#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
DOCK7	85440	hgsc.bcm.edu	37	1	62995020	62995020	+	Missense_Mutation	SNP	G	G	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:62995020G>C	ENST00000340370.5	-	29	3633	c.3616C>G	c.(3616-3618)Cga>Gga	p.R1206G	DOCK7_ENST00000251157.5_Missense_Mutation_p.R1237G	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	1237					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						ATGGCCACTCGAGCCTTTATC	0.403																																					p.R1237G		Atlas-SNP	.											.	DOCK7	184	.	0			c.C3709G						.						101.0	96.0	97.0					1																	62995020		2203	4300	6503	SO:0001583	missense	85440	exon30			CCACTCGAGCCTT		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.3616C>G	chr1.hg19:g.62995020G>C	ENSP00000340742:p.Arg1206Gly	94.0	0.0		117.0	6.0	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	hg19	CCDS30734.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.43|18.43	3.621592|3.621592	0.66787|0.66787	.|.	.|.	ENSG00000116641|ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000395441|ENST00000454575	T;T|.	0.18338|.	2.22;2.22|.	5.84|5.84	3.89|3.89	0.44902|0.44902	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.74419|0.74419	0.3714|0.3714	M|M	0.78285|0.78285	2.405|2.405	0.80722|0.80722	D|D	1|1	P;D;P;P;P;P|.	0.54207|.	0.802;0.965;0.702;0.702;0.706;0.862|.	B;P;B;B;B;P|.	0.54965|.	0.326;0.765;0.355;0.355;0.325;0.702|.	T|T	0.76599|0.76599	-0.2900|-0.2900	10|5	0.87932|.	D|.	0|.	.|.	14.668|14.668	0.68924|0.68924	0.0:0.0:0.6248:0.3752|0.0:0.0:0.6248:0.3752	.|.	1237;1237;1206;1206;1206;1237|.	Q96N67;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3;Q96N67-6|.	DOCK7_HUMAN;.;.;.;.;.|.	G|W	1237;1237;1206;65|408	ENSP00000251157:R1237G;ENSP00000340742:R1206G|.	ENSP00000251157:R1237G|.	R|S	-|-	1|2	2|0	DOCK7|DOCK7	62767608|62767608	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.815000|0.815000	0.46073|0.46073	3.076000|3.076000	0.50081|0.50081	1.435000|1.435000	0.47434|0.47434	0.591000|0.591000	0.81541|0.81541	CGA|TCG	.	.		0.403	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
DPYD	1806	hgsc.bcm.edu	37	1	97981322	97981322	+	Missense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:97981322C>A	ENST00000370192.3	-	13	1800	c.1700G>T	c.(1699-1701)gGa>gTa	p.G567V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	567					beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	AAAACCCCATCCAGCTTCAAA	0.363																																					p.G567V		Atlas-SNP	.											.	DPYD	219	.	0			c.G1700T						.						54.0	54.0	54.0					1																	97981322		2202	4300	6502	SO:0001583	missense	1806	exon13			CCCCATCCAGCTT	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.1700G>T	chr1.hg19:g.97981322C>A	ENSP00000359211:p.Gly567Val	61.0	0.0		72.0	18.0	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	hg19	CCDS30777.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.508698	0.85282	.	.	ENSG00000188641	ENST00000370192	D	0.83755	-1.76	5.37	5.37	0.77165	Aldolase-type TIM barrel (1);	0.000000	0.85682	D	0.000000	D	0.93546	0.7940	H	0.95004	3.61	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94713	0.7894	10	0.87932	D	0	-17.4008	19.4624	0.94922	0.0:1.0:0.0:0.0	.	567	Q12882	DPYD_HUMAN	V	567	ENSP00000359211:G567V	ENSP00000359211:G567V	G	-	2	0	DPYD	97753910	1.000000	0.71417	0.998000	0.56505	0.989000	0.77384	7.356000	0.79445	2.677000	0.91161	0.585000	0.79938	GGA	.	.		0.363	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
PLPPR5	163404	hgsc.bcm.edu	37	1	99358645	99358645	+	Missense_Mutation	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:99358645A>G	ENST00000263177.4	-	6	1170	c.949T>C	c.(949-951)Ttc>Ctc	p.F317L	LPPR5_ENST00000370188.3_Missense_Mutation_p.F312L	NM_001037317.1	NP_001032394.1	Q32ZL2	LPPR5_HUMAN		317						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)										ACTTCTGCGAAGGCAGTGATG	0.373																																					p.F317L		Atlas-SNP	.											.	.	.	.	0			c.T949C						.						112.0	106.0	108.0					1																	99358645		2203	4300	6503	SO:0001583	missense	0	exon6			CTGCGAAGGCAGT																												ENST00000263177.4:c.949T>C	chr1.hg19:g.99358645A>G	ENSP00000263177:p.Phe317Leu	116.0	0.0		115.0	52.0	NM_001037317	A8MPX4|B7UCH3|Q32ZD0|Q3ZCU7	Missense_Mutation	SNP	ENST00000263177.4	hg19	CCDS30778.1	.	.	.	.	.	.	.	.	.	.	A	12.21	1.868340	0.32977	.	.	ENSG00000117598	ENST00000370188;ENST00000263177	T;T	0.27890	1.65;1.64	5.61	5.61	0.85477	.	0.184679	0.47093	D	0.000251	T	0.08935	0.0221	N	0.22421	0.69	0.47994	D	0.999564	B;B	0.31351	0.32;0.1	B;B	0.26517	0.07;0.022	T	0.08493	-1.0719	10	0.11182	T	0.66	.	14.9872	0.71356	1.0:0.0:0.0:0.0	.	312;317	Q32ZL2-2;Q32ZL2	.;LPPR5_HUMAN	L	312;317	ENSP00000359207:F312L;ENSP00000263177:F317L	ENSP00000263177:F317L	F	-	1	0	AL161744.1	99131233	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.758000	0.74929	2.120000	0.65058	0.455000	0.32223	TTC	.	.		0.373	LPPR5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393221.1		
FLG	2312	hgsc.bcm.edu	37	1	152282032	152282032	+	Missense_Mutation	SNP	G	G	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:152282032G>C	ENST00000368799.1	-	3	5365	c.5330C>G	c.(5329-5331)tCc>tGc	p.S1777C	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1777	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.S1777Y(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCATGGGCGGACTCAGACTG	0.607									Ichthyosis																												p.S1777C		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	.	1	Substitution - Missense(1)	lung(1)	c.C5330G						.						205.0	212.0	209.0					1																	152282032		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGGGCGGACTCAG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.5330C>G	chr1.hg19:g.152282032G>C	ENSP00000357789:p.Ser1777Cys	365.0	0.0		434.0	99.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.454490	0.26161	.	.	ENSG00000143631	ENST00000368799;ENST00000271820	T	0.01745	4.66	4.64	0.35	0.16037	.	.	.	.	.	T	0.03348	0.0097	M	0.83483	2.645	0.09310	N	1	D	0.69078	0.997	D	0.73708	0.981	T	0.28681	-1.0036	9	0.87932	D	0	0.0123	5.0931	0.14720	0.1923:0.3131:0.4945:0.0	.	1777	P20930	FILA_HUMAN	C	1777;12	ENSP00000357789:S1777C	ENSP00000271820:S12C	S	-	2	0	FLG	150548656	0.001000	0.12720	0.000000	0.03702	0.036000	0.12997	0.682000	0.25335	-0.114000	0.11936	-0.259000	0.10710	TCC	.	.		0.607	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TRIM46	80128	hgsc.bcm.edu	37	1	155148663	155148663	+	Missense_Mutation	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:155148663G>T	ENST00000334634.4	+	3	625	c.625G>T	c.(625-627)Gcc>Tcc	p.A209S	TRIM46_ENST00000368385.4_Missense_Mutation_p.A209S|TRIM46_ENST00000368383.3_Missense_Mutation_p.A209S|TRIM46_ENST00000468878.1_3'UTR|TRIM46_ENST00000543729.1_Missense_Mutation_p.A216S|TRIM46_ENST00000545012.1_Missense_Mutation_p.A83S|KRTCAP2_ENST00000295682.4_5'Flank|TRIM46_ENST00000392451.2_Missense_Mutation_p.A209S|TRIM46_ENST00000368382.1_Missense_Mutation_p.A186S|RP11-201K10.3_ENST00000473363.2_Intron|KRTCAP2_ENST00000490672.1_5'Flank	NM_001256601.1|NM_001282378.1	NP_001243530.1|NP_001269307.1	Q7Z4K8	TRI46_HUMAN	tripartite motif containing 46	209						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	29	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;6.62e-10)|all cancers(21;2.68e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CACCCAGAAGGCCCAGCATGA	0.652																																					p.A209S		Atlas-SNP	.											.	TRIM46	79	.	0			c.G625T						.						37.0	38.0	38.0					1																	155148663		2202	4298	6500	SO:0001583	missense	80128	exon3			CAGAAGGCCCAGC		CCDS1097.1, CCDS58033.1, CCDS60285.1, CCDS72932.1, CCDS72931.1	1q22	2013-01-09	2011-01-25		ENSG00000163462	ENSG00000163462		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19019	protein-coding gene	gene with protein product		600986	"""tripartite motif-containing 46"""				Standard	NM_025058		Approved	FLJ23229, TRIFIC	uc001fhs.2	Q7Z4K8	OTTHUMG00000035680	ENST00000334634.4:c.625G>T	chr1.hg19:g.155148663G>T	ENSP00000334657:p.Ala209Ser	44.0	0.0		50.0	25.0	NM_025058	A0AVI6|B1AVQ4|Q5VT60|Q5VT62|Q6NT17|Q6NT41|Q6ZRL7|Q9H5P2	Missense_Mutation	SNP	ENST00000334634.4	hg19	CCDS1097.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943409	0.92593	.	.	ENSG00000163462	ENST00000543729;ENST00000430513;ENST00000368385;ENST00000545012;ENST00000392451;ENST00000368383;ENST00000368382;ENST00000334634	T;T;T;T;T;T;T	0.68624	0.71;0.4;-0.34;0.64;0.33;0.08;0.14	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	D	0.82444	0.5038	M	0.88377	2.95	0.54753	D	0.999989	D;D;D;D;D	0.89917	0.996;1.0;0.999;1.0;0.999	D;D;D;D;D	0.91635	0.986;0.999;0.987;0.999;0.994	D	0.85594	0.1248	10	0.87932	D	0	.	16.6522	0.85219	0.0:0.0:1.0:0.0	.	196;209;186;209;209	F5H5Z2;Q5VT61;B1AVQ4;Q7Z4K8;Q7Z4K8-2	.;.;.;TRI46_HUMAN;.	S	216;196;209;83;209;209;186;209	ENSP00000442719:A216S;ENSP00000357369:A209S;ENSP00000440254:A83S;ENSP00000376245:A209S;ENSP00000357367:A209S;ENSP00000357366:A186S;ENSP00000334657:A209S	ENSP00000334657:A209S	A	+	1	0	TRIM46	153415287	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.344000	0.97050	2.596000	0.87737	0.561000	0.74099	GCC	.	.		0.652	TRIM46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086728.1	NM_025058	
ASH1L	55870	hgsc.bcm.edu	37	1	155385687	155385687	+	Silent	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:155385687G>T	ENST00000368346.3	-	6	6495	c.5856C>A	c.(5854-5856)ccC>ccA	p.P1952P	snoU13_ENST00000458873.1_RNA|ASH1L_ENST00000392403.3_Silent_p.P1952P			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	1952					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			CAGAAGGACTGGGAATCTCAA	0.388																																					p.P1952P		Atlas-SNP	.											.	ASH1L	279	.	0			c.C5856A						.						75.0	75.0	75.0					1																	155385687		2203	4300	6503	SO:0001819	synonymous_variant	55870	exon6			AGGACTGGGAATC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.5856C>A	chr1.hg19:g.155385687G>T		59.0	0.0		89.0	4.0	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.		0.388	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
MROH9	80133	hgsc.bcm.edu	37	1	170967421	170967421	+	Silent	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:170967421T>C	ENST00000367758.3	+	15	1701	c.1602T>C	c.(1600-1602)agT>agC	p.S534S	MROH9_ENST00000367759.4_Intron	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	534																	CTGAAGTGAGTTTTGTAGACT	0.393																																					p.S534S		Atlas-SNP	.											.	.	.	.	0			c.T1602C						.						186.0	167.0	173.0					1																	170967421		1846	4085	5931	SO:0001819	synonymous_variant	80133	exon15			AGTGAGTTTTGTA	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.1602T>C	chr1.hg19:g.170967421T>C		79.0	0.0		83.0	4.0	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Silent	SNP	ENST00000367758.3	hg19	CCDS41436.1																																																																																			.	.		0.393	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
RGL1	23179	hgsc.bcm.edu	37	1	183891363	183891363	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:183891363G>A	ENST00000360851.3	+	17	2190	c.2012G>A	c.(2011-2013)aGc>aAc	p.S671N	RGL1_ENST00000304685.4_Missense_Mutation_p.S706N|RGL1_ENST00000536277.1_Missense_Mutation_p.S669N|RGL1_ENST00000539189.1_Missense_Mutation_p.S642N			Q9NZL6	RGL1_HUMAN	ral guanine nucleotide dissociation stimulator-like 1	671	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				cellular lipid metabolic process (GO:0044255)|positive regulation of Ral GTPase activity (GO:0032852)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(5)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(17)|ovary(4)|prostate(3)|stomach(1)	51						CAGTTGACGAGCCAGGATAAA	0.517											OREG0014047	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S706N		Atlas-SNP	.											.	RGL1	91	.	0			c.G2117A						.						70.0	64.0	66.0					1																	183891363		2203	4300	6503	SO:0001583	missense	23179	exon18			TGACGAGCCAGGA	AF186780	CCDS1359.1, CCDS72992.1	1q25.2	2008-02-05			ENSG00000143344	ENSG00000143344			30281	protein-coding gene	gene with protein product		605667				10760592, 10231032	Standard	XM_005245010		Approved	RGL	uc001gqm.3	Q9NZL6	OTTHUMG00000035328	ENST00000360851.3:c.2012G>A	chr1.hg19:g.183891363G>A	ENSP00000354097:p.Ser671Asn	140.0	0.0	1987	131.0	17.0	NM_015149	Q5SXQ2|Q5SXQ6|Q9HBY3|Q9HBY4|Q9NZL5|Q9UG43|Q9Y2G6	Missense_Mutation	SNP	ENST00000360851.3	hg19		.	.	.	.	.	.	.	.	.	.	G	13.40	2.224580	0.39300	.	.	ENSG00000143344	ENST00000304685;ENST00000367531;ENST00000536277;ENST00000360851;ENST00000539189	T;T;T;T;T	0.47177	0.85;0.85;0.85;0.85;0.85	5.29	5.29	0.74685	Ras-association (3);	0.087292	0.85682	D	0.000000	T	0.37461	0.1004	L	0.33245	0.995	0.43647	D	0.996058	B;B;B;B	0.17465	0.01;0.022;0.008;0.022	B;B;B;B	0.23716	0.02;0.048;0.028;0.028	T	0.12967	-1.0527	10	0.22109	T	0.4	.	13.2635	0.60120	0.0778:0.0:0.9222:0.0	.	642;669;671;706	F5H6U6;B7Z2W5;Q9NZL6;Q5SXQ6	.;.;RGL1_HUMAN;.	N	706;706;669;671;642	ENSP00000303192:S706N;ENSP00000356501:S706N;ENSP00000438662:S669N;ENSP00000354097:S671N;ENSP00000437355:S642N	ENSP00000303192:S706N	S	+	2	0	RGL1	182157986	1.000000	0.71417	1.000000	0.80357	0.416000	0.31233	3.166000	0.50785	2.614000	0.88457	0.655000	0.94253	AGC	.	.		0.517	RGL1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000085742.1	NM_015149	
HMCN1	83872	hgsc.bcm.edu	37	1	186120388	186120388	+	Missense_Mutation	SNP	G	G	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:186120388G>C	ENST00000271588.4	+	94	14894	c.14665G>C	c.(14665-14667)Gga>Cga	p.G4889R	HMCN1_ENST00000367492.2_Missense_Mutation_p.G4889R	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4889	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGTTGAATTTGGAATTGCTTT	0.393																																					p.G4889R		Atlas-SNP	.											.	HMCN1	797	.	0			c.G14665C						.						141.0	141.0	141.0					1																	186120388		2203	4300	6503	SO:0001583	missense	83872	exon94			GAATTTGGAATTG	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.14665G>C	chr1.hg19:g.186120388G>C	ENSP00000271588:p.Gly4889Arg	86.0	0.0		85.0	22.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	hg19	CCDS30956.1	.	.	.	.	.	.	.	.	.	.	G	27.0	4.792151	0.90453	.	.	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.32023	1.47;1.47	5.13	5.13	0.70059	G2 nidogen/fibulin G2F (2);Green fluorescent protein-like (1);	0.000000	0.85682	D	0.000000	T	0.60327	0.2260	M	0.81341	2.54	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.66388	-0.5936	10	0.87932	D	0	.	18.5888	0.91200	0.0:0.0:1.0:0.0	.	4889	Q96RW7	HMCN1_HUMAN	R	4889	ENSP00000271588:G4889R;ENSP00000356462:G4889R	ENSP00000271588:G4889R	G	+	1	0	HMCN1	184387011	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.476000	0.97823	2.373000	0.80994	0.655000	0.94253	GGA	.	.		0.393	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
PLEKHA6	22874	hgsc.bcm.edu	37	1	204197269	204197269	+	Silent	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:204197269C>A	ENST00000272203.3	-	21	3289	c.2973G>T	c.(2971-2973)cgG>cgT	p.R991R	PLEKHA6_ENST00000414478.1_Silent_p.R1011R	NM_014935.4	NP_055750.2	Q9Y2H5	PKHA6_HUMAN	pleckstrin homology domain containing, family A member 6	991										breast(2)|endometrium(6)|kidney(1)|large_intestine(9)|lung(21)|ovary(3)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_cancers(21;0.0222)|Breast(84;0.179)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|BRCA - Breast invasive adenocarcinoma(75;0.0833)|Kidney(21;0.0934)|Epithelial(59;0.229)			AGATTTCAATCCGCTTCTCCT	0.657																																					p.R991R		Atlas-SNP	.											.	PLEKHA6	115	.	0			c.G2973T						.						44.0	43.0	44.0					1																	204197269		2203	4300	6503	SO:0001819	synonymous_variant	22874	exon21			TTCAATCCGCTTC	AB023186	CCDS1444.1	1q32	2013-01-10			ENSG00000143850	ENSG00000143850		"""Pleckstrin homology (PH) domain containing"""	17053	protein-coding gene	gene with protein product		607771				11001876	Standard	NM_014935		Approved	PEPP3, KIAA0969	uc001hau.4	Q9Y2H5	OTTHUMG00000036057	ENST00000272203.3:c.2973G>T	chr1.hg19:g.204197269C>A		59.0	0.0		84.0	31.0	NM_014935	A7MD51|Q5VTI6	Silent	SNP	ENST00000272203.3	hg19	CCDS1444.1																																																																																			.	.		0.657	PLEKHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087889.3	NM_014935	
OR2L5	81466	hgsc.bcm.edu	37	1	248186037	248186037	+	Missense_Mutation	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:248186037C>T	ENST00000355281.1	+	1	788	c.788C>T	c.(787-789)tCc>tTc	p.S263F	OR2L13_ENST00000366478.2_Intron	NM_001258284.1	NP_001245213.1	Q8NG80	OR2L5_HUMAN	olfactory receptor, family 2, subfamily L, member 5	263						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)										TGTCCAAGATCCCTGCGATCT	0.493																																					p.S263F		Atlas-SNP	.											.	.	.	.	0			c.C788T						.																																			SO:0001583	missense	81466	exon1			CAAGATCCCTGCG		CCDS58068.1	1q44	2012-08-09		2004-03-10	ENSG00000197454	ENSG00000197454		"""GPCR / Class A : Olfactory receptors"""	15011	protein-coding gene	gene with protein product				OR2L11, OR2L5P			Standard	NM_001258284		Approved		uc031psy.1	Q8NG80	OTTHUMG00000040194	ENST00000355281.1:c.788C>T	chr1.hg19:g.248186037C>T	ENSP00000347428:p.Ser263Phe	144.0	0.0		191.0	67.0	NM_001258284	Q6IF04	Missense_Mutation	SNP	ENST00000355281.1	hg19	CCDS58068.1	.	.	.	.	.	.	.	.	.	.	.	3.357	-0.131294	0.06753	.	.	ENSG00000197454	ENST00000355281	T	0.00267	8.38	2.17	1.16	0.20824	.	0.287810	0.18788	U	0.131132	T	0.00210	0.0006	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.36553	-0.9743	7	0.66056	D	0.02	.	8.3483	0.32286	0.2377:0.7623:0.0:0.0	.	.	.	.	F	263	ENSP00000347428:S263F	ENSP00000347428:S263F	S	+	2	0	OR2L5	246252660	0.000000	0.05858	0.015000	0.15790	0.271000	0.26615	0.159000	0.16442	0.077000	0.16863	0.184000	0.17185	TCC	.	.		0.493	OR2L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096851.1		
TPO	7173	hgsc.bcm.edu	37	2	1437304	1437304	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:1437304G>A	ENST00000345913.4	+	4	365	c.274G>A	c.(274-276)Gag>Aag	p.E92K	TPO_ENST00000329066.4_Missense_Mutation_p.E92K|TPO_ENST00000346956.3_Missense_Mutation_p.E92K|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Missense_Mutation_p.E92K|TPO_ENST00000539820.1_Missense_Mutation_p.E92K|TPO_ENST00000337415.3_Missense_Mutation_p.E92K|TPO_ENST00000382201.3_Missense_Mutation_p.E92K|TPO_ENST00000382269.3_Missense_Mutation_p.E92K|TPO_ENST00000382198.1_Missense_Mutation_p.E92K	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	92					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	CCGAGCAGCAGAGATAATGGA	0.458																																					p.E92K		Atlas-SNP	.											.	TPO	224	.	0			c.G274A						.						119.0	107.0	111.0					2																	1437304		2203	4300	6503	SO:0001583	missense	7173	exon4			GCAGCAGAGATAA		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.274G>A	chr2.hg19:g.1437304G>A	ENSP00000318820:p.Glu92Lys	210.0	0.0		156.0	8.0	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.942694	0.53079	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198;ENST00000422464	T;T;T;T;T;T;T;T;T;T;T	0.71222	-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55;-0.55	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	D	0.83238	0.5211	M	0.78637	2.42	0.35311	D	0.78387	D;D;D;D;D	0.89917	1.0;0.974;1.0;1.0;0.999	D;P;D;D;D	0.97110	0.988;0.854;1.0;0.988;0.962	D	0.89140	0.3516	10	0.72032	D	0.01	-30.1919	13.9712	0.64242	0.0:0.0:1.0:0.0	.	92;92;92;92;92	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	K	92;92;92;92;92;92;92;92;92;92;21	ENSP00000371704:E92K;ENSP00000337263:E92K;ENSP00000318820:E92K;ENSP00000263886:E92K;ENSP00000332044:E92K;ENSP00000444840:E92K;ENSP00000329869:E92K;ENSP00000371636:E92K;ENSP00000390994:E92K;ENSP00000371633:E92K;ENSP00000405788:E21K	ENSP00000329869:E92K	E	+	1	0	TPO	1416311	1.000000	0.71417	0.256000	0.24389	0.138000	0.21146	5.001000	0.63946	2.076000	0.62316	0.563000	0.77884	GAG	.	.		0.458	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
RTN4	57142	hgsc.bcm.edu	37	2	55252314	55252314	+	Missense_Mutation	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:55252314A>G	ENST00000337526.6	-	3	3164	c.2921T>C	c.(2920-2922)gTg>gCg	p.V974A	RTN4_ENST00000405240.1_Missense_Mutation_p.V768A|RTN4_ENST00000404909.1_Missense_Mutation_p.V768A|RTN4_ENST00000354474.6_Missense_Mutation_p.V742A|RTN4_ENST00000317610.7_Intron|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000357376.3_Missense_Mutation_p.V768A|RTN4_ENST00000394611.2_Missense_Mutation_p.V768A|RTN4_ENST00000357732.4_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	974					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						AGCTTCTTTCACAAGAACTTT	0.413																																					p.V974A		Atlas-SNP	.											.	RTN4	189	.	0			c.T2921C						.						141.0	138.0	139.0					2																	55252314		2203	4300	6503	SO:0001583	missense	57142	exon3			TCTTTCACAAGAA	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.2921T>C	chr2.hg19:g.55252314A>G	ENSP00000337838:p.Val974Ala	66.0	0.0		68.0	17.0	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	hg19	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	A	0.492	-0.874843	0.02550	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.17854	2.25;2.25;2.25;2.25;2.25;2.26	5.51	-4.23	0.03789	.	1.271090	0.05534	N	0.564520	T	0.11665	0.0284	L	0.60455	1.87	0.09310	N	1	B	0.26318	0.146	B	0.21546	0.035	T	0.34800	-0.9814	10	0.09338	T	0.73	3.2446	1.0858	0.01652	0.2259:0.2147:0.3289:0.2305	.	974	Q9NQC3	RTN4_HUMAN	A	768;768;974;768;768;742	ENSP00000384471:V768A;ENSP00000349944:V768A;ENSP00000337838:V974A;ENSP00000378109:V768A;ENSP00000385650:V768A;ENSP00000346465:V742A	ENSP00000337838:V974A	V	-	2	0	RTN4	55105818	0.994000	0.37717	0.068000	0.19968	0.488000	0.33401	0.667000	0.25112	-0.678000	0.05224	-0.250000	0.11733	GTG	.	.		0.413	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1		
TBC1D8	11138	hgsc.bcm.edu	37	2	101648734	101648734	+	Silent	SNP	C	C	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:101648734C>G	ENST00000376840.4	-	11	1886	c.1887G>C	c.(1885-1887)gtG>gtC	p.V629V	TBC1D8_ENST00000409318.1_Silent_p.V644V			O95759	TBCD8_HUMAN	TBC1 domain family, member 8 (with GRAM domain)	629	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				blood circulation (GO:0008015)|positive regulation of cell proliferation (GO:0008284)	membrane (GO:0016020)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(1)|cervix(1)|endometrium(8)|kidney(3)|large_intestine(2)|lung(12)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	32						GTTTACCGATCACTCGGTGGT	0.532																																					p.V629V		Atlas-SNP	.											.	TBC1D8	169	.	0			c.G1887C						.						71.0	76.0	74.0					2																	101648734		2098	4243	6341	SO:0001819	synonymous_variant	11138	exon11			ACCGATCACTCGG	AB024057	CCDS46375.1	2q12.1	2011-11-30			ENSG00000204634	ENSG00000204634			17791	protein-coding gene	gene with protein product	"""BUB2-like protein 1"", ""vascular Rab-GAP/TBC-containing protein"""					10373574	Standard	NM_001102426		Approved	HBLP1, VRP, AD3	uc010fiv.3	O95759	OTTHUMG00000153040	ENST00000376840.4:c.1887G>C	chr2.hg19:g.101648734C>G		159.0	0.0		114.0	24.0	NM_001102426	A6NDL4|A8K9W1|B9A6K4|Q53SQ4|Q9UQ32	Silent	SNP	ENST00000376840.4	hg19	CCDS46375.1																																																																																			.	.		0.532	TBC1D8-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376092.1	NM_007063	
B3GALT1	8708	hgsc.bcm.edu	37	2	168725799	168725799	+	Missense_Mutation	SNP	A	A	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:168725799A>T	ENST00000392690.3	+	1	342	c.250A>T	c.(250-252)Atc>Ttc	p.I84F	AC016723.4_ENST00000430546.1_RNA|B3GALT1_ENST00000305861.1_Missense_Mutation_p.I84F|AC016723.4_ENST00000436982.2_RNA			Q9Y5Z6	B3GT1_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 1	84					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	18						TGTTATCCTCATCAGCACCAC	0.433																																					p.I84F		Atlas-SNP	.											.	B3GALT1	51	.	0			c.A250T						.						76.0	77.0	77.0					2																	168725799		2203	4300	6503	SO:0001583	missense	8708	exon2			ATCCTCATCAGCA	E07739	CCDS2227.1	2q24.3	2013-02-19			ENSG00000172318	ENSG00000172318		"""Beta 3-glycosyltransferases"""	916	protein-coding gene	gene with protein product		603093				9582303	Standard	NM_020981		Approved	beta3Gal-T1	uc002udz.1	Q9Y5Z6	OTTHUMG00000132163	ENST00000392690.3:c.250A>T	chr2.hg19:g.168725799A>T	ENSP00000376456:p.Ile84Phe	109.0	0.0		76.0	15.0	NM_020981	D3DPB8|Q53SS2	Missense_Mutation	SNP	ENST00000392690.3	hg19	CCDS2227.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.095921	0.76870	.	.	ENSG00000172318	ENST00000305861;ENST00000392690	T;T	0.50813	0.73;0.73	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.67683	0.2919	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.71656	0.974	T	0.70149	-0.4951	10	0.87932	D	0	-27.9029	16.8061	0.85666	1.0:0.0:0.0:0.0	.	84	Q9Y5Z6	B3GT1_HUMAN	F	84	ENSP00000303740:I84F;ENSP00000376456:I84F	ENSP00000303740:I84F	I	+	1	0	B3GALT1	168434045	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.305000	0.96197	2.367000	0.80283	0.528000	0.53228	ATC	.	.		0.433	B3GALT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255211.2	NM_020981	
ITGAV	3685	hgsc.bcm.edu	37	2	187540572	187540572	+	Missense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:187540572C>A	ENST00000261023.3	+	28	3120	c.2846C>A	c.(2845-2847)tCt>tAt	p.S949Y	ITGAV_ENST00000433736.2_Missense_Mutation_p.S903Y|AC017101.10_ENST00000453665.1_RNA|ITGAV_ENST00000374907.3_Missense_Mutation_p.S913Y	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	949					angiogenesis (GO:0001525)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)	p.S949Y(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	CATTCCTATTCTCTGAAGTCG	0.333																																					p.S949Y	Melanoma(58;108 1995 6081)	Atlas-SNP	.											ITGAV,rectum,carcinoma,0,1	ITGAV	124	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2846A						.						67.0	68.0	68.0					2																	187540572		2203	4299	6502	SO:0001583	missense	3685	exon28			CCTATTCTCTGAA		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"""CD molecules"", ""Integrins"""	6150	protein-coding gene	gene with protein product		193210	"""antigen identified by monoclonal antibody L230"", ""vitronectin receptor"", ""integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"""	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.2846C>A	chr2.hg19:g.187540572C>A	ENSP00000261023:p.Ser949Tyr	125.0	0.0		103.0	26.0	NM_002210	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Missense_Mutation	SNP	ENST00000261023.3	hg19	CCDS2292.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.96|18.96	3.733361|3.733361	0.69189|0.69189	.|.	.|.	ENSG00000138448|ENSG00000138448	ENST00000430709|ENST00000261023;ENST00000374907;ENST00000433736	.|T;T;T	.|0.50001	.|0.76;0.76;0.76	4.89|4.89	4.89|4.89	0.63831|0.63831	.|.	.|0.219770	.|0.40385	.|N	.|0.001110	T|T	0.61135|0.61135	0.2323|0.2323	L|L	0.59436|0.59436	1.845|1.845	0.42832|0.42832	D|D	0.994024|0.994024	.|P;D;P	.|0.54047	.|0.924;0.964;0.956	.|P;P;P	.|0.55824	.|0.459;0.785;0.459	T|T	0.64786|0.64786	-0.6325|-0.6325	5|10	.|0.62326	.|D	.|0.03	.|.	18.2525|18.2525	0.90009|0.90009	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|903;913;949	.|E7EWZ6;P06756-2;P06756	.|.;.;ITAV_HUMAN	I|Y	100|949;913;903	.|ENSP00000261023:S949Y;ENSP00000364042:S913Y;ENSP00000404291:S903Y	.|ENSP00000261023:S949Y	L|S	+|+	1|2	0|0	ITGAV|ITGAV	187248817|187248817	0.994000|0.994000	0.37717|0.37717	0.999000|0.999000	0.59377|0.59377	0.967000|0.967000	0.64934|0.64934	4.557000|4.557000	0.60782|0.60782	2.547000|2.547000	0.85894|0.85894	0.563000|0.563000	0.77884|0.77884	CTC|TCT	.	.		0.333	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210	
ZSWIM2	151112	hgsc.bcm.edu	37	2	187693382	187693382	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:187693382T>C	ENST00000295131.2	-	9	1270	c.1231A>G	c.(1231-1233)Aga>Gga	p.R411G		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	411					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			ATGATGTCTCTGTTTGAAACA	0.348																																					p.R411G		Atlas-SNP	.											.	ZSWIM2	119	.	0			c.A1231G						.						81.0	80.0	81.0					2																	187693382		2203	4300	6503	SO:0001583	missense	151112	exon9			TGTCTCTGTTTGA	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1231A>G	chr2.hg19:g.187693382T>C	ENSP00000295131:p.Arg411Gly	57.0	0.0		52.0	16.0	NM_182521	B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	hg19	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	T	5.928	0.355220	0.11239	.	.	ENSG00000163012	ENST00000295131	T	0.24151	1.87	5.3	0.13	0.14746	.	0.887848	0.09682	N	0.769573	T	0.13798	0.0334	N	0.22421	0.69	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.33343	-0.9872	10	0.24483	T	0.36	0.7174	3.6817	0.08313	0.1647:0.3355:0.0:0.4999	.	411	Q8NEG5	ZSWM2_HUMAN	G	411	ENSP00000295131:R411G	ENSP00000295131:R411G	R	-	1	2	ZSWIM2	187401627	0.000000	0.05858	0.053000	0.19242	0.219000	0.24729	0.295000	0.19065	0.073000	0.16731	0.482000	0.46254	AGA	.	.		0.348	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
SDPR	8436	hgsc.bcm.edu	37	2	192701015	192701015	+	Silent	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:192701015C>T	ENST00000304141.4	-	2	1241	c.912G>A	c.(910-912)gaG>gaA	p.E304E		NM_004657.5	NP_004648.1			serum deprivation response											NS(1)|central_nervous_system(1)|cervix(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(3)	23			OV - Ovarian serous cystadenocarcinoma(117;0.0647)			GGCTTTCTCCCTCTCGGACTT	0.483																																					p.E304E		Atlas-SNP	.											.	SDPR	67	.	0			c.G912A						.						98.0	106.0	103.0					2																	192701015		2203	4300	6503	SO:0001819	synonymous_variant	8436	exon2			TTCTCCCTCTCGG	AF085481	CCDS2313.1	2q32-q33	2011-04-20	2009-09-18		ENSG00000168497	ENSG00000168497			10690	protein-coding gene	gene with protein product	"""phosphatidylserine binding protein"""	606728	"""serum deprivation response (phosphatidylserine-binding protein)"", ""serum deprivation response (phosphatidylserine binding protein)"""			10191091, 8241023	Standard	NM_004657		Approved	SDR, PS-p68, cavin-2, CAVIN2	uc002utb.3	O95810	OTTHUMG00000154309	ENST00000304141.4:c.912G>A	chr2.hg19:g.192701015C>T		94.0	0.0		76.0	19.0	NM_004657		Silent	SNP	ENST00000304141.4	hg19	CCDS2313.1																																																																																			.	.		0.483	SDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334791.2	NM_004657	
HECW2	57520	hgsc.bcm.edu	37	2	197080657	197080657	+	Silent	SNP	T	T	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:197080657T>A	ENST00000260983.3	-	28	4721	c.4539A>T	c.(4537-4539)tcA>tcT	p.S1513S	HECW2_ENST00000409111.1_Silent_p.S1157S|snoU13_ENST00000459047.1_RNA	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1513	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCCCTCGGAGTGAAGCAAATC	0.443																																					p.S1513S		Atlas-SNP	.											.	HECW2	239	.	0			c.A4539T						.						76.0	76.0	76.0					2																	197080657		2203	4300	6503	SO:0001819	synonymous_variant	57520	exon28			TCGGAGTGAAGCA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4539A>T	chr2.hg19:g.197080657T>A		43.0	0.0		58.0	21.0	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	hg19	CCDS33354.1																																																																																			.	.		0.443	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
COL6A3	1293	hgsc.bcm.edu	37	2	238255172	238255172	+	Nonsense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr2:238255172C>A	ENST00000295550.4	-	32	7518	c.7066G>T	c.(7066-7068)Gga>Tga	p.G2356*	COL6A3_ENST00000409809.1_Nonsense_Mutation_p.G2150*|COL6A3_ENST00000353578.4_Nonsense_Mutation_p.G2150*|COL6A3_ENST00000472056.1_Nonsense_Mutation_p.G1749*|COL6A3_ENST00000347401.3_Nonsense_Mutation_p.G2155*|COL6A3_ENST00000346358.4_Nonsense_Mutation_p.G2156*	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2356	Collagen-like 5.|Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CCAGGGTCTCCCTTCTGTCCA	0.512																																					p.G2356X		Atlas-SNP	.											.	COL6A3	608	.	0			c.G7066T						.						102.0	99.0	100.0					2																	238255172		2203	4300	6503	SO:0001587	stop_gained	1293	exon32			GGTCTCCCTTCTG	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7066G>T	chr2.hg19:g.238255172C>A	ENSP00000295550:p.Gly2356*	102.0	0.0		91.0	21.0	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Nonsense_Mutation	SNP	ENST00000295550.4	hg19	CCDS33412.1	.	.	.	.	.	.	.	.	.	.	C	50	16.720992	0.99870	.	.	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358	.	.	.	5.23	5.23	0.72850	.	0.000000	0.52532	D	0.000075	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	19.197	0.93693	0.0:1.0:0.0:0.0	.	.	.	.	X	2356;2155;2150;1749;2150;2156	.	ENSP00000295550:G2356X	G	-	1	0	COL6A3	237919911	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.233000	0.78125	2.605000	0.88082	0.655000	0.94253	GGA	.	.		0.512	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266113	41266113	+	Missense_Mutation	SNP	C	C	T	rs121913416|rs121913403		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:41266113C>T	ENST00000349496.5	+	3	390	c.110C>T	c.(109-111)tCt>tTt	p.S37F	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30F|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37F|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37F|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37F	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	37			S -> A (in MDB and hepatocellular carcinoma; enhances transactivation of target genes). {ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> C (in PTR, hepatoblastoma and ovarian cancer). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10391090, ECO:0000269|PubMed:9927029}.|S -> F (in PTR). {ECO:0000269|PubMed:10192393}.|S -> Y (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|SG -> W (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S37F(172)|p.S37C(141)|p.A5_A80del(53)|p.S37Y(31)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.A5_Q143>E(1)|p.S37_G48>C(1)|p.A13_R151del(1)|p.H36_E53>L(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.I35_K170del(1)|p.H24_G38del(1)|p.I35_T41del(1)|p.I35_G38del(1)|p.Y30_A97del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.D32fs*9(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.GIHS34?(1)|p.S37_G38>W(1)|p.Y30_A80del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		GGAATCCATTCTGGTGCCACT	0.498	S37C(JHUEM2_ENDOMETRIUM)|S37C(SNU398_LIVER)|S37F(HUTU80_SMALL_INTESTINE)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.S37F	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,0,1	CTNNB1	4904	.	474	Substitution - Missense(344)|Deletion - In frame(102)|Complex - deletion inframe(18)|Unknown(7)|Deletion - Frameshift(3)	liver(145)|endometrium(64)|stomach(38)|skin(34)|ovary(33)|central_nervous_system(28)|pancreas(28)|large_intestine(22)|pituitary(22)|lung(21)|biliary_tract(15)|thyroid(4)|soft_tissue(4)|urinary_tract(4)|small_intestine(3)|oesophagus(3)|adrenal_gland(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|bone(1)|breast(1)	c.C110T						.						93.0	78.0	83.0					3																	41266113		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TCCATTCTGGTGC	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.110C>T	chr3.hg19:g.41266113C>T	ENSP00000344456:p.Ser37Phe	253.0	0.0		257.0	96.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.513375	0.85389	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73;0.73	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72819	0.3508	M	0.80183	2.485	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.75297	-0.3367	10	0.87932	D	0	-15.9763	19.9596	0.97236	0.0:1.0:0.0:0.0	.	37	P35222	CTNB1_HUMAN	F	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30F;ENSP00000385604:S37F;ENSP00000412219:S37F;ENSP00000379486:S37F;ENSP00000344456:S37F;ENSP00000411226:S30F;ENSP00000379488:S37F;ENSP00000409302:S37F;ENSP00000401599:S37F	ENSP00000344456:S37F	S	+	2	0	CTNNB1	41241117	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.498	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
FLNB	2317	hgsc.bcm.edu	37	3	58116537	58116537	+	Missense_Mutation	SNP	T	T	A	rs80356511		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:58116537T>A	ENST00000295956.4	+	25	4457	c.4292T>A	c.(4291-4293)cTg>cAg	p.L1431Q	FLNB_ENST00000490882.1_Missense_Mutation_p.L1431Q|FLNB_ENST00000493452.1_Missense_Mutation_p.L1262Q|FLNB_ENST00000358537.3_Missense_Mutation_p.L1431Q|FLNB_ENST00000357272.4_Missense_Mutation_p.L1431Q|FLNB_ENST00000348383.5_Missense_Mutation_p.L1431Q|FLNB_ENST00000429972.2_Missense_Mutation_p.L1431Q|FLNB_ENST00000419752.2_Missense_Mutation_p.L1262Q	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	1431	Interaction with FBLP1.		L -> R (in LRS). {ECO:0000269|PubMed:16801345}.		actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GGCCCCGGGCTGGGCTCAGGC	0.637																																					p.L1431Q		Atlas-SNP	.											.	FLNB	430	.	0			c.T4292A	GRCh37	CM070931	FLNB	M	rs80356511	.						30.0	31.0	31.0					3																	58116537		2203	4300	6503	SO:0001583	missense	2317	exon25			CCGGGCTGGGCTC	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.4292T>A	chr3.hg19:g.58116537T>A	ENSP00000295956:p.Leu1431Gln	109.0	0.0		101.0	20.0	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Missense_Mutation	SNP	ENST00000295956.4	hg19	CCDS2885.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.847091	0.91277	.	.	ENSG00000136068	ENST00000295956;ENST00000490882;ENST00000358537;ENST00000429972;ENST00000348383;ENST00000357272;ENST00000493452;ENST00000419752	D;D;D;D;D;D;D;D	0.87334	-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24;-2.24	5.51	5.51	0.81932	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.289256	0.34362	N	0.004037	D	0.95809	0.8636	H	0.97340	3.985	0.58432	D	0.999998	D;D;D;D;D;D	0.71674	0.984;0.996;0.974;0.998;0.987;0.987	P;D;D;D;D;D	0.71184	0.847;0.972;0.944;0.971;0.936;0.936	D	0.97172	0.9845	10	0.62326	D	0.03	.	15.6399	0.76989	0.0:0.0:0.0:1.0	.	1431;1431;1262;1262;1431;1431	O75369-2;B2ZZ83;E7EN95;O75369-7;Q60FE7;O75369	.;.;.;.;.;FLNB_HUMAN	Q	1431;1431;1431;1431;1431;1431;1262;1262	ENSP00000295956:L1431Q;ENSP00000420213:L1431Q;ENSP00000351339:L1431Q;ENSP00000415599:L1431Q;ENSP00000232447:L1431Q;ENSP00000349819:L1431Q;ENSP00000418510:L1262Q;ENSP00000414532:L1262Q	ENSP00000295956:L1431Q	L	+	2	0	FLNB	58091577	1.000000	0.71417	0.954000	0.39281	0.994000	0.84299	8.040000	0.89188	2.103000	0.63969	0.533000	0.62120	CTG	.	.		0.637	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
KY	339855	hgsc.bcm.edu	37	3	134338015	134338015	+	Missense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:134338015C>A	ENST00000423778.2	-	8	746	c.685G>T	c.(685-687)Gct>Tct	p.A229S	KY_ENST00000508041.1_5'UTR|KY_ENST00000508956.1_Missense_Mutation_p.A208S|KY_ENST00000503669.1_Missense_Mutation_p.A229S	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	229					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						AAGAGGCCAGCATAGCCATCA	0.562																																					p.A229S		Atlas-SNP	.											.	KY	92	.	0			c.G685T						.						149.0	154.0	152.0					3																	134338015		2116	4237	6353	SO:0001583	missense	339855	exon8			GGCCAGCATAGCC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.685G>T	chr3.hg19:g.134338015C>A	ENSP00000397598:p.Ala229Ser	176.0	0.0		206.0	53.0	NM_178554	B7Z1S4|Q6ZT15	Missense_Mutation	SNP	ENST00000423778.2	hg19	CCDS46920.1	.	.	.	.	.	.	.	.	.	.	C	16.44	3.124822	0.56613	.	.	ENSG00000174611	ENST00000508956;ENST00000423778;ENST00000503669;ENST00000310263	T;T;T	0.39787	1.06;1.06;1.06	4.61	3.7	0.42460	.	0.152126	0.43260	N	0.000592	T	0.45856	0.1363	N	0.25992	0.78	0.39035	D	0.960024	P;D;D	0.52996	0.955;0.957;0.957	P;P;P	0.59595	0.717;0.86;0.728	T	0.42172	-0.9467	10	0.37606	T	0.19	-6.4357	13.6599	0.62361	0.156:0.844:0.0:0.0	.	208;229;229	Q8NBH2-3;B4DGA7;Q8NBH2-4	.;.;.	S	208;229;229;229	ENSP00000421297:A208S;ENSP00000397598:A229S;ENSP00000426777:A229S	ENSP00000309520:A229S	A	-	1	0	KY	135820705	0.996000	0.38824	0.780000	0.31762	0.518000	0.34316	3.716000	0.54904	0.869000	0.35703	0.462000	0.41574	GCT	.	.		0.562	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
ATP13A4	84239	hgsc.bcm.edu	37	3	193159259	193159259	+	Missense_Mutation	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:193159259G>T	ENST00000342695.4	-	20	2757	c.2435C>A	c.(2434-2436)cCa>cAa	p.P812Q	ATP13A4_ENST00000392443.3_Missense_Mutation_p.P793Q	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	812						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		ACTTACCTTTGGCAGTAGGCT	0.388																																					p.P812Q		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C2435A						.						135.0	124.0	128.0					3																	193159259		2203	4300	6503	SO:0001583	missense	84239	exon20			ACCTTTGGCAGTA	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.2435C>A	chr3.hg19:g.193159259G>T	ENSP00000339182:p.Pro812Gln	164.0	0.0		149.0	64.0	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Missense_Mutation	SNP	ENST00000342695.4	hg19	CCDS3304.2	.	.	.	.	.	.	.	.	.	.	G	19.55	3.848075	0.71603	.	.	ENSG00000127249	ENST00000392443;ENST00000342695	D;D	0.85773	-1.74;-2.03	6.03	6.03	0.97812	HAD-like domain (2);	0.078821	0.53938	D	0.000042	D	0.86977	0.6063	L	0.40543	1.245	0.80722	D	1	P;P;P	0.49358	0.923;0.68;0.923	P;P;P	0.56865	0.808;0.615;0.808	D	0.86580	0.1853	10	0.52906	T	0.07	-12.8445	14.0229	0.64568	0.0:0.0:0.8489:0.1511	.	793;812;812	B7WPN9;Q4VNC1-2;Q4VNC1	.;.;AT134_HUMAN	Q	793;812	ENSP00000376238:P793Q;ENSP00000339182:P812Q	ENSP00000339182:P812Q	P	-	2	0	ATP13A4	194641953	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.763000	0.62257	2.854000	0.98071	0.655000	0.94253	CCA	.	.		0.388	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
ZNF595	152687	hgsc.bcm.edu	37	4	59340	59340	+	Missense_Mutation	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:59340G>T	ENST00000509152.2	+	2	206	c.21G>T	c.(19-21)agG>agT	p.R7S	ZNF595_ENST00000339368.6_3'UTR|ZNF595_ENST00000526473.2_Missense_Mutation_p.R7S			Q8IYB9	ZN595_HUMAN	zinc finger protein 595	7	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)	20		all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0654)|Epithelial(2;0.0921)|all cancers(2;0.146)|LUSC - Lung squamous cell carcinoma(95;0.173)		TAACATTCAGGGATGTGGCCA	0.418																																					p.R7S		Atlas-SNP	.											.	.	.	.	0			c.G21T						.						358.0	385.0	376.0					4																	59340		2203	4300	6503	SO:0001583	missense	255403	exon2			ATTCAGGGATGTG	BX537887	CCDS75075.1, CCDS75076.1, CCDS75077.1	4p16.3	2013-01-08				ENSG00000272602		"""Zinc fingers, C2H2-type"", ""-"""	27196	protein-coding gene	gene with protein product						12477932	Standard	NM_182524		Approved	FLJ31740		Q8IYB9		ENST00000509152.2:c.21G>T	chr4.hg19:g.59340G>T	ENSP00000434858:p.Arg7Ser	328.0	0.0		308.0	18.0	NM_001039127		Missense_Mutation	SNP	ENST00000509152.2	hg19		.	.	.	.	.	.	.	.	.	.	G	11.89	1.773554	0.31411	.	.	ENSG00000197701	ENST00000509152;ENST00000526473	T;T	0.01787	4.64;4.64	1.26	1.26	0.21427	Krueppel-associated box (4);	.	.	.	.	T	0.01835	0.0058	.	.	.	0.24906	N	0.992073	B	0.26775	0.159	B	0.30179	0.112	T	0.45425	-0.9262	8	0.72032	D	0.01	.	4.5605	0.12158	0.0:0.0:0.6249:0.3751	.	7	Q8IYB9	ZN595_HUMAN	S	7	ENSP00000434858:R7S;ENSP00000437878:R7S	ENSP00000434858:R7S	R	+	3	2	ZNF595	49340	0.920000	0.31207	0.528000	0.27938	0.224000	0.24922	0.731000	0.26058	0.655000	0.30866	0.484000	0.47621	AGG	.	.		0.418	ZNF595-004	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000357817.2	NM_182524	
SORCS2	57537	hgsc.bcm.edu	37	4	7726889	7726889	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:7726889C>T	ENST00000507866.2	+	20	2729	c.2620C>T	c.(2620-2622)Cag>Tag	p.Q874*	SORCS2_ENST00000329016.9_Nonsense_Mutation_p.Q702*	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	874	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.				neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						AGCCCCCCTGCAGGCCCTCTA	0.552																																					p.Q874X		Atlas-SNP	.											.	SORCS2	98	.	0			c.C2620T						.						77.0	80.0	79.0					4																	7726889		1926	4118	6044	SO:0001587	stop_gained	57537	exon20			CCCCTGCAGGCCC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.2620C>T	chr4.hg19:g.7726889C>T	ENSP00000422185:p.Gln874*	61.0	0.0		56.0	12.0	NM_020777	Q9P2L7	Nonsense_Mutation	SNP	ENST00000507866.2	hg19	CCDS47008.1	.	.	.	.	.	.	.	.	.	.	C	37	6.109498	0.97291	.	.	ENSG00000184985	ENST00000507866;ENST00000329016	.	.	.	3.41	3.41	0.39046	.	0.367852	0.24752	U	0.035899	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	14.8181	0.70050	0.0:1.0:0.0:0.0	.	.	.	.	X	874;702	.	ENSP00000329124:Q702X	Q	+	1	0	SORCS2	7777789	1.000000	0.71417	1.000000	0.80357	0.378000	0.30076	6.721000	0.74728	1.465000	0.48006	0.453000	0.30009	CAG	.	.		0.552	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
PDS5A	23244	hgsc.bcm.edu	37	4	39876002	39876002	+	Silent	SNP	T	T	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:39876002T>A	ENST00000303538.8	-	20	2723	c.2184A>T	c.(2182-2184)gcA>gcT	p.A728A		NM_001100399.1	NP_001093869.1			PDS5, regulator of cohesion maintenance, homolog A (S. cerevisiae)											breast(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(14)|prostate(3)|skin(1)|urinary_tract(1)	39						TACCCCTCTTTGCTTTTTGAT	0.358																																					p.A728A		Atlas-SNP	.											.	PDS5A	114	.	0			c.A2184T						.						127.0	116.0	119.0					4																	39876002		1822	4085	5907	SO:0001819	synonymous_variant	23244	exon20			CCTCTTTGCTTTT	AF294791	CCDS47045.1, CCDS54759.1	4p14	2007-06-20			ENSG00000121892	ENSG00000121892			29088	protein-coding gene	gene with protein product		613200				11076961, 15855230	Standard	NM_001100399		Approved	KIAA0648, PIG54, SCC-112	uc003guv.4	Q29RF7	OTTHUMG00000160582	ENST00000303538.8:c.2184A>T	chr4.hg19:g.39876002T>A		55.0	0.0		69.0	14.0	NM_001100399		Silent	SNP	ENST00000303538.8	hg19	CCDS47045.1																																																																																			.	.		0.358	PDS5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361287.1	NM_015200	
TIGD2	166815	hgsc.bcm.edu	37	4	90035516	90035516	+	Missense_Mutation	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:90035516A>G	ENST00000317005.2	+	1	1549	c.1391A>G	c.(1390-1392)aAg>aGg	p.K464R	RP11-84C13.1_ENST00000603357.1_lincRNA|FAM13A_ENST00000502459.1_5'Flank	NM_145715.2	NP_663761.1	Q4W5G0	TIGD2_HUMAN	tigger transposable element derived 2	464						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	14		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.86e-05)		CCTTCCAGTAAGAGTAGAAAA	0.453																																					p.K464R		Atlas-SNP	.											.	TIGD2	36	.	0			c.A1391G						.						51.0	50.0	51.0					4																	90035516		2203	4300	6503	SO:0001583	missense	166815	exon1			CCAGTAAGAGTAG	AK027653	CCDS3633.1	4q21.3	2013-02-21			ENSG00000180346	ENSG00000180346			18333	protein-coding gene	gene with protein product		612973					Standard	NM_145715		Approved		uc003hsk.3	Q4W5G0	OTTHUMG00000130946	ENST00000317005.2:c.1391A>G	chr4.hg19:g.90035516A>G	ENSP00000317170:p.Lys464Arg	96.0	0.0		81.0	15.0	NM_145715		Missense_Mutation	SNP	ENST00000317005.2	hg19	CCDS3633.1	.	.	.	.	.	.	.	.	.	.	A	9.901	1.206835	0.22205	.	.	ENSG00000180346	ENST00000317005	T	0.23754	1.89	4.49	3.31	0.37934	.	0.319358	0.22518	N	0.059011	T	0.13670	0.0331	L	0.36672	1.1	0.09310	N	1	P	0.35656	0.514	B	0.24394	0.053	T	0.11641	-1.0579	10	0.27785	T	0.31	-6.4638	5.2949	0.15747	0.868:0.0:0.132:0.0	.	464	Q4W5G0	TIGD2_HUMAN	R	464	ENSP00000317170:K464R	ENSP00000317170:K464R	K	+	2	0	TIGD2	90254539	0.910000	0.30920	0.133000	0.22050	0.912000	0.54170	3.019000	0.49635	1.881000	0.54492	0.383000	0.25322	AAG	.	.		0.453	TIGD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253545.2	NM_145715	
ELF2	1998	hgsc.bcm.edu	37	4	139983133	139983133	+	Missense_Mutation	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr4:139983133G>T	ENST00000394235.2	-	8	1158	c.656C>A	c.(655-657)aCt>aAt	p.T219N	ELF2_ENST00000379550.1_Missense_Mutation_p.T231N|ELF2_ENST00000379549.2_Missense_Mutation_p.T142N|ELF2_ENST00000510408.1_Missense_Mutation_p.T159N|ELF2_ENST00000265495.4_Missense_Mutation_p.T219N|ELF2_ENST00000358635.3_Missense_Mutation_p.T171N|ELF2_ENST00000515489.1_5'Flank	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					TTCTCTCTGAGTCCATTTAAT	0.363																																					p.R171K		Atlas-SNP	.											.	ELF2	43	.	0			c.G512A						.						94.0	88.0	90.0					4																	139983133		2203	4300	6503	SO:0001583	missense	1998	exon5			CTCTGAGTCCATT	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.656C>A	chr4.hg19:g.139983133G>T	ENSP00000377782:p.Thr219Asn	67.0	0.0		61.0	4.0	NM_006874		Missense_Mutation	SNP	ENST00000394235.2	hg19	CCDS3744.1	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474008	0.84640	.	.	ENSG00000109381	ENST00000358635;ENST00000394235;ENST00000379550;ENST00000265495;ENST00000379549;ENST00000540754;ENST00000510408;ENST00000420916;ENST00000512627	T;T;T;T;T;T;T;T	0.58210	0.35;0.35;0.35;0.35;0.35;0.35;0.35;0.35	5.62	5.62	0.85841	.	0.043583	0.85682	D	0.000000	T	0.75243	0.3823	M	0.85777	2.775	0.80722	D	1	P;D;P;P;D	0.56746	0.933;0.977;0.934;0.861;0.957	P;P;P;P;P	0.62813	0.857;0.907;0.892;0.846;0.9	T	0.77035	-0.2737	9	.	.	.	.	19.661	0.95871	0.0:0.0:1.0:0.0	.	34;219;142;159;171	B7Z8R4;Q15723-1;E9PCX3;B7Z720;Q15723-3	.;.;.;.;.	N	171;219;231;219;142;34;159;142;130	ENSP00000351458:T171N;ENSP00000377782:T219N;ENSP00000368868:T231N;ENSP00000265495:T219N;ENSP00000368867:T142N;ENSP00000426997:T159N;ENSP00000397796:T142N;ENSP00000426087:T130N	.	T	-	2	0	ELF2	140202583	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.835000	0.86780	2.659000	0.90383	0.655000	0.94253	ACT	.	.		0.363	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874	
CTNND2	1501	hgsc.bcm.edu	37	5	11384929	11384929	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:11384929G>A	ENST00000304623.8	-	7	1214	c.1025C>T	c.(1024-1026)tCc>tTc	p.S342F	CTNND2_ENST00000359640.2_Missense_Mutation_p.S342F|CTNND2_ENST00000495388.2_5'Flank|CTNND2_ENST00000458100.2_Intron|CTNND2_ENST00000511377.1_Missense_Mutation_p.S251F|CTNND2_ENST00000503622.1_Intron	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	342					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGGCGAGGAGGAGATGGTGGA	0.667																																					p.S342F		Atlas-SNP	.											.	CTNND2	289	.	0			c.C1025T						.						88.0	84.0	85.0					5																	11384929		2200	4299	6499	SO:0001583	missense	1501	exon7			GAGGAGGAGATGG	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.1025C>T	chr5.hg19:g.11384929G>A	ENSP00000307134:p.Ser342Phe	26.0	0.0		28.0	9.0	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	hg19	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.189372	0.78789	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000511377	T;T;T	0.79653	-1.23;-1.29;-1.25	4.19	4.19	0.49359	.	0.567752	0.16119	N	0.228731	T	0.80248	0.4588	L	0.43152	1.355	0.80722	D	1	P	0.49961	0.93	P	0.48030	0.564	T	0.82906	-0.0225	10	0.72032	D	0.01	-9.6331	16.1132	0.81278	0.0:0.0:1.0:0.0	.	342	Q9UQB3	CTND2_HUMAN	F	342;342;251	ENSP00000307134:S342F;ENSP00000352661:S342F;ENSP00000426510:S251F	ENSP00000307134:S342F	S	-	2	0	CTNND2	11437929	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	6.165000	0.71891	1.882000	0.54519	0.462000	0.41574	TCC	.	.		0.667	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
MROH2B	133558	hgsc.bcm.edu	37	5	41042223	41042223	+	Missense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:41042223C>A	ENST00000399564.4	-	19	2374	c.1924G>T	c.(1924-1926)Gct>Tct	p.A642S	MROH2B_ENST00000506092.2_Missense_Mutation_p.A197S	NM_173489.4	NP_775760.3	Q7Z745	MRO2B_HUMAN	maestro heat-like repeat family member 2B	642																	TGGTTGGGAGCAGTCAGAAAC	0.433																																					p.A642S		Atlas-SNP	.											.	.	.	.	0			c.G1924T						.						60.0	55.0	56.0					5																	41042223		1840	4092	5932	SO:0001583	missense	133558	exon19			TGGGAGCAGTCAG		CCDS47202.1	5p13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000171495	ENSG00000171495		"""maestro heat-like repeat containing"""	26857	protein-coding gene	gene with protein product			"""HEAT repeat family member 7B2"""	HEATR7B2		12477932	Standard	NM_173489		Approved	DKFZp781F0822, FLJ40243	uc003jmj.4	Q7Z745	OTTHUMG00000162151	ENST00000399564.4:c.1924G>T	chr5.hg19:g.41042223C>A	ENSP00000382476:p.Ala642Ser	87.0	0.0		80.0	32.0	NM_173489	Q68DM1|Q7Z4U4|Q8N7X3	Missense_Mutation	SNP	ENST00000399564.4	hg19	CCDS47202.1	.	.	.	.	.	.	.	.	.	.	C	11.17	1.560902	0.27827	.	.	ENSG00000171495	ENST00000506092;ENST00000296803;ENST00000399564	T;T	0.01369	4.97;5.22	5.79	-1.24	0.09435	Armadillo-type fold (1);	0.543746	0.16865	N	0.196343	T	0.01092	0.0036	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.49082	-0.8976	10	0.10636	T	0.68	.	4.9854	0.14187	0.5785:0.2413:0.0:0.1802	.	642	Q7Z745	HTRB2_HUMAN	S	197;347;642	ENSP00000441504:A197S;ENSP00000382476:A642S	ENSP00000296803:A347S	A	-	1	0	HEATR7B2	41077980	0.003000	0.15002	0.680000	0.29994	0.658000	0.38924	-0.139000	0.10358	0.053000	0.16036	0.460000	0.39030	GCT	.	.		0.433	MROH2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367558.2	NM_173489	
BDP1	55814	hgsc.bcm.edu	37	5	70840961	70840961	+	Missense_Mutation	SNP	A	A	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:70840961A>T	ENST00000358731.4	+	32	6922	c.6659A>T	c.(6658-6660)gAt>gTt	p.D2220V	BDP1_ENST00000380675.2_Missense_Mutation_p.D356V	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2220					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.D2220V(1)		NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		CTTGGTTTGGATAGGGGTCTT	0.463																																					p.D2220V		Atlas-SNP	.											BDP1,NS,carcinoma,0,1	BDP1	204	.	1	Substitution - Missense(1)	lung(1)	c.A6659T						.						115.0	109.0	111.0					5																	70840961		1845	4098	5943	SO:0001583	missense	55814	exon32			GTTTGGATAGGGG	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.6659A>T	chr5.hg19:g.70840961A>T	ENSP00000351575:p.Asp2220Val	101.0	0.0		82.0	17.0	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	hg19	CCDS43328.1	.	.	.	.	.	.	.	.	.	.	A	9.541	1.113418	0.20795	.	.	ENSG00000145734	ENST00000358731;ENST00000451951;ENST00000380675;ENST00000545546	T;T	0.45276	3.83;0.9	4.11	-8.22	0.01037	.	1.627000	0.03383	N	0.200682	T	0.32224	0.0822	L	0.44542	1.39	0.09310	N	1	P;P	0.38020	0.615;0.615	B;B	0.37091	0.124;0.241	T	0.44406	-0.9330	10	0.62326	D	0.03	.	7.8518	0.29459	0.5454:0.3054:0.1492:0.0	.	2220;2220	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	V	2220;1768;356;356	ENSP00000351575:D2220V;ENSP00000370050:D356V	ENSP00000351575:D2220V	D	+	2	0	BDP1	70876717	0.000000	0.05858	0.000000	0.03702	0.095000	0.18619	-0.446000	0.06837	-2.571000	0.00468	-0.899000	0.02877	GAT	.	.		0.463	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
GPR98	84059	hgsc.bcm.edu	37	5	89943506	89943506	+	Missense_Mutation	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:89943506A>G	ENST00000405460.2	+	17	3310	c.3214A>G	c.(3214-3216)Ata>Gta	p.I1072V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1072	Calx-beta 8. {ECO:0000255}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ACAGCAGAGCATATCCATATT	0.383																																					p.I1072V		Atlas-SNP	.											.	GPR98	605	.	0			c.A3214G						.						144.0	138.0	140.0					5																	89943506		1871	4103	5974	SO:0001583	missense	84059	exon17			CAGAGCATATCCA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3214A>G	chr5.hg19:g.89943506A>G	ENSP00000384582:p.Ile1072Val	128.0	0.0		107.0	52.0	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	hg19	CCDS47246.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	8.954|8.954	0.968848|0.968848	0.18659|0.18659	.|.	.|.	ENSG00000164199|ENSG00000164199	ENST00000504142|ENST00000405460;ENST00000296619;ENST00000399043	.|T	.|0.27890	.|1.64	5.49|5.49	-3.41|-3.41	0.04839|0.04839	.|Na-Ca exchanger/integrin-beta4 (2);	.|0.194186	.|0.53938	.|N	.|0.000058	T|T	0.25865|0.25865	0.0630|0.0630	L|L	0.60904|0.60904	1.88|1.88	0.46149|0.46149	D|D	0.998891|0.998891	.|B	.|0.31655	.|0.334	.|B	.|0.41510	.|0.359	T|T	0.13495|0.13495	-1.0507|-1.0507	5|10	.|0.49607	.|T	.|0.09	.|.	0.5087|0.5087	0.00591|0.00591	0.4146:0.1961:0.1777:0.2116|0.4146:0.1961:0.1777:0.2116	.|.	.|1072	.|Q8WXG9	.|GPR98_HUMAN	R|V	660|1072	.|ENSP00000384582:I1072V	.|ENSP00000296619:I1072V	H|I	+|+	2|1	0|0	GPR98|GPR98	89979262|89979262	0.003000|0.003000	0.15002|0.15002	0.000000|0.000000	0.03702|0.03702	0.376000|0.376000	0.30014|0.30014	0.019000|0.019000	0.13444|0.13444	-0.904000|-0.904000	0.03876|0.03876	0.528000|0.528000	0.53228|0.53228	CAT|ATA	.	.		0.383	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
KCNN2	3781	hgsc.bcm.edu	37	5	113798833	113798833	+	Silent	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:113798833C>T	ENST00000512097.3	+	5	2107	c.1089C>T	c.(1087-1089)gaC>gaT	p.D363D	KCNN2_ENST00000503706.1_Silent_p.D15D|KCNN2_ENST00000264773.3_Silent_p.D363D|KCNN2_ENST00000507750.1_3'UTR			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	363					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transport (GO:1901379)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|protein homodimerization activity (GO:0042803)|small conductance calcium-activated potassium channel activity (GO:0016286)			breast(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.86e-05)|all_epithelial(76;9.33e-06)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Breast(839;0.159)|Lung NSC(810;0.174)|all_lung(232;0.206)		OV - Ovarian serous cystadenocarcinoma(64;1.89e-08)|Epithelial(69;2.04e-08)|all cancers(49;3.74e-06)|COAD - Colon adenocarcinoma(37;0.142)|Colorectal(14;0.195)	Miconazole(DB01110)|Procaine(DB00721)	GTTATGGTGACATGGTACCTA	0.383																																					p.D363D		Atlas-SNP	.											.	KCNN2	144	.	0			c.C1089T						.						303.0	259.0	274.0					5																	113798833		2202	4300	6502	SO:0001819	synonymous_variant	3781	exon4			TGGTGACATGGTA	AF239613	CCDS4114.1, CCDS43352.1	5q22.3	2012-07-05			ENSG00000080709	ENSG00000080709		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6291	protein-coding gene	gene with protein product		605879				16382103	Standard	NM_001278204		Approved	KCa2.2, hSK2	uc003kqo.3	Q9H2S1	OTTHUMG00000128836	ENST00000512097.3:c.1089C>T	chr5.hg19:g.113798833C>T		283.0	0.0		306.0	62.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Silent	SNP	ENST00000512097.3	hg19	CCDS4114.1																																																																																			.	.		0.383	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614	
FAT2	2196	hgsc.bcm.edu	37	5	150885501	150885501	+	Silent	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:150885501G>A	ENST00000261800.5	-	23	12687	c.12675C>T	c.(12673-12675)ggC>ggT	p.G4225G		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	4225					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GGAAGGGGAAGCCCCCATAGA	0.622																																					p.G4225G		Atlas-SNP	.											.	FAT2	465	.	0			c.C12675T						.						93.0	111.0	105.0					5																	150885501		2202	4300	6502	SO:0001819	synonymous_variant	2196	exon23			GGGGAAGCCCCCA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.12675C>T	chr5.hg19:g.150885501G>A		19.0	0.0		32.0	8.0	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	hg19	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	9.683	1.149935	0.21371	.	.	ENSG00000086570	ENST00000520200	.	.	.	5.02	1.19	0.21007	.	.	.	.	.	T	0.53334	0.1790	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39251	-0.9623	4	.	.	.	.	6.2156	0.20653	0.2732:0.0:0.6077:0.1191	.	.	.	.	F	998	.	.	L	-	1	0	FAT2	150865694	1.000000	0.71417	0.997000	0.53966	0.986000	0.74619	1.567000	0.36407	-0.073000	0.12842	0.561000	0.74099	CTT	.	.		0.622	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
LCP2	3937	hgsc.bcm.edu	37	5	169689860	169689860	+	Silent	SNP	C	C	T	rs373086683		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:169689860C>T	ENST00000046794.5	-	12	1419	c.804G>A	c.(802-804)tcG>tcA	p.S268S	LCP2_ENST00000521416.1_Silent_p.S63S	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	268					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		CCGCTGGAATCGAGGGCTGCA	0.423																																					p.S268S		Atlas-SNP	.											.	LCP2	133	.	0			c.G804A						.						135.0	133.0	134.0					5																	169689860		1973	4157	6130	SO:0001819	synonymous_variant	3937	exon12			TGGAATCGAGGGC		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.804G>A	chr5.hg19:g.169689860C>T		175.0	0.0		195.0	31.0	NM_005565	A8KA25|Q53XV4	Silent	SNP	ENST00000046794.5	hg19	CCDS47339.1																																																																																			.	.		0.423	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
HRH2	3274	hgsc.bcm.edu	37	5	175110734	175110734	+	Silent	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:175110734G>A	ENST00000231683.2	+	1	2271	c.498G>A	c.(496-498)aaG>aaA	p.K166K	HRH2_ENST00000377291.2_Silent_p.K166K	NM_022304.2	NP_071640.1	P25021	HRH2_HUMAN	histamine receptor H2	166					digestive tract development (GO:0048565)|epithelial cell morphogenesis (GO:0003382)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|gastrin-induced gastric acid secretion (GO:0001698)|gland development (GO:0048732)|histamine-induced gastric acid secretion (GO:0001697)|immune response (GO:0006955)|memory (GO:0007613)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	histamine receptor activity (GO:0004969)			breast(1)|cervix(1)|endometrium(3)|large_intestine(6)|lung(10)|ovary(1)	22	all_cancers(89;0.00805)|Renal(175;0.000269)|Lung NSC(126;0.00419)|all_lung(126;0.00711)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Colorectal(1;0.0154)|COAD - Colon adenocarcinoma(1;0.149)	Amitriptyline(DB00321)|Asenapine(DB06216)|Betazole(DB00272)|Cimetidine(DB00501)|Doxepin(DB01142)|Epinastine(DB00751)|Famotidine(DB00927)|Histamine Phosphate(DB00667)|Loxapine(DB00408)|Methantheline(DB00940)|Nizatidine(DB00585)|Olanzapine(DB00334)|Ranitidine(DB00863)|Roxatidine acetate(DB08806)|Tolazoline(DB00797)	AGACCAGCAAGGGCAATCATA	0.527																																					p.K166K		Atlas-SNP	.											.	HRH2	108	.	0			c.G498A						.						114.0	94.0	101.0					5																	175110734		2203	4300	6503	SO:0001819	synonymous_variant	3274	exon2			CAGCAAGGGCAAT		CCDS4395.1, CCDS47344.1	5q35	2012-08-08			ENSG00000113749	ENSG00000113749		"""GPCR / Class A : Histamine receptors"""	5183	protein-coding gene	gene with protein product		142703				1714721	Standard	NM_022304		Approved		uc003mdc.4	P25021	OTTHUMG00000130660	ENST00000231683.2:c.498G>A	chr5.hg19:g.175110734G>A		206.0	0.0		218.0	14.0	NM_001131055	B5BUP7|Q14464|Q7Z5R9	Silent	SNP	ENST00000231683.2	hg19	CCDS4395.1																																																																																			.	.		0.527	HRH2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253151.1		
CCHCR1	54535	hgsc.bcm.edu	37	6	31113531	31113531	+	Missense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr6:31113531C>A	ENST00000376266.5	-	11	1490	c.1368G>T	c.(1366-1368)caG>caT	p.Q456H	CCHCR1_ENST00000451521.2_Missense_Mutation_p.Q509H|CCHCR1_ENST00000396268.3_Missense_Mutation_p.Q545H|CCHCR1_ENST00000396263.2_Intron	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	456					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GGCTGGGAAGCTGGGCGGCAG	0.622																																					p.Q545H		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1635T						.						92.0	80.0	84.0					6																	31113531		1511	2709	4220	SO:0001583	missense	54535	exon11			GGGAAGCTGGGCG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.1368G>T	chr6.hg19:g.31113531C>A	ENSP00000365442:p.Gln456His	92.0	0.0		78.0	25.0	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Missense_Mutation	SNP	ENST00000376266.5	hg19	CCDS4695.1	.	.	.	.	.	.	.	.	.	.	C	13.82	2.350144	0.41599	.	.	ENSG00000204536	ENST00000396268;ENST00000376266;ENST00000440185;ENST00000451521	T;T;T	0.03951	3.75;3.75;3.75	4.83	3.0	0.34707	.	0.610314	0.15113	N	0.279871	T	0.03178	0.0093	L	0.43152	1.355	0.19775	N	0.999951	P;P;P;D;P	0.54397	0.771;0.794;0.771;0.966;0.545	P;P;P;P;B	0.52267	0.606;0.601;0.606;0.694;0.371	T	0.37979	-0.9682	10	0.66056	D	0.02	-10.0625	6.7147	0.23296	0.0:0.7204:0.1804:0.0991	.	456;456;456;509;545	B4DIA2;A8K081;Q8TD31;E9PE84;Q8TD31-2	.;.;CCHCR_HUMAN;.;.	H	545;456;456;509	ENSP00000379566:Q545H;ENSP00000365442:Q456H;ENSP00000401039:Q509H	ENSP00000365442:Q456H	Q	-	3	2	CCHCR1	31221510	0.987000	0.35691	0.953000	0.39169	0.250000	0.25880	1.342000	0.33919	0.534000	0.28695	0.549000	0.68633	CAG	.	.		0.622	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
BVES	11149	hgsc.bcm.edu	37	6	105573357	105573357	+	Missense_Mutation	SNP	A	A	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr6:105573357A>T	ENST00000314641.5	-	4	664	c.448T>A	c.(448-450)Tgc>Agc	p.C150S	BVES_ENST00000446408.2_Missense_Mutation_p.C150S|BVES_ENST00000336775.5_Missense_Mutation_p.C150S	NM_001199563.1	NP_001186492.1	Q8NE79	POPD1_HUMAN	blood vessel epicardial substance	150					epithelial cell-cell adhesion (GO:0090136)|hematopoietic progenitor cell differentiation (GO:0002244)|muscle organ development (GO:0007517)|positive regulation of locomotion (GO:0040017)|positive regulation of receptor recycling (GO:0001921)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|regulation of Rac GTPase activity (GO:0032314)|sinoatrial node cell development (GO:0060931)|substrate adhesion-dependent cell spreading (GO:0034446)|vesicle-mediated transport (GO:0016192)	integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cAMP binding (GO:0030552)|structural molecule activity (GO:0005198)			NS(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|urinary_tract(1)	21		all_cancers(87;2.83e-05)|Acute lymphoblastic leukemia(125;1.95e-08)|all_hematologic(75;9.25e-07)|all_epithelial(87;0.0101)|Colorectal(196;0.204)|Lung NSC(302;0.238)				TGGATCATGCAAAACTGTCCA	0.433																																					p.C150S		Atlas-SNP	.											.	BVES	33	.	0			c.T448A						.						158.0	156.0	156.0					6																	105573357		2203	4300	6503	SO:0001583	missense	11149	exon4			TCATGCAAAACTG	AF124512	CCDS5051.1	6q21	2008-11-25			ENSG00000112276	ENSG00000112276			1152	protein-coding gene	gene with protein product	"""popeye domain containing 1"""	604577				10441744, 10882522	Standard	NM_147147		Approved	HBVES, POP1, POPDC1	uc003pqx.3	Q8NE79	OTTHUMG00000015291	ENST00000314641.5:c.448T>A	chr6.hg19:g.105573357A>T	ENSP00000313172:p.Cys150Ser	136.0	0.0		161.0	54.0	NM_001199563	A8K1R4|E1P5D8|Q5T550|Q5T551|Q8IWC6|Q9HBV0|Q9UNG6	Missense_Mutation	SNP	ENST00000314641.5	hg19	CCDS5051.1	.	.	.	.	.	.	.	.	.	.	A	25.2	4.614998	0.87359	.	.	ENSG00000112276	ENST00000314641;ENST00000336775;ENST00000446408	T;T;T	0.27402	1.67;1.67;1.67	5.76	5.76	0.90799	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.081344	0.85682	D	0.000000	T	0.26702	0.0653	L	0.40543	1.245	0.80722	D	1	D	0.63046	0.992	P	0.60117	0.869	T	0.04723	-1.0931	10	0.08837	T	0.75	-14.7206	16.0458	0.80720	1.0:0.0:0.0:0.0	.	150	Q8NE79	POPD1_HUMAN	S	150	ENSP00000313172:C150S;ENSP00000337259:C150S;ENSP00000397310:C150S	ENSP00000313172:C150S	C	-	1	0	BVES	105680050	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.830000	0.92063	2.192000	0.70111	0.533000	0.62120	TGC	.	.		0.433	BVES-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406075.1	NM_147147	
HIVEP2	3097	hgsc.bcm.edu	37	6	143095836	143095836	+	Missense_Mutation	SNP	A	A	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr6:143095836A>C	ENST00000367604.1	-	4	679	c.40T>G	c.(40-42)Tca>Gca	p.S14A	HIVEP2_ENST00000012134.2_Missense_Mutation_p.S14A|HIVEP2_ENST00000367603.2_Missense_Mutation_p.S14A			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	14					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		CCAGACCTTGAGGTAGCTTTT	0.463																																					p.S14A	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-SNP	.											.	HIVEP2	225	.	0			c.T40G						.						190.0	177.0	181.0					6																	143095836		1953	4169	6122	SO:0001583	missense	3097	exon5			ACCTTGAGGTAGC	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.40T>G	chr6.hg19:g.143095836A>C	ENSP00000356576:p.Ser14Ala	177.0	0.0		237.0	89.0	NM_006734	Q02646|Q5THT5|Q9NS05	Missense_Mutation	SNP	ENST00000367604.1	hg19	CCDS43510.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763817	0.49574	.	.	ENSG00000010818	ENST00000367604;ENST00000367603;ENST00000012134	T;T;T	0.02446	4.29;4.29;4.29	5.56	5.56	0.83823	.	0.256825	0.39834	N	0.001244	T	0.02533	0.0077	L	0.60455	1.87	0.29347	N	0.865594	P	0.43788	0.817	B	0.41764	0.366	T	0.16129	-1.0413	10	0.66056	D	0.02	-12.2929	16.0068	0.80367	1.0:0.0:0.0:0.0	.	14	P31629	ZEP2_HUMAN	A	14	ENSP00000356576:S14A;ENSP00000356575:S14A;ENSP00000012134:S14A	ENSP00000012134:S14A	S	-	1	0	HIVEP2	143137529	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.110000	0.50352	2.240000	0.73641	0.528000	0.53228	TCA	.	.		0.463	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
C7orf72	100130988	hgsc.bcm.edu	37	7	50136120	50136120	+	Missense_Mutation	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:50136120A>G	ENST00000297001.6	+	1	489	c.439A>G	c.(439-441)Aca>Gca	p.T147A		NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72	147										NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						CAGACCAGACACAGGATTTCA	0.413																																					p.T147A		Atlas-SNP	.											.	C7orf72	26	.	0			c.A439G						.						79.0	62.0	67.0					7																	50136120		692	1591	2283	SO:0001583	missense	100130988	exon1			CCAGACACAGGAT		CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.439A>G	chr7.hg19:g.50136120A>G	ENSP00000297001:p.Thr147Ala	88.0	0.0		99.0	29.0	NM_001161834	A6NDX9	Missense_Mutation	SNP	ENST00000297001.6	hg19	CCDS47585.1	.	.	.	.	.	.	.	.	.	.	A	4.074	0.011509	0.07912	.	.	ENSG00000164500	ENST00000297001	.	.	.	5.22	-4.99	0.03010	.	.	.	.	.	T	0.17365	0.0417	L	0.29908	0.895	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.28138	-1.0053	7	.	.	.	-0.0912	0.6013	0.00745	0.3702:0.1083:0.2046:0.317	.	147	A4D263	CG072_HUMAN	A	147	.	.	T	+	1	0	C7orf72	50106666	0.000000	0.05858	0.017000	0.16124	0.766000	0.43426	-0.236000	0.09003	-0.552000	0.06167	0.260000	0.18958	ACA	.	.		0.413	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	
GNAI1	2770	hgsc.bcm.edu	37	7	79833109	79833109	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:79833109T>C	ENST00000351004.3	+	5	924	c.551T>C	c.(550-552)aTt>aCt	p.I184T	GNAI1_ENST00000457358.2_Missense_Mutation_p.I132T	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	184					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						ACTACAGGAATTGTTGAAACC	0.299																																					p.I184T		Atlas-SNP	.											.	GNAI1	44	.	0			c.T551C						.						72.0	68.0	69.0					7																	79833109		2201	4298	6499	SO:0001583	missense	2770	exon5			CAGGAATTGTTGA	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.551T>C	chr7.hg19:g.79833109T>C	ENSP00000343027:p.Ile184Thr	102.0	0.0		150.0	40.0	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Missense_Mutation	SNP	ENST00000351004.3	hg19	CCDS5595.1	.	.	.	.	.	.	.	.	.	.	T	26.2	4.712836	0.89112	.	.	ENSG00000127955	ENST00000351004;ENST00000418742;ENST00000457358	D;D;D	0.91011	-2.77;-2.77;-2.77	5.86	5.86	0.93980	.	0.000000	0.85682	D	0.000000	D	0.96972	0.9011	H	0.96301	3.8	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98188	1.0461	9	.	.	.	.	16.2652	0.82574	0.0:0.0:0.0:1.0	.	184	P63096	GNAI1_HUMAN	T	184;132;132	ENSP00000343027:I184T;ENSP00000389435:I132T;ENSP00000410572:I132T	.	I	+	2	0	GNAI1	79671045	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.949000	0.87791	2.241000	0.73720	0.528000	0.53228	ATT	.	.		0.299	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
KIAA1324L	222223	hgsc.bcm.edu	37	7	86526919	86526919	+	Missense_Mutation	SNP	C	C	T	rs553991387		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:86526919C>T	ENST00000450689.2	-	19	2773	c.2588G>A	c.(2587-2589)tGt>tAt	p.C863Y	KIAA1324L_ENST00000444627.1_Missense_Mutation_p.C792Y|KIAA1324L_ENST00000416314.1_Missense_Mutation_p.C696Y|KIAA1324L_ENST00000297222.6_Missense_Mutation_p.C623Y	NM_001142749.2	NP_001136221.1	A8MWY0	K132L_HUMAN	KIAA1324-like	863						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(14)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44	Esophageal squamous(14;0.0058)					ATAGAACGTACACCCATCACA	0.453																																					p.C863Y		Atlas-SNP	.											.	KIAA1324L	225	.	0			c.G2588A						.						97.0	84.0	88.0					7																	86526919		2203	4300	6503	SO:0001583	missense	222223	exon19			AACGTACACCCAT	AK055902	CCDS34677.1, CCDS47632.1, CCDS34677.2	7q21.12	2008-09-18			ENSG00000164659	ENSG00000164659			21945	protein-coding gene	gene with protein product	"""EIG121-like"""	614048					Standard	NM_001142749		Approved	FLJ31340, EIG121L	uc011kha.2	A8MWY0	OTTHUMG00000153995	ENST00000450689.2:c.2588G>A	chr7.hg19:g.86526919C>T	ENSP00000413445:p.Cys863Tyr	98.0	0.0		122.0	30.0	NM_001142749	A4D1C9|B4DJV3|Q17RI6|Q96DP2	Missense_Mutation	SNP	ENST00000450689.2	hg19	CCDS47632.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.728619	0.89390	.	.	ENSG00000164659	ENST00000450689;ENST00000297222;ENST00000444627;ENST00000416314	T;T;T;T	0.16324	2.35;2.35;2.35;2.35	5.59	5.59	0.84812	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.49218	0.1544	M	0.85630	2.765	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.999	T	0.54302	-0.8314	10	0.87932	D	0	.	18.5874	0.91196	0.0:1.0:0.0:0.0	.	863;623;696	A8MWY0;A8MWY0-2;B4DJV3	K132L_HUMAN;.;.	Y	863;623;792;696	ENSP00000413445:C863Y;ENSP00000297222:C623Y;ENSP00000397377:C792Y;ENSP00000402390:C696Y	ENSP00000297222:C623Y	C	-	2	0	KIAA1324L	86364855	1.000000	0.71417	0.941000	0.38009	0.980000	0.70556	7.818000	0.86416	2.642000	0.89623	0.650000	0.86243	TGT	.	.		0.453	KIAA1324L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333372.3	NM_152748	
CPA4	51200	hgsc.bcm.edu	37	7	129951882	129951882	+	Missense_Mutation	SNP	A	A	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr7:129951882A>T	ENST00000222482.4	+	10	1026	c.998A>T	c.(997-999)aAg>aTg	p.K333M	CPA4_ENST00000493259.1_Missense_Mutation_p.K229M|CPA4_ENST00000445470.2_Missense_Mutation_p.K300M	NM_016352.3	NP_057436.2	Q9UI42	CBPA4_HUMAN	carboxypeptidase A4	333					histone acetylation (GO:0016573)	extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21	Melanoma(18;0.0435)					TCCCAGGACAAGGTGGCGAGG	0.537																																					p.K333M		Atlas-SNP	.											.	CPA4	47	.	0			c.A998T						.						72.0	65.0	67.0					7																	129951882		2203	4300	6503	SO:0001583	missense	51200	exon10			AGGACAAGGTGGC	AF095719	CCDS5818.1, CCDS55163.1	7q32	2008-07-18			ENSG00000128510	ENSG00000128510			15740	protein-coding gene	gene with protein product	"""carboxypeptidase A3"""	607635				10383164, 10860668	Standard	NM_016352		Approved	CPA3	uc003vpr.3	Q9UI42	OTTHUMG00000157825	ENST00000222482.4:c.998A>T	chr7.hg19:g.129951882A>T	ENSP00000222482:p.Lys333Met	99.0	0.0		127.0	34.0	NM_016352	B7Z576|Q86UY9	Missense_Mutation	SNP	ENST00000222482.4	hg19	CCDS5818.1	.	.	.	.	.	.	.	.	.	.	A	6.952	0.545519	0.13312	.	.	ENSG00000128510	ENST00000445470;ENST00000222482;ENST00000538687;ENST00000493259	T;T;T	0.11277	2.79;2.79;2.79	6.02	2.32	0.28847	Peptidase M14, carboxypeptidase A (2);	1.293600	0.04827	N	0.438014	T	0.12646	0.0307	L	0.48935	1.535	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.17098	0.017;0.008	T	0.36383	-0.9750	10	0.54805	T	0.06	.	6.6356	0.22881	0.4876:0.2615:0.0:0.251	.	300;333	B7Z576;Q9UI42	.;CBPA4_HUMAN	M	300;333;138;229	ENSP00000412947:K300M;ENSP00000222482:K333M;ENSP00000419660:K229M	ENSP00000222482:K333M	K	+	2	0	CPA4	129739118	0.000000	0.05858	0.129000	0.21949	0.068000	0.16541	-0.060000	0.11712	0.158000	0.19367	-1.139000	0.01908	AAG	.	.		0.537	CPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349725.1	NM_016352	
CSMD3	114788	hgsc.bcm.edu	37	8	113240991	113240991	+	Missense_Mutation	SNP	T	T	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr8:113240991T>G	ENST00000297405.5	-	70	11202	c.10958A>C	c.(10957-10959)aAa>aCa	p.K3653T	CSMD3_ENST00000343508.3_Missense_Mutation_p.K3613T|CSMD3_ENST00000455883.2_Missense_Mutation_p.K3484T|CSMD3_ENST00000352409.3_Missense_Mutation_p.K3583T	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3653						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTACCTTTGTTTATAAAGATA	0.299										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.K3653T		Atlas-SNP	.											.	CSMD3	2325	.	0			c.A10958C						.						64.0	70.0	68.0					8																	113240991		2203	4295	6498	SO:0001583	missense	114788	exon70			CTTTGTTTATAAA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.10958A>C	chr8.hg19:g.113240991T>G	ENSP00000297405:p.Lys3653Thr	37.0	0.0		33.0	19.0	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	hg19	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	T	25.9	4.688300	0.88639	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.41400	1.35;1.34;1.43;1.0;1.39	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	T	0.65739	0.2720	M	0.73962	2.25	0.54753	D	0.999988	D;D;D	0.89917	1.0;0.999;0.988	D;D;P	0.85130	0.997;0.994;0.693	T	0.69304	-0.5180	10	0.72032	D	0.01	.	16.2119	0.82168	0.0:0.0:0.0:1.0	.	3484;3653;3613	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	T	3613;3653;2923;3484;3583	ENSP00000345799:K3613T;ENSP00000297405:K3653T;ENSP00000341558:K2923T;ENSP00000412263:K3484T;ENSP00000343124:K3583T	ENSP00000297405:K3653T	K	-	2	0	CSMD3	113310167	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.997000	0.88414	2.288000	0.76882	0.482000	0.46254	AAA	.	.		0.299	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
TG	7038	hgsc.bcm.edu	37	8	133906037	133906037	+	Missense_Mutation	SNP	A	A	T	rs61736740		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr8:133906037A>T	ENST00000220616.4	+	11	2904	c.2864A>T	c.(2863-2865)gAg>gTg	p.E955V	TG_ENST00000377869.1_Missense_Mutation_p.E955V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	955	Thyroglobulin type-1 8. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CCTCTGGGGGAGAGTTTCCTG	0.582																																					p.E955V		Atlas-SNP	.											.	TG	416	.	0			c.A2864T						.						126.0	118.0	120.0					8																	133906037		2203	4300	6503	SO:0001583	missense	7038	exon11			TGGGGGAGAGTTT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.2864A>T	chr8.hg19:g.133906037A>T	ENSP00000220616:p.Glu955Val	236.0	1.0		247.0	109.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	a	14.62	2.589216	0.46110	.	.	ENSG00000042832	ENST00000377869;ENST00000220616	T;T	0.65916	-0.18;-0.18	5.14	5.14	0.70334	.	0.000000	0.64402	D	0.000015	T	0.54127	0.1839	L	0.46157	1.445	0.28834	N	0.896988	B	0.20671	0.047	B	0.21708	0.036	T	0.56068	-0.8040	10	0.72032	D	0.01	.	9.279	0.37716	0.8392:0.0:0.0:0.1608	.	955	P01266	THYG_HUMAN	V	955	ENSP00000367100:E955V;ENSP00000220616:E955V	ENSP00000220616:E955V	E	+	2	0	TG	133975219	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	3.711000	0.54868	1.950000	0.56595	0.313000	0.20887	GAG	.	A|0.987;C|0.013		0.582	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
KIAA2026	158358	hgsc.bcm.edu	37	9	5922603	5922603	+	Silent	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr9:5922603A>G	ENST00000399933.3	-	8	3392	c.3393T>C	c.(3391-3393)ggT>ggC	p.G1131G	KIAA2026_ENST00000381461.2_Silent_p.G1101G	NM_001017969.2	NP_001017969.2	Q5HYC2	K2026_HUMAN	KIAA2026	1131										breast(6)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(1)	46		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00155)|Lung(218;0.124)		GTTGTTCTGTACCTTTCTGTT	0.368																																					p.G1131G		Atlas-SNP	.											.	KIAA2026	231	.	0			c.T3393C						.						129.0	123.0	125.0					9																	5922603		1883	4111	5994	SO:0001819	synonymous_variant	158358	exon8			TTCTGTACCTTTC	AB095946		9p24.1	2014-01-10			ENSG00000183354	ENSG00000183354			23378	protein-coding gene	gene with protein product							Standard	NM_001017969		Approved	FLJ20375	uc003zjq.4	Q5HYC2	OTTHUMG00000019507	ENST00000399933.3:c.3393T>C	chr9.hg19:g.5922603A>G		105.0	0.0		93.0	36.0	NM_001017969	A8MTP2|B9EGW7|Q4VXA2|Q8IVE5	Silent	SNP	ENST00000399933.3	hg19																																																																																				.	.		0.368	KIAA2026-002	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051652.2	NM_001017969	
SVEP1	79987	hgsc.bcm.edu	37	9	113312196	113312196	+	Silent	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr9:113312196C>T	ENST00000401783.2	-	2	1056	c.720G>A	c.(718-720)gaG>gaA	p.E240E	SVEP1_ENST00000374469.1_Silent_p.E217E|SVEP1_ENST00000374461.1_Silent_p.E217E|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000302728.8_Silent_p.E240E	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	240	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						AACAGTGCTCCTCCTTTGGGG	0.478																																					p.E240E		Atlas-SNP	.											.	SVEP1	326	.	0			c.G720A						.						94.0	89.0	91.0					9																	113312196		1945	4144	6089	SO:0001819	synonymous_variant	79987	exon2			GTGCTCCTCCTTT	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.720G>A	chr9.hg19:g.113312196C>T		207.0	0.0		189.0	38.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	hg19	CCDS48004.1																																																																																			.	.		0.478	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
NLRP14	338323	hgsc.bcm.edu	37	11	7064361	7064361	+	Silent	SNP	C	C	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:7064361C>G	ENST00000299481.4	+	4	1450	c.1104C>G	c.(1102-1104)gtC>gtG	p.V368V		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	368	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TGTGCCAAGTCCCCCTAGTGT	0.453																																					p.V368V		Atlas-SNP	.											.	NLRP14	187	.	0			c.C1104G						.						131.0	130.0	131.0					11																	7064361		2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			CCAAGTCCCCCTA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1104C>G	chr11.hg19:g.7064361C>G		77.0	0.0		102.0	15.0	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	hg19	CCDS7776.1																																																																																			.	.		0.453	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955438	18955438	+	Silent	SNP	C	C	A	rs374955450		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:18955438C>A	ENST00000302797.3	-	1	1118	c.894G>T	c.(892-894)gcG>gcT	p.A298A	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'Flank	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	298				AS -> TP (in Ref. 2; AAL86880). {ECO:0000305}.	acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCACCTCAGACGCGTCCTGCA	0.562																																					p.A298A		Atlas-SNP	.											.	MRGPRX1	84	.	0			c.G894T						.						72.0	68.0	69.0					11																	18955438		2194	4286	6480	SO:0001819	synonymous_variant	259249	exon1			CTCAGACGCGTCC		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.894G>T	chr11.hg19:g.18955438C>A		67.0	0.0		89.0	22.0	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Silent	SNP	ENST00000302797.3	hg19	CCDS7846.1																																																																																			.	.		0.562	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
NELL1	4745	hgsc.bcm.edu	37	11	20699518	20699518	+	Silent	SNP	C	C	A	rs146112225		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:20699518C>A	ENST00000357134.5	+	2	248	c.96C>A	c.(94-96)atC>atA	p.I32I	NELL1_ENST00000532434.1_Silent_p.I32I|NELL1_ENST00000325319.5_Silent_p.I32I|NELL1_ENST00000298925.5_Silent_p.I60I	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	32					cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGATGGATATCGTCACCGAGC	0.473																																					p.I32I		Atlas-SNP	.											.	NELL1	179	.	0			c.C96A						.						176.0	161.0	166.0					11																	20699518		2203	4300	6503	SO:0001819	synonymous_variant	4745	exon2			GGATATCGTCACC	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.96C>A	chr11.hg19:g.20699518C>A		178.0	0.0		231.0	79.0	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	hg19	CCDS7855.1																																																																																			.	C|1.000;T|0.000		0.473	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
OR5W2	390148	hgsc.bcm.edu	37	11	55681596	55681596	+	Missense_Mutation	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:55681596C>T	ENST00000344514.1	-	1	462	c.463G>A	c.(463-465)Gat>Aat	p.D155N		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						ATCAAAGCATCTGCTATTCCC	0.448																																					p.D155N	Melanoma(48;171 1190 15239 43886 49348)	Atlas-SNP	.											.	OR5W2	112	.	0			c.G463A						.						81.0	71.0	74.0					11																	55681596		2201	4296	6497	SO:0001583	missense	390148	exon1			AAGCATCTGCTAT	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.463G>A	chr11.hg19:g.55681596C>T	ENSP00000342448:p.Asp155Asn	77.0	0.0		83.0	35.0	NM_001001960		Missense_Mutation	SNP	ENST00000344514.1	hg19	CCDS31513.1	.	.	.	.	.	.	.	.	.	.	C	0.115	-1.133505	0.01756	.	.	ENSG00000187612	ENST00000344514	T	0.36520	1.25	5.01	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41712	D	0.000824	T	0.10551	0.0258	N	0.01656	-0.775	0.09310	N	1	B	0.14012	0.009	B	0.24269	0.052	T	0.40001	-0.9586	10	0.02654	T	1	.	5.6206	0.17455	0.1968:0.7044:0.0:0.0987	.	155	Q8NH69	OR5W2_HUMAN	N	155	ENSP00000342448:D155N	ENSP00000342448:D155N	D	-	1	0	OR5W2	55438172	0.000000	0.05858	0.192000	0.23308	0.115000	0.19883	-1.037000	0.03557	2.311000	0.77944	0.549000	0.68633	GAT	.	.		0.448	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
ENDOD1	23052	hgsc.bcm.edu	37	11	94861677	94861677	+	Missense_Mutation	SNP	C	C	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:94861677C>G	ENST00000278505.4	+	2	555	c.437C>G	c.(436-438)cCa>cGa	p.P146R		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	146						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.00824)				CAGCTTTACCCATTCTCCCTT	0.483																																					p.P146R		Atlas-SNP	.											.	ENDOD1	26	.	0			c.C437G						.						122.0	120.0	121.0					11																	94861677		2016	4189	6205	SO:0001583	missense	23052	exon2			TTTACCCATTCTC	BC026191	CCDS41699.1	11q21	2010-03-19			ENSG00000149218	ENSG00000149218			29129	protein-coding gene	gene with protein product						10048485	Standard	NM_015036		Approved	KIAA0830	uc001pfh.3	O94919	OTTHUMG00000167835	ENST00000278505.4:c.437C>G	chr11.hg19:g.94861677C>G	ENSP00000278505:p.Pro146Arg	262.0	0.0		254.0	81.0	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	hg19	CCDS41699.1	.	.	.	.	.	.	.	.	.	.	C	11.54	1.669913	0.29693	.	.	ENSG00000149218	ENST00000278505	T	0.80566	-1.39	5.52	4.41	0.53225	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.137701	0.47455	D	0.000235	D	0.89832	0.6829	M	0.87971	2.92	0.32620	N	0.523472	D	0.89917	1.0	D	0.74023	0.982	D	0.92133	0.5714	10	0.72032	D	0.01	-2.9771	13.1853	0.59677	0.0:0.9112:0.0:0.0888	.	146	O94919	ENDD1_HUMAN	R	146	ENSP00000278505:P146R	ENSP00000278505:P146R	P	+	2	0	ENDOD1	94501325	0.964000	0.33143	0.907000	0.35723	0.027000	0.11550	2.173000	0.42472	2.591000	0.87537	0.455000	0.32223	CCA	.	.		0.483	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036	
RAB39A	54734	hgsc.bcm.edu	37	11	107799388	107799388	+	Missense_Mutation	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:107799388C>T	ENST00000320578.2	+	1	160	c.94C>T	c.(94-96)Cgc>Tgc	p.R32C	SLC35F2_ENST00000525071.1_5'Flank|SLC35F2_ENST00000429869.1_5'Flank	NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	32					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)										CACCCAGGGCCGCTTCCCCGG	0.662																																					p.R32C		Atlas-SNP	.											.	.	.	.	0			c.C94T						.						41.0	39.0	40.0					11																	107799388		2201	4298	6499	SO:0001583	missense	54734	exon1			CAGGGCCGCTTCC	X99962	CCDS8338.1	11q22.3	2011-11-22	2011-11-22	2011-11-22	ENSG00000179331	ENSG00000179331		"""RAB, member RAS oncogene"""	16521	protein-coding gene	gene with protein product	"""rab-related GTP-binding protein"""		"""RAB39, member RAS oncogene family"""	RAB39		9119394	Standard	NM_017516		Approved		uc001pjt.3	Q14964	OTTHUMG00000166367	ENST00000320578.2:c.94C>T	chr11.hg19:g.107799388C>T	ENSP00000322594:p.Arg32Cys	15.0	0.0		19.0	8.0	NM_017516	A8KAA4|Q8N6W2	Missense_Mutation	SNP	ENST00000320578.2	hg19	CCDS8338.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.986337	0.74589	.	.	ENSG00000179331	ENST00000320578	T	0.77750	-1.12	4.61	4.61	0.57282	Small GTP-binding protein domain (1);	0.000000	0.51477	D	0.000097	T	0.78916	0.4359	M	0.78223	2.4	0.80722	D	1	B	0.11235	0.004	B	0.04013	0.001	T	0.78211	-0.2292	10	0.66056	D	0.02	.	16.7242	0.85417	0.0:1.0:0.0:0.0	.	32	Q14964	RB39A_HUMAN	C	32	ENSP00000322594:R32C	ENSP00000322594:R32C	R	+	1	0	RAB39	107304598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.923000	0.48868	2.548000	0.85928	0.555000	0.69702	CGC	.	.		0.662	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516	
APOA4	337	hgsc.bcm.edu	37	11	116693445	116693445	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr11:116693445T>C	ENST00000357780.3	-	2	220	c.106A>G	c.(106-108)Agc>Ggc	p.S36G		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	36	13 X 22 AA approximate tandem repeats.				cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		CTCAGCTGGCTGAAGTAGTCC	0.567																																					p.S36G		Atlas-SNP	.											.	APOA4	51	.	0			c.A106G						.						176.0	150.0	159.0					11																	116693445		2201	4296	6497	SO:0001583	missense	337	exon2			GCTGGCTGAAGTA		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.106A>G	chr11.hg19:g.116693445T>C	ENSP00000350425:p.Ser36Gly	97.0	0.0		119.0	41.0	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	hg19	CCDS31681.1	.	.	.	.	.	.	.	.	.	.	T	19.93	3.917991	0.73098	.	.	ENSG00000110244	ENST00000357780	T	0.75821	-0.97	5.19	4.04	0.47022	Apolipoprotein/apolipophorin (1);	1.228650	0.05431	N	0.545956	T	0.80934	0.4719	M	0.75264	2.295	0.24514	N	0.994196	D	0.53885	0.963	P	0.50825	0.651	T	0.62282	-0.6887	10	0.51188	T	0.08	-11.9228	8.5031	0.33170	0.426:0.0:0.0:0.574	.	36	P06727	APOA4_HUMAN	G	36	ENSP00000350425:S36G	ENSP00000350425:S36G	S	-	1	0	APOA4	116198655	0.940000	0.31905	0.999000	0.59377	0.996000	0.88848	1.306000	0.33505	0.957000	0.37930	0.533000	0.62120	AGC	.	.		0.567	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
CACNA2D4	93589	hgsc.bcm.edu	37	12	1993990	1993990	+	Missense_Mutation	SNP	C	C	A	rs375148197		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr12:1993990C>A	ENST00000382722.5	-	11	1578	c.1216G>T	c.(1216-1218)Ggc>Tgc	p.G406C	CACNA2D4_ENST00000585708.1_Missense_Mutation_p.G342C|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.G406C|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.G322C|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.G406C|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.G342C	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	406	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		TCCACGGCGCCGTCGCTGATG	0.577																																					p.G406C	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.G1216T						.						48.0	55.0	53.0					12																	1993990		2055	4189	6244	SO:0001583	missense	93589	exon11			CGGCGCCGTCGCT	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.1216G>T	chr12.hg19:g.1993990C>A	ENSP00000372169:p.Gly406Cys	197.0	0.0		184.0	42.0	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	hg19	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.785734	0.70337	.	.	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.33216	1.42	5.4	5.4	0.78164	von Willebrand factor, type A (3);	0.000000	0.85682	D	0.000000	T	0.66307	0.2776	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.74771	-0.3552	10	0.87932	D	0	.	19.178	0.93611	0.0:1.0:0.0:0.0	.	406;406	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	C	342;406;406	ENSP00000372169:G406C	ENSP00000280663:G406C	G	-	1	0	CACNA2D4	1864251	1.000000	0.71417	0.465000	0.27155	0.257000	0.26127	7.818000	0.86416	2.528000	0.85240	0.511000	0.50034	GGC	.	.		0.577	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
PTPRB	5787	hgsc.bcm.edu	37	12	70986132	70986132	+	Silent	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr12:70986132T>C	ENST00000261266.5	-	5	1085	c.1056A>G	c.(1054-1056)cgA>cgG	p.R352R	PTPRB_ENST00000538174.2_5'UTR|PTPRB_ENST00000550358.1_Silent_p.R570R|PTPRB_ENST00000538708.1_Silent_p.R352R|PTPRB_ENST00000551525.1_Silent_p.R569R|PTPRB_ENST00000451516.2_Silent_p.R352R|PTPRB_ENST00000550857.1_Silent_p.R352R|PTPRB_ENST00000334414.6_Silent_p.R570R	NM_002837.4	NP_002828.3	P23467	PTPRB_HUMAN	protein tyrosine phosphatase, receptor type, B	352	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|protein dephosphorylation (GO:0006470)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(4)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(8)|lung(46)|prostate(4)|skin(18)|upper_aerodigestive_tract(1)|urinary_tract(3)	107	Renal(347;0.236)		GBM - Glioblastoma multiforme(2;2.17e-05)|Lung(24;0.000636)|OV - Ovarian serous cystadenocarcinoma(12;0.00306)|STAD - Stomach adenocarcinoma(21;0.149)			CTTGATAAAGTCGACCGGGGA	0.463																																					p.R570R		Atlas-SNP	.											.	PTPRB	676	.	0			c.A1710G						.						94.0	91.0	92.0					12																	70986132		1932	4140	6072	SO:0001819	synonymous_variant	5787	exon7			ATAAAGTCGACCG	X54131	CCDS44943.1, CCDS44944.1, CCDS55845.1, CCDS55846.1	12q15-q21	2013-02-11						"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9665	protein-coding gene	gene with protein product		176882		PTPB		2169617	Standard	NM_001109754		Approved		uc001swc.4	P23467	OTTHUMG00000169499	ENST00000261266.5:c.1056A>G	chr12.hg19:g.70986132T>C		114.0	0.0		97.0	11.0	NM_001109754	B7ZKS8|B7ZKT0|C9JX87|F5H3G6|Q14D85|Q3MIV7	Silent	SNP	ENST00000261266.5	hg19	CCDS44944.1																																																																																			.	.		0.463	PTPRB-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404439.1		
TAOK3	51347	hgsc.bcm.edu	37	12	118639243	118639243	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr12:118639243G>A	ENST00000392533.3	-	12	1335	c.845C>T	c.(844-846)cCa>cTa	p.P282L	TAOK3_ENST00000419821.2_Missense_Mutation_p.P282L	NM_016281.3	NP_057365.3	Q9H2K8	TAOK3_HUMAN	TAO kinase 3	282					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|MAPK cascade (GO:0000165)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of JNK cascade (GO:0046329)|negative regulation of protein kinase activity (GO:0006469)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			central_nervous_system(1)|lung(5)|skin(1)	7	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GACACGTAGTGGCCGGTCTCG	0.403																																					p.P282L		Atlas-SNP	.											.	TAOK3	151	.	0			c.C845T						.						100.0	92.0	95.0					12																	118639243		2203	4300	6503	SO:0001583	missense	51347	exon12			CGTAGTGGCCGGT	AF135158	CCDS9188.1	12q	2007-08-03				ENSG00000135090			18133	protein-coding gene	gene with protein product						10559204, 10924369	Standard	NM_016281		Approved	JIK, DPK, MAP3K18	uc001twy.4	Q9H2K8		ENST00000392533.3:c.845C>T	chr12.hg19:g.118639243G>A	ENSP00000376317:p.Pro282Leu	82.0	0.0		107.0	44.0	NM_016281	Q658N1|Q8IUM4|Q9HC79|Q9NZM9|Q9UHG7	Missense_Mutation	SNP	ENST00000392533.3	hg19	CCDS9188.1	.	.	.	.	.	.	.	.	.	.	G	18.56	3.649689	0.67358	.	.	ENSG00000135090	ENST00000419821;ENST00000392533;ENST00000538601	D;D;D	0.85411	-1.98;-1.98;-1.98	4.65	4.65	0.58169	Protein kinase-like domain (1);	0.070349	0.64402	D	0.000015	D	0.83399	0.5246	L	0.56396	1.775	0.80722	D	1	B	0.25772	0.134	B	0.23716	0.048	T	0.81536	-0.0888	10	0.44086	T	0.13	.	17.703	0.88301	0.0:0.0:1.0:0.0	.	282	Q9H2K8	TAOK3_HUMAN	L	282;282;180	ENSP00000416374:P282L;ENSP00000376317:P282L;ENSP00000437389:P180L	ENSP00000376317:P282L	P	-	2	0	TAOK3	117123626	1.000000	0.71417	0.874000	0.34290	0.936000	0.57629	9.564000	0.98151	2.401000	0.81631	0.591000	0.81541	CCA	.	.		0.403	TAOK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401456.2	NM_016281	
NBEA	26960	hgsc.bcm.edu	37	13	35692392	35692392	+	Nonsense_Mutation	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:35692392C>T	ENST00000400445.3	+	15	2644	c.2110C>T	c.(2110-2112)Cag>Tag	p.Q704*	NBEA_ENST00000310336.4_Nonsense_Mutation_p.Q704*|NBEA_ENST00000379939.2_Nonsense_Mutation_p.Q704*|NBEA_ENST00000540320.1_Nonsense_Mutation_p.Q704*	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	704					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)		AGATGAACTTCAGAGTATATT	0.239																																					p.Q704X		Atlas-SNP	.											.	NBEA	340	.	0			c.C2110T						.						51.0	45.0	47.0					13																	35692392		1785	4049	5834	SO:0001587	stop_gained	26960	exon15			GAACTTCAGAGTA	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.2110C>T	chr13.hg19:g.35692392C>T	ENSP00000383295:p.Gln704*	111.0	0.0		54.0	13.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Nonsense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	C	45	11.441239	0.99561	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	.	.	.	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.37606	T	0.19	.	16.7133	0.85391	0.0:1.0:0.0:0.0	.	.	.	.	X	704	.	ENSP00000308534:Q704X	Q	+	1	0	NBEA	34590392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.345000	0.79337	1.929000	0.55896	0.460000	0.39030	CAG	.	.		0.239	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
NBEA	26960	hgsc.bcm.edu	37	13	35692394	35692394	+	Missense_Mutation	SNP	G	G	C	rs376099257		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:35692394G>C	ENST00000400445.3	+	15	2646	c.2112G>C	c.(2110-2112)caG>caC	p.Q704H	NBEA_ENST00000310336.4_Missense_Mutation_p.Q704H|NBEA_ENST00000379939.2_Missense_Mutation_p.Q704H|NBEA_ENST00000540320.1_Missense_Mutation_p.Q704H	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	704					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)		ATGAACTTCAGAGTATATTAA	0.244																																					p.Q704H		Atlas-SNP	.											.	NBEA	340	.	0			c.G2112C						.						52.0	46.0	48.0					13																	35692394		1785	4050	5835	SO:0001583	missense	26960	exon15			ACTTCAGAGTATA	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.2112G>C	chr13.hg19:g.35692394G>C	ENSP00000383295:p.Gln704His	112.0	0.0		56.0	13.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	G	15.64	2.893891	0.52121	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.56941	0.43;0.43;0.43;0.43	4.29	4.29	0.51040	.	0.000000	0.64402	D	0.000001	T	0.67524	0.2902	M	0.67953	2.075	0.80722	D	1	D	0.65815	0.995	D	0.77557	0.99	T	0.68089	-0.5501	10	0.45353	T	0.12	.	11.3759	0.49728	0.0896:0.0:0.9104:0.0	.	704	Q5T321	.	H	704	ENSP00000440951:Q704H;ENSP00000383295:Q704H;ENSP00000369271:Q704H;ENSP00000308534:Q704H	ENSP00000308534:Q704H	Q	+	3	2	NBEA	34590394	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	1.357000	0.34090	1.929000	0.55896	0.460000	0.39030	CAG	.	.		0.244	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
NBEA	26960	hgsc.bcm.edu	37	13	35734090	35734090	+	Missense_Mutation	SNP	T	T	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:35734090T>G	ENST00000400445.3	+	22	4316	c.3782T>G	c.(3781-3783)aTt>aGt	p.I1261S	NBEA_ENST00000310336.4_Missense_Mutation_p.I1261S|NBEA_ENST00000379939.2_Missense_Mutation_p.I1261S|NBEA_ENST00000540320.1_Missense_Mutation_p.I1261S	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	1261					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)		GGAAGTATAATTTCAGATACT	0.378																																					p.I1261S		Atlas-SNP	.											.	NBEA	340	.	0			c.T3782G						.						40.0	42.0	42.0					13																	35734090		1839	4074	5913	SO:0001583	missense	26960	exon22			GTATAATTTCAGA	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.3782T>G	chr13.hg19:g.35734090T>G	ENSP00000383295:p.Ile1261Ser	38.0	0.0		62.0	22.0	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Missense_Mutation	SNP	ENST00000400445.3	hg19	CCDS45026.1	.	.	.	.	.	.	.	.	.	.	T	12.38	1.920176	0.33908	.	.	ENSG00000172915	ENST00000540320;ENST00000400445;ENST00000379939;ENST00000310336	T;T;T;T	0.50813	0.73;0.73;0.73;0.73	5.8	5.8	0.92144	.	0.542704	0.19638	N	0.109515	T	0.34395	0.0896	N	0.19112	0.55	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12734	-1.0536	10	0.18710	T	0.47	.	16.134	0.81465	0.0:0.0:0.0:1.0	.	1261	Q5T321	.	S	1261	ENSP00000440951:I1261S;ENSP00000383295:I1261S;ENSP00000369271:I1261S;ENSP00000308534:I1261S	ENSP00000308534:I1261S	I	+	2	0	NBEA	34632090	0.997000	0.39634	0.994000	0.49952	0.995000	0.86356	4.731000	0.62022	2.216000	0.71823	0.528000	0.53228	ATT	.	.		0.378	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
ARHGEF7	8874	hgsc.bcm.edu	37	13	111932983	111932983	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr13:111932983G>A	ENST00000375741.2	+	16	1997	c.1747G>A	c.(1747-1749)Gga>Aga	p.G583R	ARHGEF7_ENST00000375723.1_Missense_Mutation_p.G405R|ARHGEF7_ENST00000218789.5_Missense_Mutation_p.G405R|ARHGEF7_ENST00000370623.3_Missense_Mutation_p.G490R|ARHGEF7_ENST00000375739.2_Missense_Mutation_p.G533R|ARHGEF7_ENST00000544132.1_3'UTR|ARHGEF7_ENST00000426073.2_Missense_Mutation_p.G405R|ARHGEF7_ENST00000317133.5_Missense_Mutation_p.G562R|ARHGEF7_ENST00000375736.4_Missense_Mutation_p.G405R|ARHGEF7_ENST00000478679.1_Missense_Mutation_p.G327R|ARHGEF7_ENST00000375737.5_Missense_Mutation_p.G480R	NM_001113511.1|NM_145735.2	NP_001106983.1|NP_663788.1	Q14155	ARHG7_HUMAN	Rho guanine nucleotide exchange factor (GEF) 7	583					apoptotic signaling pathway (GO:0097190)|epidermal growth factor receptor signaling pathway (GO:0007173)|focal adhesion assembly (GO:0048041)|hematopoietic progenitor cell differentiation (GO:0002244)|lamellipodium assembly (GO:0030032)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of GTPase activity (GO:0043547)|positive regulation of lamellipodium morphogenesis (GO:2000394)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase binding (GO:0019901)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|soft_tissue(1)	41	all_lung(23;3.96e-05)|Lung NSC(43;0.00156)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Medulloblastoma(90;0.163)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CACGTCTGTGGGAAACCCCAC	0.542																																					p.G583R		Atlas-SNP	.											.	ARHGEF7	157	.	0			c.G1747A						.						210.0	158.0	176.0					13																	111932983		2203	4300	6503	SO:0001583	missense	8874	exon16			TCTGTGGGAAACC	D63476	CCDS9521.1, CCDS32009.1, CCDS45068.1, CCDS45069.1	13q33.3	2013-01-10			ENSG00000102606	ENSG00000102606		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	15607	protein-coding gene	gene with protein product	"""SH3 domain-containing proline-rich protein"", ""PAK-interacting exchange factor beta"", ""rho"", ""guanine nucleotide exchange factor 7"""	605477				9207241, 9726964	Standard	NM_003899		Approved	KIAA0142, PIXB, DKFZp761K1021, Nbla10314, DKFZp686C12170, BETA-PIX, COOL1, P85SPR, P85, P85COOL1, P50BP, PAK3, P50	uc001vrs.2	Q14155	OTTHUMG00000017357	ENST00000375741.2:c.1747G>A	chr13.hg19:g.111932983G>A	ENSP00000364893:p.Gly583Arg	120.0	0.0		119.0	32.0	NM_001113511	B1ALK6|B1ALK8|Q3LIA4|Q5W9H0|Q6P9G3|Q6PII2|Q86W63|Q8N3M1	Missense_Mutation	SNP	ENST00000375741.2	hg19	CCDS45068.1	.	.	.	.	.	.	.	.	.	.	G	3.869	-0.028348	0.07589	.	.	ENSG00000102606	ENST00000317133;ENST00000375741;ENST00000375739;ENST00000370623;ENST00000545635;ENST00000466143;ENST00000218789;ENST00000375736;ENST00000426073;ENST00000375737;ENST00000375723;ENST00000478679	T;T;T;T;T;T;T;T;T;T;T	0.60672	0.75;0.76;0.76;0.72;0.74;0.71;0.72;0.72;0.76;0.7;0.17	4.91	0.798	0.18660	.	0.334721	0.33092	N	0.005291	T	0.37461	0.1004	N	0.24115	0.695	0.09310	N	0.999999	B;B;B;B;B	0.25850	0.044;0.105;0.068;0.136;0.07	B;B;B;B;B	0.30716	0.025;0.045;0.093;0.056;0.119	T	0.18524	-1.0334	10	0.39692	T	0.17	.	4.3244	0.11032	0.338:0.0:0.5151:0.1469	.	327;480;533;583;562	E9PDQ5;B7Z6G2;Q14155-2;Q14155;Q14155-3	.;.;.;ARHG7_HUMAN;.	R	562;583;533;490;560;405;405;405;405;480;405;327	ENSP00000325994:G562R;ENSP00000364893:G583R;ENSP00000364891:G533R;ENSP00000359657:G490R;ENSP00000418067:G405R;ENSP00000218789:G405R;ENSP00000364888:G405R;ENSP00000397068:G405R;ENSP00000364889:G480R;ENSP00000364875:G405R;ENSP00000417596:G327R	ENSP00000218789:G405R	G	+	1	0	ARHGEF7	110730984	0.981000	0.34729	0.001000	0.08648	0.005000	0.04900	2.237000	0.43061	-0.199000	0.10317	-0.188000	0.12872	GGA	.	.		0.542	ARHGEF7-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001113511	
NDRG2	57447	hgsc.bcm.edu	37	14	21487891	21487892	+	Missense_Mutation	DNP	GA	GA	TG			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:21487891_21487892GA>TG	ENST00000556147.1	-	10	1562_1563	c.622_623TC>CA	c.(622-624)TCt>CAt	p.S208H	NDRG2_ENST00000350792.3_Missense_Mutation_p.S194H|NDRG2_ENST00000397853.3_Missense_Mutation_p.S208H|NDRG2_ENST00000397856.3_Missense_Mutation_p.S194H|NDRG2_ENST00000397847.2_Missense_Mutation_p.S208H|NDRG2_ENST00000397855.3_Missense_Mutation_p.S165H|NDRG2_ENST00000397858.1_Missense_Mutation_p.S208H|NDRG2_ENST00000397851.2_Missense_Mutation_p.S208H|NDRG2_ENST00000298687.5_Missense_Mutation_p.S208H|NDRG2_ENST00000553503.1_Missense_Mutation_p.S194H|NDRG2_ENST00000298684.5_Missense_Mutation_p.S165H|NDRG2_ENST00000360463.3_Missense_Mutation_p.S194H|NDRG2_ENST00000554143.1_Missense_Mutation_p.S194H|NDRG2_ENST00000554104.1_Missense_Mutation_p.S121H|NDRG2_ENST00000555158.1_Missense_Mutation_p.S194H|NDRG2_ENST00000403829.3_Missense_Mutation_p.S204H|NDRG2_ENST00000554277.1_5'UTR|NDRG2_ENST00000397844.2_Missense_Mutation_p.S194H			Q9UN36	NDRG2_HUMAN	NDRG family member 2	208					cell differentiation (GO:0030154)|negative regulation of cytokine production (GO:0001818)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of smooth muscle cell proliferation (GO:0048662)|regulation of platelet-derived growth factor production (GO:0090361)|regulation of vascular endothelial growth factor production (GO:0010574)|substantia nigra development (GO:0021762)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)				breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	23	all_cancers(95;0.00185)		OV - Ovarian serous cystadenocarcinoma(11;6.85e-11)|Epithelial(56;9.49e-09)|all cancers(55;3.84e-08)	GBM - Glioblastoma multiforme(265;0.0191)		AGAATTTCCAGAGAGCTCTTCC	0.401																																					p.S208Y|p.S208P		Atlas-SNP	.											.	NDRG2	37	.	0			c.C623A|c.T622C						.																																			SO:0001583	missense	57447	exon10			TTTCCAGAGAGCT|TTCCAGAGAGCTC	AB033074	CCDS9564.1, CCDS9565.1, CCDS61384.1, CCDS61386.1, CCDS73613.1	14q11.2	2008-07-09			ENSG00000165795	ENSG00000165795			14460	protein-coding gene	gene with protein product		605272				10831399	Standard	NM_201535		Approved	KIAA1248, SYLD	uc001vyx.3	Q9UN36	OTTHUMG00000029619	ENST00000556147.1:c.622_623delinsTG	chr14.hg19:g.21487891_21487892delinsTG	ENSP00000451712:p.Ser208His	72.0|71.0	0.0		87.0	27.0	NM_201537	B3KUE3|B4DE86|B7WP11|B7WPD5|D3DS07|D3DS10|Q567T1|Q68DW2|Q86U08|Q86U46|Q96FD3|Q96FT0|Q96JU0|Q96PN0|Q9BQH5|Q9ULH2	Missense_Mutation	SNP	ENST00000556147.1	hg19	CCDS9565.1																																																																																			.	.		0.401	NDRG2-013	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411717.1		
SYNE2	23224	hgsc.bcm.edu	37	14	64554464	64554464	+	Missense_Mutation	SNP	A	A	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:64554464A>C	ENST00000344113.4	+	58	11772	c.11560A>C	c.(11560-11562)Att>Ctt	p.I3854L	SYNE2_ENST00000358025.3_Missense_Mutation_p.I3854L|SYNE2_ENST00000554584.1_Missense_Mutation_p.I3887L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Missense_Mutation_p.I488L|SYNE2_ENST00000357395.3_Missense_Mutation_p.I239L|SYNE2_ENST00000394768.2_Missense_Mutation_p.I239L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	3854					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CCTGTCAATAATTTTTGAAAC	0.333																																					p.I3854L		Atlas-SNP	.											.	SYNE2	577	.	0			c.A11560C						.						82.0	88.0	86.0					14																	64554464		2202	4300	6502	SO:0001583	missense	23224	exon58			TCAATAATTTTTG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.11560A>C	chr14.hg19:g.64554464A>C	ENSP00000341781:p.Ile3854Leu	107.0	0.0		110.0	34.0	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	15.25	2.777228	0.49786	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	T;T;T;T;T;T	0.34275	1.37;3.93;1.37;1.37;1.37;3.93	5.36	5.36	0.76844	.	0.115504	0.38778	N	0.001576	T	0.35098	0.0920	M	0.68317	2.08	0.80722	D	1	P;B;B;B	0.35507	0.506;0.402;0.372;0.183	B;B;B;B	0.32211	0.131;0.142;0.062;0.069	T	0.23797	-1.0178	10	0.46703	T	0.11	.	10.8822	0.46946	0.859:0.0:0.0:0.141	.	239;3888;3854;3854	Q8WXH0-7;D4YW74;Q8WXH0;Q8WXH0-2	.;.;SYNE2_HUMAN;.	L	3854;239;3854;3887;3887;488;239	ENSP00000350719:I3854L;ENSP00000349969:I239L;ENSP00000341781:I3854L;ENSP00000452570:I3887L;ENSP00000450831:I488L;ENSP00000378249:I239L	ENSP00000261678:I3887L	I	+	1	0	SYNE2	63624217	0.959000	0.32827	0.933000	0.37362	0.875000	0.50365	2.139000	0.42149	2.024000	0.59613	0.482000	0.46254	ATT	.	.		0.333	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259685	69259685	+	5'UTR	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:69259685G>A	ENST00000439696.2	-	0	272				ZFP36L1_ENST00000336440.3_5'UTR|ZFP36L1_ENST00000555997.1_5'Flank	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		CAGGGGCGAGGATCTGGTGTG	0.647																																					p.P60S		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C178T						.						92.0	89.0	90.0					14																	69259685		2203	4300	6503	SO:0001623	5_prime_UTR_variant	677	exon2			GGCGAGGATCTGG	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.-30C>T	chr14.hg19:g.69259685G>A		46.0	0.0		30.0	7.0	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	hg19	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	G	8.520	0.868501	0.17322	.	.	ENSG00000185650	ENST00000553375	.	.	.	4.56	1.06	0.20224	.	.	.	.	.	T	0.21590	0.0520	.	.	.	0.09310	N	0.999993	.	.	.	.	.	.	T	0.21314	-1.0249	4	.	.	.	.	2.0988	0.03675	0.3613:0.0:0.3611:0.2776	.	.	.	.	S	60	.	.	P	-	1	0	ZFP36L1	68329438	0.000000	0.05858	0.062000	0.19696	0.706000	0.40770	-0.028000	0.12350	0.320000	0.23234	-0.397000	0.06425	CCT	.	.		0.647	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
EML5	161436	hgsc.bcm.edu	37	14	89206879	89206879	+	Missense_Mutation	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:89206879C>T	ENST00000380664.5	-	5	562	c.563G>A	c.(562-564)cGa>cAa	p.R188Q	EML5_ENST00000554922.1_Missense_Mutation_p.R188Q|EML5_ENST00000352093.5_Missense_Mutation_p.R188Q			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	188						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						AAAGACACCTCGTTTTGGGGT	0.368																																					p.R188Q		Atlas-SNP	.											.	EML5	141	.	0			c.G563A						.						143.0	135.0	138.0					14																	89206879		1860	4102	5962	SO:0001583	missense	161436	exon5			ACACCTCGTTTTG	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.563G>A	chr14.hg19:g.89206879C>T	ENSP00000370039:p.Arg188Gln	121.0	0.0		125.0	35.0	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Missense_Mutation	SNP	ENST00000380664.5	hg19	CCDS45148.1	.	.	.	.	.	.	.	.	.	.	C	34	5.331765	0.95733	.	.	ENSG00000165521	ENST00000554922;ENST00000352093;ENST00000380664	T;T;T	0.21734	1.99;1.99;1.99	5.21	5.21	0.72293	WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000001	T	0.35278	0.0926	L	0.52364	1.645	0.53005	D	0.999962	D	0.71674	0.998	P	0.59703	0.862	T	0.04268	-1.0964	10	0.11485	T	0.65	-7.7252	18.7549	0.91828	0.0:1.0:0.0:0.0	.	188	Q05BV3	EMAL5_HUMAN	Q	188	ENSP00000451998:R188Q;ENSP00000298315:R188Q;ENSP00000370039:R188Q	ENSP00000298315:R188Q	R	-	2	0	EML5	88276632	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.412000	0.80091	2.417000	0.82017	0.591000	0.81541	CGA	.	.		0.368	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
ZNF839	55778	hgsc.bcm.edu	37	14	102792471	102792471	+	Silent	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr14:102792471C>T	ENST00000558850.1	+	2	440	c.90C>T	c.(88-90)gcC>gcT	p.A30A	ZNF839_ENST00000262236.5_Silent_p.A30A|ZNF839_ENST00000559185.1_Silent_p.A30A|ZNF839_ENST00000442396.2_Silent_p.A146A	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	30							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						TCCATATCGCCAGCCCTCAGC	0.582																																					p.A146A		Atlas-SNP	.											.	ZNF839	41	.	0			c.C438T						.						39.0	45.0	43.0					14																	102792471		1944	4154	6098	SO:0001819	synonymous_variant	55778	exon2			TATCGCCAGCCCT	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.90C>T	chr14.hg19:g.102792471C>T		98.0	0.0		67.0	14.0	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	hg19	CCDS58336.1																																																																																			.	.		0.582	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
MKRN3	7681	hgsc.bcm.edu	37	15	23812394	23812394	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:23812394G>T	ENST00000314520.3	+	1	1941	c.1465G>T	c.(1465-1467)Gag>Tag	p.E489*	RP11-73C9.1_ENST00000563044.1_RNA|MKRN3_ENST00000568252.1_Intron|MKRN3_ENST00000564592.1_Intron|MKRN3_ENST00000568945.1_Intron	NM_005664.3	NP_005655.1	Q13064	MKRN3_HUMAN	makorin ring finger protein 3	489					protein ubiquitination (GO:0016567)	ribonucleoprotein complex (GO:0030529)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)	p.E489*(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(33)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		all_cancers(20;8.44e-25)|all_epithelial(15;3.69e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000353)|Colorectal(260;0.14)		all cancers(64;3.02e-06)|Epithelial(43;1.94e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0012)		ACCCTTCTCTGAGGACCAGTG	0.453																																					p.E489X		Atlas-SNP	.											MKRN3,NS,carcinoma,0,1	MKRN3	155	.	1	Substitution - Nonsense(1)	lung(1)	c.G1465T						.						149.0	141.0	144.0					15																	23812394		2203	4300	6503	SO:0001587	stop_gained	7681	exon1			TTCTCTGAGGACC	U19107	CCDS10013.1	15q11-q13	2013-01-09	2008-08-13		ENSG00000179455	ENSG00000179455		"""RING-type (C3HC4) zinc fingers"""	7114	protein-coding gene	gene with protein product	"""zinc finger protein 127"""	603856		ZNF127, D15S9		10196367	Standard	NM_005664		Approved	RNF63, ZFP127, MGC88288	uc001ywh.4	Q13064	OTTHUMG00000129160	ENST00000314520.3:c.1465G>T	chr15.hg19:g.23812394G>T	ENSP00000313881:p.Glu489*	121.0	0.0		124.0	40.0	NM_005664		Nonsense_Mutation	SNP	ENST00000314520.3	hg19	CCDS10013.1	.	.	.	.	.	.	.	.	.	.	G	36	5.955527	0.97145	.	.	ENSG00000179455	ENST00000314520	.	.	.	4.09	-0.159	0.13379	.	0.358986	0.23431	N	0.048259	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	3.643	0.08174	0.3435:0.1888:0.4677:0.0	.	.	.	.	X	489	.	ENSP00000313881:E489X	E	+	1	0	MKRN3	21363487	1.000000	0.71417	0.006000	0.13384	0.292000	0.27327	4.316000	0.59178	-0.008000	0.14320	0.563000	0.77884	GAG	.	.		0.453	MKRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251225.1	NM_005664	
DMXL2	23312	hgsc.bcm.edu	37	15	51756896	51756896	+	Missense_Mutation	SNP	A	A	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:51756896A>C	ENST00000251076.5	-	32	8068	c.7781T>G	c.(7780-7782)cTa>cGa	p.L2594R	DMXL2_ENST00000449909.3_Missense_Mutation_p.L1958R|DMXL2_ENST00000543779.2_Missense_Mutation_p.L2595R|RP11-707P17.1_ENST00000561007.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2594						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		TTCAGGTTCTAGCATTGCTTT	0.398																																					p.L2595R		Atlas-SNP	.											.	DMXL2	262	.	0			c.T7784G						.						87.0	82.0	84.0					15																	51756896		2196	4293	6489	SO:0001583	missense	23312	exon32			GGTTCTAGCATTG	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.7781T>G	chr15.hg19:g.51756896A>C	ENSP00000251076:p.Leu2594Arg	120.0	0.0		65.0	15.0	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.792617	0.90453	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.37584	1.34;1.35;1.19	5.55	5.55	0.83447	.	0.153974	0.44285	D	0.000465	T	0.59514	0.2199	M	0.81942	2.565	0.53688	D	0.999974	P;D;P;D	0.67145	0.929;0.996;0.857;0.99	P;P;P;P	0.60415	0.724;0.823;0.451;0.874	T	0.65676	-0.6110	10	0.87932	D	0	.	15.8527	0.78947	1.0:0.0:0.0:0.0	.	2595;1958;2594;2595	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	R	2594;2595;1958;139	ENSP00000251076:L2594R;ENSP00000441858:L2595R;ENSP00000400855:L1958R	ENSP00000251076:L2594R	L	-	2	0	DMXL2	49544188	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.761000	0.91691	2.330000	0.79161	0.477000	0.44152	CTA	.	.		0.398	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
PEAK1	79834	hgsc.bcm.edu	37	15	77471864	77471864	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:77471864T>C	ENST00000560626.2	-	4	2880	c.2405A>G	c.(2404-2406)gAt>gGt	p.D802G	PEAK1_ENST00000312493.4_Missense_Mutation_p.D802G|PEAK1_ENST00000558305.1_Missense_Mutation_p.D802G			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	802	Pro-rich.				cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										AACATCAGCATCTGGAGGAAT	0.512																																					p.D802G		Atlas-SNP	.											.	.	.	.	0			c.A2405G						.						82.0	84.0	83.0					15																	77471864		2013	4187	6200	SO:0001583	missense	0	exon5			TCAGCATCTGGAG		CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.2405A>G	chr15.hg19:g.77471864T>C	ENSP00000452796:p.Asp802Gly	122.0	0.0		87.0	19.0	NM_024776	Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	hg19	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	T	12.78	2.040023	0.35989	.	.	ENSG00000173517	ENST00000312493	T	0.72725	-0.68	5.78	3.17	0.36434	.	0.181563	0.31415	N	0.007693	T	0.55529	0.1926	N	0.20986	0.625	0.44918	D	0.997935	B	0.11235	0.004	B	0.10450	0.005	T	0.55088	-0.8195	10	0.72032	D	0.01	-3.4663	10.6403	0.45590	0.0:0.1508:0.0:0.8492	.	802	Q9H792	PEAK1_HUMAN	G	802	ENSP00000309230:D802G	ENSP00000309230:D802G	D	-	2	0	AC087465.1	75258919	1.000000	0.71417	0.564000	0.28396	0.538000	0.34931	3.785000	0.55424	1.031000	0.39867	0.533000	0.62120	GAT	.	.		0.512	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3		
BAIAP3	8938	hgsc.bcm.edu	37	16	1384728	1384728	+	Silent	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr16:1384728C>A	ENST00000324385.5	+	1	224	c.66C>A	c.(64-66)atC>atA	p.I22I	BAIAP3_ENST00000562208.1_Intron|BAIAP3_ENST00000421665.2_5'Flank|BAIAP3_ENST00000397488.2_Intron|BAIAP3_ENST00000397489.1_5'UTR|BAIAP3_ENST00000426824.3_Intron|BAIAP3_ENST00000568887.1_Intron	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	22					G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GCACCGCCATCGGCTTCGCAG	0.662																																					p.I22I		Atlas-SNP	.											.	BAIAP3	88	.	0			c.C66A						.						8.0	9.0	9.0					16																	1384728		2113	4180	6293	SO:0001819	synonymous_variant	8938	exon1			CGCCATCGGCTTC	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.66C>A	chr16.hg19:g.1384728C>A		99.0	0.0		79.0	35.0	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	hg19	CCDS10434.1																																																																																			.	.		0.662	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
TP53	7157	hgsc.bcm.edu	37	17	7578275	7578275	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:7578275G>A	ENST00000269305.4	-	6	763	c.574C>T	c.(574-576)Cag>Tag	p.Q192*	TP53_ENST00000574684.1_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.Q192*|TP53_ENST00000420246.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000445888.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000413465.2_Nonsense_Mutation_p.Q192*|TP53_ENST00000455263.2_Nonsense_Mutation_p.Q192*	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	192	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Q -> H (in sporadic cancers; somatic mutation).|Q -> K (in a sporadic cancer; somatic mutation).|Q -> L (in sporadic cancers; somatic mutation).|Q -> P (in sporadic cancers; somatic mutation).|Q -> R (in sporadic cancers; somatic mutation).|QH -> HN (in a sporadic cancer; somatic mutation).|QH -> HY (in a sporadic cancer; 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.Q192*(83)|p.0?(8)|p.Q99*(6)|p.?(6)|p.Q60*(6)|p.P191del(4)|p.P191delP(4)|p.A189_V197delAPPQHLIRV(4)|p.P191_E198>Q(3)|p.P191fs*53(2)|p.G187fs*16(2)|p.P59delP(2)|p.P98delP(2)|p.P191fs*6(1)|p.A189_Q192>E(1)|p.P59_E66>Q(1)|p.P191fs*15(1)|p.P191_Q192delPQ(1)|p.Q192K(1)|p.P98_E105>Q(1)|p.A189fs*53(1)|p.Q192del(1)|p.Q192fs*16(1)|p.L188_P191del(1)|p.Q192fs*30(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)	ATAAGATGCTGAGGAGGGGCC	0.557		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.Q192X	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_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	144	Substitution - Nonsense(95)|Deletion - In frame(19)|Whole gene deletion(8)|Deletion - Frameshift(7)|Complex - deletion inframe(6)|Unknown(6)|Insertion - Frameshift(1)|Complex - frameshift(1)|Substitution - Missense(1)	breast(26)|ovary(20)|urinary_tract(15)|lung(12)|upper_aerodigestive_tract(10)|skin(8)|biliary_tract(7)|oesophagus(7)|large_intestine(6)|kidney(6)|stomach(5)|haematopoietic_and_lymphoid_tissue(5)|liver(5)|bone(4)|central_nervous_system(3)|pancreas(2)|cervix(1)|endometrium(1)|eye(1)	c.C574T						.						89.0	80.0	83.0					17																	7578275		2203	4300	6503	SO:0001587	stop_gained	7157	exon6	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;	GATGCTGAGGAGG	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.574C>T	chr17.hg19:g.7578275G>A	ENSP00000269305:p.Gln192*	167.0	0.0		113.0	47.0	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	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	13.54	2.269040	0.40095	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944;ENST00000414315	.	.	.	5.41	3.36	0.38483	.	0.242461	0.43260	D	0.000594	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-22.6404	8.6971	0.34303	0.0:0.1484:0.545:0.3066	.	.	.	.	X	192;192;192;192;192;192;181;99;60;99;60	.	ENSP00000269305:Q192X	Q	-	1	0	TP53	7519000	1.000000	0.71417	0.987000	0.45799	0.035000	0.12851	2.163000	0.42377	0.732000	0.32470	0.655000	0.94253	CAG	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
PIGS	94005	hgsc.bcm.edu	37	17	26888556	26888556	+	Missense_Mutation	SNP	A	A	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:26888556A>T	ENST00000308360.7	-	6	935	c.560T>A	c.(559-561)gTc>gAc	p.V187D	PIGS_ENST00000543734.1_Missense_Mutation_p.V126D|PIGS_ENST00000395346.2_Missense_Mutation_p.V179D|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	187					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					GGCCACCTGGACTATGCGGCG	0.597																																					p.V187D		Atlas-SNP	.											.	PIGS	42	.	0			c.T560A						.						81.0	64.0	70.0					17																	26888556		2203	4300	6503	SO:0001583	missense	94005	exon6			ACCTGGACTATGC		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"""Phosphatidylinositol glycan anchor biosynthesis"""	14937	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610271	"""phosphatidylinositol glycan, class S"""				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.560T>A	chr17.hg19:g.26888556A>T	ENSP00000309430:p.Val187Asp	144.0	0.0		130.0	49.0	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	hg19	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	A	11.52	1.662267	0.29515	.	.	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.43294	0.95;0.95;0.95	5.68	3.27	0.37495	.	0.552930	0.21428	N	0.074703	T	0.28532	0.0706	L	0.34521	1.04	0.39722	D	0.971482	B;B	0.16802	0.019;0.016	B;B	0.20384	0.026;0.029	T	0.06954	-1.0798	10	0.14656	T	0.56	-3.8239	9.2515	0.37557	0.4912:0.0:0.0:0.5088	.	187;179	Q96S52;Q96S52-2	PIGS_HUMAN;.	D	179;187;126	ENSP00000378755:V179D;ENSP00000309430:V187D;ENSP00000438447:V126D	ENSP00000309430:V187D	V	-	2	0	PIGS	23912683	0.170000	0.23016	0.494000	0.27515	0.961000	0.63080	0.457000	0.21875	0.930000	0.37217	0.533000	0.62120	GTC	.	.		0.597	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198	
MED13	9969	hgsc.bcm.edu	37	17	60038954	60038954	+	Missense_Mutation	SNP	G	G	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:60038954G>T	ENST00000397786.2	-	22	5327	c.5251C>A	c.(5251-5253)Cct>Act	p.P1751T		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1751					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTTACATCAGGACTTCTAAGG	0.408																																					p.P1751T		Atlas-SNP	.											.	MED13	181	.	0			c.C5251A						.						99.0	96.0	97.0					17																	60038954		1870	4098	5968	SO:0001583	missense	9969	exon22			CATCAGGACTTCT	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.5251C>A	chr17.hg19:g.60038954G>T	ENSP00000380888:p.Pro1751Thr	87.0	0.0		81.0	31.0	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	hg19	CCDS42366.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.074063	0.76415	.	.	ENSG00000108510	ENST00000397786;ENST00000262436	D	0.82619	-1.63	5.34	4.37	0.52481	.	0.051925	0.85682	D	0.000000	T	0.80008	0.4545	L	0.33485	1.01	0.80722	D	1	B	0.29936	0.262	B	0.41440	0.357	T	0.78122	-0.2327	10	0.40728	T	0.16	0.261	13.4147	0.60961	0.0755:0.0:0.9245:0.0	.	1751	Q9UHV7	MED13_HUMAN	T	1751;1750	ENSP00000380888:P1751T	ENSP00000262436:P1750T	P	-	1	0	MED13	57393736	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.399000	0.79935	2.496000	0.84212	0.591000	0.81541	CCT	.	.		0.408	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
LAMA1	284217	hgsc.bcm.edu	37	18	6958645	6958645	+	Silent	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr18:6958645A>G	ENST00000389658.3	-	55	7888	c.7795T>C	c.(7795-7797)Ttg>Ctg	p.L2599L	RP11-781P6.1_ENST00000584722.1_RNA	NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2599	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTCTCATCCAATTGGACAGTG	0.363																																					p.L2599L		Atlas-SNP	.											.	LAMA1	458	.	0			c.T7795C						.						80.0	71.0	74.0					18																	6958645		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon55			CATCCAATTGGAC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7795T>C	chr18.hg19:g.6958645A>G		98.0	0.0		89.0	24.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.363	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
TAF4B	6875	hgsc.bcm.edu	37	18	23854650	23854650	+	Silent	SNP	C	C	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr18:23854650C>T	ENST00000269142.5	+	4	1619	c.621C>T	c.(619-621)gtC>gtT	p.V207V	TAF4B_ENST00000578121.1_Silent_p.V207V|TAF4B_ENST00000400466.2_Silent_p.V207V	NM_005640.1	NP_005631.1	Q92750	TAF4B_HUMAN	TAF4b RNA polymerase II, TATA box binding protein (TBP)-associated factor, 105kDa	207					gene expression (GO:0010467)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|NF-kappaB binding (GO:0051059)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(13)|prostate(1)|skin(1)	29	all_cancers(21;0.00151)|Lung NSC(5;0.000401)|all_lung(6;0.00115)|Ovarian(20;0.124)		Epithelial(2;9.57e-07)|all cancers(3;5.15e-06)|OV - Ovarian serous cystadenocarcinoma(3;1.96e-05)|LUSC - Lung squamous cell carcinoma(2;0.00594)|Lung(2;0.0267)			CAACCAGTGTCGTCACAGTTA	0.413																																					p.V207V		Atlas-SNP	.											.	TAF4B	71	.	0			c.C621T						.						117.0	112.0	113.0					18																	23854650		1896	4119	6015	SO:0001819	synonymous_variant	6875	exon4			CAGTGTCGTCACA	Y09321	CCDS42421.1	18q11.1	2008-08-01	2002-08-29	2001-12-07		ENSG00000141384			11538	protein-coding gene	gene with protein product	"""TATA box binding protein (TBP)-associated factor 4B"""	601689	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C2, 105kD"""	TAF2C2		8858156, 10849440	Standard	XM_005258339		Approved	TAFII105	uc002kvu.4	Q92750		ENST00000269142.5:c.621C>T	chr18.hg19:g.23854650C>T		187.0	0.0		129.0	21.0	NM_005640	Q29YA4|Q29YA5	Silent	SNP	ENST00000269142.5	hg19	CCDS42421.1																																																																																			.	.		0.413	TAF4B-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000446260.3	NM_005640	
ELAVL1	1994	hgsc.bcm.edu	37	19	8032602	8032602	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:8032602T>C	ENST00000407627.2	-	5	632	c.503A>G	c.(502-504)aAt>aGt	p.N168S	ELAVL1_ENST00000351593.5_Missense_Mutation_p.N195S|ELAVL1_ENST00000593807.1_Intron|ELAVL1_ENST00000596459.1_Missense_Mutation_p.N168S	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	168	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						TTTATGACCATTGAAACTGGT	0.493																																					p.N168S		Atlas-SNP	.											.	ELAVL1	44	.	0			c.A503G						.						148.0	117.0	128.0					19																	8032602		2203	4300	6503	SO:0001583	missense	1994	exon5			TGACCATTGAAAC	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"""RNA binding motif (RRM) containing"""	3312	protein-coding gene	gene with protein product	"""embryonic lethal, abnormal vision, drosophila, homolog-like 1"", ""Hu antigen R"""	603466	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"""	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.503A>G	chr19.hg19:g.8032602T>C	ENSP00000385269:p.Asn168Ser	146.0	0.0		146.0	46.0	NM_001419	B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	hg19	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.546629	0.86022	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.09163	3.01;3.01	6.17	6.17	0.99709	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.23611	0.0571	M	0.72894	2.215	0.80722	D	1	D	0.61697	0.99	P	0.51135	0.66	T	0.00501	-1.1702	10	0.59425	D	0.04	.	14.7743	0.69713	0.0:0.0:0.0:1.0	.	168	Q15717	ELAV1_HUMAN	S	168;195	ENSP00000385269:N168S;ENSP00000264073:N195S	ENSP00000264073:N195S	N	-	2	0	ELAVL1	7938602	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.698000	0.84413	2.371000	0.80710	0.533000	0.62120	AAT	.	.		0.493	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419	
FBN3	84467	hgsc.bcm.edu	37	19	8196686	8196686	+	Missense_Mutation	SNP	A	A	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:8196686A>G	ENST00000600128.1	-	15	2156	c.1742T>C	c.(1741-1743)aTc>aCc	p.I581T	FBN3_ENST00000601739.1_Missense_Mutation_p.I581T|FBN3_ENST00000270509.2_Missense_Mutation_p.I581T			Q75N90	FBN3_HUMAN	fibrillin 3	581	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GTTCACGCAGATGCCGGGCGT	0.672																																					p.I581T		Atlas-SNP	.											.	FBN3	300	.	0			c.T1742C						.						24.0	26.0	25.0					19																	8196686		2203	4300	6503	SO:0001583	missense	84467	exon14			ACGCAGATGCCGG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.1742T>C	chr19.hg19:g.8196686A>G	ENSP00000470498:p.Ile581Thr	42.0	0.0		54.0	8.0	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	hg19	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	a	14.18	2.458988	0.43634	.	.	ENSG00000142449	ENST00000270509	D	0.86865	-2.18	2.92	2.92	0.33932	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	U	0.000000	D	0.82917	0.5141	L	0.35793	1.09	0.42019	D	0.990978	P	0.48089	0.905	P	0.47299	0.543	T	0.80703	-0.1264	10	0.37606	T	0.19	.	10.9744	0.47456	1.0:0.0:0.0:0.0	.	581	Q75N90	FBN3_HUMAN	T	581	ENSP00000270509:I581T	ENSP00000270509:I581T	I	-	2	0	FBN3	8102686	1.000000	0.71417	0.625000	0.29200	0.037000	0.13140	6.212000	0.72188	0.961000	0.38030	0.155000	0.16302	ATC	.	.		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
MUC16	94025	hgsc.bcm.edu	37	19	9015640	9015640	+	Missense_Mutation	SNP	T	T	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:9015640T>G	ENST00000397910.4	-	29	38386	c.38183A>C	c.(38182-38184)gAg>gCg	p.E12728A		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12730	SEA 5. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CAGGACTCTCTCTGTGGTGTT	0.542																																					p.E12728A		Atlas-SNP	.											.	MUC16	4315	.	0			c.A38183C						.						186.0	166.0	173.0					19																	9015640		2024	4164	6188	SO:0001583	missense	94025	exon29			ACTCTCTCTGTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38183A>C	chr19.hg19:g.9015640T>G	ENSP00000381008:p.Glu12728Ala	201.0	0.0		172.0	58.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	9.701	1.154433	0.21371	.	.	ENSG00000181143	ENST00000397910	T	0.29397	1.57	3.34	2.27	0.28462	.	.	.	.	.	T	0.52885	0.1762	M	0.88310	2.945	.	.	.	D	0.57899	0.981	D	0.62955	0.909	T	0.63646	-0.6590	8	0.87932	D	0	.	5.6416	0.17567	0.0:0.1464:0.0:0.8536	.	12728	B5ME49	.	A	12728	ENSP00000381008:E12728A	ENSP00000381008:E12728A	E	-	2	0	MUC16	8876640	0.024000	0.19004	0.002000	0.10522	0.013000	0.08279	2.372000	0.44257	1.274000	0.44362	0.254000	0.18369	GAG	.	.		0.542	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CC2D1A	54862	hgsc.bcm.edu	37	19	14024108	14024108	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:14024108G>A	ENST00000318003.7	+	5	747	c.506G>A	c.(505-507)gGg>gAg	p.G169E	CC2D1A_ENST00000589606.1_Missense_Mutation_p.G169E	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	169					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			TACGATCGGGGGCTTAAAGTA	0.602																																					p.G169E		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G506A						.						25.0	31.0	29.0					19																	14024108		1964	4142	6106	SO:0001583	missense	54862	exon5			ATCGGGGGCTTAA	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.506G>A	chr19.hg19:g.14024108G>A	ENSP00000313601:p.Gly169Glu	86.0	0.0		86.0	30.0	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	hg19	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.710151	0.68730	.	.	ENSG00000132024	ENST00000318003;ENST00000254346;ENST00000389233	D	0.91068	-2.78	4.8	4.8	0.61643	Domain of unknown function DM14 (1);	0.056252	0.64402	D	0.000001	D	0.95287	0.8471	M	0.83603	2.65	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.94511	0.7718	10	0.36615	T	0.2	-26.0657	16.7813	0.85563	0.0:0.0:1.0:0.0	.	169;169	Q6P1N0-2;Q6P1N0	.;C2D1A_HUMAN	E	169;7;144	ENSP00000313601:G169E	ENSP00000254346:G7E	G	+	2	0	CC2D1A	13885108	1.000000	0.71417	0.926000	0.36857	0.200000	0.23975	7.883000	0.87264	2.494000	0.84150	0.561000	0.74099	GGG	.	.		0.602	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
ZNF714	148206	hgsc.bcm.edu	37	19	21299717	21299717	+	Missense_Mutation	SNP	T	T	G			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:21299717T>G	ENST00000596143.1	+	5	572	c.247T>G	c.(247-249)Tta>Gta	p.L83V	ZNF714_ENST00000596053.1_Intron|ZNF714_ENST00000291770.7_3'UTR|ZNF714_ENST00000601416.1_3'UTR	NM_182515.3	NP_872321	Q96N38	ZN714_HUMAN	zinc finger protein 714	83					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|lung(11)|urinary_tract(2)	18						ACATGAGAATTTACAGTTAAG	0.373																																					p.L83V		Atlas-SNP	.											.	ZNF714	121	.	0			c.T247G						.						63.0	63.0	63.0					19																	21299717		2199	4298	6497	SO:0001583	missense	148206	exon5			GAGAATTTACAGT	AK056006	CCDS54239.1	19p12	2013-01-08				ENSG00000160352		"""Zinc fingers, C2H2-type"""	27124	protein-coding gene	gene with protein product						12477932	Standard	NM_182515		Approved		uc002npo.4	Q96N38		ENST00000596143.1:c.247T>G	chr19.hg19:g.21299717T>G	ENSP00000472368:p.Leu83Val	171.0	0.0		177.0	51.0	NM_182515	Q49AI1|Q86W65|Q8ND40	Missense_Mutation	SNP	ENST00000596143.1	hg19	CCDS54239.1	.	.	.	.	.	.	.	.	.	.	.	9.034	0.987923	0.18966	.	.	ENSG00000160352	ENST00000343332;ENST00000291770	.	.	.	0.601	-0.984	0.10259	.	.	.	.	.	T	0.54271	0.1848	M	0.72894	2.215	0.09310	N	1	D;D	0.63880	0.971;0.993	P;D	0.73708	0.721;0.981	T	0.42582	-0.9443	8	0.48119	T	0.1	.	3.8304	0.08871	0.3218:0.0:0.0:0.6781	.	83;83	Q96N38-2;A6NEM4	.;.	V	83	.	ENSP00000291770:L83V	L	+	1	2	ZNF714	21091557	0.007000	0.16637	0.005000	0.12908	0.008000	0.06430	0.095000	0.15127	-0.425000	0.07371	-0.714000	0.03626	TTA	.	.		0.373	ZNF714-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463930.1	NM_182515	
CCNE1	898	hgsc.bcm.edu	37	19	30311721	30311721	+	Missense_Mutation	SNP	G	G	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:30311721G>C	ENST00000262643.3	+	7	854	c.575G>C	c.(574-576)gGg>gCg	p.G192A	CCNE1_ENST00000444983.2_Missense_Mutation_p.G177A|CCNE1_ENST00000357943.5_Intron	NM_001238.2	NP_001229.1	P24864	CCNE1_HUMAN	cyclin E1	192					androgen receptor signaling pathway (GO:0030521)|cell division (GO:0051301)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|Wnt signaling pathway (GO:0016055)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(2)|large_intestine(4)|lung(12)|skin(1)	20	all_cancers(1;2.19e-31)|all_epithelial(1;1.49e-30)|all_lung(1;1.37e-11)|Lung NSC(1;2.35e-11)|Ovarian(5;0.000902)|Breast(6;0.0203)|Esophageal squamous(110;0.195)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|Epithelial(1;6.85e-98)|all cancers(1;1.38e-94)|OV - Ovarian serous cystadenocarcinoma(1;1.38e-90)|STAD - Stomach adenocarcinoma(5;5.8e-07)|GBM - Glioblastoma multiforme(4;0.0394)|Lung(7;0.092)|LUAD - Lung adenocarcinoma(5;0.115)|BRCA - Breast invasive adenocarcinoma(6;0.183)|COAD - Colon adenocarcinoma(1;0.188)|Colorectal(1;0.202)			CAGCTTATTGGGATTTCATCT	0.348			A		serous ovarian																																p.G192A		Atlas-SNP	.		Dom	yes		19	19q12	898	cyclin E1		E	.	CCNE1	49	.	0			c.G575C						.						69.0	72.0	71.0					19																	30311721		2203	4300	6503	SO:0001583	missense	898	exon7			TTATTGGGATTTC	M73812	CCDS12419.1	19q12	2014-07-03			ENSG00000105173	ENSG00000105173			1589	protein-coding gene	gene with protein product	"""cyclin Es"", ""cyclin Et"""	123837		CCNE		1833066	Standard	NM_001238		Approved		uc002nsn.3	P24864	OTTHUMG00000177626	ENST00000262643.3:c.575G>C	chr19.hg19:g.30311721G>C	ENSP00000262643:p.Gly192Ala	117.0	0.0		89.0	22.0	NM_001238	A8K684|Q14091|Q8NFG1|Q92501|Q9UD21	Missense_Mutation	SNP	ENST00000262643.3	hg19	CCDS12419.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919889	0.92249	.	.	ENSG00000105173	ENST00000262643;ENST00000444983	T;T	0.11604	2.76;2.76	5.97	5.97	0.96955	Cyclin, N-terminal (1);Cyclin-like (3);	0.000000	0.85682	D	0.000000	T	0.38665	0.1049	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.08848	-1.0702	10	0.87932	D	0	.	19.4017	0.94632	0.0:0.0:1.0:0.0	.	192	P24864	CCNE1_HUMAN	A	192;177	ENSP00000262643:G192A;ENSP00000410179:G177A	ENSP00000262643:G192A	G	+	2	0	CCNE1	35003561	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	9.860000	0.99555	2.835000	0.97688	0.591000	0.81541	GGG	.	.		0.348	CCNE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438138.1	NM_001238	
PROSER3	148137	hgsc.bcm.edu	37	19	36256039	36256039	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:36256039T>C	ENST00000544099.1	+	7	794	c.731T>C	c.(730-732)aTc>aCc	p.I244T	C19orf55_ENST00000396908.4_Missense_Mutation_p.I244T			Q2NL68	PRSR3_HUMAN		244	Ser-rich.									cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GAGACCTTCATCCCTGACTCC	0.627																																					p.I244T		Atlas-SNP	.											.	C19orf55	39	.	0			c.T731C						.						87.0	90.0	89.0					19																	36256039		2107	4242	6349	SO:0001583	missense	148137	exon7			CCTTCATCCCTGA																												ENST00000544099.1:c.731T>C	chr19.hg19:g.36256039T>C	ENSP00000467267:p.Ile244Thr	79.0	0.0		68.0	15.0	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000544099.1	hg19		.	.	.	.	.	.	.	.	.	.	T	0.013	-1.610108	0.00835	.	.	ENSG00000167595	ENST00000396908;ENST00000301165	T;T	0.40476	1.03;1.03	4.42	-5.24	0.02789	.	1.025080	0.07815	N	0.958850	T	0.10937	0.0267	N	0.02802	-0.49	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.28964	-1.0027	10	0.02654	T	1	-2.4375	0.3981	0.00421	0.2784:0.2354:0.1297:0.3565	.	244	E5RFB9	.	T	244;243	ENSP00000380116:I244T;ENSP00000301165:I243T	ENSP00000301165:I243T	I	+	2	0	C19orf55	40947879	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	-0.856000	0.04290	-0.671000	0.05274	-0.379000	0.06801	ATC	.	.		0.627	C19orf55-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000398160.2		
DYRK1B	9149	hgsc.bcm.edu	37	19	40316849	40316849	+	Missense_Mutation	SNP	T	T	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:40316849T>C	ENST00000593685.1	-	10	1957	c.1489A>G	c.(1489-1491)Atc>Gtc	p.I497V	DYRK1B_ENST00000430012.2_Missense_Mutation_p.I457V|DYRK1B_ENST00000348817.3_Missense_Mutation_p.I469V|DYRK1B_ENST00000597639.1_Missense_Mutation_p.I469V|DYRK1B_ENST00000323039.5_Missense_Mutation_p.I497V			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B	497	Interaction with RANBP9.				adipose tissue development (GO:0060612)|myoblast fusion (GO:0007520)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(7)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	24	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)			CAGTCTGTGATAGGGGGCCCA	0.622																																					p.I497V		Atlas-SNP	.											.	DYRK1B	114	.	0			c.A1489G						.						51.0	55.0	53.0					19																	40316849		2203	4300	6503	SO:0001583	missense	9149	exon10			CTGTGATAGGGGG	Y17999	CCDS12543.1, CCDS12544.1, CCDS46075.1	19q13.2	2012-10-02			ENSG00000105204	ENSG00000105204	2.7.12.1		3092	protein-coding gene	gene with protein product	"""minibrain-related kinase"""	604556				9918863	Standard	XM_005259395		Approved	MIRK	uc002omj.3	Q9Y463		ENST00000593685.1:c.1489A>G	chr19.hg19:g.40316849T>C	ENSP00000469863:p.Ile497Val	46.0	0.0		32.0	7.0	NM_004714	O75258|O75788|O75789	Missense_Mutation	SNP	ENST00000593685.1	hg19	CCDS12543.1	.	.	.	.	.	.	.	.	.	.	T	3.615	-0.078772	0.07141	.	.	ENSG00000105204	ENST00000323039;ENST00000348817;ENST00000430012	T;T;T	0.55052	0.56;0.54;0.55	4.18	0.313	0.15842	.	0.664334	0.13789	N	0.362640	T	0.19765	0.0475	N	0.03608	-0.345	0.20975	N	0.999813	P;B;B	0.36086	0.536;0.007;0.003	B;B;B	0.34038	0.174;0.003;0.007	T	0.10917	-1.0609	10	0.16896	T	0.51	.	2.2481	0.04036	0.2223:0.2714:0.0:0.5063	.	457;497;469	Q9Y463-2;Q9Y463;Q9Y463-3	.;DYR1B_HUMAN;.	V	497;469;457	ENSP00000312789:I497V;ENSP00000221803:I469V;ENSP00000403182:I457V	ENSP00000312789:I497V	I	-	1	0	DYRK1B	45008689	0.984000	0.35163	0.997000	0.53966	0.991000	0.79684	0.829000	0.27449	0.445000	0.26639	0.379000	0.24179	ATC	.	.		0.622	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462874.2	NM_004714	
CEACAM5	1048	hgsc.bcm.edu	37	19	42212653	42212653	+	Start_Codon_SNP	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr19:42212653G>A	ENST00000221992.6	+	1	117	c.3G>A	c.(1-3)atG>atA	p.M1I	CEACAM5_ENST00000398599.4_Start_Codon_SNP_p.M1I|CEA_ENST00000598976.1_Start_Codon_SNP_p.M1I|CEACAM7_ENST00000599715.1_5'Flank|CEACAM5_ENST00000405816.1_Start_Codon_SNP_p.M1I	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	1					homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CAGAGACCATGGAGTCTCCCT	0.597																																					p.M1I		Atlas-SNP	.											.	CEACAM5	84	.	0			c.G3A						.						52.0	44.0	47.0					19																	42212653		2203	4300	6503	SO:0001582	initiator_codon_variant	1048	exon1			GACCATGGAGTCT	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.3G>A	chr19.hg19:g.42212653G>A	ENSP00000221992:p.Met1Ile	67.0	0.0		45.0	7.0	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	hg19	CCDS12584.1	.	.	.	.	.	.	.	.	.	.	-	15.07	2.723174	0.48728	.	.	ENSG00000105388	ENST00000221992;ENST00000405816;ENST00000378181	T;T	0.39592	1.07;1.07	3.01	3.01	0.34805	.	.	.	.	.	T	0.60287	0.2257	.	.	.	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.995	D;D;D	0.76071	0.98;0.987;0.956	T	0.63919	-0.6528	8	0.87932	D	0	.	9.6017	0.39607	0.0:0.0:1.0:0.0	.	1;1;1	Q8N4D0;P06731;Q53G30	.;CEAM5_HUMAN;.	I	1	ENSP00000221992:M1I;ENSP00000385072:M1I	ENSP00000221992:M1I	M	+	3	0	CEACAM5	46904493	0.975000	0.34042	0.096000	0.21009	0.034000	0.12701	3.510000	0.53393	1.694000	0.51137	0.313000	0.20887	ATG	.	.		0.597	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	Missense_Mutation
ERG	2078	hgsc.bcm.edu	37	21	39817538	39817538	+	Missense_Mutation	SNP	A	A	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr21:39817538A>C	ENST00000417133.2	-	4	231	c.46T>G	c.(46-48)Tta>Gta	p.L16V	ERG_ENST00000398907.1_Missense_Mutation_p.L9V|ERG_ENST00000429727.2_Missense_Mutation_p.L9V|ERG_ENST00000398910.1_Missense_Mutation_p.L16V|ERG_ENST00000398905.1_Missense_Mutation_p.L9V|ERG_ENST00000398919.2_Missense_Mutation_p.L16V|ERG_ENST00000442448.1_Missense_Mutation_p.L16V|ERG_ENST00000398911.1_Missense_Mutation_p.L16V|ERG_ENST00000453032.2_Intron|ERG_ENST00000288319.7_Missense_Mutation_p.L9V|ERG_ENST00000398897.1_Intron	NM_001136154.1|NM_001243432.1	NP_001129626.1|NP_001230361.1	Q12809	KCNH2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog	0					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)		EWSR1/ERG(178)|NDRG1/ERG(5)|TMPRSS2/ERG(3582)|FUS/ERG(167)|SLC45A3/ERG(50)	lung(2)|ovary(1)|skin(1)	4		Prostate(19;3.6e-06)			Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	ACAACTGATAAGGCTTCCTGA	0.478			T	"""EWSR1, TMPRSS2, ELF4, FUS, HERPUD1, NDRG1"""	"""Ewing sarcoma, prostate, AML"""																																p.L16V	Esophageal Squamous(130;336 1700 3010 3083 40589)	Atlas-SNP	.		Dom	yes		21	21q22.3	2078	v-ets erythroblastosis virus E26 oncogene like (avian)		"""M, E, L"""	.	ERG	78	.	0			c.T46G						.						87.0	71.0	77.0					21																	39817538		2203	4300	6503	SO:0001583	missense	2078	exon4			CTGATAAGGCTTC		CCDS13657.1, CCDS13658.1, CCDS46648.1, CCDS46649.1, CCDS58789.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157554	ENSG00000157554			3446	protein-coding gene	gene with protein product	"""v-ets avian erythroblastosis virus E26 oncogene related"", ""transcriptional regulator ERG (transforming protein ERG)"", ""v-ets erythroblastosis virus E26 oncogene like"", ""TMPRSS2-ERG prostate cancer specific"""	165080	"""v-ets avian erythroblastosis virus E26 oncogene related"""			3274086	Standard	NM_001136154		Approved	erg-3, p55	uc002yxa.3	P11308	OTTHUMG00000090767	ENST00000417133.2:c.46T>G	chr21.hg19:g.39817538A>C	ENSP00000414150:p.Leu16Val	248.0	0.0		291.0	56.0	NM_001243432	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000417133.2	hg19	CCDS46648.1	.	.	.	.	.	.	.	.	.	.	A	15.63	2.891027	0.52014	.	.	ENSG00000157554	ENST00000398905;ENST00000398907;ENST00000288319;ENST00000398911;ENST00000417133;ENST00000398910;ENST00000442448;ENST00000398919;ENST00000429727	T;T;T;T;T;T;T;T	0.37915	1.54;1.48;1.35;1.38;1.17;1.37;1.38;1.17	5.77	-3.5	0.04710	.	0.000000	0.64402	D	0.000003	T	0.50990	0.1648	M	0.64404	1.975	0.26945	N	0.966165	D;D;D;D;D	0.89917	0.998;1.0;1.0;0.999;0.998	D;D;D;D;D	0.91635	0.996;0.998;0.999;0.996;0.996	T	0.53151	-0.8479	10	0.87932	D	0	.	13.5166	0.61543	0.4795:0.0:0.5205:0.0	.	9;16;16;16;9	B4E3C5;P11308;P11308-6;P11308-1;P11308-4	.;ERG_HUMAN;.;.;.	V	9;9;9;16;16;16;16;16;9	ENSP00000381877:L9V;ENSP00000381879:L9V;ENSP00000288319:L9V;ENSP00000381882:L16V;ENSP00000414150:L16V;ENSP00000381881:L16V;ENSP00000394694:L16V;ENSP00000381891:L16V	ENSP00000288319:L9V	L	-	1	2	ERG	38739408	0.103000	0.21917	0.003000	0.11579	0.778000	0.44026	0.645000	0.24782	-0.664000	0.05324	-0.993000	0.02533	TTA	.	.		0.478	ERG-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207532.2	NM_182918	
TXN2	25828	hgsc.bcm.edu	37	22	36876748	36876748	+	Missense_Mutation	SNP	G	G	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr22:36876748G>A	ENST00000216185.2	-	2	603	c.137C>T	c.(136-138)cCc>cTc	p.P46L	TXN2_ENST00000416967.1_5'UTR|TXN2_ENST00000403313.1_Missense_Mutation_p.P46L|TXN2_ENST00000487725.1_5'UTR			Q99757	THIOM_HUMAN	thioredoxin 2	46					cell redox homeostasis (GO:0045454)|cellular response to nutrient levels (GO:0031669)|glycerol ether metabolic process (GO:0006662)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|response to oxidative stress (GO:0006979)	dendrite (GO:0030425)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)	protein disulfide oxidoreductase activity (GO:0015035)			breast(1)|lung(1)|prostate(1)	3						GGCTGGGTTGGGTGTTACAGT	0.547																																					p.P46L		Atlas-SNP	.											.	TXN2	15	.	0			c.C137T						.						155.0	132.0	140.0					22																	36876748		2203	4300	6503	SO:0001583	missense	25828	exon2			GGGTTGGGTGTTA	U78678	CCDS13928.1	22q13.1	2008-06-11			ENSG00000100348	ENSG00000100348			17772	protein-coding gene	gene with protein product		609063				9006939, 17220299	Standard	NM_012473		Approved	MT-TRX	uc003apk.1	Q99757	OTTHUMG00000150596	ENST00000216185.2:c.137C>T	chr22.hg19:g.36876748G>A	ENSP00000216185:p.Pro46Leu	113.0	0.0		66.0	15.0	NM_012473	Q5JZA0|Q6FH60|Q9UH29	Missense_Mutation	SNP	ENST00000216185.2	hg19	CCDS13928.1	.	.	.	.	.	.	.	.	.	.	g	2.067	-0.413949	0.04799	.	.	ENSG00000100348	ENST00000216185;ENST00000403313	T;T	0.12672	2.66;2.66	5.36	-1.28	0.09318	.	0.254450	0.39407	N	0.001368	T	0.12860	0.0312	M	0.69823	2.125	0.26776	N	0.969698	B	0.02656	0.0	B	0.01281	0.0	T	0.16988	-1.0384	10	0.39692	T	0.17	-23.1098	6.5833	0.22607	0.2285:0.3384:0.4331:0.0	.	46	Q99757	THIOM_HUMAN	L	46	ENSP00000216185:P46L;ENSP00000385393:P46L	ENSP00000216185:P46L	P	-	2	0	TXN2	35206694	0.000000	0.05858	0.305000	0.25099	0.037000	0.13140	-0.025000	0.12413	-0.092000	0.12417	-0.738000	0.03535	CCC	.	.		0.547	TXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319016.1	NM_012473	
KIAA2022	340533	hgsc.bcm.edu	37	X	73960550	73960550	+	Missense_Mutation	SNP	C	C	A			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chrX:73960550C>A	ENST00000055682.6	-	3	4453	c.3842G>T	c.(3841-3843)gGa>gTa	p.G1281V		NM_001008537.2	NP_001008537.1	Q5QGS0	K2022_HUMAN	KIAA2022	1281					base-excision repair, gap-filling (GO:0006287)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|nervous system development (GO:0007399)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)	delta DNA polymerase complex (GO:0043625)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(23)|liver(1)|lung(41)|ovary(7)|pancreas(2)|prostate(4)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	109						GGCCCAATCTCCAGAAAGTCC	0.517																																					p.G1281V		Atlas-SNP	.											.	KIAA2022	262	.	0			c.G3842T						.						88.0	73.0	78.0					X																	73960550		2203	4300	6503	SO:0001583	missense	340533	exon3			CAATCTCCAGAAA		CCDS35337.1	Xq13.3	2014-02-19			ENSG00000050030	ENSG00000050030			29433	protein-coding gene	gene with protein product	"""XLMR-related protein, neurite extension"""	300524				15466006, 23615299	Standard	NM_001008537		Approved	XPN, MRX98	uc004eby.3	Q5QGS0	OTTHUMG00000021860	ENST00000055682.6:c.3842G>T	chrX.hg19:g.73960550C>A	ENSP00000055682:p.Gly1281Val	53.0	0.0		44.0	22.0	NM_001008537	A7YY87|Q5JUX9|Q8IVE9	Missense_Mutation	SNP	ENST00000055682.6	hg19	CCDS35337.1	.	.	.	.	.	.	.	.	.	.	C	14.56	2.570404	0.45798	.	.	ENSG00000050030	ENST00000373468;ENST00000055682	T;T	0.30714	1.52;1.52	5.11	3.33	0.38152	.	0.503490	0.23414	N	0.048438	T	0.28034	0.0691	L	0.29908	0.895	0.80722	D	1	P	0.45827	0.867	P	0.47206	0.541	T	0.02844	-1.1103	10	0.87932	D	0	-1.3178	9.7619	0.40537	0.0:0.7849:0.1373:0.0778	.	1281	Q5QGS0	K2022_HUMAN	V	1281	ENSP00000362567:G1281V;ENSP00000055682:G1281V	ENSP00000055682:G1281V	G	-	2	0	KIAA2022	73877275	0.999000	0.42202	0.992000	0.48379	0.915000	0.54546	2.181000	0.42547	0.538000	0.28769	0.600000	0.82982	GGA	.	.		0.517	KIAA2022-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057270.2	NM_001008537	
RAP2C	57826	hgsc.bcm.edu	37	X	131348421	131348421	+	Silent	SNP	G	G	C			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chrX:131348421G>C	ENST00000342983.2	-	3	1073	c.327C>G	c.(325-327)gtC>gtG	p.V109V	RAP2C_ENST00000460462.1_5'UTR|RAP2C-AS1_ENST00000421483.2_RNA|RAP2C_ENST00000370874.1_Silent_p.V109V	NM_001271187.1|NM_021183.4	NP_001258116.1|NP_067006.3	Q9Y3L5	RAP2C_HUMAN	RAP2C, member of RAS oncogene family	109					GTP catabolic process (GO:0006184)|negative regulation of cell migration (GO:0030336)|positive regulation of protein autophosphorylation (GO:0031954)|Rap protein signal transduction (GO:0032486)|regulation of protein tyrosine kinase activity (GO:0061097)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|transcription coactivator activity (GO:0003713)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	8	Acute lymphoblastic leukemia(192;0.000127)					GGATTAGTGGGACTTTTTCAT	0.393																																					p.V109V		Atlas-SNP	.											.	RAP2C	22	.	0			c.C327G						.						91.0	72.0	78.0					X																	131348421		2203	4300	6503	SO:0001819	synonymous_variant	57826	exon3			TAGTGGGACTTTT	BC051467	CCDS14632.1, CCDS76024.1	Xq25	2014-05-09			ENSG00000123728	ENSG00000123728			21165	protein-coding gene	gene with protein product							Standard	NM_001271186		Approved	DKFZp313B211	uc004ewp.4	Q9Y3L5	OTTHUMG00000022424	ENST00000342983.2:c.327C>G	chrX.hg19:g.131348421G>C		104.0	0.0		71.0	33.0	NM_021183	B3KWD6|Q5H9H9|Q9BTS0	Silent	SNP	ENST00000342983.2	hg19	CCDS14632.1																																																																																			.	.		0.393	RAP2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058312.1	NM_021183	
VEPH1	79674	hgsc.bcm.edu	37	3	157146119	157146120	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr3:157146119_157146120insT	ENST00000362010.2	-	5	994_995	c.687_688insA	c.(685-690)aaacaafs	p.Q230fs	VEPH1_ENST00000469007.1_5'UTR|VEPH1_ENST00000543418.1_Frame_Shift_Ins_p.Q230fs|VEPH1_ENST00000392832.2_Frame_Shift_Ins_p.Q230fs|VEPH1_ENST00000392833.2_Frame_Shift_Ins_p.Q230fs	NM_001167912.1	NP_001161384.1	Q14D04	MELT_HUMAN	ventricular zone expressed PH domain-containing 1	230						plasma membrane (GO:0005886)		p.K229N(1)		autonomic_ganglia(1)|breast(5)|cervix(1)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|pancreas(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48			Lung(72;0.0272)|LUSC - Lung squamous cell carcinoma(72;0.0461)			ACCTCGAGTTGTTTTTTCTTTG	0.431																																					p.Q230fs		Atlas-INDEL	.											.	VEPH1	129	.	1	Substitution - Missense(1)	large_intestine(1)	c.688_689insA						.																																			SO:0001589	frameshift_variant	79674	exon5			.	AL713656	CCDS3179.1, CCDS54661.1, CCDS54662.1, CCDS54663.1	3q24-q25	2013-01-10	2012-12-10		ENSG00000197415	ENSG00000197415		"""Pleckstrin homology (PH) domain containing"""	25735	protein-coding gene	gene with protein product		609594	"""ventricular zone expressed PH domain homolog 1 (zebrafish)"""			11214970, 15388229	Standard	NM_024621		Approved	FLJ12604, KIAA1692	uc003fbk.2	Q14D04	OTTHUMG00000158711	ENST00000362010.2:c.688dupA	chr3.hg19:g.157146125_157146125dupT	ENSP00000354919:p.Gln230fs	122.0	0.0		132.0	40.0	NM_024621	D3DNL0|F5GZ91|Q2TAA9|Q3MIX2|Q6PEL3|Q86TL5|Q8TCR3|Q96SP7|Q9C0H1|Q9H9Q7	Frame_Shift_Ins	INS	ENST00000362010.2	hg19	CCDS3179.1																																																																																			.	.		0.431	VEPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351845.3	NM_024621	
NLRP3	114548	hgsc.bcm.edu	37	1	247588695	247588695	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:247588695delC	ENST00000336119.3	+	3	2696	c.1950delC	c.(1948-1950)ttcfs	p.F650fs	NLRP3_ENST00000348069.2_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000391827.2_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000366496.2_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000391828.3_Frame_Shift_Del_p.F650fs|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000366497.2_Frame_Shift_Del_p.F650fs	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	650					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TGGACTATTTCCCCAAGATTG	0.493																																					p.F650fs		Atlas-Indel,Pindel	.											.	NLRP3	286	.	0			c.1949delT						.						94.0	80.0	85.0					1																	247588695		2203	4300	6503	SO:0001589	frameshift_variant	114548	exon3			.	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1950delC	chr1.hg19:g.247588695delC	ENSP00000337383:p.Phe650fs	253.0	0.0		236.0	96.0	NM_004895	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Frame_Shift_Del	DEL	ENST00000336119.3	hg19	CCDS1632.1																																																																																			.	.		0.493	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
LCP2	3937	hgsc.bcm.edu	37	5	169689858	169689859	+	Frame_Shift_Ins	INS	-	-	T			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:169689858_169689859insT	ENST00000046794.5	-	12	1420_1421	c.805_806insA	c.(805-807)attfs	p.I269fs	LCP2_ENST00000521416.1_Frame_Shift_Ins_p.I64fs	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	269					blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		TCCCGCTGGAATCGAGGGCTGC	0.426																																					p.I269fs		Atlas-INDEL	.											.	LCP2	133	.	0			c.806_807insA						.																																			SO:0001589	frameshift_variant	3937	exon12			.		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.806dupA	chr5.hg19:g.169689859_169689859dupT	ENSP00000046794:p.Ile269fs	179.0	0.0		194.0	30.0	NM_005565	A8KA25|Q53XV4	Frame_Shift_Ins	INS	ENST00000046794.5	hg19	CCDS47339.1																																																																																			.	.		0.426	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
MAP2K4	6416	hgsc.bcm.edu	37	17	12013730	12013731	+	In_Frame_Ins	INS	-	-	ATT			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr17:12013730_12013731insATT	ENST00000353533.5	+	6	735_736	c.672_673insATT	c.(673-675)att>ATTatt	p.225_225I>II	MAP2K4_ENST00000415385.3_In_Frame_Ins_p.236_236I>II|MAP2K4_ENST00000581941.1_3'UTR	NM_003010.2	NP_003001.1	P45985	MP2K4_HUMAN	mitogen-activated protein kinase kinase 4	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|cellular response to sorbitol (GO:0072709)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of DNA replication (GO:0045740)|positive regulation of neuron apoptotic process (GO:0043525)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|nucleus (GO:0005634)|perikaryon (GO:0043204)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.0?(10)|p.?(1)		NS(1)|biliary_tract(2)|breast(22)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(26)|lung(15)|ovary(8)|pancreas(11)|skin(3)|stomach(2)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	100		all_cancers(5;0.0413)|Breast(5;0.000625)|all_epithelial(5;0.00978)|all_lung(20;0.0449)|Lung NSC(33;0.163)		Epithelial(2;4.12e-09)|all cancers(2;6.86e-07)|BRCA - Breast invasive adenocarcinoma(2;8.74e-07)|Colorectal(4;5.32e-05)|COAD - Colon adenocarcinoma(4;0.0039)|READ - Rectum adenocarcinoma(10;0.0681)		AAAACTTGAAAATTATTCACAG	0.322			"""D, Mis, N"""		"""pancreatic, breast, colorectal"""																																p.K224delinsKI		Atlas-INDEL	.		Rec	yes		17	17p11.2	6416	mitogen-activated protein kinase kinase 4		E	.	MAP2K4	176	.	11	Whole gene deletion(10)|Unknown(1)	ovary(4)|breast(4)|biliary_tract(1)|large_intestine(1)|pancreas(1)	c.672_673insATT						.																																			SO:0001652	inframe_insertion	6416	exon6			.	L36870	CCDS11162.1, CCDS62095.1	17p12	2012-03-23			ENSG00000065559	ENSG00000065559	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6844	protein-coding gene	gene with protein product		601335		SERK1		7716521	Standard	NM_003010		Approved	MEK4, JNKK1, PRKMK4, MKK4	uc002gnj.3	P45985		ENST00000353533.5:c.676_678dupATT	chr17.hg19:g.12013734_12013736dupATT	ENSP00000262445:p.Ile226dup	103.0	0.0		48.0	14.0	NM_003010	B2R7N7|B3KYB2|D3DTS5|Q5U0B8|Q6FHX4|Q6P9H2|Q6PIE6	In_Frame_Ins	INS	ENST00000353533.5	hg19	CCDS11162.1																																																																																			.	.		0.322	MAP2K4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441226.1		
RASGRF1	5923	hgsc.bcm.edu	37	15	79382797	79382799	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr15:79382797_79382799delAGG	ENST00000419573.3	-	1	316_318	c.42_44delCCT	c.(40-45)tccctg>tcg	p.L15del	RASGRF1_ENST00000558480.2_In_Frame_Del_p.L15del	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	15					activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						CAGCAGTCCCAGGGACGCGACGT	0.635																																					p.15_15del		Atlas-INDEL	.											.	RASGRF1	168	.	0			c.43_45del						.																																			SO:0001651	inframe_deletion	5923	exon1			.	M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.42_44delCCT	chr15.hg19:g.79382797_79382799delAGG	ENSP00000405963:p.Leu15del	94.0	0.0		55.0	10.0	NM_001145648	F8VPA5|H0YKF2|J3KQP9|Q16027	In_Frame_Del	DEL	ENST00000419573.3	hg19	CCDS10309.1																																																																																			.	.		0.635	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3	NM_002891	
ARID1A	8289	hgsc.bcm.edu	37	1	27106299	27106300	+	Frame_Shift_Ins	INS	-	-	CTGGA	rs372543523		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr1:27106299_27106300insCTGGA	ENST00000324856.7	+	20	6281_6282	c.5910_5911insCTGGA	c.(5911-5913)ctgfs	p.-1972fs	ARID1A_ENST00000540690.1_Frame_Shift_Ins_p.-300fs|ARID1A_ENST00000457599.2_Frame_Shift_Ins_p.-1755fs|ARID1A_ENST00000374152.2_Frame_Shift_Ins_p.-1589fs	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)						androgen receptor signaling pathway (GO:0030521)|ATP-dependent chromatin remodeling (GO:0043044)|cardiac chamber development (GO:0003205)|chromatin remodeling (GO:0006338)|chromatin-mediated maintenance of transcription (GO:0048096)|forebrain development (GO:0030900)|glucocorticoid receptor signaling pathway (GO:0042921)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nucleosome disassembly (GO:0006337)|nucleosome mobilization (GO:0042766)|optic cup formation involved in camera-type eye development (GO:0003408)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|transcription coactivator activity (GO:0003713)		ARID1A/MAST2_ENST00000361297(2)	NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(13)|central_nervous_system(6)|cervix(2)|endometrium(56)|haematopoietic_and_lymphoid_tissue(8)|kidney(10)|large_intestine(41)|liver(31)|lung(34)|ovary(130)|pancreas(18)|prostate(8)|skin(9)|stomach(14)|upper_aerodigestive_tract(4)|urinary_tract(24)	411		all_cancers(24;6.36e-27)|all_epithelial(13;5.93e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Breast(348;9.7e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|all cancers(4;2.61e-56)|Epithelial(14;7.53e-55)|OV - Ovarian serous cystadenocarcinoma(117;4.5e-30)|Colorectal(126;2.07e-09)|COAD - Colon adenocarcinoma(152;4.29e-07)|BRCA - Breast invasive adenocarcinoma(304;4.13e-05)|STAD - Stomach adenocarcinoma(196;0.000279)|KIRC - Kidney renal clear cell carcinoma(1967;0.000794)|GBM - Glioblastoma multiforme(114;0.0132)|READ - Rectum adenocarcinoma(331;0.0469)|Lung(427;0.167)|LUSC - Lung squamous cell carcinoma(448;0.242)		TGTGTACCCTTCTGGACTGGCA	0.515			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.L1970fs		Atlas-INDEL	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.5910_5911insCTGGA						.																																			SO:0001589	frameshift_variant	8289	exon20			.	AB001895	CCDS285.1, CCDS44091.1	1p36.1-p35	2014-09-17	2006-11-08	2004-01-30	ENSG00000117713	ENSG00000117713		"""-"""	11110	protein-coding gene	gene with protein product		603024	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily f, member 1"", ""AT rich interactive domain 1A (SWI- like)"""	C1orf4, SMARCF1		9630625, 9434167	Standard	NM_139135		Approved	B120, P270, C10rf4, BAF250, BAF250a	uc001bmv.1	O14497	OTTHUMG00000004004	ENST00000324856.7:c.5911_5915dupCTGGA	chr1.hg19:g.27106300_27106304dupCTGGA	ENSP00000320485:p.Asp1972fs	103.0	0.0		106.0	22.0	NM_006015	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	Frame_Shift_Ins	INS	ENST00000324856.7	hg19	CCDS285.1																																																																																			.	.		0.515	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
AFF4	27125	hgsc.bcm.edu	37	5	132269980	132269980	+	Frame_Shift_Del	DEL	G	G	-	rs200345107		TCGA-BW-A5NQ-01A-11D-A27I-10	TCGA-BW-A5NQ-10A-01D-A27I-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	e30c64d5-e796-4cfc-8dc8-6e62bf97822f	62616abe-8ebe-46fc-b24e-32d8cca79e40	g.chr5:132269980delG	ENST00000265343.5	-	3	1156	c.777delC	c.(775-777)cccfs	p.P259fs	AFF4_ENST00000491831.1_5'UTR|AFF4_ENST00000378595.3_Frame_Shift_Del_p.P259fs	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	259	Ser-rich.				spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			GTCCGTCCATGGGCCGCACAT	0.507																																					p.M260fs	Ovarian(126;889 1733 2942 10745 11605)	Pindel	.											.	AFF4	120	.	0			c.778delA						.						168.0	151.0	157.0					5																	132269980		2203	4300	6503	SO:0001589	frameshift_variant	27125	exon3			.	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.777delC	chr5.hg19:g.132269980delG	ENSP00000265343:p.Pro259fs	274.0	0.0		368.0	86.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Del	DEL	ENST00000265343.5	hg19	CCDS4164.1																																																																																			.	.		0.507	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
