#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
NPHP4	261734	hgsc.bcm.edu	37	1	6029260	6029260	+	Silent	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:6029260G>A	ENST00000378156.4	-	4	604	c.339C>T	c.(337-339)gtC>gtT	p.V113V	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	113					actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCCTCAGCGACCACTTCCA	0.527																																					p.V113V		Atlas-SNP	.											.	NPHP4	119	.	0			c.C339T						.						78.0	86.0	83.0					1																	6029260		2004	4151	6155	SO:0001819	synonymous_variant	261734	exon4			CTCAGCGACCACT	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.339C>T	chr1.hg19:g.6029260G>A		115.0	0.0		148.0	59.0	NM_015102	Q8IWC0	Silent	SNP	ENST00000378156.4	hg19	CCDS44052.1																																																																																			.	.		0.527	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
CAMTA1	23261	hgsc.bcm.edu	37	1	7796520	7796520	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:7796520G>C	ENST00000303635.7	+	13	3390	c.3183G>C	c.(3181-3183)aaG>aaC	p.K1061N	CAMTA1_ENST00000439411.2_Missense_Mutation_p.K1061N	NM_015215.2	NP_056030.1	Q9Y6Y1	CMTA1_HUMAN	calmodulin binding transcription activator 1	1061					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(11)|lung(29)|ovary(5)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	85	Ovarian(185;0.0634)	all_epithelial(116;8.38e-23)|all_lung(118;5.87e-07)|Lung NSC(185;3.43e-06)|Renal(390;0.000219)|Breast(487;0.000307)|Colorectal(325;0.000615)|Hepatocellular(190;0.0088)|Myeloproliferative disorder(586;0.0303)|Ovarian(437;0.0388)		UCEC - Uterine corpus endometrioid carcinoma (279;0.101)|Colorectal(212;1.33e-05)|COAD - Colon adenocarcinoma(227;0.000235)|BRCA - Breast invasive adenocarcinoma(304;0.000864)|Kidney(185;0.00244)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0179)|READ - Rectum adenocarcinoma(331;0.133)		TCCACTCAAAGACTTTCCGCG	0.592			T	WWTR1	epitheliod hemangioendothelioma																																p.K1061N		Atlas-SNP	.		Dom	yes		1	1p36.31-p36.23	611501	calmodulin binding transcription activator 1		M	.	CAMTA1	226	.	0			c.G3183C						.						138.0	124.0	129.0					1																	7796520		2203	4300	6503	SO:0001583	missense	23261	exon13			CTCAAAGACTTTC	AB020640	CCDS30576.1, CCDS55574.1, CCDS55575.1	1p36.31-p36.23	2008-07-18			ENSG00000171735	ENSG00000171735			18806	protein-coding gene	gene with protein product		611501				11925432	Standard	NM_001195563		Approved	KIAA0833	uc001aoi.3	Q9Y6Y1	OTTHUMG00000001212	ENST00000303635.7:c.3183G>C	chr1.hg19:g.7796520G>C	ENSP00000306522:p.Lys1061Asn	160.0	0.0		163.0	7.0	NM_015215	A7MBM4|G3V3Z7|Q5VUE1|Q6V701|Q8WYI3|Q96S92	Missense_Mutation	SNP	ENST00000303635.7	hg19	CCDS30576.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.252809|4.252809	0.80135|0.80135	.|.	.|.	ENSG00000171735|ENSG00000171735	ENST00000303635;ENST00000439411;ENST00000414738;ENST00000303646|ENST00000495233	T;T|.	0.45276|.	0.9;0.9|.	5.58|5.58	3.73|3.73	0.42828|0.42828	Ankyrin repeat-containing domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.60011|0.60011	0.2236|0.2236	L|L	0.51422|0.51422	1.61|1.61	0.54753|0.54753	D|D	0.999989|0.999989	D;D;D;D|.	0.76494|.	0.995;0.999;0.996;0.997|.	D;D;P;D|.	0.80764|.	0.969;0.994;0.873;0.931|.	T|T	0.55425|0.55425	-0.8143|-0.8143	10|5	0.17369|.	T|.	0.5|.	-25.379|-25.379	12.042|12.042	0.53458|0.53458	0.1384:0.0:0.8616:0.0|0.1384:0.0:0.8616:0.0	.|.	1061;148;17;1061|.	Q9Y6Y1-2;B4DXR3;Q7Z7P1;Q9Y6Y1|.	.;.;.;CMTA1_HUMAN|.	N|T	1061;1061;148;17|18	ENSP00000306522:K1061N;ENSP00000402561:K1061N|.	ENSP00000306522:K1061N|.	K|R	+|+	3|2	2|0	CAMTA1|CAMTA1	7719107|7719107	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.832000|0.832000	0.47134|0.47134	4.090000|4.090000	0.57693|0.57693	0.736000|0.736000	0.32559|0.32559	-0.122000|-0.122000	0.15005|0.15005	AAG|AGA	.	.		0.592	CAMTA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003588.3	NM_015215	
VPS13D	55187	hgsc.bcm.edu	37	1	12359278	12359278	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:12359278G>T	ENST00000358136.3	+	25	6183	c.6053G>T	c.(6052-6054)cGc>cTc	p.R2018L	VPS13D_ENST00000356315.4_Missense_Mutation_p.R2018L	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		CAAGCCCAGCGCTGTTCACGG	0.438																																					p.R2018L		Atlas-SNP	.											VPS13D,NS,carcinoma,0,1	VPS13D	316	.	0			c.G6053T						.						96.0	96.0	96.0					1																	12359278		2203	4300	6503	SO:0001583	missense	55187	exon25			CCCAGCGCTGTTC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.6053G>T	chr1.hg19:g.12359278G>T	ENSP00000350854:p.Arg2018Leu	76.0	0.0		87.0	4.0	NM_015378		Missense_Mutation	SNP	ENST00000358136.3	hg19	CCDS30588.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	29.8|29.8	5.037451|5.037451	0.93630|0.93630	.|.	.|.	ENSG00000048707|ENSG00000048707	ENST00000011700|ENST00000356315;ENST00000358136	.|T;T	.|0.56941	.|0.43;0.44	5.77|5.77	5.77|5.77	0.91146|0.91146	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.71904|0.71904	0.3395|0.3395	M|M	0.74647|0.74647	2.275|2.275	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.998;0.997	.|D;P	.|0.65684	.|0.937;0.866	T|T	0.66945|0.66945	-0.5795|-0.5795	5|10	.|0.27785	.|T	.|0.31	.|.	19.9983|19.9983	0.97395|0.97395	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|2018;2018	.|Q5THJ4-2;Q5THJ4	.|.;VP13D_HUMAN	S|L	841|2018	.|ENSP00000348666:R2018L;ENSP00000350854:R2018L	.|ENSP00000348666:R2018L	A|R	+|+	1|2	0|0	VPS13D|VPS13D	12281865|12281865	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.906000|0.906000	0.53458|0.53458	9.402000|9.402000	0.97298|0.97298	2.724000|2.724000	0.93272|0.93272	0.561000|0.561000	0.74099|0.74099	GCT|CGC	.	.		0.438	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
C1orf158	93190	hgsc.bcm.edu	37	1	12820859	12820859	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:12820859G>T	ENST00000288048.5	+	4	776	c.560G>T	c.(559-561)cGc>cTc	p.R187L	C1orf158_ENST00000376210.3_Missense_Mutation_p.R149L	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	187								p.R187P(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		CCTCCCCATCGCCTGCATCCT	0.577																																					p.R187L		Atlas-SNP	.											C1orf158,NS,lymphoid_neoplasm,0,2	C1orf158	28	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G560T						.						89.0	78.0	82.0					1																	12820859		2203	4300	6503	SO:0001583	missense	93190	exon4			CCCATCGCCTGCA	BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330			28567	protein-coding gene	gene with protein product						12477932	Standard	NM_152290		Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.560G>T	chr1.hg19:g.12820859G>T	ENSP00000288048:p.Arg187Leu	70.0	0.0		76.0	18.0	NM_152290	Q5VUY4	Missense_Mutation	SNP	ENST00000288048.5	hg19	CCDS147.1	.	.	.	.	.	.	.	.	.	.	.	12.10	1.835737	0.32421	.	.	ENSG00000157330	ENST00000288048;ENST00000376210	T;T	0.48522	0.82;0.81	4.55	1.53	0.23141	.	0.476202	0.23712	N	0.045317	T	0.39384	0.1076	M	0.68317	2.08	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.33420	-0.9869	10	0.46703	T	0.11	-6.9156	3.9984	0.09569	0.2048:0.0:0.6083:0.1869	.	187	Q8N1D5	CA158_HUMAN	L	187;149	ENSP00000288048:R187L;ENSP00000365383:R149L	ENSP00000288048:R187L	R	+	2	0	C1orf158	12743446	0.002000	0.14202	0.028000	0.17463	0.003000	0.03518	0.745000	0.26259	0.520000	0.28426	0.563000	0.77884	CGC	.	.		0.577	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290	
PRAMEF18	391003	hgsc.bcm.edu	37	1	13475241	13475241	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:13475241C>T	ENST00000376126.2	-	3	887	c.888G>A	c.(886-888)gaG>gaA	p.E296E		NM_001099850.1	NP_001093320.1	Q5VWM3	PRA18_HUMAN	PRAME family member 18	296					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					lung(2)|ovary(1)	3	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.00224)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATGCCAATGTCTCCAACGGGC	0.498																																					p.E296E		Atlas-SNP	.											PRAMEF18,NS,carcinoma,0,1	PRAMEF19	6	.	0			c.G888A						.						3.0	3.0	3.0					1																	13475241		1541	3394	4935	SO:0001819	synonymous_variant	645414	exon3			CAATGTCTCCAAC			1p36.21	2013-01-17			ENSG00000204491			"""-"""	30693	protein-coding gene	gene with protein product							Standard			Approved	OTTHUMG00000002932		Q5VWM3	OTTHUMG00000002932	ENST00000376126.2:c.888G>A	chr1.hg19:g.13475241C>T		263.0	0.0		272.0	17.0	NM_001099790		Silent	SNP	ENST00000376126.2	hg19	CCDS41258.1																																																																																			.	.		0.498	PRAMEF18-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008177.2	NM_001099850	
PHC2	1912	hgsc.bcm.edu	37	1	33832725	33832725	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:33832725A>G	ENST00000257118.5	-	6	1021	c.968T>C	c.(967-969)aTt>aCt	p.I323T	PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000419414.2_Missense_Mutation_p.I323T|PHC2_ENST00000431992.1_Missense_Mutation_p.I294T	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	323					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				ACCTGGTGCAATGAGGGGGTG	0.567																																					p.I323T		Atlas-SNP	.											.	PHC2	78	.	0			c.T968C						.						67.0	71.0	69.0					1																	33832725		2201	4300	6501	SO:0001583	missense	1912	exon6			GGTGCAATGAGGG	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.968T>C	chr1.hg19:g.33832725A>G	ENSP00000257118:p.Ile323Thr	62.0	0.0		74.0	5.0	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	hg19	CCDS378.1	.	.	.	.	.	.	.	.	.	.	A	14.67	2.605231	0.46423	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000419414	T;T;T	0.36340	1.53;1.26;1.65	5.88	4.73	0.59995	.	0.284540	0.38326	N	0.001721	T	0.30135	0.0755	L	0.51422	1.61	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.07404	-1.0774	10	0.24483	T	0.36	-0.2548	9.0205	0.36198	0.9158:0.0:0.0842:0.0	.	323;294;323	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	T	294;323;323	ENSP00000389436:I294T;ENSP00000257118:I323T;ENSP00000391440:I323T	ENSP00000257118:I323T	I	-	2	0	PHC2	33605312	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.526000	0.53509	1.008000	0.39264	0.533000	0.62120	ATT	.	.		0.567	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
FOXE3	2301	hgsc.bcm.edu	37	1	47882609	47882609	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:47882609C>A	ENST00000335071.2	+	1	866	c.622C>A	c.(622-624)Ccg>Acg	p.P208T		NM_012186.2	NP_036318.1	Q13461	FOXE3_HUMAN	forkhead box E3	208					camera-type eye development (GO:0043010)|cell development (GO:0048468)|positive regulation of epithelial cell proliferation (GO:0050679)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(3)|prostate(1)|upper_aerodigestive_tract(1)	5				READ - Rectum adenocarcinoma(2;0.0908)		TTCTGCCGGACCGGGCCCCTC	0.811																																					p.P208T		Atlas-SNP	.											.	FOXE3	8	.	0			c.C622A						.						1.0	1.0	1.0					1																	47882609		364	692	1056	SO:0001583	missense	2301	exon1			GCCGGACCGGGCC	AF275722	CCDS550.1	1p32	2008-02-05			ENSG00000186790	ENSG00000186790		"""Forkhead boxes"""	3808	protein-coding gene	gene with protein product		601094		FKHL12		8825632	Standard	NM_012186		Approved	FREAC8	uc001crk.3	Q13461	OTTHUMG00000007954	ENST00000335071.2:c.622C>A	chr1.hg19:g.47882609C>A	ENSP00000334472:p.Pro208Thr	21.0	0.0		26.0	8.0	NM_012186	Q5SVY9|Q9NQV9	Missense_Mutation	SNP	ENST00000335071.2	hg19	CCDS550.1	.	.	.	.	.	.	.	.	.	.	c	11.95	1.791118	0.31685	.	.	ENSG00000186790	ENST00000335071	D	0.94897	-3.55	3.35	3.35	0.38373	.	0.831414	0.09635	U	0.775714	D	0.87865	0.6285	N	0.19112	0.55	0.27231	N	0.959403	B	0.19331	0.035	B	0.17098	0.017	T	0.74034	-0.3794	10	0.08381	T	0.77	.	11.0831	0.48072	0.0:0.8116:0.1884:0.0	.	208	Q13461	FOXE3_HUMAN	T	208	ENSP00000334472:P208T	ENSP00000334472:P208T	P	+	1	0	FOXE3	47655196	0.008000	0.16893	0.035000	0.18076	0.017000	0.09413	0.981000	0.29526	1.706000	0.51276	0.448000	0.29417	CCG	.	.		0.811	FOXE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021836.1	NM_012186	
USP24	23358	hgsc.bcm.edu	37	1	55624658	55624658	+	Missense_Mutation	SNP	G	G	A	rs374277857		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:55624658G>A	ENST00000294383.6	-	10	1119	c.1120C>T	c.(1120-1122)Cgc>Tgc	p.R374C	USP24_ENST00000407756.1_Missense_Mutation_p.R262C	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	374					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						GGTTGGAAGCGCATGCAAAGT	0.378																																					p.R374C		Atlas-SNP	.											.	USP24	323	.	0			c.C1120T						.	G	CYS/ARG	0,3846		0,0,1923	62.0	59.0	60.0		1120	5.4	1.0	1		60	2,8296		0,2,4147	no	missense	USP24	NM_015306.2	180	0,2,6070	AA,AG,GG		0.0241,0.0,0.0165	probably-damaging	374/2621	55624658	2,12142	1923	4149	6072	SO:0001583	missense	23358	exon10			GGAAGCGCATGCA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.1120C>T	chr1.hg19:g.55624658G>A	ENSP00000294383:p.Arg374Cys	242.0	0.0		253.0	88.0	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	hg19	CCDS44154.2	.	.	.	.	.	.	.	.	.	.	G	15.74	2.923658	0.52653	0.0	2.41E-4	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.37915	1.17;1.17	5.44	5.44	0.79542	.	0.064020	0.64402	D	0.000013	T	0.33381	0.0861	N	0.25485	0.75	0.54753	D	0.99998	D	0.63880	0.993	B	0.44315	0.446	T	0.09751	-1.0660	10	0.51188	T	0.08	.	19.6122	0.95610	0.0:0.0:1.0:0.0	.	262	B7WPF4	.	C	374;262	ENSP00000294383:R374C;ENSP00000385700:R262C	ENSP00000294383:R374C	R	-	1	0	USP24	55397246	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.116000	0.57871	2.709000	0.92574	0.591000	0.81541	CGC	.	.		0.378	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
INADL	10207	hgsc.bcm.edu	37	1	62550246	62550246	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:62550246G>A	ENST00000371158.2	+	33	4417	c.4303G>A	c.(4303-4305)Gaa>Aaa	p.E1435K	INADL_ENST00000316485.6_Missense_Mutation_p.E1435K|INADL_ENST00000545929.1_Missense_Mutation_p.E108K|INADL_ENST00000543708.1_Missense_Mutation_p.E219K	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1435					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						CCCTGGACAGGAAATGATTAT	0.468																																					p.E1435K		Atlas-SNP	.											.	INADL	179	.	0			c.G4303A						.						92.0	89.0	90.0					1																	62550246		2203	4300	6503	SO:0001583	missense	10207	exon33			GGACAGGAAATGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.4303G>A	chr1.hg19:g.62550246G>A	ENSP00000360200:p.Glu1435Lys	131.0	0.0		150.0	10.0	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	hg19	CCDS617.2	.	.	.	.	.	.	.	.	.	.	G	28.4	4.915842	0.92178	.	.	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000543708;ENST00000545929	T;T;T;T	0.24350	2.27;2.14;1.86;2.27	5.02	5.02	0.67125	PDZ/DHR/GLGF (1);	0.000000	0.64402	D	0.000003	T	0.57519	0.2059	M	0.85777	2.775	0.58432	D	0.999999	D;P;D;D;P;D	0.89917	1.0;0.87;0.997;1.0;0.574;1.0	D;D;D;D;P;D	0.91635	0.997;0.951;0.995;0.999;0.861;0.977	T	0.63594	-0.6602	10	0.56958	D	0.05	.	18.6965	0.91603	0.0:0.0:1.0:0.0	.	108;219;894;1435;1435;1435	F5GY89;B4DE90;Q8NI35-5;F8W8T2;Q8NI35;Q8NI35-4	.;.;.;.;INADL_HUMAN;.	K	1435;1435;1435;1435;219;108	ENSP00000360200:E1435K;ENSP00000326199:E1435K;ENSP00000445790:E219K;ENSP00000440094:E108K	ENSP00000326199:E1435K	E	+	1	0	INADL	62322834	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.067000	0.89488	2.477000	0.83638	0.655000	0.94253	GAA	.	.		0.468	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
CSDE1	7812	hgsc.bcm.edu	37	1	115267860	115267860	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:115267860C>T	ENST00000358528.4	-	15	2161	c.1735G>A	c.(1735-1737)Gtg>Atg	p.V579M	Y_RNA_ENST00000365030.1_RNA|CSDE1_ENST00000369530.1_Missense_Mutation_p.V594M|CSDE1_ENST00000438362.2_Missense_Mutation_p.V625M|CSDE1_ENST00000530886.1_Missense_Mutation_p.V449M|CSDE1_ENST00000339438.6_Missense_Mutation_p.V548M|CSDE1_ENST00000261443.5_Missense_Mutation_p.V548M|CSDE1_ENST00000534699.1_Missense_Mutation_p.V579M	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	579	CSD 7.				male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTTTGTTCACTTTTTCTGCA	0.438																																					p.V625M		Atlas-SNP	.											.	CSDE1	145	.	0			c.G1873A						.						260.0	220.0	233.0					1																	115267860		2203	4300	6503	SO:0001583	missense	7812	exon16			TGTTCACTTTTTC		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.1735G>A	chr1.hg19:g.115267860C>T	ENSP00000351329:p.Val579Met	118.0	0.0		128.0	35.0	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.989671	0.93106	.	.	ENSG00000009307	ENST00000339438;ENST00000438362;ENST00000358528;ENST00000261443;ENST00000530886;ENST00000369530;ENST00000534699	.	.	.	6.16	6.16	0.99307	Cold shock protein (1);Nucleic acid-binding, OB-fold-like (1);Cold-shock protein, DNA-binding (1);Nucleic acid-binding, OB-fold (1);	0.000000	0.85682	D	0.000000	D	0.89508	0.6735	H	0.96175	3.78	0.80722	D	1	D;D;B	0.76494	0.999;0.999;0.226	D;D;B	0.85130	0.983;0.997;0.244	D	0.91254	0.5031	9	0.87932	D	0	-4.3418	20.8598	0.99761	0.0:1.0:0.0:0.0	.	594;579;625	E9PGZ0;O75534;G5E9Q2	.;CSDE1_HUMAN;.	M	548;625;579;548;449;594;579	.	ENSP00000261443:V548M	V	-	1	0	CSDE1	115069383	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.107000	0.77047	2.937000	0.99478	0.650000	0.86243	GTG	.	.		0.438	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
RPTN	126638	hgsc.bcm.edu	37	1	152128252	152128252	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:152128252C>A	ENST00000316073.3	-	3	1387	c.1323G>T	c.(1321-1323)caG>caT	p.Q441H		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	441	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GTCTGTCTGGCTGACCATAGT	0.542																																					p.Q441H		Atlas-SNP	.											.	RPTN	123	.	0			c.G1323T						.						794.0	699.0	728.0					1																	152128252		1568	3582	5150	SO:0001583	missense	126638	exon3			GTCTGGCTGACCA	AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1323G>T	chr1.hg19:g.152128252C>A	ENSP00000317895:p.Gln441His	108.0	0.0		199.0	44.0	NM_001122965	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	hg19	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	14.26	2.482137	0.44147	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.15256	2.44	5.32	2.42	0.29668	.	.	.	.	.	T	0.09949	0.0244	M	0.89478	3.035	0.09310	N	0.999999	B	0.17852	0.024	B	0.18263	0.021	T	0.29274	-1.0017	9	0.33940	T	0.23	-5.7869	6.3659	0.21455	0.148:0.691:0.0:0.161	.	441	Q6XPR3	RPTN_HUMAN	H	441;96	ENSP00000317895:Q441H	ENSP00000317895:Q441H	Q	-	3	2	RPTN	150394876	0.001000	0.12720	0.021000	0.16686	0.001000	0.01503	-0.349000	0.07731	0.242000	0.21303	-0.302000	0.09304	CAG	.	.		0.542	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1	XM_371312	
HMCN1	83872	hgsc.bcm.edu	37	1	186113435	186113435	+	Silent	SNP	A	A	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:186113435A>C	ENST00000271588.4	+	90	14284	c.14055A>C	c.(14053-14055)gcA>gcC	p.A4685A	HMCN1_ENST00000367492.2_Silent_p.A4685A	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4685	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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						GTGATGGAGCAGAAACACAGA	0.403																																					p.A4685A		Atlas-SNP	.											.	HMCN1	797	.	0			c.A14055C						.						142.0	144.0	143.0					1																	186113435		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon90			TGGAGCAGAAACA	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.14055A>C	chr1.hg19:g.186113435A>C		123.0	0.0		165.0	9.0	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.		0.403	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
NLRP3	114548	hgsc.bcm.edu	37	1	247587388	247587388	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:247587388C>A	ENST00000336119.3	+	3	1389	c.643C>A	c.(643-645)Cat>Aat	p.H215N	NLRP3_ENST00000391827.2_Missense_Mutation_p.H215N|NLRP3_ENST00000391828.3_Missense_Mutation_p.H215N|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000348069.2_Missense_Mutation_p.H215N|NLRP3_ENST00000366497.2_Missense_Mutation_p.H215N|NLRP3_ENST00000366496.2_Missense_Mutation_p.H215N	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	215					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)			CGATGATGAGCATTCTGAGCC	0.582																																					p.H215N		Atlas-SNP	.											.	NLRP3	286	.	0			c.C643A						.						88.0	79.0	82.0					1																	247587388		2203	4300	6503	SO:0001583	missense	114548	exon3			GATGAGCATTCTG	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.643C>A	chr1.hg19:g.247587388C>A	ENSP00000337383:p.His215Asn	172.0	0.0		223.0	37.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	C	0.749	-0.773546	0.02951	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.79845	-1.31;-1.31;-1.31;-1.31;-1.31;-1.31	4.27	-3.14	0.05250	.	1.401910	0.04258	N	0.339853	T	0.70325	0.3211	L	0.55481	1.735	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.001;0.0;0.005;0.001;0.002	T	0.43212	-0.9405	10	0.27785	T	0.31	.	0.3018	0.00274	0.3576:0.2142:0.1332:0.295	.	215;215;215;215;215	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	N	215	ENSP00000375704:H215N;ENSP00000355453:H215N;ENSP00000337383:H215N;ENSP00000294752:H215N;ENSP00000355452:H215N;ENSP00000375703:H215N	ENSP00000337383:H215N	H	+	1	0	NLRP3	245654011	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.534000	0.06150	-0.618000	0.05656	-0.895000	0.02911	CAT	.	.		0.582	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
TPO	7173	hgsc.bcm.edu	37	2	1499810	1499810	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:1499810C>A	ENST00000345913.4	+	12	2147	c.2056C>A	c.(2056-2058)Ctg>Atg	p.L686M	TPO_ENST00000346956.3_Missense_Mutation_p.L686M|TPO_ENST00000382198.1_Missense_Mutation_p.L513M|TPO_ENST00000329066.4_Missense_Mutation_p.L686M|TPO_ENST00000337415.3_Missense_Mutation_p.L686M|TPO_ENST00000349624.3_Missense_Mutation_p.L513M|TPO_ENST00000382201.3_Missense_Mutation_p.L629M|TPO_ENST00000497517.2_Intron	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	686					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)	GAGGCGTGAGCTGGAGAAGCA	0.562																																					p.L686M		Atlas-SNP	.											.	TPO	224	.	0			c.C2056A						.						80.0	65.0	70.0					2																	1499810		2203	4300	6503	SO:0001583	missense	7173	exon12			CGTGAGCTGGAGA		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.2056C>A	chr2.hg19:g.1499810C>A	ENSP00000318820:p.Leu686Met	61.0	0.0		67.0	22.0	NM_001206744	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	hg19	CCDS1643.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.05|15.05	2.717134|2.717134	0.48622|0.48622	.|.	.|.	ENSG00000115705|ENSG00000115705	ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000329066;ENST00000382201;ENST00000382198;ENST00000422464;ENST00000469607|ENST00000446278	T;T;T;T;T;T;T;T;T|.	0.71579|.	-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58;-0.58|.	4.52|4.52	3.64|3.64	0.41730|0.41730	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79335|0.79335	0.4428|0.4428	M|M	0.90759|0.90759	3.145|3.145	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	1.0;1.0;1.0;1.0|.	D;D;D;D|.	0.97110|.	1.0;0.999;1.0;1.0|.	T|T	0.82604|0.82604	-0.0375|-0.0375	10|5	0.72032|.	D|.	0.01|.	-23.3431|-23.3431	12.5955|12.5955	0.56468|0.56468	0.0:0.9181:0.0:0.0819|0.0:0.9181:0.0:0.0819	.|.	686;513;629;686|.	P07202-4;P07202-5;P07202-2;P07202|.	.;.;.;PERT_HUMAN|.	M|R	686;686;686;513;686;629;513;615;160|160	ENSP00000337263:L686M;ENSP00000318820:L686M;ENSP00000263886:L686M;ENSP00000332044:L513M;ENSP00000329869:L686M;ENSP00000371636:L629M;ENSP00000371633:L513M;ENSP00000405788:L615M;ENSP00000419461:L160M|.	ENSP00000329869:L686M|.	L|S	+|+	1|3	2|2	TPO|TPO	1478817|1478817	1.000000|1.000000	0.71417|0.71417	0.226000|0.226000	0.23910|0.23910	0.339000|0.339000	0.28857|0.28857	4.317000|4.317000	0.59184|0.59184	1.032000|1.032000	0.39892|0.39892	0.561000|0.561000	0.74099|0.74099	CTG|AGC	.	.		0.562	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
APOB	338	hgsc.bcm.edu	37	2	21228569	21228569	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:21228569T>C	ENST00000233242.1	-	26	11298	c.11171A>G	c.(11170-11172)aAa>aGa	p.K3724R		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	3724					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCCAAAACTTTTACAGGGAT	0.408																																					p.K3724R		Atlas-SNP	.											.	APOB	761	.	0			c.A11171G						.						97.0	101.0	100.0					2																	21228569		2203	4300	6503	SO:0001583	missense	338	exon26			AAAACTTTTACAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.11171A>G	chr2.hg19:g.21228569T>C	ENSP00000233242:p.Lys3724Arg	90.0	0.0		83.0	31.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	T	12.90	2.077494	0.36662	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.69175	-0.38	5.53	5.53	0.82687	.	0.582952	0.15920	N	0.238180	T	0.53367	0.1792	L	0.29908	0.895	0.80722	D	1	B	0.14805	0.011	B	0.17098	0.017	T	0.46569	-0.9182	10	0.16896	T	0.51	.	11.9727	0.53071	0.1296:0.0:0.0:0.8704	.	3724	P04114	APOB_HUMAN	R	3724	ENSP00000233242:K3724R	ENSP00000233242:K3724R	K	-	2	0	APOB	21082074	0.996000	0.38824	0.991000	0.47740	0.078000	0.17371	1.812000	0.38952	2.103000	0.63969	0.533000	0.62120	AAA	.	.		0.408	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
HEATR5B	54497	hgsc.bcm.edu	37	2	37297440	37297440	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:37297440T>C	ENST00000233099.5	-	7	955	c.860A>G	c.(859-861)aAg>aGg	p.K287R	HEATR5B_ENST00000354531.2_Missense_Mutation_p.K287R	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	287						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				TCCACCGCTCTTTAAGAAACC	0.433																																					p.K287R		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A860G						.						153.0	145.0	148.0					2																	37297440		2203	4300	6503	SO:0001583	missense	54497	exon7			CCGCTCTTTAAGA	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.860A>G	chr2.hg19:g.37297440T>C	ENSP00000233099:p.Lys287Arg	135.0	0.0		136.0	9.0	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	hg19	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	T	12.99	2.102515	0.37145	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08458	3.09;3.09	4.95	4.95	0.65309	Armadillo-like helical (1);Armadillo-type fold (1);	0.147769	0.56097	D	0.000031	T	0.04815	0.0130	N	0.04320	-0.23	0.58432	D	0.999997	B	0.22414	0.069	B	0.29942	0.109	T	0.42361	-0.9456	10	0.10377	T	0.69	-10.7144	14.9046	0.70709	0.0:0.0:0.0:1.0	.	287	Q9P2D3	HTR5B_HUMAN	R	287	ENSP00000233099:K287R;ENSP00000346531:K287R	ENSP00000233099:K287R	K	-	2	0	HEATR5B	37150944	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.747000	0.47475	1.969000	0.57287	0.460000	0.39030	AAG	.	.		0.433	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
ZFP36L2	678	hgsc.bcm.edu	37	2	43452453	43452453	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:43452453C>A	ENST00000282388.3	-	2	783	c.490G>T	c.(490-492)Gag>Tag	p.E164*	THADA_ENST00000330266.7_Intron	NM_006887.4	NP_008818.3	P47974	TISD_HUMAN	ZFP36 ring finger protein-like 2	164					cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|hemopoiesis (GO:0030097)|mRNA catabolic process (GO:0006402)|negative regulation of stem cell differentiation (GO:2000737)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(82;0.00323)|all_hematologic(82;0.00824)				GTGCCGCTCTCCTCGAAGGGC	0.647																																					p.E164X		Atlas-SNP	.											.	ZFP36L2	56	.	0			c.G490T						.						42.0	40.0	41.0					2																	43452453		2203	4300	6503	SO:0001587	stop_gained	678	exon2			CGCTCTCCTCGAA	X78992	CCDS1811.1	2p22.3-p21	2012-11-27	2012-11-27	2001-11-23	ENSG00000152518	ENSG00000152518		"""RING-type (C3HC4) zinc fingers"""	1108	protein-coding gene	gene with protein product		612053	"""zinc finger protein 36, C3H type-like 1"", ""zinc finger protein 36, C3H type-like 2"""	BRF2		7835719, 8545129, 14981510, 17172869	Standard	NM_006887		Approved	ERF2, RNF162C, TIS11D	uc002rsv.4	P47974	OTTHUMG00000128642	ENST00000282388.3:c.490G>T	chr2.hg19:g.43452453C>A	ENSP00000282388:p.Glu164*	36.0	0.0		58.0	21.0	NM_006887	Q53TB4|Q9BSJ3	Nonsense_Mutation	SNP	ENST00000282388.3	hg19	CCDS1811.1	.	.	.	.	.	.	.	.	.	.	C	39	7.785279	0.98489	.	.	ENSG00000152518	ENST00000282388	.	.	.	4.65	4.65	0.58169	.	0.062027	0.64402	D	0.000006	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-24.0185	16.3858	0.83504	0.0:1.0:0.0:0.0	.	.	.	.	X	164	.	ENSP00000282388:E164X	E	-	1	0	ZFP36L2	43305957	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	7.321000	0.79088	2.144000	0.66660	0.555000	0.69702	GAG	.	.		0.647	ZFP36L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250513.2	NM_006887	
USP34	9736	hgsc.bcm.edu	37	2	61542016	61542016	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:61542016T>C	ENST00000398571.2	-	24	3452	c.3376A>G	c.(3376-3378)Att>Gtt	p.I1126V		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	1126					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TTACCATTAATATAATAGGAG	0.338																																					p.I1126V		Atlas-SNP	.											.	USP34	334	.	0			c.A3376G						.						86.0	81.0	82.0					2																	61542016		1830	4076	5906	SO:0001583	missense	9736	exon24			CATTAATATAATA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.3376A>G	chr2.hg19:g.61542016T>C	ENSP00000381577:p.Ile1126Val	298.0	0.0		287.0	12.0	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	hg19	CCDS42686.1	.	.	.	.	.	.	.	.	.	.	T	19.43	3.826192	0.71143	.	.	ENSG00000115464	ENST00000263989;ENST00000398569;ENST00000398571	T	0.03524	3.9	5.41	5.41	0.78517	.	0.048630	0.85682	D	0.000000	T	0.06188	0.0160	L	0.50333	1.59	0.58432	D	0.999995	B	0.18461	0.028	B	0.19391	0.025	T	0.22661	-1.0210	10	0.46703	T	0.11	.	15.7339	0.77827	0.0:0.0:0.0:1.0	.	1126	Q70CQ2	UBP34_HUMAN	V	974;974;1126	ENSP00000381577:I1126V	ENSP00000263989:I974V	I	-	1	0	USP34	61395520	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.803000	0.85983	2.169000	0.68431	0.477000	0.44152	ATT	.	.		0.338	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
TEKT4	150483	hgsc.bcm.edu	37	2	95542383	95542383	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:95542383C>A	ENST00000295201.4	+	6	1314	c.1177C>A	c.(1177-1179)Ctc>Atc	p.L393I	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	393					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						CCTGCGCAACCTCGAGGACAT	0.587																																					p.L393I		Atlas-SNP	.											.	TEKT4	72	.	0			c.C1177A						.						74.0	57.0	63.0					2																	95542383		2203	4300	6503	SO:0001583	missense	150483	exon6			CGCAACCTCGAGG	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.1177C>A	chr2.hg19:g.95542383C>A	ENSP00000295201:p.Leu393Ile	19.0	0.0		23.0	8.0	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	hg19	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	17.48	3.399242	0.62177	.	.	ENSG00000163060	ENST00000295201	T	0.10288	2.89	2.43	2.43	0.29744	.	0.000000	0.64402	D	0.000003	T	0.40398	0.1115	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.51624	-0.8682	10	0.66056	D	0.02	-14.2001	10.5484	0.45072	0.0:1.0:0.0:0.0	.	393	Q8WW24	TEKT4_HUMAN	I	393	ENSP00000295201:L393I	ENSP00000295201:L393I	L	+	1	0	TEKT4	94906110	0.688000	0.27680	0.998000	0.56505	0.509000	0.34042	0.438000	0.21559	1.049000	0.40321	0.281000	0.19383	CTC	.	.		0.587	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
CNGA3	1261	hgsc.bcm.edu	37	2	99012463	99012463	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:99012463G>T	ENST00000272602.2	+	7	869	c.830G>T	c.(829-831)cGc>cTc	p.R277L	CNGA3_ENST00000393504.1_Missense_Mutation_p.R277L|CNGA3_ENST00000409937.1_Missense_Mutation_p.R281L|CNGA3_ENST00000436404.2_Missense_Mutation_p.R259L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	277			R -> C (in ACHM2; also found in patients with cone-rod dystrophy). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:15712225, ECO:0000269|PubMed:18521937, ECO:0000269|PubMed:24903488}.|R -> H (in ACHM2; also found in patients with cone-rod dystrophy; does not form functional homomeric or heteromeric channels). {ECO:0000269|PubMed:11536077, ECO:0000269|PubMed:24903488}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGGTTCAACCGCCTACTGAAG	0.498																																					p.R277L		Atlas-SNP	.											.	CNGA3	118	.	0			c.G830T	GRCh37	CM014539	CNGA3	M		.						89.0	81.0	84.0					2																	99012463		2203	4300	6503	SO:0001583	missense	1261	exon8			TCAACCGCCTACT	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.830G>T	chr2.hg19:g.99012463G>T	ENSP00000272602:p.Arg277Leu	192.0	0.0		200.0	48.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.538890	0.85917	.	.	ENSG00000144191	ENST00000393504;ENST00000436404;ENST00000272602;ENST00000409937	D;D;D;D	0.99338	-5.76;-5.76;-5.76;-5.76	5.15	5.15	0.70609	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.99645	0.9869	H	0.96777	3.88	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.998;0.997;1.0	D	0.97631	1.0142	10	0.87932	D	0	.	17.5731	0.87940	0.0:0.0:1.0:0.0	.	281;259;277	E9PF93;Q4VAP7;Q16281	.;.;CNGA3_HUMAN	L	277;259;277;281	ENSP00000377140:R277L;ENSP00000410070:R259L;ENSP00000272602:R277L;ENSP00000386761:R281L	ENSP00000272602:R277L	R	+	2	0	CNGA3	98378895	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.487000	0.81328	2.677000	0.91161	0.563000	0.77884	CGC	.	.		0.498	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131801059	131801059	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:131801059T>A	ENST00000326016.5	+	11	2021	c.1502T>A	c.(1501-1503)aTc>aAc	p.I501N	ARHGEF4_ENST00000409303.1_Missense_Mutation_p.I441N|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.I501N|ARHGEF4_ENST00000428230.2_Intron|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.I430N|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.I501N	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	501	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		TCAGAACTCATCTACTCGGGG	0.537																																					p.I501N		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.T1502A						.						99.0	91.0	94.0					2																	131801059		2203	4300	6503	SO:0001583	missense	50649	exon11			AACTCATCTACTC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1502T>A	chr2.hg19:g.131801059T>A	ENSP00000316845:p.Ile501Asn	82.0	0.0		93.0	30.0	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	24.2|24.2	4.506640|4.506640	0.85282|0.85282	.|.	.|.	ENSG00000136002|ENSG00000136002	ENST00000532720|ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	.|D;D;D;D;D	.|0.90261	.|-2.64;-2.64;-2.64;-2.64;-2.64	5.02|5.02	5.02|5.02	0.67125|0.67125	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.95121|0.95121	0.8419|0.8419	M|M	0.84326|0.84326	2.69|2.69	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.87578	.|0.998;0.997;0.998	D|D	0.95598|0.95598	0.8660|0.8660	5|10	.|0.87932	.|D	.|0	.|.	12.6975|12.6975	0.57012|0.57012	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|441;501;501	.|E9PEM0;Q9NR80-4;Q9NR80	.|.;.;ARHG4_HUMAN	Q|N	117|501;501;501;441;430	.|ENSP00000316845:I501N;ENSP00000376680:I501N;ENSP00000432267:I501N;ENSP00000387285:I441N;ENSP00000348017:I430N	.|ENSP00000316845:I501N	H|I	+|+	3|2	2|0	ARHGEF4|ARHGEF4	131517529|131517529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	5.768000|5.768000	0.68858|0.68858	1.891000|1.891000	0.54761|0.54761	0.459000|0.459000	0.35465|0.35465	CAT|ATC	.	.		0.537	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
HOXD4	3233	hgsc.bcm.edu	37	2	177016412	177016412	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:177016412C>G	ENST00000306324.3	+	1	463	c.51C>G	c.(49-51)ttC>ttG	p.F17L	MIR10B_ENST00000385011.1_RNA|HOXD3_ENST00000468418.3_5'UTR	NM_014621.2	NP_055436.2	P09016	HXD4_HUMAN	homeobox D4	17					multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.F17L(1)		kidney(1)|large_intestine(1)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.00765)|Epithelial(96;0.105)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ACCCCAAGTTCCCTCCGTGCG	0.542																																					p.F17L		Atlas-SNP	.											HOXD4,NS,carcinoma,0,1	HOXD4	32	.	1	Substitution - Missense(1)	kidney(1)	c.C51G						.						48.0	52.0	50.0					2																	177016412		2187	4235	6422	SO:0001583	missense	3233	exon1			CAAGTTCCCTCCG		CCDS2269.1	2q31.1	2011-06-20	2005-12-22		ENSG00000170166	ENSG00000170166		"""Homeoboxes / ANTP class : HOXL subclass"""	5138	protein-coding gene	gene with protein product		142981	"""homeo box D4"""	HOX4B, HOX4		1973146, 1358459	Standard	NM_014621		Approved		uc002uks.3	P09016	OTTHUMG00000132515	ENST00000306324.3:c.51C>G	chr2.hg19:g.177016412C>G	ENSP00000302548:p.Phe17Leu	177.0	0.0		178.0	72.0	NM_014621	B2R9R3|Q96AU0	Missense_Mutation	SNP	ENST00000306324.3	hg19	CCDS2269.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447955	0.63178	.	.	ENSG00000170166	ENST00000306324	T	0.59772	0.24	5.12	-1.86	0.07760	.	0.249724	0.40728	N	0.001026	T	0.76364	0.3977	M	0.91717	3.235	0.53005	D	0.999968	D	0.89917	1.0	D	0.83275	0.996	T	0.78540	-0.2165	10	0.87932	D	0	.	11.2747	0.49159	0.0:0.3812:0.0:0.6188	.	17	P09016	HXD4_HUMAN	L	17	ENSP00000302548:F17L	ENSP00000302548:F17L	F	+	3	2	HOXD4	176724658	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	2.070000	0.41491	-0.223000	0.09943	0.655000	0.94253	TTC	.	.		0.542	HOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255697.2		
DNAH7	56171	hgsc.bcm.edu	37	2	196765131	196765131	+	Silent	SNP	G	G	T	rs376085913		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:196765131G>T	ENST00000312428.6	-	28	4523	c.4423C>A	c.(4423-4425)Cga>Aga	p.R1475R		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1475	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GACAGTGGTCGAGCAGTGACA	0.463																																					p.R1475R		Atlas-SNP	.											.	DNAH7	512	.	0			c.C4423A						.						177.0	176.0	176.0					2																	196765131		1982	4180	6162	SO:0001819	synonymous_variant	56171	exon28			GTGGTCGAGCAGT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4423C>A	chr2.hg19:g.196765131G>T		183.0	0.0		188.0	71.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.463	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
KCTD18	130535	hgsc.bcm.edu	37	2	201357908	201357908	+	Missense_Mutation	SNP	G	G	T	rs146790839		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:201357908G>T	ENST00000359878.3	-	6	1261	c.751C>A	c.(751-753)Cca>Aca	p.P251T	KCTD18_ENST00000468413.1_5'Flank|KCTD18_ENST00000409157.1_Missense_Mutation_p.P251T	NM_152387.2	NP_689600.2	Q6PI47	KCD18_HUMAN	potassium channel tetramerization domain containing 18	251					protein homooligomerization (GO:0051260)					endometrium(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15						TTTCGAATTGGAGCCATGTGA	0.408																																					p.P251T		Atlas-SNP	.											.	KCTD18	44	.	0			c.C751A						.						76.0	70.0	72.0					2																	201357908		2203	4300	6503	SO:0001583	missense	130535	exon6			GAATTGGAGCCAT	AK055884	CCDS2330.1	2q33.1	2013-06-20	2013-06-20		ENSG00000155729	ENSG00000155729			26446	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 18"""				Standard	NM_152387		Approved	FLJ31322, 6530404F10Rik, FLJ37818	uc002uvs.3	Q6PI47	OTTHUMG00000132781	ENST00000359878.3:c.751C>A	chr2.hg19:g.201357908G>T	ENSP00000352941:p.Pro251Thr	80.0	0.0		78.0	28.0	NM_152387	Q53T21|Q6NW26|Q6PCD8|Q8N9B7|Q96N73	Missense_Mutation	SNP	ENST00000359878.3	hg19	CCDS2330.1	.	.	.	.	.	.	.	.	.	.	G	15.69	2.907482	0.52333	.	.	ENSG00000155729	ENST00000359878;ENST00000409157	T;T	0.43294	0.95;0.95	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000017	T	0.54303	0.1850	L	0.32530	0.975	0.43351	D	0.995412	D	0.76494	0.999	D	0.68353	0.957	T	0.52064	-0.8625	10	0.48119	T	0.1	-18.7757	18.7156	0.91673	0.0:0.0:1.0:0.0	.	251	Q6PI47	KCD18_HUMAN	T	251	ENSP00000352941:P251T;ENSP00000386751:P251T	ENSP00000352941:P251T	P	-	1	0	KCTD18	201066153	1.000000	0.71417	0.728000	0.30774	0.004000	0.04260	5.299000	0.65716	2.810000	0.96702	0.650000	0.86243	CCA	.	G|1.000;A|0.000		0.408	KCTD18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256188.1	NM_152387	
BMPR2	659	hgsc.bcm.edu	37	2	203383670	203383670	+	Silent	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:203383670G>A	ENST00000374580.4	+	6	1286	c.747G>A	c.(745-747)gtG>gtA	p.V249V	BMPR2_ENST00000374574.2_Silent_p.V249V	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						TTTACAGAGTGCCTTTGATGG	0.413																																					p.V249V		Atlas-SNP	.											.	BMPR2	142	.	0			c.G747A						.						169.0	155.0	160.0					2																	203383670		2203	4300	6503	SO:0001819	synonymous_variant	659	exon6			CAGAGTGCCTTTG	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.747G>A	chr2.hg19:g.203383670G>A		132.0	0.0		137.0	9.0	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Silent	SNP	ENST00000374580.4	hg19	CCDS33361.1																																																																																			.	.		0.413	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
MDH1B	130752	hgsc.bcm.edu	37	2	207622077	207622077	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:207622077A>T	ENST00000374412.3	-	3	429	c.154T>A	c.(154-156)Tgt>Agt	p.C52S	MDH1B_ENST00000454776.2_Missense_Mutation_p.C52S|MDH1B_ENST00000392214.2_Missense_Mutation_p.C52S|MDH1B_ENST00000449792.1_5'UTR	NM_001039845.1|NM_001282940.1	NP_001034934.1|NP_001269869.1	Q5I0G3	MDH1B_HUMAN	malate dehydrogenase 1B, NAD (soluble)	52					carbohydrate metabolic process (GO:0005975)|malate metabolic process (GO:0006108)|tricarboxylic acid cycle (GO:0006099)		malate dehydrogenase activity (GO:0016615)|oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor (GO:0016616)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(14)|ovary(4)|stomach(1)	34				LUSC - Lung squamous cell carcinoma(261;0.0763)|Epithelial(149;0.131)|Lung(261;0.145)		TTCTTTTCACACACATCTTTT	0.363																																					p.C52S	Pancreas(76;29 1355 28675 37177 51207)	Atlas-SNP	.											.	MDH1B	89	.	0			c.T154A						.						118.0	115.0	116.0					2																	207622077		2203	4300	6503	SO:0001583	missense	130752	exon3			TTTCACACACATC		CCDS33365.1, CCDS63102.1	2q33.3	2008-05-27			ENSG00000138400	ENSG00000138400			17836	protein-coding gene	gene with protein product							Standard	NM_001039845		Approved	FLJ25341, RP11-95H11	uc002vbs.3	Q5I0G3	OTTHUMG00000132918	ENST00000374412.3:c.154T>A	chr2.hg19:g.207622077A>T	ENSP00000363533:p.Cys52Ser	55.0	0.0		41.0	19.0	NM_001039845	A8K8M1|Q53TK9|Q8IV51	Missense_Mutation	SNP	ENST00000374412.3	hg19	CCDS33365.1	.	.	.	.	.	.	.	.	.	.	A	16.53	3.148788	0.57151	.	.	ENSG00000138400	ENST00000374412;ENST00000454776;ENST00000392214	T;T;T	0.57436	0.4;0.4;0.4	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.74397	0.3711	M	0.81497	2.545	0.53688	D	0.99997	D;D	0.89917	1.0;0.999	D;D	0.80764	0.994;0.987	T	0.78298	-0.2258	10	0.87932	D	0	-26.2499	16.2159	0.82217	1.0:0.0:0.0:0.0	.	52;52	Q5I0G3-2;Q5I0G3	.;MDH1B_HUMAN	S	52	ENSP00000363533:C52S;ENSP00000389916:C52S;ENSP00000376049:C52S	ENSP00000363533:C52S	C	-	1	0	MDH1B	207330322	1.000000	0.71417	0.847000	0.33407	0.018000	0.09664	8.383000	0.90157	2.243000	0.73865	0.533000	0.62120	TGT	.	.		0.363	MDH1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256429.2	NM_001039845	
PRKAG3	53632	hgsc.bcm.edu	37	2	219689003	219689003	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:219689003A>G	ENST00000529249.1	-	12	1610	c.1295T>C	c.(1294-1296)cTt>cCt	p.L432P	PRKAG3_ENST00000439262.2_Missense_Mutation_p.L407P|PRKAG3_ENST00000545803.1_Missense_Mutation_p.L248P			Q9UGI9	AAKG3_HUMAN	protein kinase, AMP-activated, gamma 3 non-catalytic subunit	432	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				cell cycle arrest (GO:0007050)|fatty acid biosynthetic process (GO:0006633)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|protein phosphorylation (GO:0006468)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)	AMP-activated protein kinase activity (GO:0004679)|ATP binding (GO:0005524)|protein kinase binding (GO:0019901)			large_intestine(7)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	20		Renal(207;0.0474)		Epithelial(149;4.35e-07)|all cancers(144;8.96e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	Acetylsalicylic acid(DB00945)	CTGGCAGGAAAGGACTCCCTC	0.597																																					p.L432P		Atlas-SNP	.											.	PRKAG3	47	.	0			c.T1295C						.						85.0	82.0	83.0					2																	219689003		2203	4300	6503	SO:0001583	missense	53632	exon12			CAGGAAAGGACTC	AF214519	CCDS2424.1	2q35	2012-09-20			ENSG00000115592	ENSG00000115592			9387	protein-coding gene	gene with protein product		604976				10818001	Standard	NM_017431		Approved		uc002vjb.1	Q9UGI9	OTTHUMG00000133078	ENST00000529249.1:c.1295T>C	chr2.hg19:g.219689003A>G	ENSP00000436068:p.Leu432Pro	137.0	0.0		133.0	7.0	NM_017431	Q4QQG8|Q4V779|Q9NRL1	Missense_Mutation	SNP	ENST00000529249.1	hg19	CCDS2424.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.185248	0.78677	.	.	ENSG00000115592	ENST00000439262;ENST00000545803;ENST00000529249	D;D;D	0.93426	-3.22;-3.22;-3.22	5.08	5.08	0.68730	Cystathionine beta-synthase, core (3);	0.063176	0.64402	D	0.000004	D	0.95230	0.8453	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.94725	0.7904	10	0.41790	T	0.15	-6.502	14.0592	0.64788	1.0:0.0:0.0:0.0	.	432	Q9UGI9	AAKG3_HUMAN	P	407;248;432	ENSP00000397133:L407P;ENSP00000444536:L248P;ENSP00000436068:L432P	ENSP00000233944:L432P	L	-	2	0	PRKAG3	219397247	1.000000	0.71417	0.990000	0.47175	0.989000	0.77384	9.084000	0.94076	1.904000	0.55121	0.533000	0.62120	CTT	.	.		0.597	PRKAG3-006	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385992.1		
KCNJ13	3769	hgsc.bcm.edu	37	2	233633278	233633278	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:233633278A>T	ENST00000233826.3	-	3	845	c.706T>A	c.(706-708)Ttc>Atc	p.F236I	GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.F236I|AC064852.4_ENST00000427571.1_RNA	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	236					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		AAGATGAAGAATGGACATTCG	0.443																																					p.F236I		Atlas-SNP	.											.	KCNJ13	18	.	0			c.T706A						.						173.0	141.0	151.0					2																	233633278		2203	4300	6503	SO:0001583	missense	3769	exon3			TGAAGAATGGACA	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.706T>A	chr2.hg19:g.233633278A>T	ENSP00000233826:p.Phe236Ile	180.0	0.0		194.0	60.0	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Missense_Mutation	SNP	ENST00000233826.3	hg19	CCDS2498.1	.	.	.	.	.	.	.	.	.	.	A	14.65	2.600030	0.46318	.	.	ENSG00000115474	ENST00000233826;ENST00000410029;ENST00000438786	D;D;D	0.95238	-3.65;-3.65;-3.65	6.07	4.91	0.64330	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (2);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.088508	0.85682	D	0.000000	D	0.92835	0.7721	L	0.56199	1.76	0.44175	D	0.996982	P	0.38300	0.626	B	0.40782	0.34	D	0.93322	0.6693	10	0.87932	D	0	.	12.5221	0.56065	0.9341:0.0:0.0659:0.0	.	236	O60928	IRK13_HUMAN	I	236;236;156	ENSP00000233826:F236I;ENSP00000386251:F236I;ENSP00000407284:F156I	ENSP00000233826:F236I	F	-	1	0	KCNJ13	233341522	1.000000	0.71417	0.985000	0.45067	0.958000	0.62258	4.987000	0.63857	2.326000	0.78906	0.533000	0.62120	TTC	.	.		0.443	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242	
GIGYF2	26058	hgsc.bcm.edu	37	2	233674449	233674449	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:233674449G>T	ENST00000409547.1	+	18	2137	c.1826G>T	c.(1825-1827)cGa>cTa	p.R609L	GIGYF2_ENST00000409196.3_Missense_Mutation_p.R603L|GIGYF2_ENST00000373563.4_Missense_Mutation_p.R609L|GIGYF2_ENST00000409451.3_Missense_Mutation_p.R630L|GIGYF2_ENST00000373566.3_Missense_Mutation_p.R631L|GIGYF2_ENST00000409480.1_Missense_Mutation_p.R631L|GIGYF2_ENST00000452341.2_Missense_Mutation_p.R440L	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	609	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		GACCAGGAACGACTGACCAGG	0.428																																					p.R630L		Atlas-SNP	.											.	GIGYF2	288	.	0			c.G1889T						.						115.0	106.0	109.0					2																	233674449		2203	4300	6503	SO:0001583	missense	26058	exon18			AGGAACGACTGAC	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.1826G>T	chr2.hg19:g.233674449G>T	ENSP00000386537:p.Arg609Leu	257.0	0.0		297.0	127.0	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	hg19	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	G	29.1	4.977409	0.92982	.	.	ENSG00000204120	ENST00000373566;ENST00000414511;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000535418;ENST00000423659;ENST00000409196;ENST00000409451;ENST00000440945;ENST00000452341	T;T;T;T;T;T;T;T;T	0.75704	-0.8;-0.81;-0.8;-0.81;-0.94;-0.81;-0.8;-0.96;-0.68	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.85974	0.5822	M	0.66939	2.045	0.58432	D	0.999999	D;D;D;D	0.89917	0.999;1.0;0.967;0.995	D;D;B;D	0.87578	0.996;0.998;0.386;0.968	D	0.83454	0.0050	10	0.41790	T	0.15	-11.169	20.6208	0.99490	0.0:0.0:1.0:0.0	.	440;630;609;603	E9PC50;A6H8W4;Q6Y7W6;E9PBB0	.;.;PERQ2_HUMAN;.	L	631;552;609;631;609;609;552;603;630;603;440	ENSP00000362667:R631L;ENSP00000362664:R609L;ENSP00000386765:R631L;ENSP00000386537:R609L;ENSP00000404195:R552L;ENSP00000387070:R603L;ENSP00000387170:R630L;ENSP00000410297:R603L;ENSP00000411505:R440L	ENSP00000362664:R609L	R	+	2	0	GIGYF2	233382693	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.199000	0.95003	2.882000	0.98803	0.655000	0.94253	CGA	.	.		0.428	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
USP40	55230	hgsc.bcm.edu	37	2	234399852	234399852	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr2:234399852C>A	ENST00000427112.2	-	25	3005	c.2970G>T	c.(2968-2970)gaG>gaT	p.E990D	USP40_ENST00000251722.6_Missense_Mutation_p.E990D|USP40_ENST00000450966.1_Missense_Mutation_p.E1002D|USP40_ENST00000496298.1_5'Flank			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	990					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CTTCTGAGATCTCTATGTCTC	0.478																																					p.E1002D		Atlas-SNP	.											.	USP40	174	.	0			c.G3006T						.						46.0	46.0	46.0					2																	234399852		1905	4127	6032	SO:0001583	missense	55230	exon25			TGAGATCTCTATG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.2970G>T	chr2.hg19:g.234399852C>A	ENSP00000387898:p.Glu990Asp	379.0	1.0		400.0	158.0	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	hg19	CCDS46547.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	8.710|8.710	0.911866|0.911866	0.17907|0.17907	.|.	.|.	ENSG00000085982|ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112|ENST00000430158	T;T;T|.	0.08458|.	3.09;3.09;3.09|.	5.28|5.28	-10.6|-10.6	0.00265|0.00265	.|.	2.570310|.	0.01121|.	N|.	0.005789|.	T|T	0.27594|0.27594	0.0678|0.0678	L|L	0.41961|0.41961	1.31|1.31	0.29144|0.29144	N|N	0.878836|0.878836	B;B|.	0.31383|.	0.321;0.046|.	B;B|.	0.37239|.	0.244;0.027|.	T|T	0.09707|0.09707	-1.0662|-1.0662	10|5	0.59425|.	D|.	0.04|.	.|.	4.4271|4.4271	0.11509|0.11509	0.0739:0.3001:0.3266:0.2994|0.0739:0.3001:0.3266:0.2994	.|.	1002;650|.	Q9NVE5-3;B4DN96|.	.;.|.	D|I	1002;990;990|166	ENSP00000415434:E1002D;ENSP00000251722:E990D;ENSP00000387898:E990D|.	ENSP00000251722:E990D|.	E|R	-|-	3|2	2|0	USP40|USP40	234064591|234064591	0.031000|0.031000	0.19500|0.19500	0.007000|0.007000	0.13788|0.13788	0.011000|0.011000	0.07611|0.07611	-1.403000|-1.403000	0.02497|0.02497	-2.892000|-2.892000	0.00315|0.00315	0.655000|0.655000	0.94253|0.94253	GAG|AGA	.	.		0.478	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
ITPR1	3708	hgsc.bcm.edu	37	3	4853115	4853115	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:4853115A>G	ENST00000443694.2	+	53	7394	c.7394A>G	c.(7393-7395)gAt>gGt	p.D2465G	ITPR1_ENST00000354582.6_Missense_Mutation_p.D2465G|ITPR1_ENST00000302640.8_Missense_Mutation_p.D2465G|ITPR1_ENST00000456211.2_Missense_Mutation_p.D2417G|ITPR1_ENST00000463980.1_3'UTR|ITPR1_ENST00000544951.1_Missense_Mutation_p.D443G|ITPR1_ENST00000357086.4_Missense_Mutation_p.D2432G|ITPR1_ENST00000423119.2_Missense_Mutation_p.D2432G|AC018816.3_ENST00000489771.1_5'Flank			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	2480					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	TTGGAAGTAGATAGGCTGCCC	0.403																																					p.D2465G		Atlas-SNP	.											.	ITPR1	659	.	0			c.A7394G						.						129.0	127.0	128.0					3																	4853115		1903	4118	6021	SO:0001583	missense	3708	exon55			AAGTAGATAGGCT	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.7394A>G	chr3.hg19:g.4853115A>G	ENSP00000401671:p.Asp2465Gly	66.0	0.0		68.0	36.0	NM_001168272	E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	hg19	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	A	27.0	4.790428	0.90367	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000426160;ENST00000357086;ENST00000456211;ENST00000544951;ENST00000443694	D;D;D;D;D;D;D	0.98512	-4.97;-4.97;-4.97;-4.97;-4.97;-4.97;-4.97	5.62	5.62	0.85841	Ion transport (1);	0.141833	0.64402	D	0.000007	D	0.99089	0.9687	M	0.90369	3.11	0.80722	D	1	D;P;P	0.71674	0.998;0.555;0.586	D;B;P	0.77557	0.99;0.257;0.46	D	0.99552	1.0966	10	0.87932	D	0	.	15.8153	0.78595	1.0:0.0:0.0:0.0	.	443;2480;2432	B7ZMI3;Q14643;G5E9P1	.;ITPR1_HUMAN;.	G	2480;2465;2465;2432;926;2432;2417;443;2465	ENSP00000306253:D2465G;ENSP00000346595:D2465G;ENSP00000405934:D2432G;ENSP00000349597:D2432G;ENSP00000397885:D2417G;ENSP00000440564:D443G;ENSP00000401671:D2465G	ENSP00000306253:D2465G	D	+	2	0	ITPR1	4828115	1.000000	0.71417	0.644000	0.29465	0.888000	0.51559	9.224000	0.95209	2.143000	0.66587	0.460000	0.39030	GAT	.	.		0.403	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266113	41266113	+	Missense_Mutation	SNP	C	C	G	rs121913416|rs121913403		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:41266113C>G	ENST00000349496.5	+	3	390	c.110C>G	c.(109-111)tCt>tGt	p.S37C	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S30C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S37C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S37C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S37C	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.S37C	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.C110G						.						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>G	chr3.hg19:g.41266113C>G	ENSP00000344456:p.Ser37Cys	140.0	0.0		142.0	44.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.407996	0.83340	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51325	0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71;0.71	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	C	30;37;37;37;37;30;37;37;37	ENSP00000400508:S30C;ENSP00000385604:S37C;ENSP00000412219:S37C;ENSP00000379486:S37C;ENSP00000344456:S37C;ENSP00000411226:S30C;ENSP00000379488:S37C;ENSP00000409302:S37C;ENSP00000401599:S37C	ENSP00000344456:S37C	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	
CCR5	1234	hgsc.bcm.edu	37	3	46414720	46414720	+	Silent	SNP	T	T	C	rs558483026		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:46414720T>C	ENST00000292303.4	+	2	473	c.327T>C	c.(325-327)ttT>ttC	p.F109F	CCR5_ENST00000343801.4_Silent_p.F109F|RP11-24F11.2_ENST00000451485.1_RNA|CCR5_ENST00000445772.1_Silent_p.F109F	NM_001100168.1	NP_001093638.1	P51681	CCR5_HUMAN	chemokine (C-C motif) receptor 5 (gene/pseudogene)	109					calcium ion transport (GO:0006816)|calcium-mediated signaling (GO:0019722)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|entry into host cell (GO:0030260)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|MAPK cascade (GO:0000165)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to cholesterol (GO:0070723)|signaling (GO:0023052)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|C-C chemokine binding (GO:0019957)|C-C chemokine receptor activity (GO:0016493)|chemokine (C-C motif) ligand 5 binding (GO:0071791)|chemokine receptor activity (GO:0004950)|coreceptor activity (GO:0015026)|phosphatidylinositol phospholipase C activity (GO:0004435)			central_nervous_system(1)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(193;0.00112)|KIRC - Kidney renal clear cell carcinoma(197;0.017)|Kidney(197;0.02)	Maraviroc(DB04835)	GGCTCTATTTTATAGGCTTCT	0.473																																					p.F109F		Atlas-SNP	.											.	CCR5	128	.	0			c.T327C						.						146.0	159.0	155.0					3																	46414720		2203	4296	6499	SO:0001819	synonymous_variant	1234	exon3			CTATTTTATAGGC		CCDS2739.1	3p21	2012-08-08	2012-01-23		ENSG00000160791	ENSG00000160791		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1606	protein-coding gene	gene with protein product		601373	"""chemokine (C-C motif) receptor 5"""	CMKBR5		8639485	Standard	NM_001100168		Approved	CKR-5, CC-CKR-5, CKR5, CD195, IDDM22	uc003cpo.4	P51681	OTTHUMG00000133481	ENST00000292303.4:c.327T>C	chr3.hg19:g.46414720T>C		113.0	0.0		127.0	51.0	NM_000579	O14692|O14693|O14695|O14696|O14697|O14698|O14699|O14700|O14701|O14702|O14703|O14704|O14705|O14706|O14707|O14708|O15538|Q9UPA4	Silent	SNP	ENST00000292303.4	hg19	CCDS2739.1																																																																																			.	.		0.473	CCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257377.2	NM_000579	
CADPS	8618	hgsc.bcm.edu	37	3	62459851	62459851	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:62459851T>A	ENST00000383710.4	-	24	3823	c.3474A>T	c.(3472-3474)caA>caT	p.Q1158H	CADPS_ENST00000357948.3_Missense_Mutation_p.Q1079H|CADPS_ENST00000283269.9_Missense_Mutation_p.Q1119H	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1158					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TTTTTACCTCTTGGCCCATTT	0.353																																					p.Q1158H		Atlas-SNP	.											.	CADPS	387	.	0			c.A3474T						.						85.0	87.0	86.0					3																	62459851		2203	4300	6503	SO:0001583	missense	8618	exon24			TACCTCTTGGCCC	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3474A>T	chr3.hg19:g.62459851T>A	ENSP00000373215:p.Gln1158His	44.0	0.0		60.0	17.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Missense_Mutation	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	T|T|T	16.02|16.02|16.02	3.003747|3.003747|3.003747	0.54254|0.54254|0.54254	.|.|.	.|.|.	ENSG00000163618|ENSG00000163618|ENSG00000163618	ENST00000473635|ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269|ENST00000466621	.|T;T;T|.	.|0.32272|.	.|1.46;1.46;1.46|.	5.97|5.97|5.97	3.54|3.54|3.54	0.40534|0.40534|0.40534	.|.|.	.|0.000000|.	.|0.85682|.	.|D|.	.|0.000000|.	T|T|.	0.69860|0.69860|.	0.3158|0.3158|.	M|M|M	0.75447|0.75447|0.75447	2.3|2.3|2.3	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D;D|.	.|0.69078|.	.|0.997;0.995;0.996;0.997|.	.|D;D;D;D|.	.|0.77004|.	.|0.951;0.989;0.986;0.935|.	T|T|.	0.66846|0.66846|.	-0.5820|-0.5820|.	5|10|.	.|0.72032|.	.|D|.	.|0.01|.	.|.|.	10.0951|10.0951|10.0951	0.42471|0.42471|0.42471	0.0:0.1963:0.0:0.8037|0.0:0.1963:0.0:0.8037|0.0:0.1963:0.0:0.8037	.|.|.	.|1079;1119;1158;1158|.	.|Q9ULU8-2;Q9ULU8-3;Q9ULU8;Q9ULU8-4|.	.|.;.;CAPS1_HUMAN;.|.	M|H|X	145|1158;1158;1079;1119|70	.|ENSP00000373215:Q1158H;ENSP00000350632:Q1079H;ENSP00000283269:Q1119H|.	.|ENSP00000283269:Q1119H|.	K|Q|R	-|-|-	2|3|1	0|2|2	CADPS|CADPS|CADPS	62434891|62434891|62434891	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.999000|0.999000|0.999000	0.98932|0.98932|0.98932	1.421000|1.421000|1.421000	0.34815|0.34815|0.34815	0.485000|0.485000|0.485000	0.27652|0.27652|0.27652	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	AAG|CAA|AGA	.	.		0.353	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
CADPS	8618	hgsc.bcm.edu	37	3	62459893	62459893	+	Silent	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:62459893G>A	ENST00000383710.4	-	24	3781	c.3432C>T	c.(3430-3432)gcC>gcT	p.A1144A	CADPS_ENST00000357948.3_Silent_p.A1065A|CADPS_ENST00000283269.9_Silent_p.A1105A	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	1144					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		ATTGAGCTTTGGCATCAACCA	0.358																																					p.A1144A		Atlas-SNP	.											.	CADPS	387	.	0			c.C3432T						.						156.0	156.0	156.0					3																	62459893		2203	4300	6503	SO:0001819	synonymous_variant	8618	exon24			AGCTTTGGCATCA	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.3432C>T	chr3.hg19:g.62459893G>A		66.0	0.0		97.0	5.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.310|7.310	0.614793|0.614793	0.14129|0.14129	.|.	.|.	ENSG00000163618|ENSG00000163618	ENST00000473635|ENST00000466621	.|.	.|.	.|.	5.97|5.97	4.19|4.19	0.49359|0.49359	.|.	.|.	.|.	.|.	.|.	T|.	0.63522|.	0.2518|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.60505|.	-0.7250|.	4|.	.|.	.|.	.|.	.|.	12.4934|12.4934	0.55914|0.55914	0.1344:0.0:0.8656:0.0|0.1344:0.0:0.8656:0.0	.|.	.|.	.|.	.|.	L|X	131|56	.|.	.|.	P|Q	-|-	2|1	0|0	CADPS|CADPS	62434933|62434933	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	6.634000|6.634000	0.74290|0.74290	0.867000|0.867000	0.35654|0.35654	0.655000|0.655000	0.94253|0.94253	CCA|CAA	.	.		0.358	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
C3orf17	25871	hgsc.bcm.edu	37	3	112729968	112729968	+	Silent	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:112729968T>C	ENST00000314400.5	-	6	1028	c.837A>G	c.(835-837)aaA>aaG	p.K279K	C3orf17_ENST00000393857.2_Silent_p.K143K|C3orf17_ENST00000472762.1_5'UTR|C3orf17_ENST00000383675.2_Silent_p.K209K	NM_015412.3	NP_056227.2	Q6NW34	CC017_HUMAN	chromosome 3 open reading frame 17	279					negative regulation of neuron differentiation (GO:0045665)|positive regulation of Notch signaling pathway (GO:0045747)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(1)|kidney(2)|lung(6)|prostate(2)|skin(1)	13						TTTGTTTAGCTTTTTTTGAAA	0.328																																					p.K279K		Atlas-SNP	.											.	C3orf17	37	.	0			c.A837G						.						80.0	83.0	82.0					3																	112729968		2200	4296	6496	SO:0001819	synonymous_variant	25871	exon6			TTTAGCTTTTTTT	AL117573	CCDS33824.1	3q13.2	2009-11-06			ENSG00000163608	ENSG00000163608			24496	protein-coding gene	gene with protein product						12477932	Standard	NR_027794		Approved	DKFZP434F2021, NET17	uc003dzr.3	Q6NW34	OTTHUMG00000159286	ENST00000314400.5:c.837A>G	chr3.hg19:g.112729968T>C		108.0	0.0		139.0	39.0	NM_015412	D3DN69|Q68DM6|Q9H7U0|Q9UFM4	Silent	SNP	ENST00000314400.5	hg19	CCDS33824.1																																																																																			.	.		0.328	C3orf17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354405.3	NM_015412	
TRPC1	7220	hgsc.bcm.edu	37	3	142522995	142522995	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:142522995T>A	ENST00000476941.1	+	11	2420	c.1934T>A	c.(1933-1935)cTt>cAt	p.L645H	TRPC1_ENST00000273482.6_Missense_Mutation_p.L611H|RNU7-47P_ENST00000515978.1_RNA	NM_001251845.1	NP_001238774.1	P48995	TRPC1_HUMAN	transient receptor potential cation channel, subfamily C, member 1	645					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to calcium ion (GO:0051592)|saliva secretion (GO:0046541)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|sarcomere (GO:0030017)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|inositol 1,4,5 trisphosphate binding (GO:0070679)|ion channel binding (GO:0044325)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(2)|stomach(3)|urinary_tract(1)	37						GTGGCAATGCTTCATAAAAGC	0.383																																					p.L645H		Atlas-SNP	.											.	TRPC1	82	.	0			c.T1934A						.						160.0	138.0	146.0					3																	142522995		2203	4300	6503	SO:0001583	missense	7220	exon11			CAATGCTTCATAA	X89066	CCDS3126.1, CCDS58856.1	3q23	2011-12-14			ENSG00000144935	ENSG00000144935		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12333	protein-coding gene	gene with protein product		602343				7568191, 16382100	Standard	NM_001251845		Approved	HTRP-1	uc003evc.3	P48995	OTTHUMG00000159301	ENST00000476941.1:c.1934T>A	chr3.hg19:g.142522995T>A	ENSP00000419313:p.Leu645His	121.0	0.0		152.0	55.0	NM_001251845	Q14CE4	Missense_Mutation	SNP	ENST00000476941.1	hg19	CCDS58856.1	.	.	.	.	.	.	.	.	.	.	T	25.5	4.646844	0.87958	.	.	ENSG00000144935	ENST00000476941;ENST00000273482	T;T	0.81330	-1.16;-1.48	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.86585	0.5968	L	0.47716	1.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.91635	0.999;0.999;0.973	D	0.88011	0.2762	10	0.87932	D	0	-12.5585	15.6063	0.76676	0.0:0.0:0.0:1.0	.	611;645;611	A7VJS2;P48995;P48995-2	.;TRPC1_HUMAN;.	H	645;611	ENSP00000419313:L645H;ENSP00000273482:L611H	ENSP00000273482:L611H	L	+	2	0	TRPC1	144005685	1.000000	0.71417	0.996000	0.52242	0.996000	0.88848	7.710000	0.84655	2.144000	0.66660	0.528000	0.53228	CTT	.	.		0.383	TRPC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354520.1	NM_003304	
IL12A	3592	hgsc.bcm.edu	37	3	159713248	159713248	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:159713248T>A	ENST00000305579.2	+	7	971	c.664T>A	c.(664-666)Ttt>Att	p.F222I	IL12A-AS1_ENST00000462431.1_RNA|IL12A_ENST00000466512.1_Missense_Mutation_p.F208I|IL12A_ENST00000480787.1_Missense_Mutation_p.F184I|IL12A-AS1_ENST00000497452.1_RNA	NM_000882.3	NP_000873.2	P29459	IL12A_HUMAN	interleukin 12A	188					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|defense response to Gram-positive bacterium (GO:0050830)|defense response to protozoan (GO:0042832)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cell adhesion (GO:0045785)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of lymphocyte proliferation (GO:0050671)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|positive regulation of NK T cell activation (GO:0051135)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat4 protein (GO:0042520)|response to lipopolysaccharide (GO:0032496)|response to UV-B (GO:0010224)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|interleukin-12 complex (GO:0043514)	interleukin-12 beta subunit binding (GO:0042163)|interleukin-12 receptor binding (GO:0005143)|interleukin-27 binding (GO:0045513)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)	9			Lung(72;0.00334)|LUSC - Lung squamous cell carcinoma(72;0.00523)			AGAACCGGATTTTTATAAAAC	0.388																																					p.F222I		Atlas-SNP	.											.	IL12A	23	.	0			c.T664A						.						92.0	94.0	93.0					3																	159713248		2203	4300	6503	SO:0001583	missense	3592	exon7			CCGGATTTTTATA	M65271	CCDS3187.1	3q25.33	2014-04-04	2014-04-04		ENSG00000168811	ENSG00000168811		"""Interleukins and interleukin receptors"""	5969	protein-coding gene	gene with protein product	"""natural killer cell stimulatory factor 1, 35 kD subunit"", ""cytotoxic lymphocyte maturation factor 1, p35"", ""interleukin 12, p35"", ""IL-12, subunit p35"", ""NF cell stimulatory factor chain 1"", ""interleukin-12 alpha chain"", ""IL35 subunit"""	161560	"""interleukin 12A (natural killer cell stimulatory factor 1, cytotoxic lymphocyte maturation factor 1, p35)"""	NKSF1		1673147	Standard	NM_000882		Approved	CLMF, IL-12A, p35, NFSK	uc003fcx.3	P29459	OTTHUMG00000158942	ENST00000305579.2:c.664T>A	chr3.hg19:g.159713248T>A	ENSP00000303231:p.Phe222Ile	124.0	0.0		130.0	13.0	NM_000882	Q96QZ1	Missense_Mutation	SNP	ENST00000305579.2	hg19	CCDS3187.1	.	.	.	.	.	.	.	.	.	.	T	10.07	1.250340	0.22880	.	.	ENSG00000168811	ENST00000305579;ENST00000480787;ENST00000466512	.	.	.	5.48	-1.08	0.09936	.	0.608922	0.18471	N	0.140220	T	0.38719	0.1051	M	0.69823	2.125	0.21386	N	0.999708	P	0.41643	0.758	B	0.39971	0.315	T	0.30475	-0.9977	9	0.52906	T	0.07	-1.1898	8.9887	0.36010	0.0:0.4387:0.0:0.5613	.	222	O60595	.	I	222;184;208	.	ENSP00000303231:F222I	F	+	1	0	IL12A	161195942	0.947000	0.32204	0.021000	0.16686	0.641000	0.38312	0.860000	0.27871	-0.424000	0.07382	0.533000	0.62120	TTT	.	.		0.388	IL12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352602.2	NM_000882	
FGF12	2257	hgsc.bcm.edu	37	3	192078328	192078328	+	Splice_Site	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr3:192078328C>T	ENST00000454309.2	-	2	1025		c.e2-1		FGF12_ENST00000264730.3_Splice_Site|FGF12_ENST00000430714.1_Intron|FGF12_ENST00000445105.2_Splice_Site|FGF12_ENST00000450716.1_Splice_Site	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12						adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		AGCTGGGGTTCTGCAAAACAA	0.383																																					.		Atlas-SNP	.											.	FGF12	88	.	0			c.14-1G>A						.						89.0	87.0	88.0					3																	192078328		2203	4300	6503	SO:0001630	splice_region_variant	2257	exon4			GGGGTTCTGCAAA	U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"""fibroblast growth factor 12B"", ""fibroblast growth factor homologous factor 1"", ""myocyte-activating factor"", ""fibroblast growth factor FGF-12b"""	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.200-1G>A	chr3.hg19:g.192078328C>T		120.0	0.0		124.0	49.0	NM_004113	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Splice_Site	SNP	ENST00000454309.2	hg19	CCDS3301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.3|24.3	4.515649|4.515649	0.85389|0.85389	.|.	.|.	ENSG00000114279|ENSG00000114279	ENST00000264730;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000418610|ENST00000392454	.|.	.|.	.|.	5.53|5.53	5.53|5.53	0.82687|0.82687	.|.	.|.	.|.	.|.	.|.	.|T	.|0.74619	.|0.3740	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.72940	.|-0.4139	.|4	.|.	.|.	.|.	.|.	18.4573|18.4573	0.90725|0.90725	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	.|K	-1|5	.|.	.|.	.|E	-|-	.|1	.|0	FGF12|FGF12	193561022|193561022	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	7.398000|7.398000	0.79919|0.79919	2.613000|2.613000	0.88420|0.88420	0.591000|0.591000	0.81541|0.81541	.|GAA	.	.		0.383	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032	Intron
HTT	3064	hgsc.bcm.edu	37	4	3129224	3129224	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:3129224A>G	ENST00000355072.5	+	12	1781	c.1636A>G	c.(1636-1638)Atg>Gtg	p.M546V		NM_002111.6	NP_002102	P42858	HD_HUMAN	huntingtin	546					anterior/posterior pattern specification (GO:0009952)|axon cargo transport (GO:0008088)|cell aging (GO:0007569)|citrulline metabolic process (GO:0000052)|determination of adult lifespan (GO:0008340)|dopamine receptor signaling pathway (GO:0007212)|endoplasmic reticulum organization (GO:0007029)|endosomal transport (GO:0016197)|ER to Golgi vesicle-mediated transport (GO:0006888)|establishment of mitotic spindle orientation (GO:0000132)|Golgi organization (GO:0007030)|grooming behavior (GO:0007625)|hormone metabolic process (GO:0042445)|insulin secretion (GO:0030073)|iron ion homeostasis (GO:0055072)|L-glutamate import (GO:0051938)|lactate biosynthetic process from pyruvate (GO:0019244)|locomotory behavior (GO:0007626)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|neural plate formation (GO:0021990)|neuron apoptotic process (GO:0051402)|neuron development (GO:0048666)|olfactory lobe development (GO:0021988)|organ development (GO:0048513)|paraxial mesoderm formation (GO:0048341)|positive regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031587)|protein import into nucleus (GO:0006606)|quinolinate biosynthetic process (GO:0019805)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of protein phosphatase type 2A activity (GO:0034047)|regulation of synaptic plasticity (GO:0048167)|response to calcium ion (GO:0051592)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|social behavior (GO:0035176)|spermatogenesis (GO:0007283)|striatum development (GO:0021756)|urea cycle (GO:0000050)|vesicle transport along microtubule (GO:0047496)|visual learning (GO:0008542)	autophagic vacuole (GO:0005776)|axon (GO:0030424)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|inclusion body (GO:0016234)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|diazepam binding (GO:0050809)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|identical protein binding (GO:0042802)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|transcription factor binding (GO:0008134)			breast(1)|cervix(2)|endometrium(14)|kidney(5)|large_intestine(23)|lung(28)|ovary(4)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	87		all_epithelial(65;0.18)		UCEC - Uterine corpus endometrioid carcinoma (64;0.187)		TGACCCTGCCATGGACCTGAA	0.602																																					p.M546V		Atlas-SNP	.											.	HTT	221	.	0			c.A1636G						.						55.0	61.0	59.0					4																	3129224		2107	4217	6324	SO:0001583	missense	3064	exon12			CCTGCCATGGACC	L12392	CCDS43206.1	4p16.3	2014-09-17	2007-12-04	2007-12-04	ENSG00000197386	ENSG00000197386		"""Endogenous ligands"""	4851	protein-coding gene	gene with protein product		613004	"""huntingtin (Huntington disease)"""	HD		8458085	Standard	NM_002111		Approved	IT15	uc021xkv.1	P42858	OTTHUMG00000159916	ENST00000355072.5:c.1636A>G	chr4.hg19:g.3129224A>G	ENSP00000347184:p.Met546Val	221.0	1.0		174.0	80.0	NM_002111	Q9UQB7	Missense_Mutation	SNP	ENST00000355072.5	hg19	CCDS43206.1	.	.	.	.	.	.	.	.	.	.	A	8.567	0.879088	0.17395	.	.	ENSG00000197386	ENST00000355072	T	0.04706	3.57	4.71	0.76	0.18442	Armadillo-type fold (1);	0.456130	0.27349	N	0.019767	T	0.02970	0.0088	N	0.20986	0.625	0.19575	N	0.999963	B	0.02656	0.0	B	0.01281	0.0	T	0.42189	-0.9466	10	0.31617	T	0.26	.	5.5418	0.17041	0.6356:0.1378:0.2266:0.0	.	546	P42858	HD_HUMAN	V	546	ENSP00000347184:M546V	ENSP00000347184:M546V	M	+	1	0	HTT	3099022	0.983000	0.35010	0.991000	0.47740	0.983000	0.72400	1.554000	0.36266	0.306000	0.22856	0.460000	0.39030	ATG	.	.		0.602	HTT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358234.2	NM_002111	
PCDH7	5099	hgsc.bcm.edu	37	4	30921844	30921844	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:30921844T>A	ENST00000543491.1	+	2	3244	c.3244T>A	c.(3244-3246)Tgc>Agc	p.C1082S	PCDH7_ENST00000509925.1_3'UTR			O60245	PCDH7_HUMAN	protocadherin 7	0					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						ACTGCAGAGTTGCTATGACAG	0.502																																					p.C1082S		Atlas-SNP	.											.	PCDH7	215	.	0			c.T3244A						.						92.0	99.0	97.0					4																	30921844		2105	4240	6345	SO:0001583	missense	5099	exon2			CAGAGTTGCTATG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000543491.1:c.3244T>A	chr4.hg19:g.30921844T>A	ENSP00000441802:p.Cys1082Ser	141.0	0.0		123.0	49.0	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000543491.1	hg19	CCDS54753.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.56|14.56	2.571339|2.571339	0.45798|0.45798	.|.	.|.	ENSG00000169851|ENSG00000169851	ENST00000543491;ENST00000333135|ENST00000511884	T|.	0.52754|.	0.65|.	5.9|5.9	5.9|5.9	0.94986|0.94986	.|.	.|.	.|.	.|.	.|.	T|.	0.56615|.	0.1997|.	L|L	0.29908|0.29908	0.895|0.895	0.54753|0.54753	D|D	0.999989|0.999989	D;D|.	0.64830|.	0.99;0.994|.	P;P|.	0.59221|.	0.854;0.854|.	T|.	0.52756|.	-0.8533|.	9|.	0.12766|.	T|.	0.61|.	.|.	16.3322|16.3322	0.83039|0.83039	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1082;1035|.	F5GWJ1;O60245-3|.	.;.|.	S|X	1082;1035|771	ENSP00000441802:C1082S|.	ENSP00000330302:C1035S|.	C|L	+|+	1|2	0|0	PCDH7|PCDH7	30530942|30530942	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.698000|7.698000	0.84413|0.84413	2.251000|2.251000	0.74343|0.74343	0.528000|0.528000	0.53228|0.53228	TGC|TTG	.	.		0.502	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032457, NM_002589	
GABRB1	2560	hgsc.bcm.edu	37	4	47163447	47163447	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:47163447T>A	ENST00000295454.3	+	4	714	c.422T>A	c.(421-423)aTt>aAt	p.I141N	GABRB1_ENST00000538619.1_Missense_Mutation_p.I71N	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	141					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	AATCGAATGATTCGACTGCAT	0.388																																					p.I141N		Atlas-SNP	.											.	GABRB1	107	.	0			c.T422A						.						156.0	144.0	148.0					4																	47163447		2203	4300	6503	SO:0001583	missense	2560	exon4			GAATGATTCGACT		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.422T>A	chr4.hg19:g.47163447T>A	ENSP00000295454:p.Ile141Asn	72.0	0.0		72.0	5.0	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Missense_Mutation	SNP	ENST00000295454.3	hg19	CCDS3474.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.384909	0.82792	.	.	ENSG00000163288	ENST00000513567;ENST00000295454;ENST00000538619	T;T;T	0.80304	-1.36;-1.36;-1.36	4.85	4.85	0.62838	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.64402	D	0.000002	D	0.90331	0.6975	M	0.86864	2.845	0.58432	D	0.999996	D;D	0.76494	0.999;0.997	D;D	0.83275	0.987;0.996	D	0.92021	0.5626	10	0.87932	D	0	-17.8598	13.7596	0.62956	0.0:0.0:0.0:1.0	.	71;141	F5GXV5;P18505	.;GBRB1_HUMAN	N	108;141;71	ENSP00000426753:I108N;ENSP00000295454:I141N;ENSP00000440330:I71N	ENSP00000295454:I141N	I	+	2	0	GABRB1	46858204	1.000000	0.71417	1.000000	0.80357	0.891000	0.51852	7.868000	0.87116	2.030000	0.59900	0.454000	0.30748	ATT	.	.		0.388	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
FRYL	285527	hgsc.bcm.edu	37	4	48512966	48512966	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:48512966C>T	ENST00000503238.1	-	55	8180	c.8181G>A	c.(8179-8181)gaG>gaA	p.E2727E	FRYL_ENST00000537810.1_Silent_p.E2727E|FRYL_ENST00000507873.2_Silent_p.E123E|FRYL_ENST00000358350.4_Silent_p.E2727E|FRYL_ENST00000264319.7_Silent_p.E123E			O94915	FRYL_HUMAN	FRY-like	2727					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						AGCTGACTGCCTCATTAGTTA	0.368																																					p.E2727E		Atlas-SNP	.											.	FRYL	242	.	0			c.G8181A						.						85.0	79.0	81.0					4																	48512966		1896	4104	6000	SO:0001819	synonymous_variant	285527	exon58			GACTGCCTCATTA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.8181G>A	chr4.hg19:g.48512966C>T		295.0	0.0		295.0	103.0	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	hg19	CCDS43227.1																																																																																			.	.		0.368	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
AMBN	258	hgsc.bcm.edu	37	4	71467187	71467187	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:71467187T>C	ENST00000322937.6	+	6	450	c.347T>C	c.(346-348)tTg>tCg	p.L116S	AMBN_ENST00000449493.2_Missense_Mutation_p.L101S	NM_016519.5	NP_057603.1	Q9NP70	AMBN_HUMAN	ameloblastin (enamel matrix protein)	116					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|odontogenesis of dentin-containing tooth (GO:0042475)	proteinaceous extracellular matrix (GO:0005578)	growth factor activity (GO:0008083)|structural constituent of tooth enamel (GO:0030345)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(3)|prostate(2)|skin(1)	29			Lung(101;0.235)			CAGCCATCCTTGAAGCCTCAA	0.488											OREG0016218	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L116S		Atlas-SNP	.											.	AMBN	73	.	0			c.T347C						.						140.0	142.0	141.0					4																	71467187		2203	4300	6503	SO:0001583	missense	258	exon6			CATCCTTGAAGCC	AF209780	CCDS3543.1	4q21	2006-11-28	2006-04-27		ENSG00000178522	ENSG00000178522			452	protein-coding gene	gene with protein product		601259	"""ameloblastin, enamel matrix protein"""			9126491	Standard	NM_016519		Approved		uc003hfl.3	Q9NP70	OTTHUMG00000129913	ENST00000322937.6:c.347T>C	chr4.hg19:g.71467187T>C	ENSP00000313809:p.Leu116Ser	106.0	0.0	1130	111.0	38.0	NM_016519	Q3B862|Q9H2X1|Q9H4L1	Missense_Mutation	SNP	ENST00000322937.6	hg19	CCDS3543.1	.	.	.	.	.	.	.	.	.	.	T	12.09	1.832518	0.32421	.	.	ENSG00000178522	ENST00000322937;ENST00000538728;ENST00000449493	T;T	0.36157	1.27;1.27	5.65	3.11	0.35812	.	0.228662	0.30658	N	0.009159	T	0.50292	0.1607	M	0.62723	1.935	0.29718	N	0.838909	D	0.71674	0.998	D	0.64877	0.93	T	0.50250	-0.8850	10	0.66056	D	0.02	-4.8433	8.4246	0.32720	0.3133:0.0:0.0:0.6867	.	116	Q9NP70	AMBN_HUMAN	S	116;116;101	ENSP00000313809:L116S;ENSP00000391234:L101S	ENSP00000313809:L116S	L	+	2	0	AMBN	71501776	1.000000	0.71417	1.000000	0.80357	0.069000	0.16628	1.602000	0.36783	0.458000	0.26988	-0.490000	0.04691	TTG	.	.		0.488	AMBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252165.1	NM_016519	
LIN54	132660	hgsc.bcm.edu	37	4	83891563	83891563	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:83891563T>C	ENST00000340417.3	-	4	1245	c.868A>G	c.(868-870)Agt>Ggt	p.S290G	LIN54_ENST00000446851.2_Missense_Mutation_p.S69G|LIN54_ENST00000395283.2_Intron|LIN54_ENST00000506560.1_Intron|LIN54_ENST00000510557.1_Missense_Mutation_p.S69G|LIN54_ENST00000442461.2_Missense_Mutation_p.S69G|LIN54_ENST00000395282.2_3'UTR|LIN54_ENST00000505397.1_Missense_Mutation_p.S290G	NM_194282.2	NP_919258.2	Q6MZP7	LIN54_HUMAN	lin-54 DREAM MuvB core complex component	290					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(5)	14		Hepatocellular(203;0.114)				ATAACACCACTTTCAGATATT	0.358																																					p.S290G		Atlas-SNP	.											.	LIN54	50	.	0			c.A868G						.						175.0	169.0	171.0					4																	83891563		2203	4300	6503	SO:0001583	missense	132660	exon4			CACCACTTTCAGA	BX537919	CCDS3599.1, CCDS47089.1, CCDS75157.1	4q21.22	2014-07-17	2014-07-17		ENSG00000189308	ENSG00000189308			25397	protein-coding gene	gene with protein product	"""CXC domain containing 1"""	613367	"""lin-54 homolog (C. elegans)"""			21498570	Standard	XM_005262749		Approved	MIP120, DKFZp686L1814, JC8.6, CXCDC1	uc003hnx.3	Q6MZP7	OTTHUMG00000130287	ENST00000340417.3:c.868A>G	chr4.hg19:g.83891563T>C	ENSP00000341947:p.Ser290Gly	106.0	0.0		128.0	53.0	NM_194282	Q32M68|Q32M69|Q6N071|Q76B60	Missense_Mutation	SNP	ENST00000340417.3	hg19	CCDS3599.1	.	.	.	.	.	.	.	.	.	.	T	15.12	2.739611	0.49045	.	.	ENSG00000189308	ENST00000340417;ENST00000442461;ENST00000446851;ENST00000510557;ENST00000505397	.	.	.	5.81	5.81	0.92471	.	0.247257	0.47455	D	0.000230	T	0.33177	0.0854	N	0.14661	0.345	0.80722	D	1	B;P	0.38827	0.0;0.649	B;B	0.32090	0.0;0.14	T	0.18366	-1.0339	9	0.17832	T	0.49	-7.2614	16.1756	0.81847	0.0:0.0:0.0:1.0	.	162;290	Q7Z3G2;Q6MZP7	.;LIN54_HUMAN	G	290;69;69;69;290	.	ENSP00000341947:S290G	S	-	1	0	LIN54	84110587	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.505000	0.66981	2.213000	0.71641	0.528000	0.53228	AGT	.	.		0.358	LIN54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252626.2	NM_194282	
PITX2	5308	hgsc.bcm.edu	37	4	111539720	111539720	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:111539720G>T	ENST00000354925.2	-	7	2220	c.515C>A	c.(514-516)cCa>cAa	p.P172Q	PITX2_ENST00000556049.1_5'UTR|PITX2_ENST00000306732.3_Missense_Mutation_p.P179Q|PITX2_ENST00000355080.5_Missense_Mutation_p.P126Q|PITX2_ENST00000394595.3_Silent_p.P103P|PITX2_ENST00000394598.2_Missense_Mutation_p.P172Q	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	172					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|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)|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 transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		GGAATAGCCTGGGTACATGTC	0.562																																					p.P179Q		Atlas-SNP	.											.	PITX2	73	.	0			c.C536A						.						83.0	73.0	76.0					4																	111539720		2203	4300	6503	SO:0001583	missense	5308	exon3			TAGCCTGGGTACA	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"""Homeoboxes / PRD class"""	9005	protein-coding gene	gene with protein product		601542	"""paired-like homeodomain transcription factor 2"""	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.515C>A	chr4.hg19:g.111539720G>T	ENSP00000347004:p.Pro172Gln	120.0	0.0		113.0	41.0	NM_000325	A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	hg19	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.380658	0.61845	.	.	ENSG00000164093	ENST00000306732;ENST00000394598;ENST00000355080;ENST00000354925;ENST00000511837;ENST00000556049	D;D;D;D;D;T	0.94000	-2.96;-3.09;-3.23;-3.09;-3.33;-0.74	4.89	4.89	0.63831	.	0.106120	0.64402	D	0.000003	D	0.95595	0.8568	L	0.59436	1.845	0.80722	D	1	P;D;D;D	0.69078	0.904;0.997;0.984;0.973	P;D;P;P	0.63793	0.536;0.918;0.616;0.786	D	0.95878	0.8896	10	0.87932	D	0	.	18.6339	0.91370	0.0:0.0:1.0:0.0	.	126;126;172;179	A8K6C6;Q99697-3;Q99697;Q99697-2	.;.;PITX2_HUMAN;.	Q	179;172;126;172;172;96	ENSP00000304169:P179Q;ENSP00000378097:P172Q;ENSP00000347192:P126Q;ENSP00000347004:P172Q;ENSP00000421454:P172Q;ENSP00000450938:P96Q	ENSP00000304169:P179Q	P	-	2	0	PITX2	111759169	1.000000	0.71417	0.996000	0.52242	0.911000	0.54048	9.263000	0.95617	2.712000	0.92718	0.563000	0.77884	CCA	.	.		0.562	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2		
CCRN4L	25819	hgsc.bcm.edu	37	4	139965969	139965969	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:139965969C>A	ENST00000280614.2	+	3	830	c.637C>A	c.(637-639)Caa>Aaa	p.Q213K	ELF2_ENST00000515489.1_Intron	NM_012118.2	NP_036250.2	Q9UK39	NOCT_HUMAN	CCR4 carbon catabolite repression 4-like (S. cerevisiae)	213					circadian regulation of gene expression (GO:0032922)|cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of gene expression (GO:0010629)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|regulation of circadian rhythm (GO:0042752)|regulation of embryonic development (GO:0045995)|regulation of transcription, DNA-templated (GO:0006355)|response to extracellular stimulus (GO:0009991)|response to lipopolysaccharide (GO:0032496)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A)-specific ribonuclease activity (GO:0004535)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(2)|large_intestine(3)|lung(3)|ovary(1)	9	all_hematologic(180;0.162)					ACTAGGCTATCAAGGCACGTT	0.463																																					p.Q213K	Ovarian(144;566 1842 19130 21379 22209)	Atlas-SNP	.											.	CCRN4L	22	.	0			c.C637A						.						130.0	112.0	118.0					4																	139965969		2203	4300	6503	SO:0001583	missense	25819	exon3			GGCTATCAAGGCA	AF183961	CCDS3743.1	4q31.1	2014-06-18	2001-11-28		ENSG00000151014	ENSG00000151014			14254	protein-coding gene	gene with protein product		608468	"""CCR4-like (carbon catabolite repression 4, S.cerevisiae)"""			10521507	Standard	NM_012118		Approved	CCR4L, Ccr4c	uc003ihl.3	Q9UK39	OTTHUMG00000161271	ENST00000280614.2:c.637C>A	chr4.hg19:g.139965969C>A	ENSP00000280614:p.Gln213Lys	160.0	0.0		166.0	64.0	NM_012118	D3DNY5|Q14D51|Q9HD93|Q9HD94|Q9HD95	Missense_Mutation	SNP	ENST00000280614.2	hg19	CCDS3743.1	.	.	.	.	.	.	.	.	.	.	C	10.31	1.313869	0.23908	.	.	ENSG00000151014	ENST00000280614	T	0.27720	1.65	5.5	5.5	0.81552	Endonuclease/exonuclease/phosphatase (2);	0.168168	0.52532	D	0.000062	T	0.24624	0.0597	N	0.20986	0.625	0.80722	D	1	B	0.25563	0.129	B	0.26517	0.07	T	0.04693	-1.0933	9	.	.	.	-7.1442	19.3911	0.94583	0.0:1.0:0.0:0.0	.	213	Q9UK39	NOCT_HUMAN	K	213	ENSP00000280614:Q213K	.	Q	+	1	0	CCRN4L	140185419	1.000000	0.71417	0.975000	0.42487	0.947000	0.59692	2.591000	0.46163	2.600000	0.87896	0.555000	0.69702	CAA	.	.		0.463	CCRN4L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257231.3	NM_012118	
GALNTL6	442117	hgsc.bcm.edu	37	4	173730589	173730589	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:173730589G>A	ENST00000506823.1	+	6	1288	c.631G>A	c.(631-633)Gga>Aga	p.G211R	GALNTL6_ENST00000508122.1_Missense_Mutation_p.G194R	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	211	Catalytic subdomain A.				protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						GAAAAGAGAAGGACTCATCCG	0.512																																					p.G211R		Atlas-SNP	.											.	GALNTL6	102	.	0			c.G631A						.						99.0	92.0	94.0					4																	173730589		2203	4300	6503	SO:0001583	missense	442117	exon6			AGAGAAGGACTCA		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"""Glycosyltransferase family 2 domain containing"""	33844	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 6"""	615138	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"""				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.631G>A	chr4.hg19:g.173730589G>A	ENSP00000423313:p.Gly211Arg	140.0	0.0		142.0	9.0	NM_001034845	Q2L4S6	Missense_Mutation	SNP	ENST00000506823.1	hg19	CCDS34104.1	.	.	.	.	.	.	.	.	.	.	G	26.1	4.703718	0.88924	.	.	ENSG00000174473	ENST00000506823;ENST00000404275;ENST00000508122	T;T	0.80214	-1.35;-1.35	5.45	5.45	0.79879	Glycosyl transferase, family 2 (1);	0.000000	0.64402	D	0.000009	D	0.94745	0.8304	H	0.99117	4.435	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96726	0.9536	10	0.87932	D	0	.	19.6346	0.95724	0.0:0.0:1.0:0.0	.	211	Q49A17	GLTL6_HUMAN	R	211;211;194	ENSP00000423313:G211R;ENSP00000423827:G194R	ENSP00000385382:G211R	G	+	1	0	GALNTL6	173967164	1.000000	0.71417	1.000000	0.80357	0.702000	0.40608	9.813000	0.99286	2.720000	0.93068	0.491000	0.48974	GGA	.	.		0.512	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
SORBS2	8470	hgsc.bcm.edu	37	4	186544895	186544895	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:186544895T>C	ENST00000284776.7	-	13	2185	c.1676A>G	c.(1675-1677)aAt>aGt	p.N559S	SORBS2_ENST00000355634.5_Missense_Mutation_p.N659S|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000431808.1_Missense_Mutation_p.N559S|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.N463S|SORBS2_ENST00000448662.2_Intron	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	559					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		GCCGCTTTGATTTTCTTCCTC	0.577																																					p.N659S	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.A1976G						.						30.0	35.0	33.0					4																	186544895		2202	4299	6501	SO:0001583	missense	8470	exon16			CTTTGATTTTCTT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1676A>G	chr4.hg19:g.186544895T>C	ENSP00000284776:p.Asn559Ser	166.0	0.0		189.0	76.0	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	hg19	CCDS3845.1	.	.	.	.	.	.	.	.	.	.	T	0.441	-0.898616	0.02472	.	.	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.35973	1.38;1.38;1.28;1.38	5.36	-2.46	0.06461	.	1.102740	0.06553	N	0.745425	T	0.18676	0.0448	N	0.12182	0.205	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.28038	-1.0056	10	0.18710	T	0.47	-5.2441	8.5184	0.33259	0.0:0.2149:0.5245:0.2606	.	463;659;559	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	S	559;559;463;659	ENSP00000284776:N559S;ENSP00000411764:N559S;ENSP00000397482:N463S;ENSP00000347852:N659S	ENSP00000284776:N559S	N	-	2	0	SORBS2	186781889	0.389000	0.25205	0.001000	0.08648	0.007000	0.05969	0.215000	0.17562	-0.525000	0.06391	-0.488000	0.04728	AAT	.	.		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
PRDM9	56979	hgsc.bcm.edu	37	5	23527459	23527459	+	Silent	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:23527459G>A	ENST00000296682.3	+	11	2444	c.2262G>A	c.(2260-2262)ggG>ggA	p.G754G		NM_020227.2	NP_064612.2	Q9NQV7	PRDM9_HUMAN	PR domain containing 9	754					meiotic gene conversion (GO:0006311)|positive regulation of meiosis I (GO:0060903)|positive regulation of reciprocal meiotic recombination (GO:0010845)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|metal ion binding (GO:0046872)|recombination hotspot binding (GO:0010844)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(27)|lung(87)|ovary(6)|pancreas(2)|prostate(4)|skin(10)|upper_aerodigestive_tract(11)	172						GGGAGTGTGGGCGGGGCTTTC	0.582										HNSCC(3;0.000094)																											p.G754G		Atlas-SNP	.											.	PRDM9	344	.	0			c.G2262A						.						52.0	73.0	66.0					5																	23527459		2112	4293	6405	SO:0001819	synonymous_variant	56979	exon11			GTGTGGGCGGGGC	AF275816	CCDS43307.1	5p14.2	2014-06-03			ENSG00000164256	ENSG00000164256		"""-"", ""Zinc fingers, C2H2-type"""	13994	protein-coding gene	gene with protein product	"""PR-domain containing protein 9"""	609760	"""minisatellite binding protein 3, 115kDa"", ""minisatellite binding protein 3 (115kD)"""	MSBP3		10668202, 2062643, 24634223	Standard	NM_020227		Approved	PFM6, ZNF899	uc003jgo.3	Q9NQV7	OTTHUMG00000161918	ENST00000296682.3:c.2262G>A	chr5.hg19:g.23527459G>A		273.0	0.0		185.0	19.0	NM_020227	B4DX22|Q27Q50	Silent	SNP	ENST00000296682.3	hg19	CCDS43307.1																																																																																			.	.		0.582	PRDM9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366375.1	NM_020227	
NUP155	9631	hgsc.bcm.edu	37	5	37302983	37302983	+	Silent	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:37302983T>C	ENST00000231498.3	-	29	3548	c.3345A>G	c.(3343-3345)ctA>ctG	p.L1115L	NUP155_ENST00000381843.2_Silent_p.L1056L|NUP155_ENST00000513532.1_Silent_p.L1051L|NUP155_ENST00000502533.1_5'UTR	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1115					atrial cardiac muscle cell action potential (GO:0086014)|carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CAATGTACTCTAGTCGCTGCT	0.363																																					p.L1115L		Atlas-SNP	.											.	NUP155	116	.	0			c.A3345G						.						120.0	118.0	119.0					5																	37302983		2203	4300	6503	SO:0001819	synonymous_variant	9631	exon29			GTACTCTAGTCGC	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"""nucleoporin 155kD"""			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.3345A>G	chr5.hg19:g.37302983T>C		53.0	0.0		59.0	26.0	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	hg19	CCDS3921.1																																																																																			.	.		0.363	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
SLC30A5	64924	hgsc.bcm.edu	37	5	68411780	68411780	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:68411780A>G	ENST00000396591.3	+	9	1421	c.811A>G	c.(811-813)Att>Gtt	p.I271V	CTC-498J12.3_ENST00000504129.1_RNA	NM_022902.4	NP_075053.2	Q8TAD4	ZNT5_HUMAN	solute carrier family 30 (zinc transporter), member 5	271					cellular protein metabolic process (GO:0044267)|cellular zinc ion homeostasis (GO:0006882)|cobalt ion transport (GO:0006824)|regulation of proton transport (GO:0010155)|response to zinc ion (GO:0010043)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	apical plasma membrane (GO:0016324)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Lung NSC(167;0.000986)|Prostate(74;0.00809)|Colorectal(97;0.0508)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		GTTTTCTCTCATTATGCCTTT	0.328																																					p.I271V		Atlas-SNP	.											.	SLC30A5	54	.	0			c.A811G						.						158.0	149.0	152.0					5																	68411780		2203	4300	6503	SO:0001583	missense	64924	exon9			TCTCTCATTATGC	AF212235	CCDS3996.1, CCDS34173.1, CCDS58955.1	5q13.1	2013-05-22			ENSG00000145740	ENSG00000145740		"""Solute carriers"""	19089	protein-coding gene	gene with protein product		607819				11937503, 11904301	Standard	NM_022902		Approved	ZTL1, ZnT-5, FLJ12496, FLJ12756, ZNT5, MGC5499, ZNTL1	uc003jvh.3	Q8TAD4	OTTHUMG00000131253	ENST00000396591.3:c.811A>G	chr5.hg19:g.68411780A>G	ENSP00000379836:p.Ile271Val	120.0	0.0		109.0	34.0	NM_022902	B7ZM89|Q6UX54|Q7L4M4|Q8TDG3|Q9BVY8|Q9H9H1	Missense_Mutation	SNP	ENST00000396591.3	hg19	CCDS3996.1	.	.	.	.	.	.	.	.	.	.	A	13.02	2.112247	0.37242	.	.	ENSG00000145740	ENST00000396591	T	0.62788	-0.0	5.47	5.47	0.80525	.	0.087522	0.85682	D	0.000000	T	0.53433	0.1796	L	0.43152	1.355	0.80722	D	1	B;B	0.18166	0.004;0.026	B;B	0.14578	0.011;0.008	T	0.49370	-0.8947	10	0.15952	T	0.53	.	15.4982	0.75673	1.0:0.0:0.0:0.0	.	100;271	Q8TAD4-2;Q8TAD4	.;ZNT5_HUMAN	V	271	ENSP00000379836:I271V	ENSP00000379836:I271V	I	+	1	0	SLC30A5	68447536	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.328000	0.43867	2.206000	0.71126	0.477000	0.44152	ATT	.	.		0.328	SLC30A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254017.2		
NUDT12	83594	hgsc.bcm.edu	37	5	102887925	102887925	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:102887925C>G	ENST00000230792.2	-	6	1367	c.1271G>C	c.(1270-1272)aGa>aCa	p.R424T	NUDT12_ENST00000515407.1_5'Flank|NUDT12_ENST00000507423.1_Missense_Mutation_p.R406T	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	424	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		TACCTGTTCTCTAGTGAACCA	0.393																																					p.R424T		Atlas-SNP	.											.	NUDT12	27	.	0			c.G1271C						.						136.0	133.0	134.0					5																	102887925		2202	4300	6502	SO:0001583	missense	83594	exon6			TGTTCTCTAGTGA	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.1271G>C	chr5.hg19:g.102887925C>G	ENSP00000230792:p.Arg424Thr	94.0	0.0		124.0	25.0	NM_031438	B3KUW2|Q8TAL7	Missense_Mutation	SNP	ENST00000230792.2	hg19	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.148630	0.78001	.	.	ENSG00000112874	ENST00000230792;ENST00000507423	T;T	0.08193	3.12;3.12	5.46	4.57	0.56435	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.042117	0.85682	D	0.000000	T	0.32823	0.0842	M	0.86651	2.83	0.58432	D	0.999994	D;D	0.67145	0.993;0.996	D;D	0.72625	0.911;0.978	T	0.09729	-1.0661	10	0.56958	D	0.05	-26.4578	15.1505	0.72692	0.0:0.9285:0.0:0.0715	.	406;424	E7EM93;Q9BQG2	.;NUD12_HUMAN	T	424;406	ENSP00000230792:R424T;ENSP00000424521:R406T	ENSP00000230792:R424T	R	-	2	0	NUDT12	102915824	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.624000	0.61254	2.724000	0.93272	0.650000	0.86243	AGA	.	.		0.393	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250650.1	NM_031438	
KCNN2	3781	hgsc.bcm.edu	37	5	113698857	113698857	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:113698857G>T	ENST00000512097.3	+	2	1403	c.385G>T	c.(385-387)Gaa>Taa	p.E129*	KCNN2_ENST00000507750.1_3'UTR|KCNN2_ENST00000264773.3_Nonsense_Mutation_p.E129*			Q9H2S1	KCNN2_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 2	129					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)	CGCCCTGTTCGAAAAGCGCAA	0.622																																					p.E129X		Atlas-SNP	.											.	KCNN2	144	.	0			c.G385T						.						38.0	39.0	38.0					5																	113698857		2202	4300	6502	SO:0001587	stop_gained	3781	exon1			CTGTTCGAAAAGC	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.385G>T	chr5.hg19:g.113698857G>T	ENSP00000427120:p.Glu129*	76.0	0.0		115.0	29.0	NM_021614	A6NF94|Q0VFZ4|Q6PJI0|Q6X2Y2	Nonsense_Mutation	SNP	ENST00000512097.3	hg19	CCDS4114.1	.	.	.	.	.	.	.	.	.	.	G	48	14.308480	0.99789	.	.	ENSG00000080709	ENST00000512097;ENST00000264773	.	.	.	5.44	4.57	0.56435	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	.	13.8883	0.63721	0.0741:0.0:0.9259:0.0	.	.	.	.	X	129	.	ENSP00000264773:E129X	E	+	1	0	KCNN2	113726756	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	7.695000	0.84257	1.293000	0.44690	0.655000	0.94253	GAA	.	.		0.622	KCNN2-001	KNOWN	not_organism_supported|upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250775.2	NM_021614	
FTMT	94033	hgsc.bcm.edu	37	5	121187759	121187759	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:121187759C>A	ENST00000321339.1	+	1	110	c.101C>A	c.(100-102)cCg>cAg	p.P34Q		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	34					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		CGTTGGGCCCCGGGGCGCCCC	0.766																																					p.P34Q		Atlas-SNP	.											.	FTMT	71	.	0			c.C101A						.						8.0	9.0	9.0					5																	121187759		2156	4207	6363	SO:0001583	missense	94033	exon1			GGGCCCCGGGGCG	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.101C>A	chr5.hg19:g.121187759C>A	ENSP00000313691:p.Pro34Gln	22.0	0.0		56.0	19.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	C	10.33	1.320220	0.23994	.	.	ENSG00000181867	ENST00000321339	T	0.64438	-0.1	3.06	1.21	0.21127	.	.	.	.	.	T	0.38214	0.1032	N	0.24115	0.695	0.09310	N	1	P	0.42357	0.777	B	0.32864	0.154	T	0.20207	-1.0282	9	0.48119	T	0.1	.	4.4736	0.11724	0.0:0.6377:0.23:0.1323	.	34	Q8N4E7	FTMT_HUMAN	Q	34	ENSP00000313691:P34Q	ENSP00000313691:P34Q	P	+	2	0	FTMT	121215658	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.154000	0.16343	0.303000	0.22785	-0.182000	0.12963	CCG	.	.		0.766	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478	
SKP1	6500	hgsc.bcm.edu	37	5	133481891	133481891	+	IGR	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:133481891G>A	ENST00000353411.6	-	0	9467				TCF7_ENST00000321603.6_Splice_Site|TCF7_ENST00000342854.5_Intron|TCF7_ENST00000395023.1_Intron|TCF7_ENST00000432532.2_Intron|TCF7_ENST00000395029.1_Intron|TCF7_ENST00000378560.4_Splice_Site|TCF7_ENST00000520958.1_Intron	NM_170679.2	NP_733779.1	P63208	SKP1_HUMAN	S-phase kinase-associated protein 1						anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H2A monoubiquitination (GO:0035518)|mitotic cell cycle (GO:0000278)|Notch signaling pathway (GO:0007219)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein ubiquitination (GO:0016567)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)|viral process (GO:0016032)	Cul7-RING ubiquitin ligase complex (GO:0031467)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|SCF ubiquitin ligase complex (GO:0019005)	ubiquitin-protein transferase activity (GO:0004842)			large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCTGTTTACAGATAACTCTCT	0.502											OREG0016787	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									.		Atlas-SNP	.											.	TCF7	81	.	0			c.804-1G>A						.						114.0	123.0	120.0					5																	133481891		2203	4300	6503	SO:0001628	intergenic_variant	6932	exon10			TTTACAGATAACT	U33760	CCDS4171.1, CCDS4172.1	5q31	2011-11-18	2007-11-13	2007-11-13	ENSG00000113558	ENSG00000113558			10899	protein-coding gene	gene with protein product		601434	"""S-phase kinase-associated protein 1A (p19A)"""	SKP1A		7553852, 8646875	Standard	NM_006930		Approved	EMC19, OCP2, TCEB1L, MGC34403, OCP-II, p19A	uc003kzc.4	P63208	OTTHUMG00000129117		chr5.hg19:g.133481891G>A		93.0	0.0	1603	143.0	34.0	NM_201634	D3DQ97|D3DQ98|P34991|Q8TAY2	Splice_Site	SNP	ENST00000353411.6	hg19	CCDS4171.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.345643	0.82022	.	.	ENSG00000081059	ENST00000321603;ENST00000378560	.	.	.	5.51	5.51	0.81932	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.4191	0.94713	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TCF7	133509790	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.942000	0.70203	2.586000	0.87340	0.563000	0.77884	.	.	.		0.502	SKP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251162.2	NM_170679	
RBM27	54439	hgsc.bcm.edu	37	5	145640456	145640456	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:145640456A>G	ENST00000265271.5	+	12	2054	c.1888A>G	c.(1888-1890)Atc>Gtc	p.I630V	RBM27_ENST00000506502.1_Missense_Mutation_p.I575V	NM_018989.1	NP_061862.1	Q9P2N5	RBM27_HUMAN	RNA binding motif protein 27	630	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA processing (GO:0006397)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(4)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TATTGTTAATATCCAGGTAAA	0.363																																					p.I630V		Atlas-SNP	.											.	RBM27	119	.	0			c.A1888G						.						164.0	143.0	149.0					5																	145640456		1568	3582	5150	SO:0001583	missense	54439	exon12			GTTAATATCCAGG	AL833706	CCDS43378.1	5q32	2013-01-09				ENSG00000091009		"""Zinc fingers, CCCH-type domain containing"", ""RNA binding motif (RRM) containing"""	29243	protein-coding gene	gene with protein product	"""acidic rich RS domain containing 1"""					10718198, 15741184	Standard	NM_018989		Approved	KIAA1311, ARRS1, Psc1, ZC3H18	uc003lnz.4	Q9P2N5		ENST00000265271.5:c.1888A>G	chr5.hg19:g.145640456A>G	ENSP00000265271:p.Ile630Val	292.0	0.0		432.0	23.0	NM_018989	Q8IYW9	Missense_Mutation	SNP	ENST00000265271.5	hg19	CCDS43378.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.726745	0.89298	.	.	ENSG00000091009	ENST00000265271	T	0.51817	0.69	6.17	6.17	0.99709	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	D	0.000000	T	0.59865	0.2225	L	0.37466	1.105	0.80722	D	1	P;D	0.58620	0.898;0.983	D;D	0.73708	0.956;0.981	T	0.56232	-0.8013	10	0.36615	T	0.2	-11.4254	16.8222	0.85835	1.0:0.0:0.0:0.0	.	630;575	Q9P2N5;B3KY61	RBM27_HUMAN;.	V	630	ENSP00000265271:I630V	ENSP00000265271:I630V	I	+	1	0	RBM27	145620649	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.763000	0.91715	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.363	RBM27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373420.1	XM_291128	
GRM6	2916	hgsc.bcm.edu	37	5	178418902	178418902	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:178418902C>T	ENST00000517717.1	-	3	725	c.687G>A	c.(685-687)ggG>ggA	p.G229G	GRM6_ENST00000231188.5_Silent_p.G229G|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	229					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.245)		AGGCCTCAACCCCACTTTCGC	0.637																																					p.G229G		Atlas-SNP	.											.	GRM6	149	.	0			c.G687A						.						72.0	61.0	64.0					5																	178418902		2203	4300	6503	SO:0001819	synonymous_variant	2916	exon2			CTCAACCCCACTT	U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.687G>A	chr5.hg19:g.178418902C>T		120.0	0.0		135.0	18.0	NM_000843		Silent	SNP	ENST00000517717.1	hg19	CCDS4442.1																																																																																			.	.		0.637	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
C5orf60	285679	hgsc.bcm.edu	37	5	179069928	179069928	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:179069928G>C	ENST00000448248.2	-	4	650	c.625C>G	c.(625-627)Cac>Gac	p.H209D	C5orf60_ENST00000506142.1_5'UTR	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	209	Ser-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						GGTGGCTGGTGTGAAGGGTGC	0.592																																					p.H209D		Atlas-SNP	.											.	C5orf60	24	.	0			c.C625G						.						70.0	72.0	71.0					5																	179069928		692	1591	2283	SO:0001583	missense	285679	exon4			GCTGGTGTGAAGG	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.625C>G	chr5.hg19:g.179069928G>C	ENSP00000404583:p.His209Asp	209.0	0.0		253.0	56.0	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	hg19	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	g	0.027	-1.363086	0.01235	.	.	ENSG00000204661	ENST00000448248	T	0.25579	1.79	0.118	0.118	0.14667	.	.	.	.	.	T	0.18593	0.0446	N	0.08118	0	0.09310	N	1	P;P	0.47106	0.89;0.89	P;P	0.52554	0.702;0.702	T	0.16541	-1.0399	8	0.46703	T	0.11	.	.	.	.	.	209;209	A6NFR6-2;A6NFR6-4	.;.	D	209	ENSP00000404583:H209D	ENSP00000404583:H209D	H	-	1	0	C5orf60	179002534	0.017000	0.18338	0.008000	0.14137	0.007000	0.05969	0.233000	0.17911	0.191000	0.20236	0.194000	0.17425	CAC	.	.		0.592	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
PRPF4B	8899	hgsc.bcm.edu	37	6	4032939	4032939	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:4032939C>T	ENST00000337659.6	+	2	1288	c.1188C>T	c.(1186-1188)tcC>tcT	p.S396S	PRPF4B_ENST00000538861.1_Silent_p.S382S	NM_003913.4	NP_003904.3	Q13523	PRP4B_HUMAN	pre-mRNA processing factor 4B	396	Arg/Lys-rich (basic).				mRNA splicing, via spliceosome (GO:0000398)|protein phosphorylation (GO:0006468)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|chromosome (GO:0005694)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(6)|endometrium(3)|large_intestine(5)|lung(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	22	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				AGAGCCGATCCTTAGAAAGAA	0.443																																					p.S396S		Atlas-SNP	.											.	PRPF4B	140	.	0			c.C1188T						.						73.0	82.0	79.0					6																	4032939		2203	4300	6503	SO:0001819	synonymous_variant	8899	exon2			CCGATCCTTAGAA	U48736	CCDS4488.1	6p24.2	2013-10-03	2013-10-03		ENSG00000112739	ENSG00000112739			17346	protein-coding gene	gene with protein product		602338	"""PRP4 pre-mRNA processing factor 4 homolog B (yeast)"""			9628581, 11418604	Standard	XR_241936		Approved	Prp4, PR4H, KIAA0536	uc003mvv.3	Q13523	OTTHUMG00000014157	ENST00000337659.6:c.1188C>T	chr6.hg19:g.4032939C>T		153.0	0.0		236.0	30.0	NM_003913	A8K5C9|Q5D0F6|Q5TAY8|Q8IVC3|Q8TDP2|Q96QT7|Q9UEE6	Silent	SNP	ENST00000337659.6	hg19	CCDS4488.1																																																																																			.	.		0.443	PRPF4B-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314018.2		
GFOD1	54438	hgsc.bcm.edu	37	6	13365293	13365293	+	Silent	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:13365293C>G	ENST00000379287.3	-	2	1519	c.855G>C	c.(853-855)gtG>gtC	p.V285V	GFOD1_ENST00000379284.1_Silent_p.V182V	NM_018988.3	NP_061861.1	Q9NXC2	GFOD1_HUMAN	glucose-fructose oxidoreductase domain containing 1	285						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)	18	Breast(50;0.0296)|Ovarian(93;0.0454)	all_hematologic(90;0.135)	Epithelial(50;0.0348)|BRCA - Breast invasive adenocarcinoma(129;0.1)|all cancers(50;0.108)			GGGAGTTGCTCACCGGCGTGG	0.701																																					p.V285V		Atlas-SNP	.											.	GFOD1	38	.	0			c.G855C						.						40.0	42.0	41.0					6																	13365293		2203	4300	6503	SO:0001819	synonymous_variant	54438	exon2			GTTGCTCACCGGC	AK000337	CCDS4524.1, CCDS56397.1, CCDS64351.1	6p24.1-p23	2013-09-19			ENSG00000145990	ENSG00000145990			21096	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 114"""	C6orf114			Standard	NM_018988		Approved	FLJ20330, ADG-90	uc003nat.2	Q9NXC2	OTTHUMG00000014276	ENST00000379287.3:c.855G>C	chr6.hg19:g.13365293C>G		58.0	0.0		89.0	32.0	NM_018988	A8E4L6|Q5T058|Q96JD4|Q9H5K2	Silent	SNP	ENST00000379287.3	hg19	CCDS4524.1																																																																																			.	.		0.701	GFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039902.1	NM_018988	
FAM8A1	51439	hgsc.bcm.edu	37	6	17601130	17601130	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:17601130C>G	ENST00000259963.3	+	1	545	c.490C>G	c.(490-492)Ccg>Gcg	p.P164A		NM_016255.2	NP_057339.1	Q9UBU6	FA8A1_HUMAN	family with sequence similarity 8, member A1	164	Poly-Pro.					integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(3)	6	Breast(50;0.0259)|Ovarian(93;0.0584)	all_hematologic(90;0.143)	all cancers(50;0.176)|Epithelial(50;0.204)			ggccgcggcgccgccgccccc	0.751																																					p.P164A		Atlas-SNP	.											.	FAM8A1	26	.	0			c.C490G						.						4.0	6.0	6.0					6																	17601130		1472	3232	4704	SO:0001583	missense	51439	exon1			GCGGCGCCGCCGC	AF097027	CCDS4540.1	6p23	2010-11-22			ENSG00000137414	ENSG00000137414			16372	protein-coding gene	gene with protein product						11707071	Standard	NM_016255		Approved	AHCP	uc003ncc.3	Q9UBU6	OTTHUMG00000014309	ENST00000259963.3:c.490C>G	chr6.hg19:g.17601130C>G	ENSP00000259963:p.Pro164Ala	83.0	0.0		123.0	9.0	NM_016255	B2R725	Missense_Mutation	SNP	ENST00000259963.3	hg19	CCDS4540.1	.	.	.	.	.	.	.	.	.	.	C	3.098	-0.185400	0.06340	.	.	ENSG00000137414	ENST00000259963	.	.	.	3.8	1.95	0.26073	.	0.921406	0.09105	N	0.847962	T	0.08758	0.0217	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.39313	-0.9620	9	0.15952	T	0.53	-0.1795	6.4769	0.22041	0.0:0.7112:0.1834:0.1054	.	164	Q9UBU6	FA8A1_HUMAN	A	164	.	ENSP00000259963:P164A	P	+	1	0	FAM8A1	17709109	0.001000	0.12720	0.173000	0.22940	0.158000	0.22134	1.059000	0.30517	0.208000	0.20626	0.484000	0.47621	CCG	.	.		0.751	FAM8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039950.1		
GOPC	57120	hgsc.bcm.edu	37	6	117890868	117890868	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:117890868A>C	ENST00000368498.2	-	7	1019	c.944T>G	c.(943-945)aTc>aGc	p.I315S	GOPC_ENST00000535237.1_Missense_Mutation_p.I315S|DCBLD1_ENST00000296955.8_3'UTR|GOPC_ENST00000052569.6_Missense_Mutation_p.I307S|GOPC_ENST00000467125.1_5'UTR	NM_020399.3	NP_065132.1	Q9HD26	GOPC_HUMAN	golgi-associated PDZ and coiled-coil motif containing	315	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apical protein localization (GO:0045176)|cytoplasmic sequestering of CFTR protein (GO:0043004)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi to plasma membrane transport (GO:0006893)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|spermatid nucleus differentiation (GO:0007289)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|trans-Golgi network transport vesicle (GO:0030140)	ion channel binding (GO:0044325)|small GTPase regulator activity (GO:0005083)		GOPC/ROS1(14)	endometrium(1)|large_intestine(3)|lung(4)|ovary(1)	9		all_cancers(87;0.00844)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0363)|OV - Ovarian serous cystadenocarcinoma(136;0.0821)|all cancers(137;0.0976)		GATCTCAGAGATGAGGATTGG	0.458			O	ROS1	glioblastoma																																p.I315S		Atlas-SNP	.		Dom	yes		6	6q21	57120	golgi associated PDZ and coiled-coil motif containing		O	GOPC,NS,carcinoma,0,1	GOPC	29	.	0			c.T944G						.						153.0	150.0	151.0					6																	117890868		2203	4300	6503	SO:0001583	missense	57120	exon7			TCAGAGATGAGGA	AF287894	CCDS5117.1, CCDS34523.1	6q21	2010-02-12	2010-02-12		ENSG00000047932	ENSG00000047932			17643	protein-coding gene	gene with protein product		606845				11162552, 11520064	Standard	NM_020399		Approved	dJ94G16.2, PIST, FIG, GOPC1, CAL		Q9HD26	OTTHUMG00000015457	ENST00000368498.2:c.944T>G	chr6.hg19:g.117890868A>C	ENSP00000357484:p.Ile315Ser	141.0	0.0		154.0	12.0	NM_020399	A6NM30|Q59FS4|Q969U8	Missense_Mutation	SNP	ENST00000368498.2	hg19	CCDS5117.1	.	.	.	.	.	.	.	.	.	.	A	29.4	5.001761	0.93227	.	.	ENSG00000047932	ENST00000052569;ENST00000368498;ENST00000535237	T;T;T	0.62941	-0.01;-0.01;-0.01	5.44	5.44	0.79542	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	D	0.85080	0.5615	H	0.97874	4.095	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.992;0.996;0.992	D	0.90820	0.4708	10	0.87932	D	0	-20.112	15.7835	0.78281	1.0:0.0:0.0:0.0	.	307;315;315	Q9HD26-2;Q9HD26;F5H1Y4	.;GOPC_HUMAN;.	S	307;315;315	ENSP00000052569:I307S;ENSP00000357484:I315S;ENSP00000445690:I315S	ENSP00000052569:I307S	I	-	2	0	GOPC	117997561	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.257000	0.95545	2.185000	0.69588	0.455000	0.32223	ATC	.	.		0.458	GOPC-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041988.1	NM_020399	
EPB41L2	2037	hgsc.bcm.edu	37	6	131216151	131216151	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:131216151A>C	ENST00000337057.3	-	9	1526	c.1345T>G	c.(1345-1347)Tcc>Gcc	p.S449A	EPB41L2_ENST00000528282.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000445890.2_Missense_Mutation_p.S449A|EPB41L2_ENST00000527411.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000525193.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000529208.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000530481.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000392427.3_Missense_Mutation_p.S449A|EPB41L2_ENST00000525271.1_Missense_Mutation_p.S449A|EPB41L2_ENST00000368128.2_Missense_Mutation_p.S449A|EPB41L2_ENST00000527659.1_Missense_Mutation_p.S449A	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	449	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		CGTTTATAGGAAATTTTTAAG	0.418																																					p.S449A		Atlas-SNP	.											.	EPB41L2	96	.	0			c.T1345G						.						103.0	94.0	97.0					6																	131216151		2203	4300	6503	SO:0001583	missense	2037	exon9			TATAGGAAATTTT	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.1345T>G	chr6.hg19:g.131216151A>C	ENSP00000338481:p.Ser449Ala	116.0	0.0		106.0	21.0	NM_001135554	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Missense_Mutation	SNP	ENST00000337057.3	hg19	CCDS5141.1	.	.	.	.	.	.	.	.	.	.	A	28.1	4.894923	0.91962	.	.	ENSG00000079819	ENST00000528282;ENST00000530481;ENST00000445890;ENST00000337057;ENST00000392427;ENST00000425439;ENST00000368128;ENST00000527411;ENST00000525271;ENST00000525193;ENST00000527659;ENST00000529208	D;D;D;D;D;D;D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52;-2.52	5.68	5.68	0.88126	FERM, C-terminal PH-like domain (1);FERM domain (1);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	D	0.95085	0.8408	M	0.91663	3.23	0.80722	D	1	D;D;D;D;D	0.57571	0.98;0.98;0.98;0.977;0.98	D;D;D;D;D	0.85130	0.995;0.993;0.995;0.997;0.993	D	0.95799	0.8831	10	0.62326	D	0.03	.	15.9369	0.79717	1.0:0.0:0.0:0.0	.	449;449;449;449;449	E9PHY5;B4DHI8;E9PPD9;O43491;Q68DV2	.;.;.;E41L2_HUMAN;.	A	449	ENSP00000434308:S449A;ENSP00000434576:S449A;ENSP00000402041:S449A;ENSP00000338481:S449A;ENSP00000376222:S449A;ENSP00000357110:S449A;ENSP00000436348:S449A;ENSP00000432803:S449A;ENSP00000431988:S449A;ENSP00000431647:S449A;ENSP00000436641:S449A	ENSP00000338481:S449A	S	-	1	0	EPB41L2	131257844	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.303000	0.96183	2.172000	0.68678	0.533000	0.62120	TCC	.	.		0.418	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
KDELR2	11014	hgsc.bcm.edu	37	7	6505873	6505873	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:6505873C>A	ENST00000258739.4	-	4	617	c.433G>T	c.(433-435)Gag>Tag	p.E145*	DAGLB_ENST00000436575.1_Intron|KDELR2_ENST00000490996.1_Intron|KDELR2_ENST00000463747.1_Intron	NM_006854.3	NP_006845.1	P33947	ERD22_HUMAN	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2	145					intracellular protein transport (GO:0006886)|protein retention in ER lumen (GO:0006621)|vesicle-mediated transport (GO:0016192)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	KDEL sequence binding (GO:0005046)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	10		Ovarian(82;0.0776)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)		GTGATGGTCTCGGCCTCCCCA	0.517																																					p.E145X		Atlas-SNP	.											.	KDELR2	31	.	0			c.G433T						.						123.0	107.0	113.0					7																	6505873		2203	4300	6503	SO:0001587	stop_gained	11014	exon4			TGGTCTCGGCCTC	X63745	CCDS5351.1, CCDS43550.1	7p	2008-05-02			ENSG00000136240	ENSG00000136240			6305	protein-coding gene	gene with protein product		609024				1316805, 1325562	Standard	NM_006854		Approved	ELP-1, ERD2.2	uc003sqe.4	P33947	OTTHUMG00000023103	ENST00000258739.4:c.433G>T	chr7.hg19:g.6505873C>A	ENSP00000258739:p.Glu145*	88.0	0.0		76.0	22.0	NM_006854	A4D2P4|Q6IPC5|Q96E30	Nonsense_Mutation	SNP	ENST00000258739.4	hg19	CCDS5351.1	.	.	.	.	.	.	.	.	.	.	C	38	6.918416	0.97936	.	.	ENSG00000136240	ENST00000258739	.	.	.	5.18	4.29	0.51040	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	-13.6006	13.9242	0.63952	0.0:0.9261:0.0:0.0739	.	.	.	.	X	145	.	ENSP00000258739:E145X	E	-	1	0	KDELR2	6472398	1.000000	0.71417	0.981000	0.43875	0.986000	0.74619	7.692000	0.84203	1.311000	0.45024	0.460000	0.39030	GAG	.	.		0.517	KDELR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059424.2		
TWIST1	7291	hgsc.bcm.edu	37	7	19156374	19156374	+	Missense_Mutation	SNP	T	T	C	rs200369729		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:19156374T>C	ENST00000242261.5	-	1	921	c.571A>G	c.(571-573)Agg>Ggg	p.R191G	AC003986.6_ENST00000419944.1_RNA	NM_000474.3	NP_000465.1	Q15672	TWST1_HUMAN	twist family bHLH transcription factor 1	191	Sufficient for transactivation activity. {ECO:0000250}.				aortic valve morphogenesis (GO:0003180)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in heart valve development (GO:2000793)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hypoxia (GO:0071456)|cranial suture morphogenesis (GO:0060363)|embryonic camera-type eye formation (GO:0060900)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cushion morphogenesis (GO:0003203)|eyelid development in camera-type eye (GO:0061029)|in utero embryonic development (GO:0001701)|mitral valve morphogenesis (GO:0003183)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone phosphorylation (GO:0033128)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of oxidative phosphorylation uncoupler activity (GO:2000276)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoblast differentiation (GO:0001649)|outer ear morphogenesis (GO:0042473)|palate development (GO:0060021)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell motility (GO:2000147)|positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation (GO:2000802)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of gene expression (GO:0010628)|positive regulation of interleukin-6 secretion (GO:2000778)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of bone mineralization (GO:0030500)|rhythmic process (GO:0048511)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription factor binding (GO:0008134)			lung(2)|upper_aerodigestive_tract(1)	3						CCCTCCATCCTCCAGACCGAG	0.662																																					p.R191G		Atlas-SNP	.											.	TWIST1	18	.	0			c.A571G						.						38.0	34.0	35.0					7																	19156374		2203	4300	6503	SO:0001583	missense	7291	exon1			CCATCCTCCAGAC	U80998	CCDS5367.1	7p21	2014-02-07	2013-10-17	2003-03-28	ENSG00000122691	ENSG00000122691		"""Basic helix-loop-helix proteins"""	12428	protein-coding gene	gene with protein product	"""Saethre-Chotzen syndrome"""	601622	"""blepharophimosis, epicanthus inversus and ptosis 3"", ""acrocephalosyndactyly 3"", ""twist homolog 1 (Drosophila)"", ""twist basic helix-loop-helix transcription factor 1"", ""craniosynostosis"""	ACS3, BPES3, TWIST, CRS		8995765, 11474656, 17343269	Standard	XR_428085		Approved	SCS, H-twist, BPES2, bHLHa38, CRS1	uc003sum.3	Q15672	OTTHUMG00000090821	ENST00000242261.5:c.571A>G	chr7.hg19:g.19156374T>C	ENSP00000242261:p.Arg191Gly	204.0	0.0		200.0	79.0	NM_000474	A4D128|Q92487|Q99804	Missense_Mutation	SNP	ENST00000242261.5	hg19	CCDS5367.1	.	.	.	.	.	.	.	.	.	.	t	15.48	2.846069	0.51164	.	.	ENSG00000122691	ENST00000242261	D	0.98178	-4.77	4.29	3.11	0.35812	Helix-loop-helix DNA-binding (1);	0.000000	0.41605	D	0.000844	D	0.98748	0.9579	M	0.85945	2.785	0.58432	D	0.999992	D	0.89917	1.0	D	0.91635	0.999	D	0.98925	1.0785	10	0.87932	D	0	-19.5452	11.3659	0.49671	0.0:0.0:0.2112:0.7888	.	191	Q15672	TWST1_HUMAN	G	191	ENSP00000242261:R191G	ENSP00000242261:R191G	R	-	1	2	TWIST1	19122899	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.627000	0.46469	1.798000	0.52647	0.369000	0.22263	AGG	.	T|0.998;G|0.002		0.662	TWIST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207625.1	NM_000474	
ABCA13	154664	hgsc.bcm.edu	37	7	48314641	48314641	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:48314641T>C	ENST00000435803.1	+	17	5402	c.5378T>C	c.(5377-5379)aTt>aCt	p.I1793T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1793					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GACTTCGCAATTGTGATAAAA	0.378																																					p.I1793T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.T5378C						.						43.0	42.0	42.0					7																	48314641		1847	4106	5953	SO:0001583	missense	154664	exon17			TCGCAATTGTGAT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5378T>C	chr7.hg19:g.48314641T>C	ENSP00000411096:p.Ile1793Thr	121.0	0.0		121.0	45.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	hg19	CCDS47584.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.254972	0.00265	.	.	ENSG00000179869	ENST00000435803	T	0.14266	2.52	5.92	-11.8	0.00035	.	2.777580	0.01395	N	0.013385	T	0.07773	0.0195	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20605	-1.0270	9	.	.	.	.	2.2718	0.04093	0.3058:0.3327:0.2423:0.1192	.	1793	Q86UQ4	ABCAD_HUMAN	T	1793	ENSP00000411096:I1793T	.	I	+	2	0	ABCA13	48285187	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.859000	0.04277	-2.135000	0.00811	-0.374000	0.07098	ATT	.	.		0.378	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
POM121	9883	hgsc.bcm.edu	37	7	72413572	72413572	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:72413572A>G	ENST00000434423.2	+	11	3040	c.3040A>G	c.(3040-3042)Atg>Gtg	p.M1014V	POM121_ENST00000358357.3_Missense_Mutation_p.M749V|POM121_ENST00000257622.4_Missense_Mutation_p.M749V|POM121_ENST00000395270.1_Missense_Mutation_p.M749V|POM121_ENST00000446813.1_Missense_Mutation_p.M749V			Q96HA1	P121A_HUMAN	POM121 transmembrane nucleoporin	1014	Pore side. {ECO:0000255}.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				NS(1)|breast(1)|endometrium(9)|kidney(4)|large_intestine(6)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Lung NSC(55;0.163)				ACCTCCGTCCATGATCAAGGT	0.632																																					p.M749V		Atlas-SNP	.											.	POM121	131	.	0			c.A2245G						.						91.0	88.0	89.0					7																	72413572		2203	4300	6503	SO:0001583	missense	9883	exon11			CCGTCCATGATCA	AB014518	CCDS5542.1, CCDS59059.1	7q11.23	2013-01-08	2012-03-13		ENSG00000196313	ENSG00000196313		"""-"""	19702	protein-coding gene	gene with protein product		615753	"""POM121 membrane glycoprotein (rat)"", ""POM121 membrane glycoprotein"""			8335683, 9734811, 17900573	Standard	NM_172020		Approved	KIAA0618, DKFZP586G1822, DKFZP586P2220, POM121A	uc003twk.2	Q96HA1	OTTHUMG00000023527	ENST00000434423.2:c.3040A>G	chr7.hg19:g.72413572A>G	ENSP00000405562:p.Met1014Val	217.0	0.0		333.0	55.0	NM_172020	A6NFS9|A8CDT4|A8K933|A8MXF9|O75115|Q96DI0|Q9H9X1|Q9Y2N3|Q9Y4S7	Missense_Mutation	SNP	ENST00000434423.2	hg19		.	.	.	.	.	.	.	.	.	.	A	0.009	-1.805423	0.00606	.	.	ENSG00000196313	ENST00000446813;ENST00000257622;ENST00000395270;ENST00000358357;ENST00000434423	T;T;T;T;T	0.04970	3.52;3.54;3.52;3.54;3.77	0.1	0.1	0.14510	.	.	.	.	.	T	0.02929	0.0087	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.47018	-0.9149	8	0.24483	T	0.36	.	.	.	.	.	749;1014	A8MXF9;Q96HA1	.;P121A_HUMAN	V	749;749;749;749;1014	ENSP00000393020:M749V;ENSP00000257622:M749V;ENSP00000378687:M749V;ENSP00000351124:M749V;ENSP00000405562:M1014V	ENSP00000257622:M749V	M	+	1	0	POM121	72051508	0.001000	0.12720	0.010000	0.14722	0.008000	0.06430	-0.585000	0.05794	0.147000	0.19030	0.145000	0.16022	ATG	.	.		0.632	POM121-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347344.1		
HSPB1	3315	hgsc.bcm.edu	37	7	75932030	75932030	+	Start_Codon_SNP	SNP	A	A	G	rs200190722		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:75932030A>G	ENST00000248553.6	+	1	170	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	HSPB1_ENST00000429938.1_5'Flank	NM_001540.3	NP_001531.1	P04792	HSPB1_HUMAN	heat shock 27kDa protein 1	1					cell death (GO:0008219)|cellular component movement (GO:0006928)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of protein kinase activity (GO:0006469)|platelet aggregation (GO:0070527)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of translational initiation (GO:0006446)|response to unfolded protein (GO:0006986)|response to virus (GO:0009615)|retina homeostasis (GO:0001895)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein kinase C inhibitor activity (GO:0008426)|ubiquitin binding (GO:0043130)			large_intestine(1)|lung(3)	4						GTCAGCCAGCATGACCGAGCG	0.657																																					p.M1V		Atlas-SNP	.											.	HSPB1	6	.	0			c.A1G						.						11.0	14.0	13.0					7																	75932030		2119	4197	6316	SO:0001582	initiator_codon_variant	3315	exon1			GCCAGCATGACCG	X54079	CCDS5583.1	7q11.23	2014-09-17	2002-08-29		ENSG00000106211	ENSG00000106211		"""Heat shock proteins / HSPB"""	5246	protein-coding gene	gene with protein product		602195	"""heat shock 27kD protein 1"""			2243808, 9344682	Standard	NM_001540		Approved	HSP27, HSP28, Hs.76067, Hsp25	uc003uew.3	P04792	OTTHUMG00000023228	ENST00000248553.6:c.1A>G	chr7.hg19:g.75932030A>G	ENSP00000248553:p.Met1Val	101.0	0.0		147.0	39.0	NM_001540	B2R4N8|Q6FI47|Q96C20|Q96EI7|Q9UC31|Q9UC34|Q9UC35|Q9UC36	Missense_Mutation	SNP	ENST00000248553.6	hg19	CCDS5583.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.654087	0.88056	.	.	ENSG00000106211	ENST00000248553;ENST00000432276	D	0.90844	-2.74	4.88	4.88	0.63580	.	0.000000	0.85682	D	0.000000	D	0.94981	0.8376	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.95552	0.8621	9	0.87932	D	0	-31.1993	13.8592	0.63550	1.0:0.0:0.0:0.0	.	1	P04792	HSPB1_HUMAN	V	1	ENSP00000248553:M1V	ENSP00000248553:M1V	M	+	1	0	HSPB1	75769966	1.000000	0.71417	0.993000	0.49108	0.927000	0.56198	8.486000	0.90451	2.057000	0.61298	0.459000	0.35465	ATG	.	.		0.657	HSPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252958.1		Missense_Mutation
PCLO	27445	hgsc.bcm.edu	37	7	82538312	82538312	+	Nonsense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:82538312C>A	ENST00000333891.9	-	8	13655	c.13318G>T	c.(13318-13320)Gag>Tag	p.E4440*	PCLO_ENST00000423517.2_Nonsense_Mutation_p.E4440*	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TCTGTTTCCTCACGACGCAGA	0.458																																					p.E4440X		Atlas-SNP	.											.	PCLO	1506	.	0			c.G13318T						.						93.0	84.0	87.0					7																	82538312		1934	4148	6082	SO:0001587	stop_gained	27445	exon8			TTTCCTCACGACG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13318G>T	chr7.hg19:g.82538312C>A	ENSP00000334319:p.Glu4440*	75.0	0.0		94.0	29.0	NM_014510		Nonsense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	C	56	26.217464	0.99968	.	.	ENSG00000186472	ENST00000333891;ENST00000423517	.	.	.	5.39	4.51	0.55191	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	14.2833	0.66228	0.0:0.9281:0.0:0.0719	.	.	.	.	X	4440	.	ENSP00000334319:E4440X	E	-	1	0	PCLO	82376248	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.647000	0.83462	1.409000	0.46915	0.591000	0.81541	GAG	.	.		0.458	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
COL1A2	1278	hgsc.bcm.edu	37	7	94057146	94057146	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:94057146C>G	ENST00000297268.6	+	49	3946	c.3475C>G	c.(3475-3477)Cca>Gca	p.P1159A		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1159	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	TAGAAAGAACCCAGCTCGCAC	0.502										HNSCC(75;0.22)																											p.P1159A		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3475G						.						66.0	62.0	63.0					7																	94057146		2203	4300	6503	SO:0001583	missense	1278	exon49			AAGAACCCAGCTC	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3475C>G	chr7.hg19:g.94057146C>G	ENSP00000297268:p.Pro1159Ala	58.0	0.0		83.0	20.0	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	hg19	CCDS34682.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.159600	0.78226	.	.	ENSG00000164692	ENST00000297268;ENST00000545487	T	0.80653	-1.4	5.65	5.65	0.86999	Fibrillar collagen, C-terminal (3);	0.000000	0.85682	D	0.000000	D	0.91855	0.7422	M	0.88512	2.96	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.92493	0.6002	10	0.87932	D	0	.	20.1065	0.97896	0.0:1.0:0.0:0.0	.	1159	P08123	CO1A2_HUMAN	A	1159;1160	ENSP00000297268:P1159A	ENSP00000297268:P1159A	P	+	1	0	COL1A2	93895082	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	7.818000	0.86416	2.836000	0.97738	0.655000	0.94253	CCA	.	.		0.502	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
GRM8	2918	hgsc.bcm.edu	37	7	126173564	126173564	+	Silent	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:126173564C>A	ENST00000339582.2	-	9	2680	c.1872G>T	c.(1870-1872)gtG>gtT	p.V624V	GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000444921.2_Silent_p.V624V|GRM8_ENST00000358373.3_Silent_p.V624V			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	624					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				CCGTTAGGAGCACGTAACTAA	0.458										HNSCC(24;0.065)																											p.V624V		Atlas-SNP	.											.	GRM8	377	.	0			c.G1872T						.						107.0	106.0	106.0					7																	126173564		2203	4300	6503	SO:0001819	synonymous_variant	2918	exon8			TAGGAGCACGTAA		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1872G>T	chr7.hg19:g.126173564C>A		143.0	0.0		184.0	59.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Silent	SNP	ENST00000339582.2	hg19	CCDS5794.1																																																																																			.	.		0.458	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
MGAM	8972	hgsc.bcm.edu	37	7	141735987	141735988	+	Missense_Mutation	DNP	GG	GG	TT			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:141735987_141735988GG>TT	ENST00000549489.2	+	17	2073_2074	c.1978_1979GG>TT	c.(1978-1980)GGc>TTc	p.G660F	MGAM_ENST00000475668.2_Missense_Mutation_p.G660F	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	660	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGACATATGTGGCTTTGCTTTG	0.51																																					p.G660C|p.G660V		Atlas-SNP	.											.	MGAM	767	.	0			c.G1978T|c.G1979T						.																																			SO:0001583	missense	8972	exon17			ATATGTGGCTTTG|TATGTGGCTTTGC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	Exception_encountered	chr7.hg19:g.141735987_141735988delinsTT	ENSP00000447378:p.Gly660Phe	121.0	0.0		161.0|165.0	36.0|38.0	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1																																																																																			.	.		0.510	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
RP1	6101	hgsc.bcm.edu	37	8	55539282	55539282	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:55539282G>T	ENST00000220676.1	+	4	2988	c.2840G>T	c.(2839-2841)tGt>tTt	p.C947F		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	947					axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			GTGGTAAATTGTAGCAATAAT	0.313																																					p.C947F	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G2840T						.						41.0	45.0	43.0					8																	55539282		2203	4300	6503	SO:0001583	missense	6101	exon4			TAAATTGTAGCAA	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.2840G>T	chr8.hg19:g.55539282G>T	ENSP00000220676:p.Cys947Phe	233.0	0.0		195.0	11.0	NM_006269		Missense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	0.812	-0.751697	0.03041	.	.	ENSG00000104237	ENST00000220676	T	0.46063	0.88	5.58	-1.12	0.09808	.	0.838095	0.10610	N	0.654635	T	0.26159	0.0638	L	0.43152	1.355	0.09310	N	1	P	0.41947	0.766	B	0.37198	0.243	T	0.13980	-1.0489	10	0.27082	T	0.32	.	2.9909	0.05982	0.2755:0.124:0.4864:0.114	.	947	P56715	RP1_HUMAN	F	947	ENSP00000220676:C947F	ENSP00000220676:C947F	C	+	2	0	RP1	55701835	0.000000	0.05858	0.011000	0.14972	0.020000	0.10135	-0.076000	0.11412	-0.100000	0.12241	-0.211000	0.12701	TGT	.	.		0.313	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
OXR1	55074	hgsc.bcm.edu	37	8	107705036	107705036	+	Silent	SNP	T	T	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:107705036T>G	ENST00000442977.2	+	6	708	c.609T>G	c.(607-609)acT>acG	p.T203T	OXR1_ENST00000445937.1_Silent_p.T202T|OXR1_ENST00000497705.1_Silent_p.T135T|OXR1_ENST00000452423.2_5'UTR|OXR1_ENST00000531443.1_Silent_p.T202T|OXR1_ENST00000517566.2_Silent_p.T202T|OXR1_ENST00000312046.6_Silent_p.T195T	NM_001198532.1	NP_001185461.1	Q8N573	OXR1_HUMAN	oxidation resistance 1	203					adult walking behavior (GO:0007628)|cellular response to hydroperoxide (GO:0071447)|negative regulation of neuron apoptotic process (GO:0043524)|response to oxidative stress (GO:0006979)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)	oxidoreductase activity (GO:0016491)			NS(2)|breast(2)|endometrium(2)|large_intestine(9)|lung(10)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	31			OV - Ovarian serous cystadenocarcinoma(57;1.81e-09)			TATCTTCAACTTCTGAGGAGG	0.358																																					p.T203T		Atlas-SNP	.											.	OXR1	190	.	0			c.T609G						.						77.0	78.0	77.0					8																	107705036		2203	4300	6503	SO:0001819	synonymous_variant	55074	exon6			TTCAACTTCTGAG	AF309387	CCDS6304.2, CCDS47909.1, CCDS56547.1, CCDS56548.1, CCDS56549.1, CCDS56550.1	8q23	2013-03-14			ENSG00000164830	ENSG00000164830			15822	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 3"""	605609				11114193	Standard	NM_181354		Approved	TLDC3	uc011lht.2	Q8N573	OTTHUMG00000167682	ENST00000442977.2:c.609T>G	chr8.hg19:g.107705036T>G		91.0	0.0		105.0	42.0	NM_001198532	A6NK11|A8KA34|B3KXL1|B7Z402|B7Z8N5|D3HIS6|Q3LIB5|Q6ZVK9|Q8N8V0|Q9H266|Q9NWC7	Silent	SNP	ENST00000442977.2	hg19	CCDS56548.1	.	.	.	.	.	.	.	.	.	.	T	5.147	0.212736	0.09757	.	.	ENSG00000164830	ENST00000517455	.	.	.	5.06	1.06	0.20224	.	.	.	.	.	T	0.51092	0.1654	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33904	-0.9850	4	.	.	.	-18.6337	5.0572	0.14539	0.4086:0.0762:0.0:0.5152	.	.	.	.	R	119	.	.	L	+	2	0	OXR1	107774212	0.867000	0.29959	0.998000	0.56505	0.453000	0.32348	0.087000	0.14958	-0.065000	0.13021	0.383000	0.25322	CTT	.	.		0.358	OXR1-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_181354	
EIF3E	3646	hgsc.bcm.edu	37	8	109226846	109226846	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:109226846T>C	ENST00000220849.5	-	10	1113	c.1051A>G	c.(1051-1053)Atc>Gtc	p.I351V	EIF3E_ENST00000519517.1_5'UTR|EIF3E_ENST00000519030.1_Missense_Mutation_p.I258V	NM_001568.2	NP_001559.1			eukaryotic translation initiation factor 3, subunit E										EIF3E/RSPO2(6)	NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30			OV - Ovarian serous cystadenocarcinoma(57;6.84e-10)			TTAATGCTGATACACTGGTGG	0.363																																					p.I351V	GBM(15;360 410 8460 34179 52246)	Atlas-SNP	.											.	EIF3E	73	.	0			c.A1051G						.						75.0	72.0	73.0					8																	109226846		2203	4300	6503	SO:0001583	missense	3646	exon10			TGCTGATACACTG	U94175	CCDS6308.1	8q22-q23	2010-03-10	2007-07-27	2007-07-27	ENSG00000104408	ENSG00000104408			3277	protein-coding gene	gene with protein product		602210	"""eukaryotic translation initiation factor 3, subunit 6 48kDa"""	INT6, EIF3S6		9403073, 9295280	Standard	NM_001568		Approved	eIF3-p48, eIF3e	uc003ymu.3	P60228	OTTHUMG00000164858	ENST00000220849.5:c.1051A>G	chr8.hg19:g.109226846T>C	ENSP00000220849:p.Ile351Val	250.0	0.0		244.0	13.0	NM_001568		Missense_Mutation	SNP	ENST00000220849.5	hg19	CCDS6308.1	.	.	.	.	.	.	.	.	.	.	T	23.4	4.417337	0.83449	.	.	ENSG00000104408	ENST00000220849;ENST00000519030;ENST00000519627	T;T;T	0.54675	1.05;1.05;0.56	5.52	5.52	0.82312	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.000000	0.85682	D	0.000000	T	0.70945	0.3282	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.72795	-0.4185	10	0.54805	T	0.06	-16.4334	15.9416	0.79758	0.0:0.0:0.0:1.0	.	351	P60228	EIF3E_HUMAN	V	351;258;224	ENSP00000220849:I351V;ENSP00000428796:I258V;ENSP00000430839:I224V	ENSP00000220849:I351V	I	-	1	0	EIF3E	109296022	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.993000	0.88291	2.225000	0.72522	0.533000	0.62120	ATC	.	.		0.363	EIF3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380612.2	NM_001568	
COL14A1	7373	hgsc.bcm.edu	37	8	121296007	121296007	+	Silent	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:121296007T>A	ENST00000297848.3	+	32	4227	c.3957T>A	c.(3955-3957)gtT>gtA	p.V1319V	COL14A1_ENST00000247781.3_Silent_p.V1224V|COL14A1_ENST00000309791.4_Silent_p.V1319V	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TGGTTGGGGTTATTTTAGACA	0.358																																					p.V1319V		Atlas-SNP	.											.	COL14A1	292	.	0			c.T3957A						.						65.0	64.0	64.0					8																	121296007		2203	4300	6503	SO:0001819	synonymous_variant	7373	exon32			TGGGGTTATTTTA		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.3957T>A	chr8.hg19:g.121296007T>A		91.0	0.0		101.0	45.0	NM_021110		Silent	SNP	ENST00000297848.3	hg19	CCDS34938.1																																																																																			.	.		0.358	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
MTBP	27085	hgsc.bcm.edu	37	8	121468896	121468896	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:121468896A>T	ENST00000305949.1	+	7	778	c.733A>T	c.(733-735)Ata>Tta	p.I245L		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	245					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			GAAAATACAGATATGGGAAAG	0.308																																					p.I245L		Atlas-SNP	.											.	MTBP	77	.	0			c.A733T						.						99.0	114.0	109.0					8																	121468896		2203	4291	6494	SO:0001583	missense	27085	exon7			ATACAGATATGGG		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.733A>T	chr8.hg19:g.121468896A>T	ENSP00000303398:p.Ile245Leu	54.0	0.0		56.0	17.0	NM_022045	B4DUR5|Q9HA89	Missense_Mutation	SNP	ENST00000305949.1	hg19	CCDS6333.1	.	.	.	.	.	.	.	.	.	.	A	17.28	3.349396	0.61183	.	.	ENSG00000172167	ENST00000305949	.	.	.	5.56	5.56	0.83823	.	0.118223	0.53938	D	0.000049	T	0.52629	0.1746	M	0.68952	2.095	0.50467	D	0.999872	P	0.40211	0.707	B	0.28916	0.096	T	0.59166	-0.7505	9	0.46703	T	0.11	-13.7942	15.7142	0.77655	1.0:0.0:0.0:0.0	.	245	Q96DY7	MTBP_HUMAN	L	245	.	ENSP00000303398:I245L	I	+	1	0	MTBP	121538077	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	7.143000	0.77348	2.120000	0.65058	0.372000	0.22366	ATA	.	.		0.308	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
ANXA13	312	hgsc.bcm.edu	37	8	124696885	124696886	+	Nonsense_Mutation	DNP	CC	CC	AA			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:124696885_124696886CC>AA	ENST00000419625.1	-	10	867_868	c.795_796GG>TT	c.(793-798)gaGGag>gaTTag	p.265_266EE>D*	ANXA13_ENST00000262219.6_Nonsense_Mutation_p.306_307EE>D*	NM_004306.2	NP_004297.2	P27216	ANX13_HUMAN	annexin A13	265					cell differentiation (GO:0030154)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|exocytic vesicle (GO:0070382)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phosphatidylglycerol binding (GO:1901611)|phosphatidylserine binding (GO:0001786)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	25	Lung NSC(37;2.06e-11)|Ovarian(258;0.00579)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00288)			ATCAACGTCTCCTCATCGGTCC	0.52																																					p.E307X|p.E306D		Atlas-SNP	.											.	ANXA13	38	.	0			c.G919T|c.G918T						.																																			SO:0001587	stop_gained	312	exon11			ACGTCTCCTCATC|CGTCTCCTCATCG	Z11502	CCDS34939.1, CCDS47917.1	8q24.13	2005-11-09			ENSG00000104537	ENSG00000104537		"""Annexins"""	536	protein-coding gene	gene with protein product		602573		ANX13		9503022	Standard	NM_004306		Approved		uc003yqt.3	P27216	OTTHUMG00000164987	ENST00000419625.1:c.795_796delinsAA	chr8.hg19:g.124696885_124696886delinsAA	ENSP00000390809:p.E265_E266delinsD*	116.0	0.0		124.0|126.0	41.0	NM_001003954	Q9BQR5	Nonsense_Mutation|Missense_Mutation	SNP	ENST00000419625.1	hg19	CCDS47917.1																																																																																			.	.		0.520	ANXA13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381308.1	NM_004306	
LYNX1	66004	hgsc.bcm.edu	37	8	143857324	143857324	+	Splice_Site	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr8:143857324C>T	ENST00000335822.5	-	2	679	c.52G>A	c.(52-54)Gcc>Acc	p.A18T	LYNX1_ENST00000345173.6_Splice_Site_p.A18T|LYNX1_ENST00000523332.1_Splice_Site_p.A18T|LYNX1_ENST00000522906.1_Intron|LYNX1_ENST00000398906.1_Splice_Site_p.A18T|LYNX1_ENST00000395192.2_Splice_Site_p.A18T	NM_023946.2	NP_076435.1	Q9BZG9	LYNX1_HUMAN	Ly6/neurotoxin 1	18						anchored component of membrane (GO:0031225)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|lung(2)|skin(1)	4	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCCATCTTACCCAGAGGTAAG	0.602																																					p.A18T		Atlas-SNP	.											.	LYNX1	40	.	0			c.G52A						.						93.0	72.0	80.0					8																	143857324		2203	4300	6503	SO:0001630	splice_region_variant	66004	exon2			TCTTACCCAGAGG	AF321824	CCDS6389.1, CCDS34951.1, CCDS34952.1	8q24.3	2008-03-12			ENSG00000180155	ENSG00000180155			29604	protein-coding gene	gene with protein product		606110				12573258, 10402197	Standard	NM_023946		Approved	SLURP2	uc003yxd.1	Q9BZG9	OTTHUMG00000164694	ENST00000335822.5:c.52+1G>A	chr8.hg19:g.143857324C>T		45.0	0.0		67.0	22.0	NM_177477	D3DWI7|G3XAC2|Q86SR0	Missense_Mutation	SNP	ENST00000335822.5	hg19	CCDS34951.1	.	.	.	.	.	.	.	.	.	.	c	16.93	3.258937	0.59321	.	.	ENSG00000180155	ENST00000523332;ENST00000335822;ENST00000395192;ENST00000398906;ENST00000345173;ENST00000522929;ENST00000520131	T;T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63;1.63	3.34	3.34	0.38264	.	0.211384	0.26387	N	0.024675	T	0.32194	0.0821	M	0.70595	2.14	0.24881	N	0.992224	B;B	0.22683	0.043;0.073	B;B	0.27887	0.02;0.084	T	0.16837	-1.0389	9	.	.	.	-18.4559	10.3623	0.44001	0.0:1.0:0.0:0.0	.	18;18	Q9BZG9;G3XAC2	LYNX1_HUMAN;.	T	18	ENSP00000428713:A18T;ENSP00000337950:A18T;ENSP00000378618:A18T;ENSP00000381878:A18T;ENSP00000332495:A18T;ENSP00000429261:A18T;ENSP00000428157:A18T	.	A	-	1	0	LYNX1	143854326	0.998000	0.40836	1.000000	0.80357	0.996000	0.88848	3.350000	0.52224	1.865000	0.54081	0.650000	0.86243	GCC	.	.		0.602	LYNX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379786.3	NM_177476	Missense_Mutation
ACO1	48	hgsc.bcm.edu	37	9	32424547	32424547	+	Splice_Site	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:32424547G>A	ENST00000309951.6	+	10	1210	c.1072G>A	c.(1072-1074)Gtt>Att	p.V358I	ACO1_ENST00000379923.1_Splice_Site_p.V358I|ACO1_ENST00000541043.1_Splice_Site_p.V259I	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	358					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		GGGTCAACAGGTTGTGGAATT	0.383																																					p.V358I		Atlas-SNP	.											.	ACO1	149	.	0			c.G1072A						.						107.0	116.0	113.0					9																	32424547		2203	4300	6503	SO:0001630	splice_region_variant	48	exon10			CAACAGGTTGTGG	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1072-1G>A	chr9.hg19:g.32424547G>A		115.0	0.0		95.0	6.0	NM_002197	D3DRK7|Q14652|Q5VZA7	Missense_Mutation	SNP	ENST00000309951.6	hg19	CCDS6525.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.917520	0.33815	.	.	ENSG00000122729	ENST00000432017;ENST00000309951;ENST00000379923;ENST00000379921;ENST00000541043	T;T;T	0.19250	2.16;2.16;2.16	5.86	2.0	0.26442	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (2);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 2 (1);	0.270323	0.41500	N	0.000863	T	0.18509	0.0444	L	0.55103	1.725	0.80722	D	1	B;B	0.06786	0.001;0.0	B;B	0.12837	0.008;0.002	T	0.06023	-1.0850	9	.	.	.	-9.0754	9.9743	0.41774	0.3496:0.0:0.6504:0.0	.	394;358	Q59FI0;P21399	.;ACOC_HUMAN	I	394;358;358;358;259	ENSP00000309477:V358I;ENSP00000369255:V358I;ENSP00000438733:V259I	.	V	+	1	0	ACO1	32414547	1.000000	0.71417	0.998000	0.56505	0.682000	0.39822	3.758000	0.55220	0.501000	0.28013	-0.157000	0.13467	GTT	.	.		0.383	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	Missense_Mutation
GNAQ	2776	hgsc.bcm.edu	37	9	80537112	80537112	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:80537112T>A	ENST00000286548.4	-	2	508	c.286A>T	c.(286-288)Aca>Tca	p.T96S		NM_002072.3	NP_002063.2	P50148	GNAQ_HUMAN	guanine nucleotide binding protein (G protein), q polypeptide	96					action potential (GO:0001508)|activation of phospholipase C activity (GO:0007202)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|developmental pigmentation (GO:0048066)|embryonic digit morphogenesis (GO:0042733)|forebrain neuron development (GO:0021884)|glutamate receptor signaling pathway (GO:0007215)|heart development (GO:0007507)|maternal behavior (GO:0042711)|negative regulation of protein kinase activity (GO:0006469)|neuron remodeling (GO:0016322)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|post-embryonic development (GO:0009791)|protein stabilization (GO:0050821)|regulation of catenin import into nucleus (GO:0035412)|regulation of melanocyte differentiation (GO:0045634)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.T96S(1)		NS(1)|endometrium(3)|eye(229)|kidney(1)|large_intestine(4)|lung(6)|meninges(11)|ovary(1)|prostate(1)|skin(44)|upper_aerodigestive_tract(1)	302						ATCTTGAGTGTGTCCATGGCT	0.473			Mis		uveal melanoma																																p.T96S		Atlas-SNP	.		Dom	yes		9	9q21	2776	"""guanine nucleotide binding protein (G protein), q polypeptide"""		E	GNAQ,NS,carcinoma,0,2	GNAQ	384	.	1	Substitution - Missense(1)	prostate(1)	c.A286T						.																																			SO:0001583	missense	2776	exon2			TGAGTGTGTCCAT		CCDS6658.1	9q21	2010-03-17			ENSG00000156052	ENSG00000156052			4390	protein-coding gene	gene with protein product		600998				8825633	Standard	NM_002072		Approved	G-ALPHA-q, GAQ	uc004akw.3	P50148	OTTHUMG00000020059	ENST00000286548.4:c.286A>T	chr9.hg19:g.80537112T>A	ENSP00000286548:p.Thr96Ser	46.0	1.0		53.0	4.0	NM_002072	O15108|Q13462|Q6NT27|Q92471|Q9BZB9	Missense_Mutation	SNP	ENST00000286548.4	hg19	CCDS6658.1	.	.	.	.	.	.	.	.	.	.	T	13.12	2.141103	0.37825	.	.	ENSG00000156052	ENST00000286548;ENST00000411677	D;D	0.87809	-2.3;-2.3	5.86	5.86	0.93980	G protein alpha subunit, helical insertion (2);	0.000000	0.85682	D	0.000000	D	0.84170	0.5413	L	0.52126	1.63	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.79122	-0.1933	10	0.29301	T	0.29	.	16.2652	0.82574	0.0:0.0:0.0:1.0	.	96	P50148	GNAQ_HUMAN	S	96;67	ENSP00000286548:T96S;ENSP00000391501:T67S	ENSP00000286548:T96S	T	-	1	0	GNAQ	79726932	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.145000	0.64839	2.241000	0.73720	0.528000	0.53228	ACA	.	.		0.473	GNAQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052761.1	NM_002072	
MUSK	4593	hgsc.bcm.edu	37	9	113550073	113550073	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:113550073G>A	ENST00000374448.4	+	14	2016	c.1882G>A	c.(1882-1884)Gcc>Acc	p.A628T	MUSK_ENST00000374438.1_Missense_Mutation_p.A144T|MUSK_ENST00000416899.2_Missense_Mutation_p.A620T|MUSK_ENST00000189978.5_Missense_Mutation_p.A628T	NM_001166281.1|NM_005592.3	NP_001159753.1|NP_005583.1	O15146	MUSK_HUMAN	muscle, skeletal, receptor tyrosine kinase	628	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|memory (GO:0007613)|multicellular organismal development (GO:0007275)|neuromuscular junction development (GO:0007528)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein geranylgeranylation (GO:2000541)|positive regulation of protein phosphorylation (GO:0001934)|protein autophosphorylation (GO:0046777)|regulation of synaptic growth at neuromuscular junction (GO:0008582)|regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|lung(23)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)	49						GAGGGAGGCAGCCCTCATGGC	0.438																																					p.A628T		Atlas-SNP	.											.	MUSK	112	.	0			c.G1882A						.						56.0	53.0	54.0					9																	113550073		1882	4115	5997	SO:0001583	missense	4593	exon13			GAGGCAGCCCTCA	AF006464	CCDS48005.1, CCDS75874.1	9q31.3-q32	2013-01-29			ENSG00000030304	ENSG00000030304		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7525	protein-coding gene	gene with protein product		601296				7546737	Standard	NM_005592		Approved		uc022blv.1	O15146	OTTHUMG00000020485	ENST00000374448.4:c.1882G>A	chr9.hg19:g.113550073G>A	ENSP00000363571:p.Ala628Thr	90.0	0.0		80.0	26.0	NM_005592	Q32MJ8|Q32MJ9|Q5VZW7|Q5VZW8	Missense_Mutation	SNP	ENST00000374448.4	hg19	CCDS48005.1	.	.	.	.	.	.	.	.	.	.	G	32	5.140558	0.94560	.	.	ENSG00000030304	ENST00000189978;ENST00000374448;ENST00000543335;ENST00000374447;ENST00000545907;ENST00000374441;ENST00000416899;ENST00000374438	D;D	0.82893	-1.66;-1.66	5.93	5.93	0.95920	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83797	0.5332	N	0.16037	0.36	0.80722	D	1	D	0.63046	0.992	D	0.70016	0.967	D	0.83678	0.0170	10	0.36615	T	0.2	.	17.4968	0.87719	0.0:0.0:1.0:0.0	.	628	O15146	MUSK_HUMAN	T	634;628;628;542;542;144;626;144	ENSP00000363571:A628T;ENSP00000363561:A144T	ENSP00000189978:A634T	A	+	1	0	MUSK	112589894	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	9.476000	0.97823	2.814000	0.96858	0.655000	0.94253	GCC	.	.		0.438	MUSK-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
RGS3	5998	hgsc.bcm.edu	37	9	116247941	116247941	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:116247941G>T	ENST00000374140.2	+	8	866	c.657G>T	c.(655-657)ttG>ttT	p.L219F	RGS3_ENST00000350696.5_Missense_Mutation_p.L219F|RGS3_ENST00000317613.6_Missense_Mutation_p.L107F	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	219	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						AGCGTCTCTTGGTTACTGTGT	0.577																																					p.L219F		Atlas-SNP	.											.	RGS3	251	.	0			c.G657T						.						92.0	78.0	82.0					9																	116247941		2201	4299	6500	SO:0001583	missense	5998	exon8			TCTCTTGGTTACT	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.657G>T	chr9.hg19:g.116247941G>T	ENSP00000363255:p.Leu219Phe	89.0	0.0		81.0	30.0	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	hg19	CCDS43869.1	.	.	.	.	.	.	.	.	.	.	G	17.69	3.451695	0.63290	.	.	ENSG00000138835	ENST00000374140;ENST00000350696;ENST00000317613	T;T;T	0.69175	-0.38;-0.38;-0.38	4.66	2.75	0.32379	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.282287	0.24067	N	0.041852	T	0.78534	0.4298	M	0.83384	2.64	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.77004	0.989;0.981;0.984	T	0.74777	-0.3550	10	0.28530	T	0.3	.	7.9414	0.29961	0.1948:0.0:0.8052:0.0	.	109;107;219	B3KWG8;P49796-5;P49796	.;.;RGS3_HUMAN	F	219;219;107	ENSP00000363255:L219F;ENSP00000259406:L219F;ENSP00000312844:L107F	ENSP00000312844:L107F	L	+	3	2	RGS3	115287762	1.000000	0.71417	0.555000	0.28281	0.989000	0.77384	1.926000	0.40084	0.642000	0.30620	0.561000	0.74099	TTG	.	.		0.577	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123298694	123298694	+	Silent	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:123298694G>A	ENST00000349780.4	-	7	797	c.618C>T	c.(616-618)caC>caT	p.H206H	CDK5RAP2_ENST00000360822.3_Silent_p.H206H|CDK5RAP2_ENST00000359309.3_Silent_p.H206H|CDK5RAP2_ENST00000360190.4_Silent_p.H206H	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	206					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)			breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGTCCCCCTCGTGCATCTTCT	0.547																																					p.H206H		Atlas-SNP	.											.	CDK5RAP2	157	.	0			c.C618T						.						144.0	124.0	131.0					9																	123298694		2203	4300	6503	SO:0001819	synonymous_variant	55755	exon7			CCCCTCGTGCATC	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.618C>T	chr9.hg19:g.123298694G>A		58.0	0.0		60.0	24.0	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Silent	SNP	ENST00000349780.4	hg19	CCDS6823.1																																																																																			.	.		0.547	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
SLC29A3	55315	hgsc.bcm.edu	37	10	73111483	73111483	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:73111483G>C	ENST00000373189.5	+	4	600	c.548G>C	c.(547-549)aGc>aCc	p.S183T	SLC29A3_ENST00000469204.1_3'UTR	NM_001174098.1|NM_018344.5	NP_001167569.1|NP_060814.4	Q9BZD2	S29A3_HUMAN	solute carrier family 29 (equilibrative nucleoside transporter), member 3	183					transmembrane transport (GO:0055085)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleoside transmembrane transporter activity (GO:0005337)			endometrium(3)|kidney(2)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	15						ACTGTCTTCAGCAGCAGCATC	0.577																																					p.S183T	Esophageal Squamous(200;1319 2142 18949 31248 39672)	Atlas-SNP	.											.	SLC29A3	51	.	0			c.G548C						.						115.0	89.0	97.0					10																	73111483		2203	4300	6503	SO:0001583	missense	55315	exon4			TCTTCAGCAGCAG	AF326987	CCDS7310.1	10q22.2	2013-07-17	2013-07-17		ENSG00000198246	ENSG00000198246		"""Solute carriers"""	23096	protein-coding gene	gene with protein product		612373	"""solute carrier family 29 (nucleoside transporters), member 3"""			11396612	Standard	NM_018344		Approved	ENT3, FLJ11160	uc001jrr.4	Q9BZD2	OTTHUMG00000018424	ENST00000373189.5:c.548G>C	chr10.hg19:g.73111483G>C	ENSP00000362285:p.Ser183Thr	67.0	0.0		59.0	18.0	NM_018344	B2RB50|B4E2Z9|B7ZA37|Q0VAM9|Q5T465|Q7RTT8|Q8IVZ0|Q9BWI2|Q9NUS9	Missense_Mutation	SNP	ENST00000373189.5	hg19	CCDS7310.1	.	.	.	.	.	.	.	.	.	.	G	11.70	1.717128	0.30413	.	.	ENSG00000198246	ENST00000373189	T	0.63096	-0.02	5.83	-8.01	0.01122	.	0.608811	0.19482	N	0.113198	T	0.41419	0.1158	N	0.25890	0.77	0.32100	N	0.590761	B	0.14805	0.011	B	0.19666	0.026	T	0.04029	-1.0983	9	0.41790	T	0.15	-7.3834	12.8029	0.57596	0.6701:0.0835:0.2464:0.0	.	183	Q9BZD2	S29A3_HUMAN	T	183	ENSP00000362285:S183T	ENSP00000362285:S183T	S	+	2	0	SLC29A3	72781489	0.000000	0.05858	0.274000	0.24659	0.728000	0.41692	-0.879000	0.04188	-1.468000	0.01892	-0.266000	0.10368	AGC	.	.		0.577	SLC29A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048544.1	NM_018344	
DNAJB12	54788	hgsc.bcm.edu	37	10	74114738	74114738	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:74114738C>T	ENST00000338820.3	-	1	169	c.20G>A	c.(19-21)cGg>cAg	p.R7Q	DNAJB12_ENST00000461919.1_5'Flank|DNAJB12_ENST00000444643.2_5'UTR|DNAJB12_ENST00000394903.2_Missense_Mutation_p.R7Q	NM_001002762.2	NP_001002762.2	Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	0						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						CGCGGGCAGCCGGGCGCGGAG	0.657																																					p.R7Q		Atlas-SNP	.											.	DNAJB12	22	.	0			c.G20A						.						12.0	17.0	15.0					10																	74114738		687	1576	2263	SO:0001583	missense	54788	exon1			GGCAGCCGGGCGC	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"""Heat shock proteins / DNAJ (HSP40)"""	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000338820.3:c.20G>A	chr10.hg19:g.74114738C>T	ENSP00000345575:p.Arg7Gln	44.0	0.0		55.0	33.0	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000338820.3	hg19	CCDS7316.2	.	.	.	.	.	.	.	.	.	.	C	20.8	4.045610	0.75846	.	.	ENSG00000148719	ENST00000338820;ENST00000394903	T;T	0.63580	-0.05;-0.05	5.68	5.68	0.88126	.	.	.	.	.	T	0.73651	0.3614	.	.	.	0.26250	N	0.978734	.	.	.	.	.	.	T	0.68603	-0.5365	6	0.87932	D	0	.	18.5439	0.91039	0.0:1.0:0.0:0.0	.	.	.	.	Q	7	ENSP00000345575:R7Q;ENSP00000378363:R7Q	ENSP00000345575:R7Q	R	-	2	0	DNAJB12	73784744	0.792000	0.28813	0.946000	0.38457	0.097000	0.18754	1.525000	0.35953	2.669000	0.90835	0.561000	0.74099	CGG	.	.		0.657	DNAJB12-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
PPP3CB	5532	hgsc.bcm.edu	37	10	75238300	75238300	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:75238300A>G	ENST00000360663.5	-	3	479	c.368T>C	c.(367-369)cTt>cCt	p.L123P	PPP3CB_ENST00000342558.3_Missense_Mutation_p.L123P|PPP3CB_ENST00000394822.2_Missense_Mutation_p.L123P|PPP3CB_ENST00000394829.2_Missense_Mutation_p.L123P|PPP3CB_ENST00000545874.1_Missense_Mutation_p.L37P|PPP3CB_ENST00000394828.2_Missense_Mutation_p.L123P			P16298	PP2BB_HUMAN	protein phosphatase 3, catalytic subunit, beta isozyme	123	Catalytic.				axon extension (GO:0048675)|calcium ion-dependent exocytosis (GO:0017156)|cellular response to drug (GO:0035690)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|innate immune response (GO:0045087)|learning (GO:0007612)|locomotion involved in locomotory behavior (GO:0031987)|memory (GO:0007613)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of transcription, DNA-templated (GO:0045893)|protein dephosphorylation (GO:0006470)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|regulation of synaptic plasticity (GO:0048167)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)|social behavior (GO:0035176)|T cell activation (GO:0042110)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|T cell proliferation (GO:0042098)	calcineurin complex (GO:0005955)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein phosphatase 2B binding (GO:0030346)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(7)|skin(1)|urinary_tract(1)	22	Prostate(51;0.0119)					GCCAAGAAAAAGGTATCGTGT	0.348																																					p.L123P		Atlas-SNP	.											.	PPP3CB	68	.	0			c.T368C						.						112.0	108.0	109.0					10																	75238300		2203	4300	6503	SO:0001583	missense	5532	exon3			AGAAAAAGGTATC	M29551	CCDS7328.1, CCDS44436.1, CCDS44437.1	10q22.2	2010-03-17	2010-03-05		ENSG00000107758	ENSG00000107758	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9315	protein-coding gene	gene with protein product	"""calcineurin A beta"", ""protein phosphatase 2B, catalytic subunit, beta isoform"""	114106	"""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform (calcineurin A beta)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, beta isoform"""	CALNB		1659808, 2558868	Standard	XM_005269944		Approved	CALNA2, CNA2, PP2Bbeta	uc001juf.3	P16298	OTTHUMG00000018472	ENST00000360663.5:c.368T>C	chr10.hg19:g.75238300A>G	ENSP00000353881:p.Leu123Pro	60.0	0.0		82.0	4.0	NM_001142354	P16299|Q5F2F9|Q8N1F0|Q8N3W4	Missense_Mutation	SNP	ENST00000360663.5	hg19	CCDS7328.1	.	.	.	.	.	.	.	.	.	.	A	26.6	4.754681	0.89843	.	.	ENSG00000107758	ENST00000360663;ENST00000394829;ENST00000394828;ENST00000342558;ENST00000545874;ENST00000394822	D;D;D;D;D;D	0.88201	-2.35;-2.35;-2.35;-2.35;-2.35;-2.35	5.83	5.83	0.93111	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (2);Metallophosphoesterase domain (1);	0.092215	0.47093	D	0.000260	D	0.97648	0.9229	H	0.99967	5.1	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;0.999;0.999;1.0;1.0	D	0.99640	1.0988	10	0.87932	D	0	.	16.1946	0.82018	1.0:0.0:0.0:0.0	.	123;37;123;123;123	P16298-2;F5H0F8;P16298-3;Q8N1F0;P16298	.;.;.;.;PP2BB_HUMAN	P	123;123;123;123;37;123	ENSP00000353881:L123P;ENSP00000378306:L123P;ENSP00000378305:L123P;ENSP00000343147:L123P;ENSP00000439876:L37P;ENSP00000378299:L123P	ENSP00000343147:L123P	L	-	2	0	PPP3CB	74908306	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.329000	0.96413	2.228000	0.72767	0.528000	0.53228	CTT	.	.		0.348	PPP3CB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048669.1	NM_021132	
CH25H	9023	hgsc.bcm.edu	37	10	90966684	90966684	+	Silent	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:90966684G>T	ENST00000371852.2	-	1	387	c.366C>A	c.(364-366)ctC>ctA	p.L122L		NM_003956.3	NP_003947.1	O95992	CH25H_HUMAN	cholesterol 25-hydroxylase	122					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|fatty acid biosynthetic process (GO:0006633)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cholesterol 25-hydroxylase activity (GO:0001567)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)			kidney(1)|large_intestine(2)|lung(3)|stomach(1)	7		Colorectal(252;0.0161)		GBM - Glioblastoma multiforme(2;0.000133)		GCAGCAGCAGGAGCAGCTCGG	0.627																																					p.L122L		Atlas-SNP	.											.	CH25H	19	.	0			c.C366A						.						45.0	48.0	47.0					10																	90966684		2203	4300	6503	SO:0001819	synonymous_variant	9023	exon1			CAGCAGGAGCAGC	AF059212	CCDS7400.1	10q23	2013-03-04			ENSG00000138135	ENSG00000138135	1.14.99.38	"""Fatty acid hydroxylase domain containing"""	1907	protein-coding gene	gene with protein product		604551				9852097	Standard	NM_003956		Approved		uc001kfz.3	O95992	OTTHUMG00000018705	ENST00000371852.2:c.366C>A	chr10.hg19:g.90966684G>T		109.0	0.0		123.0	36.0	NM_003956	B2RBY3	Silent	SNP	ENST00000371852.2	hg19	CCDS7400.1																																																																																			.	.		0.627	CH25H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049291.1	NM_003956	
DNMBP	23268	hgsc.bcm.edu	37	10	101715378	101715378	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:101715378G>A	ENST00000324109.4	-	4	1944	c.1853C>T	c.(1852-1854)cCg>cTg	p.P618L	DNMBP-AS1_ENST00000434409.1_RNA|DNMBP_ENST00000342239.3_Missense_Mutation_p.P618L	NM_015221.2	NP_056036.1	Q6XZF7	DNMBP_HUMAN	dynamin binding protein	618	Pro-rich.				intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(4)|endometrium(9)|large_intestine(14)|lung(19)|ovary(5)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	61		Colorectal(252;0.234)		Epithelial(162;2.94e-10)|all cancers(201;3.15e-08)		AGTGGATACCGGAGTACAGGG	0.582																																					p.P618L		Atlas-SNP	.											.	DNMBP	173	.	0			c.C1853T						.						56.0	52.0	53.0					10																	101715378		2203	4300	6503	SO:0001583	missense	23268	exon4			GATACCGGAGTAC	AL833283	CCDS7485.1	10q24.31	2012-07-24			ENSG00000107554	ENSG00000107554		"""Rho guanine nucleotide exchange factors"""	30373	protein-coding gene	gene with protein product	"""scaffold protein TUBA"""	611282				10231032, 14506234	Standard	NM_015221		Approved	KIAA1010, Tuba, ARHGEF36	uc001kqj.2	Q6XZF7	OTTHUMG00000018897	ENST00000324109.4:c.1853C>T	chr10.hg19:g.101715378G>A	ENSP00000315659:p.Pro618Leu	65.0	0.0		73.0	5.0	NM_015221	Q8IVY3|Q9Y2L3	Missense_Mutation	SNP	ENST00000324109.4	hg19	CCDS7485.1	.	.	.	.	.	.	.	.	.	.	G	5.836	0.338469	0.11069	.	.	ENSG00000107554	ENST00000342239;ENST00000324109	T;T	0.12672	2.72;2.66	5.9	4.99	0.66335	.	0.295265	0.24497	N	0.038016	T	0.12008	0.0292	L	0.41356	1.27	0.33465	D	0.585458	B	0.17465	0.022	B	0.12156	0.007	T	0.12319	-1.0552	10	0.22706	T	0.39	-1.0546	11.6108	0.51057	0.1532:0.0:0.8468:0.0	.	618	Q6XZF7	DNMBP_HUMAN	L	618	ENSP00000344914:P618L;ENSP00000315659:P618L	ENSP00000315659:P618L	P	-	2	0	DNMBP	101705368	1.000000	0.71417	0.003000	0.11579	0.038000	0.13279	5.907000	0.69908	1.483000	0.48342	0.561000	0.74099	CCG	.	.		0.582	DNMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049832.2	NM_015221	
SFXN2	118980	hgsc.bcm.edu	37	10	104489078	104489078	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:104489078A>G	ENST00000369893.5	+	5	601	c.434A>G	c.(433-435)cAg>cGg	p.Q145R		NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	145				QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 4). {ECO:0000305}.	iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		TCCCCCAGGCAGATGGCCCTT	0.627											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q145R		Atlas-SNP	.											.	SFXN2	40	.	0			c.A434G						.						47.0	40.0	42.0					10																	104489078		2203	4300	6503	SO:0001583	missense	118980	exon5			CCAGGCAGATGGC	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.434A>G	chr10.hg19:g.104489078A>G	ENSP00000358909:p.Gln145Arg	45.0	0.0	1382	74.0	31.0	NM_178858	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	hg19	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447746	0.84101	.	.	ENSG00000156398	ENST00000369893	T	0.32988	1.43	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.52741	0.1753	M	0.65498	2.005	0.80722	D	1	D	0.67145	0.996	D	0.74023	0.982	T	0.50558	-0.8814	10	0.40728	T	0.16	-20.7158	14.5699	0.68203	1.0:0.0:0.0:0.0	.	145	Q96NB2	SFXN2_HUMAN	R	145	ENSP00000358909:Q145R	ENSP00000358909:Q145R	Q	+	2	0	SFXN2	104479068	1.000000	0.71417	1.000000	0.80357	0.816000	0.46133	8.363000	0.90103	2.179000	0.69175	0.482000	0.46254	CAG	.	.		0.627	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
ATRNL1	26033	hgsc.bcm.edu	37	10	117061424	117061424	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:117061424T>C	ENST00000355044.3	+	17	2815	c.2689T>C	c.(2689-2691)Tcc>Ccc	p.S897P	ATRNL1_ENST00000423111.2_5'UTR|ATRNL1_ENST00000303745.7_5'Flank	NM_207303.2	NP_997186.1	Q5VV63	ATRN1_HUMAN	attractin-like 1	897	PSI 4.				G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(11)|liver(2)|lung(44)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_lung(145;0.0686)|Breast(234;0.0969)|Lung NSC(174;0.17)|Colorectal(252;0.234)		Epithelial(162;0.00031)|all cancers(201;0.000753)|LUSC - Lung squamous cell carcinoma(1;0.0515)|Lung(30;0.0827)		GACATCATGTTCCAACTGTAC	0.383																																					p.S897P		Atlas-SNP	.											.	ATRNL1	219	.	0			c.T2689C						.						240.0	171.0	194.0					10																	117061424		2203	4300	6503	SO:0001583	missense	26033	exon17			TCATGTTCCAACT	AB011106	CCDS7592.1, CCDS73204.1	10q26	2004-03-04			ENSG00000107518	ENSG00000107518			29063	protein-coding gene	gene with protein product		612869				9628581	Standard	NM_001276282		Approved	KIAA0534, FLJ45344, ALP	uc001lcg.3	Q5VV63	OTTHUMG00000019096	ENST00000355044.3:c.2689T>C	chr10.hg19:g.117061424T>C	ENSP00000347152:p.Ser897Pro	85.0	0.0		95.0	40.0	NM_207303	O60283|Q5JSE8|Q5T5Y9|Q6T256|Q6ZSN4|Q86WX2	Missense_Mutation	SNP	ENST00000355044.3	hg19	CCDS7592.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.41|15.41	2.825704|2.825704	0.50739|0.50739	.|.	.|.	ENSG00000107518|ENSG00000107518	ENST00000526373|ENST00000355044	.|T	.|0.20738	.|2.05	5.31|5.31	0.218|0.218	0.15270|0.15270	.|.	.|0.560072	.|0.20925	.|N	.|0.083203	T|T	0.17066|0.17066	0.0410|0.0410	L|L	0.38175|0.38175	1.15|1.15	0.80722|0.80722	D|D	1|1	.|P	.|0.42584	.|0.784	.|P	.|0.45753	.|0.492	T|T	0.06463|0.06463	-1.0825|-1.0825	5|10	.|0.30854	.|T	.|0.27	-0.3001|-0.3001	6.3877|6.3877	0.21569|0.21569	0.0:0.1208:0.2636:0.6155|0.0:0.1208:0.2636:0.6155	.|.	.|897	.|Q5VV63	.|ATRN1_HUMAN	S|P	26|897	.|ENSP00000347152:S897P	.|ENSP00000347152:S897P	F|S	+|+	2|1	0|0	ATRNL1|ATRNL1	117051414|117051414	0.981000|0.981000	0.34729|0.34729	0.518000|0.518000	0.27811|0.27811	0.946000|0.946000	0.59487|0.59487	1.500000|1.500000	0.35682|0.35682	-0.203000|-0.203000	0.10251|0.10251	-0.435000|-0.435000	0.05868|0.05868	TTC|TCC	.	.		0.383	ATRNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050507.3	XM_049349	
OR52R1	119695	hgsc.bcm.edu	37	11	4824778	4824778	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:4824778A>T	ENST00000356069.2	-	1	832	c.833T>A	c.(832-834)cTg>cAg	p.L278Q	OR52R1_ENST00000380382.1_Missense_Mutation_p.L357Q|MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		ATTAGCAAACAGGATGTGTAC	0.463																																					p.L278Q		Atlas-SNP	.											.	OR52R1	81	.	0			c.T833A						.						142.0	143.0	142.0					11																	4824778		2201	4298	6499	SO:0001583	missense	119695	exon1			GCAAACAGGATGT	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.833T>A	chr11.hg19:g.4824778A>T	ENSP00000348368:p.Leu278Gln	165.0	0.0		145.0	51.0	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	hg19	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	A	12.79	2.042329	0.35989	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00188	8.59;8.59	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.259956	0.28057	N	0.016768	T	0.00666	0.0022	H	0.96430	3.82	0.09310	N	0.999999	P	0.50066	0.931	P	0.52554	0.702	T	0.17289	-1.0374	10	0.87932	D	0	.	14.7065	0.69194	1.0:0.0:0.0:0.0	.	278	Q8NGF1	O52R1_HUMAN	Q	278;357	ENSP00000348368:L278Q;ENSP00000369742:L357Q	ENSP00000348368:L278Q	L	-	2	0	OR52R1	4781354	0.024000	0.19004	0.111000	0.21465	0.027000	0.11550	3.058000	0.49939	2.340000	0.79590	0.528000	0.53228	CTG	.	.		0.463	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
OR52N4	390072	hgsc.bcm.edu	37	11	5776539	5776540	+	Missense_Mutation	DNP	CC	CC	AT			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:5776539_5776540CC>AT	ENST00000317254.3	+	1	617_618	c.569_570CC>AT	c.(568-570)tCC>tAT	p.S190Y	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	190						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		GCCAAATTGTCCTGTGGTAATG	0.46																																					p.S190Y|p.S190S		Atlas-SNP	.											.	OR52N4	55	.	0			c.C569A|c.C570T						.																																			SO:0001583	missense	390072	exon1			AATTGTCCTGTGG|ATTGTCCTGTGGT	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"""GPCR / Class A : Olfactory receptors"""	15230	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily N, member 4"""				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	Exception_encountered	chr11.hg19:g.5776539_5776540delinsAT	ENSP00000323224:p.Ser190Tyr	69.0	0.0		74.0|73.0	5.0	NM_001005175	B2RNP8|Q6IF77	Missense_Mutation|Silent	SNP	ENST00000317254.3	hg19	CCDS44528.1																																																																																			.	.		0.460	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175	
PAMR1	25891	hgsc.bcm.edu	37	11	35454063	35454063	+	Silent	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:35454063G>T	ENST00000378880.2	-	11	2449	c.2004C>A	c.(2002-2004)atC>atA	p.I668I	PAMR1_ENST00000532848.1_Silent_p.I628I|PAMR1_ENST00000378878.3_Silent_p.I557I|PAMR1_ENST00000278360.3_Silent_p.I685I	NM_001001991.1	NP_001001991.1	Q6UXH9	PAMR1_HUMAN	peptidase domain containing associated with muscle regeneration 1	668	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	26						ACACAGCCGCGATGCCTCCTG	0.567																																					p.I685I		Atlas-SNP	.											PAMR1,NS,carcinoma,0,1	PAMR1	85	.	0			c.C2055A						.						81.0	74.0	76.0					11																	35454063		2202	4298	6500	SO:0001819	synonymous_variant	25891	exon12			AGCCGCGATGCCT		CCDS7898.1, CCDS31460.1, CCDS60759.1, CCDS60760.1	11p13	2009-09-30			ENSG00000149090	ENSG00000149090			24554	protein-coding gene	gene with protein product	"""regeneration-associated muscle protease"""					15111323	Standard	NM_001282675		Approved	RAMP, DKFZP586H2123	uc001mwf.3	Q6UXH9	OTTHUMG00000166328	ENST00000378880.2:c.2004C>A	chr11.hg19:g.35454063G>T		70.0	0.0		70.0	3.0	NM_015430	A8MQ58|B7ZA73|Q5EBL7|Q5JPI4|Q6N062|Q71RE9|Q96JW2|Q9Y432	Silent	SNP	ENST00000378880.2	hg19	CCDS31460.1																																																																																			.	.		0.567	PAMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389177.1	NM_015430	
CKAP5	9793	hgsc.bcm.edu	37	11	46771955	46771955	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:46771955T>C	ENST00000529230.1	-	42	5619	c.5573A>G	c.(5572-5574)aAg>aGg	p.K1858R	MIR5582_ENST00000579697.1_RNA|CKAP5_ENST00000354558.3_Missense_Mutation_p.K1798R|CKAP5_ENST00000312055.5_Missense_Mutation_p.K1798R|CKAP5_ENST00000415402.1_Missense_Mutation_p.K1865R			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1858					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						TGAGTATTTCTTCTTATATTC	0.433																																					p.K1858R	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.A5573G						.						106.0	103.0	104.0					11																	46771955		2201	4299	6500	SO:0001583	missense	9793	exon42			TATTTCTTCTTAT		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.5573A>G	chr11.hg19:g.46771955T>C	ENSP00000432768:p.Lys1858Arg	106.0	0.0		92.0	6.0	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	hg19	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	T	16.18	3.049826	0.55218	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.64803	-0.12;-0.12;0.77;0.77	5.58	5.58	0.84498	Armadillo-like helical (1);Armadillo-type fold (1);	0.140992	0.64402	D	0.000004	T	0.52092	0.1713	L	0.40543	1.245	0.49051	D	0.999744	P;B;B	0.42248	0.774;0.386;0.267	B;B;B	0.36608	0.229;0.085;0.039	T	0.51601	-0.8685	10	0.26408	T	0.33	-12.3852	15.8087	0.78538	0.0:0.0:0.0:1.0	.	1865;1798;1858	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	R	1858;1865;1798;1798	ENSP00000432768:K1858R;ENSP00000395302:K1865R;ENSP00000310227:K1798R;ENSP00000346566:K1798R	ENSP00000310227:K1798R	K	-	2	0	CKAP5	46728531	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.759000	0.62227	2.140000	0.66376	0.449000	0.29647	AAG	.	.		0.433	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
OR6Q1	219952	hgsc.bcm.edu	37	11	57798664	57798664	+	Silent	SNP	G	G	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:57798664G>C	ENST00000302622.3	+	1	263	c.240G>C	c.(238-240)gtG>gtC	p.V80V	OR9Q1_ENST00000335397.3_Intron	NM_001005186.2	NP_001005186.2	Q8NGQ2	OR6Q1_HUMAN	olfactory receptor, family 6, subfamily Q, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			biliary_tract(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(21;0.0707)|all_epithelial(135;0.142)				CTGTTACAGTGCCCAAGATGC	0.473																																					p.V80V		Atlas-SNP	.											.	OR6Q1	58	.	0			c.G240C						.						174.0	166.0	168.0					11																	57798664		2201	4296	6497	SO:0001819	synonymous_variant	219952	exon1			TACAGTGCCCAAG	AB065737	CCDS31541.1	11q12.1	2012-08-09			ENSG00000172381	ENSG00000172381		"""GPCR / Class A : Olfactory receptors"""	15302	protein-coding gene	gene with protein product							Standard	NM_001005186		Approved		uc010rjz.2	Q8NGQ2	OTTHUMG00000168831	ENST00000302622.3:c.240G>C	chr11.hg19:g.57798664G>C		172.0	0.0		181.0	18.0	NM_001005186	B9EKW1|Q6IFH1|Q96R34	Silent	SNP	ENST00000302622.3	hg19	CCDS31541.1																																																																																			.	.		0.473	OR6Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401257.1	NM_001005186	
OR9I1	219954	hgsc.bcm.edu	37	11	57886498	57886498	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:57886498A>G	ENST00000302610.1	-	1	418	c.419T>C	c.(418-420)cTc>cCc	p.L140P	OR9Q1_ENST00000335397.3_Intron	NM_001005211.1	NP_001005211.1	Q8NGQ6	OR9I1_HUMAN	olfactory receptor, family 9, subfamily I, member 1	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|liver(1)|lung(15)|pancreas(1)|skin(1)|urinary_tract(1)	23		Breast(21;0.0589)				GCTCCAGCAGAGCCTGGGATT	0.557																																					p.L140P		Atlas-SNP	.											.	OR9I1	53	.	0			c.T419C						.						42.0	42.0	42.0					11																	57886498		2201	4296	6497	SO:0001583	missense	219954	exon1			CAGCAGAGCCTGG	AB065733	CCDS31542.1	11q12.1	2012-08-09			ENSG00000172377	ENSG00000172377		"""GPCR / Class A : Olfactory receptors"""	14718	protein-coding gene	gene with protein product							Standard	NM_001005211		Approved		uc021qjl.1	Q8NGQ6	OTTHUMG00000167404	ENST00000302610.1:c.419T>C	chr11.hg19:g.57886498A>G	ENSP00000302606:p.Leu140Pro	80.0	0.0		71.0	7.0	NM_001005211	Q6IFH0|Q96RA8	Missense_Mutation	SNP	ENST00000302610.1	hg19	CCDS31542.1	.	.	.	.	.	.	.	.	.	.	A	5.924	0.354601	0.11239	.	.	ENSG00000172377	ENST00000302610	T	0.00241	8.46	5.05	1.08	0.20341	GPCR, rhodopsin-like superfamily (1);	0.837659	0.10227	N	0.700170	T	0.00241	0.0007	M	0.76433	2.335	0.09310	N	0.999997	P	0.38642	0.641	B	0.41764	0.366	T	0.29761	-1.0001	10	0.87932	D	0	-5.7039	2.6704	0.05065	0.4103:0.0:0.2456:0.3441	.	140	Q8NGQ6	OR9I1_HUMAN	P	140	ENSP00000302606:L140P	ENSP00000302606:L140P	L	-	2	0	OR9I1	57643074	0.000000	0.05858	0.485000	0.27403	0.019000	0.09904	0.569000	0.23638	0.372000	0.24591	0.377000	0.23210	CTC	.	.		0.557	OR9I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394539.1	NM_001005211	
ZFP91	80829	hgsc.bcm.edu	37	11	58381796	58381796	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:58381796G>T	ENST00000316059.6	+	9	1253	c.1082G>T	c.(1081-1083)cGa>cTa	p.R361L	ZFP91-CNTF_ENST00000389919.4_Missense_Mutation_p.R361L	NM_001197051.1|NM_053023.4	NP_001183980.1|NP_444251.1	Q96JP5	ZFP91_HUMAN	ZFP91 zinc finger protein	361	Interaction with MAP3K14/NIK.				activation of NF-kappaB-inducing kinase activity (GO:0007250)|protein K63-linked ubiquitination (GO:0070534)	nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|ubiquitin-protein transferase activity (GO:0004842)			cervix(1)|endometrium(4)|kidney(4)|large_intestine(4)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	26		Breast(21;0.00725)|all_epithelial(135;0.0101)|all_lung(304;0.24)				CAACTTCTGCGACATGCCAAA	0.383																																					p.R361L		Atlas-SNP	.											.	ZFP91	66	.	0			c.G1082T						.						90.0	82.0	84.0					11																	58381796		2201	4294	6495	SO:0001583	missense	80829	exon9			TTCTGCGACATGC	AB056107	CCDS31553.1	11q12	2012-11-27	2012-11-27		ENSG00000186660	ENSG00000186660		"""Zinc fingers, C2H2-type"""	14983	protein-coding gene	gene with protein product			"""zinc finger protein homologous to Zfp91 in mouse"", ""zinc finger protein 91 homolog (mouse)"""			12738986, 20682767	Standard	NM_053023		Approved	PZF, ZNF757	uc001nmx.4	Q96JP5	OTTHUMG00000137391	ENST00000316059.6:c.1082G>T	chr11.hg19:g.58381796G>T	ENSP00000339030:p.Arg361Leu	51.0	0.0		57.0	21.0	NM_053023	A6NHC4|A8MSG7|Q86V47|Q96JP4|Q96QA3	Missense_Mutation	SNP	ENST00000316059.6	hg19	CCDS31553.1	.	.	.	.	.	.	.	.	.	.	G	34	5.315890	0.95655	.	.	ENSG00000186660	ENST00000316059;ENST00000389918	T	0.15372	2.43	5.97	5.97	0.96955	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000007	T	0.38453	0.1041	L	0.49513	1.565	0.80722	D	1	D;D	0.76494	0.998;0.999	D;D	0.85130	0.994;0.997	T	0.00533	-1.1685	10	0.34782	T	0.22	-7.0583	19.2039	0.93722	0.0:0.0:1.0:0.0	.	361;361	Q96JP5-2;Q96JP5	.;ZFP91_HUMAN	L	361	ENSP00000339030:R361L	ENSP00000374569:R361L	R	+	2	0	ZFP91	58138372	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	9.476000	0.97823	2.833000	0.97629	0.585000	0.79938	CGA	.	.		0.383	ZFP91-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268674.1	NM_053023	
STIP1	10963	hgsc.bcm.edu	37	11	63963275	63963275	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:63963275A>G	ENST00000305218.4	+	5	809	c.662A>G	c.(661-663)aAt>aGt	p.N221S	STIP1_ENST00000538945.1_Missense_Mutation_p.N197S|STIP1_ENST00000358794.5_Missense_Mutation_p.N268S|STIP1_ENST00000540501.1_3'UTR|STIP1_ENST00000543847.1_Missense_Mutation_p.N221S	NM_006819.2	NP_006810.1	P31948	STIP1_HUMAN	stress-induced phosphoprotein 1	221					response to stress (GO:0006950)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(1)|skin(1)	27						CTTCCAGAGAATAAGAAGCAG	0.448																																					p.N221S		Atlas-SNP	.											.	STIP1	63	.	0			c.A662G						.						138.0	149.0	145.0					11																	63963275		2201	4297	6498	SO:0001583	missense	10963	exon5			CAGAGAATAAGAA	BC039299	CCDS8058.1, CCDS60827.1, CCDS60828.1	11q13	2014-01-13	2014-01-13		ENSG00000168439	ENSG00000168439		"""Tetratricopeptide (TTC) repeat domain containing"""	11387	protein-coding gene	gene with protein product	"""Hsp70/Hsp90-organizing protein"""	605063	"""stress-induced-phosphoprotein 1"""			1569099	Standard	NM_006819		Approved	HOP, STI1	uc001nyk.1	P31948	OTTHUMG00000167789	ENST00000305218.4:c.662A>G	chr11.hg19:g.63963275A>G	ENSP00000305958:p.Asn221Ser	239.0	0.0		260.0	109.0	NM_006819	B4DM70|F5H0T1|G3XAD8|Q3ZCU9|Q5TZU9	Missense_Mutation	SNP	ENST00000305218.4	hg19	CCDS8058.1	.	.	.	.	.	.	.	.	.	.	A	8.371	0.835428	0.16820	.	.	ENSG00000168439	ENST00000358794;ENST00000305218;ENST00000538945;ENST00000543847	T;T;T;T	0.70986	2.54;2.77;2.55;-0.53	5.05	3.9	0.45041	.	0.000000	0.85682	D	0.000000	T	0.68650	0.3024	M	0.62723	1.935	0.53688	D	0.999971	B;B;P	0.36048	0.2;0.245;0.534	B;B;B	0.42282	0.069;0.032;0.382	T	0.62435	-0.6855	10	0.19147	T	0.46	-43.5292	10.9318	0.47222	0.8591:0.0:0.0:0.1409	.	197;221;221	F5H0T1;P31948;F5H783	.;STIP1_HUMAN;.	S	268;221;197;221	ENSP00000351646:N268S;ENSP00000305958:N221S;ENSP00000445957:N197S;ENSP00000442704:N221S	ENSP00000305958:N221S	N	+	2	0	STIP1	63719851	1.000000	0.71417	1.000000	0.80357	0.349000	0.29174	7.731000	0.84895	1.005000	0.39183	-0.516000	0.04426	AAT	.	.		0.448	STIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396289.2	NM_006819	
CBL	867	hgsc.bcm.edu	37	11	119170325	119170325	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr11:119170325C>T	ENST00000264033.4	+	16	2931	c.2555C>T	c.(2554-2556)aCc>aTc	p.T852I		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	852	Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCTGCTGCCACCGCCTCACCT	0.562			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies																												p.T852I		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.C2555T						.						154.0	154.0	154.0					11																	119170325		2199	4295	6494	SO:0001583	missense	867	exon16	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	CTGCCACCGCCTC	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2555C>T	chr11.hg19:g.119170325C>T	ENSP00000264033:p.Thr852Ile	92.0	0.0		88.0	5.0	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	hg19	CCDS8418.1	.	.	.	.	.	.	.	.	.	.	C	5.511	0.279276	0.10458	.	.	ENSG00000110395	ENST00000264033	T	0.77358	-1.09	5.59	5.59	0.84812	.	0.495098	0.21803	N	0.068896	T	0.62502	0.2433	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.11329	0.006	T	0.59172	-0.7504	10	0.72032	D	0.01	-2.9898	15.4319	0.75105	0.0:0.8218:0.1782:0.0	.	852	P22681	CBL_HUMAN	I	852	ENSP00000264033:T852I	ENSP00000264033:T852I	T	+	2	0	CBL	118675535	0.177000	0.23109	0.084000	0.20598	0.190000	0.23558	2.726000	0.47302	2.639000	0.89480	0.655000	0.94253	ACC	.	.		0.562	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
ATF7IP	55729	hgsc.bcm.edu	37	12	14577886	14577886	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:14577886A>C	ENST00000540793.1	+	1	1192	c.1037A>C	c.(1036-1038)gAt>gCt	p.D346A	ATF7IP_ENST00000543189.1_Missense_Mutation_p.D346A|ATF7IP_ENST00000261168.4_Missense_Mutation_p.D346A|ATF7IP_ENST00000541654.1_3'UTR|ATF7IP_ENST00000544627.1_Missense_Mutation_p.D354A|ATF7IP_ENST00000536444.1_Missense_Mutation_p.D346A			Q6VMQ6	MCAF1_HUMAN	activating transcription factor 7 interacting protein	346					DNA methylation (GO:0006306)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045898)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)				cervix(1)|endometrium(7)|kidney(5)|large_intestine(10)|liver(2)|lung(22)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	54						AATAATATTGATGCTAATGAA	0.313																																					p.D346A		Atlas-SNP	.											.	ATF7IP	136	.	0			c.A1037C						.						56.0	63.0	60.0					12																	14577886		2202	4298	6500	SO:0001583	missense	55729	exon2			ATATTGATGCTAA	AJ242978	CCDS8663.1, CCDS66326.1, CCDS66327.1, CCDS73449.1	12p13.1	2005-11-18				ENSG00000171681			20092	protein-coding gene	gene with protein product		613644				10976766, 10777215	Standard	XM_005253424		Approved	FLJ10688, p621	uc001rbw.3	Q6VMQ6		ENST00000540793.1:c.1037A>C	chr12.hg19:g.14577886A>C	ENSP00000444589:p.Asp346Ala	122.0	0.0		90.0	34.0	NM_018179	F5GX74|G3V1U0|Q4G0T9|Q6P3T3|Q86XW5|Q9NVJ9|Q9NWC2|Q9Y4X8	Missense_Mutation	SNP	ENST00000540793.1	hg19	CCDS8663.1	.	.	.	.	.	.	.	.	.	.	A	8.855	0.945614	0.18356	.	.	ENSG00000171681	ENST00000261168;ENST00000543189;ENST00000536444;ENST00000544627;ENST00000396279;ENST00000540793	T;T;T;T;T;T	0.23147	2.24;2.23;2.24;2.23;1.92;2.24	5.55	0.497	0.16902	.	0.456909	0.20727	N	0.086784	T	0.11153	0.0272	N	0.16478	0.41	0.09310	N	1	B;B;B;B;B	0.24721	0.11;0.11;0.01;0.01;0.01	B;B;B;B;B	0.23419	0.046;0.046;0.006;0.006;0.006	T	0.18903	-1.0322	10	0.25751	T	0.34	-7.0378	2.1934	0.03905	0.5645:0.1135:0.1035:0.2185	.	354;346;346;346;346	B4E2A2;B4DRL6;G3V1U0;Q6VMQ6;Q6VMQ6-2	.;.;.;MCAF1_HUMAN;.	A	346;346;346;354;346;346	ENSP00000261168:D346A;ENSP00000443179:D346A;ENSP00000445955:D346A;ENSP00000440440:D354A;ENSP00000379575:D346A;ENSP00000444589:D346A	ENSP00000261168:D346A	D	+	2	0	ATF7IP	14469153	0.182000	0.23173	0.005000	0.12908	0.962000	0.63368	0.852000	0.27764	-0.083000	0.12618	0.533000	0.62120	GAT	.	.		0.313	ATF7IP-024	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000401400.1	NM_018179	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20852565	20852565	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:20852565C>A	ENST00000266509.2	+	2	423	c.55C>A	c.(55-57)Cct>Act	p.P19T	SLCO1C1_ENST00000381552.1_Missense_Mutation_p.P19T|SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.P19T|SLCO1C1_ENST00000545604.1_Missense_Mutation_p.P19T	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	19					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	TTCAGTGCAACCTGTTGGAAG	0.373																																					p.P19T		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.C55A						.						65.0	64.0	64.0					12																	20852565		2203	4299	6502	SO:0001583	missense	53919	exon2			GTGCAACCTGTTG	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.55C>A	chr12.hg19:g.20852565C>A	ENSP00000266509:p.Pro19Thr	286.0	0.0		254.0	94.0	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	hg19	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627460	0.46944	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552	T;T;T;T	0.38077	1.16;1.24;1.22;1.16	4.86	4.86	0.63082	Major facilitator superfamily domain, general substrate transporter (1);	1.596860	0.03301	N	0.189018	T	0.25938	0.0632	N	0.08118	0	0.36994	D	0.894924	B;B;B	0.28233	0.054;0.204;0.054	B;B;B	0.27500	0.034;0.08;0.05	T	0.08330	-1.0727	10	0.51188	T	0.08	.	10.8646	0.46847	0.0:0.9137:0.0:0.0863	.	19;19;19	B7Z3Q3;Q5JPA4;Q9NYB5	.;.;SO1C1_HUMAN	T	19	ENSP00000444149:P19T;ENSP00000438665:P19T;ENSP00000266509:P19T;ENSP00000370964:P19T	ENSP00000266509:P19T	P	+	1	0	SLCO1C1	20743832	0.290000	0.24343	0.996000	0.52242	0.967000	0.64934	1.561000	0.36342	2.532000	0.85374	0.655000	0.94253	CCT	.	.		0.373	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
SLC38A2	54407	hgsc.bcm.edu	37	12	46758276	46758276	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:46758276T>C	ENST00000256689.5	-	10	1213	c.769A>G	c.(769-771)Ata>Gta	p.I257V	SLC38A2_ENST00000551374.1_Missense_Mutation_p.I95V|SLC38A2_ENST00000547252.1_5'Flank	NM_018976.4	NP_061849.2	Q96QD8	S38A2_HUMAN	solute carrier family 38, member 2	257					amino acid transport (GO:0006865)|glutamate secretion (GO:0014047)|ion transport (GO:0006811)|neurotransmitter secretion (GO:0007269)|sodium ion transport (GO:0006814)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|symporter activity (GO:0015293)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	18	Lung SC(27;0.192)|Renal(347;0.236)		OV - Ovarian serous cystadenocarcinoma(5;0.0048)|Epithelial(2;0.0374)	GBM - Glioblastoma multiforme(48;0.226)		GTGGTGTTTATTGTTTCGTTA	0.363																																					p.I257V	Ovarian(9;448 492 8335 28722 40361)	Atlas-SNP	.											.	SLC38A2	36	.	0			c.A769G						.						252.0	252.0	252.0					12																	46758276		2203	4300	6503	SO:0001583	missense	54407	exon10			TGTTTATTGTTTC	AB037803	CCDS8749.1	12q13.11	2014-08-12			ENSG00000134294	ENSG00000134294		"""Solute carriers"""	13448	protein-coding gene	gene with protein product		605180				10747860, 17237199	Standard	NM_018976		Approved	SAT2, ATA2, KIAA1382, SNAT2	uc001rpg.3	Q96QD8	OTTHUMG00000169471	ENST00000256689.5:c.769A>G	chr12.hg19:g.46758276T>C	ENSP00000256689:p.Ile257Val	157.0	0.0		126.0	33.0	NM_018976	Q6IA88|Q6ZMG2|Q9HAV3|Q9NVA8|Q9P2G5	Missense_Mutation	SNP	ENST00000256689.5	hg19	CCDS8749.1	.	.	.	.	.	.	.	.	.	.	T	8.536	0.872107	0.17322	.	.	ENSG00000134294	ENST00000256689;ENST00000551374	T;T	0.02421	4.3;4.3	5.43	-5.76	0.02376	.	2.500020	0.01439	N	0.015034	T	0.01387	0.0045	N	0.04203	-0.255	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.46091	-0.9216	10	0.09084	T	0.74	0.7757	6.9081	0.24321	0.1459:0.5961:0.0856:0.1724	.	95;157;257	F8VQW8;Q96QD8-2;Q96QD8	.;.;S38A2_HUMAN	V	257;95	ENSP00000256689:I257V;ENSP00000450406:I95V	ENSP00000256689:I257V	I	-	1	0	SLC38A2	45044543	0.000000	0.05858	0.000000	0.03702	0.926000	0.56050	-2.806000	0.00758	-0.967000	0.03582	0.377000	0.23210	ATA	.	.		0.363	SLC38A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404226.1		
TFCP2	7024	hgsc.bcm.edu	37	12	51510198	51510198	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:51510198T>C	ENST00000257915.5	-	4	815	c.357A>G	c.(355-357)atA>atG	p.I119M	TFCP2_ENST00000549867.1_Missense_Mutation_p.I119M|TFCP2_ENST00000307660.4_Missense_Mutation_p.I119M|TFCP2_ENST00000548115.1_Missense_Mutation_p.I119M	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	119					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						CCACACGGAATATACTCTAAA	0.433																																					p.I119M		Atlas-SNP	.											.	TFCP2	49	.	0			c.A357G						.						91.0	84.0	87.0					12																	51510198		2203	4300	6503	SO:0001583	missense	7024	exon4			ACGGAATATACTC	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.357A>G	chr12.hg19:g.51510198T>C	ENSP00000257915:p.Ile119Met	96.0	0.0		74.0	37.0	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	hg19	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	T	12.52	1.963013	0.34659	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.18016	2.24;2.24;2.24;2.24;2.24	4.86	3.69	0.42338	CP2 transcription factor (1);	0.000000	0.85682	D	0.000000	T	0.21550	0.0519	L	0.55743	1.74	0.49051	D	0.999746	B;P;B;B	0.36733	0.021;0.567;0.372;0.185	B;P;B;B	0.44696	0.009;0.458;0.209;0.132	T	0.02161	-1.1203	10	0.87932	D	0	-18.7396	6.809	0.23794	0.1502:0.0:0.1565:0.6933	.	119;119;119;119	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	M	119;119;119;119;21	ENSP00000257915:I119M;ENSP00000304411:I119M;ENSP00000449742:I119M;ENSP00000447991:I119M;ENSP00000449280:I21M	ENSP00000257915:I119M	I	-	3	3	TFCP2	49796465	0.866000	0.29940	1.000000	0.80357	0.835000	0.47333	-0.078000	0.11375	0.968000	0.38212	0.533000	0.62120	ATA	.	.		0.433	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653	
SLC26A10	65012	hgsc.bcm.edu	37	12	58018905	58018905	+	Splice_Site	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:58018905G>A	ENST00000320442.4	+	11	1655		c.e11-1		SLC26A10_ENST00000379218.2_Splice_Site|SLC26A10_ENST00000490243.1_Splice_Site	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10							integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					TTTACTTATAGGAGACTTCAA	0.532																																					.		Atlas-SNP	.											.	SLC26A10	89	.	0			c.1345-1G>A						.						267.0	262.0	264.0					12																	58018905		2203	4300	6503	SO:0001630	splice_region_variant	65012	exon11			CTTATAGGAGACT		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"""Solute carriers"""	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1345-1G>A	chr12.hg19:g.58018905G>A		138.0	0.0		169.0	66.0	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Splice_Site	SNP	ENST00000320442.4	hg19	CCDS8949.2	.	.	.	.	.	.	.	.	.	.	G	8.345	0.829641	0.16749	.	.	ENSG00000135502	ENST00000320442	.	.	.	4.44	4.44	0.53790	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4261	0.55548	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC26A10	56305172	0.207000	0.23482	0.942000	0.38095	0.266000	0.26442	2.021000	0.41020	2.297000	0.77311	0.561000	0.74099	.	.	.		0.532	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		Intron
NAV3	89795	hgsc.bcm.edu	37	12	78522622	78522622	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:78522622G>A	ENST00000397909.2	+	18	4590	c.4417G>A	c.(4417-4419)Gga>Aga	p.G1473R	NAV3_ENST00000228327.6_Missense_Mutation_p.G1473R|NAV3_ENST00000266692.7_Missense_Mutation_p.G1296R|NAV3_ENST00000536525.2_Missense_Mutation_p.G1473R			Q8IVL0	NAV3_HUMAN	neuron navigator 3	1473	Ser-rich.					membrane (GO:0016020)|nuclear envelope (GO:0005635)				NS(2)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(13)|kidney(16)|large_intestine(39)|liver(2)|lung(126)|ovary(5)|pancreas(3)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(1)	236						TTCTGCAGCTGGAAAATACCA	0.443										HNSCC(70;0.22)																											p.G1473R		Atlas-SNP	.											.	NAV3	506	.	0			c.G4417A						.						93.0	88.0	89.0					12																	78522622		1859	4111	5970	SO:0001583	missense	89795	exon18			GCAGCTGGAAAAT	AB023155	CCDS41815.1, CCDS66432.1	12q14.3	2008-08-05				ENSG00000067798			15998	protein-coding gene	gene with protein product	"""pore membrane and/or filament interacting like protein 1"", ""steerin 3"""	611629				12079279, 12062803	Standard	XM_005269215		Approved	KIAA0938, POMFIL1	uc001syo.3	Q8IVL0	OTTHUMG00000170001	ENST00000397909.2:c.4417G>A	chr12.hg19:g.78522622G>A	ENSP00000381007:p.Gly1473Arg	93.0	0.0		87.0	35.0	NM_014903	Q8NFW7|Q9Y2E7	Missense_Mutation	SNP	ENST00000397909.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	23.1|23.1	4.374909|4.374909	0.82573|0.82573	.|.	.|.	ENSG00000067798|ENSG00000067798	ENST00000536525;ENST00000397909;ENST00000228327;ENST00000266692;ENST00000378640;ENST00000550788|ENST00000552895	T;T;T;T;T|.	0.32515|.	1.48;1.51;1.5;1.45;2.24|.	5.81|5.81	5.81|5.81	0.92471|0.92471	.|.	0.000000|.	0.39146|.	U|.	0.001455|.	T|.	0.75583|.	0.3869|.	M|M	0.65498|0.65498	2.005|2.005	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.89917|.	0.999;0.996;1.0;1.0|.	D;D;D;D|.	0.97110|.	0.98;0.953;1.0;0.982|.	T|.	0.72367|.	-0.4315|.	10|.	0.36615|.	T|.	0.2|.	-15.7635|-15.7635	20.0755|20.0755	0.97742|0.97742	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	1473;1296;1473;1473|.	E7EUC6;Q8IVL0-3;Q8IVL0;Q8IVL0-2|.	.;.;NAV3_HUMAN;.|.	R|X	1473;1473;1473;1296;94;102|367	ENSP00000446132:G1473R;ENSP00000381007:G1473R;ENSP00000228327:G1473R;ENSP00000266692:G1296R;ENSP00000448303:G102R|.	ENSP00000228327:G1473R|.	G|W	+|+	1|2	0|0	NAV3|NAV3	77046753|77046753	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.958000|0.958000	0.62258|0.62258	6.435000|6.435000	0.73412|0.73412	2.749000|2.749000	0.94314|0.94314	0.460000|0.460000	0.39030|0.39030	GGA|TGG	.	.		0.443	NAV3-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000406812.1	NM_001024383	
METTL25	84190	hgsc.bcm.edu	37	12	82792710	82792710	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:82792710A>G	ENST00000248306.3	+	4	737	c.668A>G	c.(667-669)cAt>cGt	p.H223R	METTL25_ENST00000547357.1_3'UTR	NM_032230.2	NP_115606.2	Q8N6Q8	MET25_HUMAN	methyltransferase like 25	223							methyltransferase activity (GO:0008168)										TTGAAGAAACATTGGAAACTC	0.323																																					p.H223R		Atlas-SNP	.											.	.	.	.	0			c.A668G						.						61.0	59.0	60.0					12																	82792710		2203	4299	6502	SO:0001583	missense	84190	exon4			AGAAACATTGGAA	BC029120	CCDS9024.1	12q21.31	2012-08-13	2012-08-13	2012-08-13	ENSG00000127720	ENSG00000127720			26228	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 26"""	C12orf26			Standard	NM_032230		Approved	FLJ22789	uc001szq.3	Q8N6Q8	OTTHUMG00000170252	ENST00000248306.3:c.668A>G	chr12.hg19:g.82792710A>G	ENSP00000248306:p.His223Arg	102.0	0.0		97.0	44.0	NM_032230	Q9H5Y3	Missense_Mutation	SNP	ENST00000248306.3	hg19	CCDS9024.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	10.57|10.57	1.386405|1.386405	0.25031|0.25031	.|.	.|.	ENSG00000127720|ENSG00000127720	ENST00000248306;ENST00000548200|ENST00000550058	T;T|.	0.18960|.	2.18;2.18|.	5.43|5.43	4.29|4.29	0.51040|0.51040	.|.	0.199004|.	0.56097|.	D|.	0.000040|.	T|T	0.54464|0.54464	0.1860|0.1860	L|L	0.49640|0.49640	1.575|1.575	0.33617|0.33617	D|D	0.604316|0.604316	B|.	0.19331|.	0.035|.	B|.	0.19666|.	0.026|.	T|T	0.63761|0.63761	-0.6564|-0.6564	10|5	0.25106|.	T|.	0.35|.	-8.0965|-8.0965	11.2669|11.2669	0.49116|0.49116	0.9282:0.0:0.0717:0.0|0.9282:0.0:0.0717:0.0	.|.	223|.	Q8N6Q8|.	CL026_HUMAN|.	R|V	223|182	ENSP00000248306:H223R;ENSP00000446878:H223R|.	ENSP00000248306:H223R|.	H|I	+|+	2|1	0|0	C12orf26|C12orf26	81316841|81316841	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.454000|0.454000	0.32378|0.32378	4.731000|4.731000	0.62022|0.62022	1.009000|1.009000	0.39289|0.39289	0.477000|0.477000	0.44152|0.44152	CAT|ATT	.	.		0.323	METTL25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408192.1	NM_032230	
NAA25	80018	hgsc.bcm.edu	37	12	112516482	112516482	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:112516482C>T	ENST00000261745.4	-	6	789	c.541G>A	c.(541-543)Gtc>Atc	p.V181I		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	181						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						ATTTTTTCGACCATTCTCTCA	0.358																																					p.V181I		Atlas-SNP	.											.	NAA25	105	.	0			c.G541A						.						170.0	154.0	159.0					12																	112516482		2203	4300	6503	SO:0001583	missense	80018	exon6			TTTCGACCATTCT	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.541G>A	chr12.hg19:g.112516482C>T	ENSP00000261745:p.Val181Ile	129.0	0.0		128.0	28.0	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	hg19	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	36	5.760438	0.96906	.	.	ENSG00000111300	ENST00000261745	T	0.37235	1.21	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	T	0.48114	0.1482	L	0.31752	0.955	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.13335	-1.0513	10	0.10111	T	0.7	-14.0427	20.6013	0.99457	0.0:1.0:0.0:0.0	.	181;181	A8K8X0;Q14CX7	.;NAA25_HUMAN	I	181	ENSP00000261745:V181I	ENSP00000261745:V181I	V	-	1	0	NAA25	111000865	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.251000	0.78297	2.878000	0.98634	0.650000	0.86243	GTC	.	.		0.358	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
GCN1L1	10985	hgsc.bcm.edu	37	12	120595713	120595713	+	Silent	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:120595713G>T	ENST00000300648.6	-	26	3039	c.3027C>A	c.(3025-3027)atC>atA	p.I1009I	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1009					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GGACAGTGAGGATCTGAAGAA	0.602																																					p.I1009I		Atlas-SNP	.											.	GCN1L1	207	.	0			c.C3027A						.						50.0	57.0	55.0					12																	120595713		1971	4152	6123	SO:0001819	synonymous_variant	10985	exon26			AGTGAGGATCTGA	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3027C>A	chr12.hg19:g.120595713G>T		98.0	0.0		113.0	39.0	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Silent	SNP	ENST00000300648.6	hg19	CCDS41847.1																																																																																			.	.		0.602	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
AKAP11	11215	hgsc.bcm.edu	37	13	42874405	42874405	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr13:42874405A>G	ENST00000025301.2	+	8	1698	c.1523A>G	c.(1522-1524)cAt>cGt	p.H508R		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	508					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CGTACCCACCATACTAATACC	0.299																																					p.H508R		Atlas-SNP	.											.	AKAP11	146	.	0			c.A1523G						.						68.0	69.0	69.0					13																	42874405		2203	4299	6502	SO:0001583	missense	11215	exon8			CCCACCATACTAA	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.1523A>G	chr13.hg19:g.42874405A>G	ENSP00000025301:p.His508Arg	220.0	0.0		219.0	13.0	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	hg19	CCDS9383.1	.	.	.	.	.	.	.	.	.	.	A	0.948	-0.707207	0.03230	.	.	ENSG00000023516	ENST00000025301	T	0.48522	0.81	5.63	0.322	0.15888	.	0.610881	0.17589	N	0.168822	T	0.35537	0.0935	M	0.63428	1.95	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.17745	-1.0359	10	0.30854	T	0.27	.	1.9061	0.03278	0.4875:0.2515:0.1395:0.1215	.	508	Q9UKA4	AKA11_HUMAN	R	508	ENSP00000025301:H508R	ENSP00000025301:H508R	H	+	2	0	AKAP11	41772405	0.000000	0.05858	0.003000	0.11579	0.011000	0.07611	0.305000	0.19254	0.473000	0.27368	0.477000	0.44152	CAT	.	.		0.299	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
TRIM13	10206	hgsc.bcm.edu	37	13	50586458	50586458	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr13:50586458T>C	ENST00000378182.3	+	2	1120	c.382T>C	c.(382-384)Ttc>Ctc	p.F128L	TRIM13_ENST00000420995.2_Missense_Mutation_p.F128L|TRIM13_ENST00000457662.2_Missense_Mutation_p.F128L|KCNRG_ENST00000312942.1_5'Flank|TRIM13_ENST00000478111.1_Intron|TRIM13_ENST00000298772.5_Missense_Mutation_p.F131L|KCNRG_ENST00000360473.4_5'Flank|TRIM13_ENST00000356017.4_Missense_Mutation_p.F131L	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13	128					anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		CAAACATGTCTTCTGTTCTAT	0.507																																					p.F131L		Atlas-SNP	.											.	TRIM13	30	.	0			c.T391C						.						136.0	124.0	128.0					13																	50586458		2203	4300	6503	SO:0001583	missense	10206	exon4			CATGTCTTCTGTT	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.382T>C	chr13.hg19:g.50586458T>C	ENSP00000367424:p.Phe128Leu	126.0	0.0		174.0	10.0	NM_001007278	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	Missense_Mutation	SNP	ENST00000378182.3	hg19	CCDS9423.1	.	.	.	.	.	.	.	.	.	.	T	19.89	3.911178	0.72983	.	.	ENSG00000204977	ENST00000442421;ENST00000378183;ENST00000420995;ENST00000378182;ENST00000356017;ENST00000457662;ENST00000298772	T;T;T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11;1.11;1.11	5.4	5.4	0.78164	Zinc finger, B-box (3);	0.000000	0.85682	D	0.000000	T	0.33644	0.0870	L	0.37800	1.135	0.47994	D	0.999563	P;P	0.39094	0.659;0.607	B;B	0.34873	0.191;0.12	T	0.11470	-1.0586	10	0.36615	T	0.2	-6.2555	15.4114	0.74923	0.0:0.0:0.0:1.0	.	128;131	O60858;O60858-3	TRI13_HUMAN;.	L	128;128;128;128;131;128;131	ENSP00000404586:F128L;ENSP00000367425:F128L;ENSP00000412943:F128L;ENSP00000367424:F128L;ENSP00000348299:F131L;ENSP00000399206:F128L;ENSP00000298772:F131L	ENSP00000298772:F131L	F	+	1	0	TRIM13	49484459	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.323000	0.52014	2.041000	0.60428	0.533000	0.62120	TTC	.	.		0.507	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
OR4N5	390437	hgsc.bcm.edu	37	14	20612471	20612471	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:20612471T>C	ENST00000333629.1	+	1	577	c.577T>C	c.(577-579)Ttt>Ctt	p.F193L	RNA5SP381_ENST00000516076.1_RNA	NM_001004724.1	NP_001004724.1	Q8IXE1	OR4N5_HUMAN	olfactory receptor, family 4, subfamily N, member 5	193						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(23)|ovary(1)|skin(2)|urinary_tract(1)	29	all_cancers(95;0.00108)		Epithelial(56;7.58e-07)|all cancers(55;3.84e-06)	GBM - Glioblastoma multiforme(265;0.0143)		CACCAATACCTTTGTGGTGGA	0.532																																					p.F193L		Atlas-SNP	.											.	OR4N5	72	.	0			c.T577C						.						103.0	85.0	91.0					14																	20612471		2203	4300	6503	SO:0001583	missense	390437	exon1			AATACCTTTGTGG		CCDS32031.1	14q11.2	2013-09-23			ENSG00000184394	ENSG00000184394		"""GPCR / Class A : Olfactory receptors"""	15358	protein-coding gene	gene with protein product							Standard	NM_001004724		Approved		uc010tla.2	Q8IXE1	OTTHUMG00000170784	ENST00000333629.1:c.577T>C	chr14.hg19:g.20612471T>C	ENSP00000332110:p.Phe193Leu	67.0	0.0		72.0	20.0	NM_001004724	Q6IF11	Missense_Mutation	SNP	ENST00000333629.1	hg19	CCDS32031.1	.	.	.	.	.	.	.	.	.	.	T	4.266	0.048476	0.08243	.	.	ENSG00000184394	ENST00000333629	T	0.00137	8.68	3.74	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.000000	0.45126	D	0.000400	T	0.00144	0.0004	L	0.49778	1.585	0.09310	N	1	B	0.18741	0.03	B	0.31751	0.135	T	0.33189	-0.9878	10	0.62326	D	0.03	.	4.9155	0.13844	0.0:0.1081:0.1911:0.7008	.	193	Q8IXE1	OR4N5_HUMAN	L	193	ENSP00000332110:F193L	ENSP00000332110:F193L	F	+	1	0	OR4N5	19682311	0.000000	0.05858	0.577000	0.28562	0.009000	0.06853	-0.484000	0.06528	0.587000	0.29643	-0.291000	0.09656	TTT	.	.		0.532	OR4N5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410347.1		
OR11H4	390442	hgsc.bcm.edu	37	14	20711205	20711205	+	Silent	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:20711205C>G	ENST00000315409.2	+	1	308	c.255C>G	c.(253-255)tcC>tcG	p.S85S		NM_001004479.1	NP_001004479.1	Q8NGC9	O11H4_HUMAN	olfactory receptor, family 11, subfamily H, member 4	85						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S85S(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(3)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	29	all_cancers(95;0.000888)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0146)		GGTATGTGTCCTCCACTATTC	0.453																																					p.S85S		Atlas-SNP	.											OR11H4,rectum,carcinoma,0,3	OR11H4	63	.	1	Substitution - coding silent(1)	ovary(1)	c.C255G						.						168.0	162.0	164.0					14																	20711205		2203	4300	6503	SO:0001819	synonymous_variant	390442	exon1			TGTGTCCTCCACT		CCDS32034.1	14q11.2	2013-09-24			ENSG00000176198	ENSG00000176198		"""GPCR / Class A : Olfactory receptors"""	15347	protein-coding gene	gene with protein product							Standard	NM_001004479		Approved		uc010tld.2	Q8NGC9	OTTHUMG00000170852	ENST00000315409.2:c.255C>G	chr14.hg19:g.20711205C>G		137.0	0.0		145.0	12.0	NM_001004479	B2RNQ4|Q6IF07	Silent	SNP	ENST00000315409.2	hg19	CCDS32034.1																																																																																			.	.		0.453	OR11H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410678.1		
FANCM	57697	hgsc.bcm.edu	37	14	45658480	45658480	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:45658480A>G	ENST00000267430.5	+	20	5340	c.5255A>G	c.(5254-5256)aAt>aGt	p.N1752S	FANCM_ENST00000542564.2_Missense_Mutation_p.N1726S	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	1752	Interaction with FAAP24 and EME1.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						AAACCTCAGAATCATAATGAA	0.398								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.N1752S		Atlas-SNP	.											.	FANCM	225	.	0			c.A5255G						.						125.0	128.0	127.0					14																	45658480		2203	4300	6503	SO:0001583	missense	57697	exon20	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTCAGAATCATAA	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.5255A>G	chr14.hg19:g.45658480A>G	ENSP00000267430:p.Asn1752Ser	350.0	0.0		300.0	107.0	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Missense_Mutation	SNP	ENST00000267430.5	hg19	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	1.172	-0.640659	0.03557	.	.	ENSG00000187790	ENST00000267430;ENST00000542564;ENST00000556250	T;T;T	0.15952	2.96;2.96;2.38	5.32	0.883	0.19177	.	1.390360	0.04022	N	0.299994	T	0.04634	0.0126	N	0.00972	-1.085	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.35301	-0.9794	10	0.02654	T	1	.	3.8973	0.09144	0.3582:0.1772:0.4645:0.0	.	1726;1752	B2RTQ9;Q8IYD8	.;FANCM_HUMAN	S	1752;1726;1268	ENSP00000267430:N1752S;ENSP00000442493:N1726S;ENSP00000452033:N1268S	ENSP00000267430:N1752S	N	+	2	0	FANCM	44728230	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.183000	0.16919	-0.049000	0.13379	0.477000	0.44152	AAT	.	.		0.398	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
SIX6	4990	hgsc.bcm.edu	37	14	60976599	60976599	+	Silent	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:60976599C>A	ENST00000327720.5	+	1	931	c.483C>A	c.(481-483)ctC>ctA	p.L161L		NM_007374.2	NP_031400.2	O95475	SIX6_HUMAN	SIX homeobox 6	161					organ morphogenesis (GO:0009887)|visual perception (GO:0007601)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)	p.L161L(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)	11				OV - Ovarian serous cystadenocarcinoma(108;0.088)		AACGTGAGCTCGCCCAGGCAA	0.597																																					p.L161L		Atlas-SNP	.											SIX6,NS,carcinoma,0,1	SIX6	27	.	1	Substitution - coding silent(1)	endometrium(1)	c.C483A						.						49.0	43.0	45.0					14																	60976599		2201	4300	6501	SO:0001819	synonymous_variant	4990	exon1			TGAGCTCGCCCAG	AF141651	CCDS9747.1	14q23.1	2011-06-20	2007-07-13		ENSG00000184302	ENSG00000184302		"""Homeoboxes / SINE class"""	10892	protein-coding gene	gene with protein product		606326	"""sine oculis homeobox (Drosophila) homolog 6"", ""sine oculis homeobox homolog 6 (Drosophila)"""	OPTX2		10512683	Standard	NM_007374		Approved	Six9	uc001xfa.4	O95475	OTTHUMG00000152339	ENST00000327720.5:c.483C>A	chr14.hg19:g.60976599C>A		235.0	0.0		270.0	96.0	NM_007374	Q6NT42|Q9P1X8	Silent	SNP	ENST00000327720.5	hg19	CCDS9747.1																																																																																			.	.		0.597	SIX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276952.2		
MLH3	27030	hgsc.bcm.edu	37	14	75500136	75500136	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:75500136T>A	ENST00000556740.1	-	6	3736	c.3701A>T	c.(3700-3702)gAg>gTg	p.E1234V	MLH3_ENST00000355774.2_Missense_Mutation_p.E1234V|MLH3_ENST00000238662.7_Intron|MLH3_ENST00000544985.1_3'UTR|MLH3_ENST00000556257.1_Intron|MLH3_ENST00000380968.2_Missense_Mutation_p.E180V			Q9UHC1	MLH3_HUMAN	mutL homolog 3	1234					ATP catabolic process (GO:0006200)|female meiosis I (GO:0007144)|male meiosis (GO:0007140)|mismatch repair (GO:0006298)|protein localization (GO:0008104)|reciprocal meiotic recombination (GO:0007131)|synaptonemal complex assembly (GO:0007130)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|mismatch repair complex (GO:0032300)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|mismatched DNA binding (GO:0030983)|satellite DNA binding (GO:0003696)|single-stranded DNA binding (GO:0003697)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	44				BRCA - Breast invasive adenocarcinoma(234;0.00688)		GATAAGCTGCTCCAGACGTAT	0.473								Mismatch excision repair (MMR)																													p.E1234V		Atlas-SNP	.											.	MLH3	200	.	0			c.A3701T						.						73.0	58.0	63.0					14																	75500136		2203	4300	6503	SO:0001583	missense	27030	exon7			AGCTGCTCCAGAC	AF195657	CCDS9837.1, CCDS32123.1	14q24.3	2014-09-17	2013-09-12			ENSG00000119684			7128	protein-coding gene	gene with protein product		604395	"""mutL (E. coli) homolog 3"", ""mutL homolog 3 (E. coli)"""			10615123	Standard	XR_245681		Approved		uc001xrd.1	Q9UHC1		ENST00000556740.1:c.3701A>T	chr14.hg19:g.75500136T>A	ENSP00000452316:p.Glu1234Val	59.0	0.0		60.0	14.0	NM_001040108	P49751|Q56DK9|Q9P292|Q9UHC0	Missense_Mutation	SNP	ENST00000556740.1	hg19	CCDS32123.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.89|16.89	3.246788|3.246788	0.59103|0.59103	.|.	.|.	ENSG00000119684|ENSG00000119684	ENST00000355774;ENST00000380968;ENST00000556740|ENST00000553713	T;T;T|.	0.80566|.	-1.39;-1.39;-1.39|.	5.68|5.68	5.68|5.68	0.88126|0.88126	MutL, C-terminal, dimerisation (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.85457|0.85457	0.5701|0.5701	M|M	0.92649|0.92649	3.33|3.33	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.89152|0.89152	0.3524|0.3524	10|5	0.87932|.	D|.	0|.	-15.2893|-15.2893	15.9394|15.9394	0.79743|0.79743	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1234|.	Q9UHC1|.	MLH3_HUMAN|.	V|C	1234;180;1234|258	ENSP00000348020:E1234V;ENSP00000370355:E180V;ENSP00000452316:E1234V|.	ENSP00000348020:E1234V|.	E|S	-|-	2|1	0|0	MLH3|MLH3	74569889|74569889	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.038000|0.038000	0.13279|0.13279	7.458000|7.458000	0.80787|0.80787	2.169000|2.169000	0.68431|0.68431	0.519000|0.519000	0.50382|0.50382	GAG|AGC	.	.		0.473	MLH3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415006.1	NM_014381	
SLIRP	81892	hgsc.bcm.edu	37	14	78174474	78174474	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:78174474G>A	ENST00000557342.1	+	1	61	c.20G>A	c.(19-21)aGa>aAa	p.R7K	ALKBH1_ENST00000216489.3_5'Flank|SLIRP_ENST00000557623.1_Missense_Mutation_p.R7K|SLIRP_ENST00000238688.5_Missense_Mutation_p.R7K|SLIRP_ENST00000557431.1_Missense_Mutation_p.R7K	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	7					mitochondrion morphogenesis (GO:0070584)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	acrosomal vesicle (GO:0001669)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|sperm flagellum (GO:0036126)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			kidney(1)|prostate(1)	2						TCAGCAGCGAGAGGTGCTGCG	0.557																																					p.R7K		Atlas-SNP	.											SLIRP,NS,carcinoma,0,1	SLIRP	6	.	0			c.G20A						.						64.0	65.0	65.0					14																	78174474		2203	4300	6503	SO:0001583	missense	81892	exon1			CAGCGAGAGGTGC	AF253980	CCDS9866.1, CCDS58331.1, CCDS73668.1	14q24.3	2013-02-12	2011-06-17	2011-06-17	ENSG00000119705	ENSG00000119705		"""RNA binding motif (RRM) containing"""	20495	protein-coding gene	gene with protein product		610211	"""chromosome 14 open reading frame 156"""	C14orf156		16762838	Standard	NM_031210		Approved	DC50	uc001xue.5	Q9GZT3		ENST00000557342.1:c.20G>A	chr14.hg19:g.78174474G>A	ENSP00000450909:p.Arg7Lys	89.0	0.0		93.0	43.0	NM_001267864	J3KMY7	Missense_Mutation	SNP	ENST00000557342.1	hg19	CCDS9866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.43|10.43	1.347405|1.347405	0.24426|0.24426	.|.	.|.	ENSG00000119705|ENSG00000119705	ENST00000556831|ENST00000557342;ENST00000238688;ENST00000557623;ENST00000557431	.|T;T;T;T	.|0.53857	.|1.02;1.04;1.33;0.6	5.93|5.93	2.05|2.05	0.26809|0.26809	.|.	.|0.367509	.|0.26776	.|N	.|0.022550	T|T	0.27384|0.27384	0.0672|0.0672	N|N	0.16307|0.16307	0.4|0.4	0.09310|0.09310	N|N	1|1	.|B	.|0.09022	.|0.002	.|B	.|0.10450	.|0.005	T|T	0.22277|0.22277	-1.0221|-1.0221	5|10	.|0.07325	.|T	.|0.83	-6.9568|-6.9568	5.6755|5.6755	0.17745|0.17745	0.2371:0.1418:0.6211:0.0|0.2371:0.1418:0.6211:0.0	.|.	.|7	.|Q9GZT3	.|SLIRP_HUMAN	K|K	5|7	.|ENSP00000450909:R7K;ENSP00000238688:R7K;ENSP00000452057:R7K;ENSP00000450849:R7K	.|ENSP00000238688:R7K	E|R	+|+	1|2	0|0	SLIRP|SLIRP	77244227|77244227	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-0.177000|-0.177000	0.09796|0.09796	0.109000|0.109000	0.17891|0.17891	-0.155000|-0.155000	0.13514|0.13514	GAG|AGA	.	.		0.557	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210	
CEP170B	283638	hgsc.bcm.edu	37	14	105350819	105350819	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr14:105350819G>A	ENST00000414716.3	+	9	1931	c.1703G>A	c.(1702-1704)gGg>gAg	p.G568E	CEP170B_ENST00000556508.1_Missense_Mutation_p.G498E|CEP170B_ENST00000418279.1_Missense_Mutation_p.G498E|CEP170B_ENST00000453495.1_Missense_Mutation_p.G569E	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	568						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGTGACGCAGGGACATACACC	0.697																																					p.G568E		Atlas-SNP	.											.	.	.	.	0			c.G1703A						.						6.0	5.0	6.0					14																	105350819		1924	3925	5849	SO:0001583	missense	283638	exon9			ACGCAGGGACATA	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.1703G>A	chr14.hg19:g.105350819G>A	ENSP00000404151:p.Gly568Glu	179.0	0.0		174.0	78.0	NM_001112726	Q2KHR7|Q86TI7	Missense_Mutation	SNP	ENST00000414716.3	hg19	CCDS45175.1	.	.	.	.	.	.	.	.	.	.	G	19.29	3.799953	0.70567	.	.	ENSG00000099814	ENST00000556508;ENST00000414716;ENST00000453495;ENST00000418279	T;T;T;T	0.23552	1.9;1.9;1.9;1.9	4.26	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.54127	0.1839	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.63510	-0.6621	10	0.87932	D	0	-32.3908	16.6737	0.85273	0.0:0.0:1.0:0.0	.	568;568;498	Q9Y4F5-2;Q9Y4F5;E9PFC1	.;K0284_HUMAN;.	E	498;568;569;498	ENSP00000451249:G498E;ENSP00000404151:G568E;ENSP00000407238:G569E;ENSP00000415006:G498E	ENSP00000404151:G568E	G	+	2	0	KIAA0284	104421864	1.000000	0.71417	0.284000	0.24805	0.299000	0.27559	9.545000	0.98095	1.908000	0.55244	0.313000	0.20887	GGG	.	.		0.697	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
GPR176	11245	hgsc.bcm.edu	37	15	40093462	40093462	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr15:40093462C>T	ENST00000561100.1	-	3	2284	c.1419G>A	c.(1417-1419)aaG>aaA	p.K473K	RP11-37C7.1_ENST00000558616.1_RNA|GPR176_ENST00000560729.1_5'Flank|GPR176_ENST00000299092.3_Silent_p.K472K|GPR176_ENST00000543580.1_Silent_p.K428K	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	473					G-protein coupled receptor signaling pathway (GO:0007186)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)	23		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		GAAGCAGCCGCTTCTTGCTGT	0.532																																					p.K473K		Atlas-SNP	.											.	GPR176	41	.	0			c.G1419A						.						66.0	68.0	67.0					15																	40093462		2203	4300	6503	SO:0001819	synonymous_variant	11245	exon3			CAGCCGCTTCTTG	BC067106	CCDS10051.1, CCDS61588.1, CCDS61589.1	15q14-q15.1	2012-08-21			ENSG00000166073	ENSG00000166073		"""GPCR / Class A : Orphans"""	32370	protein-coding gene	gene with protein product		612183				7893747	Standard	NM_007223		Approved	Gm1012	uc010uck.2	Q14439	OTTHUMG00000129873	ENST00000561100.1:c.1419G>A	chr15.hg19:g.40093462C>T		82.0	0.0		116.0	8.0	NM_007223	Q6NXF6	Silent	SNP	ENST00000561100.1	hg19	CCDS10051.1																																																																																			.	.		0.532	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252117.2	NM_007223	
CHST14	113189	hgsc.bcm.edu	37	15	40763663	40763664	+	Missense_Mutation	DNP	GC	GC	AA			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr15:40763663_40763664GC>AA	ENST00000306243.5	+	1	504_505	c.251_252GC>AA	c.(250-252)cGC>cAA	p.R84Q	CHST14_ENST00000559991.1_Missense_Mutation_p.R84Q	NM_130468.3	NP_569735.1	Q8NCH0	CHSTE_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 14	84					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|dermatan sulfate proteoglycan metabolic process (GO:0050655)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)|phosphate ion binding (GO:0042301)			cervix(1)|large_intestine(1)|prostate(2)	4		all_cancers(109;2.34e-14)|all_epithelial(112;1.08e-11)|Lung NSC(122;2.95e-09)|all_lung(180;6.03e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;3e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0781)		ACAGCCTGGCGCGGGAAAGCCC	0.733																																					p.R84H|p.R84R		Atlas-SNP	.											.	CHST14	19	.	0			c.G251A|c.C252A						.																																			SO:0001583	missense	113189	exon1			CCTGGCGCGGGAA|CTGGCGCGGGAAA	AF401222	CCDS10059.1	15q15.1	2014-09-17	2007-03-27	2007-03-27	ENSG00000169105	ENSG00000169105		"""Sulfotransferases, membrane-bound"""	24464	protein-coding gene	gene with protein product		608429	"""dermatan 4 sulfotransferase 1"""	D4ST1		11470797	Standard	NM_130468		Approved	HD4ST, D4ST-1	uc001zlw.3	Q8NCH0	OTTHUMG00000129985	Exception_encountered	chr15.hg19:g.40763663_40763664delinsAA	ENSP00000307297:p.Arg84Gln	563.0|561.0	0.0		773.0|760.0	258.0|254.0	NM_130468	Q6PJ31|Q6UXA0|Q96P94	Missense_Mutation|Silent	SNP	ENST00000306243.5	hg19	CCDS10059.1																																																																																			.	.		0.733	CHST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252251.1	NM_130468	
SEMA6D	80031	hgsc.bcm.edu	37	15	48063146	48063146	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr15:48063146C>T	ENST00000316364.5	+	19	2825	c.2386C>T	c.(2386-2388)Cat>Tat	p.H796Y	SEMA6D_ENST00000389432.2_Missense_Mutation_p.H753Y|SEMA6D_ENST00000558014.1_Missense_Mutation_p.H734Y|SEMA6D_ENST00000536845.2_Missense_Mutation_p.H796Y|SEMA6D_ENST00000354744.4_Missense_Mutation_p.H740Y|SEMA6D_ENST00000355997.3_3'UTR|SEMA6D_ENST00000389433.2_Missense_Mutation_p.H777Y|SEMA6D_ENST00000389428.3_Missense_Mutation_p.H721Y|SEMA6D_ENST00000358066.4_Missense_Mutation_p.H734Y|SEMA6D_ENST00000558816.1_3'UTR|SEMA6D_ENST00000537942.1_Missense_Mutation_p.H734Y	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	796					axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		AGAAAAGGCCCATGGCCATGG	0.537																																					p.H796Y		Atlas-SNP	.											.	SEMA6D	322	.	0			c.C2386T						.						61.0	65.0	63.0					15																	48063146		2198	4297	6495	SO:0001583	missense	80031	exon19			AAGGCCCATGGCC	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.2386C>T	chr15.hg19:g.48063146C>T	ENSP00000324857:p.His796Tyr	142.0	0.0		175.0	11.0	NM_153618	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	hg19	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	C	17.09	3.300879	0.60195	.	.	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428	T;T;T;T;T;T;T;T	0.18016	2.24;2.27;2.27;2.27;2.24;2.24;2.24;2.25	5.19	5.19	0.71726	.	0.655751	0.16337	N	0.218873	T	0.23926	0.0579	L	0.36672	1.1	0.80722	D	1	P;P;P;D	0.54964	0.933;0.883;0.814;0.969	P;P;P;P	0.50440	0.641;0.641;0.589;0.641	T	0.01309	-1.1389	10	0.26408	T	0.33	.	18.8873	0.92383	0.0:1.0:0.0:0.0	.	721;740;796;734	Q8NFY4-3;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;SEM6D_HUMAN;.	Y	734;796;796;777;753;740;734;721	ENSP00000442040:H734Y;ENSP00000446152:H796Y;ENSP00000324857:H796Y;ENSP00000374084:H777Y;ENSP00000374083:H753Y;ENSP00000346786:H740Y;ENSP00000350770:H734Y;ENSP00000374079:H721Y	ENSP00000324857:H796Y	H	+	1	0	SEMA6D	45850438	0.999000	0.42202	0.997000	0.53966	0.925000	0.55904	4.420000	0.59841	2.681000	0.91329	0.655000	0.94253	CAT	.	.		0.537	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
PRR35	146325	hgsc.bcm.edu	37	16	613776	613776	+	Nonsense_Mutation	SNP	C	C	A	rs368085414		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr16:613776C>A	ENST00000409413.3	+	2	761	c.482C>A	c.(481-483)tCg>tAg	p.S161*		NM_145270.2	NP_660313.1	P0CG20	PRR35_HUMAN		161	Pro-rich.									central_nervous_system(1)|endometrium(1)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10						CTGCCTGAGTCGTGGAAGCCG	0.741																																					p.S161X		Atlas-SNP	.											.	C16orf11	27	.	0			c.C482A						.						4.0	5.0	5.0					16																	613776		1783	3930	5713	SO:0001587	stop_gained	146325	exon2			CTGAGTCGTGGAA																												ENST00000409413.3:c.482C>A	chr16.hg19:g.613776C>A	ENSP00000386499:p.Ser161*	67.0	0.0		64.0	5.0	NM_145270	B8ZZ27|Q8N233|Q96AX3|Q96S23	Nonsense_Mutation	SNP	ENST00000409413.3	hg19	CCDS45365.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.930759	0.92389	.	.	ENSG00000161992	ENST00000409413	.	.	.	4.96	0.245	0.15512	.	1.194090	0.06296	N	0.700005	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.1771	0.31289	0.3994:0.3924:0.2082:0.0	.	.	.	.	X	161	.	ENSP00000386499:S161X	S	+	2	0	C16orf11	553777	0.002000	0.14202	0.029000	0.17559	0.289000	0.27227	0.499000	0.22546	0.460000	0.27045	0.563000	0.77884	TCG	.	.		0.741	C16orf11-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000333913.1		
CLEC16A	23274	hgsc.bcm.edu	37	16	11217616	11217616	+	Silent	SNP	C	C	T	rs200993240		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr16:11217616C>T	ENST00000409790.1	+	21	2516	c.2286C>T	c.(2284-2286)ggC>ggT	p.G762G	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000381822.2_5'Flank|CLEC16A_ENST00000409552.3_Silent_p.G744G	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGGTGACTGGCGTGGAGGACG	0.577																																					p.G762G		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2286T						.						79.0	86.0	84.0					16																	11217616		2141	4240	6381	SO:0001819	synonymous_variant	23274	exon20			GACTGGCGTGGAG	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2286C>T	chr16.hg19:g.11217616C>T		49.0	0.0		70.0	12.0	NM_015226		Silent	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	C	8.075	0.771132	0.16051	.	.	ENSG00000038532	ENST00000428742	.	.	.	5.55	-11.1	0.00147	.	.	.	.	.	T	0.40522	0.1120	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50583	-0.8811	4	.	.	.	-16.5506	4.4251	0.11498	0.2912:0.0882:0.0612:0.5594	.	.	.	.	V	6	.	.	A	+	2	0	CLEC16A	11125117	0.003000	0.15002	0.044000	0.18714	0.922000	0.55478	-1.222000	0.02965	-3.244000	0.00206	-1.251000	0.01509	GCG	.	.		0.577	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
TBX6	6911	hgsc.bcm.edu	37	16	30097548	30097548	+	Nonstop_Mutation	SNP	A	A	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr16:30097548A>C	ENST00000395224.2	-	9	1368	c.1309T>G	c.(1309-1311)Tga>Gga	p.*437G	TBX6_ENST00000279386.2_Nonstop_Mutation_p.*437G	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	0					anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						GCAGTGGTTCAGTACATGGGT	0.657																																					p.X437G		Atlas-SNP	.											.	TBX6	29	.	0			c.T1309G						.						45.0	51.0	49.0					16																	30097548		2197	4300	6497	SO:0001578	stop_lost	6911	exon9			TGGTTCAGTACAT	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.1309T>G	chr16.hg19:g.30097548A>C	ENSP00000378650:p.*437Argext*81	139.0	0.0		169.0	37.0	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	hg19	CCDS10670.1	.	.	.	.	.	.	.	.	.	.	A	6.243	0.412985	0.11812	.	.	ENSG00000149922	ENST00000395224;ENST00000279386	.	.	.	4.69	4.69	0.59074	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.1969	0.54303	1.0:0.0:0.0:0.0	.	.	.	.	G	437	.	.	X	-	1	0	TBX6	30005049	1.000000	0.71417	0.997000	0.53966	0.020000	0.10135	3.003000	0.49505	1.989000	0.58080	0.449000	0.29647	TGA	.	.		0.657	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
P2RX1	5023	hgsc.bcm.edu	37	17	3806860	3806860	+	Missense_Mutation	SNP	C	C	A	rs367615874		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:3806860C>A	ENST00000225538.3	-	6	864	c.590G>T	c.(589-591)cGc>cTc	p.R197L		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	197					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		GACCTTGAAGCGTGGAAAGCT	0.607																																					p.R197L		Atlas-SNP	.											.	P2RX1	38	.	0			c.G590T						.						81.0	81.0	81.0					17																	3806860		2203	4300	6503	SO:0001583	missense	5023	exon6			TTGAAGCGTGGAA	X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.590G>T	chr17.hg19:g.3806860C>A	ENSP00000225538:p.Arg197Leu	29.0	0.0		24.0	15.0	NM_002558	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	hg19	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270514	0.59540	.	.	ENSG00000108405	ENST00000225538	T	0.04119	3.7	5.56	5.56	0.83823	.	0.265230	0.37393	N	0.002101	T	0.03915	0.0110	N	0.16266	0.395	0.37740	D	0.92558	B	0.19817	0.039	B	0.18561	0.022	T	0.48670	-0.9015	10	0.36615	T	0.2	-2.7716	11.84	0.52348	0.0:0.9116:0.0:0.0884	.	197	P51575	P2RX1_HUMAN	L	197	ENSP00000225538:R197L	ENSP00000225538:R197L	R	-	2	0	P2RX1	3753609	0.920000	0.31207	1.000000	0.80357	0.994000	0.84299	0.035000	0.13797	2.608000	0.88229	0.655000	0.94253	CGC	.	.		0.607	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558	
SMCR8	140775	hgsc.bcm.edu	37	17	18220404	18220404	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:18220404G>A	ENST00000406438.3	+	1	1781	c.1301G>A	c.(1300-1302)gGa>gAa	p.G434E	TOP3A_ENST00000321105.5_5'Flank|TOP3A_ENST00000582230.1_5'Flank|TOP3A_ENST00000542570.1_5'Flank	NM_144775.2	NP_658988.2	Q8TEV9	SMCR8_HUMAN	Smith-Magenis syndrome chromosome region, candidate 8	434						nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(7)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	21						CAGGAACTGGGAGATGAGGAG	0.448																																					p.G434E		Atlas-SNP	.											.	SMCR8	62	.	0			c.G1301A						.						115.0	108.0	110.0					17																	18220404		2203	4300	6503	SO:0001583	missense	140775	exon1			AACTGGGAGATGA	AF467440	CCDS11195.2	17p11.2	2014-06-12			ENSG00000176994	ENSG00000176994			17921	protein-coding gene	gene with protein product						11997338, 23248642	Standard	NM_144775		Approved	FLJ34716	uc002gsy.4	Q8TEV9	OTTHUMG00000059394	ENST00000406438.3:c.1301G>A	chr17.hg19:g.18220404G>A	ENSP00000385025:p.Gly434Glu	131.0	0.0		85.0	12.0	NM_144775	A5PKZ5|Q3ZCN0|Q6PJL3	Missense_Mutation	SNP	ENST00000406438.3	hg19	CCDS11195.2	.	.	.	.	.	.	.	.	.	.	g	1.215	-0.628558	0.03610	.	.	ENSG00000176994	ENST00000406438	T	0.21361	2.01	5.8	2.74	0.32292	.	0.123741	0.53938	N	0.000047	T	0.14743	0.0356	L	0.53249	1.67	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.24225	-1.0166	10	0.15952	T	0.53	-35.0175	2.8074	0.05431	0.3239:0.0:0.4621:0.214	.	434	Q8TEV9	SMCR8_HUMAN	E	434	ENSP00000385025:G434E	ENSP00000385025:G434E	G	+	2	0	SMCR8	18161129	0.998000	0.40836	0.006000	0.13384	0.920000	0.55202	1.494000	0.35616	0.785000	0.33685	-0.119000	0.15052	GGA	.	.		0.448	SMCR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132065.2	NM_144775	
SUZ12	23512	hgsc.bcm.edu	37	17	30320261	30320261	+	Splice_Site	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:30320261C>T	ENST00000322652.5	+	11	1431	c.1202C>T	c.(1201-1203)gCt>gTt	p.A401V	SUZ12_ENST00000580398.1_Splice_Site_p.A378V	NM_015355.2	NP_056170.2	Q15022	SUZ12_HUMAN	SUZ12 polycomb repressive complex 2 subunit	401					histone ubiquitination (GO:0016574)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	ESC/E(Z) complex (GO:0035098)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|sex chromatin (GO:0001739)	chromatin binding (GO:0003682)|histone methyltransferase activity (GO:0042054)|metal ion binding (GO:0046872)|methylated histone binding (GO:0035064)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)		SSH2/SUZ12(2)|JAZF1/SUZ12(133)	breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|lung(5)|skin(1)	21		Myeloproliferative disorder(56;0.0255)|all_hematologic(16;0.041)|Ovarian(249;0.182)|Breast(31;0.231)				ATGTTTTCAGCTGTTAAAGAA	0.254			T	JAZF1	endometrial stromal tumours																																p.A401V		Atlas-SNP	.		Dom	yes		17	17q11.2	23512	suppressor of zeste 12 homolog (Drosophila)		M	.	SUZ12	61	.	0			c.C1202T						.						33.0	34.0	34.0					17																	30320261		2189	4278	6467	SO:0001630	splice_region_variant	23512	exon11			TTTCAGCTGTTAA	D63881	CCDS11270.1	17q21	2013-06-05	2013-06-05		ENSG00000178691	ENSG00000178691		"""Zinc fingers, C2H2-type"""	17101	protein-coding gene	gene with protein product		606245	"""suppressor of zeste 12 homolog (Drosophila)"""			8590280, 11371647, 18784248	Standard	NM_015355		Approved	JJAZ1, KIAA0160, CHET9	uc002hgs.2	Q15022	OTTHUMG00000132813	ENST00000322652.5:c.1202-1C>T	chr17.hg19:g.30320261C>T		633.0	0.0		457.0	27.0	NM_015355	Q96BD9	Missense_Mutation	SNP	ENST00000322652.5	hg19	CCDS11270.1	.	.	.	.	.	.	.	.	.	.	c	16.14	3.038045	0.54896	.	.	ENSG00000178691	ENST00000322652	T	0.48201	0.82	5.18	5.18	0.71444	.	0.153345	0.56097	D	0.000023	T	0.56804	0.2010	L	0.29908	0.895	0.80722	D	1	B;D	0.63880	0.267;0.993	B;D	0.65443	0.058;0.935	T	0.52373	-0.8584	9	.	.	.	.	19.097	0.93257	0.0:1.0:0.0:0.0	.	401;401	A8K1U9;Q15022	.;SUZ12_HUMAN	V	401	ENSP00000316578:A401V	.	A	+	2	0	SUZ12	27344374	1.000000	0.71417	1.000000	0.80357	0.899000	0.52679	5.459000	0.66685	2.592000	0.87571	0.644000	0.83932	GCT	.	.		0.254	SUZ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256260.2	NM_015355	Missense_Mutation
LUC7L3	51747	hgsc.bcm.edu	37	17	48817694	48817694	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:48817694A>T	ENST00000505658.1	+	3	383	c.194A>T	c.(193-195)aAt>aTt	p.N65I	LUC7L3_ENST00000240304.1_Missense_Mutation_p.N65I|LUC7L3_ENST00000544170.1_5'UTR|LUC7L3_ENST00000393227.2_Missense_Mutation_p.N65I			O95232	LC7L3_HUMAN	LUC7-like 3 (S. cerevisiae)	65					mRNA splice site selection (GO:0006376)|RNA splicing (GO:0008380)	focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|U1 snRNP (GO:0005685)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	12						CATGATGAAAATCTACGAAAA	0.328																																					p.N65I		Atlas-SNP	.											.	LUC7L3	32	.	0			c.A194T						.						103.0	104.0	104.0					17																	48817694		2203	4300	6503	SO:0001583	missense	51747	exon3			ATGAAAATCTACG		CCDS11573.1	17q21.33	2010-02-17			ENSG00000108848	ENSG00000108848			24309	protein-coding gene	gene with protein product	"""cisplatin resistance associated overexpressed protein"", ""CRE-associated protein"""	609434				10631324, 12565863	Standard	NM_016424		Approved	LUC7A, CROP, OA48-18, CREAP-1, FLJ11063, CRA, hLuc7A	uc002iss.3	O95232	OTTHUMG00000162257	ENST00000505658.1:c.194A>T	chr17.hg19:g.48817694A>T	ENSP00000425092:p.Asn65Ile	94.0	0.0		119.0	65.0	NM_006107	B3KN54|D3DTY1|Q6PHR9|Q9NUY0|Q9P2S7	Missense_Mutation	SNP	ENST00000505658.1	hg19	CCDS11573.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.835289	0.71373	.	.	ENSG00000108848	ENST00000505658;ENST00000393227;ENST00000240304;ENST00000542316;ENST00000505619	T;T;T;T	0.44083	1.23;1.23;1.23;0.93	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	T	0.56761	0.2007	L	0.46741	1.465	0.80722	D	1	D;D	0.69078	0.997;0.997	D;D	0.81914	0.995;0.995	T	0.54146	-0.8337	10	0.38643	T	0.18	-21.411	14.7778	0.69743	1.0:0.0:0.0:0.0	.	65;65	O95232;A8K3C5	LC7L3_HUMAN;.	I	65;65;65;65;114	ENSP00000425092:N65I;ENSP00000376919:N65I;ENSP00000240304:N65I;ENSP00000420933:N114I	ENSP00000240304:N65I	N	+	2	0	LUC7L3	46172693	1.000000	0.71417	0.998000	0.56505	0.980000	0.70556	8.296000	0.89940	2.149000	0.67028	0.477000	0.44152	AAT	.	.		0.328	LUC7L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368205.2	NM_016424	
VEZF1	7716	hgsc.bcm.edu	37	17	56060489	56060489	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:56060489T>G	ENST00000581208.1	-	2	339	c.299A>C	c.(298-300)aAg>aCg	p.K100T	VEZF1_ENST00000584396.1_Missense_Mutation_p.K91T	NM_007146.2	NP_009077.2	Q14119	VEZF1_HUMAN	vascular endothelial zinc finger 1	100					angiogenesis (GO:0001525)|cellular defense response (GO:0006968)|endothelial cell development (GO:0001885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(2)|lung(5)|ovary(1)	10						GGACACCAACTTGATCCCTGT	0.522																																					p.K100T		Atlas-SNP	.											.	VEZF1	50	.	0			c.A299C						.						100.0	100.0	100.0					17																	56060489		2203	4300	6503	SO:0001583	missense	7716	exon2			ACCAACTTGATCC	D28118	CCDS32687.1	17q22	2012-10-05	2006-08-16	2006-08-16	ENSG00000136451	ENSG00000136451		"""Zinc fingers, C2H2-type"""	12949	protein-coding gene	gene with protein product		606747	"""zinc finger protein 161"""	ZNF161		8035792	Standard	XM_005257643		Approved	DB1	uc002ivf.1	Q14119	OTTHUMG00000178777	ENST00000581208.1:c.299A>C	chr17.hg19:g.56060489T>G	ENSP00000462337:p.Lys100Thr	80.0	0.0		97.0	27.0	NM_007146		Missense_Mutation	SNP	ENST00000581208.1	hg19	CCDS32687.1	.	.	.	.	.	.	.	.	.	.	T	20.1	3.937276	0.73557	.	.	ENSG00000136451	ENST00000258963	.	.	.	5.48	5.48	0.80851	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.64605	0.2613	L	0.27053	0.805	0.80722	D	1	D	0.57899	0.981	D	0.67900	0.954	T	0.69135	-0.5225	9	0.87932	D	0	-8.5753	15.5805	0.76432	0.0:0.0:0.0:1.0	.	100	Q14119	VEZF1_HUMAN	T	100	.	ENSP00000258963:K100T	K	-	2	0	VEZF1	53415488	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.690000	0.84178	2.094000	0.63399	0.523000	0.50628	AAG	.	.		0.522	VEZF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000443321.1		
RPTOR	57521	hgsc.bcm.edu	37	17	78704430	78704430	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:78704430T>C	ENST00000306801.3	+	5	940	c.578T>C	c.(577-579)gTc>gCc	p.V193A	RPTOR_ENST00000570891.1_Missense_Mutation_p.V193A|RPTOR_ENST00000537330.1_Missense_Mutation_p.V8A|RPTOR_ENST00000544334.2_Missense_Mutation_p.V193A	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	193					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						TCGATCTTCGTCTACGACTGC	0.542																																					p.V193A		Atlas-SNP	.											RPTOR,caecum,carcinoma,0,1	RPTOR	122	.	0			c.T578C						.						138.0	100.0	113.0					17																	78704430		2203	4300	6503	SO:0001583	missense	57521	exon5			TCTTCGTCTACGA		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.578T>C	chr17.hg19:g.78704430T>C	ENSP00000307272:p.Val193Ala	66.0	0.0		83.0	27.0	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	T	16.92	3.255592	0.59321	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T	0.63913	-0.07;-0.02	4.77	4.77	0.60923	.	0.000000	0.64402	D	0.000001	D	0.82930	0.5144	M	0.93678	3.445	0.80722	D	1	P;P;D	0.76494	0.954;0.946;0.999	D;P;D	0.67900	0.954;0.592;0.925	D	0.87850	0.2657	10	0.87932	D	0	.	14.4433	0.67333	0.0:0.0:0.0:1.0	.	193;8;193	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	A	8;193;193	ENSP00000307272:V193A;ENSP00000442479:V193A	ENSP00000307272:V193A	V	+	2	0	RPTOR	76319025	1.000000	0.71417	0.988000	0.46212	0.341000	0.28922	7.772000	0.85439	1.980000	0.57719	0.533000	0.62120	GTC	.	.		0.542	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
FSCN2	25794	hgsc.bcm.edu	37	17	79495626	79495626	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:79495626C>T	ENST00000417245.2	+	1	205	c.69C>T	c.(67-69)taC>taT	p.Y23Y	FSCN2_ENST00000334850.7_Silent_p.Y23Y|RP13-766D20.2_ENST00000430912.1_RNA|RP13-766D20.2_ENST00000442532.1_RNA	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	23					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			CTGACCGCTACCTGACAGCTG	0.637																																					p.Y23Y		Atlas-SNP	.											.	FSCN2	35	.	0			c.C69T						.						27.0	29.0	28.0					17																	79495626		2083	4208	6291	SO:0001819	synonymous_variant	25794	exon1			CCGCTACCTGACA	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"""Fascins"""	3960	protein-coding gene	gene with protein product		607643	"""fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)"", ""fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"""			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.69C>T	chr17.hg19:g.79495626C>T		143.0	0.0		211.0	59.0	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	hg19	CCDS45811.1																																																																																			.	.		0.637	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418	
FASN	2194	hgsc.bcm.edu	37	17	80038048	80038048	+	Missense_Mutation	SNP	C	C	G	rs147197890		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr17:80038048C>G	ENST00000306749.2	-	41	7332	c.7114G>C	c.(7114-7116)Gtg>Ctg	p.V2372L	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2372	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	AACTGCTGCACGAAGAAGCAT	0.612																																					p.V2372L	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G7114C						.						133.0	115.0	121.0					17																	80038048		2202	4300	6502	SO:0001583	missense	2194	exon41			GCTGCACGAAGAA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.7114G>C	chr17.hg19:g.80038048C>G	ENSP00000304592:p.Val2372Leu	79.0	0.0		103.0	49.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	8.317	0.823405	0.16678	.	.	ENSG00000169710	ENST00000306749	T	0.25414	1.8	4.68	-0.893	0.10567	Fatty acid synthase, domain 2 (1);Thioesterase (1);	0.494333	0.19981	N	0.101766	T	0.11495	0.0280	N	0.17474	0.49	0.34609	D	0.71739	B	0.09022	0.002	B	0.10450	0.005	T	0.21075	-1.0256	10	0.22109	T	0.4	-5.6822	5.308	0.15815	0.0:0.4874:0.1343:0.3783	.	2372	P49327	FAS_HUMAN	L	2372	ENSP00000304592:V2372L	ENSP00000304592:V2372L	V	-	1	0	FASN	77631337	0.819000	0.29175	0.879000	0.34478	0.495000	0.33615	-0.030000	0.12308	-0.272000	0.09259	0.591000	0.81541	GTG	.	C|1.000;T|0.000		0.612	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
DSC1	1823	hgsc.bcm.edu	37	18	28719849	28719849	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr18:28719849G>A	ENST00000257198.5	-	11	1786	c.1525C>T	c.(1525-1527)Cag>Tag	p.Q509*	DSC1_ENST00000257197.3_Nonsense_Mutation_p.Q509*|RP11-408H20.2_ENST00000581836.1_RNA	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	509	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CCTAACTTCTGATACCTAATT	0.294																																					p.Q509X		Atlas-SNP	.											.	DSC1	240	.	0			c.C1525T						.						39.0	39.0	39.0					18																	28719849		2202	4296	6498	SO:0001587	stop_gained	1823	exon11			ACTTCTGATACCT	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.1525C>T	chr18.hg19:g.28719849G>A	ENSP00000257198:p.Gln509*	119.0	0.0		110.0	44.0	NM_004948	Q9HB01	Nonsense_Mutation	SNP	ENST00000257198.5	hg19	CCDS11894.1	.	.	.	.	.	.	.	.	.	.	G	36	5.627017	0.96671	.	.	ENSG00000134765	ENST00000257197;ENST00000257198	.	.	.	5.59	-7.33	0.01431	.	1.130530	0.06668	N	0.765600	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	15.1612	0.72788	0.0:0.0603:0.6806:0.2591	.	.	.	.	X	509	.	ENSP00000257197:Q509X	Q	-	1	0	DSC1	26973847	0.010000	0.17322	0.039000	0.18376	0.703000	0.40648	-0.498000	0.06420	-1.044000	0.03254	-1.350000	0.01237	CAG	.	.		0.294	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
DSG3	1830	hgsc.bcm.edu	37	18	29052251	29052251	+	Silent	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr18:29052251C>T	ENST00000257189.4	+	13	1985	c.1902C>T	c.(1900-1902)gcC>gcT	p.A634A		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	634					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			CACTAGTGGCCCCCCTTCTGC	0.403																																					p.A634A		Atlas-SNP	.											.	DSG3	172	.	0			c.C1902T						.						92.0	97.0	95.0					18																	29052251		2203	4300	6503	SO:0001819	synonymous_variant	1830	exon13			AGTGGCCCCCCTT	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.1902C>T	chr18.hg19:g.29052251C>T		104.0	0.0		96.0	27.0	NM_001944	A8K2V2	Silent	SNP	ENST00000257189.4	hg19	CCDS11898.1																																																																																			.	.		0.403	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
NFATC1	4772	hgsc.bcm.edu	37	18	77208981	77208981	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr18:77208981C>A	ENST00000427363.2	+	4	1586	c.1586C>A	c.(1585-1587)gCc>gAc	p.A529D	NFATC1_ENST00000253506.5_Missense_Mutation_p.A529D|NFATC1_ENST00000318065.5_Missense_Mutation_p.A516D|NFATC1_ENST00000592223.1_Missense_Mutation_p.A516D|NFATC1_ENST00000586434.1_Missense_Mutation_p.A516D|NFATC1_ENST00000397790.2_Missense_Mutation_p.A57D|NFATC1_ENST00000587635.1_Missense_Mutation_p.A529D|NFATC1_ENST00000542384.1_Missense_Mutation_p.A529D|NFATC1_ENST00000591814.1_Missense_Mutation_p.A529D|NFATC1_ENST00000329101.4_Missense_Mutation_p.A516D|NFATC1_ENST00000545796.1_Missense_Mutation_p.A57D			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	529	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	AGCATGCGAGCCGTGTAAGCC	0.692																																					p.A529D	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C1586A						.						37.0	32.0	33.0					18																	77208981		2200	4297	6497	SO:0001583	missense	4772	exon4			TGCGAGCCGTGTA	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.1586C>A	chr18.hg19:g.77208981C>A	ENSP00000389377:p.Ala529Asp	95.0	0.0		86.0	42.0	NM_006162	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	hg19		.	.	.	.	.	.	.	.	.	.	C	22.2	4.256904	0.80246	.	.	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000397790;ENST00000542384;ENST00000329101;ENST00000545796;ENST00000427363;ENST00000397794	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	4.97	4.97	0.65823	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.054535	0.64402	D	0.000001	T	0.70850	0.3271	M	0.79123	2.44	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;1.0;1.0;0.999	D;D;D;D;D;D;D	0.87578	0.99;0.99;0.986;0.998;0.998;0.996;0.986	T	0.75766	-0.3202	10	0.87932	D	0	-29.192	18.2452	0.89982	0.0:1.0:0.0:0.0	.	516;516;529;529;529;516;529	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	D	529;529;57;529;516;57;516;493	ENSP00000253506:A529D;ENSP00000380892:A57D;ENSP00000442435:A529D;ENSP00000327850:A516D;ENSP00000439992:A57D	ENSP00000253506:A529D	A	+	2	0	NFATC1	75309969	1.000000	0.71417	0.670000	0.29842	0.547000	0.35210	7.450000	0.80656	2.301000	0.77427	0.655000	0.94253	GCC	.	.		0.692	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
RANBP3	8498	hgsc.bcm.edu	37	19	5925741	5925741	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:5925741T>A	ENST00000340578.6	-	10	878	c.821A>T	c.(820-822)aAt>aTt	p.N274I	RANBP3_ENST00000034275.8_Missense_Mutation_p.N206I|RANBP3_ENST00000439268.2_Missense_Mutation_p.N269I|RANBP3_ENST00000591092.1_Missense_Mutation_p.N201I|RANBP3_ENST00000541471.1_Missense_Mutation_p.N146I	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3	274					intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						CACGCTCTCATTTATCAGCTG	0.577																																					p.N274I		Atlas-SNP	.											.	RANBP3	36	.	0			c.A821T						.						64.0	69.0	67.0					19																	5925741		2066	4189	6255	SO:0001583	missense	8498	exon10			CTCTCATTTATCA	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4		ENST00000340578.6:c.821A>T	chr19.hg19:g.5925741T>A	ENSP00000341483:p.Asn274Ile	33.0	0.0		25.0	8.0	NM_007322	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	hg19	CCDS42478.1	.	.	.	.	.	.	.	.	.	.	T	12.67	2.008564	0.35415	.	.	ENSG00000031823	ENST00000340578;ENST00000439268;ENST00000034275;ENST00000324807;ENST00000541471	T;T;T;T	0.32272	1.46;1.46;2.21;1.48	5.19	3.09	0.35607	.	0.706833	0.13753	N	0.365158	T	0.21103	0.0508	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B;P;B	0.34977	0.33;0.346;0.222;0.138;0.216;0.478;0.346	B;B;B;B;B;B;B	0.29716	0.045;0.08;0.049;0.049;0.106;0.106;0.08	T	0.12091	-1.0561	10	0.41790	T	0.15	-6.5517	6.3179	0.21200	0.0:0.1931:0.0:0.8069	.	146;269;146;201;206;269;274	F5H4C2;Q53GE1;B7Z5P4;B7Z7F3;Q9H6Z4-3;Q9H6Z4-2;Q9H6Z4	.;.;.;.;.;.;RANB3_HUMAN	I	274;269;206;205;146	ENSP00000341483:N274I;ENSP00000404837:N269I;ENSP00000034275:N206I;ENSP00000445071:N146I	ENSP00000034275:N206I	N	-	2	0	RANBP3	5876741	0.002000	0.14202	0.001000	0.08648	0.024000	0.10985	1.038000	0.30254	0.919000	0.36945	0.459000	0.35465	AAT	.	.		0.577	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
TRIP10	9322	hgsc.bcm.edu	37	19	6743800	6743800	+	Nonsense_Mutation	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:6743800C>T	ENST00000313244.9	+	7	630	c.595C>T	c.(595-597)Cga>Tga	p.R199*	TRIP10_ENST00000313285.8_Nonsense_Mutation_p.R199*|TRIP10_ENST00000600428.1_Nonsense_Mutation_p.R91*|TRIP10_ENST00000596758.1_Nonsense_Mutation_p.R199*			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	199	F-BAR domain.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)			NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						GCGCTTCAACCGAGACCAAGC	0.517																																					p.R199X		Atlas-SNP	.											TRIP10_ENST00000313244,NS,carcinoma,0,2	TRIP10	104	.	0			c.C595T						.						187.0	171.0	176.0					19																	6743800		2203	4300	6503	SO:0001587	stop_gained	9322	exon7			TTCAACCGAGACC	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"""Cdc42-interacting protein"""	604504	"""salt tolerator"""	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.595C>T	chr19.hg19:g.6743800C>T	ENSP00000320117:p.Arg199*	130.0	1.0		118.0	35.0	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Nonsense_Mutation	SNP	ENST00000313244.9	hg19		.	.	.	.	.	.	.	.	.	.	C	33	5.286356	0.95517	.	.	ENSG00000125733	ENST00000313285;ENST00000313244;ENST00000420690	.	.	.	4.78	3.73	0.42828	.	0.069844	0.56097	D	0.000023	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09084	T	0.74	-6.3457	10.5836	0.45269	0.193:0.807:0.0:0.0	.	.	.	.	X	199	.	ENSP00000320117:R199X	R	+	1	2	TRIP10	6694800	1.000000	0.71417	1.000000	0.80357	0.876000	0.50452	1.430000	0.34914	1.121000	0.41925	0.462000	0.41574	CGA	.	.		0.517	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2		
COL5A3	50509	hgsc.bcm.edu	37	19	10092740	10092740	+	Splice_Site	SNP	C	C	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:10092740C>T	ENST00000264828.3	-	32	2546		c.e32+1			NM_015719.3	NP_056534.2	P25940	CO5A3_HUMAN	collagen, type V, alpha 3						axon guidance (GO:0007411)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)			NS(2)|breast(3)|central_nervous_system(2)|endometrium(11)|kidney(23)|large_intestine(12)|liver(2)|lung(35)|ovary(8)|prostate(5)|skin(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	116			Epithelial(33;7.11e-05)			TCATGACTCACCGACTTCCCT	0.532																																					.		Atlas-SNP	.											.	COL5A3	243	.	0			c.2460+1G>A						.						152.0	133.0	139.0					19																	10092740		2203	4300	6503	SO:0001630	splice_region_variant	50509	exon33			GACTCACCGACTT	AF177941	CCDS12222.1	19p13.2	2013-01-16			ENSG00000080573	ENSG00000080573		"""Collagens"""	14864	protein-coding gene	gene with protein product		120216				10722718	Standard	NM_015719		Approved		uc002mmq.1	P25940	OTTHUMG00000150019	ENST00000264828.3:c.2460+1G>A	chr19.hg19:g.10092740C>T		101.0	0.0		119.0	47.0	NM_015719	Q9NZQ6	Splice_Site	SNP	ENST00000264828.3	hg19	CCDS12222.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.149855	0.57151	.	.	ENSG00000080573	ENST00000264828	.	.	.	4.48	4.48	0.54585	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6721	0.68951	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	COL5A3	9953740	1.000000	0.71417	1.000000	0.80357	0.581000	0.36288	4.128000	0.57951	2.027000	0.59764	0.313000	0.20887	.	.	.		0.532	COL5A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315788.1	NM_015719	Intron
CYP4F3	4051	hgsc.bcm.edu	37	19	15758109	15758109	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:15758109T>C	ENST00000221307.8	+	5	547	c.500T>C	c.(499-501)tTc>tCc	p.F167S	CYP4F3_ENST00000591058.1_Missense_Mutation_p.F167S|CYP4F3_ENST00000586182.2_Missense_Mutation_p.F167S|CYP4F3_ENST00000585846.1_Missense_Mutation_p.F167S	NM_000896.2	NP_000887.2	Q08477	CP4F3_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 3	167					arachidonic acid metabolic process (GO:0019369)|icosanoid metabolic process (GO:0006690)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-tocopherol omega-hydroxylase activity (GO:0052871)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|monooxygenase activity (GO:0004497)			endometrium(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|stomach(1)	34						ATGAAGATTTTCAATGAGAGT	0.507																																					p.F167S		Atlas-SNP	.											.	CYP4F3	69	.	0			c.T500C						.						113.0	119.0	117.0					19																	15758109		2203	4300	6503	SO:0001583	missense	4051	exon5			AGATTTTCAATGA	AB002454	CCDS12332.1, CCDS59362.1	19p13.12	2013-02-21	2003-01-14		ENSG00000186529	ENSG00000186529		"""Cytochrome P450s"""	2646	protein-coding gene	gene with protein product		601270	"""cytochrome P450, subfamily IVF, polypeptide 3 (leukotriene B4 omega hydroxylase)"""	LTB4H		8486631, 9539102	Standard	NM_000896		Approved	CYP4F	uc010xol.2	Q08477	OTTHUMG00000182374	ENST00000221307.8:c.500T>C	chr19.hg19:g.15758109T>C	ENSP00000221307:p.Phe167Ser	111.0	0.0		118.0	8.0	NM_001199209	B7Z8Z3|O60634|Q5U740	Missense_Mutation	SNP	ENST00000221307.8	hg19	CCDS12332.1	.	.	.	.	.	.	.	.	.	.	.	18.52	3.642685	0.67244	.	.	ENSG00000186529	ENST00000538865;ENST00000221307	T	0.69685	-0.42	3.4	3.4	0.38934	.	0.000000	0.64402	U	0.000001	D	0.84969	0.5590	H	0.95574	3.69	0.52099	D	0.999948	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.87298	0.2303	10	0.87932	D	0	.	9.8126	0.40833	0.0:0.0:0.0:1.0	.	167;167	B7Z8Z3;Q08477	.;CP4F3_HUMAN	S	94;167	ENSP00000221307:F167S	ENSP00000221307:F167S	F	+	2	0	CYP4F3	15619109	1.000000	0.71417	0.014000	0.15608	0.969000	0.65631	6.724000	0.74747	1.400000	0.46741	0.358000	0.22013	TTC	.	.		0.507	CYP4F3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460819.3	NM_000896	
ATP13A1	57130	hgsc.bcm.edu	37	19	19756765	19756765	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:19756765T>G	ENST00000357324.6	-	24	3304	c.3278A>C	c.(3277-3279)gAg>gCg	p.E1093A	GMIP_ENST00000587238.1_5'Flank|GMIP_ENST00000203556.4_5'Flank|ATP13A1_ENST00000291503.5_Missense_Mutation_p.E975A|GMIP_ENST00000445806.2_5'Flank	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	1093						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						TGGCTCAAACTCCTTGTACAA	0.582																																					p.E1093A	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.A3278C						.						254.0	220.0	231.0					19																	19756765		2203	4300	6503	SO:0001583	missense	57130	exon24			TCAAACTCCTTGT	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"""ATPases / P-type"""	24215	protein-coding gene	gene with protein product	"""cation transporting ATPase"""		"""ATPase type 13A"""	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.3278A>C	chr19.hg19:g.19756765T>G	ENSP00000349877:p.Glu1093Ala	28.0	0.0		28.0	7.0	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Missense_Mutation	SNP	ENST00000357324.6	hg19	CCDS32970.2	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346574	0.41599	.	.	ENSG00000105726	ENST00000291503;ENST00000357324	T;T	0.71698	-0.59;-0.59	5.13	3.01	0.34805	.	0.205916	0.49916	D	0.000132	T	0.64114	0.2569	M	0.65975	2.015	0.46499	D	0.999075	B;B	0.19445	0.01;0.036	B;B	0.20384	0.013;0.029	T	0.56613	-0.7950	10	0.42905	T	0.14	-31.3201	6.2417	0.20795	0.0:0.0864:0.1616:0.752	.	1093;975	Q9HD20;Q9HD20-2	AT131_HUMAN;.	A	975;1093	ENSP00000291503:E975A;ENSP00000349877:E1093A	ENSP00000291503:E975A	E	-	2	0	ATP13A1	19617765	1.000000	0.71417	0.559000	0.28332	0.899000	0.52679	4.745000	0.62125	0.280000	0.22209	0.402000	0.26972	GAG	.	.		0.582	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410	
TSHZ3	57616	hgsc.bcm.edu	37	19	31769256	31769256	+	Silent	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:31769256A>G	ENST00000240587.4	-	2	1770	c.1443T>C	c.(1441-1443)acT>acC	p.T481T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	481					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GTTTCTCGTCAGTGACCGCTT	0.478																																					p.T481T		Atlas-SNP	.											.	TSHZ3	549	.	0			c.T1443C						.						184.0	186.0	186.0					19																	31769256		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTCGTCAGTGACC	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1443T>C	chr19.hg19:g.31769256A>G		61.0	0.0		70.0	23.0	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.		0.478	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
KMT2B	9757	hgsc.bcm.edu	37	19	36216399	36216399	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:36216399G>T	ENST00000222270.7	+	12	3662	c.3662G>T	c.(3661-3663)tGc>tTc	p.C1221F	KMT2B_ENST00000420124.1_Missense_Mutation_p.C1221F|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	1221					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TGTCAAGTCTGCTGTGACCCA	0.617																																					p.C1221F		Atlas-SNP	.											.	MLL4	229	.	0			c.G3662T						.						209.0	224.0	219.0					19																	36216399		2101	4229	6330	SO:0001583	missense	8085	exon12			AAGTCTGCTGTGA	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.3662G>T	chr19.hg19:g.36216399G>T	ENSP00000222270:p.Cys1221Phe	32.0	0.0		25.0	11.0	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Missense_Mutation	SNP	ENST00000222270.7	hg19	CCDS46055.1	.	.	.	.	.	.	.	.	.	.	G	14.18	2.459881	0.43736	.	.	ENSG00000105663	ENST00000222270;ENST00000420124	D;D	0.99983	-11.16;-11.16	5.54	5.54	0.83059	Zinc finger, PHD-finger (1);Zinc finger, PHD-type (1);	0.000000	0.49305	D	0.000155	D	0.99984	0.9995	M	0.77313	2.365	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.95146	0.8268	10	0.87932	D	0	.	18.4191	0.90582	0.0:0.0:1.0:0.0	.	1221	Q9UMN6	MLL4_HUMAN	F	1221	ENSP00000222270:C1221F;ENSP00000398837:C1221F	ENSP00000222270:C1221F	C	+	2	0	AD000671.1	40908239	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	9.077000	0.94016	2.884000	0.98904	0.655000	0.94253	TGC	.	.		0.617	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
ZC3H4	23211	hgsc.bcm.edu	37	19	47587632	47587632	+	Nonsense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:47587632G>T	ENST00000253048.5	-	9	1225	c.1188C>A	c.(1186-1188)tgC>tgA	p.C396*	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	396							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CGAAGTACTTGCAAATGACTT	0.587																																					p.C396X		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1188A						.						78.0	83.0	81.0					19																	47587632		2101	4231	6332	SO:0001587	stop_gained	23211	exon9			GTACTTGCAAATG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1188C>A	chr19.hg19:g.47587632G>T	ENSP00000253048:p.Cys396*	62.0	0.0		94.0	4.0	NM_015168	Q9Y420	Nonsense_Mutation	SNP	ENST00000253048.5	hg19	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	G	38	6.933444	0.97944	.	.	ENSG00000130749	ENST00000253048	.	.	.	5.67	4.64	0.57946	.	0.105254	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.923	0.63945	0.0747:0.0:0.9253:0.0	.	.	.	.	X	396	.	ENSP00000253048:C396X	C	-	3	2	ZC3H4	52279472	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	5.910000	0.69931	1.542000	0.49330	-0.140000	0.14226	TGC	.	.		0.587	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
SIGLEC6	946	hgsc.bcm.edu	37	19	52031019	52031019	+	Silent	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:52031019G>T	ENST00000425629.3	-	7	1324	c.1170C>A	c.(1168-1170)gtC>gtA	p.V390V	SIGLEC6_ENST00000343300.4_Intron|SIGLEC6_ENST00000474054.1_5'UTR|SIGLEC6_ENST00000391797.3_Intron|SIGLEC6_ENST00000359982.4_Intron|SIGLEC6_ENST00000436458.1_Silent_p.V338V|SIGLEC6_ENST00000346477.3_Silent_p.V374V	NM_001245.5	NP_001236.4	O43699	SIGL6_HUMAN	sialic acid binding Ig-like lectin 6	390					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(15)|ovary(1)|stomach(1)	28		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00115)|OV - Ovarian serous cystadenocarcinoma(262;0.0165)		CTGAGACCATGACGGGGTTCA	0.493																																					p.V390V		Atlas-SNP	.											.	SIGLEC6	142	.	0			c.C1170A						.						196.0	196.0	196.0					19																	52031019		1959	4154	6113	SO:0001819	synonymous_variant	946	exon7			GACCATGACGGGG	D86358	CCDS12834.3, CCDS12835.3, CCDS12836.3, CCDS54307.1, CCDS54308.1, CCDS59417.1	19q13.3	2013-01-29			ENSG00000105492	ENSG00000105492		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10875	protein-coding gene	gene with protein product		604405		CD33L, CD33L1		9465907	Standard	NM_001245		Approved	OB-BP1, SIGLEC-6, CD327	uc002pwy.3	O43699	OTTHUMG00000133571	ENST00000425629.3:c.1170C>A	chr19.hg19:g.52031019G>T		72.0	0.0		64.0	8.0	NM_001245	A8MV71|B2RTS8|C9JBE5|F8WA78|O15388|O43700	Silent	SNP	ENST00000425629.3	hg19	CCDS12834.3																																																																																			.	.		0.493	SIGLEC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257670.3	NM_001245	
PRKCG	5582	hgsc.bcm.edu	37	19	54395040	54395040	+	Silent	SNP	G	G	T	rs77550964	byFrequency	TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:54395040G>T	ENST00000263431.3	+	6	924	c.642G>T	c.(640-642)acG>acT	p.T214T	PRKCG_ENST00000536044.1_Silent_p.T214T|PRKCG_ENST00000540413.1_Silent_p.T214T|PRKCG_ENST00000542049.1_Silent_p.T101T	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	214	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	AGACCCGAACGGTGAAAGCCA	0.512																																					p.T214T		Atlas-SNP	.											.	PRKCG	246	.	0			c.G642T						.						136.0	104.0	115.0					19																	54395040		2203	4300	6503	SO:0001819	synonymous_variant	5582	exon6			CCGAACGGTGAAA	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.642G>T	chr19.hg19:g.54395040G>T		131.0	0.0		179.0	70.0	NM_002739	B7Z8Q0	Silent	SNP	ENST00000263431.3	hg19	CCDS12867.1																																																																																			.	G|0.999;A|0.001		0.512	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
ZSCAN22	342945	hgsc.bcm.edu	37	19	58850111	58850111	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:58850111A>T	ENST00000329665.4	+	3	1042	c.895A>T	c.(895-897)Agc>Tgc	p.S299C		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	299					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		ATATGCCTGCAGCGAGTGTGG	0.597																																					p.S299C		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.A895T						.						128.0	134.0	132.0					19																	58850111		2203	4300	6503	SO:0001583	missense	342945	exon3			GCCTGCAGCGAGT	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"""-"", ""Zinc fingers, C2H2-type"""	4929	protein-coding gene	gene with protein product	"""oncogene HKR2"""	165260	"""zinc finger protein 50"", ""GLI-Kruppel family member HKR2"""	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.895A>T	chr19.hg19:g.58850111A>T	ENSP00000332433:p.Ser299Cys	94.0	0.0		94.0	37.0	NM_181846	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	hg19	CCDS12975.1	.	.	.	.	.	.	.	.	.	.	A	7.262	0.605325	0.14002	.	.	ENSG00000182318	ENST00000329665	T	0.08008	3.14	3.8	2.78	0.32641	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11879	0.0289	M	0.75447	2.3	0.09310	N	1	P	0.46020	0.871	B	0.43536	0.423	T	0.25047	-1.0143	9	0.62326	D	0.03	.	3.2886	0.06940	0.6847:0.0:0.1127:0.2025	.	299	P10073	ZSC22_HUMAN	C	299	ENSP00000332433:S299C	ENSP00000332433:S299C	S	+	1	0	ZSCAN22	63541923	0.000000	0.05858	0.299000	0.25016	0.381000	0.30169	-4.570000	0.00214	0.626000	0.30322	0.379000	0.24179	AGC	.	.		0.597	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846	
CST9L	128821	hgsc.bcm.edu	37	20	23549024	23549024	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr20:23549024G>T	ENST00000376979.3	-	1	362	c.64C>A	c.(64-66)Cag>Aag	p.Q22K		NM_080610.2	NP_542177.1	Q9H4G1	CST9L_HUMAN	cystatin 9-like	22						extracellular region (GO:0005576)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8	Colorectal(13;0.0431)|Lung NSC(19;0.235)					AGCAGGATCTGGGAGCCTAAG	0.572																																					p.Q22K		Atlas-SNP	.											.	CST9L	25	.	0			c.C64A						.						106.0	94.0	98.0					20																	23549024		2203	4300	6503	SO:0001583	missense	128821	exon1			GGATCTGGGAGCC		CCDS13157.1	20p11.21	2012-08-14	2008-03-06		ENSG00000101435	ENSG00000101435			16233	protein-coding gene	gene with protein product			"""cystatin 9 (mouse)-like"""			20565543	Standard	NM_080610		Approved	bA218C14.1, CTES7B	uc002wtk.4	Q9H4G1	OTTHUMG00000032073	ENST00000376979.3:c.64C>A	chr20.hg19:g.23549024G>T	ENSP00000366178:p.Gln22Lys	83.0	0.0		101.0	40.0	NM_080610	B2R5A1	Missense_Mutation	SNP	ENST00000376979.3	hg19	CCDS13157.1	.	.	.	.	.	.	.	.	.	.	G	6.184	0.402212	0.11696	.	.	ENSG00000101435	ENST00000376979	T	0.13196	2.61	2.03	-1.67	0.08238	.	1.922710	0.03608	N	0.234429	T	0.05960	0.0155	N	0.08118	0	0.09310	N	1	B	0.25007	0.116	B	0.14578	0.011	T	0.26360	-1.0105	10	0.30078	T	0.28	.	1.9722	0.03409	0.3802:0.0:0.3577:0.2622	.	22	Q9H4G1	CST9L_HUMAN	K	22	ENSP00000366178:Q22K	ENSP00000366178:Q22K	Q	-	1	0	CST9L	23497024	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.197000	0.09518	-0.428000	0.07339	0.313000	0.20887	CAG	.	.		0.572	CST9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078338.1	NM_080610	
ZNF831	128611	hgsc.bcm.edu	37	20	57829044	57829044	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr20:57829044T>C	ENST00000371030.2	+	5	4280	c.4280T>C	c.(4279-4281)cTg>cCg	p.L1427P		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	1427							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GACACCTGCCTGGCAGTGGTT	0.522																																					p.L1427P		Atlas-SNP	.											.	ZNF831	287	.	0			c.T4280C						.						81.0	84.0	83.0					20																	57829044		2032	4207	6239	SO:0001583	missense	128611	exon5			CCTGCCTGGCAGT	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.4280T>C	chr20.hg19:g.57829044T>C	ENSP00000360069:p.Leu1427Pro	111.0	0.0		78.0	24.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	T	10.56	1.384367	0.25031	.	.	ENSG00000124203	ENST00000371030	T	0.10860	2.83	5.34	2.99	0.34606	.	0.521716	0.15872	N	0.240474	T	0.12817	0.0311	L	0.38175	1.15	0.09310	N	0.99999	D	0.55385	0.971	P	0.50440	0.641	T	0.15435	-1.0437	10	0.28530	T	0.3	-0.0836	9.5268	0.39169	0.0:0.0:0.3457:0.6543	.	1427	Q5JPB2	ZN831_HUMAN	P	1427	ENSP00000360069:L1427P	ENSP00000360069:L1427P	L	+	2	0	ZNF831	57262439	0.018000	0.18449	0.004000	0.12327	0.003000	0.03518	1.210000	0.32370	0.311000	0.23014	-0.321000	0.08615	CTG	.	.		0.522	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19726182	19726182	+	Splice_Site	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr21:19726182T>A	ENST00000284885.3	-	9	914		c.e9-2			NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15							brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						AAATAGAAGCTACAAAATAAA	0.333																																					.		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.881-2A>T						.						48.0	53.0	51.0					21																	19726182		2202	4284	6486	SO:0001630	splice_region_variant	5651	exon10			AGAAGCTACAAAA		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.881-2A>T	chr21.hg19:g.19726182T>A		311.0	0.0		304.0	22.0	NM_002772	Q2NKL7	Splice_Site	SNP	ENST00000284885.3	hg19	CCDS13571.1	.	.	.	.	.	.	.	.	.	.	T	13.18	2.158960	0.38119	.	.	ENSG00000154646	ENST00000284885	.	.	.	4.6	4.6	0.57074	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9538	0.58415	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	TMPRSS15	18648053	1.000000	0.71417	0.951000	0.38953	0.424000	0.31475	4.858000	0.62947	1.934000	0.56057	0.528000	0.53228	.	.	.		0.333	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	Intron
TMPRSS3	64699	hgsc.bcm.edu	37	21	43802299	43802299	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr21:43802299G>A	ENST00000291532.3	-	9	1782	c.827C>T	c.(826-828)tCc>tTc	p.S276F	TMPRSS3_ENST00000433957.2_Missense_Mutation_p.S276F|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.S276F|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.S360F|TMPRSS3_ENST00000398405.1_Missense_Mutation_p.S274F	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	276	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						GTCCAACAGGGAAACTAGACC	0.502																																					p.S276F		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.C827T						.						106.0	81.0	89.0					21																	43802299		2203	4300	6503	SO:0001583	missense	64699	exon9			AACAGGGAAACTA	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.827C>T	chr21.hg19:g.43802299G>A	ENSP00000291532:p.Ser276Phe	95.0	0.0		90.0	27.0	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	hg19	CCDS13686.1	.	.	.	.	.	.	.	.	.	.	G	8.537	0.872348	0.17322	.	.	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	T;D;D;T;D	0.81821	0.17;-1.54;-1.54;0.17;-1.54	4.8	2.98	0.34508	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.358897	0.25762	N	0.028471	T	0.66703	0.2816	L	0.28344	0.845	0.23010	N	0.998432	B;P;B;P	0.47034	0.21;0.646;0.075;0.889	B;B;B;B	0.43575	0.096;0.111;0.063;0.424	T	0.57516	-0.7798	9	.	.	.	.	5.2162	0.15344	0.2401:0.1533:0.6065:0.0	.	276;276;276;274	P57727-3;P57727-5;P57727;B7WPR2	.;.;TMPS3_HUMAN;.	F	276;276;274;360;276	ENSP00000291532:S276F;ENSP00000411013:S276F;ENSP00000381442:S274F;ENSP00000369762:S360F;ENSP00000381434:S276F	.	S	-	2	0	TMPRSS3	42675368	0.998000	0.40836	0.692000	0.30179	0.101000	0.19017	1.938000	0.40203	1.020000	0.39573	-0.137000	0.14449	TCC	.	.		0.502	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
C22orf42	150297	hgsc.bcm.edu	37	22	32546378	32546378	+	Silent	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:32546378A>G	ENST00000382097.3	-	7	654	c.582T>C	c.(580-582)ctT>ctC	p.L194L	C22orf42_ENST00000490640.1_5'Flank	NM_001010859.1	NP_001010859.1	Q6IC83	CV042_HUMAN	chromosome 22 open reading frame 42	194										NS(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(2)	24						TGAAGTCTTCAAGAGAGACAG	0.438																																					p.L194L		Atlas-SNP	.											.	C22orf42	37	.	0			c.T582C						.						145.0	132.0	136.0					22																	32546378		2203	4300	6503	SO:0001819	synonymous_variant	150297	exon7			GTCTTCAAGAGAG	BC040263	CCDS33639.1	22q12.3	2009-03-05			ENSG00000205856	ENSG00000205856			27160	protein-coding gene	gene with protein product						12477932	Standard	XM_005261369		Approved		uc003amd.3	Q6IC83	OTTHUMG00000030380	ENST00000382097.3:c.582T>C	chr22.hg19:g.32546378A>G		437.0	1.0		450.0	172.0	NM_001010859	A4QPH5	Silent	SNP	ENST00000382097.3	hg19	CCDS33639.1																																																																																			.	.		0.438	C22orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075268.2	NM_001010859	
L3MBTL2	83746	hgsc.bcm.edu	37	22	41616753	41616753	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:41616753T>A	ENST00000216237.5	+	7	892	c.734T>A	c.(733-735)cTt>cAt	p.L245H		NM_031488.4	NP_113676.2	Q969R5	LMBL2_HUMAN	l(3)mbt-like 2 (Drosophila)	245					chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CGGGTGCTGCTTCGGTATGAA	0.502																																					p.L245H		Atlas-SNP	.											.	L3MBTL2	61	.	0			c.T734A						.						109.0	98.0	102.0					22																	41616753		2203	4300	6503	SO:0001583	missense	83746	exon7			TGCTGCTTCGGTA	AJ305226	CCDS14011.1	22q13.31-q13.33	2008-06-11			ENSG00000100395	ENSG00000100395			18594	protein-coding gene	gene with protein product		611865				11682070	Standard	NM_031488		Approved	H-l(3)mbt-l, DKFZP761I141, dJ756G23.3	uc003azo.3	Q969R5	OTTHUMG00000150942	ENST00000216237.5:c.734T>A	chr22.hg19:g.41616753T>A	ENSP00000216237:p.Leu245His	54.0	0.0		59.0	26.0	NM_031488	Q8TEN1|Q96SC4|Q9BQI2|Q9UGS4	Missense_Mutation	SNP	ENST00000216237.5	hg19	CCDS14011.1	.	.	.	.	.	.	.	.	.	.	T	21.5	4.156726	0.78114	.	.	ENSG00000100395	ENST00000216237	T	0.58940	0.3	5.37	5.37	0.77165	.	0.318671	0.32608	N	0.005861	T	0.80904	0.4713	M	0.91717	3.235	0.58432	D	0.999999	D;D	0.89917	0.999;1.0	D;D	0.79108	0.939;0.992	D	0.85647	0.1280	10	0.87932	D	0	.	15.677	0.77336	0.0:0.0:0.0:1.0	.	245;245	Q969R5-3;Q969R5	.;LMBL2_HUMAN	H	245	ENSP00000216237:L245H	ENSP00000216237:L245H	L	+	2	0	L3MBTL2	39946699	1.000000	0.71417	0.977000	0.42913	0.834000	0.47266	7.990000	0.88215	2.169000	0.68431	0.374000	0.22700	CTT	.	.		0.502	L3MBTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320613.1	NM_031488	
SULT4A1	25830	hgsc.bcm.edu	37	22	44237809	44237809	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:44237809G>A	ENST00000330884.4	-	2	293	c.173C>T	c.(172-174)aCc>aTc	p.T58I	SULT4A1_ENST00000249130.5_Missense_Mutation_p.T58I|SULT4A1_ENST00000540422.1_Intron	NM_014351.3	NP_055166.1	Q9BR01	ST4A1_HUMAN	sulfotransferase family 4A, member 1	58					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	sulfotransferase activity (GO:0008146)			kidney(1)|large_intestine(3)|lung(4)|ovary(1)	9		Ovarian(80;0.024)|all_neural(38;0.0416)		Colorectal(1;0.00242)|READ - Rectum adenocarcinoma(1;0.0419)		CAGCAAGCTGGTGCCTGGAGG	0.662																																					p.T58I		Atlas-SNP	.											.	SULT4A1	26	.	0			c.C173T						.						33.0	33.0	33.0					22																	44237809		2203	4299	6502	SO:0001583	missense	25830	exon2			AAGCTGGTGCCTG	AF188698	CCDS14051.1	22q13.2	2012-11-05			ENSG00000130540	ENSG00000130540		"""Sulfotransferases, cytosolic"""	14903	protein-coding gene	gene with protein product		608359				10698717	Standard	NM_014351		Approved	SULTX3, hBR-STL-1	uc003bee.1	Q9BR01	OTTHUMG00000141314	ENST00000330884.4:c.173C>T	chr22.hg19:g.44237809G>A	ENSP00000332565:p.Thr58Ile	35.0	0.0		47.0	17.0	NM_014351	B2R7N3|O43728	Missense_Mutation	SNP	ENST00000330884.4	hg19	CCDS14051.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625606	0.87560	.	.	ENSG00000130540	ENST00000330884;ENST00000249130	T;T	0.05199	3.48;3.48	4.4	4.4	0.53042	Sulfotransferase domain (1);	0.000000	0.85682	D	0.000000	T	0.31638	0.0803	M	0.89840	3.065	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.40403	-0.9565	10	0.87932	D	0	.	15.943	0.79771	0.0:0.0:1.0:0.0	.	58	Q9BR01	ST4A1_HUMAN	I	58	ENSP00000332565:T58I;ENSP00000249130:T58I	ENSP00000249130:T58I	T	-	2	0	SULT4A1	42569142	1.000000	0.71417	0.945000	0.38365	0.953000	0.61014	9.066000	0.93949	1.999000	0.58509	0.650000	0.86243	ACC	.	.		0.662	SULT4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280660.2	NM_014351	
DMD	1756	hgsc.bcm.edu	37	X	32827649	32827649	+	Nonsense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:32827649T>A	ENST00000357033.4	-	7	816	c.610A>T	c.(610-612)Aga>Tga	p.R204*	DMD_ENST00000378677.2_Nonsense_Mutation_p.R200*|DMD_ENST00000288447.4_Nonsense_Mutation_p.R196*	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	204	Actin-binding.|CH 2. {ECO:0000255|PROSITE- ProRule:PRU00044}.				cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AATTGATATCTGGCGATGTTG	0.413																																					p.R204X		Atlas-SNP	.											.	DMD	2127	.	0			c.A610T						.						186.0	138.0	154.0					X																	32827649		2202	4300	6502	SO:0001587	stop_gained	1756	exon7			GATATCTGGCGAT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.610A>T	chrX.hg19:g.32827649T>A	ENSP00000354923:p.Arg204*	56.0	0.0		63.0	38.0	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Nonsense_Mutation	SNP	ENST00000357033.4	hg19	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	T	40	7.989021	0.98596	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280;ENST00000288447	.	.	.	5.17	4.02	0.46733	.	0.514114	0.13704	U	0.368623	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	.	5.8858	0.18880	0.0:0.087:0.1646:0.7484	.	.	.	.	X	196;200;204;204;81;196	.	ENSP00000288447:R196X	R	-	1	2	DMD	32737570	1.000000	0.71417	0.285000	0.24819	0.952000	0.60782	2.851000	0.48302	0.642000	0.30620	0.345000	0.21793	AGA	.	.		0.413	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
AMER1	139285	hgsc.bcm.edu	37	X	63412647	63412647	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:63412647T>C	ENST00000330258.3	-	2	792	c.520A>G	c.(520-522)Agc>Ggc	p.S174G	AMER1_ENST00000374869.3_Missense_Mutation_p.S174G|AMER1_ENST00000403336.1_Missense_Mutation_p.S174G	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	174					adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									CGGATACTGCTAAAAAAGCCT	0.557																																					p.S174G		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A520G						.						53.0	50.0	51.0					X																	63412647		2203	4300	6503	SO:0001583	missense	139285	exon2			TACTGCTAAAAAA	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.520A>G	chrX.hg19:g.63412647T>C	ENSP00000329117:p.Ser174Gly	48.0	0.0		44.0	32.0	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	hg19	CCDS14377.2	.	.	.	.	.	.	.	.	.	.	T	14.39	2.521541	0.44866	.	.	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.23147	1.92;1.92;1.92	4.74	4.74	0.60224	.	0.458634	0.25058	N	0.033470	T	0.32793	0.0841	M	0.65975	2.015	0.29060	N	0.883973	P	0.52692	0.955	P	0.45753	0.492	T	0.36187	-0.9758	10	0.62326	D	0.03	-2.908	12.3652	0.55224	0.0:0.0:0.0:1.0	.	174	Q5JTC6	F123B_HUMAN	G	174	ENSP00000364003:S174G;ENSP00000329117:S174G;ENSP00000384722:S174G	ENSP00000329117:S174G	S	-	1	0	FAM123B	63329372	1.000000	0.71417	0.992000	0.48379	0.978000	0.69477	4.440000	0.59975	1.867000	0.54127	0.486000	0.48141	AGC	.	.		0.557	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
ATP7A	538	hgsc.bcm.edu	37	X	77258571	77258571	+	Splice_Site	SNP	A	A	T			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:77258571A>T	ENST00000341514.6	+	6	1700	c.1545A>T	c.(1543-1545)ggA>ggT	p.G515G	ATP7A_ENST00000343533.5_Splice_Site_p.G515G|ATP7A_ENST00000350425.4_Intron	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	515	HMA 5. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	TGCTCTTAGGAATATATTCTA	0.338																																					p.G515G		Atlas-SNP	.											.	ATP7A	248	.	0			c.A1545T						.						105.0	98.0	100.0					X																	77258571		2203	4295	6498	SO:0001630	splice_region_variant	538	exon6			CTTAGGAATATAT	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1544-1A>T	chrX.hg19:g.77258571A>T		82.0	0.0		82.0	70.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Silent	SNP	ENST00000341514.6	hg19	CCDS35339.1																																																																																			.	.		0.338	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	Silent
IGSF1	3547	hgsc.bcm.edu	37	X	130420012	130420012	+	Silent	SNP	A	A	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:130420012A>G	ENST00000361420.3	-	4	187	c.108T>C	c.(106-108)ccT>ccC	p.P36P	IGSF1_ENST00000370903.3_Silent_p.P36P|IGSF1_ENST00000370910.1_Silent_p.P27P|IGSF1_ENST00000370901.4_Silent_p.P36P|IGSF1_ENST00000370904.1_Silent_p.P27P|IGSF1_ENST00000370900.1_Silent_p.P36P			Q8N6C5	IGSF1_HUMAN	immunoglobulin superfamily, member 1	36					regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	coreceptor activity (GO:0015026)|inhibin binding (GO:0034711)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(15)|liver(1)|lung(37)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)	78						ACTCTGGTTGAGGGTCCATCA	0.507																																					p.P36P		Atlas-SNP	.											.	IGSF1	231	.	0			c.T108C						.						78.0	77.0	77.0					X																	130420012		2203	4300	6503	SO:0001819	synonymous_variant	3547	exon4			TGGTTGAGGGTCC	AF034198	CCDS14629.1, CCDS14630.1, CCDS55490.1, CCDS55491.1	Xq25	2013-01-11			ENSG00000147255	ENSG00000147255		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5948	protein-coding gene	gene with protein product		300137				9521868, 9729118	Standard	NM_001555		Approved	KIAA0364, IGDC1, IGCD1, INHBP, MGC75490, PGSF2	uc004ewe.4	Q8N6C5	OTTHUMG00000022406	ENST00000361420.3:c.108T>C	chrX.hg19:g.130420012A>G		65.0	0.0		49.0	30.0	NM_001555	B5MEG2|H9KV64|O15070|Q9NTC8	Silent	SNP	ENST00000361420.3	hg19	CCDS14629.1																																																																																			.	.		0.507	IGSF1-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058288.1		
SLITRK4	139065	hgsc.bcm.edu	37	X	142716502	142716502	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:142716502T>A	ENST00000381779.4	-	2	2648	c.2423A>T	c.(2422-2424)aAg>aTg	p.K808M	SLITRK4_ENST00000356928.1_Missense_Mutation_p.K808M|SLITRK4_ENST00000338017.4_Missense_Mutation_p.K808M	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	808						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					ATACTCACTCTTCCTTTGTTC	0.423																																					p.K808M		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A2423T						.						148.0	126.0	133.0					X																	142716502		2203	4300	6503	SO:0001583	missense	139065	exon2			TCACTCTTCCTTT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.2423A>T	chrX.hg19:g.142716502T>A	ENSP00000371198:p.Lys808Met	67.0	0.0		72.0	8.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	T	18.90	3.722420	0.68959	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.62105	0.05;0.05;0.05	5.39	5.39	0.77823	.	0.000000	0.85682	U	0.000000	T	0.74876	0.3774	M	0.62723	1.935	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.77838	-0.2439	10	0.87932	D	0	-8.2631	13.1568	0.59522	0.0:0.0:0.0:1.0	.	808	Q8IW52	SLIK4_HUMAN	M	808	ENSP00000371198:K808M;ENSP00000349400:K808M;ENSP00000336627:K808M	ENSP00000336627:K808M	K	-	2	0	SLITRK4	142544168	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	1.789000	0.52484	0.486000	0.48141	AAG	.	.		0.423	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
SLITRK4	139065	hgsc.bcm.edu	37	X	142716504	142716504	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:142716504C>G	ENST00000381779.4	-	2	2646	c.2421G>C	c.(2419-2421)agG>agC	p.R807S	SLITRK4_ENST00000356928.1_Missense_Mutation_p.R807S|SLITRK4_ENST00000338017.4_Missense_Mutation_p.R807S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	807						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					ACTCACTCTTCCTTTGTTCCA	0.428																																					p.R807S		Atlas-SNP	.											.	SLITRK4	162	.	0			c.G2421C						.						148.0	126.0	133.0					X																	142716504		2203	4300	6503	SO:0001583	missense	139065	exon2			ACTCTTCCTTTGT	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.2421G>C	chrX.hg19:g.142716504C>G	ENSP00000371198:p.Arg807Ser	64.0	0.0		71.0	8.0	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Missense_Mutation	SNP	ENST00000381779.4	hg19	CCDS14679.1	.	.	.	.	.	.	.	.	.	.	C	4.735	0.136613	0.09032	.	.	ENSG00000179542	ENST00000381779;ENST00000356928;ENST00000338017	T;T;T	0.50813	0.73;0.73;0.73	5.39	2.18	0.27775	.	0.000000	0.85682	U	0.000000	T	0.25419	0.0618	N	0.20530	0.585	0.53688	D	0.999977	B	0.15473	0.013	B	0.17433	0.018	T	0.04767	-1.0928	10	0.11794	T	0.64	-6.163	5.7057	0.17907	0.0:0.4243:0.0:0.5757	.	807	Q8IW52	SLIK4_HUMAN	S	807	ENSP00000371198:R807S;ENSP00000349400:R807S;ENSP00000336627:R807S	ENSP00000336627:R807S	R	-	3	2	SLITRK4	142544170	0.690000	0.27699	1.000000	0.80357	0.996000	0.88848	-0.143000	0.10296	0.450000	0.26774	0.600000	0.82982	AGG	.	.		0.428	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
MAGEA1	4100	hgsc.bcm.edu	37	X	152482572	152482572	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrX:152482572C>A	ENST00000356661.5	-	3	657	c.439G>T	c.(439-441)Gcc>Tcc	p.A147S		NM_004988.4	NP_004979.3	P43355	MAGA1_HUMAN	melanoma antigen family A, 1 (directs expression of antigen MZ2-E)	147	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(7)|kidney(2)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					GACTCAGAGGCTTTGCCGAAG	0.512																																					p.A147S		Atlas-SNP	.											.	MAGEA1	57	.	0			c.G439T						.						135.0	130.0	132.0					X																	152482572		2203	4300	6503	SO:0001583	missense	4100	exon3			CAGAGGCTTTGCC		CCDS76051.1	Xq28	2010-05-26			ENSG00000198681	ENSG00000198681			6796	protein-coding gene	gene with protein product	"""melanoma-associated antigen 1"", ""melanoma-associated antigen MZ2-E"", ""melanoma antigen MAGE-1"", ""melanoma antigen family A 1"", ""cancer/testis antigen family 1, member 1"""	300016		MAGE1		1840703	Standard	NM_004988		Approved	MGC9326, CT1.1	uc004fhf.2	P43355	OTTHUMG00000024192	ENST00000356661.5:c.439G>T	chrX.hg19:g.152482572C>A	ENSP00000349085:p.Ala147Ser	116.0	0.0		131.0	8.0	NM_004988	B2RC81|O00346	Missense_Mutation	SNP	ENST00000356661.5	hg19	CCDS14720.1	.	.	.	.	.	.	.	.	.	.	C	10.80	1.452124	0.26074	.	.	ENSG00000198681	ENST00000356661	T	0.11277	2.79	1.28	0.37	0.16160	.	0.336075	0.33959	N	0.004387	T	0.28699	0.0711	M	0.88906	2.99	0.09310	N	1	P	0.49358	0.923	D	0.64506	0.926	T	0.07195	-1.0785	10	0.66056	D	0.02	.	3.7344	0.08504	0.0:0.7313:0.0:0.2687	.	147	P43355	MAGA1_HUMAN	S	147	ENSP00000349085:A147S	ENSP00000349085:A147S	A	-	1	0	MAGEA1	152135766	0.001000	0.12720	0.003000	0.11579	0.008000	0.06430	0.196000	0.17176	0.053000	0.16036	-1.130000	0.01982	GCC	.	.		0.512	MAGEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060940.1	NM_004988	
MT-ND3	4537	hgsc.bcm.edu	37	M	10251	10251	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chrM:10251T>C	ENST00000361227.2	+	1	193	c.193T>C	c.(193-195)Ttt>Ctt	p.F65L	MT-TG_ENST00000387429.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TS2_ENST00000387449.1_RNA			P03897	NU3M_HUMAN	mitochondrially encoded NADH dehydrogenase 3	65					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)										CCTTCTTATTATTTGATCTAG	0.428																																					p.F65L		Atlas-SNP	.											.	.	.	.	0			c.T193C						.																																			SO:0001583	missense	0	exon1			TTATTATTTGATC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198840	ENSG00000198840	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7458	protein-coding gene	gene with protein product	"""complex I ND3 subunit"", ""NADH-ubiquinone oxidoreductase chain 3"""	516002	"""NADH dehydrogenase 3"""	MTND3			Standard			Approved	ND3, NAD3		P03897		ENST00000361227.2:c.193T>C	chrM.hg19:g.10251T>C	ENSP00000355206:p.Phe65Leu	19.0	0.0		38.0	17.0	ENST00000361227		Missense_Mutation	SNP	ENST00000361227.2	hg19																																																																																				.	.		0.428	MT-ND3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024033	
MIER1	57708	hgsc.bcm.edu	37	1	67450363	67450364	+	In_Frame_Ins	INS	-	-	GAT			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:67450363_67450364insGAT	ENST00000355356.3	+	13	1468_1469	c.1319_1320insGAT	c.(1318-1323)gatatg>gaGATtatg	p.440_440D>EI	MIER1_ENST00000401042.3_Intron|MIER1_ENST00000357692.2_In_Frame_Ins_p.457_457D>EI|MIER1_ENST00000371016.1_Intron|MIER1_ENST00000371018.3_Intron|MIER1_ENST00000371014.1_Intron|MIER1_ENST00000355977.6_Intron|MIER1_ENST00000401041.1_In_Frame_Ins_p.493_493D>EI	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	440					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						CTTCATGCAGATATGGATACTA	0.351																																					p.D493delinsEI		Atlas-INDEL	.											.	MIER1	86	.	0			c.1478_1479insGAT						.																																			SO:0001652	inframe_insertion	57708	exon14			.		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"""mesoderm induction early response 1 homolog (Xenopus laevis)"""			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	Exception_encountered	chr1.hg19:g.67450363_67450364insGAT	ENSP00000347514:p.Asp440delinsGluIle	193.0	0.0		184.0	64.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	In_Frame_Ins	INS	ENST00000355356.3	hg19	CCDS41348.1																																																																																			.	.		0.351	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	
EFCAB7	84455	hgsc.bcm.edu	37	1	64021164	64021165	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:64021164_64021165insTA	ENST00000371088.4	+	9	1438_1439	c.1192_1193insTA	c.(1192-1194)ttafs	p.L398fs	EFCAB7_ENST00000461039.1_3'UTR	NM_032437.2	NP_115813.2	A8K855	EFCB7_HUMAN	EF-hand calcium binding domain 7	398							calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	19						AACAGGGGAATTATTCCTTACA	0.342																																					p.L398fs		Atlas-INDEL	.											.	EFCAB7	45	.	0			c.1192_1193insTA						.																																			SO:0001589	frameshift_variant	84455	exon9			.	BC015814	CCDS30737.1	1p31.3	2013-01-10			ENSG00000203965	ENSG00000203965		"""EF-hand domain containing"""	29379	protein-coding gene	gene with protein product						11347906	Standard	NM_032437		Approved	KIAA1799, RP4-534K7.1	uc001dbf.3	A8K855	OTTHUMG00000008983	ENST00000371088.4:c.1193_1194dupTA	chr1.hg19:g.64021165_64021166dupTA	ENSP00000360129:p.Leu398fs	213.0	0.0		231.0	93.0	NM_032437	Q658P0|Q96B95|Q96JM6	Frame_Shift_Ins	INS	ENST00000371088.4	hg19	CCDS30737.1																																																																																			.	.		0.342	EFCAB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024910.1	NM_032437	
ALB	213	hgsc.bcm.edu	37	4	74282058	74282071	+	Splice_Site	DEL	AATTCCAGAATGCG	AATTCCAGAATGCG	-	rs370819889		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	AATTCCAGAATGCG	AATTCCAGAATGCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:74282058_74282071delAATTCCAGAATGCG	ENST00000503124.1	+	8	1034_1046	c.827_839delAATTCCAGAATGCG	c.(826-840)aaattccagaatgcg>ag	p.KFQNA276fs	ALB_ENST00000505649.1_3'UTR|ALB_ENST00000401494.3_Splice_Site_p.KFQNA311fs|ALB_ENST00000415165.2_Splice_Site_p.KFQNA234fs|ALB_ENST00000509063.1_Splice_Site_p.KFQNA426fs|ALB_ENST00000295897.4_Splice_Site_p.KFQNA426fs			Q8TES7	FBF1_HUMAN	albumin	0					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)		p.A430V(1)		NS(1)|endometrium(4)|kidney(1)|large_intestine(6)|liver(9)|lung(16)|ovary(3)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	48	Breast(15;0.00102)		Epithelial(6;4.8e-05)|OV - Ovarian serous cystadenocarcinoma(6;0.000263)|all cancers(17;0.000472)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GGAGAGTACAAATTCCAGAATGCGTAAGTAATTT	0.29																																					p.426_430del		Atlas-INDEL	.											.	ALB	132	.	1	Substitution - Missense(1)	stomach(1)	c.1276_1289del						.																																			SO:0001630	splice_region_variant	213	exon10			.	V00494	CCDS3555.1	4q13.3	2008-02-05	2006-06-30	2006-06-30	ENSG00000163631	ENSG00000163631			399	protein-coding gene	gene with protein product		103600				6292049, 6192711	Standard	NM_000477		Approved		uc003hgs.4	P02768	OTTHUMG00000129919	ENST00000503124.1:c.839+1AATTCCAGAATGCG>-	chr4.hg19:g.74282058_74282071delAATTCCAGAATGCG		231.0	0.0		178.0	56.0	NM_000477	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Frame_Shift_Del	DEL	ENST00000503124.1	hg19																																																																																				.	.		0.290	ALB-011	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000365419.1	NM_000477	Frame_Shift_Del
C19orf80	55908	hgsc.bcm.edu	37	19	11350417	11350428	+	In_Frame_Del	DEL	TGACCCTGCTCT	TGACCCTGCTCT	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	TGACCCTGCTCT	TGACCCTGCTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr19:11350417_11350428delTGACCCTGCTCT	ENST00000252453.8	+	1	123_134	c.104_115delTGACCCTGCTCT	c.(103-117)ctgaccctgctcttc>ctc	p.TLLF36del	DOCK6_ENST00000319867.7_5'Flank|DOCK6_ENST00000294618.7_Intron|C19orf80_ENST00000591200.1_Intron	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	36					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CATGAGGAGCTGACCCTGCTCTTCCATGGGAC	0.67																																					p.35_38del		Atlas-INDEL	.											.	C19orf80	8	.	0			c.103_114del						.																																			SO:0001651	inframe_deletion	55908	exon1			.		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"""lipasin"", ""betatrophin"""					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.104_115delTGACCCTGCTCT	chr19.hg19:g.11350417_11350428delTGACCCTGCTCT	ENSP00000252453:p.Thr36_Phe39del	103.0	0.0		115.0	32.0	NM_018687	Q9NQZ1	In_Frame_Del	DEL	ENST00000252453.8	hg19	CCDS54220.1																																																																																			.	.		0.670	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687	
DAPK1	1612	hgsc.bcm.edu	37	9	90219888	90219888	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:90219888delA	ENST00000408954.3	+	3	417	c.82delA	c.(82-84)aagfs	p.K29fs	DAPK1_ENST00000469640.2_Frame_Shift_Del_p.K29fs|DAPK1_ENST00000358077.5_Frame_Shift_Del_p.K29fs|DAPK1_ENST00000472284.1_Frame_Shift_Del_p.K29fs|DAPK1_ENST00000491893.1_Frame_Shift_Del_p.K29fs	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	29	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						TGCGGTTGTGAAGAAATGCCG	0.498									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.V27fs		Atlas-INDEL	.											.	DAPK1	329	.	0			c.81delG						.						33.0	34.0	33.0					9																	90219888		1997	4184	6181	SO:0001589	frameshift_variant	1612	exon3	Familial Cancer Database	Familial CLL	.	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.82delA	chr9.hg19:g.90219888delA	ENSP00000386135:p.Lys29fs	120.0	0.0		89.0	36.0	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Frame_Shift_Del	DEL	ENST00000408954.3	hg19	CCDS43842.1																																																																																			.	.		0.498	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
IFIT5	24138	hgsc.bcm.edu	37	10	91177145	91177145	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr10:91177145delA	ENST00000371795.4	+	2	402	c.189delA	c.(187-189)ctafs	p.L63fs	IFIT5_ENST00000416601.1_Frame_Shift_Del_p.L63fs|LIPA_ENST00000371837.1_5'Flank	NM_012420.2	NP_036552.1	Q13325	IFIT5_HUMAN	interferon-induced protein with tetratricopeptide repeats 5	63					defense response to virus (GO:0051607)|innate immune response (GO:0045087)	actin cytoskeleton (GO:0015629)|apical part of cell (GO:0045177)|ruffle membrane (GO:0032587)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)|tRNA binding (GO:0000049)			endometrium(1)|large_intestine(4)|lung(4)	9						TGAAACACCTAAAAGGCCAAA	0.398																																					p.L63fs		Atlas-INDEL	.											.	IFIT5	32	.	0			c.188delT						.						69.0	71.0	71.0					10																	91177145		2203	4300	6503	SO:0001589	frameshift_variant	24138	exon2			.	U34605	CCDS7403.1	10q23.31	2013-01-10			ENSG00000152778	ENSG00000152778		"""Tetratricopeptide (TTC) repeat domain containing"""	13328	protein-coding gene	gene with protein product	"""retinoic acid- and interferon-inducible protein (58kD)"""					9398535	Standard	NM_012420		Approved	RI58	uc010qnh.2	Q13325	OTTHUMG00000018713	ENST00000371795.4:c.189delA	chr10.hg19:g.91177145delA	ENSP00000360860:p.Leu63fs	167.0	0.0		160.0	51.0	NM_012420	B2R5X9|B4DDV1|Q5T7I9|Q6IAX3	Frame_Shift_Del	DEL	ENST00000371795.4	hg19	CCDS7403.1																																																																																			.	.		0.398	IFIT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049303.1	NM_012420	
LAG3	3902	hgsc.bcm.edu	37	12	6887494	6887511	+	In_Frame_Del	DEL	CCGGAGCCGGAGCCGGAG	CCGGAGCCGGAGCCGGAG	-	rs566439838|rs566081528|rs149606091	byFrequency	TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	CCGGAGCCGGAGCCGGAG	CCGGAGCCGGAGCCGGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr12:6887494_6887511delCCGGAGCCGGAGCCGGAG	ENST00000203629.2	+	8	1849_1866	c.1516_1533delCCGGAGCCGGAGCCGGAG	c.(1516-1533)ccggagccggagccggagdel	p.PEPEPE518del		NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	518	12 X 2 AA tandem repeats of E-X.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						GGAGCAAGAAccggagccggagccggagccggaaccgg	0.615																																					p.505_511del		Atlas-INDEL	.											.	LAG3	35	.	0			c.1515_1532del						.																																			SO:0001651	inframe_deletion	3902	exon8			.		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.1516_1533delCCGGAGCCGGAGCCGGAG	chr12.hg19:g.6887494_6887511delCCGGAGCCGGAGCCGGAG	ENSP00000203629:p.Pro518_Glu523del	67.0	0.0		56.0	22.0	NM_002286	A8K7T9|Q7Z643	In_Frame_Del	DEL	ENST00000203629.2	hg19	CCDS8561.1																																																																																			.	.		0.615	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1		
CDC5L	988	hgsc.bcm.edu	37	6	44414400	44414400	+	Frame_Shift_Del	DEL	A	A	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr6:44414400delA	ENST00000371477.3	+	16	2660	c.2361delA	c.(2359-2361)agafs	p.R787fs		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	787	Interaction with PLRG1.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTCAACATAGATATGCTGATT	0.308																																					p.R787fs		Atlas-INDEL	.											CDC5L,NS,carcinoma,0,1	CDC5L	86	.	0			c.2360delG						.						106.0	115.0	112.0					6																	44414400		2203	4300	6503	SO:0001589	frameshift_variant	988	exon16			.	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"""CDC5 (cell division cycle 5, S. pombe, homolog)-like"", ""CDC5 cell division cycle 5-like (S. pombe)"""			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.2361delA	chr6.hg19:g.44414400delA	ENSP00000360532:p.Arg787fs	62.0	0.0		108.0	27.0	NM_001253	Q76N46|Q99974	Frame_Shift_Del	DEL	ENST00000371477.3	hg19	CCDS4912.1																																																																																			.	.		0.308	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
CCT8L2	150160	hgsc.bcm.edu	37	22	17073436	17073439	+	Start_Codon_Del	DEL	TCCA	TCCA	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	TCCA	TCCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr22:17073436_17073439delTCCA	ENST00000359963.3	-	0	261_264					NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2						anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				GACTGTGCTGTCCATGGCCCGCAG	0.623																																					p.1_2del		Atlas-INDEL	.											.	CCT8L2	150	.	0			c.3_6del						.																																			SO:0001582	initiator_codon_variant	150160	exon1			.	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302		chr22.hg19:g.17073436_17073439delTCCA		74.0	0.0		65.0	27.0	NM_014406	A4QPH3|Q9UJS3	Frame_Shift_Del	DEL	ENST00000359963.3	hg19	CCDS13738.1																																																																																			.	.		0.623	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
DSPP	1834	hgsc.bcm.edu	37	4	88537080	88537088	+	In_Frame_Del	DEL	ACAGCAGCA	ACAGCAGCA	-	rs367717407|rs201754564|rs370267258|rs553101049	byFrequency	TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	ACAGCAGCA	ACAGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr4:88537080_88537088delACAGCAGCA	ENST00000282478.7	+	4	3299_3307	c.3266_3274delACAGCAGCA	c.(3265-3276)gacagcagcaat>gat	p.SSN1090del	DSPP_ENST00000399271.1_In_Frame_Del_p.SSN1090del|RP11-742B18.1_ENST00000506480.1_RNA			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1090	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		gatagcagtgacagcagcaatagcagtga	0.536																																					p.1089_1091del		Atlas-INDEL	.											.	DSPP	174	.	0			c.3265_3273del						.			1444,630		641,162,234						0.5	0.0			23	2259,1617		893,473,572	no	coding	DSPP	NM_014208.3		1534,635,806	A1A1,A1R,RR		41.7183,30.3761,37.7647				3703,2247				SO:0001651	inframe_deletion	1834	exon5			.	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3266_3274delACAGCAGCA	chr4.hg19:g.88537080_88537088delACAGCAGCA	ENSP00000282478:p.Ser1090_Asn1092del	233.0	0.0		256.0	51.0	NM_014208	A8MUI0|O95815	In_Frame_Del	DEL	ENST00000282478.7	hg19	CCDS43248.1																																																																																			.	.		0.536	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
NAA38	84316	hgsc.bcm.edu	37	7	117832038	117832043	+	In_Frame_Del	DEL	AAATTC	AAATTC	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	AAATTC	AAATTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr7:117832038_117832043delAAATTC	ENST00000249299.2	+	4	465_470	c.273_278delAAATTC	c.(271-279)ttaaattct>ttt	p.91_93LNS>F	NAA38_ENST00000424702.1_3'UTR|NAA38_ENST00000422760.1_In_Frame_Del_p.70_72LNS>F	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	0					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						CAGAACCTTTAAATTCTGTAGCACAC	0.354																																					p.91_93del		Atlas-INDEL	.											.	NAA38	16	.	0			c.272_277del						.																																			SO:0001651	inframe_deletion	51691	exon4			.		CCDS11122.1	17p13.1	2014-01-21	2014-01-21	2014-01-21		ENSG00000183011		"""N(alpha)-acetyltransferase subunits"""	28212	protein-coding gene	gene with protein product			"""LSM domain containing 1"""	LSMD1		16484612, 19398576	Standard	NM_032356		Approved	MGC14151, PFAAP2	uc002gja.3	Q9BRA0		ENST00000249299.2:c.273_278delAAATTC	chr7.hg19:g.117832038_117832043delAAATTC	ENSP00000249299:p.Leu91_Ser93delinsPhe	132.0	0.0		149.0	34.0	NM_016200	Q8N4M0	In_Frame_Del	DEL	ENST00000249299.2	hg19	CCDS5775.1																																																																																			.	.		0.354	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356	
MIER1	57708	hgsc.bcm.edu	37	1	67450362	67450363	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr1:67450362_67450363insC	ENST00000355356.3	+	13	1467_1468	c.1318_1319insC	c.(1318-1320)gatfs	p.D440fs	MIER1_ENST00000401042.3_Intron|MIER1_ENST00000357692.2_Frame_Shift_Ins_p.D457fs|MIER1_ENST00000371016.1_Intron|MIER1_ENST00000371018.3_Intron|MIER1_ENST00000371014.1_Intron|MIER1_ENST00000355977.6_Intron|MIER1_ENST00000401041.1_Frame_Shift_Ins_p.D493fs	NM_001077701.2|NM_001077704.2	NP_001071169.1|NP_001071172.1	Q8N108	MIER1_HUMAN	mesoderm induction early response 1, transcriptional regulator	440					positive regulation of chromatin silencing (GO:0031937)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|urinary_tract(3)	15						ACTTCATGCAGATATGGATACT	0.351																																					p.D493fs		Atlas-INDEL	.											.	MIER1	86	.	0			c.1477_1478insC						.																																			SO:0001589	frameshift_variant	57708	exon14			.		CCDS41347.1, CCDS41348.1, CCDS53325.1, CCDS53326.1, CCDS53327.1, CCDS53328.1, CCDS53329.1, CCDS53330.1, CCDS60163.1	1p31.2	2013-07-23	2013-07-23		ENSG00000198160	ENSG00000198160			29657	protein-coding gene	gene with protein product			"""mesoderm induction early response 1 homolog (Xenopus laevis)"""			12242014, 12482978	Standard	NM_020948		Approved	hMI-ER1, MI-ER1, KIAA1610	uc001dde.2	Q8N108	OTTHUMG00000009194	Exception_encountered	chr1.hg19:g.67450362_67450363insC	ENSP00000347514:p.Asp440fs	195.0	0.0		186.0	65.0	NM_001077700	C9JFD4|Q08AE0|Q32NC4|Q5T104|Q5TAD1|Q5TAD2|Q5TAD4|Q5TAD5|Q6AHY8|Q86TB4|Q8N156|Q8N161|Q8NC37|Q8NES4|Q8NES5|Q8NES6|Q8WWG2|Q9HCG2	Frame_Shift_Ins	INS	ENST00000355356.3	hg19	CCDS41348.1																																																																																			.	.		0.351	MIER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025491.2	NM_020948	
CDKN2A	1029	hgsc.bcm.edu	37	9	21974751	21974760	+	Frame_Shift_Del	DEL	CTACCCGACC	CTACCCGACC	-	rs104894097		TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	CTACCCGACC	CTACCCGACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr9:21974751_21974760delCTACCCGACC	ENST00000304494.5	-	1	337_346	c.67_76delGGTCGGGTAG	c.(67-78)ggtcgggtagagfs	p.GRVE23fs	RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000498124.1_Frame_Shift_Del_p.GRVE23fs|CDKN2A_ENST00000579122.1_Frame_Shift_Del_p.GRVE23fs|CDKN2A_ENST00000494262.1_Intron|CDKN2A_ENST00000361570.3_Intron|CDKN2A_ENST00000579755.1_Intron|CDKN2A_ENST00000498628.2_Intron|CDKN2A_ENST00000530628.2_Intron|CDKN2A_ENST00000446177.1_Frame_Shift_Del_p.GRVE23fs	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	23			G -> D (in a pancreas tumor and a melanoma; loss of CDK4 binding).		cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(23)|p.E26*(3)|p.R24P(2)|p.V25fs*1(2)|p.G23S(1)|p.0(1)|p.S12fs*20(1)|p.R24fs*20(1)|p.R22fs*14(1)|p.G23G(1)|p.G23D(1)|p.R24Q(1)|p.E26K(1)|p.G23fs*3(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		CGCACCTCCTCTACCCGACCCCGGGCCGCG	0.743		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.23_26del		Atlas-INDEL	.											.	CDKN2A	4810	.	1355	Whole gene deletion(1316)|Unknown(23)|Substitution - Missense(6)|Deletion - Frameshift(5)|Substitution - Nonsense(3)|Insertion - Frameshift(1)|Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(281)|skin(169)|central_nervous_system(164)|lung(148)|urinary_tract(90)|bone(73)|soft_tissue(58)|pleura(52)|oesophagus(50)|upper_aerodigestive_tract(49)|ovary(36)|kidney(31)|pancreas(30)|breast(30)|thyroid(14)|biliary_tract(14)|NS(12)|stomach(12)|large_intestine(7)|autonomic_ganglia(7)|liver(7)|meninges(7)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.68_77del	GRCh37	CM024657|CM056560|CM056561|CM072932|CM950224|CM980322	CDKN2A	M	rs104894097	.																																			SO:0001589	frameshift_variant	1029	exon1			.	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.67_76delGGTCGGGTAG	chr9.hg19:g.21974751_21974760delCTACCCGACC	ENSP00000307101:p.Gly23fs	79.0	0.0		83.0	26.0	NM_058197	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Frame_Shift_Del	DEL	ENST00000304494.5	hg19	CCDS6510.1																																																																																			.	.		0.743	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
GPRIN1	114787	hgsc.bcm.edu	37	5	176026192	176026192	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-AADG-01A-11D-A40R-10	TCGA-DD-AADG-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	bc83c53e-cd19-48a9-ae9c-a59c69b55438	54f60e9c-e44d-435e-8f76-5525282b610b	g.chr5:176026192delC	ENST00000303991.4	-	2	821	c.644delG	c.(643-645)ggafs	p.G215fs		NM_052899.2	NP_443131.2	Q7Z2K8	GRIN1_HUMAN	G protein regulated inducer of neurite outgrowth 1	215					neuron projection development (GO:0031175)	cell projection (GO:0042995)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(15)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(89;0.00263)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			ATCTACTTTTCCCAGGGATCC	0.502																																					p.G215fs		Atlas-INDEL	.											.	GPRIN1	77	.	0			c.645delA						.						77.0	78.0	77.0					5																	176026192		2203	4299	6502	SO:0001589	frameshift_variant	114787	exon2			.	AB067480	CCDS4405.1	5q35.2	2008-02-05			ENSG00000169258	ENSG00000169258			24835	protein-coding gene	gene with protein product		611239				11572484	Standard	NM_052899		Approved	GRIN1, KIAA1893	uc003meo.1	Q7Z2K8	OTTHUMG00000130659	ENST00000303991.4:c.644delG	chr5.hg19:g.176026192delC	ENSP00000305839:p.Gly215fs	56.0	0.0		103.0	22.0	NM_052899	C9JM70|Q8ND74|Q96PZ4	Frame_Shift_Del	DEL	ENST00000303991.4	hg19	CCDS4405.1																																																																																			.	.		0.502	GPRIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253149.1	NM_052899	
