ENST00000359597.4_Missense_Mutation_p.R249S|TP53_ENST00000420246.2_Missense_Mutation_p.R249S|TP53_ENST00000445888.2_Missense_Mutation_p.R249S|TP53_ENST00000413465.2_Missense_Mutation_p.R249S|TP53_ENST00000574684.1_5'Flank	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	249	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		R -> G (in sporadic cancers; somatic mutation).|R -> I (in a sporadic cancer; somatic mutation).|R -> K (in sporadic cancers; somatic mutation).|R -> M (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|R -> N (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|R -> S (in sporadic cancers; somatic mutation; does not induce SNAI1 degradation; dbSNP:rs28934571). {ECO:0000269|PubMed:1694291, ECO:0000269|PubMed:16959974}.|R -> T (in sporadic cancers; somatic mutation).|R -> W (in sporadic cancers; somatic mutation).|RP -> SA (in a sporadic cancer; somatic mutation).|RP -> SS (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|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 by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.R249S(348)|p.0?(8)|p.R249R(5)|p.?(5)|p.M246_P250delMNRRP(2)|p.R248_P250delRRP(1)|p.R249_P250delRP(1)|p.R249_P250insR(1)|p.R249_P250>SS(1)|p.N247_R249delNRR(1)|p.N247_P250delNRRP(1)|p.R249fs*14(1)|p.R249_T256delRPILTIIT(1)|p.P250fs*14(1)|p.R249_I251delRPI(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TGAGGATGGGCCTCCGGTTCA	0.572		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.R249S	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000455263,right_lower_lobe,carcinoma,-2,1	TP53	33396	.	378	Substitution - Missense(348)|Deletion - In frame(8)|Whole gene deletion(8)|Unknown(5)|Substitution - coding silent(5)|Insertion - Frameshift(1)|Insertion - In frame(1)|Deletion - Frameshift(1)|Complex - compound substitution(1)	liver(240)|lung(44)|upper_aerodigestive_tract(12)|breast(12)|central_nervous_system(10)|stomach(7)|ovary(6)|prostate(6)|cervix(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(5)|biliary_tract(5)|urinary_tract(5)|bone(4)|endometrium(3)|oesophagus(3)|skin(2)|peritoneum(1)|kidney(1)|salivary_gland(1)|pancreas(1)	c.G747T						.						155.0	113.0	127.0					17																	7577534		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GATGGGCCTCCGG	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.747G>T	chr17.hg19:g.7577534C>A	ENSP00000269305:p.Arg249Ser	83.0	0.0		51.0	39.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	C	17.26	3.344264	0.61073	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	D;D;D;D;D;D;D	0.99865	-7.29;-7.29;-7.29;-7.29;-7.29;-7.29;-7.29	4.62	-0.0929	0.13654	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99792	0.9912	M	0.92367	3.3	0.50039	D	0.999848	D;D;D;D;D	0.89917	0.996;0.996;0.997;0.99;1.0	D;D;D;D;D	0.79108	0.968;0.966;0.981;0.955;0.992	D	0.98720	1.0708	10	0.72032	D	0.01	-3.0658	3.2479	0.06803	0.1392:0.5551:0.1362:0.1695	rs28934571	249;249;249;249;249	P04637-2;P04637-3;P04637;Q1MSW8;E7EQX7	.;.;P53_HUMAN;.;.	S	249;249;249;249;249;249;238;117	ENSP00000410739:R249S;ENSP00000352610:R249S;ENSP00000269305:R249S;ENSP00000398846:R249S;ENSP00000391127:R249S;ENSP00000391478:R249S;ENSP00000425104:R117S	ENSP00000269305:R249S	R	-	3	2	TP53	7518259	0.011000	0.17503	0.998000	0.56505	0.783000	0.44284	-1.379000	0.02554	0.253000	0.21552	0.462000	0.41574	AGG	.	.		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
MYO18A	399687	hgsc.bcm.edu	37	17	27442787	27442787	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr17:27442787C>T	ENST00000527372.1	-	12	2302	c.2122G>A	c.(2122-2124)Gag>Aag	p.E708K	MYO18A_ENST00000533112.1_Missense_Mutation_p.E708K|MYO18A_ENST00000531253.1_Missense_Mutation_p.E708K|MYO18A_ENST00000354329.4_Missense_Mutation_p.E708K	NM_078471.3	NP_510880.2	Q92614	MY18A_HUMAN	myosin XVIIIA	708	Myosin motor.				actomyosin structure organization (GO:0031032)|cell migration (GO:0016477)|DNA metabolic process (GO:0006259)|Golgi organization (GO:0007030)|Golgi vesicle budding (GO:0048194)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein secretion (GO:0050714)	actomyosin (GO:0042641)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|myosin complex (GO:0016459)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(6)|kidney(6)|lung(20)|urinary_tract(2)	36			Epithelial(11;4.97e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000221)|all cancers(11;0.000234)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			GAGGACAGCTCCTCCAGGCTG	0.642																																					p.E708K	Esophageal Squamous(182;472 2015 7001 15270 22562)	Atlas-SNP	.											.	MYO18A	217	.	0			c.G2122A						.						30.0	37.0	35.0					17																	27442787		2041	4187	6228	SO:0001583	missense	399687	exon12			ACAGCTCCTCCAG	D86970	CCDS45641.1, CCDS45642.1	17q11.2	2011-09-27			ENSG00000196535	ENSG00000196535		"""Myosins / Myosin superfamily : Class XVIII"""	31104	protein-coding gene	gene with protein product		610067				12761286	Standard	NM_078471		Approved	KIAA0216, MysPDZ	uc002hdt.1	Q92614	OTTHUMG00000166360	ENST00000527372.1:c.2122G>A	chr17.hg19:g.27442787C>T	ENSP00000437073:p.Glu708Lys	54.0	0.0		34.0	15.0	NM_078471	Q5H9U3|Q5W9F9|Q5W9G1|Q8IXP8	Missense_Mutation	SNP	ENST00000527372.1	hg19	CCDS45642.1	.	.	.	.	.	.	.	.	.	.	C	37	6.113689	0.97296	.	.	ENSG00000196535	ENST00000354329;ENST00000359450;ENST00000533112;ENST00000531253;ENST00000527372;ENST00000458428	D;D;D;D	0.87887	-2.31;-2.31;-2.31;-2.31	5.84	5.84	0.93424	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.93006	0.7774	M	0.64170	1.965	0.58432	D	0.999998	D;D;D;D;D	0.89917	0.999;0.998;0.998;0.998;1.0	D;D;D;D;D	0.91635	0.966;0.994;0.994;0.994;0.999	D	0.92946	0.6376	10	0.87932	D	0	.	20.1379	0.98040	0.0:1.0:0.0:0.0	.	377;320;708;708;708	Q92614-2;F8W6Y3;Q92614-3;Q92614-4;Q92614	.;.;.;.;MY18A_HUMAN	K	708;708;708;708;708;320	ENSP00000346291:E708K;ENSP00000435932:E708K;ENSP00000434228:E708K;ENSP00000437073:E708K	ENSP00000346291:E708K	E	-	1	0	MYO18A	24466913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.453000	0.80700	2.779000	0.95612	0.655000	0.94253	GAG	.	.		0.642	MYO18A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389396.1	NM_078471	
PTPN2	5771	hgsc.bcm.edu	37	18	12802149	12802149	+	Splice_Site	SNP	T	T	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr18:12802149T>G	ENST00000309660.5	-	8	953	c.860A>C	c.(859-861)aAa>aCa	p.K287T	PTPN2_ENST00000591115.1_Splice_Site_p.K310T|PTPN2_ENST00000591497.1_Splice_Site_p.K258T|PTPN2_ENST00000353319.4_Splice_Site_p.K287T|PTPN2_ENST00000327283.3_Splice_Site_p.K287T	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	287					B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				TTTCCATCGTTTCTAGGTAGG	0.279																																					p.K310T		Atlas-SNP	.											.	PTPN2	37	.	0			c.A929C						.						61.0	52.0	55.0					18																	12802149		2203	4299	6502	SO:0001630	splice_region_variant	5771	exon9			CATCGTTTCTAGG	M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.859-1A>C	chr18.hg19:g.12802149T>G		66.0	0.0		98.0	51.0	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	hg19	CCDS11865.1	.	.	.	.	.	.	.	.	.	.	T	15.53	2.860965	0.51482	.	.	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000341361;ENST00000309660	T;T;T	0.04275	3.67;3.68;3.66	5.52	5.52	0.82312	.	0.000000	0.56097	D	0.000022	T	0.09555	0.0235	M	0.69823	2.125	0.80722	D	1	B;B;B;B;B	0.33135	0.399;0.066;0.107;0.085;0.04	B;B;B;B;B	0.35607	0.206;0.124;0.065;0.032;0.058	T	0.03306	-1.1050	10	0.44086	T	0.13	.	13.6713	0.62427	0.0:0.0:0.0:1.0	.	287;287;264;287;287	P17706;P17706-2;Q59F91;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.;.	T	287;287;264;287	ENSP00000320298:K287T;ENSP00000320546:K287T;ENSP00000311857:K287T	ENSP00000311857:K287T	K	-	2	0	PTPN2	12792149	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	4.869000	0.63028	2.222000	0.72286	0.455000	0.32223	AAA	.	.		0.279	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423	Missense_Mutation
PIN1	5300	hgsc.bcm.edu	37	19	9949168	9949168	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr19:9949168G>T	ENST00000247970.4	+	2	137	c.115G>T	c.(115-117)Ggc>Tgc	p.G39C	PIN1_ENST00000587625.1_Missense_Mutation_p.G39C|PIN1_ENST00000380889.6_3'UTR|PIN1_ENST00000588695.1_Missense_Mutation_p.G39C	NM_006221.3	NP_006212.1	Q13526	PIN1_HUMAN	peptidylprolyl cis/trans isomerase, NIMA-interacting 1	39	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cell cycle (GO:0007049)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|negative regulation of cell motility (GO:2000146)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)|regulation of cytokinesis (GO:0032465)|regulation of mitosis (GO:0007088)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	GTPase activating protein binding (GO:0032794)|mitogen-activated protein kinase kinase binding (GO:0031434)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|phosphoserine binding (GO:0050815)|phosphothreonine binding (GO:0050816)	p.G39C(1)		skin(3)	3						GCGGCCCAGCGGCAACAGCAG	0.652																																					p.G39C		Atlas-SNP	.											PIN1_ENST00000247970,NS,carcinoma,0,1	PIN1	7	.	1	Substitution - Missense(1)	lung(1)	c.G115T						.						17.0	19.0	18.0					19																	9949168		2201	4298	6499	SO:0001583	missense	5300	exon2			CCCAGCGGCAACA		CCDS12220.1	19p13	2014-09-17	2008-03-25		ENSG00000127445	ENSG00000127445			8988	protein-coding gene	gene with protein product		601052	"""protein (peptidyl-prolyl cis/trans isomerase) NIMA-interacting 1"""			8606777	Standard	NM_006221		Approved	dod	uc002mml.2	Q13526		ENST00000247970.4:c.115G>T	chr19.hg19:g.9949168G>T	ENSP00000247970:p.Gly39Cys	55.0	0.0		46.0	17.0	NM_006221	A8K4V9|Q53X75	Missense_Mutation	SNP	ENST00000247970.4	hg19	CCDS12220.1	.	.	.	.	.	.	.	.	.	.	G	19.07	3.755544	0.69648	.	.	ENSG00000127445	ENST00000247970;ENST00000424497	T	0.76839	-1.05	3.63	2.59	0.31030	WW/Rsp5/WWP (3);	0.327520	0.27851	N	0.017596	T	0.80969	0.4726	M	0.69185	2.1	0.42263	D	0.992026	D;P;D	0.65815	0.995;0.894;0.983	P;P;P	0.58721	0.769;0.649;0.844	T	0.79351	-0.1839	9	.	.	.	-36.7392	6.9465	0.24522	0.1238:0.0:0.8762:0.0	.	39;39;39	B3KUM4;Q13526;E7EQR5	.;PIN1_HUMAN;.	C	39	ENSP00000247970:G39C	.	G	+	1	0	PIN1	9810168	1.000000	0.71417	0.996000	0.52242	0.968000	0.65278	5.971000	0.70440	1.125000	0.41998	0.555000	0.69702	GGC	.	.		0.652	PIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451107.1		
ARHGAP33	115703	hgsc.bcm.edu	37	19	36272086	36272086	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr19:36272086T>G	ENST00000007510.4	+	12	1161	c.1017T>G	c.(1015-1017)atT>atG	p.I339M	ARHGAP33_ENST00000378944.5_Missense_Mutation_p.I203M|ARHGAP33_ENST00000314737.5_Missense_Mutation_p.I339M			O14559	RHG33_HUMAN	Rho GTPase activating protein 33	339	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				protein transport (GO:0015031)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|Rac GTPase activator activity (GO:0030675)			endometrium(7)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	37						CCGAGTTCATTGAGGCCCACG	0.657																																					p.I339M		Atlas-SNP	.											.	ARHGAP33	102	.	0			c.T1017G						.						75.0	74.0	74.0					19																	36272086		2203	4300	6503	SO:0001583	missense	115703	exon12			GTTCATTGAGGCC	AY044864	CCDS12477.1, CCDS54254.1	19q13.13	2011-06-29	2010-02-19	2010-02-19		ENSG00000004777		"""Rho GTPase activating proteins"""	23085	protein-coding gene	gene with protein product		614902	"""sorting nexin 26"""	SNX26		12297274, 12461558	Standard	NM_052948		Approved	FLJ39019, TCGAP	uc002obs.2	O14559		ENST00000007510.4:c.1017T>G	chr19.hg19:g.36272086T>G	ENSP00000007510:p.Ile339Met	34.0	0.0		42.0	19.0	NM_052948	O14552|O14560|Q6ZSP6|Q96CP3|Q9NT23	Missense_Mutation	SNP	ENST00000007510.4	hg19		.	.	.	.	.	.	.	.	.	.	T	17.70	3.454980	0.63290	.	.	ENSG00000004777	ENST00000007510;ENST00000314737;ENST00000378944	T;T;T	0.27557	1.66;1.66;1.66	5.3	-4.36	0.03645	.	0.000000	0.85682	D	0.000000	T	0.62732	0.2452	H	0.96604	3.85	0.34950	D	0.751159	D;D	0.89917	0.999;1.0	D;D	0.91635	0.999;0.996	T	0.72584	-0.4249	10	0.87932	D	0	.	13.0487	0.58942	0.1181:0.7333:0.0:0.1486	.	203;339	O14559-10;O14559-11	.;.	M	339;339;203	ENSP00000007510:I339M;ENSP00000320038:I339M;ENSP00000368227:I203M	ENSP00000007510:I339M	I	+	3	3	ARHGAP33	40963926	0.001000	0.12720	0.923000	0.36655	0.973000	0.67179	-1.984000	0.01487	-1.103000	0.03019	-0.366000	0.07423	ATT	.	.		0.657	ARHGAP33-201	KNOWN	basic	protein_coding	protein_coding		NM_052948	
AMER1	139285	hgsc.bcm.edu	37	X	63410591	63410591	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:63410591T>A	ENST00000330258.3	-	2	2848	c.2576A>T	c.(2575-2577)tAc>tTc	p.Y859F	AMER1_ENST00000374869.3_Intron|AMER1_ENST00000403336.1_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	859					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CAGGCCTTGGTAGAATCGACT	0.552																																					p.Y859F		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A2576T						.						40.0	43.0	42.0					X																	63410591		2116	4204	6320	SO:0001583	missense	139285	exon2			CCTTGGTAGAATC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.2576A>T	chrX.hg19:g.63410591T>A	ENSP00000329117:p.Tyr859Phe	107.0	0.0		82.0	36.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	8.304	0.820525	0.16678	.	.	ENSG00000184675	ENST00000330258	T	0.39056	1.1	4.79	0.735	0.18300	.	.	.	.	.	T	0.17323	0.0416	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.08249	-1.0731	8	.	.	.	-0.6102	4.4958	0.11837	0.3703:0.0941:0.0:0.5356	.	859	Q5JTC6	F123B_HUMAN	F	859	ENSP00000329117:Y859F	.	Y	-	2	0	FAM123B	63327316	1.000000	0.71417	0.999000	0.59377	0.932000	0.56968	1.635000	0.37134	0.252000	0.21531	0.430000	0.28490	TAC	.	.		0.552	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
TNMD	64102	hgsc.bcm.edu	37	X	99854571	99854571	+	Silent	SNP	C	C	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:99854571C>A	ENST00000373031.4	+	7	1028	c.811C>A	c.(811-813)Cga>Aga	p.R271R		NM_022144.2	NP_071427.2	Q9H2S6	TNMD_HUMAN	tenomodulin	271					cellular response to BMP stimulus (GO:0071773)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|tendon cell differentiation (GO:0035990)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(7)|skin(1)	16						TTACTGCCGTCGAGGCAACCG	0.478																																					p.R271R		Atlas-SNP	.											.	TNMD	40	.	0			c.C811A						.						86.0	56.0	66.0					X																	99854571		2203	4300	6503	SO:0001819	synonymous_variant	64102	exon7			TGCCGTCGAGGCA	AF191770	CCDS14469.1	Xq21.33-q23	2012-10-10			ENSG00000000005	ENSG00000000005		"""BRICHOS domain containing"""	17757	protein-coding gene	gene with protein product	"""BRICHOS domain containing 4"""	300459					Standard	NM_022144		Approved	myodulin, ChM1L, tendin, TEM, BRICD4	uc004efy.4	Q9H2S6	OTTHUMG00000022001	ENST00000373031.4:c.811C>A	chrX.hg19:g.99854571C>A		81.0	0.0		61.0	18.0	NM_022144	Q9HBX0|Q9UJG0	Silent	SNP	ENST00000373031.4	hg19	CCDS14469.1																																																																																			.	.		0.478	TNMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057481.1	NM_022144	
LONRF3	79836	hgsc.bcm.edu	37	X	118148215	118148215	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:118148215G>A	ENST00000371628.3	+	10	2051	c.2020G>A	c.(2020-2022)Gtc>Atc	p.V674I	LONRF3_ENST00000304778.7_Missense_Mutation_p.V633I|LONRF3_ENST00000472173.1_3'UTR|LONRF3_ENST00000422289.2_Missense_Mutation_p.V418I	NM_001031855.1	NP_001027026.1	Q496Y0	LONF3_HUMAN	LON peptidase N-terminal domain and ring finger 3	674	Lon.						ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	36						ACATAACTGTGTCTATCAGCA	0.448																																					p.V674I		Atlas-SNP	.											.	LONRF3	138	.	0			c.G2020A						.						332.0	266.0	288.0					X																	118148215		2203	4300	6503	SO:0001583	missense	79836	exon10			AACTGTGTCTATC	AK026265	CCDS14575.1, CCDS35374.1, CCDS76014.1	Xq24	2013-01-09	2005-08-19	2005-08-19	ENSG00000175556	ENSG00000175556		"""RING-type (C3HC4) zinc fingers"""	21152	protein-coding gene	gene with protein product			"""ring finger protein 127"""	RNF127			Standard	XM_005262476		Approved	FLJ22612	uc004eqw.3	Q496Y0	OTTHUMG00000022262	ENST00000371628.3:c.2020G>A	chrX.hg19:g.118148215G>A	ENSP00000360690:p.Val674Ile	89.0	0.0		127.0	60.0	NM_001031855	Q5JPN6|Q8NB00|Q9H647	Missense_Mutation	SNP	ENST00000371628.3	hg19	CCDS35374.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	33|33	5.224584|5.224584	0.95139|0.95139	.|.	.|.	ENSG00000175556|ENSG00000175556	ENST00000439603|ENST00000365713;ENST00000304778;ENST00000371628;ENST00000422289	T|T;T;T;T	0.40756|0.36340	1.02|1.26;1.26;1.26;1.26	5.7|5.7	5.7|5.7	0.88788|0.88788	.|Peptidase S16, lon N-terminal (1);PUA-like domain (1);	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.67785|0.67785	0.2930|0.2930	M|M	0.88310|0.88310	2.945|2.945	0.58432|0.58432	D|D	0.999998|0.999998	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.995;0.996;0.999	T|T	0.74657|0.74657	-0.3592|-0.3592	7|10	0.56958|0.87932	D|D	0.05|0	-47.094|-47.094	17.6221|17.6221	0.88084|0.88084	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|418;633;674	.|B3KUN7;Q496Y0-2;Q496Y0	.|.;.;LONF3_HUMAN	Y|I	439|633;633;674;418	ENSP00000414519:C439Y|ENSP00000360691:V633I;ENSP00000307732:V633I;ENSP00000360690:V674I;ENSP00000408894:V418I	ENSP00000414519:C439Y|ENSP00000307732:V633I	C|V	+|+	2|1	0|0	LONRF3|LONRF3	118032243|118032243	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	9.869000|9.869000	0.99810|0.99810	2.377000|2.377000	0.81083|0.81083	0.600000|0.600000	0.82982|0.82982	TGT|GTC	.	.		0.448	LONRF3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355124.2	NM_024778	
MT-ND3	4537	hgsc.bcm.edu	37	M	10114	10114	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrM:10114T>C	ENST00000361227.2	+	1	56	c.56T>C	c.(55-57)aTt>aCt	p.I19T	MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03897	NU3M_HUMAN	mitochondrially encoded NADH dehydrogenase 3	19					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)										ACTACTAATAATTATTACATT	0.398																																					p.I19T		Atlas-SNP	.											.	.	.	.	0			c.T56C						.																																			SO:0001583	missense	0	exon1			TAATAATTATTAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198840	ENSG00000198840	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7458	protein-coding gene	gene with protein product	"""complex I ND3 subunit"", ""NADH-ubiquinone oxidoreductase chain 3"""	516002	"""NADH dehydrogenase 3"""	MTND3			Standard			Approved	ND3, NAD3		P03897		ENST00000361227.2:c.56T>C	chrM.hg19:g.10114T>C	ENSP00000355206:p.Ile19Thr	166.0	0.0		147.0	136.0	ENST00000361227		Missense_Mutation	SNP	ENST00000361227.2	hg19																																																																																				.	.		0.398	MT-ND3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024033	
TEX11	56159	hgsc.bcm.edu	37	X	70053381	70053383	+	In_Frame_Del	DEL	CAA	CAA	-			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chrX:70053381_70053383delCAA	ENST00000395889.2	-	9	786_788	c.631_633delTTG	c.(631-633)ttgdel	p.L211del	TEX11_ENST00000344304.3_In_Frame_Del_p.L211del|TEX11_ENST00000374333.2_In_Frame_Del_p.L196del	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	211					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GGAGCCTCATCAACATATCTTTA	0.379																																					p.211_212del		Atlas-Indel,Pindel	.											.	TEX11	132	.	0			c.632_634del						.																																			SO:0001651	inframe_deletion	56159	exon9			.	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.631_633delTTG	chrX.hg19:g.70053381_70053383delCAA	ENSP00000379226:p.Leu211del	178.0	0.0		172.0	63.0	NM_001003811	A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	In_Frame_Del	DEL	ENST00000395889.2	hg19	CCDS35323.1																																																																																			.	.		0.379	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
CYP3A5	1577	hgsc.bcm.edu	37	7	99247719	99247721	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr7:99247719_99247721delAGG	ENST00000222982.4	-	12	1487_1489	c.1388_1390delCCT	c.(1387-1392)tccttc>ttc	p.S463del	CYP3A5_ENST00000343703.5_In_Frame_Del_p.S453del|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	463					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	CAAGGTTTGAAGGAGAAGTTCTG	0.35																																					p.463_464del		Atlas-Indel,Pindel	.											.	CYP3A5	46	.	0			c.1389_1391del						.																																			SO:0001651	inframe_deletion	1577	exon12			.	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.1388_1390delCCT	chr7.hg19:g.99247719_99247721delAGG	ENSP00000222982:p.Ser463del	192.0	0.0		172.0	69.0	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	In_Frame_Del	DEL	ENST00000222982.4	hg19	CCDS5672.1																																																																																			.	.		0.350	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
RB1	5925	hgsc.bcm.edu	37	13	48947605	48947606	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr13:48947605_48947606insA	ENST00000267163.4	+	12	1330_1331	c.1192_1193insA	c.(1192-1194)gaafs	p.E398fs		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	398	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)|p.E398L(2)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TCAACCTTCAGAAAATCTGATT	0.287		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.E398fs		Atlas-INDEL	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	.,1	RB1	1068	.	25	Whole gene deletion(15)|Unknown(8)|Substitution - Missense(2)	bone(11)|breast(5)|central_nervous_system(2)|lung(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.1192_1193insA						.																																			SO:0001589	frameshift_variant	5925	exon12	Familial Cancer Database		.	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1196dupA	chr13.hg19:g.48947609_48947609dupA	ENSP00000267163:p.Glu398fs	228.0	0.0		312.0	277.0	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Frame_Shift_Ins	INS	ENST00000267163.4	hg19	CCDS31973.1																																																																																			.	.		0.287	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
TNPO1	3842	hgsc.bcm.edu	37	5	72189531	72189532	+	Splice_Site	INS	-	-	T			TCGA-G3-A25U-01A-11D-A16V-10	TCGA-G3-A25U-10A-01D-A16V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	656f2a16-cd8a-4255-b6ff-703f560a74a7	c178796c-e0ab-403c-9ab1-95aa12c72f0e	g.chr5:72189531_72189532insT	ENST00000337273.5	+	18	2569		c.e18+1		TNPO1_ENST00000506351.2_Splice_Site|TNPO1_ENST00000454282.1_Splice_Site|TNPO1_ENST00000523768.1_Splice_Site	NM_002270.3	NP_002261.3	Q92973	TNPO1_HUMAN	transportin 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|protein import into nucleus, translocation (GO:0000060)|RNA metabolic process (GO:0016070)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(6)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	36		Lung NSC(167;0.0053)|Ovarian(174;0.0175)		OV - Ovarian serous cystadenocarcinoma(47;6.14e-54)		CCTTGTATAGGTATGAATATTT	0.327																																					.		Atlas-INDEL	.											.	TNPO1	90	.	0			c.2143+1->T						.																																			SO:0001630	splice_region_variant	3842	exon18			.	U70322	CCDS4016.1, CCDS43329.1	5q13.1	2009-01-12	2004-01-29	2004-01-30	ENSG00000083312	ENSG00000083312		"""Importins"""	6401	protein-coding gene	gene with protein product	"""importin 2"""	602901	"""karyopherin (importin) beta 2"""	KPNB2		8808633, 9144189	Standard	NM_153188		Approved	MIP, TRN, IPO2, MIP1	uc003kci.4	Q92973	OTTHUMG00000100967	ENST00000337273.5:c.2143+1->T	chr5.hg19:g.72189532_72189532dupT		81.0	0.0		74.0	35.0	NM_002270	B4DVC6|Q92957|Q92975	Splice_Site	INS	ENST00000337273.5	hg19	CCDS43329.1																																																																																			.	.		0.327	TNPO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000218577.3	NM_002270	Intron
