#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
TAS1R3	83756	hgsc.bcm.edu	37	1	1268035	1268035	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:1268035G>T	ENST00000339381.5	+	3	1156	c.1124G>T	c.(1123-1125)tGc>tTc	p.C375F		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	375					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		CAGTGTGACTGCATCACGCTG	0.647																																					p.C375F		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G1124T						.						25.0	23.0	23.0					1																	1268035		2192	4295	6487	SO:0001583	missense	83756	exon3			GTGACTGCATCAC	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1124G>T	chr1.hg19:g.1268035G>T	ENSP00000344411:p.Cys375Phe	57.0	0.0		52.0	13.0	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	hg19	CCDS30556.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.591994	0.00864	.	.	ENSG00000169962	ENST00000339381	D	0.85861	-2.04	4.71	-5.38	0.02673	Extracellular ligand-binding receptor (1);	1.852440	0.04610	U	0.400039	T	0.66934	0.2840	N	0.08118	0	0.09310	N	1	B	0.19445	0.036	B	0.10450	0.005	T	0.54603	-0.8269	10	0.22109	T	0.4	.	8.0053	0.30321	0.3924:0.132:0.4756:0.0	.	375	Q7RTX0	TS1R3_HUMAN	F	375	ENSP00000344411:C375F	ENSP00000344411:C375F	C	+	2	0	TAS1R3	1257898	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.588000	0.23924	-0.779000	0.04560	-1.036000	0.02392	TGC	.	.		0.647	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		
GPR153	387509	hgsc.bcm.edu	37	1	6314095	6314095	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:6314095A>C	ENST00000377893.2	-	3	728	c.469T>G	c.(469-471)Tac>Gac	p.Y157D		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	157						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CCATGGGTGTAGAAGCGCTCG	0.637																																					p.Y157D		Atlas-SNP	.											.	GPR153	44	.	0			c.T469G						.						56.0	61.0	59.0					1																	6314095		2201	4298	6499	SO:0001583	missense	387509	exon3			GGGTGTAGAAGCG	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.469T>G	chr1.hg19:g.6314095A>C	ENSP00000367125:p.Tyr157Asp	207.0	0.0		177.0	37.0	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	hg19	CCDS64.1	.	.	.	.	.	.	.	.	.	.	A	19.60	3.858451	0.71834	.	.	ENSG00000158292	ENST00000377893	T	0.34667	1.35	4.9	4.9	0.64082	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	L	0.34521	1.04	0.58432	D	0.999998	D	0.89917	1.0	D	0.97110	1.0	T	0.46925	-0.9156	10	0.51188	T	0.08	-39.2472	13.3635	0.60669	1.0:0.0:0.0:0.0	.	157	Q6NV75	GP153_HUMAN	D	157	ENSP00000367125:Y157D	ENSP00000367125:Y157D	Y	-	1	0	GPR153	6236682	1.000000	0.71417	1.000000	0.80357	0.722000	0.41435	9.265000	0.95647	1.833000	0.53350	0.460000	0.39030	TAC	.	.		0.637	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
CA6	765	hgsc.bcm.edu	37	1	9027785	9027785	+	Nonsense_Mutation	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:9027785C>A	ENST00000377443.2	+	6	643	c.639C>A	c.(637-639)taC>taA	p.Y213*	CA6_ENST00000377442.2_Nonsense_Mutation_p.Y153*|CA6_ENST00000476083.1_3'UTR|CA6_ENST00000377436.3_Nonsense_Mutation_p.Y213*	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	213					bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	AGCACTACTACACCTACCATG	0.517																																					p.Y213X		Atlas-SNP	.											.	CA6	47	.	0			c.C639A						.						192.0	144.0	160.0					1																	9027785		2203	4300	6503	SO:0001587	stop_gained	765	exon6			CTACTACACCTAC	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.639C>A	chr1.hg19:g.9027785C>A	ENSP00000366662:p.Tyr213*	632.0	1.0		902.0	250.0	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Nonsense_Mutation	SNP	ENST00000377443.2	hg19	CCDS30578.1	.	.	.	.	.	.	.	.	.	.	C	9.159	1.018118	0.19355	.	.	ENSG00000131686	ENST00000549778;ENST00000377443;ENST00000377436;ENST00000377442	.	.	.	5.31	2.22	0.28083	.	0.364504	0.32563	N	0.005924	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9474	0.24526	0.0:0.6794:0.0:0.3206	.	.	.	.	X	181;213;213;153	.	ENSP00000366654:Y213X	Y	+	3	2	CA6	8950372	1.000000	0.71417	0.989000	0.46669	0.006000	0.05464	0.944000	0.29043	0.159000	0.19401	-0.258000	0.10820	TAC	.	.		0.517	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
KIF1B	23095	hgsc.bcm.edu	37	1	10408722	10408722	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:10408722A>T	ENST00000377086.1	+	37	4082	c.3880A>T	c.(3880-3882)Atc>Ttc	p.I1294F	KIF1B_ENST00000377081.1_Missense_Mutation_p.I1294F|KIF1B_ENST00000465635.1_3'UTR|KIF1B_ENST00000263934.6_Missense_Mutation_p.I1248F			O60333	KIF1B_HUMAN	kinesin family member 1B	1294					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCAGCGAAGGATCACAGTGAC	0.478																																					p.I1248F		Atlas-SNP	.											.	KIF1B	242	.	0			c.A3742T						.						136.0	105.0	115.0					1																	10408722		2203	4300	6503	SO:0001583	missense	23095	exon35			CGAAGGATCACAG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.3880A>T	chr1.hg19:g.10408722A>T	ENSP00000366290:p.Ile1294Phe	253.0	0.0		368.0	115.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	A	25.8	4.673574	0.88445	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.81415	-1.41;-1.49;-1.49	5.52	4.39	0.52855	.	0.000000	0.85682	D	0.000000	D	0.89887	0.6845	M	0.87269	2.87	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.976;1.0;0.96	D;D;D;D;D;D	0.91635	0.996;0.999;0.999;0.949;0.99;0.948	D	0.90376	0.4384	10	0.87932	D	0	.	11.3155	0.49390	0.9289:0.0:0.0711:0.0	.	1280;1254;1294;1268;1294;1248	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	F	1294;1248;1294;1294	ENSP00000263934:I1248F;ENSP00000366290:I1294F;ENSP00000366284:I1294F	ENSP00000263934:I1248F	I	+	1	0	KIF1B	10331309	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.335000	0.72949	0.932000	0.37266	0.533000	0.62120	ATC	.	.		0.478	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
VPS13D	55187	hgsc.bcm.edu	37	1	12313850	12313850	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:12313850T>A	ENST00000358136.3	+	7	766	c.636T>A	c.(634-636)acT>acA	p.T212T	VPS13D_ENST00000356315.4_Silent_p.T212T	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)		TCGATTGCACTTTACTGGGGG	0.443																																					p.T212T		Atlas-SNP	.											.	VPS13D	316	.	0			c.T636A						.						207.0	188.0	195.0					1																	12313850		2203	4300	6503	SO:0001819	synonymous_variant	55187	exon7			TTGCACTTTACTG	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.636T>A	chr1.hg19:g.12313850T>A		247.0	0.0		332.0	109.0	NM_015378		Silent	SNP	ENST00000358136.3	hg19	CCDS30588.1																																																																																			.	.		0.443	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
UBR4	23352	hgsc.bcm.edu	37	1	19480377	19480377	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:19480377T>A	ENST00000375254.3	-	45	6542	c.6515A>T	c.(6514-6516)aAc>aTc	p.N2172I	UBR4_ENST00000375267.2_Missense_Mutation_p.N2172I|UBR4_ENST00000375217.2_Missense_Mutation_p.N2172I|UBR4_ENST00000375226.2_Missense_Mutation_p.N2172I	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2172					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(7)|central_nervous_system(1)|cervix(2)|endometrium(23)|kidney(25)|large_intestine(25)|liver(2)|lung(47)|ovary(10)|pancreas(2)|prostate(7)|skin(5)|stomach(5)|upper_aerodigestive_tract(4)|urinary_tract(6)	171		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000328)|Lung NSC(340;0.000406)|Breast(348;0.000814)|Ovarian(437;0.00774)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00674)|BRCA - Breast invasive adenocarcinoma(304;5.43e-05)|Kidney(64;0.000337)|KIRC - Kidney renal clear cell carcinoma(64;0.00426)|STAD - Stomach adenocarcinoma(196;0.00715)|READ - Rectum adenocarcinoma(331;0.0816)		GCCAGGGTGGTTCATCACCTC	0.493																																					p.N2172I		Atlas-SNP	.											.	UBR4	415	.	0			c.A6515T						.						104.0	97.0	100.0					1																	19480377		2203	4300	6503	SO:0001583	missense	23352	exon45			GGGTGGTTCATCA	AF348492	CCDS189.1	1p36.13	2008-06-23	2007-06-19	2007-06-19	ENSG00000127481	ENSG00000127481		"""Ubiquitin protein ligase E3 component n-recognins"""	30313	protein-coding gene	gene with protein product		609890	"""zinc finger, UBR1 type 1"""	ZUBR1		14702039, 10718198, 16055722	Standard	XM_005245802		Approved	KIAA1307, KIAA0462, RBAF600	uc001bbi.3	Q5T4S7	OTTHUMG00000002498	ENST00000375254.3:c.6515A>T	chr1.hg19:g.19480377T>A	ENSP00000364403:p.Asn2172Ile	476.0	2.0		430.0	245.0	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	hg19	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.035890	0.93630	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T	0.25749	1.79;1.79;1.78;1.78	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.44477	0.1295	L	0.48642	1.525	0.80722	D	1	D;D	0.65815	0.993;0.995	P;D	0.75484	0.905;0.986	T	0.36407	-0.9749	10	0.72032	D	0.01	.	14.6112	0.68517	0.0:0.0:0.0:1.0	.	2173;2172	Q5T4S7-5;Q5T4S7	.;UBR4_HUMAN	I	2172;2172;2172;2172;882;1389	ENSP00000364403:N2172I;ENSP00000364416:N2172I;ENSP00000364365:N2172I;ENSP00000364374:N2172I	ENSP00000364365:N2172I	N	-	2	0	UBR4	19352964	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.330000	0.79181	2.243000	0.73865	0.482000	0.46254	AAC	.	.		0.493	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
EPHB2	2048	hgsc.bcm.edu	37	1	23222044	23222044	+	Silent	SNP	T	T	A	rs141173528		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:23222044T>A	ENST00000400191.3	+	8	1689	c.1671T>A	c.(1669-1671)gcT>gcA	p.A557A	EPHB2_ENST00000374627.1_Silent_p.A552A|EPHB2_ENST00000374630.3_Silent_p.A557A|EPHB2_ENST00000374632.3_Silent_p.A557A|EPHB2_ENST00000465676.1_3'UTR	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	557					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		TCCTCATTGCTGTGGTTGTCA	0.582																																					p.A557A		Atlas-SNP	.											.	EPHB2	257	.	0			c.T1671A						.						128.0	110.0	116.0					1																	23222044		2203	4300	6503	SO:0001819	synonymous_variant	2048	exon8			CATTGCTGTGGTT	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1671T>A	chr1.hg19:g.23222044T>A		181.0	0.0		113.0	18.0	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	hg19																																																																																				.	T|1.000;C|0.000		0.582	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
MTFR1L	56181	hgsc.bcm.edu	37	1	26158452	26158452	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:26158452A>G	ENST00000374301.3	+	7	1122	c.814A>G	c.(814-816)Atc>Gtc	p.I272V	MTFR1L_ENST00000524618.1_Missense_Mutation_p.I175V|AUNIP_ENST00000538789.1_3'UTR|MTFR1L_ENST00000374303.2_Missense_Mutation_p.I272V|MTFR1L_ENST00000374307.5_Missense_Mutation_p.I260V|MTFR1L_ENST00000374300.3_Missense_Mutation_p.I272V|RP1-317E23.7_ENST00000606617.1_RNA|AUNIP_ENST00000481602.1_5'Flank|MTFR1L_ENST00000474295.1_3'UTR|MTFR1L_ENST00000469815.1_3'UTR|MTFR1L_ENST00000466284.1_3'UTR	NM_019557.5	NP_062457.3	Q9H019	MFR1L_HUMAN	mitochondrial fission regulator 1-like	272																	TGCTGTGCTTATCTCTGAGGT	0.423																																					p.I272V		Atlas-SNP	.											.	.	.	.	0			c.A814G						.						226.0	224.0	224.0					1																	26158452		1906	4106	6012	SO:0001583	missense	56181	exon7			GTGCTTATCTCTG		CCDS41284.1, CCDS44089.1	1p36.11	2012-11-30	2012-11-29	2012-11-29	ENSG00000117640	ENSG00000117640			28836	protein-coding gene	gene with protein product			"""family with sequence similarity 54, member B"""	FAM54B		8619474, 9110174	Standard	NM_019557		Approved		uc001bkq.4	Q9H019	OTTHUMG00000007377	ENST00000374301.3:c.814A>G	chr1.hg19:g.26158452A>G	ENSP00000363419:p.Ile272Val	145.0	0.0		128.0	9.0	NM_001099625	A6NCB4|B7WNV5|D3DPJ4|Q63HP1|Q7Z2S7|Q9NUI7	Missense_Mutation	SNP	ENST00000374301.3	hg19	CCDS41284.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.649922	0.87958	.	.	ENSG00000117640	ENST00000374303;ENST00000524618;ENST00000374307;ENST00000374301;ENST00000374300	T;T;T;T	0.59502	0.4;0.26;0.4;0.4	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.66446	0.2790	L	0.29908	0.895	0.80722	D	1	D;D;D	0.59357	0.985;0.978;0.963	D;D;P	0.67725	0.952;0.953;0.898	T	0.69198	-0.5208	10	0.72032	D	0.01	-7.8421	16.8222	0.85835	1.0:0.0:0.0:0.0	.	305;260;272	B4DRE5;Q9H019-3;Q9H019	.;.;FA54B_HUMAN	V	272;175;260;272;272	ENSP00000363421:I272V;ENSP00000363426:I260V;ENSP00000363419:I272V;ENSP00000363418:I272V	ENSP00000363418:I272V	I	+	1	0	FAM54B	26031039	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	8.448000	0.90335	2.371000	0.80710	0.533000	0.62120	ATC	.	.		0.423	MTFR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019319.1	NM_019557	
PIK3R3	8503	hgsc.bcm.edu	37	1	46531740	46531740	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:46531740T>C	ENST00000262741.5	-	5	1296	c.607A>G	c.(607-609)Act>Gct	p.T203A	PIK3R3_ENST00000540385.1_Missense_Mutation_p.T249A|PIK3R3_ENST00000420542.1_Missense_Mutation_p.T203A|PIK3R3_ENST00000354242.4_Missense_Mutation_p.T203A|PIK3R3_ENST00000423209.1_Missense_Mutation_p.T203A|PIK3R3_ENST00000372006.1_Missense_Mutation_p.T203A|PIK3R3_ENST00000340332.6_Missense_Mutation_p.T167A	NM_003629.3	NP_003620.3	Q92569	P55G_HUMAN	phosphoinositide-3-kinase, regulatory subunit 3 (gamma)	203					insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)			endometrium(1)|large_intestine(5)|lung(6)|prostate(2)	14	Acute lymphoblastic leukemia(166;0.155)				Isoprenaline(DB01064)	GATGTTCTAGTATATTCTTCA	0.318																																					p.T203A		Atlas-SNP	.											.	PIK3R3	41	.	0			c.A607G						.						176.0	161.0	166.0					1																	46531740		2203	4292	6495	SO:0001583	missense	8503	exon6			TTCTAGTATATTC	BC021622	CCDS529.1	1p34.1	2013-02-14	2008-02-04		ENSG00000117461	ENSG00000117461		"""SH2 domain containing"""	8981	protein-coding gene	gene with protein product		606076				9524259	Standard	NM_003629		Approved	p55	uc001cpb.4	Q92569	OTTHUMG00000008096	ENST00000262741.5:c.607A>G	chr1.hg19:g.46531740T>C	ENSP00000262741:p.Thr203Ala	75.0	0.0		116.0	14.0	NM_001114172	B2R9C1|D3DQ12|O60482|Q5T4P1|Q5T4P2	Missense_Mutation	SNP	ENST00000262741.5	hg19	CCDS529.1	.	.	.	.	.	.	.	.	.	.	T	17.48	3.400605	0.62177	.	.	ENSG00000117461	ENST00000372006;ENST00000262741;ENST00000420542;ENST00000354242;ENST00000340332;ENST00000540385;ENST00000423209;ENST00000425892	T;T;T;T;D;T;T;T	0.85556	-1.29;-1.29;-1.29;-1.43;-2.0;-1.27;-1.43;0.97	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.82199	0.4985	L	0.58583	1.82	0.80722	D	1	B;P;B;B	0.36974	0.081;0.576;0.06;0.39	B;B;B;B	0.32928	0.021;0.155;0.031;0.054	T	0.83341	-0.0008	10	0.52906	T	0.07	.	15.4406	0.75178	0.0:0.0:0.0:1.0	.	249;236;203;203	F6TDL0;Q7Z3W2;Q92569-2;Q92569	.;.;.;P55G_HUMAN	A	203;203;203;203;167;249;203;203	ENSP00000361075:T203A;ENSP00000262741:T203A;ENSP00000412546:T203A;ENSP00000346188:T203A;ENSP00000342484:T167A;ENSP00000439913:T249A;ENSP00000391431:T203A;ENSP00000416647:T203A	ENSP00000262741:T203A	T	-	1	0	PIK3R3	46304327	1.000000	0.71417	1.000000	0.80357	0.926000	0.56050	7.698000	0.84413	2.055000	0.61198	0.477000	0.44152	ACT	.	.		0.318	PIK3R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022171.1	NM_003629	
ZCCHC11	23318	hgsc.bcm.edu	37	1	52943444	52943444	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:52943444T>A	ENST00000371544.3	-	12	2221	c.1959A>T	c.(1957-1959)gtA>gtT	p.V653V	ZCCHC11_ENST00000257177.4_Silent_p.V653V|ZCCHC11_ENST00000371541.1_5'UTR	NM_001009881.2|NM_015269.2	NP_001009881.1|NP_056084.1	Q5TAX3	TUT4_HUMAN	zinc finger, CCHC domain containing 11	653	PAP-associated 1.				cytokine production (GO:0001816)|miRNA catabolic process (GO:0010587)|miRNA metabolic process (GO:0010586)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|pre-miRNA processing (GO:0031054)|regulation of lipopolysaccharide-mediated signaling pathway (GO:0031664)|RNA 3'-end processing (GO:0031123)|stem cell maintenance (GO:0019827)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(15)|lung(17)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	58						CTTGTATCCGTACACATATGA	0.358																																					p.V653V		Atlas-SNP	.											.	ZCCHC11	151	.	0			c.A1959T						.						107.0	108.0	108.0					1																	52943444		2203	4300	6503	SO:0001819	synonymous_variant	23318	exon12			TATCCGTACACAT	D83776	CCDS30715.1, CCDS30716.1	1p32.3	2014-03-05			ENSG00000134744	ENSG00000134744		"""Zinc fingers, CCHC domain containing"""	28981	protein-coding gene	gene with protein product	"""TUTase4"""	613692				8724849, 12239557	Standard	NM_015269		Approved	KIAA0191, PAPD3, TUT4	uc001cty.2	Q5TAX3	OTTHUMG00000008200	ENST00000371544.3:c.1959A>T	chr1.hg19:g.52943444T>A		103.0	0.0		122.0	11.0	NM_015269	A2RRP0|B7Z8J5|D3DQ35|Q12764|Q5TAX2|Q5TAX4|Q86XZ3	Silent	SNP	ENST00000371544.3	hg19	CCDS30716.1																																																																																			.	.		0.358	ZCCHC11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022462.1	XM_038288	
NDC1	55706	hgsc.bcm.edu	37	1	54272140	54272140	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:54272140G>T	ENST00000371429.3	-	9	1540	c.942C>A	c.(940-942)tgC>tgA	p.C314*	NDC1_ENST00000537333.1_5'UTR|NDC1_ENST00000234725.8_Nonsense_Mutation_p.C199*|NDC1_ENST00000540001.1_Nonsense_Mutation_p.C314*	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	314					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)										CTTTTGGAAGGCACTCATCTG	0.348																																					p.C314X		Atlas-SNP	.											.	TMEM48	47	.	0			c.C942A						.						97.0	96.0	96.0					1																	54272140		2203	4300	6503	SO:0001587	stop_gained	55706	exon9			TGGAAGGCACTCA	AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"""nuclear division cycle 1 homolog (S. cerevisiae)"""	610115	"""transmembrane protein 48"""	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.942C>A	chr1.hg19:g.54272140G>T	ENSP00000360483:p.Cys314*	87.0	0.0		92.0	4.0	NM_018087	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Nonsense_Mutation	SNP	ENST00000371429.3	hg19	CCDS583.1	.	.	.	.	.	.	.	.	.	.	G	38	6.979130	0.97979	.	.	ENSG00000058804	ENST00000371429;ENST00000360494;ENST00000540001;ENST00000234725	.	.	.	5.04	4.12	0.48240	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.09843	T	0.71	.	10.3319	0.43827	0.1602:0.0:0.8398:0.0	.	.	.	.	X	314;314;314;199	.	ENSP00000234725:C199X	C	-	3	2	TMEM48	54044728	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.073000	0.41519	1.352000	0.45808	0.579000	0.79373	TGC	.	.		0.348	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022101.1	NM_018087	
MROH7	374977	hgsc.bcm.edu	37	1	55130862	55130862	+	Silent	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:55130862A>G	ENST00000421030.2	+	4	1539	c.1254A>G	c.(1252-1254)tcA>tcG	p.S418S	MROH7_ENST00000409996.1_5'UTR|MROH7_ENST00000395690.2_Silent_p.S418S|MROH7_ENST00000339553.5_Silent_p.S418S|MROH7_ENST00000454855.2_5'UTR|MROH7-TTC4_ENST00000414150.2_Silent_p.S418S|MROH7_ENST00000545244.1_5'UTR	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	418						extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											AAGTGACCTCATGCCTGGTGA	0.527																																					p.S418S		Atlas-SNP	.											.	.	.	.	0			c.A1254G						.						104.0	108.0	107.0					1																	55130862		2116	4236	6352	SO:0001819	synonymous_variant	374977	exon4			GACCTCATGCCTG	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.1254A>G	chr1.hg19:g.55130862A>G		256.0	1.0		361.0	145.0	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Silent	SNP	ENST00000421030.2	hg19	CCDS41342.2																																																																																			.	.		0.527	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
LEPR	3953	hgsc.bcm.edu	37	1	66081748	66081748	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:66081748A>T	ENST00000349533.6	+	15	2238	c.2053A>T	c.(2053-2055)Act>Tct	p.T685S	LEPR_ENST00000371059.3_Missense_Mutation_p.T685S|LEPR_ENST00000344610.8_Missense_Mutation_p.T685S|LEPR_ENST00000406510.3_Intron|LEPR_ENST00000371058.1_Missense_Mutation_p.T685S|LEPR_ENST00000371060.3_Missense_Mutation_p.T685S	NM_002303.5	NP_002294.2	O15243	OBRG_HUMAN	leptin receptor	0					negative regulation of growth hormone receptor signaling pathway (GO:0060400)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of protein localization to cell surface (GO:2000009)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(22)|skin(2)	36				OV - Ovarian serous cystadenocarcinoma(397;0.00722)|KIRC - Kidney renal clear cell carcinoma(1967;0.094)		AAACCATCATACTTCCTGCAA	0.413																																					p.T685S		Atlas-SNP	.											.	LEPR	284	.	0			c.A2053T						.						139.0	125.0	130.0					1																	66081748		2203	4300	6503	SO:0001583	missense	3953	exon15			CATCATACTTCCT	U43168	CCDS631.1, CCDS30740.1, CCDS30741.1, CCDS55604.1	1p31	2014-09-17			ENSG00000116678	ENSG00000116678		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6554	protein-coding gene	gene with protein product		601007				8548812, 8812446	Standard	NM_001003680		Approved	OBR, CD295	uc001dci.3	P48357	OTTHUMG00000009115	ENST00000349533.6:c.2053A>T	chr1.hg19:g.66081748A>T	ENSP00000330393:p.Thr685Ser	161.0	0.0		257.0	13.0	NM_001003680	Q6FHL5	Missense_Mutation	SNP	ENST00000349533.6	hg19	CCDS631.1	.	.	.	.	.	.	.	.	.	.	A	14.45	2.539579	0.45176	.	.	ENSG00000116678	ENST00000344610;ENST00000349533;ENST00000371060;ENST00000371059;ENST00000371058	T;T;T;T;T	0.38887	1.11;1.11;1.11;1.11;1.11	5.37	5.37	0.77165	Fibronectin, type III (2);	0.230349	0.44483	D	0.000451	T	0.53481	0.1799	M	0.75447	2.3	0.80722	D	1	D;D;D	0.69078	0.994;0.997;0.991	D;D;D	0.74348	0.963;0.983;0.919	T	0.52555	-0.8560	10	0.26408	T	0.33	-18.9545	15.3683	0.74541	1.0:0.0:0.0:0.0	.	685;685;685	P48357;P48357-2;P48357-3	LEPR_HUMAN;.;.	S	685	ENSP00000340884:T685S;ENSP00000330393:T685S;ENSP00000360099:T685S;ENSP00000360098:T685S;ENSP00000360097:T685S	ENSP00000340884:T685S	T	+	1	0	LEPR	65854336	0.978000	0.34361	0.076000	0.20297	0.045000	0.14185	6.384000	0.73177	2.045000	0.60652	0.533000	0.62120	ACT	.	.		0.413	LEPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025275.1	NM_002303	
ZNF326	284695	hgsc.bcm.edu	37	1	90473063	90473063	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:90473063A>T	ENST00000340281.4	+	5	512	c.369A>T	c.(367-369)ggA>ggT	p.G123G	ZNF326_ENST00000455342.2_Intron|ZNF326_ENST00000370447.3_Intron	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	123	Gly-rich.|Mediates transcriptional activation. {ECO:0000250}.				mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		ACTCTTTCGGAGGTAGAAACC	0.498																																					p.G123G		Atlas-SNP	.											.	ZNF326	60	.	0			c.A369T						.						139.0	148.0	145.0					1																	90473063		2203	4300	6503	SO:0001819	synonymous_variant	284695	exon5			TTTCGGAGGTAGA	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.369A>T	chr1.hg19:g.90473063A>T		151.0	0.0		228.0	19.0	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Silent	SNP	ENST00000340281.4	hg19	CCDS727.1																																																																																			.	.		0.498	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
FRRS1	391059	hgsc.bcm.edu	37	1	100174554	100174554	+	3'UTR	SNP	T	T	A	rs553200347		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:100174554T>A	ENST00000414213.1	-	0	2410				FRRS1_ENST00000287474.5_Missense_Mutation_p.Q594L|FRRS1_ENST00000492943.1_5'Flank			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1							integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AATTATCACTTGGCCTGCAAA	0.403																																					p.Q594L		Atlas-SNP	.											.	FRRS1	50	.	0			c.A1781T						.						73.0	74.0	74.0					1																	100174554		2203	4300	6503	SO:0001624	3_prime_UTR_variant	391059	exon17			ATCACTTGGCCTG	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.*30A>T	chr1.hg19:g.100174554T>A		77.0	0.0		120.0	48.0	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	hg19		.	.	.	.	.	.	.	.	.	.	T	12.89	2.074439	0.36566	.	.	ENSG00000156869	ENST00000287474	.	.	.	5.67	-0.88	0.10610	.	3.411090	0.00597	N	0.000362	T	0.12135	0.0295	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22103	-1.0226	8	0.87932	D	0	24.6037	3.05	0.06166	0.2873:0.2354:0.0:0.4773	.	594	Q6ZNA5-2	.	L	594	.	ENSP00000287474:Q594L	Q	-	2	0	FRRS1	99947142	0.005000	0.15991	0.002000	0.10522	0.062000	0.15995	0.105000	0.15333	-0.415000	0.07484	-0.341000	0.08007	CAA	.	.		0.403	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
SLC6A17	388662	hgsc.bcm.edu	37	1	110709579	110709579	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:110709579C>A	ENST00000331565.4	+	2	513	c.28C>A	c.(28-30)Cgt>Agt	p.R10S	RP5-1028L10.1_ENST00000430098.1_RNA|RP5-1028L10.1_ENST00000418579.1_RNA|RP5-1028L10.1_ENST00000443008.1_RNA	NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	10					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		AGTGACCCAGCGTGAGCACAG	0.577																																					p.R10S		Atlas-SNP	.											.	SLC6A17	86	.	0			c.C28A						.						58.0	52.0	54.0					1																	110709579		2203	4300	6503	SO:0001583	missense	388662	exon2			ACCCAGCGTGAGC		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.28C>A	chr1.hg19:g.110709579C>A	ENSP00000330199:p.Arg10Ser	296.0	0.0		366.0	163.0	NM_001010898	A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Missense_Mutation	SNP	ENST00000331565.4	hg19	CCDS30799.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.149428	0.78001	.	.	ENSG00000197106	ENST00000331565;ENST00000450985	T	0.75589	-0.95	4.31	4.31	0.51392	.	0.060060	0.64402	D	0.000004	T	0.67297	0.2878	M	0.67397	2.05	0.49582	D	0.999809	P	0.43287	0.802	B	0.41466	0.358	T	0.73704	-0.3899	10	0.51188	T	0.08	.	16.9598	0.86269	0.0:1.0:0.0:0.0	.	10	Q9H1V8	S6A17_HUMAN	S	10	ENSP00000330199:R10S	ENSP00000330199:R10S	R	+	1	0	SLC6A17	110511102	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.457000	0.53007	2.221000	0.72209	0.563000	0.77884	CGT	.	.		0.577	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
MTMR11	10903	hgsc.bcm.edu	37	1	149904191	149904191	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:149904191T>A	ENST00000439741.2	-	11	1267	c.1017A>T	c.(1015-1017)tcA>tcT	p.S339S	MTMR11_ENST00000406732.3_Silent_p.S311S|MTMR11_ENST00000361405.6_Intron|MTMR11_ENST00000369140.3_Silent_p.S267S|MTMR11_ENST00000492824.1_5'UTR	NM_001145862.1	NP_001139334.1	A4FU01	MTMRB_HUMAN	myotubularin related protein 11	339	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.						phosphatase activity (GO:0016791)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(13)|prostate(2)|stomach(1)|urinary_tract(4)	34	Breast(34;0.0009)|Ovarian(49;0.0377)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.221)|STAD - Stomach adenocarcinoma(528;0.247)			CTTCCAGGGCTGAAAGCCATT	0.443																																					p.S339S		Atlas-SNP	.											.	MTMR11	136	.	0			c.A1017T						.						175.0	167.0	170.0					1																	149904191		2203	4300	6503	SO:0001819	synonymous_variant	10903	exon11			CAGGGCTGAAAGC	AK097000	CCDS72901.1, CCDS72902.1	1q12-q21	2011-06-09			ENSG00000014914	ENSG00000014914		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	24307	protein-coding gene	gene with protein product	"""cisplatin resistance associated"""					12495846	Standard	NM_181873		Approved	CRA	uc001etl.4	A4FU01	OTTHUMG00000012207	ENST00000439741.2:c.1017A>T	chr1.hg19:g.149904191T>A		99.0	0.0		162.0	13.0	NM_001145862	B3KUE4|B4DJI6|B4DQF5|B4E3Q6|Q3ZCP7|Q5SZ62|Q6P2Q8|Q99752|Q99753	Silent	SNP	ENST00000439741.2	hg19	CCDS53360.1																																																																																			.	.		0.443	MTMR11-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_181873	
ADAM15	8751	hgsc.bcm.edu	37	1	155030505	155030505	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:155030505A>T	ENST00000356955.2	+	14	1696	c.1595A>T	c.(1594-1596)cAg>cTg	p.Q532L	ADAM15_ENST00000447332.3_Missense_Mutation_p.Q516L|ADAM15_ENST00000271836.6_Missense_Mutation_p.Q532L|ADAM15_ENST00000359280.4_Missense_Mutation_p.Q532L|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000368413.1_Missense_Mutation_p.Q238L|ADAM15_ENST00000368412.3_Missense_Mutation_p.Q532L|ADAM15_ENST00000355956.2_Missense_Mutation_p.Q532L|ADAM15_ENST00000368410.2_Missense_Mutation_p.Q238L|ADAM15_ENST00000449910.2_Missense_Mutation_p.Q532L|ADAM15_ENST00000360674.4_Missense_Mutation_p.Q532L|ADAM15_ENST00000531455.1_Missense_Mutation_p.Q542L	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	532	Cys-rich.				angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CAGCAGTGCCAGTCACTTTGG	0.637																																					p.Q542L		Atlas-SNP	.											.	ADAM15	92	.	0			c.A1625T						.						66.0	65.0	65.0					1																	155030505		2203	4300	6503	SO:0001583	missense	8751	exon14			AGTGCCAGTCACT	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.1595A>T	chr1.hg19:g.155030505A>T	ENSP00000349436:p.Gln532Leu	80.0	0.0		69.0	5.0	NM_001261464	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	hg19	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	A	13.20	2.167177	0.38315	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	T;T;T;T;T;T;T;T;T;T	0.23348	1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91;1.91	5.4	4.28	0.50868	ADAM, cysteine-rich (2);	0.000000	0.42548	D	0.000683	T	0.32346	0.0826	M	0.76328	2.33	0.45607	D	0.998546	D;D;B;D;P;D;D;D;D;D;D	0.89917	0.999;0.999;0.198;0.995;0.741;1.0;1.0;1.0;0.99;0.996;1.0	D;D;B;D;P;D;D;D;D;D;D	0.87578	0.988;0.988;0.192;0.996;0.622;0.979;0.979;0.986;0.92;0.998;0.988	T	0.15925	-1.0420	10	0.26408	T	0.33	.	7.8003	0.29170	0.9081:0.0:0.0919:0.0	.	542;549;516;532;532;532;532;532;532;532;529	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444;Q59GF2	.;.;.;.;.;.;.;.;.;ADA15_HUMAN;.	L	532;532;532;532;532;532;238;532;238;542	ENSP00000349436:Q532L;ENSP00000403843:Q532L;ENSP00000352226:Q532L;ENSP00000353892:Q532L;ENSP00000357397:Q532L;ENSP00000348227:Q532L;ENSP00000357395:Q238L;ENSP00000271836:Q532L;ENSP00000357398:Q238L;ENSP00000432927:Q542L	ENSP00000271836:Q532L	Q	+	2	0	ADAM15	153297129	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.514000	0.45503	1.075000	0.40932	0.533000	0.62120	CAG	.	.		0.637	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
ARHGEF2	9181	hgsc.bcm.edu	37	1	155931649	155931649	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:155931649T>A	ENST00000361247.4	-	11	1370	c.1271A>T	c.(1270-1272)gAg>gTg	p.E424V	ARHGEF2_ENST00000462460.2_Missense_Mutation_p.E469V|ARHGEF2_ENST00000313667.4_Missense_Mutation_p.E423V|ARHGEF2_ENST00000368316.1_Missense_Mutation_p.E396V|ARHGEF2_ENST00000368315.4_Missense_Mutation_p.E425V|ARHGEF2_ENST00000477754.2_Intron|ARHGEF2_ENST00000313695.7_Missense_Mutation_p.E396V	NM_001162383.1|NM_001162384.1	NP_001155855.1|NP_001155856.1	Q92974	ARHG2_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 2	424	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin filament organization (GO:0007015)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular hyperosmotic response (GO:0071474)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to tumor necrosis factor (GO:0071356)|establishment of mitotic spindle orientation (GO:0000132)|innate immune response (GO:0045087)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress (GO:1902219)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of necroptotic process (GO:0060546)|negative regulation of neurogenesis (GO:0050768)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)|regulation of Rho protein signal transduction (GO:0035023)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)|vesicle (GO:0031982)	microtubule binding (GO:0008017)|Rac GTPase binding (GO:0048365)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho GTPase binding (GO:0017048)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(4)|cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|skin(2)	40	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					GGACAGCAGCTCCTTCACTAG	0.607																																					p.E424V	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A1271T						.						80.0	78.0	79.0					1																	155931649		2203	4300	6503	SO:0001583	missense	9181	exon11			AGCAGCTCCTTCA	AB014551	CCDS1125.1, CCDS53375.1, CCDS53376.1	1q21-q22	2013-01-10	2009-06-12		ENSG00000116584	ENSG00000116584		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	682	protein-coding gene	gene with protein product		607560	"""rho/rac guanine nucleotide exchange factor (GEF) 2"""			9857026, 9734811	Standard	NM_004723		Approved	LFP40, GEF-H1, KIAA0651, P40	uc001fmt.2	Q92974	OTTHUMG00000017464	ENST00000361247.4:c.1271A>T	chr1.hg19:g.155931649T>A	ENSP00000354837:p.Glu424Val	231.0	0.0		312.0	35.0	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Missense_Mutation	SNP	ENST00000361247.4	hg19	CCDS53376.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.326302	0.81580	.	.	ENSG00000116584	ENST00000313695;ENST00000361247;ENST00000368315;ENST00000368316;ENST00000435736;ENST00000543433;ENST00000313667	T;T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17;-0.17	4.86	4.86	0.63082	Dbl homology (DH) domain (5);	0.138147	0.33075	N	0.005303	T	0.73682	0.3618	M	0.83603	2.65	0.46061	D	0.998841	P;P;D;P	0.67145	0.789;0.87;0.996;0.923	P;P;D;P	0.68039	0.643;0.758;0.955;0.644	T	0.78677	-0.2111	10	0.72032	D	0.01	-25.5843	12.7091	0.57080	0.0:0.0:0.0:1.0	.	469;468;424;423	B7Z977;D3DVA5;Q92974;Q92974-2	.;.;ARHG2_HUMAN;.	V	396;424;425;396;469;397;423	ENSP00000315325:E396V;ENSP00000354837:E424V;ENSP00000357298:E425V;ENSP00000357299:E396V;ENSP00000314787:E423V	ENSP00000314787:E423V	E	-	2	0	ARHGEF2	154198273	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.540000	0.67205	2.162000	0.67917	0.482000	0.46254	GAG	.	.		0.607	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
SMG5	23381	hgsc.bcm.edu	37	1	156230352	156230352	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:156230352T>A	ENST00000361813.5	-	15	2317	c.2173A>T	c.(2173-2175)Agc>Tgc	p.S725C	SMG5_ENST00000368267.5_Intron	NM_015327.2	NP_056142.2	Q9UPR3	SMG5_HUMAN	SMG5 nonsense mediated mRNA decay factor	725					gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	protein phosphatase 2A binding (GO:0051721)			NS(1)|breast(3)|endometrium(8)|kidney(2)|large_intestine(7)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	48	Hepatocellular(266;0.158)					AGCAGAAGGCTAGAGGGGAGG	0.577																																					p.S725C		Atlas-SNP	.											.	SMG5	98	.	0			c.A2173T						.						83.0	70.0	74.0					1																	156230352		2203	4300	6503	SO:0001583	missense	23381	exon15			GAAGGCTAGAGGG	AB029012	CCDS1137.1	1q21	2013-07-02	2013-07-02		ENSG00000198952	ENSG00000198952			24644	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog B (S. cerevisiae)"""	610962	"""smg-5 homolog, nonsense mediated mRNA decay factor (C. elegans)"""			12676087, 12699629	Standard	NM_015327		Approved	KIAA1089, LPTS-RP1, LPTSRP1, RP11-54H19.7, SMG-5, EST1B	uc001foc.4	Q9UPR3	OTTHUMG00000017491	ENST00000361813.5:c.2173A>T	chr1.hg19:g.156230352T>A	ENSP00000355261:p.Ser725Cys	236.0	0.0		289.0	18.0	NM_015327	D3DVB7|Q5QJE7|Q659C7|Q8IXC0|Q8IY09|Q96IJ7	Missense_Mutation	SNP	ENST00000361813.5	hg19	CCDS1137.1	.	.	.	.	.	.	.	.	.	.	T	16.85	3.235373	0.58886	.	.	ENSG00000198952	ENST00000361813	T	0.33865	1.39	5.36	4.23	0.50019	.	0.379369	0.28772	N	0.014192	T	0.20981	0.0505	N	0.22421	0.69	0.80722	D	1	P	0.52061	0.95	P	0.56474	0.799	T	0.05632	-1.0873	10	0.39692	T	0.17	-7.092	6.1766	0.20447	0.1957:0.0:0.1229:0.6813	.	725	Q9UPR3	SMG5_HUMAN	C	725	ENSP00000355261:S725C	ENSP00000355261:S725C	S	-	1	0	SMG5	154496976	0.975000	0.34042	0.965000	0.40720	0.764000	0.43329	0.540000	0.23191	1.047000	0.40274	0.459000	0.35465	AGC	.	.		0.577	SMG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046308.1	NM_015327	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517532	158517532	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:158517532T>A	ENST00000302617.3	-	1	363	c.364A>T	c.(364-366)Atc>Ttc	p.I122F		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					AAGGCCATGATAGCAAGAAGG	0.463																																					p.I122F		Atlas-SNP	.											.	OR6Y1	73	.	0			c.A364T						.						129.0	112.0	117.0					1																	158517532		2202	4300	6502	SO:0001583	missense	391112	exon1			CCATGATAGCAAG	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"""GPCR / Class A : Olfactory receptors"""	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.364A>T	chr1.hg19:g.158517532T>A	ENSP00000304807:p.Ile122Phe	255.0	0.0		414.0	39.0	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	hg19	CCDS30899.1	.	.	.	.	.	.	.	.	.	.	T	11.38	1.621977	0.28889	.	.	ENSG00000197532	ENST00000302617	T	0.01359	4.98	4.91	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.202846	0.24052	N	0.041990	T	0.00412	0.0013	N	0.16790	0.44	0.09310	N	1	B	0.33413	0.411	B	0.25405	0.06	T	0.49799	-0.8901	10	0.72032	D	0.01	.	8.5055	0.33184	0.0:0.7449:0.0:0.2551	.	122	Q8NGX8	OR6Y1_HUMAN	F	122	ENSP00000304807:I122F	ENSP00000304807:I122F	I	-	1	0	OR6Y1	156784156	0.004000	0.15560	0.007000	0.13788	0.849000	0.48306	1.803000	0.38863	0.780000	0.33566	-0.230000	0.12252	ATC	.	.		0.463	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189	
F5	2153	hgsc.bcm.edu	37	1	169521814	169521814	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:169521814T>A	ENST00000367797.3	-	8	1478	c.1277A>T	c.(1276-1278)cAg>cTg	p.Q426L	F5_ENST00000367796.3_Missense_Mutation_p.Q426L|F5_ENST00000546081.1_Missense_Mutation_p.Q289L	NM_000130.4	NP_000121	P12259	FA5_HUMAN	coagulation factor V (proaccelerin, labile factor)	426	F5/8 type A 2.|Plastocyanin-like 3.				blood circulation (GO:0008015)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|vesicle (GO:0031982)	copper ion binding (GO:0005507)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(55)|ovary(3)|prostate(4)|skin(5)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(1)	128	all_hematologic(923;0.208)				ART-123(DB05777)|Drotrecogin alfa(DB00055)	GTCTCTGACCTGGGCTCTGAT	0.343																																					p.Q426L		Atlas-SNP	.											.	F5	301	.	0			c.A1277T						.						123.0	120.0	121.0					1																	169521814		2203	4300	6503	SO:0001583	missense	2153	exon8			CTGACCTGGGCTC	M14335	CCDS1281.1	1q23	2012-10-02			ENSG00000198734	ENSG00000198734			3542	protein-coding gene	gene with protein product		612309					Standard	NM_000130		Approved		uc001ggg.1	P12259	OTTHUMG00000034595	ENST00000367797.3:c.1277A>T	chr1.hg19:g.169521814T>A	ENSP00000356771:p.Gln426Leu	124.0	0.0		185.0	14.0	NM_000130	A8K6E8|Q14285|Q2EHR5|Q5R346|Q5R347|Q6UPU6|Q8WWQ6	Missense_Mutation	SNP	ENST00000367797.3	hg19	CCDS1281.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.578911	0.86645	.	.	ENSG00000198734	ENST00000367797;ENST00000367796;ENST00000546081	D;D;D	0.98968	-5.28;-5.28;-5.28	5.65	5.65	0.86999	Cupredoxin (2);	0.000000	0.85682	D	0.000000	D	0.99089	0.9687	M	0.84326	2.69	0.43267	D	0.995219	D	0.76494	0.999	D	0.83275	0.996	D	0.99851	1.1072	9	0.87932	D	0	-14.5758	16.1566	0.81673	0.0:0.0:0.0:1.0	.	426	P12259	FA5_HUMAN	L	426;426;289	ENSP00000356771:Q426L;ENSP00000356770:Q426L;ENSP00000439664:Q289L	ENSP00000356770:Q426L	Q	-	2	0	F5	167788438	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.420000	0.80191	2.268000	0.75426	0.533000	0.62120	CAG	.	.		0.343	F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000083712.1	NM_000130	
ASPM	259266	hgsc.bcm.edu	37	1	197108988	197108988	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:197108988G>T	ENST00000367409.4	-	4	2191	c.1935C>A	c.(1933-1935)ttC>ttA	p.F645L	ASPM_ENST00000294732.7_Missense_Mutation_p.F645L	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	645					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						TTGGAGTTCTGAATATTGATA	0.303																																					p.F645L		Atlas-SNP	.											.	ASPM	444	.	0			c.C1935A						.						120.0	122.0	121.0					1																	197108988		2203	4300	6503	SO:0001583	missense	259266	exon4			AGTTCTGAATATT	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.1935C>A	chr1.hg19:g.197108988G>T	ENSP00000356379:p.Phe645Leu	47.0	0.0		44.0	17.0	NM_001206846	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	hg19	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	G	1.589	-0.529545	0.04112	.	.	ENSG00000066279	ENST00000367409;ENST00000294732	T;T	0.56103	0.48;1.76	5.79	-0.136	0.13473	.	0.724164	0.13219	N	0.404517	T	0.18299	0.0439	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18335	-1.0340	10	0.11485	T	0.65	.	1.9633	0.03390	0.2746:0.1438:0.4079:0.1736	.	645;645	Q4G1H1;Q8IZT6	.;ASPM_HUMAN	L	645	ENSP00000356379:F645L;ENSP00000294732:F645L	ENSP00000294732:F645L	F	-	3	2	ASPM	195375611	0.000000	0.05858	0.015000	0.15790	0.017000	0.09413	-0.419000	0.07071	-0.125000	0.11703	-0.847000	0.03039	TTC	.	.		0.303	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
CR1	1378	hgsc.bcm.edu	37	1	207679331	207679331	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:207679331T>A	ENST00000367049.4	+	2	204	c.204T>A	c.(202-204)taT>taA	p.Y68*	CR1_ENST00000367051.1_Nonsense_Mutation_p.Y68*|CR1_ENST00000367052.1_Nonsense_Mutation_p.Y68*|CR1_ENST00000367050.4_3'UTR|CR1_ENST00000400960.2_Nonsense_Mutation_p.Y68*|CR1_ENST00000367053.1_Nonsense_Mutation_p.Y68*	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	68	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						TTGGGACATATCTGAACTATG	0.468																																					p.Y68X		Atlas-SNP	.											.	CR1	354	.	0			c.T204A						.						172.0	160.0	164.0					1																	207679331		1850	4080	5930	SO:0001587	stop_gained	1378	exon2			GACATATCTGAAC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.204T>A	chr1.hg19:g.207679331T>A	ENSP00000356016:p.Tyr68*	332.0	0.0		444.0	33.0	NM_000573	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Nonsense_Mutation	SNP	ENST00000367049.4	hg19	CCDS44308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.07|14.07	2.427113|2.427113	0.43122|0.43122	.|.	.|.	ENSG00000203710|ENSG00000203710	ENST00000529814|ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	.|.	.|.	.|.	4.13|4.13	4.13|4.13	0.48395|0.48395	.|.	.|.	.|.	.|.	.|.	T|.	0.53738|.	0.1815|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.64245|.	-0.6453|.	3|.	.|0.37606	.|T	.|0.19	.|.	9.7248|9.7248	0.40324|0.40324	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	N|X	44|68	.|.	.|ENSP00000356016:Y68X	I|Y	+|+	2|3	0|2	CR1|CR1	205745954|205745954	0.017000|0.017000	0.18338|0.18338	0.049000|0.049000	0.19019|0.19019	0.001000|0.001000	0.01503|0.01503	3.058000|3.058000	0.49939|0.49939	1.868000|1.868000	0.54150|0.54150	0.482000|0.482000	0.46254|0.46254	ATC|TAT	.	.		0.468	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
RD3	343035	hgsc.bcm.edu	37	1	211652560	211652560	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:211652560G>T	ENST00000367002.4	-	3	1569	c.406C>A	c.(406-408)Cac>Aac	p.H136N	RD3_ENST00000484910.1_5'UTR	NM_001164688.1|NM_183059.2	NP_001158160.1|NP_898882.1	Q7Z3Z2	RD3_HUMAN	retinal degeneration 3	136					response to stimulus (GO:0050896)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)					central_nervous_system(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	10				OV - Ovarian serous cystadenocarcinoma(81;0.00284)|all cancers(67;0.0279)|Epithelial(68;0.0689)		GTCAGCTTGTGGGCCTCCTCT	0.687																																					p.H136N		Atlas-SNP	.											.	RD3	26	.	0			c.C406A						.						23.0	22.0	23.0					1																	211652560		2200	4299	6499	SO:0001583	missense	343035	exon3			GCTTGTGGGCCTC	AY191519	CCDS1498.1	1q32.3	2008-02-05	2006-11-13	2006-11-13	ENSG00000198570	ENSG00000198570			19689	protein-coding gene	gene with protein product		180040	"""chromosome 1 open reading frame 36"""	C1orf36		12914764	Standard	NM_183059		Approved	LCA12	uc001hin.2	Q7Z3Z2	OTTHUMG00000037002	ENST00000367002.4:c.406C>A	chr1.hg19:g.211652560G>T	ENSP00000355969:p.His136Asn	61.0	0.0		44.0	11.0	NM_183059	A8K595	Missense_Mutation	SNP	ENST00000367002.4	hg19	CCDS1498.1	.	.	.	.	.	.	.	.	.	.	G	14.07	2.426968	0.43122	.	.	ENSG00000198570	ENST00000367002	T	0.09163	3.01	4.33	3.25	0.37280	.	0.489617	0.23369	N	0.048933	T	0.07548	0.0190	N	0.22421	0.69	0.26407	N	0.976325	B	0.23990	0.095	B	0.24155	0.051	T	0.21075	-1.0256	10	0.45353	T	0.12	-16.4574	9.69	0.40123	0.0:0.0:0.5192:0.4808	.	136	Q7Z3Z2	RD3_HUMAN	N	136	ENSP00000355969:H136N	ENSP00000355969:H136N	H	-	1	0	RD3	209719183	1.000000	0.71417	0.975000	0.42487	0.809000	0.45718	3.898000	0.56281	2.131000	0.65755	0.555000	0.69702	CAC	.	.		0.687	RD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089837.1	NM_183059	
USH2A	7399	hgsc.bcm.edu	37	1	215972280	215972280	+	Silent	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:215972280T>C	ENST00000307340.3	-	50	10313	c.9927A>G	c.(9925-9927)ggA>ggG	p.G3309G	USH2A_ENST00000366943.2_Silent_p.G3309G	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	3309					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		CTCCTTCTTCTCCACCACAAC	0.512										HNSCC(13;0.011)																											p.G3309G		Atlas-SNP	.											.	USH2A	1168	.	0			c.A9927G						.						178.0	151.0	160.0					1																	215972280		2203	4300	6503	SO:0001819	synonymous_variant	7399	exon50			TTCTTCTCCACCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.9927A>G	chr1.hg19:g.215972280T>C		284.0	0.0		410.0	168.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.512	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
LGALS8	3964	hgsc.bcm.edu	37	1	236708178	236708178	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:236708178T>C	ENST00000366584.4	+	9	1333	c.767T>C	c.(766-768)aTt>aCt	p.I256T	LGALS8_ENST00000526589.1_Missense_Mutation_p.I298T|LGALS8_ENST00000323938.6_Missense_Mutation_p.I229T|LGALS8_ENST00000450372.2_Missense_Mutation_p.I298T|LGALS8_ENST00000416919.2_Missense_Mutation_p.I239T|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000525042.1_Missense_Mutation_p.I239T|LGALS8_ENST00000526634.1_Missense_Mutation_p.I256T|LGALS8_ENST00000352231.2_Missense_Mutation_p.I298T|LGALS8_ENST00000341872.6_Missense_Mutation_p.I256T|LGALS8_ENST00000527974.1_Missense_Mutation_p.I298T	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	256	Galectin 2. {ECO:0000255|PROSITE- ProRule:PRU00639}.				plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			GAGAGAAATATTACCTCTTTC	0.413																																					p.I298T		Atlas-SNP	.											.	LGALS8	42	.	0			c.T893C						.						87.0	89.0	88.0					1																	236708178		2203	4300	6503	SO:0001583	missense	3964	exon11			GAAATATTACCTC	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"""Lectins, galactoside-binding"""	6569	protein-coding gene	gene with protein product	"""galectin 8"""	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.767T>C	chr1.hg19:g.236708178T>C	ENSP00000355543:p.Ile256Thr	105.0	0.0		136.0	50.0	NM_006499	O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	hg19	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	T	11.36	1.615985	0.28801	.	.	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000416919;ENST00000323938;ENST00000526634;ENST00000525042	T;T;T;T;T;T;T;T;T;T	0.04758	3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56;3.56	5.35	3.03	0.35002	Concanavalin A-like lectin/glucanase (1);Galectin, carbohydrate recognition domain (4);Concanavalin A-like lectin/glucanase, subgroup (1);	0.266713	0.37178	N	0.002220	T	0.04363	0.0120	N	0.25992	0.78	0.09310	N	1	B;B;B	0.09022	0.0;0.0;0.002	B;B;B	0.19148	0.004;0.024;0.014	T	0.35126	-0.9801	10	0.62326	D	0.03	-8.274	10.0817	0.42393	0.0:0.1363:0.0:0.8637	.	239;256;298	F6V2D4;O00214;O00214-2	.;LEG8_HUMAN;.	T	298;298;298;256;298;256;297;239;229;256;239	ENSP00000431398:I298T;ENSP00000309576:I298T;ENSP00000435460:I298T;ENSP00000342139:I256T;ENSP00000408657:I298T;ENSP00000355543:I256T;ENSP00000410843:I239T;ENSP00000434860:I229T;ENSP00000437040:I256T;ENSP00000431884:I239T	ENSP00000434860:I229T	I	+	2	0	LGALS8	234774801	0.981000	0.34729	0.850000	0.33497	0.883000	0.51084	4.166000	0.58203	0.562000	0.29204	-0.274000	0.10170	ATT	.	.		0.413	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499	
RYR2	6262	hgsc.bcm.edu	37	1	237868576	237868576	+	Silent	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:237868576G>A	ENST00000366574.2	+	67	9830	c.9513G>A	c.(9511-9513)ttG>ttA	p.L3171L	RYR2_ENST00000609119.1_3'UTR|RYR2_ENST00000542537.1_Silent_p.L3155L|RYR2_ENST00000360064.6_Silent_p.L3169L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3171					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			TAGCATTTTTGGAAACTCATC	0.393																																					p.L3171L		Atlas-SNP	.											.	RYR2	1273	.	0			c.G9513A						.						116.0	107.0	110.0					1																	237868576		1881	4126	6007	SO:0001819	synonymous_variant	6262	exon67			ATTTTTGGAAACT	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.9513G>A	chr1.hg19:g.237868576G>A		133.0	0.0		155.0	47.0	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	hg19	CCDS55691.1																																																																																			.	.		0.393	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
CEP170	9859	hgsc.bcm.edu	37	1	243354349	243354349	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:243354349T>A	ENST00000366542.1	-	8	1130	c.1079A>T	c.(1078-1080)gAt>gTt	p.D360V	CEP170_ENST00000366543.1_Missense_Mutation_p.D360V|CEP170_ENST00000366544.1_Missense_Mutation_p.D360V	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	360						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			CACTGGAACATCACTTTTAAT	0.373																																					p.D360V		Atlas-SNP	.											.	CEP170	153	.	0			c.A1079T						.						25.0	24.0	24.0					1																	243354349		1829	4071	5900	SO:0001583	missense	9859	exon8			GGAACATCACTTT	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.1079A>T	chr1.hg19:g.243354349T>A	ENSP00000355500:p.Asp360Val	218.0	0.0		257.0	16.0	NM_001042405	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.96|19.96	3.924033|3.924033	0.73213|0.73213	.|.	.|.	ENSG00000143702|ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081|ENST00000336415	T;T;T|.	0.72942|.	-0.7;-0.56;-0.56|.	4.91|4.91	4.91|4.91	0.64330|0.64330	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72969|0.72969	0.3527|0.3527	M|M	0.72353|0.72353	2.195|2.195	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.97110|.	0.999;1.0;0.999|.	T|T	0.73757|0.73757	-0.3882|-0.3882	10|5	0.87932|.	D|.	0|.	-16.166|-16.166	14.5724|14.5724	0.68220|0.68220	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	360;360;360|.	Q5SW79-3;Q5SW79-2;Q5SW79|.	.;.;CE170_HUMAN|.	V|L	360;360;360;258|262	ENSP00000355500:D360V;ENSP00000355502:D360V;ENSP00000355501:D360V|.	ENSP00000355500:D360V|.	D|M	-|-	2|1	0|0	CEP170|CEP170	241420972|241420972	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.694000|7.694000	0.84235|0.84235	1.853000|1.853000	0.53794|0.53794	0.374000|0.374000	0.22700|0.22700	GAT|ATG	.	.		0.373	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
ALK	238	hgsc.bcm.edu	37	2	29416521	29416521	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:29416521T>C	ENST00000389048.3	-	29	5338	c.4432A>G	c.(4432-4434)Atg>Gtg	p.M1478V	ALK_ENST00000431873.1_Missense_Mutation_p.M308V	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1478					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GAGAATGCCATATTCACGTGT	0.577			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome																												p.M1478V		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.A4432G						.						111.0	113.0	112.0					2																	29416521		2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ATGCCATATTCAC	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.4432A>G	chr2.hg19:g.29416521T>C	ENSP00000373700:p.Met1478Val	261.0	0.0		231.0	74.0	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	hg19	CCDS33172.1	.	.	.	.	.	.	.	.	.	.	t	9.190	1.025827	0.19512	.	.	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.76316	-1.01;2.93	5.64	3.18	0.36537	.	0.000000	0.64402	U	0.000018	T	0.70902	0.3277	M	0.63428	1.95	0.24401	N	0.994708	B	0.06786	0.001	B	0.04013	0.001	T	0.57625	-0.7779	10	0.29301	T	0.29	.	8.7607	0.34672	0.0:0.067:0.1285:0.8045	.	1478	Q9UM73	ALK_HUMAN	V	1478;308	ENSP00000373700:M1478V;ENSP00000414027:M308V	ENSP00000373700:M1478V	M	-	1	0	ALK	29270025	1.000000	0.71417	0.967000	0.41034	0.349000	0.29174	1.855000	0.39378	0.390000	0.25115	0.454000	0.30748	ATG	.	.		0.577	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
HNRNPLL	92906	hgsc.bcm.edu	37	2	38804603	38804603	+	Splice_Site	SNP	C	C	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:38804603C>G	ENST00000449105.3	-	7	1213	c.874G>C	c.(874-876)Gga>Cga	p.G292R	HNRNPLL_ENST00000378915.3_Splice_Site_p.G258R|HNRNPLL_ENST00000409636.1_Splice_Site_p.G287R|HNRNPLL_ENST00000608859.1_Splice_Site_p.G292R|HNRNPLL_ENST00000409328.1_Splice_Site_p.G258R			Q8WVV9	HNRLL_HUMAN	heterogeneous nuclear ribonucleoprotein L-like	292					mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)	membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)										GACAACTTACCATAGCCATCA	0.398																																					p.G292R		Atlas-SNP	.											.	HNRPLL	19	.	0			c.G874C						.						169.0	153.0	158.0					2																	38804603		2203	4300	6503	SO:0001630	splice_region_variant	92906	exon7			ACTTACCATAGCC	BC008217	CCDS46261.1, CCDS1796.2	2p22	2014-02-10		2013-06-12	ENSG00000143889	ENSG00000143889		"""RNA binding motif (RRM) containing"""	25127	protein-coding gene	gene with protein product		611208		HNRPLL		18669861	Standard	NM_138394		Approved		uc021vgc.1	Q8WVV9	OTTHUMG00000102075	ENST00000449105.3:c.874+1G>C	chr2.hg19:g.38804603C>G		273.0	0.0		298.0	86.0	NM_138394	Q53T80|Q5JB51|Q5JB52|Q659B9|Q8IVH5|Q8IVH6|Q96HR5	Missense_Mutation	SNP	ENST00000449105.3	hg19		.	.	.	.	.	.	.	.	.	.	C	22.7	4.318637	0.81469	.	.	ENSG00000143889	ENST00000449105;ENST00000409636;ENST00000378915;ENST00000409328	.	.	.	6.03	6.03	0.97812	.	0.134395	0.48286	D	0.000194	T	0.74076	0.3669	L	0.40543	1.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.69157	-0.5219	8	.	.	.	-5.1667	20.5568	0.99304	0.0:1.0:0.0:0.0	.	287;292	C9J9G0;D6W592	.;.	R	292;287;258;258	.	.	G	-	1	0	HNRPLL	38658107	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.645000	0.74343	2.861000	0.98227	0.655000	0.94253	GGA	.	.		0.398	HNRNPLL-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000219887.2	NM_138394	Missense_Mutation
TMEM127	55654	hgsc.bcm.edu	37	2	96919803	96919803	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:96919803T>C	ENST00000258439.3	-	4	716	c.460A>G	c.(460-462)Atc>Gtc	p.I154V	TMEM127_ENST00000435268.1_Missense_Mutation_p.I70V|TMEM127_ENST00000432959.1_Missense_Mutation_p.I154V	NM_001193304.2|NM_017849.3	NP_001180233.1|NP_060319.1	O75204	TM127_HUMAN	transmembrane protein 127	154					negative regulation of cell proliferation (GO:0008285)|negative regulation of TOR signaling (GO:0032007)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(1)|prostate(1)|stomach(1)	5						TGGGCCAAGATGAGTTCAGAA	0.537																																					p.I154V		Atlas-SNP	.											.	TMEM127	13	.	0			c.A460G						.						103.0	99.0	101.0					2																	96919803		2203	4300	6503	SO:0001583	missense	55654	exon4			CCAAGATGAGTTC	AK000514	CCDS2018.1	2q11.2	2014-09-17			ENSG00000135956	ENSG00000135956			26038	protein-coding gene	gene with protein product		613403				10493829	Standard	NM_017849		Approved	FLJ20507, FLJ22257	uc002svr.3	O75204	OTTHUMG00000130454	ENST00000258439.3:c.460A>G	chr2.hg19:g.96919803T>C	ENSP00000258439:p.Ile154Val	155.0	0.0		111.0	43.0	NM_001193304	D3DXH0	Missense_Mutation	SNP	ENST00000258439.3	hg19	CCDS2018.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.603311	0.28534	.	.	ENSG00000135956	ENST00000258439;ENST00000432959;ENST00000435268	D;D;D	0.95622	-3.76;-3.76;-2.93	6.06	6.06	0.98353	.	0.052153	0.64402	D	0.000001	D	0.90665	0.7072	N	0.14661	0.345	0.49582	D	0.999806	B	0.02656	0.0	B	0.04013	0.001	D	0.86602	0.1867	10	0.59425	D	0.04	-25.5181	15.5919	0.76537	0.0:0.0:0.0:1.0	.	154	O75204	TM127_HUMAN	V	154;154;70	ENSP00000258439:I154V;ENSP00000416660:I154V;ENSP00000411810:I70V	ENSP00000258439:I154V	I	-	1	0	TMEM127	96283530	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.660000	0.61511	2.324000	0.78689	0.533000	0.62120	ATC	.	.		0.537	TMEM127-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252845.3	NM_017849	
MAP4K4	9448	hgsc.bcm.edu	37	2	102483701	102483701	+	Missense_Mutation	SNP	C	C	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:102483701C>G	ENST00000347699.4	+	19	2150	c.2150C>G	c.(2149-2151)tCt>tGt	p.S717C	MAP4K4_ENST00000324219.4_Missense_Mutation_p.S795C|MAP4K4_ENST00000302217.5_Missense_Mutation_p.S517C|MAP4K4_ENST00000350878.4_Missense_Mutation_p.S690C|MAP4K4_ENST00000350198.4_Missense_Mutation_p.S633C|MAP4K4_ENST00000425019.1_Missense_Mutation_p.S686C|MAP4K4_ENST00000413150.2_Missense_Mutation_p.S632C|MAP4K4_ENST00000456652.1_Missense_Mutation_p.S516C	NM_001242559.1|NM_145687.3	NP_001229488.1|NP_663720.1	O95819	M4K4_HUMAN	mitogen-activated protein kinase kinase kinase kinase 4	717					intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)|regulation of JNK cascade (GO:0046328)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						GGCTCTCCATCTCAGCGCCTG	0.438																																					p.S717C		Atlas-SNP	.											.	MAP4K4	111	.	0			c.C2150G						.						69.0	69.0	69.0					2																	102483701		1911	4132	6043	SO:0001583	missense	9448	exon19			CTCCATCTCAGCG	AF096300	CCDS56130.1, CCDS74546.1	2q11.2-q12	2011-06-09			ENSG00000071054	ENSG00000071054		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6866	protein-coding gene	gene with protein product	"""HPK/GCK-like kinase"", ""hepatocyte progenitor kinase-like/germinal center kinase-like kinase"""	604666				9890973, 9734811, 9135144	Standard	NM_004834		Approved	HGK, NIK, FLH21957	uc002tbf.3	O95819	OTTHUMG00000155394	ENST00000347699.4:c.2150C>G	chr2.hg19:g.102483701C>G	ENSP00000314363:p.Ser717Cys	153.0	0.0		135.0	35.0	NM_001242559	O75172|Q9NST7	Missense_Mutation	SNP	ENST00000347699.4	hg19	CCDS56130.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.30|19.30	3.801376|3.801376	0.70567|0.70567	.|.	.|.	ENSG00000071054|ENSG00000071054	ENST00000421882|ENST00000425019;ENST00000324219;ENST00000350198;ENST00000302217;ENST00000413150;ENST00000456652;ENST00000347699;ENST00000417294;ENST00000350878	.|T;T;T;T;T;T;T;T;T	.|0.12039	.|2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72;2.72	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	.|0.176739	.|0.49305	.|D	.|0.000146	T|T	0.30665|0.30665	0.0772|0.0772	L|L	0.36672|0.36672	1.1|1.1	0.51012|0.51012	D|D	0.9999|0.9999	.|P;P;P;P;D;D;D;D;D;D	.|0.76494	.|0.94;0.94;0.94;0.94;0.965;0.994;0.999;0.965;0.989;0.996	.|P;P;P;P;P;D;D;P;D;D	.|0.78314	.|0.635;0.635;0.635;0.635;0.73;0.922;0.991;0.73;0.916;0.947	T|T	0.00726|0.00726	-1.1592|-1.1592	5|10	.|0.51188	.|T	.|0.08	.|.	19.7244|19.7244	0.96157|0.96157	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|690;710;516;517;632;717;686;633;686;795	.|B7Z388;B7Z3V5;E7EX83;C9J840;O95819-4;O95819;E7EN19;G3XAA2;O95819-2;G5E948	.|.;.;.;.;.;M4K4_HUMAN;.;.;.;.	M|C	533|686;795;633;517;632;516;717;648;690	.|ENSP00000392830:S686C;ENSP00000313644:S795C;ENSP00000281111:S633C;ENSP00000303600:S517C;ENSP00000389752:S632C;ENSP00000387370:S516C;ENSP00000314363:S717C;ENSP00000409720:S648C;ENSP00000343658:S690C	.|ENSP00000303600:S517C	I|S	+|+	3|2	3|0	MAP4K4|MAP4K4	101850133|101850133	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	4.912000|4.912000	0.63335|0.63335	2.659000|2.659000	0.90383|0.90383	0.655000|0.655000	0.94253|0.94253	ATC|TCT	.	.		0.438	MAP4K4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339839.1	NM_004834	
MYO7B	4648	hgsc.bcm.edu	37	2	128334177	128334177	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:128334177A>T	ENST00000409816.2	+	7	775	c.743A>T	c.(742-744)gAg>gTg	p.E248V	MYO7B_ENST00000389524.4_Missense_Mutation_p.E248V|MYO7B_ENST00000428314.1_Missense_Mutation_p.E248V			Q6PIF6	MYO7B_HUMAN	myosin VIIB	248	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAGGCTCCCGAGGAGCGGAAC	0.627																																					p.E248V		Atlas-SNP	.											.	MYO7B	359	.	0			c.A743T						.						41.0	47.0	45.0					2																	128334177		2040	4195	6235	SO:0001583	missense	4648	exon8			CTCCCGAGGAGCG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.743A>T	chr2.hg19:g.128334177A>T	ENSP00000386461:p.Glu248Val	52.0	0.0		53.0	12.0	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	A	16.92	3.255896	0.59321	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	T;T;T	0.72615	-0.67;-0.67;-0.67	4.94	4.94	0.65067	Myosin head, motor domain (2);	0.290858	0.31872	N	0.006934	T	0.78748	0.4332	M	0.71036	2.16	0.40794	D	0.983285	D	0.57899	0.981	P	0.60345	0.873	T	0.80331	-0.1427	10	0.51188	T	0.08	.	9.4397	0.38661	0.9196:0.0:0.0804:0.0	.	248	Q6PIF6	MYO7B_HUMAN	V	248	ENSP00000374175:E248V;ENSP00000415090:E248V;ENSP00000386461:E248V	ENSP00000374175:E248V	E	+	2	0	MYO7B	128050647	1.000000	0.71417	0.853000	0.33588	0.399000	0.30720	6.247000	0.72411	1.994000	0.58287	0.460000	0.39030	GAG	.	.		0.627	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SCN1A	6323	hgsc.bcm.edu	37	2	166897947	166897947	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:166897947A>T	ENST00000303395.4	-	13	2208	c.2209T>A	c.(2209-2211)Tgt>Agt	p.C737S	SCN1A_ENST00000375405.3_Missense_Mutation_p.C726S|AC010127.3_ENST00000595647.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.C709S|SCN1A_ENST00000423058.2_Missense_Mutation_p.C737S|AC010127.3_ENST00000599041.1_RNA|AC010127.3_ENST00000595268.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	737					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTATACCAACAGGGTGGGCAT	0.338																																					p.C737S		Atlas-SNP	.											.	SCN1A	641	.	0			c.T2209A						.						81.0	90.0	87.0					2																	166897947		2203	4300	6503	SO:0001583	missense	6323	exon13			ACCAACAGGGTGG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.2209T>A	chr2.hg19:g.166897947A>T	ENSP00000303540:p.Cys737Ser	43.0	0.0		64.0	9.0	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	hg19	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578722	0.86645	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96459	-4.02;-4.02;-3.99;-3.97	5.54	5.54	0.83059	.	0.000000	0.64402	D	0.000001	D	0.97489	0.9178	M	0.90425	3.115	0.80722	D	1	P;D;P	0.54207	0.943;0.965;0.94	P;B;P	0.49829	0.623;0.419;0.601	D	0.98239	1.0487	10	0.87932	D	0	.	15.9597	0.79918	1.0:0.0:0.0:0.0	.	726;709;737	P35498-2;E9PG49;P35498	.;.;SCN1A_HUMAN	S	737;737;726;709	ENSP00000407030:C737S;ENSP00000303540:C737S;ENSP00000364554:C726S;ENSP00000386312:C709S	ENSP00000303540:C737S	C	-	1	0	SCN1A	166606193	1.000000	0.71417	0.999000	0.59377	0.975000	0.68041	7.440000	0.80464	2.226000	0.72624	0.482000	0.46254	TGT	.	.		0.338	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
SCN9A	6335	hgsc.bcm.edu	37	2	167163108	167163108	+	Splice_Site	SNP	A	A	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:167163108A>C	ENST00000409435.1	-	3	378	c.379T>G	c.(379-381)Tta>Gta	p.L127V	SCN9A_ENST00000303354.6_Missense_Mutation_p.L128V|SCN9A_ENST00000375387.4_Missense_Mutation_p.L128V|SCN9A_ENST00000409672.1_Splice_Site_p.L127V			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	127					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATGCTGAATAAGGTAGCTTAG	0.373																																					p.L127V		Atlas-SNP	.											.	SCN9A	296	.	0			c.T379G						.						65.0	64.0	65.0					2																	167163108		1936	4196	6132	SO:0001630	splice_region_variant	6335	exon4			TGAATAAGGTAGC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.378-1T>G	chr2.hg19:g.167163108A>C		105.0	0.0		76.0	31.0	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	hg19	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	a	12.90	2.075534	0.36662	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.97480	-4.4;-4.4;-4.4;-4.4	5.96	3.59	0.41128	.	0.309084	0.23307	N	0.049614	D	0.95459	0.8525	M	0.75264	2.295	0.35953	D	0.834069	B	0.06786	0.001	B	0.13407	0.009	D	0.93250	0.6634	10	0.49607	T	0.09	.	8.8756	0.35343	0.7989:0.1352:0.0659:0.0	.	127	E7EUN6	.	V	127;128;128;127	ENSP00000386306:L127V;ENSP00000364536:L128V;ENSP00000304748:L128V;ENSP00000386330:L127V	ENSP00000304748:L128V	L	-	1	2	SCN9A	166871354	0.381000	0.25140	0.990000	0.47175	0.964000	0.63967	0.932000	0.28884	0.496000	0.27904	0.528000	0.53228	TTA	.	.		0.373	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	Missense_Mutation
ITGA6	3655	hgsc.bcm.edu	37	2	173344405	173344405	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:173344405A>T	ENST00000264106.6	+	11	1745	c.1542A>T	c.(1540-1542)acA>acT	p.T514T	ITGA6_ENST00000343713.4_Silent_p.T470T|ITGA6_ENST00000264107.7_Silent_p.T475T|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000409532.1_Silent_p.T356T|ITGA6_ENST00000375221.2_Silent_p.T514T|ITGA6_ENST00000409080.1_Silent_p.T475T			P23229	ITA6_HUMAN	integrin, alpha 6	514					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			AAACCATCACAGTAACTCCTA	0.478																																					p.T475T		Atlas-SNP	.											.	ITGA6	171	.	0			c.A1425T						.						179.0	188.0	185.0					2																	173344405		2203	4300	6503	SO:0001819	synonymous_variant	3655	exon10			CATCACAGTAACT		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.1542A>T	chr2.hg19:g.173344405A>T		111.0	0.0		85.0	31.0	NM_000210	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	hg19																																																																																				.	.		0.478	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
TTN	7273	hgsc.bcm.edu	37	2	179433349	179433349	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:179433349G>A	ENST00000591111.1	-	276	72811	c.72587C>T	c.(72586-72588)cCa>cTa	p.P24196L	TTN_ENST00000359218.5_Missense_Mutation_p.P16897L|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P16772L|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P16964L|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P25837L|TTN_ENST00000342992.6_Missense_Mutation_p.P23269L|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000586707.1_RNA			Q8WZ42	TITIN_HUMAN	titin	24196	Ig-like 121.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTGCTTCAGTGGGAGACCATC	0.418																																					p.P25837L		Atlas-SNP	.											TTN_ENST00000359218,right_upper_lobe,carcinoma,0,5	TTN	18412	.	0			c.C77510T						.						207.0	189.0	195.0					2																	179433349		1920	4146	6066	SO:0001583	missense	7273	exon326			TTCAGTGGGAGAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.72587C>T	chr2.hg19:g.179433349G>A	ENSP00000465570:p.Pro24196Leu	279.0	1.0		295.0	27.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	G	10.60	1.396793	0.25205	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3	6.03	6.03	0.97812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.63896	0.2550	L	0.41824	1.3	0.58432	D	0.999999	P;P;P;P	0.34462	0.454;0.454;0.454;0.454	B;B;B;B	0.34931	0.192;0.192;0.192;0.192	T	0.64939	-0.6289	9	0.87932	D	0	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	16772;16897;16964;24196	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	L	23269;16772;16964;16897;16770	ENSP00000343764:P23269L;ENSP00000434586:P16772L;ENSP00000340554:P16964L;ENSP00000352154:P16897L	ENSP00000340554:P16964L	P	-	2	0	TTN	179141595	1.000000	0.71417	0.901000	0.35422	0.774000	0.43823	3.386000	0.52492	2.854000	0.98071	0.655000	0.94253	CCA	.	.		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
UNC80	285175	hgsc.bcm.edu	37	2	210782504	210782504	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:210782504C>T	ENST00000439458.1	+	31	4915	c.4835C>T	c.(4834-4836)gCc>gTc	p.A1612V	UNC80_ENST00000272845.6_Missense_Mutation_p.A1607V	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1612					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						TCTCTAGCTGCCATGTTCCTG	0.498																																					p.A1612V		Atlas-SNP	.											.	UNC80	280	.	0			c.C4835T						.						74.0	58.0	63.0					2																	210782504		692	1591	2283	SO:0001583	missense	285175	exon31			TAGCTGCCATGTT	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.4835C>T	chr2.hg19:g.210782504C>T	ENSP00000391088:p.Ala1612Val	122.0	0.0		124.0	39.0	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	hg19	CCDS46504.1	.	.	.	.	.	.	.	.	.	.	C	35	5.500787	0.96371	.	.	ENSG00000144406	ENST00000439458;ENST00000272845	T;T	0.36157	1.27;1.27	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.54695	0.1874	L	0.41824	1.3	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	T	0.52852	-0.8520	10	0.66056	D	0.02	-16.6264	20.137	0.98033	0.0:1.0:0.0:0.0	.	1612	Q8N2C7	UNC80_HUMAN	V	1612;1607	ENSP00000391088:A1612V;ENSP00000272845:A1607V	ENSP00000272845:A1607V	A	+	2	0	UNC80	210490749	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.088000	0.71371	2.771000	0.95319	0.655000	0.94253	GCC	.	.		0.498	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
FN1	2335	hgsc.bcm.edu	37	2	216261912	216261912	+	Silent	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:216261912T>C	ENST00000359671.1	-	23	3817	c.3552A>G	c.(3550-3552)gcA>gcG	p.A1184A	FN1_ENST00000336916.4_Silent_p.A1184A|FN1_ENST00000346544.3_Silent_p.A1184A|FN1_ENST00000421182.1_Silent_p.A1184A|FN1_ENST00000345488.5_Silent_p.A1184A|FN1_ENST00000356005.4_Silent_p.A1184A|FN1_ENST00000446046.1_Silent_p.A1184A|FN1_ENST00000443816.1_Silent_p.A1184A|FN1_ENST00000357009.2_Silent_p.A1184A|FN1_ENST00000357867.4_Silent_p.A1184A|FN1_ENST00000354785.4_Silent_p.A1184A|FN1_ENST00000323926.6_Silent_p.A1184A|FN1_ENST00000432072.2_Silent_p.A1184A			P02751	FINC_HUMAN	fibronectin 1	1184	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316, ECO:0000255|PROSITE-ProRule:PRU00478, ECO:0000255|PROSITE-ProRule:PRU00479}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TGTCAGGGTTTGCCTCCAGAT	0.473																																					p.A1184A		Atlas-SNP	.											.	FN1	521	.	0			c.A3552G						.						190.0	188.0	188.0					2																	216261912		2203	4300	6503	SO:0001819	synonymous_variant	2335	exon23			AGGGTTTGCCTCC		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.3552A>G	chr2.hg19:g.216261912T>C		82.0	0.0		72.0	15.0	NM_212476	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Silent	SNP	ENST00000359671.1	hg19																																																																																				.	.		0.473	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
CCDC108	255101	hgsc.bcm.edu	37	2	219897276	219897276	+	Silent	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:219897276G>A	ENST00000341552.5	-	6	644	c.561C>T	c.(559-561)ttC>ttT	p.F187F	CCDC108_ENST00000453220.1_Silent_p.F187F|CCDC108_ENST00000410037.1_Silent_p.F122F|CCDC108_ENST00000441968.1_Silent_p.F187F|CCDC108_ENST00000409865.3_Silent_p.F176F	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	187						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGTGAAGAAGAACTTGGTCT	0.612																																					p.F187F		Atlas-SNP	.											.	CCDC108	208	.	0			c.C561T						.						59.0	49.0	53.0					2																	219897276		2202	4300	6502	SO:0001819	synonymous_variant	255101	exon6			GAAGAAGAACTTG	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.561C>T	chr2.hg19:g.219897276G>A		252.0	0.0		200.0	55.0	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	hg19	CCDS2430.2																																																																																			.	.		0.612	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
SPEG	10290	hgsc.bcm.edu	37	2	220333737	220333737	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:220333737T>A	ENST00000312358.7	+	12	3590	c.3458T>A	c.(3457-3459)gTa>gAa	p.V1153E	SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1153					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CAGCTGTATGTAGAAGAGCCC	0.662																																					p.V1153E		Atlas-SNP	.											.	SPEG	272	.	0			c.T3458A						.						35.0	43.0	41.0					2																	220333737		1976	4147	6123	SO:0001583	missense	10290	exon12			TGTATGTAGAAGA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.3458T>A	chr2.hg19:g.220333737T>A	ENSP00000311684:p.Val1153Glu	106.0	0.0		80.0	9.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	T	17.95	3.513685	0.64522	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	D	0.86097	-2.07	4.77	4.77	0.60923	Immunoglobulin I-set (1);Immunoglobulin-like fold (1);	0.000000	0.37955	N	0.001864	D	0.95149	0.8428	H	0.97962	4.115	0.80722	D	1	D	0.89917	1.0	D	0.77557	0.99	D	0.96857	0.9629	10	0.87932	D	0	.	14.4658	0.67482	0.0:0.0:0.0:1.0	.	1153	Q15772	SPEG_HUMAN	E	1153	ENSP00000311684:V1153E	ENSP00000265327:V1153E	V	+	2	0	SPEG	220041981	1.000000	0.71417	0.978000	0.43139	0.858000	0.48976	7.773000	0.85462	2.015000	0.59207	0.533000	0.62120	GTA	.	.		0.662	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
NCL	4691	hgsc.bcm.edu	37	2	232326345	232326345	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr2:232326345T>A	ENST00000322723.4	-	3	759	c.519A>T	c.(517-519)gcA>gcT	p.A173A	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	173					angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CTTTCATCGCTGCTGGTTCAA	0.512																																					p.A173A		Atlas-SNP	.											.	NCL	80	.	0			c.A519T						.						369.0	238.0	282.0					2																	232326345		2203	4300	6503	SO:0001819	synonymous_variant	4691	exon3			CATCGCTGCTGGT		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.519A>T	chr2.hg19:g.232326345T>A		277.0	0.0		213.0	18.0	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	hg19	CCDS33397.1																																																																																			.	.		0.512	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
TIMP4	7079	hgsc.bcm.edu	37	3	12195118	12195118	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:12195118T>A	ENST00000287814.4	-	5	1082	c.572A>T	c.(571-573)cAg>cTg	p.Q191L	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	191					central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						ATGCTGAGCCTGGTAACCATA	0.547																																					p.Q191L	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.A572T						.						179.0	159.0	166.0					3																	12195118		2203	4300	6503	SO:0001583	missense	7079	exon5			TGAGCCTGGTAAC	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"""tissue inhibitor of metalloproteinase 4"""			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.572A>T	chr3.hg19:g.12195118T>A	ENSP00000287814:p.Gln191Leu	382.0	0.0		485.0	35.0	NM_003256	B2R7K6	Missense_Mutation	SNP	ENST00000287814.4	hg19	CCDS2608.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.846978	0.91277	.	.	ENSG00000157150	ENST00000287814	D	0.93859	-3.3	4.78	4.78	0.61160	Tissue inhibitor of metalloproteinases-like, OB-fold (1);	0.064005	0.64402	D	0.000004	D	0.96664	0.8911	M	0.84846	2.72	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.97007	0.9733	10	0.56958	D	0.05	.	14.4922	0.67660	0.0:0.0:0.0:1.0	.	191	Q99727	TIMP4_HUMAN	L	191	ENSP00000287814:Q191L	ENSP00000287814:Q191L	Q	-	2	0	TIMP4	12170118	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.587000	0.82613	2.015000	0.59207	0.402000	0.26972	CAG	.	.		0.547	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256	
TIMP4	7079	hgsc.bcm.edu	37	3	12198366	12198366	+	Silent	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:12198366A>G	ENST00000287814.4	-	3	816	c.306T>C	c.(304-306)tgT>tgC	p.C102C	SYN2_ENST00000432424.2_RNA	NM_003256.3	NP_003247.1	Q99727	TIMP4_HUMAN	TIMP metallopeptidase inhibitor 4	102	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				central nervous system development (GO:0007417)|negative regulation of endopeptidase activity (GO:0010951)|ovulation cycle (GO:0042698)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to peptide hormone (GO:0043434)	extracellular space (GO:0005615)|sarcomere (GO:0030017)	metal ion binding (GO:0046872)|metalloendopeptidase inhibitor activity (GO:0008191)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	11						GTTTCACACCACAGAGGGAAG	0.403																																					p.C102C	Melanoma(199;1446 2144 30617 38794 51714)	Atlas-SNP	.											.	TIMP4	21	.	0			c.T306C						.						126.0	115.0	119.0					3																	12198366		2203	4300	6503	SO:0001819	synonymous_variant	7079	exon3			CACACCACAGAGG	U76456	CCDS2608.1	3p25	2005-10-31	2005-08-08		ENSG00000157150	ENSG00000157150			11823	protein-coding gene	gene with protein product		601915	"""tissue inhibitor of metalloproteinase 4"""			8939999, 9693046	Standard	NM_003256		Approved		uc003bwo.3	Q99727	OTTHUMG00000129763	ENST00000287814.4:c.306T>C	chr3.hg19:g.12198366A>G		135.0	0.0		177.0	53.0	NM_003256	B2R7K6	Silent	SNP	ENST00000287814.4	hg19	CCDS2608.1																																																																																			.	.		0.403	TIMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251978.1	NM_003256	
CAND2	23066	hgsc.bcm.edu	37	3	12856693	12856693	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:12856693G>T	ENST00000456430.2	+	8	1101	c.1060G>T	c.(1060-1062)Gca>Tca	p.A354S	CAND2_ENST00000295989.5_Missense_Mutation_p.A261S	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	354					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						GGTGCGCCGGGCAGCTGCCAA	0.602																																					p.A354S	GBM(43;676 868 1633 6395 37496)	Atlas-SNP	.											.	CAND2	138	.	0			c.G1060T						.						57.0	64.0	62.0					3																	12856693		2144	4252	6396	SO:0001583	missense	23066	exon8			CGCCGGGCAGCTG		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.1060G>T	chr3.hg19:g.12856693G>T	ENSP00000387641:p.Ala354Ser	260.0	0.0		194.0	76.0	NM_001162499	B9EGM9|E9KL24	Missense_Mutation	SNP	ENST00000456430.2	hg19	CCDS54554.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.933132	0.73442	.	.	ENSG00000144712	ENST00000295989;ENST00000456430	T;T	0.10763	2.84;2.84	4.86	4.86	0.63082	Armadillo-like helical (1);Armadillo-type fold (1);	0.076940	0.51477	D	0.000096	T	0.17831	0.0428	L	0.33293	1	0.80722	D	1	B;D	0.61697	0.303;0.99	B;D	0.73380	0.145;0.98	T	0.07751	-1.0756	10	0.13108	T	0.6	-26.4464	10.7022	0.45934	0.0:0.0:0.8093:0.1907	.	354;261	O75155;O75155-2	CAND2_HUMAN;.	S	261;354	ENSP00000295989:A261S;ENSP00000387641:A354S	ENSP00000295989:A261S	A	+	1	0	CAND2	12831693	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	1.761000	0.38440	2.231000	0.72958	0.561000	0.74099	GCA	.	.		0.602	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
MRPS25	64432	hgsc.bcm.edu	37	3	15093970	15093970	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:15093970A>T	ENST00000253686.2	-	4	640	c.500T>A	c.(499-501)cTg>cAg	p.L167Q	MRPS25_ENST00000444840.2_3'UTR|MRPS25_ENST00000449354.2_Intron|MRPS25_ENST00000496484.1_5'Flank	NM_022497.3	NP_071942.1	P82663	RT25_HUMAN	mitochondrial ribosomal protein S25	167						mitochondrion (GO:0005739)|ribosome (GO:0005840)				large_intestine(1)|lung(1)	2						ATCGGCTTTCAGAGCGGCTTT	0.597																																					p.L167Q		Atlas-SNP	.											.	MRPS25	14	.	0			c.T500A						.						169.0	148.0	155.0					3																	15093970		2203	4300	6503	SO:0001583	missense	64432	exon4			GCTTTCAGAGCGG	AB061208	CCDS2622.1	3p25	2012-09-13			ENSG00000131368	ENSG00000131368		"""Mitochondrial ribosomal proteins / small subunits"""	14511	protein-coding gene	gene with protein product	"""mitochondrial 28S ribosomal protein S25"""	611987				11279123	Standard	NM_022497		Approved	MRP-S25, FLJ00023, DKFZp313H0817, RPMS25	uc003bzl.3	P82663	OTTHUMG00000129836	ENST00000253686.2:c.500T>A	chr3.hg19:g.15093970A>T	ENSP00000253686:p.Leu167Gln	156.0	0.0		191.0	13.0	NM_022497	B4DFJ5|B4DQG6|Q9H7P5	Missense_Mutation	SNP	ENST00000253686.2	hg19	CCDS2622.1	.	.	.	.	.	.	.	.	.	.	A	15.72	2.916035	0.52546	.	.	ENSG00000131368	ENST00000253686	.	.	.	5.48	5.48	0.80851	.	0.169199	0.51477	D	0.000081	T	0.47451	0.1446	L	0.45581	1.43	0.80722	D	1	B	0.18741	0.03	B	0.12837	0.008	T	0.40251	-0.9573	9	0.22109	T	0.4	-29.3001	9.8852	0.41257	0.8474:0.0:0.0:0.1526	.	167	P82663	RT25_HUMAN	Q	167	.	ENSP00000253686:L167Q	L	-	2	0	MRPS25	15068974	0.585000	0.26774	0.070000	0.20053	0.034000	0.12701	2.063000	0.41423	2.079000	0.62486	0.402000	0.26972	CTG	.	.		0.597	MRPS25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252076.2	NM_022497	
SCN11A	11280	hgsc.bcm.edu	37	3	38945427	38945427	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:38945427T>A	ENST00000302328.3	-	12	1969	c.1771A>T	c.(1771-1773)Act>Tct	p.T591S	SCN11A_ENST00000450244.1_Missense_Mutation_p.T591S|SCN11A_ENST00000444237.2_Missense_Mutation_p.T591S|SCN11A_ENST00000456224.3_Missense_Mutation_p.T591S	NM_014139.2	NP_054858.2	Q9UI33	SCNBA_HUMAN	sodium channel, voltage-gated, type XI, alpha subunit	591					cell death (GO:0008219)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(3)|biliary_tract(1)|breast(4)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(29)|lung(29)|ovary(3)|pancreas(2)|prostate(12)|skin(14)|upper_aerodigestive_tract(5)|urinary_tract(3)	119				Kidney(284;0.00202)|KIRC - Kidney renal clear cell carcinoma(284;0.00226)	Cocaine(DB00907)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AAGAAGACAGTGTTGATGATG	0.433																																					p.T591S		Atlas-SNP	.											.	SCN11A	296	.	0			c.A1771T						.						143.0	124.0	130.0					3																	38945427		2203	4300	6503	SO:0001583	missense	11280	exon12			AGACAGTGTTGAT	AF126739	CCDS33737.1	3p22.2	2012-02-26	2007-01-23		ENSG00000168356	ENSG00000168356		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10583	protein-coding gene	gene with protein product		604385	"""sodium channel, voltage-gated, type XI, alpha polypeptide"", ""sodium channel, voltage-gated, type XII, alpha"""	SCN12A		10444332, 16382098	Standard	NM_014139		Approved	Nav1.9, NaN, SNS-2	uc021wvy.1	Q9UI33	OTTHUMG00000048246	ENST00000302328.3:c.1771A>T	chr3.hg19:g.38945427T>A	ENSP00000307599:p.Thr591Ser	372.0	1.0		361.0	119.0	NM_014139	A6NN05|C9JD48|C9JR31|Q68K15|Q8NDX3|Q9UHE0|Q9UHM0	Missense_Mutation	SNP	ENST00000302328.3	hg19	CCDS33737.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.976746	0.74360	.	.	ENSG00000168356	ENST00000302328;ENST00000450244;ENST00000456224;ENST00000444237	D;D;D;D	0.97378	-4.36;-4.36;-4.36;-4.36	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.98639	0.9544	M	0.90922	3.16	0.51767	D	0.999937	D	0.76494	0.999	D	0.80764	0.994	D	0.99320	1.0906	10	0.49607	T	0.09	.	14.5917	0.68371	0.0:0.0:0.0:1.0	.	591	Q9UI33	SCNBA_HUMAN	S	591	ENSP00000307599:T591S;ENSP00000400945:T591S;ENSP00000416757:T591S;ENSP00000408028:T591S	ENSP00000307599:T591S	T	-	1	0	SCN11A	38920431	1.000000	0.71417	0.989000	0.46669	0.945000	0.59286	7.993000	0.88291	2.124000	0.65301	0.477000	0.44152	ACT	.	.		0.433	SCN11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109746.4	NM_014139	
NKTR	4820	hgsc.bcm.edu	37	3	42674105	42674105	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:42674105A>G	ENST00000232978.8	+	9	751	c.563A>G	c.(562-564)aAa>aGa	p.K188R	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000434363.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	188					protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TTTGAGAAAAAAAGGAAGAAA	0.323																																					p.K188R		Atlas-SNP	.											.	NKTR	116	.	0			c.A563G						.						36.0	38.0	37.0					3																	42674105		2203	4299	6502	SO:0001583	missense	4820	exon9			AGAAAAAAAGGAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.563A>G	chr3.hg19:g.42674105A>G	ENSP00000232978:p.Lys188Arg	70.0	0.0		86.0	25.0	NM_005385		Missense_Mutation	SNP	ENST00000232978.8	hg19	CCDS2702.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.660344	0.88154	.	.	ENSG00000114857	ENST00000232978	T	0.15487	2.42	5.83	5.83	0.93111	.	0.048674	0.85682	D	0.000000	T	0.40909	0.1136	M	0.64567	1.98	0.80722	D	1	D;D	0.89917	0.997;1.0	D;D	0.83275	0.985;0.996	T	0.15954	-1.0419	10	0.59425	D	0.04	-23.7897	16.1949	0.82021	1.0:0.0:0.0:0.0	.	68;188	Q59EC3;P30414	.;NKTR_HUMAN	R	188	ENSP00000232978:K188R	ENSP00000232978:K188R	K	+	2	0	NKTR	42649109	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.777000	0.75028	2.222000	0.72286	0.533000	0.62120	AAA	.	.		0.323	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
NISCH	11188	hgsc.bcm.edu	37	3	52489713	52489713	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:52489713C>T	ENST00000479054.1	+	2	128	c.56C>T	c.(55-57)gCg>gTg	p.A19V	TNNC1_ENST00000232975.3_5'Flank|NISCH_ENST00000420808.2_Missense_Mutation_p.A19V|NISCH_ENST00000488380.1_Missense_Mutation_p.A19V|NISCH_ENST00000345716.4_Missense_Mutation_p.A19V			Q9Y2I1	NISCH_HUMAN	nischarin	19	Necessary for binding to phosphoinositide-3-P; not sufficient for targeting to endosomes.|PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				actin cytoskeleton organization (GO:0030036)|apoptotic process (GO:0006915)|glucose metabolic process (GO:0006006)|negative regulation of cell migration (GO:0030336)|norepinephrine secretion (GO:0048243)|Rac protein signal transduction (GO:0016601)|regulation of blood pressure (GO:0008217)|regulation of synaptic transmission, GABAergic (GO:0032228)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)|plasma membrane (GO:0005886)	G-protein coupled amine receptor activity (GO:0008227)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	33				BRCA - Breast invasive adenocarcinoma(193;1.93e-05)|Kidney(197;0.00216)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)|OV - Ovarian serous cystadenocarcinoma(275;0.0577)	Tizanidine(DB00697)	GCCAAGGAAGCGCGCGTCGTG	0.726																																					p.A19V		Atlas-SNP	.											.	NISCH	97	.	0			c.C56T						.						7.0	10.0	9.0					3																	52489713		2027	4089	6116	SO:0001583	missense	11188	exon1			AGGAAGCGCGCGT	AF082516	CCDS33767.1, CCDS63651.1, CCDS63652.1	3p21.1	2008-07-18			ENSG00000010322	ENSG00000010322			18006	protein-coding gene	gene with protein product	"""imidazoline receptor candidate"", ""I-1 receptor candidate protein"", ""imidazoline receptor antisera selected"""	615507				11912194, 10882231	Standard	NM_007184		Approved	KIAA0975, I-1, IRAS	uc003ded.4	Q9Y2I1	OTTHUMG00000158571	ENST00000479054.1:c.56C>T	chr3.hg19:g.52489713C>T	ENSP00000418232:p.Ala19Val	34.0	0.0		12.0	7.0	NM_001276293	C9J245|Q6PGP3|Q6PIB4|Q7L8M3|Q7Z2X6|Q9UES6|Q9UEU4|Q9UFW3	Missense_Mutation	SNP	ENST00000479054.1	hg19	CCDS33767.1	.	.	.	.	.	.	.	.	.	.	C	16.38	3.108295	0.56291	.	.	ENSG00000010322	ENST00000479054;ENST00000345716;ENST00000433196;ENST00000488380;ENST00000420808	T;T;T;T	0.07216	3.42;3.42;3.24;3.21	4.9	4.9	0.64082	Phox homologous domain (3);	0.060349	0.64402	D	0.000003	T	0.02380	0.0073	N	0.02181	-0.65	0.50467	D	0.999875	D;P	0.53619	0.961;0.806	B;B	0.38803	0.282;0.103	T	0.49969	-0.8882	10	0.02654	T	1	-23.1454	10.3167	0.43740	0.0:0.9082:0.0:0.0918	.	19;19	Q9Y2I1;C9J715	NISCH_HUMAN;.	V	19	ENSP00000418232:A19V;ENSP00000339958:A19V;ENSP00000417812:A19V;ENSP00000392484:A19V	ENSP00000339958:A19V	A	+	2	0	NISCH	52464753	1.000000	0.71417	0.999000	0.59377	0.786000	0.44442	2.593000	0.46180	2.268000	0.75426	0.655000	0.94253	GCG	.	.		0.726	NISCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351357.1	NM_007184	
CHDH	55349	hgsc.bcm.edu	37	3	53857409	53857409	+	Silent	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:53857409G>A	ENST00000315251.6	-	3	1064	c.627C>T	c.(625-627)gcC>gcT	p.A209A		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	209					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	GCGGGTAGCCGGCCTGCTGCG	0.652																																					p.A209A		Atlas-SNP	.											.	CHDH	34	.	0			c.C627T						.						37.0	39.0	38.0					3																	53857409		2202	4300	6502	SO:0001819	synonymous_variant	55349	exon3			GTAGCCGGCCTGC	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.627C>T	chr3.hg19:g.53857409G>A		143.0	0.0		99.0	11.0	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	hg19	CCDS2873.1																																																																																			.	.		0.652	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
CADPS	8618	hgsc.bcm.edu	37	3	62518735	62518735	+	Splice_Site	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:62518735T>A	ENST00000383710.4	-	13	2453		c.e13-2		CADPS_ENST00000357948.3_Splice_Site|CADPS_ENST00000283269.9_Splice_Site	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator						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)		GAACCAGCCCTATATAAAGAA	0.478																																					.		Atlas-SNP	.											.	CADPS	387	.	0			c.2104-2A>T						.						39.0	40.0	40.0					3																	62518735		2203	4300	6503	SO:0001630	splice_region_variant	8618	exon14			CAGCCCTATATAA	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.2104-2A>T	chr3.hg19:g.62518735T>A		71.0	0.0		90.0	7.0	NM_183394	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Splice_Site	SNP	ENST00000383710.4	hg19	CCDS46858.1	.	.	.	.	.	.	.	.	.	.	T	18.08	3.544072	0.65198	.	.	ENSG00000163618	ENST00000383709;ENST00000383710;ENST00000357948;ENST00000283269;ENST00000491424;ENST00000468271;ENST00000478434;ENST00000542833	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0908	0.81090	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CADPS	62493775	1.000000	0.71417	0.967000	0.41034	0.615000	0.37417	8.040000	0.89188	2.202000	0.70862	0.455000	0.32223	.	.	.		0.478	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	Intron
OR5H14	403273	hgsc.bcm.edu	37	3	97868315	97868315	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:97868315T>A	ENST00000437310.1	+	1	146	c.86T>A	c.(85-87)cTg>cAg	p.L29Q	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	29						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(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						CCCCTGTTCCTGGCATTCTTG	0.418																																					p.L29Q		Atlas-SNP	.											.	OR5H14	56	.	0			c.T86A						.						90.0	95.0	93.0					3																	97868315		2202	4279	6481	SO:0001583	missense	403273	exon1			TGTTCCTGGCATT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.86T>A	chr3.hg19:g.97868315T>A	ENSP00000401706:p.Leu29Gln	256.0	0.0		291.0	18.0	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	hg19	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	T	10.37	1.331239	0.24167	.	.	ENSG00000236032	ENST00000437310	T	0.00457	7.29	2.3	1.13	0.20643	.	0.000000	0.32819	N	0.005607	T	0.01387	0.0045	M	0.92122	3.275	0.09310	N	1	D	0.76494	0.999	D	0.69824	0.966	T	0.32161	-0.9917	10	0.62326	D	0.03	.	5.2077	0.15299	0.0:0.1723:0.0:0.8277	.	29	A6NHG9	O5H14_HUMAN	Q	29	ENSP00000401706:L29Q	ENSP00000401706:L29Q	L	+	2	0	OR5H14	99351005	0.027000	0.19231	0.649000	0.29536	0.386000	0.30323	2.309000	0.43699	1.052000	0.40392	0.164000	0.16699	CTG	.	.		0.418	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
CEP97	79598	hgsc.bcm.edu	37	3	101451370	101451370	+	Silent	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:101451370G>A	ENST00000341893.3	+	6	1352	c.600G>A	c.(598-600)ttG>ttA	p.L200L	CEP97_ENST00000327230.4_Silent_p.L200L|CEP97_ENST00000494050.1_Silent_p.L200L			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	200					cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						TGGAACAGTTGTCGATTATGA	0.418																																					p.L200L		Atlas-SNP	.											.	CEP97	122	.	0			c.G600A						.						136.0	121.0	126.0					3																	101451370		2203	4300	6503	SO:0001819	synonymous_variant	79598	exon6			ACAGTTGTCGATT	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"""leucine-rich repeats and IQ motif containing 2"""	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.600G>A	chr3.hg19:g.101451370G>A		219.0	0.0		232.0	34.0	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Silent	SNP	ENST00000341893.3	hg19	CCDS2944.1																																																																																			.	.		0.418	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548	
KALRN	8997	hgsc.bcm.edu	37	3	124048793	124048793	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:124048793A>T	ENST00000240874.3	+	8	1521	c.1364A>T	c.(1363-1365)cAc>cTc	p.H455L	KALRN_ENST00000460856.1_Missense_Mutation_p.H455L|KALRN_ENST00000360013.3_Missense_Mutation_p.H455L	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	455					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						CTGGCAATCCACCACCACCAG	0.562																																					p.H455L		Atlas-SNP	.											.	KALRN	556	.	0			c.A1364T						.						150.0	124.0	133.0					3																	124048793		2203	4300	6503	SO:0001583	missense	8997	exon8			CAATCCACCACCA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1364A>T	chr3.hg19:g.124048793A>T	ENSP00000240874:p.His455Leu	245.0	0.0		262.0	79.0	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.2|21.2	4.115741|4.115741	0.77323|0.77323	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013|ENST00000354186	T;T;T|.	0.40756|.	1.02;1.02;1.02|.	5.0|5.0	5.0|5.0	0.66597|0.66597	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.73094|0.73094	0.3543|0.3543	M|M	0.69823|0.69823	2.125|2.125	0.80722|0.80722	D|D	1|1	P;D;P|.	0.65815|.	0.895;0.995;0.936|.	P;D;P|.	0.72982|.	0.468;0.979;0.669|.	T|T	0.73633|0.73633	-0.3921|-0.3921	10|5	0.32370|.	T|.	0.25|.	.|.	15.1541|15.1541	0.72726|0.72726	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	455;455;455|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	L|S	455|433	ENSP00000418611:H455L;ENSP00000240874:H455L;ENSP00000353109:H455L|.	ENSP00000240874:H455L|.	H|T	+|+	2|1	0|0	KALRN|KALRN	125531483|125531483	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	9.087000|9.087000	0.94110|0.94110	2.225000|2.225000	0.72522|0.72522	0.533000|0.533000	0.62120|0.62120	CAC|ACC	.	.		0.562	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
ITGB5	3693	hgsc.bcm.edu	37	3	124592297	124592297	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:124592297T>A	ENST00000296181.4	-	2	448	c.152A>T	c.(151-153)aAa>aTa	p.K51I		NM_002213.3	NP_002204.2	P18084	ITB5_HUMAN	integrin, beta 5	51	PSI.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|epithelial cell-cell adhesion (GO:0090136)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle contraction (GO:0006936)|stress fiber assembly (GO:0043149)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alphav-beta5 complex (GO:0034684)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	30				GBM - Glioblastoma multiforme(114;0.163)		ACATACCTCTTTGGAGCACCA	0.483																																					p.K51I		Atlas-SNP	.											.	ITGB5	66	.	0			c.A152T						.						252.0	236.0	241.0					3																	124592297		2203	4300	6503	SO:0001583	missense	3693	exon2			ACCTCTTTGGAGC	J05633	CCDS3030.1	3q21.2	2010-03-23			ENSG00000082781	ENSG00000082781		"""Integrins"""	6160	protein-coding gene	gene with protein product		147561				2211615	Standard	NM_002213		Approved		uc003eho.3	P18084	OTTHUMG00000159432	ENST00000296181.4:c.152A>T	chr3.hg19:g.124592297T>A	ENSP00000296181:p.Lys51Ile	242.0	0.0		269.0	21.0	NM_002213	B0LPF8|B2RD70	Missense_Mutation	SNP	ENST00000296181.4	hg19	CCDS3030.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.055441	0.75960	.	.	ENSG00000082781	ENST00000296181	D	0.92965	-3.14	5.04	2.36	0.29203	Integrin beta subunit, N-terminal (2);	0.224693	0.47093	D	0.000258	D	0.92476	0.7611	M	0.67700	2.07	0.39505	D	0.968269	P	0.48016	0.904	P	0.54312	0.748	D	0.90475	0.4456	10	0.66056	D	0.02	.	6.8438	0.23977	0.0:0.2278:0.0:0.7722	.	51	P18084	ITB5_HUMAN	I	51	ENSP00000296181:K51I	ENSP00000296181:K51I	K	-	2	0	ITGB5	126074987	1.000000	0.71417	0.998000	0.56505	0.971000	0.66376	2.262000	0.43285	0.300000	0.22699	0.379000	0.24179	AAA	.	.		0.483	ITGB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355286.3	NM_002213	
MGLL	11343	hgsc.bcm.edu	37	3	127441397	127441397	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:127441397T>C	ENST00000434178.2	-	4	1141	c.245A>G	c.(244-246)cAg>cGg	p.Q82R	MGLL_ENST00000453507.2_Missense_Mutation_p.Q92R|MGLL_ENST00000398104.1_Missense_Mutation_p.Q82R|MGLL_ENST00000398101.3_Missense_Mutation_p.Q56R|MGLL_ENST00000265052.5_Missense_Mutation_p.Q92R			Q99685	MGLL_HUMAN	monoglyceride lipase	82					acylglycerol acyl-chain remodeling (GO:0036155)|acylglycerol catabolic process (GO:0046464)|arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|fatty acid biosynthetic process (GO:0006633)|glycerophospholipid biosynthetic process (GO:0046474)|inflammatory response (GO:0006954)|lipid metabolic process (GO:0006629)|long term synaptic depression (GO:0060292)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|regulation of endocannabinoid signaling pathway (GO:2000124)|regulation of inflammatory response (GO:0050727)|regulation of sensory perception of pain (GO:0051930)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acylglycerol lipase activity (GO:0047372)|lipid binding (GO:0008289)|lysophospholipase activity (GO:0004622)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6						CCCTTCGCTCTGTCCGTGGCC	0.542																																					p.Q92R		Atlas-SNP	.											.	MGLL	19	.	0			c.A275G						.						92.0	97.0	96.0					3																	127441397		2065	4224	6289	SO:0001583	missense	11343	exon4			TCGCTCTGTCCGT	BC000551	CCDS43148.1, CCDS46902.1, CCDS58852.1	3p13-q13.33	2014-03-14			ENSG00000074416	ENSG00000074416	3.1.1.23		17038	protein-coding gene	gene with protein product		609699				9495531	Standard	NM_007283		Approved	HU-K5, MGL	uc003ejx.4	Q99685	OTTHUMG00000159641	ENST00000434178.2:c.245A>G	chr3.hg19:g.127441397T>C	ENSP00000402798:p.Gln82Arg	245.0	0.0		329.0	120.0	NM_007283	B3KRC2|B7Z9D1|Q6IBG9|Q96AA5	Missense_Mutation	SNP	ENST00000434178.2	hg19	CCDS43148.1	.	.	.	.	.	.	.	.	.	.	T	11.52	1.663813	0.29515	.	.	ENSG00000074416	ENST00000434178;ENST00000265052;ENST00000398104;ENST00000398101;ENST00000487473;ENST00000536024;ENST00000453507;ENST00000484451;ENST00000493611	T;T;T;T;T;T;T	0.74315	-0.83;-0.83;-0.83;-0.83;-0.11;-0.11;-0.11	4.85	2.4	0.29515	Alpha/beta hydrolase fold-1 (1);	0.121894	0.56097	N	0.000023	T	0.50188	0.1601	N	0.11000	0.08	0.47245	D	0.999366	B;B;B;B;B	0.17465	0.01;0.019;0.022;0.004;0.003	B;B;B;B;B	0.31290	0.087;0.127;0.053;0.024;0.017	T	0.28490	-1.0042	10	0.06236	T	0.91	-12.7767	6.6136	0.22765	0.0:0.0836:0.1554:0.761	.	92;82;82;92;56	B7Z9D1;B2ZGL7;Q99685;B3KRC2;E7EWX8	.;.;MGLL_HUMAN;.;.	R	82;92;82;56;6;92;92;6;19	ENSP00000402798:Q82R;ENSP00000265052:Q92R;ENSP00000381176:Q82R;ENSP00000381173:Q56R;ENSP00000420125:Q6R;ENSP00000419340:Q6R;ENSP00000417689:Q19R	ENSP00000265052:Q92R	Q	-	2	0	MGLL	128924087	1.000000	0.71417	0.996000	0.52242	0.390000	0.30446	5.538000	0.67193	0.216000	0.20781	0.254000	0.18369	CAG	.	.		0.542	MGLL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356637.2	NM_007283	
CPNE4	131034	hgsc.bcm.edu	37	3	131418758	131418758	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:131418758T>A	ENST00000512055.1	-	8	2553	c.427A>T	c.(427-429)Atc>Ttc	p.I143F	CPNE4_ENST00000502818.1_Missense_Mutation_p.I161F|CPNE4_ENST00000512332.1_Missense_Mutation_p.I161F|CPNE4_ENST00000511604.1_Missense_Mutation_p.I143F|CPNE4_ENST00000429747.1_Missense_Mutation_p.I143F			Q96A23	CPNE4_HUMAN	copine IV	143	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|liver(1)|lung(16)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	39						CTTACCGTGATGGAAGATTTC	0.502																																					p.I143F		Atlas-SNP	.											.	CPNE4	112	.	0			c.A427T						.						74.0	66.0	69.0					3																	131418758		2203	4300	6503	SO:0001583	missense	131034	exon4			CCGTGATGGAAGA	H29499	CCDS3072.1, CCDS75010.1	3q22.1	2014-09-04			ENSG00000196353	ENSG00000196353			2317	protein-coding gene	gene with protein product	"""copine 8"""	604208				9430674, 12670487	Standard	XM_005247107		Approved	COPN4, CPN4	uc003eok.3	Q96A23	OTTHUMG00000159631	ENST00000512055.1:c.427A>T	chr3.hg19:g.131418758T>A	ENSP00000421705:p.Ile143Phe	97.0	0.0		133.0	9.0	NM_130808	D3DNC5|Q8TEX1	Missense_Mutation	SNP	ENST00000512055.1	hg19	CCDS3072.1	.	.	.	.	.	.	.	.	.	.	T	19.96	3.924203	0.73213	.	.	ENSG00000196353	ENST00000512055;ENST00000429747;ENST00000512332;ENST00000511604;ENST00000502818;ENST00000505881	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.32	5.32	0.75619	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.65249	0.2673	M	0.84948	2.725	0.80722	D	1	D;D	0.56968	0.977;0.978	P;P	0.59825	0.854;0.864	T	0.72437	-0.4294	10	0.87932	D	0	-16.7256	15.5801	0.76428	0.0:0.0:0.0:1.0	.	161;143	Q96A23-2;Q96A23	.;CPNE4_HUMAN	F	143;143;161;143;161;143	ENSP00000421705:I143F;ENSP00000411904:I143F;ENSP00000424853:I161F;ENSP00000423811:I143F;ENSP00000421646:I161F;ENSP00000425506:I143F	ENSP00000411904:I143F	I	-	1	0	CPNE4	132901448	1.000000	0.71417	1.000000	0.80357	0.489000	0.33432	6.875000	0.75551	2.153000	0.67306	0.528000	0.53228	ATC	.	.		0.502	CPNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356583.4	NM_130808	
ZIC4	84107	hgsc.bcm.edu	37	3	147108887	147108887	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:147108887T>A	ENST00000383075.3	-	4	1347	c.835A>T	c.(835-837)Agc>Tgc	p.S279C	ZIC4_ENST00000473123.1_Missense_Mutation_p.S279C|ZIC4_ENST00000491672.1_Missense_Mutation_p.S73C|ZIC4_ENST00000472749.2_5'UTR|ZIC4_ENST00000484399.1_Missense_Mutation_p.S279C|ZIC4_ENST00000425731.3_Missense_Mutation_p.S317C|ZIC4_ENST00000525172.2_Missense_Mutation_p.S329C	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	279						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						CGCAGCGAGCTGGGGTGCGTG	0.642																																					p.S329C		Atlas-SNP	.											.	ZIC4	174	.	0			c.A985T						.						40.0	46.0	44.0					3																	147108887		2203	4300	6503	SO:0001583	missense	84107	exon4			GCGAGCTGGGGTG	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"""Zinc fingers, C2H2-type"""	20393	protein-coding gene	gene with protein product		608948	"""zinc finger protein of the cerebellum 4"""				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.835A>T	chr3.hg19:g.147108887T>A	ENSP00000372553:p.Ser279Cys	172.0	0.0		80.0	7.0	NM_001168378	A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	hg19	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	T	32	5.115585	0.94339	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000491672	T;T;T;T;T;T	0.58940	0.3;0.3;0.3;0.3;0.3;1.22	5.05	5.05	0.67936	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000037	T	0.71634	0.3363	L	0.52823	1.66	0.50171	D	0.999856	D;D	0.89917	0.999;1.0	D;D	0.97110	0.982;1.0	T	0.78257	-0.2274	9	0.87932	D	0	.	14.795	0.69870	0.0:0.0:0.0:1.0	.	329;279	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	C	279;317;329;279;279;73	ENSP00000372553:S279C;ENSP00000397695:S317C;ENSP00000435509:S329C;ENSP00000417855:S279C;ENSP00000420775:S279C;ENSP00000418277:S73C	ENSP00000372553:S279C	S	-	1	0	ZIC4	148591577	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.954000	0.87848	1.894000	0.54839	0.379000	0.24179	AGC	.	.		0.642	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1		
ERICH6	131831	hgsc.bcm.edu	37	3	150398678	150398678	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:150398678T>A	ENST00000295910.6	-	8	974	c.922A>T	c.(922-924)Atc>Ttc	p.I308F	FAM194A_ENST00000491361.1_Missense_Mutation_p.I162F	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TCCTCATAGATATAGTCAATC	0.423																																					p.I308F		Atlas-SNP	.											.	FAM194A	91	.	0			c.A922T						.						120.0	119.0	119.0					3																	150398678		2203	4300	6503	SO:0001583	missense	131831	exon8			CATAGATATAGTC																												ENST00000295910.6:c.922A>T	chr3.hg19:g.150398678T>A	ENSP00000295910:p.Ile308Phe	94.0	0.0		91.0	5.0	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	hg19	CCDS3151.2	.	.	.	.	.	.	.	.	.	.	T	15.17	2.753964	0.49362	.	.	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.16196	2.5;2.36	4.73	0.946	0.19549	.	0.208889	0.33327	N	0.005025	T	0.25419	0.0618	M	0.63843	1.955	0.09310	N	0.999996	D	0.57257	0.979	P	0.57244	0.816	T	0.07366	-1.0776	10	0.62326	D	0.03	-16.9773	3.9803	0.09492	0.0:0.192:0.1817:0.6263	.	308	Q7L0X2	F194A_HUMAN	F	308;162;266	ENSP00000295910:I308F;ENSP00000419366:I162F	ENSP00000295910:I308F	I	-	1	0	FAM194A	151881368	0.979000	0.34478	0.022000	0.16811	0.072000	0.16883	0.658000	0.24979	0.081000	0.16988	-1.106000	0.02097	ATC	.	.		0.423	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
KIAA0226	9711	hgsc.bcm.edu	37	3	197427705	197427705	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr3:197427705T>A	ENST00000296343.5	-	7	1039	c.1040A>T	c.(1039-1041)gAg>gTg	p.E347V	KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000449205.1_Missense_Mutation_p.E347V|KIAA0226_ENST00000389665.5_Missense_Mutation_p.E347V|KIAA0226_ENST00000273582.5_Missense_Mutation_p.E287V	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	347	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		ACTGCTGCTCTCGGCATTGCT	0.607																																					p.E347V	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											.	KIAA0226	136	.	0			c.A1040T						.						55.0	59.0	58.0					3																	197427705		2041	4207	6248	SO:0001583	missense	9711	exon7			CTGCTCTCGGCAT	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1040A>T	chr3.hg19:g.197427705T>A	ENSP00000296343:p.Glu347Val	189.0	0.0		178.0	18.0	NM_014687	Q96CK5	Missense_Mutation	SNP	ENST00000296343.5	hg19	CCDS43195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.43|13.43	2.234821|2.234821	0.39498|0.39498	.|.	.|.	ENSG00000145016|ENSG00000145016	ENST00000273582;ENST00000296343;ENST00000389665;ENST00000449205|ENST00000415452	.|.	.|.	.|.	5.72|5.72	2.02|2.02	0.26589|0.26589	.|.	0.331648|.	0.27976|.	N|.	0.017083|.	T|.	0.21347|.	0.0514|.	N|N	0.19112|0.19112	0.55|0.55	0.26565|0.26565	N|N	0.973667|0.973667	P;P;P;P;P|.	0.47302|.	0.824;0.893;0.799;0.71;0.514|.	B;B;B;B;B|.	0.41571|.	0.345;0.36;0.217;0.281;0.05|.	T|.	0.24368|.	-1.0162|.	9|.	0.40728|.	T|.	0.16|.	.|.	5.0312|5.0312	0.14411|0.14411	0.0:0.222:0.1446:0.6335|0.0:0.222:0.1446:0.6335	.|.	347;180;347;287;347|.	E9PEM3;Q5HYI6;Q92622-3;Q92622-2;Q92622|.	.;.;.;.;RUBIC_HUMAN|.	V|X	287;347;347;347|106	.|.	ENSP00000273582:E287V|.	E|R	-|-	2|1	0|2	KIAA0226|KIAA0226	198912102|198912102	0.999000|0.999000	0.42202|0.42202	0.886000|0.886000	0.34754|0.34754	0.990000|0.990000	0.78478|0.78478	2.015000|2.015000	0.40961|0.40961	0.110000|0.110000	0.17919|0.17919	0.459000|0.459000	0.35465|0.35465	GAG|AGA	.	.		0.607	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
MAEA	10296	hgsc.bcm.edu	37	4	1332275	1332275	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:1332275A>T	ENST00000303400.4	+	8	1028	c.965A>T	c.(964-966)aAc>aTc	p.N322I	MAEA_ENST00000512289.1_3'UTR|MAEA_ENST00000514708.1_Missense_Mutation_p.N254I|MAEA_ENST00000452175.2_Missense_Mutation_p.N243I|MAEA_ENST00000505177.2_Missense_Mutation_p.N360I|MAEA_ENST00000264750.6_Missense_Mutation_p.N281I|MAEA_ENST00000505839.1_Missense_Mutation_p.N274I|MAEA_ENST00000510794.1_Missense_Mutation_p.N321I	NM_001017405.1	NP_001017405.1	Q7L5Y9	MAEA_HUMAN	macrophage erythroblast attacher	322					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cytoskeleton organization (GO:0007010)|enucleate erythrocyte development (GO:0048822)|erythrocyte maturation (GO:0043249)|negative regulation of myeloid cell apoptotic process (GO:0033033)|regulation of mitotic cell cycle (GO:0007346)	actomyosin contractile ring (GO:0005826)|cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18			OV - Ovarian serous cystadenocarcinoma(23;0.0201)		WF10(DB05389)	CGCTCCCTGAACAAGCTGGCG	0.617																																					p.N322I		Atlas-SNP	.											.	MAEA	39	.	0			c.A965T						.						55.0	52.0	53.0					4																	1332275		2203	4299	6502	SO:0001583	missense	10296	exon8			CCCTGAACAAGCT	AF084928	CCDS33936.1, CCDS33937.1, CCDS75090.1	4p16.3	2012-07-20			ENSG00000090316	ENSG00000090316			13731	protein-coding gene	gene with protein product	"""GID complex subunit 9, FYV10 homolog (S. cerevisiae)"""	606801				9763581	Standard	XM_005272243		Approved	EMP, GID9	uc003gda.3	Q7L5Y9	OTTHUMG00000160169	ENST00000303400.4:c.965A>T	chr4.hg19:g.1332275A>T	ENSP00000302830:p.Asn322Ile	112.0	0.0		102.0	7.0	NM_001017405	O95285|Q5JB54|Q6ZRD6|Q9BQ11|Q9H9V6|Q9H9Z4|Q9NW84	Missense_Mutation	SNP	ENST00000303400.4	hg19	CCDS33936.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.775632	0.90195	.	.	ENSG00000090316	ENST00000303400;ENST00000505177;ENST00000264750;ENST00000382947;ENST00000539495;ENST00000452175;ENST00000514708;ENST00000510794;ENST00000505839	T;T;T;T;T;T;T	0.11385	2.78;2.78;2.78;2.78;2.78;2.78;2.78	5.26	5.26	0.73747	.	0.079954	0.85682	D	0.000000	T	0.34542	0.0901	M	0.81614	2.55	0.80722	D	1	D;D;D;D;D;D	0.89917	0.999;1.0;0.988;0.999;0.997;0.97	D;D;P;D;D;P	0.80764	0.945;0.99;0.758;0.994;0.973;0.809	T	0.08827	-1.0703	10	0.37606	T	0.19	-32.9369	15.1708	0.72872	1.0:0.0:0.0:0.0	.	321;360;108;254;281;322	B4DVN3;E7ESC7;B3KRN7;D6RIB6;Q7L5Y9-3;Q7L5Y9	.;.;.;.;.;MAEA_HUMAN	I	322;360;281;254;301;243;254;321;274	ENSP00000302830:N322I;ENSP00000422215:N360I;ENSP00000264750:N281I;ENSP00000411415:N243I;ENSP00000427512:N254I;ENSP00000426807:N321I;ENSP00000424436:N274I	ENSP00000264750:N281I	N	+	2	0	MAEA	1322275	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	8.986000	0.93492	1.977000	0.57605	0.533000	0.62120	AAC	.	.		0.617	MAEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359511.1	NM_005882	
CD38	952	hgsc.bcm.edu	37	4	15841652	15841652	+	Silent	SNP	T	T	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:15841652T>G	ENST00000226279.3	+	6	800	c.663T>G	c.(661-663)acT>acG	p.T221T		NM_001775.2	NP_001766.2	P28907	CD38_HUMAN	CD38 molecule	221					apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|female pregnancy (GO:0007565)|long term synaptic depression (GO:0060292)|negative regulation of apoptotic process (GO:0043066)|negative regulation of bone resorption (GO:0045779)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasoconstriction (GO:0045907)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to hydroperoxide (GO:0033194)|response to hypoxia (GO:0001666)|response to interleukin-1 (GO:0070555)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	NAD(P)+ nucleosidase activity (GO:0050135)|NAD+ nucleosidase activity (GO:0003953)|phosphorus-oxygen lyase activity (GO:0016849)|transferase activity (GO:0016740)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|stomach(1)	14						ATTTTAGCACTTTTGGGAGTG	0.468																																					p.T221T		Atlas-SNP	.											.	CD38	36	.	0			c.T663G						.						215.0	234.0	228.0					4																	15841652		2203	4300	6503	SO:0001819	synonymous_variant	952	exon6			TAGCACTTTTGGG	D84276	CCDS3417.1	4p15.32	2010-05-04	2006-03-28		ENSG00000004468	ENSG00000004468	3.2.2.5	"""CD molecules"""	1667	protein-coding gene	gene with protein product	"""ADP-ribosyl cyclase 1"", ""NAD(+) nucleosidase"""	107270	"""CD38 antigen (p45)"""			9074508, 2319135	Standard	NM_001775		Approved		uc003gol.1	P28907	OTTHUMG00000048206	ENST00000226279.3:c.663T>G	chr4.hg19:g.15841652T>G		96.0	0.0		106.0	13.0	NM_001775	O00121|O00122|Q96HY4	Silent	SNP	ENST00000226279.3	hg19	CCDS3417.1																																																																																			.	.		0.468	CD38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250322.2	NM_001775	
PPARGC1A	10891	hgsc.bcm.edu	37	4	23797512	23797512	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:23797512T>A	ENST00000264867.2	-	13	2449	c.2330A>T	c.(2329-2331)aAg>aTg	p.K777M	PPARGC1A_ENST00000509702.1_5'UTR	NM_013261.3	NP_037393.1	Q9UBK2	PRGC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 alpha	777	Mediates interaction with RNF34. {ECO:0000269|PubMed:22064484}.				androgen metabolic process (GO:0008209)|androgen receptor signaling pathway (GO:0030521)|brown fat cell differentiation (GO:0050873)|cellular glucose homeostasis (GO:0001678)|cellular respiration (GO:0045333)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to nitrite (GO:0071250)|cellular response to oxidative stress (GO:0034599)|cellular response to thyroid hormone stimulus (GO:0097067)|cellular response to tumor necrosis factor (GO:0071356)|circadian regulation of gene expression (GO:0032922)|digestion (GO:0007586)|fatty acid oxidation (GO:0019395)|flavone metabolic process (GO:0051552)|galactose metabolic process (GO:0006012)|gluconeogenesis (GO:0006094)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of receptor activity (GO:2000272)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of cellular respiration (GO:1901857)|positive regulation of energy homeostasis (GO:2000507)|positive regulation of fatty acid oxidation (GO:0046321)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of histone acetylation (GO:0035066)|positive regulation of mitochondrial DNA metabolic process (GO:1901860)|positive regulation of mitochondrion organization (GO:0010822)|positive regulation of muscle tissue development (GO:1901863)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)|regulation of circadian rhythm (GO:0042752)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|response to cold (GO:0009409)|response to epinephrine (GO:0071871)|response to leucine (GO:0043201)|response to muscle activity (GO:0014850)|response to norepinephrine (GO:0071873)|response to starvation (GO:0042594)|response to statin (GO:0036273)|RNA splicing (GO:0008380)|temperature homeostasis (GO:0001659)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytosol (GO:0005829)|DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(7)|liver(1)|lung(24)|ovary(3)|skin(5)	51		Breast(46;0.0503)				ATACTTGCTCTTGGTGGAAGC	0.428																																					p.K777M	Esophageal Squamous(29;694 744 13796 34866 44181)	Atlas-SNP	.											.	PPARGC1A	129	.	0			c.A2330T						.						113.0	111.0	112.0					4																	23797512		2203	4300	6503	SO:0001583	missense	10891	exon13			TTGCTCTTGGTGG	AF106698	CCDS3429.1	4p15.1	2013-02-12	2006-10-17	2004-02-04	ENSG00000109819	ENSG00000109819		"""RNA binding motif (RRM) containing"""	9237	protein-coding gene	gene with protein product		604517	"""peroxisome proliferative activated receptor, gamma, coactivator 1"", ""peroxisome proliferative activated receptor, gamma, coactivator 1, alpha"""	PPARGC1		10585775	Standard	NM_013261		Approved	PGC1, PGC1A	uc003gqs.3	Q9UBK2	OTTHUMG00000097747	ENST00000264867.2:c.2330A>T	chr4.hg19:g.23797512T>A	ENSP00000264867:p.Lys777Met	69.0	0.0		99.0	5.0	NM_013261	B7Z406|G8DM16|I3RTT5|I3RTT6|I3RTT7|I3RTT8|I3RTT9|Q3LIG1|Q4W5M7|Q9UN32	Missense_Mutation	SNP	ENST00000264867.2	hg19	CCDS3429.1	.	.	.	.	.	.	.	.	.	.	T	17.98	3.520719	0.64747	.	.	ENSG00000109819	ENST00000264867	T	0.28895	1.59	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	M	0.69358	2.11	0.80722	D	1	D	0.76494	0.999	D	0.77557	0.99	T	0.58250	-0.7669	10	0.87932	D	0	-12.1653	15.7565	0.78030	0.0:0.0:0.0:1.0	.	777	Q9UBK2	PRGC1_HUMAN	M	777	ENSP00000264867:K777M	ENSP00000264867:K777M	K	-	2	0	PPARGC1A	23406610	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.655000	0.83696	2.177000	0.69029	0.533000	0.62120	AAG	.	.		0.428	PPARGC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214976.1	NM_013261	
UGT2B7	7364	hgsc.bcm.edu	37	4	69962549	69962549	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:69962549C>A	ENST00000508661.1	+	1	338	c.311C>A	c.(310-312)aCa>aAa	p.T104K	UGT2B7_ENST00000509763.1_Intron|UGT2B7_ENST00000305231.7_Missense_Mutation_p.T104K			P16662	UD2B7_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B7	104					androgen metabolic process (GO:0008209)|cellular glucuronidation (GO:0052695)|lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38					Atorvastatin(DB01076)|Carbamazepine(DB00564)|Chenodeoxycholic acid(DB06777)|Codeine(DB00318)|Dabigatran etexilate(DB06695)|Dapagliflozin(DB06292)|Diclofenac(DB00586)|Epirubicin(DB00445)|Etodolac(DB00749)|Ezetimibe(DB00973)|Flunitrazepam(DB01544)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Losartan(DB00678)|Lovastatin(DB00227)|Mitiglinide(DB01252)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Mycophenolic acid(DB01024)|Naproxen(DB00788)|Oxazepam(DB00842)|Pitavastatin(DB08860)|Silodosin(DB06207)|Simvastatin(DB00641)|Suprofen(DB00870)|Tapentadol(DB06204)|Valproic Acid(DB00313)|Zidovudine(DB00495)	CCAAAAGATACATTTTGGTTA	0.299																																					p.T104K		Atlas-SNP	.											.	UGT2B7	79	.	0			c.C311A						.						46.0	48.0	48.0					4																	69962549		2196	4295	6491	SO:0001583	missense	7364	exon1			AAGATACATTTTG	BC030974	CCDS3526.1	4q13	2008-02-05	2005-07-20		ENSG00000171234	ENSG00000171234		"""UDP glucuronosyltransferases"""	12554	protein-coding gene	gene with protein product		600068	"""UDP glycosyltransferase 2 family, polypeptide B7"""			2159463, 7835904	Standard	NM_001074		Approved	UGT2B9	uc003heg.4	P16662	OTTHUMG00000129404	ENST00000508661.1:c.311C>A	chr4.hg19:g.69962549C>A	ENSP00000427659:p.Thr104Lys	67.0	0.0		66.0	28.0	NM_001074	B2R810|Q6GTW0	Missense_Mutation	SNP	ENST00000508661.1	hg19		.	.	.	.	.	.	.	.	.	.	C	10.02	1.237392	0.22711	.	.	ENSG00000171234	ENST00000305231;ENST00000508661	T;T	0.59638	0.25;0.25	2.54	2.54	0.30619	.	0.985432	0.08237	U	0.976560	T	0.65333	0.2681	M	0.67517	2.055	0.09310	N	1	P;B	0.34462	0.454;0.031	P;B	0.45794	0.493;0.082	T	0.57545	-0.7793	9	.	.	.	.	10.7765	0.46353	0.0:1.0:0.0:0.0	.	104;104	E9PBP8;P16662	.;UD2B7_HUMAN	K	104	ENSP00000304811:T104K;ENSP00000427659:T104K	.	T	+	2	0	UGT2B7	69997138	0.000000	0.05858	0.015000	0.15790	0.019000	0.09904	-0.722000	0.04958	1.408000	0.46895	0.313000	0.20887	ACA	.	.		0.299	UGT2B7-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000362103.1	NM_001074	
ALPK1	80216	hgsc.bcm.edu	37	4	113353386	113353386	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:113353386A>G	ENST00000458497.1	+	11	2962	c.2683A>G	c.(2683-2685)Aac>Gac	p.N895D	ALPK1_ENST00000177648.9_Missense_Mutation_p.N895D|ALPK1_ENST00000504176.2_Missense_Mutation_p.N817D	NM_001102406.1|NM_025144.3	NP_001095876.1|NP_079420.3	Q96QP1	ALPK1_HUMAN	alpha-kinase 1	895							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(20)|ovary(6)|prostate(2)|urinary_tract(1)	53		Ovarian(17;0.0446)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00325)		TGTAAGCGGTAACATCCTCTT	0.552																																					p.N895D		Atlas-SNP	.											.	ALPK1	125	.	0			c.A2683G						.						111.0	109.0	110.0					4																	113353386		2203	4300	6503	SO:0001583	missense	80216	exon11			AGCGGTAACATCC	AY044164	CCDS3697.1, CCDS58923.1	4q26	2008-02-05			ENSG00000073331	ENSG00000073331			20917	protein-coding gene	gene with protein product	"""lymphocyte alpha-kinase"""	607347				10021370, 10819331	Standard	NM_025144		Approved	Lak, FLJ22670, KIAA1527	uc003ian.4	Q96QP1	OTTHUMG00000132911	ENST00000458497.1:c.2683A>G	chr4.hg19:g.113353386A>G	ENSP00000398048:p.Asn895Asp	224.0	0.0		145.0	75.0	NM_001102406	B4E3G1|F5H138|Q68CI9|Q6P9F9|Q6ZNK4|Q9P201	Missense_Mutation	SNP	ENST00000458497.1	hg19	CCDS3697.1	.	.	.	.	.	.	.	.	.	.	A	14.57	2.574333	0.45902	.	.	ENSG00000073331	ENST00000458497;ENST00000177648;ENST00000504176	T;T;T	0.02472	4.35;4.35;4.28	5.03	-4.26	0.03755	.	1.382570	0.04233	N	0.335492	T	0.03178	0.0093	L	0.57536	1.79	0.09310	N	1	B;B;B	0.32467	0.372;0.255;0.031	B;B;B	0.30316	0.114;0.053;0.01	T	0.41395	-0.9511	10	0.52906	T	0.07	-0.2641	1.2056	0.01894	0.3977:0.2585:0.2189:0.1249	.	817;817;895	F5H138;B4E3G1;Q96QP1	.;.;ALPK1_HUMAN	D	895;895;817	ENSP00000398048:N895D;ENSP00000177648:N895D;ENSP00000426044:N817D	ENSP00000177648:N895D	N	+	1	0	ALPK1	113572835	0.000000	0.05858	0.000000	0.03702	0.119000	0.20118	-0.065000	0.11617	-0.509000	0.06532	0.533000	0.62120	AAC	.	.		0.552	ALPK1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256421.2	NM_025144	
ZGRF1	55345	hgsc.bcm.edu	37	4	113461976	113461976	+	Splice_Site	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr4:113461976C>A	ENST00000505019.1	-	26	6036		c.e26+1		RP11-402J6.1_ENST00000504009.1_RNA	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN								integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		ATAATACCAACCTTGTACATC	0.318																																					.		Atlas-SNP	.											.	C4orf21	223	.	0			c.5910+1G>T						.						75.0	67.0	70.0					4																	113461976		2202	4299	6501	SO:0001630	splice_region_variant	55345	exon27			TACCAACCTTGTA																												ENST00000505019.1:c.5910+1G>T	chr4.hg19:g.113461976C>A		146.0	0.0		94.0	48.0	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Splice_Site	SNP	ENST00000505019.1	hg19		.	.	.	.	.	.	.	.	.	.	C	11.84	1.758574	0.31137	.	.	ENSG00000138658	ENST00000505019	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.0782	0.97758	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C4orf21	113681425	1.000000	0.71417	0.997000	0.53966	0.129000	0.20672	5.311000	0.65786	2.746000	0.94184	0.655000	0.94253	.	.	.		0.318	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		Intron
ADAMTS12	81792	hgsc.bcm.edu	37	5	33648938	33648938	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:33648938G>A	ENST00000504830.1	-	9	1803	c.1468C>T	c.(1468-1470)Cag>Tag	p.Q490*	ADAMTS12_ENST00000352040.3_Nonsense_Mutation_p.Q490*|ADAMTS12_ENST00000504582.1_5'UTR	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	490	Disintegrin.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						TCTACTTCCTGGCAGAAGGTA	0.468										HNSCC(64;0.19)																											p.Q490X		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C1468T						.						134.0	128.0	130.0					5																	33648938		2203	4300	6503	SO:0001587	stop_gained	81792	exon9			CTTCCTGGCAGAA	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.1468C>T	chr5.hg19:g.33648938G>A	ENSP00000422554:p.Gln490*	179.0	0.0		219.0	80.0	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Nonsense_Mutation	SNP	ENST00000504830.1	hg19	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	G	41	8.900709	0.98996	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	.	.	.	5.6	5.6	0.85130	.	0.450232	0.25900	N	0.027561	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	.	14.1245	0.65210	0.0:0.2698:0.7302:0.0	.	.	.	.	X	490	.	ENSP00000344847:Q490X	Q	-	1	0	ADAMTS12	33684695	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	3.159000	0.50731	2.641000	0.89580	0.549000	0.68633	CAG	.	.		0.468	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
LIFR	3977	hgsc.bcm.edu	37	5	38490325	38490325	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:38490325A>T	ENST00000263409.4	-	15	2296	c.2134T>A	c.(2134-2136)Tta>Ata	p.L712I	LIFR_ENST00000503088.1_5'Flank|LIFR_ENST00000453190.2_Missense_Mutation_p.L712I	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	712	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					ATGGAGCGTAATAATTGATAT	0.313			T	PLAG1	salivary adenoma																																p.L712I	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.T2134A						.						98.0	108.0	105.0					5																	38490325		2202	4290	6492	SO:0001583	missense	3977	exon15			AGCGTAATAATTG	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.2134T>A	chr5.hg19:g.38490325A>T	ENSP00000263409:p.Leu712Ile	129.0	0.0		148.0	20.0	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	hg19	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702168	0.68501	.	.	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.54279	0.58;0.58	6.05	-7.81	0.01210	Fibronectin, type III (1);	0.140763	0.49305	D	0.000150	T	0.56337	0.1978	M	0.80422	2.495	0.09310	N	0.999998	D	0.58268	0.982	P	0.48598	0.583	T	0.63305	-0.6667	10	0.13470	T	0.59	-16.8825	22.8685	0.99977	0.2868:0.0:0.7132:0.0	.	712	P42702	LIFR_HUMAN	I	712	ENSP00000263409:L712I;ENSP00000398368:L712I	ENSP00000263409:L712I	L	-	1	2	LIFR	38526082	0.000000	0.05858	0.003000	0.11579	0.953000	0.61014	-1.035000	0.03564	-1.854000	0.01163	-0.417000	0.06048	TTA	.	.		0.313	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
MAN2A1	4124	hgsc.bcm.edu	37	5	109026191	109026191	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:109026191A>G	ENST00000261483.4	+	1	1125	c.73A>G	c.(73-75)Atg>Gtg	p.M25V	CTC-332L22.1_ENST00000606424.1_lincRNA	NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	25					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		GCTCTACCTGATGCTGGACCG	0.617																																					p.M25V		Atlas-SNP	.											.	MAN2A1	136	.	0			c.A73G						.						181.0	153.0	163.0					5																	109026191		2202	4300	6502	SO:0001583	missense	4124	exon1			TACCTGATGCTGG		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.73A>G	chr5.hg19:g.109026191A>G	ENSP00000261483:p.Met25Val	158.0	0.0		253.0	69.0	NM_002372	Q16767	Missense_Mutation	SNP	ENST00000261483.4	hg19	CCDS34209.1	.	.	.	.	.	.	.	.	.	.	A	15.70	2.909632	0.52439	.	.	ENSG00000112893	ENST00000261483	T	0.79454	-1.27	4.45	4.45	0.53987	.	0.000000	0.85682	D	0.000000	T	0.73337	0.3574	M	0.64567	1.98	0.58432	D	0.999997	B	0.28713	0.22	B	0.26864	0.074	T	0.71487	-0.4578	10	0.33940	T	0.23	-14.0474	12.9872	0.58598	1.0:0.0:0.0:0.0	.	25	Q16706	MA2A1_HUMAN	V	25	ENSP00000261483:M25V	ENSP00000261483:M25V	M	+	1	0	MAN2A1	109054090	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	6.853000	0.75435	1.739000	0.51704	0.460000	0.39030	ATG	.	.		0.617	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
YTHDC2	64848	hgsc.bcm.edu	37	5	112889035	112889035	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:112889035A>T	ENST00000161863.4	+	13	2059	c.1846A>T	c.(1846-1848)Atc>Ttc	p.I616F	YTHDC2_ENST00000515883.1_Missense_Mutation_p.I616F	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	616	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		TCTATACAATATCTGCCATAG	0.323																																					p.I616F		Atlas-SNP	.											.	YTHDC2	118	.	0			c.A1846T						.						73.0	70.0	71.0					5																	112889035		2202	4299	6501	SO:0001583	missense	64848	exon13			TACAATATCTGCC	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.1846A>T	chr5.hg19:g.112889035A>T	ENSP00000161863:p.Ile616Phe	79.0	0.0		112.0	7.0	NM_022828	B2RP66	Missense_Mutation	SNP	ENST00000161863.4	hg19	CCDS4113.1	.	.	.	.	.	.	.	.	.	.	A	17.60	3.428757	0.62844	.	.	ENSG00000047188	ENST00000161863;ENST00000515883;ENST00000511372	T;T	0.71461	0.9;-0.57	5.7	4.55	0.56014	Helicase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77558	0.4148	H	0.96777	3.88	0.53005	D	0.999969	P	0.35272	0.493	B	0.26864	0.074	T	0.80266	-0.1454	10	0.87932	D	0	.	11.4557	0.50181	0.9295:0.0:0.0705:0.0	.	616	Q9H6S0	YTDC2_HUMAN	F	616;616;526	ENSP00000161863:I616F;ENSP00000423101:I616F	ENSP00000161863:I616F	I	+	1	0	YTHDC2	112916934	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.176000	0.77643	0.996000	0.38943	0.528000	0.53228	ATC	.	.		0.323	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
DDX46	9879	hgsc.bcm.edu	37	5	134117757	134117757	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:134117757A>T	ENST00000354283.4	+	8	1161	c.1026A>T	c.(1024-1026)ctA>ctT	p.L342L	DDX46_ENST00000452510.2_Silent_p.L342L			Q7L014	DDX46_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 46	342					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			TTCCAGAACTAGCAAAAATGT	0.343																																					p.L342L	Colon(13;391 453 4901 21675 24897)	Atlas-SNP	.											.	DDX46	77	.	0			c.A1026T						.						39.0	39.0	39.0					5																	134117757		2202	4298	6500	SO:0001819	synonymous_variant	9879	exon8			AGAACTAGCAAAA		CCDS34240.1, CCDS75306.1	5q31.1	2010-01-25			ENSG00000145833	ENSG00000145833		"""DEAD-boxes"""	18681	protein-coding gene	gene with protein product							Standard	XM_005272142		Approved	KIAA0801, FLJ25329, PRPF5, Prp5	uc003kzw.3	Q7L014	OTTHUMG00000163072	ENST00000354283.4:c.1026A>T	chr5.hg19:g.134117757A>T		177.0	0.0		202.0	13.0	NM_014829	O94894|Q96EI0|Q9Y658	Silent	SNP	ENST00000354283.4	hg19	CCDS34240.1																																																																																			.	.		0.343	DDX46-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371584.1	NM_014829	
SPOCK1	6695	hgsc.bcm.edu	37	5	136324224	136324224	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:136324224A>T	ENST00000394945.1	-	8	984	c.815T>A	c.(814-816)aTc>aAc	p.I272N	SPOCK1_ENST00000282223.7_Missense_Mutation_p.I272N|SPOCK1_ENST00000509978.1_5'UTR	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	272					cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ATCCAGGTAGATGGCATTGAT	0.488																																					p.I272N		Atlas-SNP	.											.	SPOCK1	58	.	0			c.T815A						.						172.0	153.0	160.0					5																	136324224		2203	4300	6503	SO:0001583	missense	6695	exon8			AGGTAGATGGCAT	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.815T>A	chr5.hg19:g.136324224A>T	ENSP00000378401:p.Ile272Asn	349.0	0.0		395.0	137.0	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Missense_Mutation	SNP	ENST00000394945.1	hg19	CCDS4191.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.928309	0.92389	.	.	ENSG00000152377	ENST00000394945;ENST00000282223	T;T	0.53640	0.61;0.61	6.06	6.06	0.98353	SPARC/Testican, calcium-binding domain (1);EF-hand-like domain (1);	0.054329	0.64402	D	0.000001	T	0.66228	0.2768	M	0.80183	2.485	0.58432	D	0.999999	P	0.50819	0.939	P	0.55455	0.776	T	0.71151	-0.4676	10	0.87932	D	0	.	15.7966	0.78416	1.0:0.0:0.0:0.0	.	272	Q08629	TICN1_HUMAN	N	272	ENSP00000378401:I272N;ENSP00000282223:I272N	ENSP00000282223:I272N	I	-	2	0	SPOCK1	136352123	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.335000	0.96500	2.315000	0.78130	0.533000	0.62120	ATC	.	.		0.488	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
PKD2L2	27039	hgsc.bcm.edu	37	5	137226191	137226191	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:137226191A>G	ENST00000508883.1	+	2	79	c.53A>G	c.(52-54)cAt>cGt	p.H18R	PKD2L2_ENST00000350250.4_Intron|PKD2L2_ENST00000502810.1_Missense_Mutation_p.H18R|RP11-381K20.2_ENST00000514616.1_RNA|PKD2L2_ENST00000508638.1_Missense_Mutation_p.H18R|RP11-381K20.2_ENST00000508281.2_RNA|PKD2L2_ENST00000290431.5_Missense_Mutation_p.H18R			Q9NZM6	PK2L2_HUMAN	polycystic kidney disease 2-like 2	18					calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)	integral component of membrane (GO:0016021)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			breast(1)|endometrium(7)|kidney(4)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	28			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			CATAAGTTGCATTACAGAAAG	0.294																																					p.H18R		Atlas-SNP	.											.	PKD2L2	68	.	0			c.A53G						.						90.0	91.0	91.0					5																	137226191		1803	4069	5872	SO:0001583	missense	27039	exon2			AGTTGCATTACAG	AF118125	CCDS43367.1, CCDS58971.1, CCDS58972.1	5q31	2011-12-16			ENSG00000078795	ENSG00000078795		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9012	protein-coding gene	gene with protein product		604669				10602361	Standard	NM_014386		Approved	TRPP5	uc003lbw.1	Q9NZM6	OTTHUMG00000163306	ENST00000508883.1:c.53A>G	chr5.hg19:g.137226191A>G	ENSP00000424725:p.His18Arg	194.0	0.0		195.0	61.0	NM_001258448	A6NK98|B4DXD2|E9PC91|E9PDG4|Q86YB4|Q9UNJ0	Missense_Mutation	SNP	ENST00000508883.1	hg19		.	.	.	.	.	.	.	.	.	.	A	9.545	1.114460	0.20795	.	.	ENSG00000078795	ENST00000508638;ENST00000502810;ENST00000508883;ENST00000290431	T;T;T;T	0.70986	0.38;-0.53;-0.07;-0.08	5.8	1.83	0.25207	.	0.936760	0.08927	N	0.873599	T	0.52597	0.1744	L	0.29908	0.895	0.09310	N	0.999999	B;B;B	0.31581	0.002;0.329;0.008	B;B;B	0.22152	0.001;0.038;0.009	T	0.29212	-1.0019	10	0.16420	T	0.52	-1.1853	8.6922	0.34273	0.5786:0.3125:0.0:0.1089	.	18;18;18	Q9NZM6;E9PC91;Q9NZM6-5	PK2L2_HUMAN;.;.	R	18	ENSP00000423382:H18R;ENSP00000425513:H18R;ENSP00000424725:H18R;ENSP00000290431:H18R	ENSP00000290431:H18R	H	+	2	0	PKD2L2	137254090	0.000000	0.05858	0.917000	0.36280	0.801000	0.45260	-0.195000	0.09546	0.993000	0.38866	0.377000	0.23210	CAT	.	.		0.294	PKD2L2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000372521.1	NM_014386	
DPYSL3	1809	hgsc.bcm.edu	37	5	146792244	146792244	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:146792244T>A	ENST00000398514.3	-	6	919	c.548A>T	c.(547-549)gAg>gTg	p.E183V	DPYSL3_ENST00000343218.5_Missense_Mutation_p.E297V|DPYSL3_ENST00000534907.1_Intron	NM_001387.2	NP_001378.1	Q14195	DPYL3_HUMAN	dihydropyrimidinase-like 3	183					actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|axon guidance (GO:0007411)|cellular response to cytokine stimulus (GO:0071345)|negative regulation of cell migration (GO:0030336)|negative regulation of neuron projection development (GO:0010977)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron projection development (GO:0010976)|protein homooligomerization (GO:0051260)|pyrimidine nucleobase catabolic process (GO:0006208)|response to axon injury (GO:0048678)	cell body (GO:0044297)|cytosol (GO:0005829)|extracellular space (GO:0005615)|filamentous actin (GO:0031941)|growth cone (GO:0030426)|lamellipodium (GO:0030027)	chondroitin sulfate binding (GO:0035374)|hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)|SH3 domain binding (GO:0017124)			breast(2)|endometrium(1)|kidney(4)|large_intestine(6)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGTGAAGATCTCATAGAGCTG	0.512																																					p.E297V		Atlas-SNP	.											.	DPYSL3	58	.	0			c.A890T						.						58.0	57.0	57.0					5																	146792244		1923	4121	6044	SO:0001583	missense	1809	exon6			AAGATCTCATAGA	D78014	CCDS43381.1, CCDS56387.1	5q32	2008-02-05							3015	protein-coding gene	gene with protein product		601168				8973361, 9115293	Standard	NM_001197294		Approved	DRP-3, ULIP, CRMP4	uc003loo.3	Q14195		ENST00000398514.3:c.548A>T	chr5.hg19:g.146792244T>A	ENSP00000381526:p.Glu183Val	114.0	0.0		112.0	11.0	NM_001197294	B3SXQ8|Q93012	Missense_Mutation	SNP	ENST00000398514.3	hg19	CCDS43381.1	.	.	.	.	.	.	.	.	.	.	T	28.5	4.928366	0.92389	.	.	ENSG00000113657	ENST00000398514;ENST00000343218	D;D	0.90955	-2.76;-2.76	6.02	6.02	0.97574	Amidohydrolase 1 (1);Metal-dependent hydrolase, composite domain (1);	0.109568	0.64402	D	0.000004	D	0.96463	0.8846	M	0.92604	3.325	0.80722	D	1	D;D	0.71674	0.998;0.993	D;P	0.76071	0.987;0.848	D	0.97201	0.9864	10	0.72032	D	0.01	-1.6788	16.5446	0.84426	0.0:0.0:0.0:1.0	.	297;183	B3SXQ8;Q14195	.;DPYL3_HUMAN	V	183;297	ENSP00000381526:E183V;ENSP00000343690:E297V	ENSP00000343690:E297V	E	-	2	0	DPYSL3	146772437	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.997000	0.88414	2.311000	0.77944	0.533000	0.62120	GAG	.	.		0.512	DPYSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373421.2	NM_001387	
SPDL1	54908	hgsc.bcm.edu	37	5	169023605	169023605	+	Missense_Mutation	SNP	C	C	T	rs145815866		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:169023605C>T	ENST00000265295.4	+	8	1211	c.932C>T	c.(931-933)aCt>aTt	p.T311I		NM_017785.4	NP_060255.3			spindle apparatus coiled-coil protein 1																		GGGTCTCAAACTGAATTTGAG	0.348																																					p.T311I		Atlas-SNP	.											.	.	.	.	0			c.C932T						.						82.0	86.0	85.0					5																	169023605		2203	4300	6503	SO:0001583	missense	54908	exon8			CTCAAACTGAATT	BC012568	CCDS4370.1	5q35.1	2012-09-27	2012-09-27	2012-09-27	ENSG00000040275	ENSG00000040275			26010	protein-coding gene	gene with protein product	"""spindly homolog (Drosophila)"""		"""coiled-coil domain containing 99"""	CCDC99		20427577	Standard	NM_017785		Approved	FLJ20364, hSpindly	uc003mae.4	Q96EA4	OTTHUMG00000130438	ENST00000265295.4:c.932C>T	chr5.hg19:g.169023605C>T	ENSP00000265295:p.Thr311Ile	207.0	0.0		226.0	70.0	NM_017785		Missense_Mutation	SNP	ENST00000265295.4	hg19	CCDS4370.1	.	.	.	.	.	.	.	.	.	.	C	15.53	2.861091	0.51482	.	.	ENSG00000040275	ENST00000265295;ENST00000274631	T	0.32023	1.47	5.7	5.7	0.88788	.	0.304797	0.38492	N	0.001673	T	0.44435	0.1293	L	0.54323	1.7	0.28765	N	0.900678	D;P;P	0.59767	0.986;0.773;0.573	P;B;B	0.55391	0.775;0.372;0.165	T	0.41413	-0.9510	10	0.56958	D	0.05	-4.1564	14.6759	0.68978	0.0:0.7347:0.2653:0.0	.	233;212;311	B4E393;Q96EA4-2;Q96EA4	.;.;SPDLY_HUMAN	I	311;212	ENSP00000265295:T311I	ENSP00000265295:T311I	T	+	2	0	CCDC99	168956183	1.000000	0.71417	0.916000	0.36221	0.970000	0.65996	3.958000	0.56737	2.665000	0.90641	0.655000	0.94253	ACT	.	C|1.000;G|0.000		0.348	SPDL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252829.2	NM_017785	
BTN2A2	10385	hgsc.bcm.edu	37	6	26392974	26392974	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:26392974G>T	ENST00000356709.4	+	8	1462	c.1351G>T	c.(1351-1353)Gac>Tac	p.D451Y	BTN2A2_ENST00000482536.1_Missense_Mutation_p.D241Y|BTN2A2_ENST00000432533.2_3'UTR|BTN2A2_ENST00000352867.2_Missense_Mutation_p.D335Y|BTN2A2_ENST00000469230.1_Intron|BTN2A2_ENST00000416795.2_Missense_Mutation_p.D451Y	NM_001197240.1|NM_006995.4	NP_001184169.1|NP_008926.2	Q8WVV5	BT2A2_HUMAN	butyrophilin, subfamily 2, member A2	451	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cellular metabolic process (GO:0031324)|negative regulation of cytokine secretion (GO:0050710)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|large_intestine(5)|lung(13)	23						CGTCTTCCTGGACTATGAAGC	0.547																																					p.D451Y		Atlas-SNP	.											.	BTN2A2	87	.	0			c.G1351T						.						112.0	103.0	106.0					6																	26392974		2203	4298	6501	SO:0001583	missense	10385	exon8			TTCCTGGACTATG	U90550	CCDS4606.1, CCDS4607.1, CCDS56401.1, CCDS56402.1, CCDS56403.1	6p22.1	2014-01-14			ENSG00000124508	ENSG00000124508		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1137	protein-coding gene	gene with protein product		613591				10354554, 9149941	Standard	NM_006995		Approved	BTF2, BT2.2, BTN2.2	uc003nhq.3	Q8WVV5	OTTHUMG00000014452	ENST00000356709.4:c.1351G>T	chr6.hg19:g.26392974G>T	ENSP00000349143:p.Asp451Tyr	397.0	1.0		408.0	134.0	NM_006995	A6NM84|B4DE97|B4DQ01|E9PH07|O00480	Missense_Mutation	SNP	ENST00000356709.4	hg19	CCDS4606.1	.	.	.	.	.	.	.	.	.	.	.	15.45	2.835821	0.50951	.	.	ENSG00000124508	ENST00000356709;ENST00000352867;ENST00000482536;ENST00000416795	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	3.63	1.79	0.24919	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.113821	0.39615	N	0.001301	D	0.90762	0.7100	H	0.99197	4.465	0.35580	D	0.806183	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.85130	0.938;0.986;0.997	D	0.88784	0.3273	10	0.87932	D	0	.	7.0519	0.25077	0.1049:0.1735:0.7216:0.0	.	241;335;451	E9PH07;A6NM84;Q8WVV5	.;.;BT2A2_HUMAN	Y	451;335;241;451	ENSP00000349143:D451Y;ENSP00000337117:D335Y;ENSP00000419451:D241Y;ENSP00000399308:D451Y	ENSP00000337117:D335Y	D	+	1	0	BTN2A2	26500953	1.000000	0.71417	0.705000	0.30386	0.634000	0.38068	4.649000	0.61433	0.165000	0.19558	-0.455000	0.05494	GAC	.	.		0.547	BTN2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040117.1		
DPCR1	135656	hgsc.bcm.edu	37	6	30917142	30917142	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:30917142C>T	ENST00000462446.1	+	2	929	c.901C>T	c.(901-903)Cca>Tca	p.P301S	HCG21_ENST00000419481.1_RNA|DPCR1_ENST00000304311.2_5'UTR			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	301	Thr-rich.					integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						CACACCATCCCCAGCAGAGCC	0.458																																					p.P301S		Atlas-SNP	.											.	DPCR1	99	.	0			c.C901T						.						86.0	82.0	83.0					6																	30917142		692	1591	2283	SO:0001583	missense	135656	exon2			CCATCCCCAGCAG	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.901C>T	chr6.hg19:g.30917142C>T	ENSP00000417182:p.Pro301Ser	170.0	0.0		207.0	71.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Missense_Mutation	SNP	ENST00000462446.1	hg19	CCDS4692.2	.	.	.	.	.	.	.	.	.	.	c	0.015	-1.569991	0.00895	.	.	ENSG00000168631	ENST00000462446;ENST00000450344	T	0.45668	0.89	1.36	0.31	0.15825	.	.	.	.	.	T	0.08758	0.0217	L	0.28400	0.85	0.09310	N	0.999994	P	0.40282	0.711	B	0.38194	0.267	T	0.22173	-1.0224	9	0.07482	T	0.82	.	6.4298	0.21790	0.2897:0.7103:0.0:0.0	.	301	E9PEI6	.	S	301	ENSP00000417182:P301S	ENSP00000411741:P301S	P	+	1	0	DPCR1	31025121	0.000000	0.05858	0.006000	0.13384	0.078000	0.17371	0.938000	0.28965	0.091000	0.17302	0.175000	0.17021	CCA	.	.		0.458	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
TNF	7124	hgsc.bcm.edu	37	6	31544903	31544903	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:31544903A>T	ENST00000449264.2	+	4	466	c.291A>T	c.(289-291)caA>caT	p.Q97H		NM_000594.3	NP_000585.2	P01375	TNFA_HUMAN	tumor necrosis factor	97					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|calcium-mediated signaling (GO:0019722)|cell activation (GO:0001775)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nicotine (GO:0071316)|cellular response to organic cyclic compound (GO:0071407)|chronic inflammatory response to antigenic stimulus (GO:0002439)|defense response to Gram-positive bacterium (GO:0050830)|embryonic digestive tract development (GO:0048566)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|glucose metabolic process (GO:0006006)|humoral immune response (GO:0006959)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JNK cascade (GO:0007254)|leukocyte tethering or rolling (GO:0050901)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|MAPK cascade (GO:0000165)|necroptotic signaling pathway (GO:0097527)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of branching involved in lung morphogenesis (GO:0061048)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cytokine secretion involved in immune response (GO:0002740)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of glucose import (GO:0046325)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of L-glutamate transport (GO:0002037)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of lipid storage (GO:0010888)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein complex disassembly (GO:0043242)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|organ morphogenesis (GO:0009887)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of calcidiol 1-monooxygenase activity (GO:0060559)|positive regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000343)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fever generation (GO:0031622)|positive regulation of gene expression (GO:0010628)|positive regulation of hair follicle development (GO:0051798)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of JNK cascade (GO:0046330)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of mitosis (GO:0045840)|positive regulation of mononuclear cell migration (GO:0071677)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NFAT protein import into nucleus (GO:0051533)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of podosome assembly (GO:0071803)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of protein complex disassembly (GO:0043243)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein transport (GO:0051222)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of synaptic transmission (GO:0050806)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translational initiation by iron (GO:0045994)|positive regulation of vitamin D biosynthetic process (GO:0060557)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|receptor biosynthetic process (GO:0032800)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of immunoglobulin secretion (GO:0051023)|regulation of insulin secretion (GO:0050796)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|response to salt stress (GO:0009651)|response to virus (GO:0009615)|sequestering of triglyceride (GO:0030730)|skeletal muscle contraction (GO:0003009)|transformed cell apoptotic process (GO:0006927)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	cytokine activity (GO:0005125)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|transcription regulatory region DNA binding (GO:0044212)|tumor necrosis factor receptor binding (GO:0005164)			large_intestine(1)|lung(2)|ovary(1)|pancreas(1)|skin(3)	8		Ovarian(999;0.00556)			Adalimumab(DB00051)|Amrinone(DB01427)|Certolizumab pegol(DB08904)|Chloroquine(DB00608)|Clenbuterol(DB01407)|Epinephrine(DB00668)|Etanercept(DB00005)|Glucosamine(DB01296)|golimumab(DB06674)|Infliximab(DB00065)|Pomalidomide(DB08910)|Pranlukast(DB01411)|Pseudoephedrine(DB00852)|Thalidomide(DB01041)	CAAACCCTCAAGCTGAGGGGC	0.637									Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of																												p.Q97H		Atlas-SNP	.											.	TNF	15	.	0			c.A291T						.						69.0	74.0	73.0					6																	31544903		1511	2709	4220	SO:0001583	missense	7124	exon4	Familial Cancer Database	incl.: Familial Head and Neck Cancer	CCCTCAAGCTGAG	X02910	CCDS4702.1	6p21.3	2013-05-22	2010-05-04		ENSG00000232810	ENSG00000232810		"""Tumor necrosis factor (ligand) superfamily"""	11892	protein-coding gene	gene with protein product	"""TNF superfamily, member 2"""	191160	"""tumor necrosis factor (TNF superfamily, member 2)"""	TNFA		2413547, 6392892	Standard	NM_000594		Approved	TNFSF2, DIF, TNF-alpha	uc003nui.4	P01375	OTTHUMG00000031194	ENST00000449264.2:c.291A>T	chr6.hg19:g.31544903A>T	ENSP00000398698:p.Gln97His	65.0	0.0		64.0	4.0	NM_000594	O43647|Q9P1Q2|Q9UIV3	Missense_Mutation	SNP	ENST00000449264.2	hg19	CCDS4702.1	.	.	.	.	.	.	.	.	.	.	A	5.959	0.360848	0.11296	.	.	ENSG00000232810	ENST00000449264	T	0.43688	0.94	5.41	-1.04	0.10068	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.974983	0.08449	N	0.944165	T	0.19127	0.0459	M	0.77103	2.36	0.09310	N	1	B	0.27679	0.185	B	0.25884	0.064	T	0.39961	-0.9588	10	0.66056	D	0.02	.	1.414	0.02298	0.4253:0.2989:0.1307:0.1451	.	97	P01375	TNFA_HUMAN	H	97	ENSP00000398698:Q97H	ENSP00000398698:Q97H	Q	+	3	2	TNF	31652882	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.104000	0.10923	0.042000	0.15717	-0.460000	0.05396	CAA	.	.		0.637	TNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076390.2		
RGL2	5863	hgsc.bcm.edu	37	6	33263466	33263466	+	Missense_Mutation	SNP	T	T	A	rs201427428	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:33263466T>A	ENST00000497454.1	-	7	1334	c.839A>T	c.(838-840)cAt>cTt	p.H280L	RGL2_ENST00000444031.2_Missense_Mutation_p.H198L|RGL2_ENST00000437840.2_5'UTR|PFDN6_ENST00000463584.1_Intron	NM_001243738.1|NM_004761.4	NP_001230667.1|NP_004752.1	O15211	RGL2_HUMAN	ral guanine nucleotide dissociation stimulator-like 2	280	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)	intracellular (GO:0005622)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			breast(2)|cervix(2)|endometrium(7)|kidney(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	34						GAGGTGAGAATGTCCTGGCCG	0.547																																					p.H280L		Atlas-SNP	.											.	RGL2	58	.	0			c.A839T						.						51.0	53.0	52.0					6																	33263466		2203	4300	6503	SO:0001583	missense	5863	exon7			TGAGAATGTCCTG		CCDS4774.1	6p21.3	2010-02-17	2004-06-11	2004-06-16	ENSG00000237441	ENSG00000237441			9769	protein-coding gene	gene with protein product		602306	"""RAB2, member RAS oncogene family-like"""	RAB2L		8976381	Standard	NM_001243738		Approved	KE1.5, HKE1.5	uc003odv.3	O15211	OTTHUMG00000031072	ENST00000497454.1:c.839A>T	chr6.hg19:g.33263466T>A	ENSP00000420211:p.His280Leu	163.0	0.0		190.0	13.0	NM_004761	B4DG72|Q5STK0|Q9Y3F3	Missense_Mutation	SNP	ENST00000497454.1	hg19	CCDS4774.1	.	.	.	.	.	.	.	.	.	.	T	16.08	3.021312	0.54576	.	.	ENSG00000237441	ENST00000497454;ENST00000421215;ENST00000444031	T;T	0.28666	1.6;1.6	4.61	4.61	0.57282	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.199351	0.43260	D	0.000594	T	0.13072	0.0317	N	0.11698	0.16	0.39371	D	0.966088	P;P	0.48503	0.619;0.911	B;P	0.48488	0.137;0.579	T	0.03981	-1.0987	10	0.49607	T	0.09	.	10.3073	0.43689	0.0:0.0:0.0:1.0	.	198;280	B4DG72;O15211	.;RGL2_HUMAN	L	280;144;198	ENSP00000420211:H280L;ENSP00000403070:H198L	ENSP00000400083:H144L	H	-	2	0	RGL2	33371444	0.933000	0.31639	1.000000	0.80357	0.996000	0.88848	1.234000	0.32660	1.921000	0.55644	0.523000	0.50628	CAT	.	T|0.999;C|0.001		0.547	RGL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076098.2		
SYNGAP1	8831	hgsc.bcm.edu	37	6	33403036	33403036	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:33403036T>C	ENST00000418600.2	+	6	718	c.617T>C	c.(616-618)aTc>aCc	p.I206T	SYNGAP1_ENST00000428982.2_Missense_Mutation_p.I147T|SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Missense_Mutation_p.I206T	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	206	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GATTCCATTATCAAGCCAGTG	0.537																																					p.I206T		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T617C						.						106.0	95.0	99.0					6																	33403036		2203	4300	6503	SO:0001583	missense	8831	exon6			CCATTATCAAGCC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.617T>C	chr6.hg19:g.33403036T>C	ENSP00000403636:p.Ile206Thr	147.0	0.0		176.0	50.0	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Missense_Mutation	SNP	ENST00000418600.2	hg19	CCDS34434.2	.	.	.	.	.	.	.	.	.	.	T	17.10	3.303239	0.60195	.	.	ENSG00000197283	ENST00000293748;ENST00000418600;ENST00000449372;ENST00000428982	T;T;T	0.25250	1.81;1.9;1.91	4.42	4.42	0.53409	Pleckstrin homology-type (1);Pleckstrin homology domain (1);	0.062978	0.64402	D	0.000005	T	0.27900	0.0687	M	0.68593	2.085	0.58432	D	0.999992	B;P;P	0.48694	0.421;0.557;0.914	B;B;P	0.52159	0.156;0.297;0.691	T	0.07790	-1.0754	10	0.87932	D	0	.	11.6525	0.51297	0.0:0.0:0.0:1.0	.	206;206;206	Q96PV0;Q96PV0-4;B7ZCA0	SYGP1_HUMAN;.;.	T	206;206;206;147	ENSP00000293748:I206T;ENSP00000403636:I206T;ENSP00000412475:I147T	ENSP00000293748:I206T	I	+	2	0	SYNGAP1	33511014	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.859000	0.86982	1.845000	0.53610	0.482000	0.46254	ATC	.	.		0.537	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
TAF8	129685	hgsc.bcm.edu	37	6	42036240	42036240	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:42036240A>T	ENST00000372977.3	+	7	693	c.675A>T	c.(673-675)acA>acT	p.T225T	TAF8_ENST00000456846.2_Silent_p.T225T|TAF8_ENST00000465926.1_Splice_Site|TAF8_ENST00000372982.4_Silent_p.T225T|TAF8_ENST00000494547.1_Silent_p.T225T	NM_138572.2	NP_612639.2	Q7Z7C8	TAF8_HUMAN	TAF8 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 43kDa	225					cell differentiation (GO:0030154)|inner cell mass cell proliferation (GO:0001833)|maintenance of protein location in nucleus (GO:0051457)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fat cell differentiation (GO:0045598)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|transcription factor TFIID complex (GO:0005669)				endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00179)			CCTACCTGACAGCTCTTCTTC	0.507																																					p.T225T		Atlas-SNP	.											.	TAF8	25	.	0			c.A675T						.						259.0	258.0	258.0					6																	42036240		2045	4216	6261	SO:0001819	synonymous_variant	129685	exon7			CCTGACAGCTCTT	AK057383	CCDS43462.1	6p21.1	2008-10-23	2007-07-30	2007-07-30	ENSG00000137413	ENSG00000137413			17300	protein-coding gene	gene with protein product		609514	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 45/50kDa"", ""taube nuss homolog (mouse)"""	TBN			Standard	NM_138572		Approved	FLJ32821, TAF(II)43	uc003ors.3	Q7Z7C8	OTTHUMG00000014692	ENST00000372977.3:c.675A>T	chr6.hg19:g.42036240A>T		221.0	0.0		302.0	20.0	NM_138572	Q5T0K1|Q8N4R9|Q96M52	Silent	SNP	ENST00000372977.3	hg19	CCDS43462.1	.	.	.	.	.	.	.	.	.	.	A	7.113	0.576351	0.13686	.	.	ENSG00000137413	ENST00000465926	.	.	.	6.06	-12.1	0.00011	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.8065	0.08779	0.1226:0.2962:0.3625:0.2187	.	.	.	.	.	-1	.	.	.	+	.	.	TAF8	42144218	0.000000	0.05858	0.020000	0.16555	0.999000	0.98932	-5.159000	0.00146	-3.750000	0.00111	0.533000	0.62120	.	.	.		0.507	TAF8-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000357901.1	NM_138572	
AARS2	57505	hgsc.bcm.edu	37	6	44279864	44279864	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:44279864T>A	ENST00000244571.4	-	2	382	c.380A>T	c.(379-381)cAt>cTt	p.H127L	RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GAAGGTATGATGGGAAAGGTC	0.502																																					p.H127L		Atlas-SNP	.											.	AARS2	77	.	0			c.A380T						.						200.0	167.0	179.0					6																	44279864		2203	4300	6503	SO:0001583	missense	57505	exon2			GTATGATGGGAAA	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.380A>T	chr6.hg19:g.44279864T>A	ENSP00000244571:p.His127Leu	165.0	0.0		208.0	11.0	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	hg19	CCDS34464.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.705725	0.89018	.	.	ENSG00000124608	ENST00000244571	D	0.97114	-4.25	4.9	4.9	0.64082	Alanyl-tRNA synthetase, class IIc, core domain (1);Alanyl-tRNA synthetase, class IIc, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.99086	0.9686	H	0.98446	4.235	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99104	1.0844	10	0.87932	D	0	-14.2778	14.698	0.69136	0.0:0.0:0.0:1.0	.	127	Q5JTZ9	SYAM_HUMAN	L	127	ENSP00000244571:H127L	ENSP00000244571:H127L	H	-	2	0	AARS2	44387842	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	7.868000	0.87116	2.054000	0.61138	0.358000	0.22013	CAT	.	.		0.502	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
RIMS1	22999	hgsc.bcm.edu	37	6	72967855	72967855	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:72967855G>T	ENST00000521978.1	+	17	2798	c.2798G>T	c.(2797-2799)aGt>aTt	p.S933I	RIMS1_ENST00000264839.7_Missense_Mutation_p.S933I|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.S932I|RIMS1_ENST00000518273.1_Missense_Mutation_p.S933I|RIMS1_ENST00000517960.1_Missense_Mutation_p.S932I|RIMS1_ENST00000401910.3_Missense_Mutation_p.S406I|RIMS1_ENST00000522291.1_Missense_Mutation_p.S932I|RIMS1_ENST00000523963.1_Missense_Mutation_p.S407I|RIMS1_ENST00000425662.2_Missense_Mutation_p.S326I|RIMS1_ENST00000520567.1_Missense_Mutation_p.S932I|RIMS1_ENST00000517827.1_Missense_Mutation_p.S392I|RIMS1_ENST00000491071.2_Missense_Mutation_p.S933I	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	933					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GCTAGAGAAAGTAAATCTACA	0.398																																					p.S933I		Atlas-SNP	.											.	RIMS1	278	.	0			c.G2798T						.						86.0	81.0	82.0					6																	72967855		1935	4131	6066	SO:0001583	missense	22999	exon17			GAGAAAGTAAATC	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2798G>T	chr6.hg19:g.72967855G>T	ENSP00000428417:p.Ser933Ile	78.0	0.0		78.0	23.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	G|G|G	13.06|13.06|13.06	2.125161|2.125161|2.125161	0.37533|0.37533|0.37533	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000517433|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000522211	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.18016|.	.|2.49;2.53;2.53;2.54;2.6;2.58;2.56;2.51;2.59;2.62;2.63;2.43;2.61;2.24|.	5.44|5.44|5.44	4.57|4.57|4.57	0.56435|0.56435|0.56435	.|.|.	.|0.065517|.	.|0.64402|.	.|D|.	.|0.000008|.	T|T|T	0.39937|0.39937|0.39937	0.1097|0.1097|0.1097	L|L|L	0.36672|0.36672|0.36672	1.1|1.1|1.1	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|B;B;P;D;B;D;B;P;P;B;P;P|.	.|0.60575|.	.|0.18;0.214;0.863;0.988;0.013;0.978;0.329;0.613;0.8;0.02;0.918;0.725|.	.|B;B;P;P;B;P;B;B;B;B;P;B|.	.|0.53722|.	.|0.065;0.094;0.451;0.675;0.009;0.733;0.077;0.269;0.276;0.028;0.451;0.248|.	T|T|T	0.32214|0.32214|0.32214	-0.9915|-0.9915|-0.9915	5|10|5	.|0.31617|.	.|T|.	.|0.26|.	-6.9858|-6.9858|-6.9858	11.2214|11.2214|11.2214	0.48857|0.48857|0.48857	0.1473:0.0:0.8527:0.0|0.1473:0.0:0.8527:0.0|0.1473:0.0:0.8527:0.0	.|.|.	.|392;407;933;392;406;932;185;933;932;186;933;933|.	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	N|I|L	506|933;933;933;932;933;932;933;932;933;932;932;933;406;407;326;326;392;158|24	.|ENSP00000430101:S933I;ENSP00000275037:S932I;ENSP00000264839:S933I;ENSP00000429959:S932I;ENSP00000430408:S933I;ENSP00000430502:S932I;ENSP00000430932:S932I;ENSP00000428417:S933I;ENSP00000385649:S406I;ENSP00000428328:S407I;ENSP00000411235:S326I;ENSP00000389503:S326I;ENSP00000428367:S392I;ENSP00000359448:S158I|.	.|ENSP00000264839:S933I|.	K|S|V	+|+|+	3|2|1	2|0|0	RIMS1|RIMS1|RIMS1	73024576|73024576|73024576	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.829000|0.829000|0.829000	0.46940|0.46940|0.46940	5.528000|5.528000|5.528000	0.67129|0.67129|0.67129	1.301000|1.301000|1.301000	0.44836|0.44836|0.44836	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	AAG|AGT|GTA	.	.		0.398	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
RIMS1	22999	hgsc.bcm.edu	37	6	72967911	72967911	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:72967911C>A	ENST00000521978.1	+	17	2854	c.2854C>A	c.(2854-2856)Cgt>Agt	p.R952S	RIMS1_ENST00000264839.7_Missense_Mutation_p.R952S|RIMS1_ENST00000538414.1_5'UTR|RIMS1_ENST00000348717.5_Missense_Mutation_p.R951S|RIMS1_ENST00000518273.1_Missense_Mutation_p.R952S|RIMS1_ENST00000517960.1_Missense_Mutation_p.R951S|RIMS1_ENST00000401910.3_Missense_Mutation_p.R425S|RIMS1_ENST00000522291.1_Missense_Mutation_p.R951S|RIMS1_ENST00000523963.1_Missense_Mutation_p.R426S|RIMS1_ENST00000425662.2_Missense_Mutation_p.R345S|RIMS1_ENST00000520567.1_Missense_Mutation_p.R951S|RIMS1_ENST00000517827.1_Missense_Mutation_p.R411S|RIMS1_ENST00000491071.2_Missense_Mutation_p.R952S	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	952					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				TCACCGCTCACGTTCAGTATC	0.463																																					p.R952S		Atlas-SNP	.											.	RIMS1	278	.	0			c.C2854A						.						93.0	89.0	90.0					6																	72967911		1994	4171	6165	SO:0001583	missense	22999	exon17			CGCTCACGTTCAG	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.2854C>A	chr6.hg19:g.72967911C>A	ENSP00000428417:p.Arg952Ser	122.0	0.0		121.0	30.0	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	hg19	CCDS47449.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	C|C|C	26.3|26.3|26.3	4.721823|4.721823|4.721823	0.89298|0.89298|0.89298	.|.|.	.|.|.	ENSG00000079841|ENSG00000079841|ENSG00000079841	ENST00000522211|ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978;ENST00000401910;ENST00000523963;ENST00000425662;ENST00000453976;ENST00000517827;ENST00000370420|ENST00000517433	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	.|0.26810|.	.|1.93;2.31;2.06;2.31;2.12;2.02;2.13;1.81;1.94;2.07;2.3;2.27;2.26;1.71|.	5.19|5.19|5.19	5.19|5.19|5.19	0.71726|0.71726|0.71726	.|.|.	.|0.000000|.	.|0.64402|.	.|D|.	.|0.000016|.	T|T|T	0.65923|0.65923|0.65923	0.2738|0.2738|0.2738	L|L|L	0.60455|0.60455|0.60455	1.87|1.87|1.87	0.80722|0.80722|0.80722	D|D|D	1|1|1	.|D;D;D;D;P;D;P;D;D;D;D;D|.	.|0.89917|.	.|0.957;0.993;0.998;0.998;0.956;1.0;0.76;0.978;0.995;0.997;0.999;0.998|.	.|P;D;D;D;P;D;B;P;D;D;D;D|.	.|0.87578|.	.|0.78;0.972;0.994;0.994;0.646;0.998;0.082;0.823;0.968;0.951;0.994;0.994|.	T|T|T	0.63910|0.63910|0.63910	-0.6530|-0.6530|-0.6530	5|10|5	.|0.66056|.	.|D|.	.|0.02|.	-14.3502|-14.3502|-14.3502	18.729|18.729|18.729	0.91728|0.91728|0.91728	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.|.	.|411;426;952;411;425;951;204;952;951;205;952;952|.	.|B7Z3S3;E9PHF5;E9PHR1;B7Z9Z3;E9PF48;E7EX08;Q5JY22;E7ERQ1;E7ENC2;Q5JY21;C9JNW6;Q86UR5|.	.|.;.;.;.;.;.;.;.;.;.;.;RIMS1_HUMAN|.	Q|S|K	42|952;952;952;951;952;951;952;951;952;951;951;952;425;426;345;345;411;177|525	.|ENSP00000430101:R952S;ENSP00000275037:R951S;ENSP00000264839:R952S;ENSP00000429959:R951S;ENSP00000430408:R952S;ENSP00000430502:R951S;ENSP00000430932:R951S;ENSP00000428417:R952S;ENSP00000385649:R425S;ENSP00000428328:R426S;ENSP00000411235:R345S;ENSP00000389503:R345S;ENSP00000428367:R411S;ENSP00000359448:R177S|.	.|ENSP00000264839:R952S|.	H|R|T	+|+|+	3|1|2	2|0|0	RIMS1|RIMS1|RIMS1	73024632|73024632|73024632	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.893000|0.893000|0.893000	0.52053|0.52053|0.52053	7.607000|7.607000|7.607000	0.82883|0.82883|0.82883	2.434000|2.434000|2.434000	0.82447|0.82447|0.82447	0.585000|0.585000|0.585000	0.79938|0.79938|0.79938	CAC|CGT|ACG	.	.		0.463	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
MDN1	23195	hgsc.bcm.edu	37	6	90380710	90380710	+	Silent	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:90380710A>G	ENST00000369393.3	-	83	13999	c.13884T>C	c.(13882-13884)tcT>tcC	p.S4628S	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000468568.1_5'UTR|MDN1_ENST00000428876.1_Silent_p.S4628S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4628					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GAGTTGCTAAAGACATGGTCA	0.532																																					p.S4628S		Atlas-SNP	.											.	MDN1	478	.	0			c.T13884C						.						102.0	91.0	95.0					6																	90380710		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon83			TGCTAAAGACATG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13884T>C	chr6.hg19:g.90380710A>G		188.0	0.0		175.0	50.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.532	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
MDN1	23195	hgsc.bcm.edu	37	6	90381952	90381952	+	Silent	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:90381952C>A	ENST00000369393.3	-	82	13876	c.13761G>T	c.(13759-13761)tcG>tcT	p.S4587S	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000468568.1_5'UTR|MDN1_ENST00000428876.1_Silent_p.S4587S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4587					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CCTCACCGTACGATTTCAGCC	0.468																																					p.S4587S		Atlas-SNP	.											.	MDN1	478	.	0			c.G13761T						.						122.0	109.0	114.0					6																	90381952		2203	4300	6503	SO:0001819	synonymous_variant	23195	exon82			ACCGTACGATTTC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.13761G>T	chr6.hg19:g.90381952C>A		77.0	0.0		87.0	21.0	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	hg19	CCDS5024.1																																																																																			.	.		0.468	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
GRIK2	2898	hgsc.bcm.edu	37	6	102250278	102250278	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr6:102250278G>A	ENST00000421544.1	+	8	1658	c.1168G>A	c.(1168-1170)Gat>Aat	p.D390N	GRIK2_ENST00000413795.1_Missense_Mutation_p.D390N|GRIK2_ENST00000318991.6_Missense_Mutation_p.D390N|GRIK2_ENST00000369138.1_Missense_Mutation_p.D390N|GRIK2_ENST00000369134.4_Missense_Mutation_p.D341N|GRIK2_ENST00000369137.3_Missense_Mutation_p.D390N	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	390					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	TTTTGATTTGGATGTGATCAG	0.343																																					p.D390N		Atlas-SNP	.											.	GRIK2	487	.	0			c.G1168A						.						116.0	118.0	118.0					6																	102250278		2203	4299	6502	SO:0001583	missense	2898	exon8			GATTTGGATGTGA		CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.1168G>A	chr6.hg19:g.102250278G>A	ENSP00000397026:p.Asp390Asn	104.0	0.0		112.0	29.0	NM_021956	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	ENST00000421544.1	hg19	CCDS5048.1	.	.	.	.	.	.	.	.	.	.	G	34	5.375248	0.95923	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000369134;ENST00000540076;ENST00000455610	D;D;D;D;D;D;D	0.83335	-1.71;-1.71;-1.71;-1.71;-1.71;-1.71;-1.71	5.61	5.61	0.85477	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.90786	0.7107	M	0.81682	2.555	0.54753	D	0.999989	D;D;D	0.76494	0.999;0.998;0.998	D;D;D	0.74674	0.984;0.983;0.972	D	0.91365	0.5115	10	0.87932	D	0	.	19.6406	0.95755	0.0:0.0:1.0:0.0	.	390;390;390	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	N	390;390;390;390;390;390;341;352;103	ENSP00000397026:D390N;ENSP00000405596:D390N;ENSP00000358134:D390N;ENSP00000358133:D390N;ENSP00000313276:D390N;ENSP00000358130:D341N;ENSP00000391988:D103N	ENSP00000313276:D390N	D	+	1	0	GRIK2	102356971	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.398000	0.97281	2.633000	0.89246	0.544000	0.68410	GAT	.	.		0.343	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043718.1		
AMZ1	155185	hgsc.bcm.edu	37	7	2740227	2740227	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:2740227T>A	ENST00000312371.4	+	2	510	c.142T>A	c.(142-144)Tac>Aac	p.Y48N	AMZ1_ENST00000407112.1_Missense_Mutation_p.Y48N	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	48							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		GGCCGAGGCCTACAACCCGCA	0.662																																					p.Y48N		Atlas-SNP	.											.	AMZ1	41	.	0			c.T142A						.						113.0	122.0	119.0					7																	2740227		2203	4300	6503	SO:0001583	missense	155185	exon2			GAGGCCTACAACC	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.142T>A	chr7.hg19:g.2740227T>A	ENSP00000308149:p.Tyr48Asn	92.0	0.0		45.0	5.0	NM_133463	B3KRS0|Q8TF51	Missense_Mutation	SNP	ENST00000312371.4	hg19	CCDS34589.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.242212	0.79912	.	.	ENSG00000174945	ENST00000312371;ENST00000407112	T;T	0.44881	1.3;0.91	4.34	4.34	0.51931	.	0.217682	0.31760	N	0.007109	T	0.61837	0.2379	M	0.70595	2.14	0.45946	D	0.998777	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.994	T	0.66135	-0.5999	10	0.87932	D	0	-43.205	12.1049	0.53807	0.0:0.0:0.0:1.0	.	48;48	B3KRS0;Q400G9	.;AMZ1_HUMAN	N	48	ENSP00000308149:Y48N;ENSP00000386020:Y48N	ENSP00000308149:Y48N	Y	+	1	0	AMZ1	2706753	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	5.290000	0.65661	1.603000	0.50134	0.459000	0.35465	TAC	.	.		0.662	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
NPC1L1	29881	hgsc.bcm.edu	37	7	44578770	44578770	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:44578770T>A	ENST00000289547.4	-	2	1281	c.1226A>T	c.(1225-1227)cAg>cTg	p.Q409L	NPC1L1_ENST00000381160.3_Missense_Mutation_p.Q409L|NPC1L1_ENST00000546276.1_Missense_Mutation_p.Q409L|NPC1L1_ENST00000423141.1_Missense_Mutation_p.Q409L	NM_013389.2	NP_037521.2	Q9UHC9	NPCL1_HUMAN	NPC1-like 1	409					cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intestinal cholesterol absorption (GO:0030299)|lipoprotein metabolic process (GO:0042157)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)	brush border membrane (GO:0031526)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	drug binding (GO:0008144)|hedgehog receptor activity (GO:0008158)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|large_intestine(7)|lung(27)|ovary(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	57					Ezetimibe(DB00973)	CAGGATCACCTGGTTGGTTCG	0.597																																					p.Q409L		Atlas-SNP	.											.	NPC1L1	141	.	0			c.A1226T						.						83.0	93.0	89.0					7																	44578770		2203	4300	6503	SO:0001583	missense	29881	exon2			ATCACCTGGTTGG		CCDS5491.1, CCDS43575.1, CCDS75587.1	7p13	2012-11-15	2012-11-15		ENSG00000015520	ENSG00000015520			7898	protein-coding gene	gene with protein product		608010	"""NPC1 (Niemann-Pick disease, type C1, gene)-like 1"""			10783261	Standard	NM_013389		Approved		uc003tlb.3	Q9UHC9	OTTHUMG00000023691	ENST00000289547.4:c.1226A>T	chr7.hg19:g.44578770T>A	ENSP00000289547:p.Gln409Leu	193.0	0.0		226.0	15.0	NM_001101648	A4D2J7|B7ZLE6|D3DVK9|Q17RV5|Q6R3Q4|Q9UHC8	Missense_Mutation	SNP	ENST00000289547.4	hg19	CCDS5491.1	.	.	.	.	.	.	.	.	.	.	t	21.7	4.190787	0.78789	.	.	ENSG00000015520	ENST00000289547;ENST00000381160;ENST00000546276;ENST00000423141	D;D;D;D	0.92595	-3.07;-3.07;-3.07;-3.07	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	D	0.96765	0.8944	M	0.93241	3.395	0.54753	D	0.999984	D;P;D;P	0.76494	0.999;0.946;0.999;0.533	D;P;D;B	0.78314	0.978;0.509;0.991;0.133	D	0.97343	0.9958	10	0.62326	D	0.03	-24.8398	12.7308	0.57197	0.0:0.0:0.0:1.0	.	409;409;409;409	B7ZLE6;Q9UHC9-3;Q17RV5;D3DVK9	.;.;.;.	L	409	ENSP00000289547:Q409L;ENSP00000370552:Q409L;ENSP00000438033:Q409L;ENSP00000404670:Q409L	ENSP00000289547:Q409L	Q	-	2	0	NPC1L1	44545295	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.593000	0.82686	1.897000	0.54924	0.379000	0.24179	CAG	.	.		0.597	NPC1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251256.1	NM_013389	
ZPBP	11055	hgsc.bcm.edu	37	7	50129226	50129226	+	Splice_Site	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:50129226T>A	ENST00000046087.2	-	2	276	c.207A>T	c.(205-207)ccA>ccT	p.P69P	ZPBP_ENST00000419417.1_Splice_Site_p.P69P	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	69					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					TATGAATACCTGGAAAACTTG	0.308																																					p.P69P		Atlas-SNP	.											.	ZPBP	65	.	0			c.A207T						.						27.0	28.0	28.0					7																	50129226		2202	4297	6499	SO:0001630	splice_region_variant	11055	exon2			AATACCTGGAAAA	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.208+1A>T	chr7.hg19:g.50129226T>A		97.0	0.0		103.0	10.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	hg19	CCDS5509.1																																																																																			.	.		0.308	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009	Silent
FIS1	51024	hgsc.bcm.edu	37	7	100884160	100884160	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:100884160T>A	ENST00000223136.4	-	3	286	c.206A>T	c.(205-207)gAa>gTa	p.E69V	FIS1_ENST00000482199.1_5'UTR|FIS1_ENST00000474120.1_Silent_p.G14G|FIS1_ENST00000442303.1_Silent_p.G45G|CLDN15_ENST00000308344.5_5'Flank|CLDN15_ENST00000401528.1_5'Flank	NM_016068.2	NP_057152.2	Q9Y3D6	FIS1_HUMAN	fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae)	69					calcium-mediated signaling using intracellular calcium source (GO:0035584)|mitochondrial fission (GO:0000266)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mitochondrial fusion (GO:0008053)|mitochondrion degradation (GO:0000422)|mitochondrion morphogenesis (GO:0070584)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|peroxisome fission (GO:0016559)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of mitochondrial fission (GO:0090141)|positive regulation of protein targeting to membrane (GO:0090314)|protein homooligomerization (GO:0051260)|protein targeting to mitochondrion (GO:0006626)|regulation of mitochondrion organization (GO:0010821)|release of cytochrome c from mitochondria (GO:0001836)	integral component of mitochondrial outer membrane (GO:0031307)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|protein complex (GO:0043234)	receptor binding (GO:0005102)			kidney(1)|large_intestine(2)|lung(1)	4	Lung NSC(181;0.168)|all_lung(186;0.215)					ATCCCGCTGTTCCTCCTTGCT	0.582																																					p.E69V		Atlas-SNP	.											FIS1,right_upper_lobe,carcinoma,0,1	FIS1	11	.	0			c.A206T						.						90.0	96.0	94.0					7																	100884160		2004	4159	6163	SO:0001583	missense	51024	exon3			CGCTGTTCCTCCT	AF151893	CCDS43626.1	7q22.1	2012-10-01	2006-04-04	2006-01-24	ENSG00000214253	ENSG00000214253			21689	protein-coding gene	gene with protein product	"""CGI-135 protein"""	609003	"""tetratricopeptide repeat domain 11"", ""fission 1 (mitochondrial outer membrane) homolog (yeast)"""	TTC11		14996942, 16010987	Standard	NM_016068		Approved	CGI-135, H_NH0132A01.6, Fis1	uc003uyj.4	Q9Y3D6	OTTHUMG00000157106	ENST00000223136.4:c.206A>T	chr7.hg19:g.100884160T>A	ENSP00000223136:p.Glu69Val	351.0	0.0		461.0	31.0	NM_016068	Q9BTP3	Missense_Mutation	SNP	ENST00000223136.4	hg19	CCDS43626.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.93|14.93	2.681473|2.681473	0.47991|0.47991	.|.	.|.	ENSG00000214253|ENSG00000214253	ENST00000223136|ENST00000435848	.|.	.|.	.|.	5.1|5.1	5.1|5.1	0.69264|0.69264	Tetratricopeptide-like helical (1);|.	0.087599|.	0.44902|.	U|.	0.000412|.	T|T	0.61776|0.61776	0.2374|0.2374	L|L	0.43923|0.43923	1.385|1.385	0.53688|0.53688	D|D	0.999979|0.999979	B|.	0.19583|.	0.037|.	B|.	0.21360|.	0.034|.	T|T	0.65565|0.65565	-0.6137|-0.6137	9|6	0.33940|0.87932	T|D	0.23|0	.|.	12.8187|12.8187	0.57679|0.57679	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	69|.	Q9Y3D6|.	FIS1_HUMAN|.	V|Y	69|59	.|.	ENSP00000223136:E69V|ENSP00000413500:N59Y	E|N	-|-	2|1	0|0	FIS1|FIS1	100670880|100670880	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.969000|0.969000	0.65631|0.65631	6.741000|6.741000	0.74837|0.74837	1.931000|1.931000	0.55961|0.55961	0.459000|0.459000	0.35465|0.35465	GAA|AAC	.	.		0.582	FIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347449.1	NM_016068	
PRKAR2B	5577	hgsc.bcm.edu	37	7	106781395	106781395	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:106781395A>T	ENST00000265717.4	+	5	843	c.584A>T	c.(583-585)gAt>gTt	p.D195V	PRKAR2B_ENST00000393613.2_3'UTR	NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	195					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TATGTAATTGATAGGTAAGTT	0.348																																					p.D195V		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.A584T						.						141.0	136.0	137.0					7																	106781395		2203	4299	6502	SO:0001583	missense	5577	exon5			TAATTGATAGGTA		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.584A>T	chr7.hg19:g.106781395A>T	ENSP00000265717:p.Asp195Val	146.0	0.0		199.0	10.0	NM_002736	A4D0R9	Missense_Mutation	SNP	ENST00000265717.4	hg19	CCDS5740.1	.	.	.	.	.	.	.	.	.	.	A	26.4	4.729366	0.89390	.	.	ENSG00000005249	ENST00000265717;ENST00000543645;ENST00000539794	D	0.91740	-2.9	5.25	5.25	0.73442	Cyclic nucleotide-binding, conserved site (1);Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);Cyclic nucleotide-binding domain (3);	0.043573	0.85682	D	0.000000	D	0.91952	0.7451	N	0.13327	0.33	0.80722	D	1	D	0.65815	0.995	D	0.72338	0.977	D	0.93780	0.7083	10	0.87932	D	0	-0.8069	15.4527	0.75285	1.0:0.0:0.0:0.0	.	195	P31323	KAP3_HUMAN	V	195;195;182	ENSP00000265717:D195V	ENSP00000265717:D195V	D	+	2	0	PRKAR2B	106568631	1.000000	0.71417	0.999000	0.59377	0.957000	0.61999	9.259000	0.95561	2.121000	0.65114	0.460000	0.39030	GAT	.	.		0.348	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
LRRN3	54674	hgsc.bcm.edu	37	7	110763113	110763113	+	Silent	SNP	T	T	A	rs151294396		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:110763113T>A	ENST00000422987.3	+	2	1116	c.285T>A	c.(283-285)acT>acA	p.T95T	IMMP2L_ENST00000450877.1_Intron|LRRN3_ENST00000308478.5_Silent_p.T95T|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000447215.1_Intron|LRRN3_ENST00000451085.1_Silent_p.T95T|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	95					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		TAAACCTTACTGGCCTGGATT	0.373																																					p.T95T		Atlas-SNP	.											.	LRRN3	132	.	0			c.T285A						.						56.0	55.0	55.0					7																	110763113		2203	4299	6502	SO:0001819	synonymous_variant	54674	exon2			CCTTACTGGCCTG	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.285T>A	chr7.hg19:g.110763113T>A		33.0	0.0		64.0	4.0	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	hg19	CCDS5754.1																																																																																			.	T|1.000;C|0.000		0.373	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
LRGUK	136332	hgsc.bcm.edu	37	7	133881819	133881819	+	Nonsense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:133881819A>T	ENST00000285928.2	+	13	1576	c.1507A>T	c.(1507-1509)Aga>Tga	p.R503*		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	503	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						AGGTATCGCAAGAGATGGTTT	0.363																																					p.R503X		Atlas-SNP	.											.	LRGUK	113	.	0			c.A1507T						.						182.0	168.0	173.0					7																	133881819		2203	4300	6503	SO:0001587	stop_gained	136332	exon13			ATCGCAAGAGATG	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1507A>T	chr7.hg19:g.133881819A>T	ENSP00000285928:p.Arg503*	112.0	0.0		186.0	15.0	NM_144648	Q2M3I1	Nonsense_Mutation	SNP	ENST00000285928.2	hg19	CCDS5830.1	.	.	.	.	.	.	.	.	.	.	A	38	7.261324	0.98171	.	.	ENSG00000155530	ENST00000285928	.	.	.	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-27.9895	12.2884	0.54805	0.8586:0.1414:0.0:0.0	.	.	.	.	X	503	.	ENSP00000285928:R503X	R	+	1	2	LRGUK	133532359	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	3.931000	0.56529	2.254000	0.74563	0.524000	0.50904	AGA	.	.		0.363	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
CNTNAP2	26047	hgsc.bcm.edu	37	7	147675070	147675071	+	Missense_Mutation	DNP	GC	GC	TT			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:147675070_147675071GC>TT	ENST00000361727.3	+	15	2888_2889	c.2372_2373GC>TT	c.(2371-2373)tGC>tTT	p.C791F		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	791	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			CCTCTGCGCTGCCAAGGAGACA	0.465										HNSCC(39;0.1)																											p.C791F|p.C791C		Atlas-SNP	.											.	CNTNAP2	392	.	0			c.G2372T|c.C2373T						.																																			SO:0001583	missense	26047	exon15			TGCGCTGCCAAGG|GCGCTGCCAAGGA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	Exception_encountered	chr7.hg19:g.147675070_147675071delinsTT	ENSP00000354778:p.Cys791Phe	173.0|172.0	0.0		260.0|257.0	18.0|17.0	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Missense_Mutation|Silent	SNP	ENST00000361727.3	hg19	CCDS5889.1																																																																																			.	.		0.465	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
KMT2C	58508	hgsc.bcm.edu	37	7	151878935	151878935	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:151878935T>A	ENST00000262189.6	-	36	6228	c.6010A>T	c.(6010-6012)Agt>Tgt	p.S2004C	KMT2C_ENST00000355193.2_Missense_Mutation_p.S2004C	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2004	Pro-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|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)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										AAGTGATCACTGGTTCCAGCT	0.468																																					p.S2004C		Atlas-SNP	.											.	MLL3	1564	.	0			c.A6010T						.						140.0	143.0	142.0					7																	151878935		2203	4300	6503	SO:0001583	missense	58508	exon36			GATCACTGGTTCC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.6010A>T	chr7.hg19:g.151878935T>A	ENSP00000262189:p.Ser2004Cys	120.0	0.0		248.0	66.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	hg19	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	12.37	1.917129	0.33815	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	T;T	0.44083	0.93;0.93	5.59	3.2	0.36748	.	0.474047	0.17146	U	0.185268	T	0.35451	0.0932	N	0.24115	0.695	0.80722	D	1	P;P	0.50272	0.89;0.933	B;P	0.49528	0.315;0.614	T	0.07462	-1.0771	10	0.59425	D	0.04	.	8.3035	0.32027	0.0:0.0689:0.1337:0.7973	.	2004;1065	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	C	2004	ENSP00000262189:S2004C;ENSP00000347325:S2004C	ENSP00000262189:S2004C	S	-	1	0	MLL3	151509868	0.999000	0.42202	0.004000	0.12327	0.660000	0.38997	3.059000	0.49947	0.404000	0.25506	0.456000	0.33151	AGT	.	.		0.468	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
LMBR1	64327	hgsc.bcm.edu	37	7	156556491	156556491	+	Splice_Site	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr7:156556491T>A	ENST00000353442.5	-	6	660		c.e6-2		LMBR1_ENST00000354505.4_Splice_Site|LMBR1_ENST00000540390.1_Splice_Site|LMBR1_ENST00000359422.4_Splice_Site	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1						embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		TCGGATTCCCTGAAAAATAGA	0.368																																					.		Atlas-SNP	.											.	LMBR1	35	.	0			c.424-2A>T						.						73.0	70.0	71.0					7																	156556491		2203	4300	6503	SO:0001630	splice_region_variant	64327	exon7			ATTCCCTGAAAAA	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.424-2A>T	chr7.hg19:g.156556491T>A		90.0	0.0		159.0	7.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Splice_Site	SNP	ENST00000353442.5	hg19	CCDS5945.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.082918	0.76642	.	.	ENSG00000105983	ENST00000353442;ENST00000415428;ENST00000354505;ENST00000540390;ENST00000347571	.	.	.	5.22	5.22	0.72569	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.4307	0.75092	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LMBR1	156249252	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.333000	0.79214	2.099000	0.63709	0.533000	0.62120	.	.	.		0.368	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	Intron
TEX15	56154	hgsc.bcm.edu	37	8	30703652	30703652	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:30703652T>A	ENST00000256246.2	-	1	2956	c.2882A>T	c.(2881-2883)cAa>cTa	p.Q961L	TEX15_ENST00000523186.1_5'Flank	NM_031271.3	NP_112561.2	Q9BXT5	TEX15_HUMAN	testis expressed 15	961					fertilization (GO:0009566)|homeostasis of number of cells within a tissue (GO:0048873)|male genitalia development (GO:0030539)|male meiosis (GO:0007140)|protein localization to chromosome (GO:0034502)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of protein localization (GO:0032880)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)					NS(2)|breast(3)|cervix(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|lung(56)|ovary(5)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	138				KIRC - Kidney renal clear cell carcinoma(542;0.0918)|Kidney(114;0.111)		AATTCGTCCTTGGGATAATGA	0.353																																					p.Q961L		Atlas-SNP	.											.	TEX15	350	.	0			c.A2882T						.						121.0	121.0	121.0					8																	30703652		2203	4299	6502	SO:0001583	missense	56154	exon1			CGTCCTTGGGATA	AF285605	CCDS6080.1	8p22	2009-03-25	2007-03-13			ENSG00000133863			11738	protein-coding gene	gene with protein product	"""cancer/testis antigen 42"""	605795	"""testis expressed sequence 15"""			11279525	Standard	NM_031271		Approved	CT42	uc003xil.3	Q9BXT5		ENST00000256246.2:c.2882A>T	chr8.hg19:g.30703652T>A	ENSP00000256246:p.Gln961Leu	103.0	0.0		109.0	11.0	NM_031271		Missense_Mutation	SNP	ENST00000256246.2	hg19	CCDS6080.1	.	.	.	.	.	.	.	.	.	.	T	18.88	3.716496	0.68844	.	.	ENSG00000133863	ENST00000256246	T	0.11495	2.77	5.62	4.47	0.54385	.	0.285236	0.25386	N	0.031044	T	0.17831	0.0428	L	0.50333	1.59	0.32469	N	0.543097	D	0.57571	0.98	P	0.52856	0.711	T	0.14924	-1.0455	10	0.87932	D	0	.	9.3139	0.37921	0.0:0.0829:0.0:0.9171	.	961	Q9BXT5	TEX15_HUMAN	L	961	ENSP00000256246:Q961L	ENSP00000256246:Q961L	Q	-	2	0	TEX15	30823194	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.039000	0.49791	0.963000	0.38082	0.383000	0.25322	CAA	.	.		0.353	TEX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376193.1		
RP1	6101	hgsc.bcm.edu	37	8	55541215	55541215	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:55541215G>A	ENST00000220676.1	+	4	4921	c.4773G>A	c.(4771-4773)tgG>tgA	p.W1591*		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	1591					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)			CTTCTGATTGGTCAGACTATC	0.398																																					p.W1591X	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G4773A						.						63.0	63.0	63.0					8																	55541215		2203	4300	6503	SO:0001587	stop_gained	6101	exon4			TGATTGGTCAGAC	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.4773G>A	chr8.hg19:g.55541215G>A	ENSP00000220676:p.Trp1591*	55.0	0.0		63.0	34.0	NM_006269		Nonsense_Mutation	SNP	ENST00000220676.1	hg19	CCDS6160.1	.	.	.	.	.	.	.	.	.	.	G	43	10.195949	0.99357	.	.	ENSG00000104237	ENST00000220676	.	.	.	5.74	2.82	0.32997	.	0.278923	0.26255	N	0.025422	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	0.0459	7.2585	0.26189	0.0673:0.1242:0.6796:0.1289	.	.	.	.	X	1591	.	ENSP00000220676:W1591X	W	+	3	0	RP1	55703768	1.000000	0.71417	0.972000	0.41901	0.817000	0.46193	2.517000	0.45529	0.765000	0.33221	0.655000	0.94253	TGG	.	.		0.398	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
TRPA1	8989	hgsc.bcm.edu	37	8	72958812	72958812	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:72958812G>T	ENST00000262209.4	-	17	2204	c.1997C>A	c.(1996-1998)cCa>cAa	p.P666Q	RP11-383H13.1_ENST00000524152.1_Intron|RP11-383H13.1_ENST00000457356.4_Intron|RP11-383H13.1_ENST00000537896.1_Intron	NM_007332.2	NP_015628.2	O75762	TRPA1_HUMAN	transient receptor potential cation channel, subfamily A, member 1	666					calcium ion transmembrane transport (GO:0070588)|detection of chemical stimulus involved in sensory perception of pain (GO:0050968)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|response to cold (GO:0009409)|response to drug (GO:0042493)|response to hydrogen peroxide (GO:0042542)|response to pain (GO:0048265)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium bundle (GO:0032421)	calcium channel activity (GO:0005262)|channel activity (GO:0015267)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(26)|lung(44)|ovary(4)|prostate(6)|stomach(1)	98			Epithelial(68;0.223)		Menthol(DB00825)	GAATTCTAATGGACATTGAAG	0.299																																					p.P666Q		Atlas-SNP	.											.	TRPA1	256	.	0			c.C1997A						.						140.0	150.0	147.0					8																	72958812		2203	4300	6503	SO:0001583	missense	8989	exon17			TCTAATGGACATT	Y10601	CCDS34908.1	8q13	2013-01-10	2003-11-20	2003-11-20	ENSG00000104321	ENSG00000104321		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	497	protein-coding gene	gene with protein product		604775	"""ankyrin-like with transmembrane domains 1"""	ANKTM1		16382100	Standard	NM_007332		Approved		uc003xza.3	O75762	OTTHUMG00000164516	ENST00000262209.4:c.1997C>A	chr8.hg19:g.72958812G>T	ENSP00000262209:p.Pro666Gln	37.0	0.0		39.0	4.0	NM_007332	A6NIN6	Missense_Mutation	SNP	ENST00000262209.4	hg19	CCDS34908.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.807389	0.50421	.	.	ENSG00000104321	ENST00000523582;ENST00000262209	T;T	0.78126	-1.15;-1.15	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	D	0.87888	0.6291	M	0.76574	2.34	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88096	0.2816	10	0.48119	T	0.1	-12.8801	18.3975	0.90504	0.0:0.0:1.0:0.0	.	666	O75762	TRPA1_HUMAN	Q	518;666	ENSP00000428151:P518Q;ENSP00000262209:P666Q	ENSP00000262209:P666Q	P	-	2	0	TRPA1	73121366	1.000000	0.71417	0.528000	0.27938	0.079000	0.17450	7.635000	0.83286	2.402000	0.81655	0.555000	0.69702	CCA	.	.		0.299	TRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379079.2	NM_007332	
SLC26A7	115111	hgsc.bcm.edu	37	8	92352644	92352644	+	Silent	SNP	T	T	A	rs373170016		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:92352644T>A	ENST00000276609.3	+	8	1130	c.891T>A	c.(889-891)ccT>ccA	p.P297P	SLC26A7_ENST00000309536.2_Silent_p.P297P|SLC26A7_ENST00000523719.1_Silent_p.P297P	NM_001282356.1|NM_052832.2	NP_001269285.1|NP_439897.1			solute carrier family 26 (anion exchanger), member 7											breast(1)|cervix(1)|endometrium(4)|large_intestine(10)|lung(26)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	50			BRCA - Breast invasive adenocarcinoma(11;0.00802)			TTCCCTCACCTAGAGCTCCCC	0.458																																					p.P297P		Atlas-SNP	.											.	SLC26A7	207	.	0			c.T891A						.						113.0	102.0	106.0					8																	92352644		2203	4300	6503	SO:0001819	synonymous_variant	115111	exon8			CTCACCTAGAGCT	AF331521	CCDS6254.1, CCDS6255.1, CCDS75765.1	8q23	2013-07-18	2013-07-18		ENSG00000147606	ENSG00000147606		"""Solute carriers"""	14467	protein-coding gene	gene with protein product		608479	"""solute carrier family 26, member 7"""			11834742, 11829495, 16524946	Standard	NM_134266		Approved	SUT2	uc003yez.3	Q8TE54	OTTHUMG00000164062	ENST00000276609.3:c.891T>A	chr8.hg19:g.92352644T>A		152.0	0.0		219.0	13.0	NM_134266		Silent	SNP	ENST00000276609.3	hg19	CCDS6254.1	.	.	.	.	.	.	.	.	.	.	T	1.066	-0.671378	0.03403	.	.	ENSG00000147606	ENST00000520818	.	.	.	6.02	-6.47	0.01902	.	.	.	.	.	T	0.37679	0.1012	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40961	-0.9535	4	.	.	.	.	2.907	0.05723	0.3567:0.3614:0.166:0.1159	.	.	.	.	Q	165	.	.	L	+	2	0	SLC26A7	92421820	0.000000	0.05858	0.035000	0.18076	0.195000	0.23768	-0.989000	0.03736	-1.065000	0.03168	0.533000	0.62120	CTA	.	.		0.458	SLC26A7-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377011.1		
TRHR	7201	hgsc.bcm.edu	37	8	110099893	110099893	+	Missense_Mutation	SNP	T	T	C	rs144587571		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:110099893T>C	ENST00000518632.1	+	2	503	c.152T>C	c.(151-153)aTg>aCg	p.M51T	TRHR_ENST00000311762.2_Missense_Mutation_p.M51T			P34981	TRFR_HUMAN	thyrotropin-releasing hormone receptor	51					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thyrotropin-releasing hormone receptor activity (GO:0004997)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(12)|prostate(4)|skin(4)|urinary_tract(1)	37			OV - Ovarian serous cystadenocarcinoma(57;2.3e-11)			CTGGTTGTCATGAGAACCAAG	0.522																																					p.M51T		Atlas-SNP	.											.	TRHR	74	.	0			c.T152C						.						154.0	137.0	143.0					8																	110099893		2203	4300	6503	SO:0001583	missense	7201	exon1			TTGTCATGAGAAC		CCDS6311.1	8q23.1	2013-09-20			ENSG00000174417	ENSG00000174417			12299	protein-coding gene	gene with protein product		188545				8128317	Standard	NM_003301		Approved		uc003ymz.4	P34981	OTTHUMG00000164910	ENST00000518632.1:c.152T>C	chr8.hg19:g.110099893T>C	ENSP00000430711:p.Met51Thr	183.0	0.0		237.0	101.0	NM_003301	Q2M339	Missense_Mutation	SNP	ENST00000518632.1	hg19	CCDS6311.1	.	.	.	.	.	.	.	.	.	.	T	13.99	2.402429	0.42613	.	.	ENSG00000174417	ENST00000518632;ENST00000311762	T;T	0.35421	1.31;1.31	5.85	5.85	0.93711	GPCR, rhodopsin-like superfamily (1);	0.257307	0.45126	D	0.000391	T	0.20861	0.0502	N	0.04245	-0.25	0.40689	D	0.982372	B	0.02656	0.0	B	0.04013	0.001	T	0.06373	-1.0830	10	0.42905	T	0.14	-10.4335	15.4167	0.74974	0.0:0.0:0.0:1.0	.	51	P34981	TRFR_HUMAN	T	51	ENSP00000430711:M51T;ENSP00000309818:M51T	ENSP00000309818:M51T	M	+	2	0	TRHR	110169069	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	6.264000	0.72527	2.238000	0.73509	0.533000	0.62120	ATG	.	T|1.000;G|0.000		0.522	TRHR-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380892.1		
TSNARE1	203062	hgsc.bcm.edu	37	8	143425738	143425738	+	Missense_Mutation	SNP	G	G	A	rs199897318		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr8:143425738G>A	ENST00000307180.3	-	4	451	c.334C>T	c.(334-336)Cgg>Tgg	p.R112W	TSNARE1_ENST00000520166.1_Missense_Mutation_p.R112W|TSNARE1_ENST00000519651.1_Intron|TSNARE1_ENST00000524325.1_Missense_Mutation_p.R112W	NM_145003.3	NP_659440.2	Q96NA8	TSNA1_HUMAN	t-SNARE domain containing 1	112					intracellular protein transport (GO:0006886)|synaptic vesicle exocytosis (GO:0016079)	integral component of membrane (GO:0016021)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)|SNARE binding (GO:0000149)			breast(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(6)|ovary(2)|stomach(2)|urinary_tract(1)	20	all_cancers(97;7.39e-11)|all_epithelial(106;8.98e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000332)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					CCCGCCATCCGGCCATGGGGC	0.677													G|||	1	0.000199681	0.0	0.0014	5008	,	,		11782	0.0		0.0	False		,,,				2504	0.0				p.R112W		Atlas-SNP	.											TSNARE1,caecum,carcinoma,0,1	TSNARE1	59	.	0			c.C334T						.	G	TRP/ARG	3,4305		0,3,2151	7.0	10.0	9.0		334	-4.4	0.0	8		9	0,8446		0,0,4223	yes	missense	TSNARE1	NM_145003.3	101	0,3,6374	AA,AG,GG		0.0,0.0696,0.0235	probably-damaging	112/514	143425738	3,12751	2154	4223	6377	SO:0001583	missense	203062	exon4			CCATCCGGCCATG			8q24.3	2005-08-18							26437	protein-coding gene	gene with protein product						14702039	Standard	XM_005250828		Approved	FLJ31164	uc003ywk.3	Q96NA8		ENST00000307180.3:c.334C>T	chr8.hg19:g.143425738G>A	ENSP00000303437:p.Arg112Trp	83.0	0.0		65.0	3.0	NM_145003	B7ZLB0|Q14D03	Missense_Mutation	SNP	ENST00000307180.3	hg19	CCDS6384.1	.	.	.	.	.	.	.	.	.	.	G	10.78	1.447714	0.26074	6.96E-4	0.0	ENSG00000171045	ENST00000524325;ENST00000307180;ENST00000520166;ENST00000520462;ENST00000518720	T;T;T;T;T	0.24538	2.72;2.72;2.72;1.87;1.85	3.64	-4.4	0.03600	.	0.352416	0.14877	U	0.293184	T	0.19765	0.0475	L	0.27053	0.805	0.09310	N	1	D;D;D	0.69078	0.997;0.997;0.997	P;P;P	0.55999	0.789;0.789;0.789	T	0.11867	-1.0570	10	0.87932	D	0	-5.0028	1.1029	0.01687	0.2036:0.1252:0.3468:0.3244	.	112;112;112	B7ZLB0;Q96NA8;A0AVG3	.;TSNA1_HUMAN;.	W	112;112;112;112;128	ENSP00000428763:R112W;ENSP00000303437:R112W;ENSP00000427770:R112W;ENSP00000429626:R112W;ENSP00000430789:R128W	ENSP00000303437:R112W	R	-	1	2	TSNARE1	143423645	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.266000	0.08631	-0.513000	0.06496	-0.346000	0.07831	CGG	.	.		0.677	TSNARE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_145003	
TAF1L	138474	hgsc.bcm.edu	37	9	32630489	32630489	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:32630489T>C	ENST00000242310.4	-	1	5178	c.5089A>G	c.(5089-5091)Act>Gct	p.T1697A	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1697					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		GGAGTGGCAGTGGAAATATCC	0.478																																					p.T1697A		Atlas-SNP	.											.	TAF1L	382	.	0			c.A5089G						.						171.0	156.0	161.0					9																	32630489		2203	4300	6503	SO:0001583	missense	138474	exon1			TGGCAGTGGAAAT	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.5089A>G	chr9.hg19:g.32630489T>C	ENSP00000418379:p.Thr1697Ala	281.0	0.0		215.0	36.0	NM_153809	Q0VG57	Missense_Mutation	SNP	ENST00000242310.4	hg19	CCDS35003.1	.	.	.	.	.	.	.	.	.	.	T	9.376	1.071662	0.20147	.	.	ENSG00000122728	ENST00000242310	T	0.06371	3.31	0.479	0.479	0.16796	.	0.621996	0.17394	N	0.175836	T	0.03434	0.0099	N	0.22421	0.69	0.18873	N	0.999983	B	0.02656	0.0	B	0.01281	0.0	T	0.45920	-0.9228	10	0.14656	T	0.56	.	5.1959	0.15236	0.0:1.0E-4:0.0:0.9999	.	1697	Q8IZX4	TAF1L_HUMAN	A	1697	ENSP00000418379:T1697A	ENSP00000418379:T1697A	T	-	1	0	TAF1L	32620489	1.000000	0.71417	0.971000	0.41717	0.194000	0.23727	0.684000	0.25364	0.426000	0.26116	0.164000	0.16699	ACT	.	.		0.478	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
NOL6	65083	hgsc.bcm.edu	37	9	33466415	33466415	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:33466415T>A	ENST00000379471.2	-	17	2187	c.2100A>T	c.(2098-2100)ccA>ccT	p.P700P	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Silent_p.P648P			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	700					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CTGGAGTTGGTGGGAACACCT	0.612											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P700P		Atlas-SNP	.											.	NOL6	85	.	0			c.A2100T						.						88.0	84.0	86.0					9																	33466415		2203	4300	6503	SO:0001819	synonymous_variant	65083	exon17			AGTTGGTGGGAAC	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.2100A>T	chr9.hg19:g.33466415T>A		186.0	0.0	840	169.0	72.0	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Silent	SNP	ENST00000379471.2	hg19																																																																																				.	.		0.612	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
ZNF462	58499	hgsc.bcm.edu	37	9	109734475	109734475	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:109734475T>A	ENST00000277225.5	+	8	6906	c.6617T>A	c.(6616-6618)aTc>aAc	p.I2206N	ZNF462_ENST00000457913.1_Missense_Mutation_p.I2266N|ZNF462_ENST00000441147.2_Missense_Mutation_p.I1112N|ZNF462_ENST00000542028.1_Missense_Mutation_p.I163N|RP11-508N12.2_ENST00000439901.1_RNA			Q96JM2	ZN462_HUMAN	zinc finger protein 462	2206					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						ATCCAGAGCATCAGGCGTCAT	0.502																																					p.I2206N		Atlas-SNP	.											.	ZNF462	322	.	0			c.T6617A						.						97.0	92.0	94.0					9																	109734475		2203	4300	6503	SO:0001583	missense	58499	exon8			AGAGCATCAGGCG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.6617T>A	chr9.hg19:g.109734475T>A	ENSP00000277225:p.Ile2206Asn	323.0	0.0		229.0	16.0	NM_021224	Q5T0T4|Q8N408	Missense_Mutation	SNP	ENST00000277225.5	hg19	CCDS35096.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	28.0|28.0	4.878950|4.878950	0.91740|0.91740	.|.	.|.	ENSG00000148143|ENSG00000148143	ENST00000427098|ENST00000277225;ENST00000457913;ENST00000374686;ENST00000441147;ENST00000542028	.|T;T;T;T;T	.|0.28895	.|1.59;1.59;1.59;1.59;1.59	6.13|6.13	6.13|6.13	0.99165|0.99165	.|Zinc finger, C2H2-like (1);	.|0.062819	.|0.64402	.|D	.|0.000002	T|T	0.52041|0.52041	0.1710|0.1710	L|L	0.52905|0.52905	1.665|1.665	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.76494	.|0.998;0.999;0.998	.|P;D;P	.|0.71184	.|0.905;0.972;0.896	T|T	0.51965|0.51965	-0.8638|-0.8638	5|10	.|0.87932	.|D	.|0	.|.	16.8061|16.8061	0.85666|0.85666	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|2266;107;2206	.|Q96JM2-3;Q5T0T2;Q96JM2	.|.;.;ZN462_HUMAN	Q|N	107|2206;2266;1149;1112;163	.|ENSP00000277225:I2206N;ENSP00000414570:I2266N;ENSP00000363818:I1149N;ENSP00000397306:I1112N;ENSP00000439771:I163N	.|ENSP00000277225:I2206N	H|I	+|+	3|2	2|0	ZNF462|ZNF462	108774296|108774296	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.946000|0.946000	0.59487|0.59487	7.662000|7.662000	0.83803|0.83803	2.367000|2.367000	0.80283|0.80283	0.529000|0.529000	0.55759|0.55759	CAT|ATC	.	.		0.502	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
TNC	3371	hgsc.bcm.edu	37	9	117844994	117844994	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:117844994A>T	ENST00000350763.4	-	5	2635	c.2224T>A	c.(2224-2226)Tgg>Agg	p.W742R	TNC_ENST00000346706.3_Missense_Mutation_p.W742R|TNC_ENST00000340094.3_Missense_Mutation_p.W742R|TNC_ENST00000542877.1_Missense_Mutation_p.W742R|TNC_ENST00000423613.2_Missense_Mutation_p.W742R|TNC_ENST00000535648.1_Missense_Mutation_p.W742R|TNC_ENST00000537320.1_Missense_Mutation_p.W742R|TNC_ENST00000345230.3_Missense_Mutation_p.W742R|TNC_ENST00000341037.4_Missense_Mutation_p.W742R	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	742	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						ATGATCTCCCAGGTTTCAAAA	0.433																																					p.W742R		Atlas-SNP	.											.	TNC	282	.	0			c.T2224A						.						117.0	109.0	111.0					9																	117844994		2203	4300	6503	SO:0001583	missense	3371	exon5			TCTCCCAGGTTTC		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.2224T>A	chr9.hg19:g.117844994A>T	ENSP00000265131:p.Trp742Arg	198.0	0.0		146.0	61.0	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	hg19	CCDS6811.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210080	0.79240	.	.	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	T;T;T;T;T;T;T;T;T	0.53857	0.6;0.61;0.6;0.61;0.61;0.61;0.61;0.61;0.61	5.88	5.88	0.94601	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.73916	0.3648	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.77469	-0.2576	10	0.87932	D	0	.	16.268	0.82600	1.0:0.0:0.0:0.0	.	742;742	E9PC84;P24821	.;TENA_HUMAN	R	742	ENSP00000344400:W742R;ENSP00000438152:W742R;ENSP00000344555:W742R;ENSP00000345861:W742R;ENSP00000265131:W742R;ENSP00000339553:W742R;ENSP00000411406:W742R;ENSP00000443478:W742R;ENSP00000442242:W742R	ENSP00000344400:W742R	W	-	1	0	TNC	116884815	1.000000	0.71417	0.944000	0.38274	0.708000	0.40852	9.339000	0.96797	2.240000	0.73641	0.533000	0.62120	TGG	.	.		0.433	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
LHX6	26468	hgsc.bcm.edu	37	9	124979380	124979380	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:124979380T>A	ENST00000373755.2	-	4	670	c.562A>T	c.(562-564)Atg>Ttg	p.M188L	LHX6_ENST00000559895.1_Start_Codon_SNP_p.M1L|LHX6_ENST00000373754.2_Missense_Mutation_p.M188L|LHX6_ENST00000541397.2_Missense_Mutation_p.M206L|LHX6_ENST00000394319.4_Missense_Mutation_p.M217L|LHX6_ENST00000340587.3_Missense_Mutation_p.M217L	NM_001242334.1	NP_001229263.1	Q9UPM6	LHX6_HUMAN	LIM homeobox 6	188	Required for interaction with LDB1. {ECO:0000250}.				cell maturation (GO:0048469)|cerebral cortex GABAergic interneuron migration (GO:0021853)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|forebrain neuron fate commitment (GO:0021877)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(5)	8						TTCTCAATCATGGTGTCGTAG	0.652																																					p.M217L		Atlas-SNP	.											.	LHX6	73	.	0			c.A649T						.						90.0	81.0	84.0					9																	124979380		2203	4300	6503	SO:0001583	missense	26468	exon5			CAATCATGGTGTC	AB031041	CCDS6837.2, CCDS6838.2, CCDS56583.1, CCDS56584.1, CCDS59144.1	9q33.2	2011-06-20			ENSG00000106852	ENSG00000106852		"""Homeoboxes / LIM class"""	21735	protein-coding gene	gene with protein product		608215				10393337	Standard	NM_014368		Approved	LHX6.1	uc004blx.4	Q9UPM6	OTTHUMG00000020601	ENST00000373755.2:c.562A>T	chr9.hg19:g.124979380T>A	ENSP00000362860:p.Met188Leu	200.0	0.0		126.0	8.0	NM_014368	A6PVQ1|A6PVQ2|A8K1B2|B7Z4D0|H0YN76|Q5T7S7|Q5T7S8|Q9NTK3|Q9UPM5	Missense_Mutation	SNP	ENST00000373755.2	hg19	CCDS56583.1	.	.	.	.	.	.	.	.	.	.	T	24.6	4.554457	0.86231	.	.	ENSG00000106852	ENST00000373755;ENST00000373754;ENST00000394319;ENST00000340587;ENST00000541397	D;D;D;D;D	0.85484	-1.99;-1.96;-1.89;-1.83;-1.89	5.87	5.87	0.94306	Zinc finger, LIM-type (2);	0.000000	0.85682	D	0.000000	T	0.78660	0.4318	N	0.26042	0.785	0.80722	D	1	B;B;B	0.27264	0.173;0.024;0.144	B;B;B	0.36186	0.071;0.029;0.219	T	0.72584	-0.4249	10	0.07482	T	0.82	.	15.45	0.75265	0.0:0.0:0.0:1.0	.	188;217;217	Q9UPM6;Q9UPM6-4;Q9UPM6-3	LHX6_HUMAN;.;.	L	188;188;217;217;206	ENSP00000362860:M188L;ENSP00000362859:M188L;ENSP00000377854:M217L;ENSP00000340137:M217L;ENSP00000441464:M206L	ENSP00000340137:M217L	M	-	1	0	LHX6	124019201	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.698000	0.84413	2.244000	0.73946	0.533000	0.62120	ATG	.	.		0.652	LHX6-002	KNOWN	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053924.2	NM_014368	
GLE1	2733	hgsc.bcm.edu	37	9	131287658	131287658	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:131287658A>G	ENST00000309971.4	+	7	1191	c.1085A>G	c.(1084-1086)gAg>gGg	p.E362G	GLE1_ENST00000539582.1_Missense_Mutation_p.E108G|GLE1_ENST00000494417.1_3'UTR|GLE1_ENST00000372770.4_Missense_Mutation_p.E362G	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	362					mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						GCCCACAAAGAGCCCCCAGCT	0.537																																					p.E362G		Atlas-SNP	.											.	GLE1	42	.	0			c.A1085G						.						40.0	40.0	40.0					9																	131287658		2200	4299	6499	SO:0001583	missense	2733	exon7			ACAAAGAGCCCCC	AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"""GLE1 (yeast homolog)-like, RNA export mediator"", ""GLE1 RNA export mediator-like (yeast)"", ""GLE1 RNA export mediator (yeast)"", ""lethal congenital contracture syndrome 1"", ""GLE1 RNA export mediator homolog (yeast)"""	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.1085A>G	chr9.hg19:g.131287658A>G	ENSP00000308622:p.Glu362Gly	102.0	0.0		82.0	28.0	NM_001499	O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	hg19	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	A	10.00	1.233194	0.22626	.	.	ENSG00000119392	ENST00000309971;ENST00000372770;ENST00000539582	T;T;T	0.79247	-0.27;0.15;-1.25	5.59	1.79	0.24919	.	0.876442	0.10354	N	0.684813	T	0.67135	0.2861	L	0.43152	1.355	0.09310	N	1	B;B	0.31625	0.224;0.332	B;B	0.29598	0.055;0.104	T	0.52079	-0.8623	10	0.35671	T	0.21	-2.2002	7.1116	0.25392	0.6462:0.2797:0.0741:0.0	.	362;362	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	G	362;362;108	ENSP00000308622:E362G;ENSP00000361856:E362G;ENSP00000438670:E108G	ENSP00000308622:E362G	E	+	2	0	GLE1	130327479	0.998000	0.40836	0.000000	0.03702	0.744000	0.42396	3.423000	0.52756	0.057000	0.16193	0.379000	0.24179	GAG	.	.		0.537	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1	NM_001003722	
CRAT	1384	hgsc.bcm.edu	37	9	131860591	131860591	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:131860591G>A	ENST00000318080.2	-	10	1559	c.1265C>T	c.(1264-1266)cCc>cTc	p.P422L	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	422					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	CTCCGACTTGGGGAAGTCTTT	0.587																																					p.P422L		Atlas-SNP	.											.	CRAT	43	.	0			c.C1265T						.						87.0	85.0	86.0					9																	131860591		2203	4300	6503	SO:0001583	missense	1384	exon10			GACTTGGGGAAGT	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1265C>T	chr9.hg19:g.131860591G>A	ENSP00000315013:p.Pro422Leu	202.0	0.0		179.0	28.0	NM_000755	Q5T952|Q9BW16	Missense_Mutation	SNP	ENST00000318080.2	hg19	CCDS6919.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.859754	0.51376	.	.	ENSG00000095321	ENST00000351352;ENST00000318080	D	0.87966	-2.32	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.89065	0.6609	L	0.35723	1.085	0.80722	D	1	P	0.48834	0.916	P	0.58454	0.839	D	0.88299	0.2948	10	0.41790	T	0.15	-40.7892	17.7377	0.88399	0.0:0.0:1.0:0.0	.	422	P43155	CACP_HUMAN	L	341;422	ENSP00000315013:P422L	ENSP00000315013:P422L	P	-	2	0	CRAT	130900412	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	9.657000	0.98554	2.667000	0.90743	0.561000	0.74099	CCC	.	.		0.587	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1		
AK8	158067	hgsc.bcm.edu	37	9	135739158	135739158	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr9:135739158C>T	ENST00000298545.3	-	4	748	c.227G>A	c.(226-228)tGg>tAg	p.W76*	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	76	Adenylate kinase 1.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						TTTGCAGAGCCACATTGCCTG	0.423																																					p.W76X		Atlas-SNP	.											.	AK8	45	.	0			c.G227A						.						74.0	67.0	69.0					9																	135739158		2203	4300	6503	SO:0001587	stop_gained	158067	exon4			CAGAGCCACATTG	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.227G>A	chr9.hg19:g.135739158C>T	ENSP00000298545:p.Trp76*	136.0	0.0		127.0	17.0	NM_152572	A8K821|Q8N9W9	Nonsense_Mutation	SNP	ENST00000298545.3	hg19	CCDS6954.1	.	.	.	.	.	.	.	.	.	.	C	41	9.072439	0.99057	.	.	ENSG00000165695	ENST00000298545	.	.	.	5.05	5.05	0.67936	.	0.315252	0.30565	N	0.009346	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-16.959	12.8217	0.57696	0.1633:0.8367:0.0:0.0	.	.	.	.	X	76	.	ENSP00000298545:W76X	W	-	2	0	AK8	134728979	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	3.043000	0.49823	2.492000	0.84095	0.563000	0.77884	TGG	.	.		0.423	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
ITIH5	80760	hgsc.bcm.edu	37	10	7627889	7627889	+	Nonsense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:7627889G>T	ENST00000256861.6	-	8	1161	c.1083C>A	c.(1081-1083)taC>taA	p.Y361*	ITIH5_ENST00000298441.6_Nonsense_Mutation_p.Y147*|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397145.2_Nonsense_Mutation_p.Y361*|ITIH5_ENST00000446830.2_Nonsense_Mutation_p.Y143*|ITIH5_ENST00000397146.2_Nonsense_Mutation_p.Y361*	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	361	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						TATGGTGAATGTACACTTTCC	0.383																																					p.Y361X		Atlas-SNP	.											ITIH5_ENST00000397145,NS,carcinoma,0,2	ITIH5	343	.	0			c.C1083A						.						180.0	144.0	156.0					10																	7627889		2203	4300	6503	SO:0001587	stop_gained	80760	exon8			GTGAATGTACACT			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.1083C>A	chr10.hg19:g.7627889G>T	ENSP00000256861:p.Tyr361*	305.0	1.0		410.0	79.0	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Nonsense_Mutation	SNP	ENST00000256861.6	hg19		.	.	.	.	.	.	.	.	.	.	G	36	5.846805	0.97016	.	.	ENSG00000123243	ENST00000256861;ENST00000397146;ENST00000298441;ENST00000446830;ENST00000397145	.	.	.	5.3	2.36	0.29203	.	0.054481	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.7311	8.7698	0.34724	0.3863:0.0:0.6137:0.0	.	.	.	.	X	361;361;147;143;361	.	ENSP00000256861:Y361X	Y	-	3	2	ITIH5	7667895	1.000000	0.71417	0.992000	0.48379	0.836000	0.47400	1.685000	0.37659	0.200000	0.20447	0.561000	0.74099	TAC	.	.		0.383	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
MYO3A	53904	hgsc.bcm.edu	37	10	26462749	26462749	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:26462749T>A	ENST00000265944.5	+	30	3722	c.3556T>A	c.(3556-3558)Tat>Aat	p.Y1186N	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1186					ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CAACAGAGTGTATCAGACTCC	0.398																																					p.Y1186N		Atlas-SNP	.											.	MYO3A	371	.	0			c.T3556A						.						69.0	67.0	68.0					10																	26462749		2203	4300	6503	SO:0001583	missense	53904	exon30			AGAGTGTATCAGA	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3556T>A	chr10.hg19:g.26462749T>A	ENSP00000265944:p.Tyr1186Asn	109.0	0.0		122.0	11.0	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	hg19	CCDS7148.1	.	.	.	.	.	.	.	.	.	.	T	4.270	0.049165	0.08243	.	.	ENSG00000095777	ENST00000265944	T	0.76448	-1.02	5.29	1.69	0.24217	.	1.446850	0.03518	N	0.220553	T	0.67069	0.2854	L	0.27053	0.805	0.19575	N	0.999961	B	0.24823	0.112	B	0.21360	0.034	T	0.51196	-0.8736	10	0.28530	T	0.3	.	8.7328	0.34510	0.0:0.2236:0.0:0.7764	.	1186	Q8NEV4	MYO3A_HUMAN	N	1186	ENSP00000265944:Y1186N	ENSP00000265944:Y1186N	Y	+	1	0	MYO3A	26502755	0.000000	0.05858	0.016000	0.15963	0.024000	0.10985	0.491000	0.22419	0.413000	0.25759	0.533000	0.62120	TAT	.	.		0.398	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
PDSS1	23590	hgsc.bcm.edu	37	10	27024491	27024491	+	Silent	SNP	C	C	T	rs541206852		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:27024491C>T	ENST00000376215.5	+	10	1062	c.1009C>T	c.(1009-1011)Ctg>Ttg	p.L337L	PDSS1_ENST00000470978.1_3'UTR|PDSS1_ENST00000376203.5_Intron	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	337					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						TGGTCCTGTCCTGTTTGCCTG	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		21830	0.0		0.0	False		,,,				2504	0.001				p.L337L		Atlas-SNP	.											.	PDSS1	36	.	0			c.C1009T						.						118.0	104.0	109.0					10																	27024491		2203	4300	6503	SO:0001819	synonymous_variant	23590	exon10			CCTGTCCTGTTTG	AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"""coenzyme Q1 homolog (yeast)"""	607429	"""trans-prenyltransferase"""	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1009C>T	chr10.hg19:g.27024491C>T		199.0	0.0		331.0	85.0	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Silent	SNP	ENST00000376215.5	hg19	CCDS31168.1																																																																																			.	.		0.507	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1		
OIT3	170392	hgsc.bcm.edu	37	10	74660156	74660156	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:74660156A>T	ENST00000334011.5	+	3	676	c.458A>T	c.(457-459)gAg>gTg	p.E153V		NM_152635.1	NP_689848.1	Q8WWZ8	OIT3_HUMAN	oncoprotein induced transcript 3	153						nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|liver(2)|lung(14)|ovary(2)|prostate(1)|skin(2)	35	Prostate(51;0.0198)					ATCTGCGACGAGGACTGCCAT	0.483																																					p.E153V	Colon(7;19 345 13446 17537)	Atlas-SNP	.											.	OIT3	62	.	0			c.A458T						.						51.0	49.0	49.0					10																	74660156		2203	4300	6503	SO:0001583	missense	170392	exon3			GCGACGAGGACTG		CCDS7318.1	10q22.2-q22.3	2004-04-21			ENSG00000138315	ENSG00000138315			29953	protein-coding gene	gene with protein product		609330				12975309, 12939600	Standard	NM_152635		Approved	LZP, FLJ39116	uc001jte.1	Q8WWZ8	OTTHUMG00000018444	ENST00000334011.5:c.458A>T	chr10.hg19:g.74660156A>T	ENSP00000333900:p.Glu153Val	113.0	0.0		120.0	35.0	NM_152635	A0AVP3|Q8N1M8	Missense_Mutation	SNP	ENST00000334011.5	hg19	CCDS7318.1	.	.	.	.	.	.	.	.	.	.	A	13.29	2.193942	0.38707	.	.	ENSG00000138315	ENST00000334011;ENST00000415725	T	0.40476	1.03	5.22	4.03	0.46877	.	0.542530	0.16138	N	0.227863	T	0.16214	0.0390	N	0.02539	-0.55	0.26426	N	0.976028	B	0.02656	0.0	B	0.06405	0.002	T	0.16012	-1.0417	10	0.15066	T	0.55	-17.7355	7.9603	0.30068	0.7248:0.0:0.0:0.2752	.	153	Q8WWZ8	OIT3_HUMAN	V	153	ENSP00000333900:E153V	ENSP00000333900:E153V	E	+	2	0	OIT3	74330162	1.000000	0.71417	0.999000	0.59377	0.843000	0.47879	3.809000	0.55606	2.197000	0.70478	0.528000	0.53228	GAG	.	.		0.483	OIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048596.1	NM_152635	
ANXA7	310	hgsc.bcm.edu	37	10	75147463	75147463	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:75147463T>A	ENST00000372921.5	-	7	673	c.617A>T	c.(616-618)aAg>aTg	p.K206M	ANXA7_ENST00000535178.1_Missense_Mutation_p.K76M|ANXA7_ENST00000492380.1_5'UTR	NM_001156.3	NP_001147.1	P20073	ANXA7_HUMAN	annexin A7	228					autophagy (GO:0006914)|cell proliferation (GO:0008283)|cellular calcium ion homeostasis (GO:0006874)|cellular water homeostasis (GO:0009992)|epithelial cell differentiation (GO:0030855)|hemostasis (GO:0007599)|membrane fusion (GO:0061025)|negative regulation of gene expression (GO:0010629)|regulation of cell shape (GO:0008360)|response to calcium ion (GO:0051592)|response to organic cyclic compound (GO:0014070)|response to salt stress (GO:0009651)|social behavior (GO:0035176)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|calcium-dependent protein binding (GO:0048306)|integrin binding (GO:0005178)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	26	Prostate(51;0.0119)					ATAGGAGGTCTTAAATGCTGC	0.428																																					p.K228M		Atlas-SNP	.											.	ANXA7	50	.	0			c.A683T						.						217.0	206.0	210.0					10																	75147463		2203	4300	6503	SO:0001583	missense	310	exon8			GAGGTCTTAAATG	J04543	CCDS7325.1, CCDS7326.1	10q22.2	2005-11-09			ENSG00000138279	ENSG00000138279		"""Annexins"""	545	protein-coding gene	gene with protein product		186360		ANX7		7515686	Standard	NM_001156		Approved		uc001jtz.2	P20073	OTTHUMG00000018463	ENST00000372921.5:c.617A>T	chr10.hg19:g.75147463T>A	ENSP00000362012:p.Lys206Met	213.0	0.0		255.0	31.0	NM_004034	Q5F2H3|Q5T0M6|Q5T0M7	Missense_Mutation	SNP	ENST00000372921.5	hg19	CCDS7325.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.437420	0.83885	.	.	ENSG00000138279	ENST00000372921;ENST00000372919;ENST00000535178	T;T;T	0.06608	3.28;3.28;3.28	5.96	5.96	0.96718	Annexin repeat, conserved site (1);	0.146548	0.47455	D	0.000227	T	0.30166	0.0756	M	0.87097	2.86	0.58432	D	0.999994	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.996;0.993;0.988;0.993	T	0.06734	-1.0810	10	0.87932	D	0	.	14.3967	0.67015	0.0:0.0:0.0:1.0	.	206;206;133;206;228	Q53HM8;B2R7L2;B4DWU2;P20073-2;P20073	.;.;.;.;ANXA7_HUMAN	M	206;228;76	ENSP00000362012:K206M;ENSP00000362010:K228M;ENSP00000442864:K76M	ENSP00000362010:K228M	K	-	2	0	ANXA7	74817469	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.190000	0.72057	2.284000	0.76573	0.528000	0.53228	AAG	.	.		0.428	ANXA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048646.2	NM_001156	
MYOF	26509	hgsc.bcm.edu	37	10	95116494	95116494	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:95116494T>A	ENST00000359263.4	-	30	3231	c.3232A>T	c.(3232-3234)Aga>Tga	p.R1078*	MYOF_ENST00000371502.4_Nonsense_Mutation_p.R1078*|MYOF_ENST00000358334.5_Nonsense_Mutation_p.R1065*|MYOF_ENST00000371501.4_Nonsense_Mutation_p.R1078*	NM_013451.3	NP_038479.1	Q9NZM1	MYOF_HUMAN	myoferlin	1078	Poly-Arg.				blood circulation (GO:0008015)|cellular response to heat (GO:0034605)|muscle contraction (GO:0006936)|plasma membrane repair (GO:0001778)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)	caveola (GO:0005901)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)			NS(2)|autonomic_ganglia(1)|breast(3)|endometrium(7)|kidney(7)|large_intestine(15)|lung(14)|ovary(4)|prostate(4)|skin(6)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						GCCATTTTTCTCCTCCAGCGT	0.473																																					p.R1078X		Atlas-SNP	.											.	MYOF	177	.	0			c.A3232T						.						120.0	112.0	115.0					10																	95116494		1913	4121	6034	SO:0001587	stop_gained	26509	exon30			TTTTTCTCCTCCA	AB033033	CCDS41550.1, CCDS41551.1	10q24	2014-06-27	2008-11-26	2008-11-26	ENSG00000138119	ENSG00000138119			3656	protein-coding gene	gene with protein product	"""fer-1-like family member 3"""	604603	"""fer-1 (C.elegans)-like 3 (myoferlin)"", ""fer-1-like 3, myoferlin (C. elegans)"""	FER1L3		10607832, 10995573, 17702744	Standard	NM_013451		Approved	KIAA1207	uc001kin.3	Q9NZM1	OTTHUMG00000018772	ENST00000359263.4:c.3232A>T	chr10.hg19:g.95116494T>A	ENSP00000352208:p.Arg1078*	218.0	0.0		213.0	14.0	NM_013451	B3KQN5|Q5VWW2|Q5VWW3|Q5VWW4|Q5VWW5|Q7Z642|Q8IWH0|Q9HBU3|Q9NZM0|Q9ULL3|Q9Y4U4	Nonsense_Mutation	SNP	ENST00000359263.4	hg19	CCDS41551.1	.	.	.	.	.	.	.	.	.	.	T	44	10.772633	0.99465	.	.	ENSG00000138119	ENST00000358334;ENST00000359263;ENST00000371501;ENST00000371502	.	.	.	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-24.1745	12.9678	0.58494	0.0:0.0:0.1436:0.8564	.	.	.	.	X	1065;1078;1078;1078	.	ENSP00000351094:R1065X	R	-	1	2	MYOF	95106484	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.224000	0.65288	2.253000	0.74438	0.454000	0.30748	AGA	.	.		0.473	MYOF-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049423.2	NM_013451	
SFXN4	119559	hgsc.bcm.edu	37	10	120914639	120914639	+	Nonsense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr10:120914639T>A	ENST00000355697.2	-	11	686	c.667A>T	c.(667-669)Aag>Tag	p.K223*	SFXN4_ENST00000330036.6_Nonsense_Mutation_p.K214*|SFXN4_ENST00000461438.1_5'UTR	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	223					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		GCAATCCCCTTAATGGATTCA	0.468																																					p.K223X		Atlas-SNP	.											.	SFXN4	24	.	0			c.A667T						.						142.0	121.0	128.0					10																	120914639		2203	4300	6503	SO:0001587	stop_gained	119559	exon11			TCCCCTTAATGGA		CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"""Sideroflexins"""	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.667A>T	chr10.hg19:g.120914639T>A	ENSP00000347924:p.Lys223*	251.0	0.0		204.0	15.0	NM_213649	Q6WSU4|Q86TD9	Nonsense_Mutation	SNP	ENST00000355697.2	hg19	CCDS7610.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.774647	0.90108	.	.	ENSG00000183605	ENST00000355697;ENST00000330036;ENST00000392875;ENST00000369131	.	.	.	4.77	2.73	0.32206	.	0.855801	0.09976	N	0.731614	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.4705	9.8113	0.40824	0.0:0.0:0.5066:0.4934	.	.	.	.	X	223;214;106;107	.	ENSP00000333200:K214X	K	-	1	0	SFXN4	120904629	0.000000	0.05858	0.106000	0.21319	0.016000	0.09150	0.511000	0.22739	1.215000	0.43411	-0.226000	0.12346	AAG	.	.		0.468	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3	XM_058406	
UBQLNL	143630	hgsc.bcm.edu	37	11	5537570	5537570	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:5537570T>A	ENST00000380184.1	-	1	365	c.102A>T	c.(100-102)atA>atT	p.I34I	HBG2_ENST00000380259.2_Intron	NM_145053.4	NP_659490.4	Q8IYU4	UBQLN_HUMAN	ubiquilin-like	34	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.									endometrium(1)|kidney(3)|large_intestine(9)|lung(13)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	33		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.92e-09)|BRCA - Breast invasive adenocarcinoma(625;0.136)		CAGTCTTCACTATCACTCGAG	0.488																																					p.I34I		Atlas-SNP	.											.	UBQLNL	74	.	0			c.A102T						.						124.0	112.0	116.0					11																	5537570		2201	4297	6498	SO:0001819	synonymous_variant	143630	exon1			CTTCACTATCACT	AK127987	CCDS31385.1	11p15.4	2014-02-12			ENSG00000175518	ENSG00000175518		"""Ubiquilin family"""	28294	protein-coding gene	gene with protein product							Standard	NM_145053		Approved	MGC20470, MGC26958	uc001maz.4	Q8IYU4	OTTHUMG00000066903	ENST00000380184.1:c.102A>T	chr11.hg19:g.5537570T>A		110.0	0.0		138.0	10.0	NM_145053	Q6ZRU1|Q96EK3|Q96MB0	Silent	SNP	ENST00000380184.1	hg19	CCDS31385.1																																																																																			.	.		0.488	UBQLNL-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143386.1	NM_145053	
CCKBR	887	hgsc.bcm.edu	37	11	6291552	6291552	+	Missense_Mutation	SNP	G	G	A	rs200729292		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:6291552G>A	ENST00000334619.2	+	3	831	c.638G>A	c.(637-639)cGg>cAg	p.R213Q	CCKBR_ENST00000525462.1_Missense_Mutation_p.R213Q|CCKBR_ENST00000532715.1_Missense_Mutation_p.R129Q	NM_176875.3	NP_795344.1	P32239	GASR_HUMAN	cholecystokinin B receptor	213					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cholecystokinin signaling pathway (GO:0038188)|digestion (GO:0007586)|digestive tract development (GO:0048565)|feeding behavior (GO:0007631)|gastric acid secretion (GO:0001696)|gland development (GO:0048732)|metabolic process (GO:0008152)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|cholecystokinin receptor activity (GO:0004951)|gastrin receptor activity (GO:0015054)|phosphatidylinositol phospholipase C activity (GO:0004435)|type B gastrin/cholecystokinin receptor binding (GO:0031741)			NS(2)|breast(2)|endometrium(4)|kidney(13)|large_intestine(10)|lung(22)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	61		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.139)	Pentagastrin(DB00183)	CCCAGTGCGCGGGTCCGCCAG	0.582																																					p.R213Q		Atlas-SNP	.											CCKBR_ENST00000525462,right_upper_lobe,carcinoma,0,2	CCKBR	232	.	0			c.G638A						.						86.0	88.0	88.0					11																	6291552		2201	4296	6497	SO:0001583	missense	887	exon3			GTGCGCGGGTCCG	D13305	CCDS7761.1	11p15.4	2012-08-10			ENSG00000110148	ENSG00000110148		"""GPCR / Class A : Cholecystokinin receptors"""	1571	protein-coding gene	gene with protein product		118445				1280419	Standard	NM_176875		Approved		uc001mcp.3	P32239	OTTHUMG00000133380	ENST00000334619.2:c.638G>A	chr11.hg19:g.6291552G>A	ENSP00000335544:p.Arg213Gln	113.0	0.0		97.0	48.0	NM_176875	A8K7P9|O75824|Q16144|Q92492|Q96LC6|Q9NYK7|Q9UBV1	Missense_Mutation	SNP	ENST00000334619.2	hg19	CCDS7761.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.328675	0.24167	.	.	ENSG00000110148	ENST00000334619;ENST00000532715;ENST00000525462	T;T;T	0.37752	1.18;1.18;1.18	5.09	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.230162	0.38164	N	0.001783	T	0.25717	0.0626	N	0.10809	0.05	0.09310	N	1	D;B;B	0.76494	0.999;0.052;0.122	P;B;B	0.60012	0.867;0.019;0.058	T	0.13818	-1.0495	10	0.13108	T	0.6	.	3.9652	0.09428	0.3551:0.172:0.473:0.0	.	213;147;213	P32239-2;P32239-3;P32239	.;.;GASR_HUMAN	Q	213;129;213	ENSP00000335544:R213Q;ENSP00000432079:R129Q;ENSP00000435534:R213Q	ENSP00000335544:R213Q	R	+	2	0	CCKBR	6248128	0.000000	0.05858	0.726000	0.30738	0.995000	0.86356	-0.202000	0.09451	0.560000	0.29169	0.655000	0.94253	CGG	.	.		0.582	CCKBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257230.2	NM_176875	
DENND5A	23258	hgsc.bcm.edu	37	11	9182408	9182408	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:9182408T>G	ENST00000328194.3	-	12	2608	c.2288A>C	c.(2287-2289)aAg>aCg	p.K763T	DENND5A_ENST00000530044.1_Missense_Mutation_p.K763T|DENND5A_ENST00000527700.1_Missense_Mutation_p.K106T	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	763					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CAGCATCCTCTTGGTCTACAA	0.517																																					p.K763T		Atlas-SNP	.											.	DENND5A	84	.	0			c.A2288C						.						146.0	133.0	137.0					11																	9182408		2201	4296	6497	SO:0001583	missense	23258	exon12			ATCCTCTTGGTCT	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.2288A>C	chr11.hg19:g.9182408T>G	ENSP00000328524:p.Lys763Thr	224.0	0.0		286.0	17.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	T	23.8	4.461535	0.84317	.	.	ENSG00000184014	ENST00000328194;ENST00000530044;ENST00000527700	T;T;T	0.16196	2.36;2.36;2.36	5.81	4.68	0.58851	.	0.000000	0.85682	D	0.000000	T	0.43897	0.1268	M	0.80422	2.495	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.992;0.999	T	0.44862	-0.9300	10	0.72032	D	0.01	.	13.2774	0.60194	0.0:0.0:0.1323:0.8677	.	763;763	E9PS91;Q6IQ26	.;DEN5A_HUMAN	T	763;763;106	ENSP00000328524:K763T;ENSP00000435866:K763T;ENSP00000432549:K106T	ENSP00000328524:K763T	K	-	2	0	DENND5A	9138984	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	8.040000	0.89188	1.019000	0.39547	0.529000	0.55759	AAG	.	.		0.517	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
TPH1	7166	hgsc.bcm.edu	37	11	18057649	18057649	+	Nonsense_Mutation	SNP	G	G	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:18057649G>C	ENST00000250018.2	-	2	720	c.158C>G	c.(157-159)tCa>tGa	p.S53*	TPH1_ENST00000341556.2_Nonsense_Mutation_p.S53*	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	53	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.				aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	TCTTCTTTTTGATTTTCGGGA	0.348																																					p.S53X		Atlas-SNP	.											.	TPH1	44	.	0			c.C158G						.						115.0	109.0	111.0					11																	18057649		2200	4293	6493	SO:0001587	stop_gained	7166	exon2			CTTTTTGATTTTC	X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"""tryptophan 5-monooxygenase"""	191060	"""tryptophan hydroxylase (tryptophan 5-monooxygenase)"""	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.158C>G	chr11.hg19:g.18057649G>C	ENSP00000250018:p.Ser53*	51.0	0.0		58.0	13.0	NM_004179	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Nonsense_Mutation	SNP	ENST00000250018.2	hg19	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	G	36	5.857374	0.97030	.	.	ENSG00000129167	ENST00000250018;ENST00000341556;ENST00000528338	.	.	.	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.40728	T	0.16	-14.2116	19.7758	0.96391	0.0:0.0:1.0:0.0	.	.	.	.	X	53;53;63	.	ENSP00000250018:S53X	S	-	2	0	TPH1	18014225	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.768000	0.98965	2.752000	0.94435	0.655000	0.94253	TCA	.	.		0.348	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1	NM_004179	
METTL15	196074	hgsc.bcm.edu	37	11	28135039	28135039	+	Missense_Mutation	SNP	A	A	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:28135039A>C	ENST00000407364.3	+	3	510	c.158A>C	c.(157-159)cAa>cCa	p.Q53P	METTL15_ENST00000403099.1_Missense_Mutation_p.Q53P|METTL15_ENST00000379199.2_Missense_Mutation_p.Q53P|METTL15_ENST00000342303.5_Missense_Mutation_p.Q53P|METTL15_ENST00000303459.6_Missense_Mutation_p.Q53P|METTL15_ENST00000406787.3_Missense_Mutation_p.Q53P			A6NJ78	MET15_HUMAN	methyltransferase like 15	53							methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						GATCAAACTCAAGCCCAGGAG	0.383																																					p.Q53P		Atlas-SNP	.											.	METTL15	63	.	0			c.A158C						.						58.0	65.0	62.0					11																	28135039		2202	4299	6501	SO:0001583	missense	196074	exon3			AAACTCAAGCCCA	AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"""methyltransferase 5 domain containing 1"""	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.158A>C	chr11.hg19:g.28135039A>C	ENSP00000384369:p.Gln53Pro	124.0	0.0		152.0	53.0	NM_152636	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	hg19	CCDS44559.1	.	.	.	.	.	.	.	.	.	.	A	5.952	0.359640	0.11239	.	.	ENSG00000169519	ENST00000406787;ENST00000342303;ENST00000403099;ENST00000407364;ENST00000379199;ENST00000303459	T;T;T;T;T;T	0.45668	1.48;1.51;0.9;1.93;0.89;1.51	5.68	-3.3	0.05003	.	0.857111	0.10391	N	0.680392	T	0.24547	0.0595	N	0.22421	0.69	0.09310	N	1	B;B;P	0.38420	0.022;0.34;0.63	B;B;B	0.31495	0.019;0.093;0.131	T	0.08722	-1.0708	10	0.46703	T	0.11	.	12.8532	0.57869	0.6363:0.0:0.3637:0.0	.	53;53;53	A6NJ78;A6NJ78-2;A6NJ78-4	MET15_HUMAN;.;.	P	53	ENSP00000385507:Q53P;ENSP00000342259:Q53P;ENSP00000385860:Q53P;ENSP00000384369:Q53P;ENSP00000368497:Q53P;ENSP00000307251:Q53P	ENSP00000307251:Q53P	Q	+	2	0	METTL15	28091615	0.202000	0.23423	0.000000	0.03702	0.105000	0.19272	0.241000	0.18065	-0.559000	0.06110	-0.353000	0.07706	CAA	.	.		0.383	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636	
PATL1	219988	hgsc.bcm.edu	37	11	59420493	59420493	+	Splice_Site	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:59420493T>A	ENST00000300146.9	-	10	1206		c.e10-2			NM_152716.2	NP_689929.2	Q86TB9	PATL1_HUMAN	protein associated with topoisomerase II homolog 1 (yeast)						cytoplasmic mRNA processing body assembly (GO:0033962)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(2)|lung(5)|ovary(1)|prostate(2)	11						CGATGCTGACTGAAAAACATA	0.393																																					.		Atlas-SNP	.											.	PATL1	92	.	0			c.1122-2A>T						.						154.0	142.0	146.0					11																	59420493		1900	4126	6026	SO:0001630	splice_region_variant	219988	exon11			GCTGACTGAAAAA	AK094193	CCDS44613.1	11q12.1	2012-06-07	2007-10-18		ENSG00000166889	ENSG00000166889			26721	protein-coding gene	gene with protein product		614660				17936923	Standard	NM_152716		Approved	FLJ36874, Pat1b	uc001noe.4	Q86TB9	OTTHUMG00000167423	ENST00000300146.9:c.1122-2A>T	chr11.hg19:g.59420493T>A		92.0	0.0		117.0	12.0	NM_152716	B3KXT9|Q2TA86|Q6P166|Q8N9M6|Q8NI63	Splice_Site	SNP	ENST00000300146.9	hg19	CCDS44613.1	.	.	.	.	.	.	.	.	.	.	T	19.09	3.760179	0.69763	.	.	ENSG00000166889	ENST00000300146;ENST00000428532	.	.	.	5.14	5.14	0.70334	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.9127	0.70770	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	PATL1	59177069	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	4.008000	0.57103	2.073000	0.62155	0.482000	0.46254	.	.	.		0.393	PATL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394559.1	NM_152716	Intron
MS4A2	2206	hgsc.bcm.edu	37	11	59857913	59857913	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:59857913A>T	ENST00000278888.3	+	3	393	c.291A>T	c.(289-291)aaA>aaT	p.K97N		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	97					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	CATCATTTAAAGCAGGTTATC	0.348																																					p.K97N		Atlas-SNP	.											.	MS4A2	41	.	0			c.A291T						.						173.0	166.0	169.0					11																	59857913		2200	4294	6494	SO:0001583	missense	2206	exon3			ATTTAAAGCAGGT	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"""Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"""	147138	"""IgE responsiveness (atopic)"", ""membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"""	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.291A>T	chr11.hg19:g.59857913A>T	ENSP00000278888:p.Lys97Asn	43.0	0.0		50.0	9.0	NM_000139	Q54A81	Missense_Mutation	SNP	ENST00000278888.3	hg19	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	A	15.75	2.927106	0.52759	.	.	ENSG00000149534	ENST00000278888	T	0.02446	4.29	4.68	-0.461	0.12172	.	2.377010	0.01012	N	0.003859	T	0.04137	0.0115	M	0.68317	2.08	0.09310	N	1	B;B	0.33280	0.405;0.031	B;B	0.33254	0.16;0.078	T	0.41858	-0.9485	10	0.21014	T	0.42	-7.1959	1.106	0.01693	0.4213:0.1667:0.0906:0.3214	.	27;97	Q14298;Q01362	.;FCERB_HUMAN	N	97	ENSP00000278888:K97N	ENSP00000278888:K97N	K	+	3	2	MS4A2	59614489	0.038000	0.19896	0.000000	0.03702	0.986000	0.74619	0.199000	0.17237	-0.078000	0.12730	0.528000	0.53228	AAA	.	.		0.348	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1		
CD6	923	hgsc.bcm.edu	37	11	60777231	60777231	+	Silent	SNP	C	C	G	rs150066453		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:60777231C>G	ENST00000313421.7	+	5	1155	c.969C>G	c.(967-969)tcC>tcG	p.S323S	CD6_ENST00000452451.2_Silent_p.S323S|CD6_ENST00000346437.4_Silent_p.S323S|CD6_ENST00000352009.5_Silent_p.S323S|CD6_ENST00000344028.5_Silent_p.S323S|CD6_ENST00000545105.1_Intron	NM_006725.4	NP_006716.3	P30203	CD6_HUMAN	CD6 molecule	323	SRCR 3. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	scavenger receptor activity (GO:0005044)			endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)	18						ACTCCTTGTCCGGCAGGATGT	0.612																																					p.S323S	Pancreas(169;904 2017 4767 38890 42505)	Atlas-SNP	.											.	CD6	122	.	0			c.C969G						.						75.0	68.0	70.0					11																	60777231		2203	4299	6502	SO:0001819	synonymous_variant	923	exon5			CTTGTCCGGCAGG		CCDS7999.1, CCDS58137.1, CCDS58138.1	11q12.2	2006-03-28	2006-03-28		ENSG00000013725	ENSG00000013725		"""CD molecules"""	1691	protein-coding gene	gene with protein product		186720	"""CD6 antigen"""			9013954	Standard	NM_006725		Approved	Tp120	uc001nqq.3	P30203	OTTHUMG00000167823	ENST00000313421.7:c.969C>G	chr11.hg19:g.60777231C>G		120.0	0.0		127.0	39.0	NM_006725	A4KAD4|A4KAD5|Q9UMF2|Q9Y4K7|Q9Y4K8|Q9Y4K9|Q9Y4L0	Silent	SNP	ENST00000313421.7	hg19	CCDS7999.1																																																																																			.	C|1.000;T|0.000		0.612	CD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396449.1	NM_006725	
VWCE	220001	hgsc.bcm.edu	37	11	61026645	61026645	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:61026645T>A	ENST00000335613.5	-	20	2756	c.2370A>T	c.(2368-2370)tcA>tcT	p.S790S	VWCE_ENST00000535710.1_Silent_p.S255S	NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	790						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GCCTCGAGGGTGATGCTGTCG	0.562																																					p.S790S		Atlas-SNP	.											.	VWCE	84	.	0			c.A2370T						.						41.0	43.0	42.0					11																	61026645		2203	4299	6502	SO:0001819	synonymous_variant	220001	exon20			CGAGGGTGATGCT	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.2370A>T	chr11.hg19:g.61026645T>A		112.0	0.0		145.0	8.0	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	hg19	CCDS8002.1																																																																																			.	.		0.562	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
PLCB3	5331	hgsc.bcm.edu	37	11	64023034	64023034	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64023034A>T	ENST00000540288.1	+	7	646	c.543A>T	c.(541-543)gcA>gcT	p.A181A	PLCB3_ENST00000325234.5_Silent_p.A114A|PLCB3_ENST00000279230.6_Silent_p.A181A	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	181					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						TGTTCTCAGCAGACAAGAAGC	0.622																																					p.A181A		Atlas-SNP	.											.	PLCB3	103	.	0			c.A543T						.						108.0	106.0	107.0					11																	64023034		2201	4297	6498	SO:0001819	synonymous_variant	5331	exon7			CTCAGCAGACAAG	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.543A>T	chr11.hg19:g.64023034A>T		134.0	0.0		136.0	7.0	NM_000932	A5PKZ6|G5E960|Q8N1A4	Silent	SNP	ENST00000540288.1	hg19	CCDS8064.1																																																																																			.	.		0.622	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
SLC22A12	116085	hgsc.bcm.edu	37	11	64366298	64366298	+	Silent	SNP	C	C	A	rs150255373		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64366298C>A	ENST00000377574.1	+	6	1720	c.973C>A	c.(973-975)Cgg>Agg	p.R325R	SLC22A12_ENST00000336464.7_Silent_p.R291R|SLC22A12_ENST00000377567.2_Silent_p.R217R|SLC22A12_ENST00000377572.1_Silent_p.R217R|SLC22A12_ENST00000473690.1_Silent_p.R104R	NM_144585.2	NP_653186.2	Q96S37	S22AC_HUMAN	solute carrier family 22 (organic anion/urate transporter), member 12	325			Missing (affects urate transport). {ECO:0000269|PubMed:15327384}.		cellular homeostasis (GO:0019725)|response to drug (GO:0042493)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)|urate transport (GO:0015747)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|urate transmembrane transporter activity (GO:0015143)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	27					Losartan(DB00678)|Probenecid(DB01032)	TTCAGCCATGCGGGAGGAGCT	0.662																																					p.R325R		Atlas-SNP	.											.	SLC22A12	68	.	0			c.C973A						.						33.0	32.0	32.0					11																	64366298		2201	4296	6497	SO:0001819	synonymous_variant	116085	exon6			GCCATGCGGGAGG	AB071863	CCDS8075.1, CCDS60835.1, CCDS60836.1	11q13.1	2013-05-22	2008-01-11		ENSG00000197891	ENSG00000197891		"""Solute carriers"""	17989	protein-coding gene	gene with protein product		607096	"""solute carrier family 22 (organic anion/cation transporter), member 12"""			12024214	Standard	NM_144585		Approved	OAT4L, RST, URAT1	uc009yps.2	Q96S37	OTTHUMG00000045213	ENST00000377574.1:c.973C>A	chr11.hg19:g.64366298C>A		46.0	0.0		34.0	19.0	NM_144585	B7WPG1|G3XAN7|Q19PF7|Q19PF8|Q19PF9|Q19PG0|Q6UXW3|Q96DT2	Silent	SNP	ENST00000377574.1	hg19	CCDS8075.1																																																																																			.	C|1.000;T|0.000		0.662	SLC22A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104966.2	NM_144585	
MRPL49	740	hgsc.bcm.edu	37	11	64888161	64888161	+	5'Flank	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64888161T>A	ENST00000279242.2	+	0	0				FAU_ENST00000531743.1_Missense_Mutation_p.N132Y|MRPL49_ENST00000534078.1_5'Flank|FAU_ENST00000529639.1_Missense_Mutation_p.N132Y|FAU_ENST00000279259.3_3'UTR|FAU_ENST00000527548.1_Missense_Mutation_p.N132Y|MRPL49_ENST00000526171.1_5'Flank|ZNHIT2_ENST00000310597.4_5'Flank|MRPL49_ENST00000531705.1_5'Flank|FAU_ENST00000525297.1_Missense_Mutation_p.N97Y	NM_004927.3	NP_004918.1	Q13405	RM49_HUMAN	mitochondrial ribosomal protein L49						translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			endometrium(1)|ovary(1)	2						ACTTAAGAGTTGGCATTGGGG	0.478																																					p.N132Y		Atlas-SNP	.											.	FAU	17	.	0			c.A394T						.						61.0	68.0	66.0					11																	64888161		2201	4297	6498	SO:0001631	upstream_gene_variant	2197	exon5			AAGAGTTGGCATT		CCDS8096.1	11q13.1	2012-11-14	2001-10-16	2001-10-19	ENSG00000149792	ENSG00000149792		"""Mitochondrial ribosomal proteins / large subunits"""	1176	protein-coding gene	gene with protein product	"""neighbor of FAU"", ""next to FAU"""	606866	"""chromosome 11 open reading frame 4"""	C11orf4		8786148	Standard	NM_004927		Approved	NOF, NOF1, L49mt	uc001oda.2	Q13405	OTTHUMG00000165608		chr11.hg19:g.64888161T>A	Exception_encountered	118.0	0.0		137.0	7.0	NM_001997	B2R4G6	Missense_Mutation	SNP	ENST00000279242.2	hg19	CCDS8096.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.557611	0.86231	.	.	ENSG00000149806	ENST00000529639;ENST00000531743;ENST00000525297;ENST00000527548	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.62514	0.2434	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66732	-0.5849	7	0.87932	D	0	.	13.4889	0.61382	0.0:0.0:0.0:1.0	.	.	.	.	Y	132;132;97;132	ENSP00000435370:N132Y;ENSP00000431822:N132Y;ENSP00000436110:N97Y;ENSP00000434440:N132Y	ENSP00000436110:N97Y	N	-	1	0	FAU	64644737	1.000000	0.71417	1.000000	0.80357	0.898000	0.52572	7.771000	0.85420	2.090000	0.63153	0.533000	0.62120	AAC	.	.		0.478	MRPL49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385293.1	NM_004927	
SPDYC	387778	hgsc.bcm.edu	37	11	64939933	64939933	+	Silent	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:64939933C>T	ENST00000377185.2	+	5	455	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	AP003068.18_ENST00000534819.1_RNA	NM_001008778.1	NP_001008778.1			speedy/RINGO cell cycle regulator family member C											breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(1)	16						GGAGGAGGACCTGGAGGGCCC	0.552																																					p.L125L		Atlas-SNP	.											.	SPDYC	31	.	0			c.C373T						.						116.0	119.0	118.0					11																	64939933		2201	4297	6498	SO:0001819	synonymous_variant	387778	exon5			GAGGACCTGGAGG	AY820305	CCDS31606.1	11q13.1	2013-05-08	2013-05-08		ENSG00000204710	ENSG00000204710		"""Speedy homologs"""	32681	protein-coding gene	gene with protein product		614030	"""speedy homolog C (Xenopus laevis)"""			15611625	Standard	NM_001008778		Approved	Ringo2	uc010rnz.2	Q5MJ68	OTTHUMG00000165611	ENST00000377185.2:c.373C>T	chr11.hg19:g.64939933C>T		206.0	0.0		263.0	17.0	NM_001008778		Silent	SNP	ENST00000377185.2	hg19	CCDS31606.1																																																																																			.	.		0.552	SPDYC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385299.1	NM_001008778	
TAF1D	79101	hgsc.bcm.edu	37	11	93471382	93471382	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:93471382A>G	ENST00000448108.2	-	3	1002	c.352T>C	c.(352-354)Tca>Cca	p.S118P	TAF1D_ENST00000546088.1_5'Flank|SNORA40_ENST00000388090.1_RNA	NM_024116.3	NP_077021.1	Q9H5J8	TAF1D_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, D, 41kDa	118					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	microtubule organizing center (GO:0005815)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(3)|prostate(1)|skin(2)	7						TCTATTAGTGAGTATATAGGA	0.368																																					p.S118P		Atlas-SNP	.											.	TAF1D	18	.	0			c.T352C						.						146.0	151.0	149.0					11																	93471382		2201	4298	6499	SO:0001583	missense	79101	exon3			TTAGTGAGTATAT		CCDS8293.1	11q21	2012-05-30	2008-09-30	2008-09-30	ENSG00000166012	ENSG00000166012			28759	protein-coding gene	gene with protein product		612823	"""Josephin domain containing 3"""	JOSD3		15520167, 17318177	Standard	NM_024116		Approved	MGC5306, TAF(I)41	uc001pec.3	Q9H5J8	OTTHUMG00000167451	ENST00000448108.2:c.352T>C	chr11.hg19:g.93471382A>G	ENSP00000410409:p.Ser118Pro	31.0	0.0		22.0	8.0	NM_024116	Q6I9Y6	Missense_Mutation	SNP	ENST00000448108.2	hg19	CCDS8293.1	.	.	.	.	.	.	.	.	.	.	A	8.461	0.855386	0.17106	.	.	ENSG00000166012	ENST00000448108	.	.	.	5.25	2.92	0.33932	.	0.431966	0.21800	N	0.068940	T	0.34890	0.0913	L	0.52364	1.645	0.09310	N	0.999999	B	0.31769	0.339	B	0.33620	0.167	T	0.33929	-0.9849	9	0.87932	D	0	-14.656	6.3122	0.21171	0.8063:0.0:0.1937:0.0	.	118	Q9H5J8	TAF1D_HUMAN	P	118	.	ENSP00000314971:S118P	S	-	1	0	TAF1D	93111030	0.675000	0.27558	0.026000	0.17262	0.002000	0.02628	2.391000	0.44424	0.938000	0.37419	0.528000	0.53228	TCA	.	.		0.368	TAF1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394662.2	NM_024116	
KIAA1377	57562	hgsc.bcm.edu	37	11	101834387	101834387	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:101834387C>T	ENST00000263468.8	+	6	2891	c.2621C>T	c.(2620-2622)tCa>tTa	p.S874L	KIAA1377_ENST00000537689.1_Missense_Mutation_p.S675L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	874										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		GTGATACCATCACTGCCATCA	0.413																																					p.S874L		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C2621T						.						96.0	84.0	88.0					11																	101834387		2203	4299	6502	SO:0001583	missense	57562	exon6			TACCATCACTGCC	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.2621C>T	chr11.hg19:g.101834387C>T	ENSP00000263468:p.Ser874Leu	127.0	0.0		183.0	55.0	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	hg19	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	8.758	0.922990	0.18056	.	.	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.10382	2.88;2.88	5.77	3.89	0.44902	.	0.501227	0.20139	N	0.098412	T	0.13286	0.0322	M	0.64997	1.995	0.09310	N	1	B	0.27351	0.176	B	0.26202	0.067	T	0.10847	-1.0612	10	0.51188	T	0.08	-6.3323	11.2068	0.48773	0.0:0.8529:0.0:0.1471	.	874	Q9P2H0	K1377_HUMAN	L	874;675	ENSP00000263468:S874L;ENSP00000443184:S675L	ENSP00000263468:S874L	S	+	2	0	KIAA1377	101339597	0.004000	0.15560	0.017000	0.16124	0.030000	0.12068	1.924000	0.40065	1.582000	0.49881	0.655000	0.94253	TCA	.	.		0.413	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
IL10RA	3587	hgsc.bcm.edu	37	11	117869879	117869879	+	Silent	SNP	G	G	T	rs199604463	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:117869879G>T	ENST00000227752.3	+	7	1380	c.1260G>T	c.(1258-1260)tcG>tcT	p.S420S	IL10RA_ENST00000533700.1_3'UTR|IL10RA_ENST00000541785.1_Silent_p.S400S|IL10RA_ENST00000545409.1_Silent_p.S271S	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	420			S -> L (in dbSNP:rs2229114). {ECO:0000269|Ref.2}.		cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		AGGGTGGCTCGGCCTTGGGCC	0.627																																					p.S420S		Atlas-SNP	.											.	IL10RA	46	.	0			c.G1260T						.						48.0	51.0	50.0					11																	117869879		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			TGGCTCGGCCTTG	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1260G>T	chr11.hg19:g.117869879G>T		130.0	0.0		126.0	42.0	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	hg19	CCDS8388.1																																																																																			.	G|1.000;A|0.000		0.627	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
ITFG2	55846	hgsc.bcm.edu	37	12	2927434	2927434	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:2927434A>T	ENST00000228799.2	+	4	536	c.397A>T	c.(397-399)Agc>Tgc	p.S133C	ITFG2_ENST00000419778.2_Intron|ITFG2_ENST00000542548.1_5'UTR	NM_018463.3	NP_060933.3	Q969R8	ITFG2_HUMAN	integrin alpha FG-GAP repeat containing 2	133					germinal center B cell differentiation (GO:0002314)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(31;0.000818)			CATGCTGATCAGCGACATCGG	0.557																																					p.S133C		Atlas-SNP	.											.	ITFG2	38	.	0			c.A397T						.						155.0	117.0	130.0					12																	2927434		2203	4300	6503	SO:0001583	missense	55846	exon4			CTGATCAGCGACA	AF220048	CCDS8513.1	12p13.33	2006-11-29		2006-07-25	ENSG00000111203	ENSG00000111203			30879	protein-coding gene	gene with protein product						12477932	Standard	NM_018463		Approved	MDS028	uc001qlb.2	Q969R8	OTTHUMG00000130617	ENST00000228799.2:c.397A>T	chr12.hg19:g.2927434A>T	ENSP00000228799:p.Ser133Cys	142.0	0.0		144.0	54.0	NM_018463	A8K4Z5|D3DUQ2|Q6PKU5|Q96SX6	Missense_Mutation	SNP	ENST00000228799.2	hg19	CCDS8513.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.447864	0.84101	.	.	ENSG00000111203	ENST00000228799	T	0.71461	-0.57	4.69	3.55	0.40652	.	0.039659	0.85682	D	0.000000	T	0.75376	0.3841	M	0.77820	2.39	0.80722	D	1	D;D	0.56287	0.975;0.975	P;P	0.50659	0.594;0.647	T	0.76583	-0.2906	10	0.66056	D	0.02	-21.1302	9.4155	0.38519	0.9158:0.0:0.0842:0.0	.	133;133	Q969R8;Q6PKU5	ITFG2_HUMAN;.	C	133	ENSP00000228799:S133C	ENSP00000228799:S133C	S	+	1	0	ITFG2	2797695	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.080000	0.64437	0.830000	0.34757	0.533000	0.62120	AGC	.	.		0.557	ITFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253091.1	NM_018463	
PRH1	5554	hgsc.bcm.edu	37	12	11036772	11036772	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:11036772T>A	ENST00000428168.2	-	1	82	c.45A>T	c.(43-45)tcA>tcT	p.S15S	PRR4_ENST00000536668.1_5'UTR	NM_006250.3	NP_006241.2	P02810	PRPC_HUMAN	proline-rich protein HaeIII subfamily 1	15						extracellular space (GO:0005615)				endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	5				BRCA - Breast invasive adenocarcinoma(232;0.245)		AATCCTGAGCTGAGCTGAAGG	0.493																																					p.S15S		Atlas-SNP	.											.	PRH1	17	.	0			c.A45T						.						80.0	79.0	80.0					12																	11036772		2203	4300	6503	SO:0001819	synonymous_variant	5554	exon1			CTGAGCTGAGCTG			12p13.2	2013-05-10			ENSG00000231887	ENSG00000231887			9366	protein-coding gene	gene with protein product		168730				3009472	Standard	NM_001291314		Approved	Pa	uc021qvf.1	P02810		ENST00000428168.2:c.45A>T	chr12.hg19:g.11036772T>A		214.0	0.0		218.0	15.0	NM_006250	A2VCM0|A3KN66|A5D902|B2RMW2|Q4VBP2|Q53XA2|Q6P2F6	Silent	SNP	ENST00000428168.2	hg19																																																																																				.	.		0.493	PRH1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_006250	
NELL2	4753	hgsc.bcm.edu	37	12	44913954	44913954	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:44913954A>T	ENST00000429094.2	-	19	2738	c.2234T>A	c.(2233-2235)aTt>aAt	p.I745N	NELL2_ENST00000452445.2_Missense_Mutation_p.I745N|NELL2_ENST00000333837.4_Missense_Mutation_p.I768N|NELL2_ENST00000549027.1_Missense_Mutation_p.I744N|NELL2_ENST00000551601.1_Missense_Mutation_p.I697N|NELL2_ENST00000395487.2_Missense_Mutation_p.I744N|NELL2_ENST00000437801.2_Missense_Mutation_p.I795N	NM_001145108.1	NP_001138580.1	Q99435	NELL2_HUMAN	NEL-like 2 (chicken)	745	VWFC 3. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(16)|lung(30)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	65	Lung SC(27;0.192)	Lung NSC(34;0.144)		GBM - Glioblastoma multiforme(48;0.092)		CTCTGGGAGAATGCTGAATTC	0.547																																					p.I795N		Atlas-SNP	.											.	NELL2	286	.	0			c.T2384A						.						80.0	67.0	72.0					12																	44913954		2203	4300	6503	SO:0001583	missense	4753	exon20			GGGAGAATGCTGA	D83018	CCDS8746.1, CCDS44863.1, CCDS44864.1, CCDS53781.1	12q12	2012-01-30	2001-11-28		ENSG00000184613	ENSG00000184613			7751	protein-coding gene	gene with protein product		602320	"""nel (chicken)-like 2"""			19249368	Standard	NM_006159		Approved	NRP2	uc010skz.1	Q99435	OTTHUMG00000169464	ENST00000429094.2:c.2234T>A	chr12.hg19:g.44913954A>T	ENSP00000390680:p.Ile745Asn	125.0	0.0		171.0	48.0	NM_001145107	B7Z2U7|B7Z5Q4|B7Z9J5|B7Z9U3|Q96JS2	Missense_Mutation	SNP	ENST00000429094.2	hg19	CCDS8746.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.781160	0.49891	.	.	ENSG00000184613	ENST00000395487;ENST00000429094;ENST00000551601;ENST00000452445;ENST00000549027;ENST00000333837;ENST00000437801	T;T;T;T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21;-0.21;-0.21;-0.21	5.07	5.07	0.68467	von Willebrand factor, type C (4);	0.136036	0.48767	D	0.000172	T	0.66426	0.2788	L	0.60455	1.87	0.30030	N	0.813516	B;B;B;B;B	0.27013	0.044;0.166;0.145;0.055;0.166	B;B;B;B;B	0.34346	0.084;0.18;0.039;0.066;0.116	T	0.66304	-0.5957	10	0.39692	T	0.17	-8.2482	14.8307	0.70146	1.0:0.0:0.0:0.0	.	768;795;697;745;744	B7Z2U7;B7Z9U3;F8VVB6;Q99435;Q96JS2	.;.;.;NELL2_HUMAN;.	N	744;745;697;745;744;768;795	ENSP00000378866:I744N;ENSP00000390680:I745N;ENSP00000449332:I697N;ENSP00000394612:I745N;ENSP00000447927:I744N;ENSP00000327988:I768N;ENSP00000416341:I795N	ENSP00000327988:I768N	I	-	2	0	NELL2	43200221	1.000000	0.71417	0.990000	0.47175	0.897000	0.52465	4.483000	0.60264	1.885000	0.54596	0.528000	0.53228	ATT	.	.		0.547	NELL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404180.1	NM_006159	
KRT86	3892	hgsc.bcm.edu	37	12	52699941	52699941	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:52699941T>A	ENST00000423955.2	+	9	1302	c.1124T>A	c.(1123-1125)cTg>cAg	p.L375Q	RP11-845M18.6_ENST00000552441.1_RNA|KRT86_ENST00000544024.1_Missense_Mutation_p.L375Q|KRT86_ENST00000293525.5_Missense_Mutation_p.L375Q			O43790	KRT86_HUMAN	keratin 86	375	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		GAGGGTGCCCTGCAGAAGGCC	0.637											OREG0021845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L375Q		Atlas-SNP	.											.	KRT86	33	.	0			c.T1124A						.						63.0	63.0	63.0					12																	52699941		2203	4300	6503	SO:0001583	missense	3892	exon7			GTGCCCTGCAGAA	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.1124T>A	chr12.hg19:g.52699941T>A	ENSP00000444533:p.Leu375Gln	204.0	0.0	987	116.0	6.0	NM_002284	P78387	Missense_Mutation	SNP	ENST00000423955.2	hg19	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	T	24.0	4.485795	0.84854	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	D;D;D	0.92299	-3.01;-3.01;-3.01	5.49	5.49	0.81192	Filament (1);	0.000000	0.33005	U	0.005395	D	0.97688	0.9242	H	0.98664	4.295	0.48341	D	0.999633	D	0.89917	1.0	D	0.97110	1.0	D	0.99004	1.0812	10	0.87932	D	0	.	14.1668	0.65483	0.0:0.0:0.0:1.0	.	375	O43790	KRT86_HUMAN	Q	375	ENSP00000443169:L375Q;ENSP00000444533:L375Q;ENSP00000293525:L375Q	ENSP00000293525:L375Q	L	+	2	0	AC021066.1;KRT86	50986208	1.000000	0.71417	1.000000	0.80357	0.878000	0.50629	7.947000	0.87758	2.089000	0.63090	0.454000	0.30748	CTG	.	.		0.637	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284	
ANKRD52	283373	hgsc.bcm.edu	37	12	56636966	56636966	+	Missense_Mutation	SNP	C	C	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:56636966C>A	ENST00000267116.7	-	28	3312	c.3191G>T	c.(3190-3192)cGg>cTg	p.R1064L	ANKRD52_ENST00000548241.1_Intron	NM_173595.3	NP_775866.2	Q8NB46	ANR52_HUMAN	ankyrin repeat domain 52	1064										endometrium(9)|kidney(2)|large_intestine(8)|lung(6)|ovary(2)|prostate(1)|skin(1)	29						GGCGCCGGGCCGCTCCTGGCT	0.607																																					p.R1064L		Atlas-SNP	.											.	ANKRD52	81	.	0			c.G3191T						.						11.0	12.0	12.0					12																	56636966		1875	4081	5956	SO:0001583	missense	283373	exon28			CCGGGCCGCTCCT	AK091555	CCDS44920.1	12q13.3	2013-01-10			ENSG00000139645	ENSG00000139645		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"", ""Ankyrin repeat domain containing"""	26614	protein-coding gene	gene with protein product	"""protein phosphatase 6 ankyrin repeat subunit C"""						Standard	NM_173595		Approved	FLJ34236, PP6-ARS-C	uc001skm.4	Q8NB46	OTTHUMG00000170329	ENST00000267116.7:c.3191G>T	chr12.hg19:g.56636966C>A	ENSP00000267116:p.Arg1064Leu	24.0	0.0		18.0	5.0	NM_173595	A6NE79|B1Q2K2	Missense_Mutation	SNP	ENST00000267116.7	hg19	CCDS44920.1	.	.	.	.	.	.	.	.	.	.	C	14.28	2.487538	0.44249	.	.	ENSG00000139645	ENST00000267116;ENST00000417002	T	0.64803	-0.12	3.62	3.62	0.41486	.	0.077520	0.52532	D	0.000067	T	0.47911	0.1471	N	0.19112	0.55	0.58432	D	0.999999	P	0.40875	0.731	B	0.39562	0.303	T	0.54938	-0.8218	10	0.46703	T	0.11	.	14.6424	0.68734	0.0:1.0:0.0:0.0	.	1064	Q8NB46	ANR52_HUMAN	L	1064	ENSP00000267116:R1064L	ENSP00000267116:R1064L	R	-	2	0	ANKRD52	54923233	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	5.460000	0.66691	2.049000	0.60858	0.555000	0.69702	CGG	.	.		0.607	ANKRD52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408539.1	NM_173595	
NACA	4666	hgsc.bcm.edu	37	12	57114439	57114439	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:57114439G>T	ENST00000454682.1	-	3	1156	c.875C>A	c.(874-876)aCt>aAt	p.T292N	NACA_ENST00000546392.1_Intron|NACA_ENST00000356769.3_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Missense_Mutation_p.T292N|NACA_ENST00000548563.1_Intron|NACA_ENST00000552540.1_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	292	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						GGGACCCGCAGTCTTTTGAGA	0.498			T	BCL6	NHL																																p.T292N		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.C875A						.						65.0	64.0	65.0					12																	57114439		1568	3582	5150	SO:0001583	missense	4666	exon3			CCCGCAGTCTTTT	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.875C>A	chr12.hg19:g.57114439G>T	ENSP00000403817:p.Thr292Asn	30.0	0.0		37.0	4.0	NM_001113203		Missense_Mutation	SNP	ENST00000454682.1	hg19		.	.	.	.	.	.	.	.	.	.	g	12.99	2.103170	0.37145	.	.	ENSG00000196531	ENST00000454682;ENST00000550952	T;T	0.60171	0.21;0.74	3.92	2.93	0.34026	.	.	.	.	.	T	0.36580	0.0972	N	0.08118	0	0.09310	N	1	D;P	0.59357	0.985;0.941	B;B	0.42422	0.387;0.203	T	0.16364	-1.0405	9	0.87932	D	0	.	8.9241	0.35630	0.0:0.2297:0.7703:0.0	.	292;292	E9PAV3;F8VU71	.;.	N	292	ENSP00000403817:T292N;ENSP00000448035:T292N	ENSP00000403817:T292N	T	-	2	0	NACA	55400706	0.044000	0.20184	0.079000	0.20413	0.259000	0.26198	1.666000	0.37460	1.928000	0.55862	0.282000	0.19409	ACT	.	.		0.498	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
SDR9C7	121214	hgsc.bcm.edu	37	12	57324233	57324233	+	Silent	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:57324233G>A	ENST00000293502.1	-	2	480	c.337C>T	c.(337-339)Ctg>Ttg	p.L113L		NM_148897.2	NP_683695.1	Q8NEX9	DR9C7_HUMAN	short chain dehydrogenase/reductase family 9C, member 7	113					oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	retinol dehydrogenase activity (GO:0004745)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|pancreas(1)	7						CCACTGGGCAGGCCCACACCA	0.552																																					p.L113L		Atlas-SNP	.											.	SDR9C7	31	.	0			c.C337T						.						68.0	61.0	63.0					12																	57324233		2203	4300	6503	SO:0001819	synonymous_variant	121214	exon2			TGGGCAGGCCCAC	AY044434	CCDS8926.1	12q13.3	2014-09-04			ENSG00000170426	ENSG00000170426	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	29958	protein-coding gene	gene with protein product		609769				12234675, 19027726	Standard	NM_148897		Approved	SDR-O, RDHS	uc010sqw.2	Q8NEX9	OTTHUMG00000171004	ENST00000293502.1:c.337C>T	chr12.hg19:g.57324233G>A		141.0	0.0		196.0	11.0	NM_148897	B3KVB4	Silent	SNP	ENST00000293502.1	hg19	CCDS8926.1																																																																																			.	.		0.552	SDR9C7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411211.1	NM_148897	
SLC6A15	55117	hgsc.bcm.edu	37	12	85279337	85279337	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:85279337A>G	ENST00000266682.5	-	4	992	c.451T>C	c.(451-453)Tgc>Cgc	p.C151R	SLC6A15_ENST00000551388.1_Intron|SLC6A15_ENST00000450363.3_Missense_Mutation_p.C151R|SLC6A15_ENST00000552192.1_Missense_Mutation_p.C44R	NM_182767.5	NP_877499.1	Q9H2J7	S6A15_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 15	151					amino acid transport (GO:0006865)|ion transport (GO:0006811)|leucine transport (GO:0015820)|neurotransmitter transport (GO:0006836)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)|proline:sodium symporter activity (GO:0005298)			kidney(1)|large_intestine(18)|lung(15)|ovary(1)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	44						ACAAAATAGCACACCTGCAAA	0.343																																					p.C151R		Atlas-SNP	.											.	SLC6A15	159	.	0			c.T451C						.						89.0	86.0	87.0					12																	85279337		2203	4300	6503	SO:0001583	missense	55117	exon4			AATAGCACACCTG	AF265577	CCDS9026.1, CCDS9027.1, CCDS53816.1	12q21.31	2013-07-15	2008-09-02		ENSG00000072041	ENSG00000072041		"""Solute carriers"""	13621	protein-coding gene	gene with protein product	"""homolog of rat orphan transporter v7-3"", ""sodium/chloride dependent neurotransmitter transporter Homo sapiens orphan neurotransmitter transporter NTT7"""	607971	"""solute carrier family 6 (neurotransmitter transporter), member 15"""			10471414, 11112352, 16185194	Standard	NM_182767		Approved	hv7-3, NTT73, FLJ10316, V7-3, SBAT1	uc001szv.4	Q9H2J7	OTTHUMG00000169742	ENST00000266682.5:c.451T>C	chr12.hg19:g.85279337A>G	ENSP00000266682:p.Cys151Arg	115.0	0.0		135.0	45.0	NM_018057	A8K592|B7Z2P7|E7ESJ5|Q9H9F5	Missense_Mutation	SNP	ENST00000266682.5	hg19	CCDS9026.1	.	.	.	.	.	.	.	.	.	.	A	18.08	3.544481	0.65198	.	.	ENSG00000072041	ENST00000266682;ENST00000552192;ENST00000450363	T;T;T	0.74632	-0.86;-0.86;-0.86	5.11	3.94	0.45596	.	0.000000	0.85682	D	0.000000	D	0.85792	0.5779	M	0.85710	2.77	0.80722	D	1	P;D	0.67145	0.915;0.996	P;D	0.72075	0.821;0.976	D	0.86458	0.1777	10	0.62326	D	0.03	.	11.5065	0.50471	0.8654:0.0:0.0:0.1346	.	151;151	Q9H9F5;Q9H2J7	.;S6A15_HUMAN	R	151;44;151	ENSP00000266682:C151R;ENSP00000450145:C44R;ENSP00000390706:C151R	ENSP00000266682:C151R	C	-	1	0	SLC6A15	83803468	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.026000	0.76455	0.874000	0.35823	0.477000	0.44152	TGC	.	.		0.343	SLC6A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405678.1	NM_018057, NM_182767	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85449747	85449747	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:85449747A>T	ENST00000393217.2	+	8	1237	c.1176A>T	c.(1174-1176)caA>caT	p.Q392H		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	392										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		ATGCAAGCCAACAGCTAATAA	0.294																																					p.Q392H		Atlas-SNP	.											.	LRRIQ1	512	.	0			c.A1176T						.						51.0	57.0	55.0					12																	85449747		2201	4292	6493	SO:0001583	missense	84125	exon8			AAGCCAACAGCTA	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.1176A>T	chr12.hg19:g.85449747A>T	ENSP00000376910:p.Gln392His	27.0	0.0		45.0	5.0	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	hg19	CCDS41816.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291674	0.40594	.	.	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.52983	0.64	4.95	2.49	0.30216	.	0.464479	0.20777	N	0.085877	T	0.33059	0.0850	N	0.22421	0.69	0.09310	N	1	P;P	0.51653	0.804;0.947	B;P	0.44561	0.258;0.453	T	0.13361	-1.0512	10	0.54805	T	0.06	.	7.1546	0.25630	0.6749:0.0:0.3251:0.0	.	392;367	Q96JM4;C9JI57	LRIQ1_HUMAN;.	H	392;367;392	ENSP00000376910:Q392H	ENSP00000256007:Q392H	Q	+	3	2	LRRIQ1	83973878	0.000000	0.05858	0.013000	0.15412	0.069000	0.16628	0.718000	0.25866	0.214000	0.20742	-0.856000	0.03024	CAA	.	.		0.294	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
NTS	4922	hgsc.bcm.edu	37	12	86276027	86276027	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:86276027T>A	ENST00000256010.6	+	4	494	c.387T>A	c.(385-387)acT>acA	p.T129T	NTS_ENST00000551529.1_Silent_p.T54T	NM_006183.4	NP_006174.1	P30990	NEUT_HUMAN	neurotensin	129					regulation of blood vessel size (GO:0050880)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)				large_intestine(2)|lung(6)	8						TTCTTGATACTGGAAATGACA	0.323																																					p.T129T		Atlas-SNP	.											.	NTS	25	.	0			c.T387A						.						60.0	65.0	63.0					12																	86276027		2203	4296	6499	SO:0001819	synonymous_variant	4922	exon4			TGATACTGGAAAT		CCDS9029.1	12q21.31	2013-02-26			ENSG00000133636	ENSG00000133636		"""Endogenous ligands"""	8038	protein-coding gene	gene with protein product	"""neuromedin N"", ""pro-neurotensin/neuromedin"""	162650					Standard	NM_006183		Approved		uc001tag.3	P30990	OTTHUMG00000169832	ENST00000256010.6:c.387T>A	chr12.hg19:g.86276027T>A		107.0	0.0		127.0	9.0	NM_006183		Silent	SNP	ENST00000256010.6	hg19	CCDS9029.1																																																																																			.	.		0.323	NTS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406111.2		
KITLG	4254	hgsc.bcm.edu	37	12	88900157	88900157	+	Splice_Site	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:88900157T>A	ENST00000228280.5	-	8	897		c.e8-2		KITLG_ENST00000347404.5_Splice_Site|KITLG_ENST00000357116.4_Splice_Site|KITLG_ENST00000378535.4_Splice_Site	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand						cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						CTGTCTCTTCTGGAAAAAGAA	0.323									Testicular Cancer, Familial Clustering of																												.		Atlas-SNP	.											.	KITLG	26	.	0			c.715-2A>T						.						140.0	146.0	144.0					12																	88900157		2203	4300	6503	SO:0001630	splice_region_variant	4254	exon9	Familial Cancer Database		CTCTTCTGGAAAA	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"""mast cell growth factor"", ""stem cell factor"", ""steel factor"", ""familial progressive hyperpigmentation 2"""	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.715-2A>T	chr12.hg19:g.88900157T>A		80.0	0.0		96.0	10.0	NM_000899	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Splice_Site	SNP	ENST00000228280.5	hg19	CCDS31868.1	.	.	.	.	.	.	.	.	.	.	T	18.21	3.572537	0.65765	.	.	ENSG00000049130	ENST00000378535;ENST00000228280;ENST00000347404	.	.	.	5.47	5.47	0.80525	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.31	0.60374	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	KITLG	87424288	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	3.640000	0.54350	2.070000	0.61991	0.477000	0.44152	.	.	.		0.323	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994	Intron
STAB2	55576	hgsc.bcm.edu	37	12	104067722	104067722	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:104067722A>T	ENST00000388887.2	+	23	2613	c.2409A>T	c.(2407-2409)atA>atT	p.I803I		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ATAACAGGATAGACAGCGATG	0.582																																					p.I803I		Atlas-SNP	.											.	STAB2	370	.	0			c.A2409T						.						88.0	76.0	80.0					12																	104067722		2203	4300	6503	SO:0001819	synonymous_variant	55576	exon23			CAGGATAGACAGC	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.2409A>T	chr12.hg19:g.104067722A>T		150.0	0.0		141.0	13.0	NM_017564		Silent	SNP	ENST00000388887.2	hg19	CCDS31888.1																																																																																			.	.		0.582	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
ALKBH2	121642	hgsc.bcm.edu	37	12	109526088	109526088	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:109526088T>G	ENST00000429722.2	-	4	1072	c.709A>C	c.(709-711)Agt>Cgt	p.S237R	ALKBH2_ENST00000343075.3_Missense_Mutation_p.S237R|ALKBH2_ENST00000440112.2_3'UTR	NM_001145374.1	NP_001138846.1	Q6NS38	ALKB2_HUMAN	alkB, alkylation repair homolog 2 (E. coli)	237	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|DNA repair (GO:0006281)|oxidative demethylation (GO:0070989)|oxidative DNA demethylation (GO:0035511)	nucleoplasm (GO:0005654)	cytosine C-5 DNA demethylase activity (GO:0051747)|DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)			endometrium(1)|kidney(3)|large_intestine(1)|lung(3)	8					Vitamin C(DB00126)	ACGGGAAGACTGTGGTACCAG	0.488								Direct reversal of damage																													p.S237R		Atlas-SNP	.											.	ALKBH2	16	.	0			c.A709C						.						121.0	122.0	121.0					12																	109526088		2203	4300	6503	SO:0001583	missense	121642	exon4			GAAGACTGTGGTA	AY754389	CCDS31897.1, CCDS55883.1	12q24.11	2008-04-24			ENSG00000189046	ENSG00000189046		"""Alkylation repair homologs"""	32487	protein-coding gene	gene with protein product		610602					Standard	NM_001145374		Approved	MGC90512, ABH2	uc010sxj.1	Q6NS38	OTTHUMG00000169246	ENST00000429722.2:c.709A>C	chr12.hg19:g.109526088T>G	ENSP00000398181:p.Ser237Arg	67.0	0.0		63.0	23.0	NM_001001655	A4PET2|Q5XLE3	Missense_Mutation	SNP	ENST00000429722.2	hg19	CCDS31897.1	.	.	.	.	.	.	.	.	.	.	T	24.7	4.561254	0.86335	.	.	ENSG00000189046	ENST00000429722;ENST00000343075;ENST00000435370	T;T	0.15372	2.43;2.43	5.49	5.49	0.81192	Oxoglutarate/iron-dependent oxygenase (2);	0.000000	0.85682	D	0.000000	T	0.33206	0.0855	L	0.48218	1.51	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.03077	-1.1075	10	0.20046	T	0.44	-26.5377	14.7744	0.69713	0.0:0.0:0.0:1.0	.	237	Q6NS38	ALKB2_HUMAN	R	237	ENSP00000398181:S237R;ENSP00000343021:S237R	ENSP00000343021:S237R	S	-	1	0	ALKBH2	108010471	1.000000	0.71417	0.999000	0.59377	0.791000	0.44710	7.401000	0.79962	2.074000	0.62210	0.460000	0.39030	AGT	.	.		0.488	ALKBH2-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403063.2	NM_001001655	
OASL	8638	hgsc.bcm.edu	37	12	121458369	121458369	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:121458369T>A	ENST00000257570.5	-	6	1810	c.1540A>T	c.(1540-1542)Agt>Tgt	p.S514C	OASL_ENST00000339275.5_3'UTR	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	514					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GAAAACTAACTGGCTGGAAAC	0.502																																					p.S514C	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.A1540T						.						70.0	72.0	71.0					12																	121458369		2203	4300	6503	SO:0001583	missense	8638	exon6			ACTAACTGGCTGG	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.1540A>T	chr12.hg19:g.121458369T>A	ENSP00000257570:p.Ser514Cys	72.0	0.0		58.0	8.0	NM_003733	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Missense_Mutation	SNP	ENST00000257570.5	hg19	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	T	11.94	1.789833	0.31685	.	.	ENSG00000135114	ENST00000257570	T	0.06371	3.31	4.8	-0.206	0.13193	.	1.817350	0.03138	N	0.166123	T	0.06462	0.0166	L	0.36672	1.1	0.09310	N	1	B	0.12013	0.005	B	0.12156	0.007	T	0.42189	-0.9466	10	0.87932	D	0	-14.9306	3.2323	0.06752	0.172:0.286:0.0:0.542	.	514	Q15646	OASL_HUMAN	C	514	ENSP00000257570:S514C	ENSP00000257570:S514C	S	-	1	0	OASL	119942752	0.003000	0.15002	0.001000	0.08648	0.036000	0.12997	0.206000	0.17375	0.075000	0.16796	0.533000	0.62120	AGT	.	.		0.502	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733	
OASL	8638	hgsc.bcm.edu	37	12	121458371	121458371	+	Missense_Mutation	SNP	G	G	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:121458371G>C	ENST00000257570.5	-	6	1808	c.1538C>G	c.(1537-1539)gCc>gGc	p.A513G	OASL_ENST00000339275.5_3'UTR	NM_003733.3	NP_003724.1	Q15646	OASL_HUMAN	2'-5'-oligoadenylate synthetase-like	513					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|thyroid hormone receptor binding (GO:0046966)|transferase activity (GO:0016740)			NS(1)|endometrium(3)|large_intestine(4)|lung(4)|skin(2)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					AAACTAACTGGCTGGAAACAG	0.507																																					p.A513G	Colon(192;517 2041 31392 31913 39966)	Atlas-SNP	.											.	OASL	49	.	0			c.C1538G						.						71.0	72.0	72.0					12																	121458371		2203	4300	6503	SO:0001583	missense	8638	exon6			TAACTGGCTGGAA	AF063611	CCDS9211.1, CCDS9212.1, CCDS73536.1	12q24.2	2008-08-05			ENSG00000135114	ENSG00000135114			8090	protein-coding gene	gene with protein product		603281				10087211	Standard	NM_003733		Approved	TRIP14, p59OASL	uc001tzj.2	Q15646	OTTHUMG00000154981	ENST00000257570.5:c.1538C>G	chr12.hg19:g.121458371G>C	ENSP00000257570:p.Ala513Gly	74.0	0.0		58.0	8.0	NM_003733	B2RAZ2|I1YDD2|O75686|Q17R95|Q9Y6K6|Q9Y6K7	Missense_Mutation	SNP	ENST00000257570.5	hg19	CCDS9211.1	.	.	.	.	.	.	.	.	.	.	G	6.597	0.478568	0.12521	.	.	ENSG00000135114	ENST00000257570	T	0.05855	3.38	4.8	-6.94	0.01633	.	30.692100	0.01045	N	0.004377	T	0.03783	0.0107	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33163	-0.9879	10	0.41790	T	0.15	-20.326	0.8567	0.01184	0.2006:0.2009:0.1907:0.4078	.	513	Q15646	OASL_HUMAN	G	513	ENSP00000257570:A513G	ENSP00000257570:A513G	A	-	2	0	OASL	119942754	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.177000	0.09796	-1.740000	0.01345	-0.140000	0.14226	GCC	.	.		0.507	OASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337875.2	NM_003733	
B3GNT4	79369	hgsc.bcm.edu	37	12	122691677	122691677	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:122691677T>A	ENST00000324189.4	+	3	1235	c.879T>A	c.(877-879)gcT>gcA	p.A293A	B3GNT4_ENST00000535274.1_Silent_p.A268A|B3GNT4_ENST00000546192.1_Silent_p.A268A|B3GNT4_ENST00000545141.1_Intron	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	293					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		GCCTCCAGGCTATCATGGAAG	0.567																																					p.A293A		Atlas-SNP	.											.	B3GNT4	35	.	0			c.T879A						.						119.0	105.0	110.0					12																	122691677		2203	4300	6503	SO:0001819	synonymous_variant	79369	exon3			CCAGGCTATCATG	AB049586	CCDS9227.1	12q24	2013-02-19						"""Beta 3-glycosyltransferases"""	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.879T>A	chr12.hg19:g.122691677T>A		142.0	0.0		95.0	11.0	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Silent	SNP	ENST00000324189.4	hg19	CCDS9227.1																																																																																			.	.		0.567	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765	
MMP17	4326	hgsc.bcm.edu	37	12	132334436	132334436	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr12:132334436G>A	ENST00000360564.1	+	9	1396	c.1294G>A	c.(1294-1296)Gac>Aac	p.D432N	MMP17_ENST00000535004.1_Intron|MMP17_ENST00000535291.1_Missense_Mutation_p.D348N	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	432					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	TGGCGGCATCGACGCTGCCTT	0.597																																					p.D432N		Atlas-SNP	.											MMP17_ENST00000360564,NS,carcinoma,0,2	MMP17	77	.	0			c.G1294A						.						107.0	112.0	111.0					12																	132334436		2203	4300	6503	SO:0001583	missense	4326	exon9			GGCATCGACGCTG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.1294G>A	chr12.hg19:g.132334436G>A	ENSP00000353767:p.Asp432Asn	311.0	1.0		188.0	26.0	NM_016155	Q14850	Missense_Mutation	SNP	ENST00000360564.1	hg19	CCDS31927.1	.	.	.	.	.	.	.	.	.	.	G	19.90	3.911954	0.72983	.	.	ENSG00000198598	ENST00000360564;ENST00000535291;ENST00000534865;ENST00000542648	T;T;T;T	0.08282	3.11;3.11;3.11;3.11	4.58	4.58	0.56647	Hemopexin/matrixin (2);	0.000000	0.85682	D	0.000000	T	0.36082	0.0954	M	0.88570	2.965	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.47661	-0.9100	10	0.87932	D	0	.	17.3957	0.87444	0.0:0.0:1.0:0.0	.	432	Q9ULZ9	MMP17_HUMAN	N	432;348;273;62	ENSP00000353767:D432N;ENSP00000441106:D348N;ENSP00000442104:D273N;ENSP00000439542:D62N	ENSP00000353767:D432N	D	+	1	0	MMP17	130900389	1.000000	0.71417	0.046000	0.18839	0.181000	0.23173	9.750000	0.98875	2.112000	0.64535	0.471000	0.43371	GAC	.	.		0.597	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
SLITRK5	26050	hgsc.bcm.edu	37	13	88330413	88330414	+	Missense_Mutation	DNP	TT	TT	AA			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr13:88330413_88330414TT>AA	ENST00000325089.6	+	2	2989_2990	c.2770_2771TT>AA	c.(2770-2772)TTt>AAt	p.F924N	SLITRK5_ENST00000400028.3_Missense_Mutation_p.F683N	NM_015567.1	NP_056382.1	O94991	SLIK5_HUMAN	SLIT and NTRK-like family, member 5	924					adult behavior (GO:0030534)|axonogenesis (GO:0007409)|cardiovascular system development (GO:0072358)|dendrite morphogenesis (GO:0048813)|grooming behavior (GO:0007625)|response to xenobiotic stimulus (GO:0009410)|skin development (GO:0043588)|striatum development (GO:0021756)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)				breast(1)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(14)|lung(40)|ovary(2)|pancreas(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(4)	81	all_neural(89;0.101)|Medulloblastoma(90;0.163)					GAGTGCTGTCTTTGTAGAACCC	0.55																																					p.F924I|p.F924Y		Atlas-SNP	.											.	SLITRK5	192	.	0			c.T2770A|c.T2771A						.																																			SO:0001583	missense	26050	exon2			GCTGTCTTTGTAG|CTGTCTTTGTAGA	AB020725	CCDS9465.1	13q31.1	2004-04-16	2004-01-08		ENSG00000165300	ENSG00000165300			20295	protein-coding gene	gene with protein product		609680	"""leucine rich repeat containing 11"""	LRRC11		10048485, 14557068	Standard	NM_015567		Approved	bA364G4.2, KIAA0918	uc001vln.3	O94991	OTTHUMG00000017167	Exception_encountered	chr13.hg19:g.88330413_88330414delinsAA	ENSP00000366283:p.Phe924Asn	88.0|87.0	0.0		97.0	8.0|7.0	NM_015567	B3KNB8|B4DSH5|Q5VT81	Missense_Mutation	SNP	ENST00000325089.6	hg19	CCDS9465.1																																																																																			.	.		0.550	SLITRK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045416.3		
RALGAPA1	253959	hgsc.bcm.edu	37	14	36154285	36154285	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr14:36154285T>C	ENST00000389698.3	-	19	3016	c.2626A>G	c.(2626-2628)Aac>Gac	p.N876D	RALGAPA1_ENST00000307138.6_Missense_Mutation_p.N876D|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.N923D|RALGAPA1_ENST00000382366.3_Missense_Mutation_p.N889D	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	876					activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TTCTGCTTGTTTAGAATATCA	0.453																																					p.N876D		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.A2626G						.						30.0	28.0	28.0					14																	36154285		2199	4294	6493	SO:0001583	missense	253959	exon19			GCTTGTTTAGAAT	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.2626A>G	chr14.hg19:g.36154285T>C	ENSP00000374348:p.Asn876Asp	104.0	0.0		80.0	37.0	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	T	15.88	2.962179	0.53400	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000382366;ENST00000553892	D;D;D;D;D	0.94184	-3.33;-3.33;-3.37;-3.37;-3.37	6.07	6.07	0.98685	.	0.095237	0.64402	D	0.000001	D	0.90369	0.6986	L	0.32530	0.975	0.41780	D	0.989818	B;B;B;B;B	0.33212	0.353;0.089;0.402;0.167;0.025	B;B;B;B;B	0.39339	0.154;0.049;0.297;0.079;0.024	D	0.87928	0.2708	10	0.14252	T	0.57	-13.6835	16.6277	0.84984	0.0:0.0:0.0:1.0	.	923;889;923;876;876	Q6GYQ0-6;B9EK38;Q6GYQ0-3;Q6GYQ0-2;Q6GYQ0	.;.;.;.;RGPA1_HUMAN	D	876;876;876;923;889;923	ENSP00000374348:N876D;ENSP00000302647:N876D;ENSP00000258840:N923D;ENSP00000371803:N889D;ENSP00000451877:N923D	ENSP00000258840:N923D	N	-	1	0	RALGAPA1	35224036	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.399000	0.59703	2.330000	0.79161	0.528000	0.53228	AAC	.	.		0.453	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
BTBD7	55727	hgsc.bcm.edu	37	14	93714872	93714872	+	Nonsense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr14:93714872G>A	ENST00000334746.5	-	9	2378	c.2071C>T	c.(2071-2073)Cga>Tga	p.R691*	BTBD7_ENST00000554565.1_Nonsense_Mutation_p.R340*|BTBD7_ENST00000393170.2_Nonsense_Mutation_p.R265*	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	691					multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)		p.R691*(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		CTTAGCACTCGAATCTGAATT	0.527																																					p.R691X		Atlas-SNP	.											BTBD7,colon,carcinoma,0,1	BTBD7	112	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.C2071T						.						87.0	80.0	82.0					14																	93714872		2203	4300	6503	SO:0001587	stop_gained	55727	exon9			GCACTCGAATCTG	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2071C>T	chr14.hg19:g.93714872G>A	ENSP00000335615:p.Arg691*	93.0	0.0		89.0	25.0	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Nonsense_Mutation	SNP	ENST00000334746.5	hg19	CCDS32146.1	.	.	.	.	.	.	.	.	.	.	G	37	6.226650	0.97394	.	.	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	.	.	.	5.81	4.84	0.62591	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	17.6058	0.88037	0.0:0.0:0.8683:0.1317	.	.	.	.	X	691;340;306;265	.	ENSP00000335615:R691X	R	-	1	2	BTBD7	92784625	1.000000	0.71417	0.716000	0.30569	0.977000	0.68977	6.258000	0.72487	2.753000	0.94483	0.563000	0.77884	CGA	.	.		0.527	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860	
TRPM1	4308	hgsc.bcm.edu	37	15	31325077	31325077	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:31325077T>A	ENST00000256552.6	-	22	2914	c.2767A>T	c.(2767-2769)Atc>Ttc	p.I923F	RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.I940F|TRPM1_ENST00000397795.2_Missense_Mutation_p.I901F|RP11-348B17.1_ENST00000561299.1_RNA	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AGATCTGTGATGTTCCAGTAC	0.463																																					p.I940F		Atlas-SNP	.											.	TRPM1	183	.	0			c.A2818T						.						170.0	161.0	164.0					15																	31325077		1938	4138	6076	SO:0001583	missense	4308	exon21			CTGTGATGTTCCA	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2767A>T	chr15.hg19:g.31325077T>A	ENSP00000256552:p.Ile923Phe	253.0	0.0		236.0	10.0	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	hg19	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	T	24.5	4.535466	0.85812	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	D;D;D	0.98849	-5.18;-5.18;-5.18	5.59	5.59	0.84812	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.97901	0.9310	L	0.45470	1.425	0.80722	D	1	P;P	0.41929	0.765;0.594	B;P	0.48334	0.439;0.574	D	0.99044	1.0825	10	0.87932	D	0	-29.3404	15.7614	0.78082	0.0:0.0:0.0:1.0	.	895;901	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	F	901;940;923;901	ENSP00000380897:I901F;ENSP00000437849:I940F;ENSP00000256552:I923F	ENSP00000256552:I923F	I	-	1	0	TRPM1	29112369	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.260000	0.72502	2.114000	0.64651	0.523000	0.50628	ATC	.	.		0.463	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
RASGRP1	10125	hgsc.bcm.edu	37	15	38818572	38818572	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:38818572A>T	ENST00000310803.5	-	3	431	c.254T>A	c.(253-255)cTg>cAg	p.L85Q	RASGRP1_ENST00000561180.1_Missense_Mutation_p.L136Q|RP11-275I4.1_ENST00000559544.1_RNA|RASGRP1_ENST00000539159.1_Missense_Mutation_p.L37Q|RASGRP1_ENST00000558164.1_Missense_Mutation_p.L85Q|RASGRP1_ENST00000450598.2_Missense_Mutation_p.L85Q|RASGRP1_ENST00000559830.1_Missense_Mutation_p.L85Q	NM_001128602.1|NM_005739.3	NP_001122074.1|NP_005730.2	O95267	GRP1_HUMAN	RAS guanyl releasing protein 1 (calcium and DAG-regulated)	85	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.|Ras exchanger motif region; required for transforming activity. {ECO:0000250}.				activation of Rho GTPase activity (GO:0032862)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|mast cell degranulation (GO:0043303)|platelet activation (GO:0030168)|Ras protein signal transduction (GO:0007265)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)|secretory granule localization (GO:0032252)|signal transduction (GO:0007165)|vesicle transport along microtubule (GO:0047496)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|guanyl-nucleotide exchange factor activity (GO:0005085)|lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(2)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20		all_cancers(109;6.38e-17)|all_epithelial(112;5.51e-15)|Lung NSC(122;2.12e-11)|all_lung(180;5.63e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;1.97e-07)|BRCA - Breast invasive adenocarcinoma(123;0.00248)		GACTTGCAACAGTTGGTTACT	0.458																																					p.L85Q		Atlas-SNP	.											.	RASGRP1	50	.	0			c.T254A						.						134.0	130.0	131.0					15																	38818572		1948	4147	6095	SO:0001583	missense	10125	exon3			TGCAACAGTTGGT	AF106071	CCDS45221.1, CCDS45222.1	15q15	2013-01-10				ENSG00000172575		"""EF-hand domain containing"""	9878	protein-coding gene	gene with protein product		603962				10087292, 9789079	Standard	NM_005739		Approved	CalDAG-GEFII, RASGRP	uc001zke.4	O95267		ENST00000310803.5:c.254T>A	chr15.hg19:g.38818572A>T	ENSP00000310244:p.Leu85Gln	85.0	0.0		99.0	26.0	NM_001128602	Q56CZ0|Q58G75|Q59HB1|Q5I3A8|Q6GV31|Q6NX39|Q7LDG6|Q9UI94|Q9UNN9	Missense_Mutation	SNP	ENST00000310803.5	hg19	CCDS45222.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.047458	0.36085	.	.	ENSG00000172575	ENST00000310803;ENST00000450598;ENST00000415523;ENST00000431814;ENST00000539159;ENST00000414708;ENST00000541438	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	4.62	3.48	0.39840	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.160455	0.43260	N	0.000594	T	0.50154	0.1599	L	0.60845	1.875	0.52501	D	0.99995	B;B	0.24317	0.062;0.101	B;B	0.30782	0.12;0.098	T	0.51371	-0.8714	10	0.72032	D	0.01	-3.4223	10.6141	0.45441	0.8559:0.0:0.0:0.1441	.	85;85	O95267;O95267-2	GRP1_HUMAN;.	Q	85;85;85;85;37;85;85	ENSP00000310244:L85Q;ENSP00000388540:L85Q;ENSP00000444762:L37Q;ENSP00000413105:L85Q	ENSP00000310244:L85Q	L	-	2	0	RASGRP1	36605864	1.000000	0.71417	0.810000	0.32431	0.390000	0.30446	6.019000	0.70818	0.782000	0.33613	0.379000	0.24179	CTG	.	.		0.458	RASGRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418223.1	NM_005739	
KNSTRN	90417	hgsc.bcm.edu	37	15	40675114	40675114	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:40675114A>T	ENST00000249776.8	+	1	193	c.78A>T	c.(76-78)ccA>ccT	p.P26P	KNSTRN_ENST00000416151.2_Silent_p.P26P|KNSTRN_ENST00000608100.1_5'Flank|KNSTRN_ENST00000448395.2_Silent_p.P26P	NM_033286.3	NP_150628.3			kinetochore-localized astrin/SPAG5 binding protein																		ATTCCCACCCACTTCCGCCTA	0.562																																					p.P26P		Atlas-SNP	.											.	.	.	.	0			c.A78T						.						44.0	48.0	46.0					15																	40675114		1872	4108	5980	SO:0001819	synonymous_variant	90417	exon1			CCACCCACTTCCG	AK027408	CCDS42021.1, CCDS45226.1, CCDS45227.1	15q15.1	2013-01-17	2012-12-04	2012-12-04	ENSG00000128944	ENSG00000128944			30767	protein-coding gene	gene with protein product	"""small kinetochore-associated protein"", ""kinetochore-localized astrin-binding protein"", ""TRAF4 associated factor 1"""	614718	"""chromosome 15 open reading frame 23"""	C15orf23		12477932	Standard	NM_033286		Approved	FLJ14502, SKAP, kinastrin, TRAF4AF1	uc001zll.3	Q9Y448	OTTHUMG00000172454	ENST00000249776.8:c.78A>T	chr15.hg19:g.40675114A>T		108.0	0.0		122.0	9.0	NM_033286		Silent	SNP	ENST00000249776.8	hg19	CCDS42021.1																																																																																			.	.		0.562	KNSTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418636.1	NM_001142761	
CASC5	57082	hgsc.bcm.edu	37	15	40917526	40917526	+	Silent	SNP	G	G	T	rs369221746		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:40917526G>T	ENST00000346991.5	+	11	5532	c.5142G>T	c.(5140-5142)ccG>ccT	p.P1714P	CASC5_ENST00000399668.2_Silent_p.P1688P			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1714					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		AAACTCAGCCGGTCTCTAGCA	0.398																																					p.P1714P		Atlas-SNP	.											.	CASC5	269	.	0			c.G5142T						.						79.0	76.0	77.0					15																	40917526		1828	4080	5908	SO:0001819	synonymous_variant	57082	exon11			TCAGCCGGTCTCT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.5142G>T	chr15.hg19:g.40917526G>T		66.0	0.0		82.0	5.0	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	hg19	CCDS42023.1																																																																																			.	.		0.398	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
TGM7	116179	hgsc.bcm.edu	37	15	43571320	43571320	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:43571320T>C	ENST00000452443.2	-	11	1838	c.1834A>G	c.(1834-1836)Att>Gtt	p.I612V		NM_052955.2	NP_443187.1	Q96PF1	TGM7_HUMAN	transglutaminase 7	612					peptide cross-linking (GO:0018149)		metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(2)|prostate(4)|skin(1)	39		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.14e-07)	L-Glutamine(DB00130)	ACTACCTCAATAGACAAGTGG	0.572																																					p.I612V		Atlas-SNP	.											.	TGM7	86	.	0			c.A1834G						.						72.0	61.0	65.0					15																	43571320		2202	4299	6501	SO:0001583	missense	116179	exon11			CCTCAATAGACAA	AF363393	CCDS32213.1	15q15.2	2004-07-01				ENSG00000159495		"""Transglutaminases"""	30790	protein-coding gene	gene with protein product	"""transglutaminase Z"""	606776				11390390	Standard	NM_052955		Approved	TGMZ	uc001zrf.1	Q96PF1		ENST00000452443.2:c.1834A>G	chr15.hg19:g.43571320T>C	ENSP00000389466:p.Ile612Val	90.0	0.0		113.0	6.0	NM_052955		Missense_Mutation	SNP	ENST00000452443.2	hg19	CCDS32213.1	.	.	.	.	.	.	.	.	.	.	T	15.98	2.991898	0.54041	.	.	ENSG00000159495	ENST00000452443	T	0.71222	-0.55	5.17	5.17	0.71159	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78426	0.4281	L	0.55990	1.75	0.28708	N	0.9037	D	0.69078	0.997	D	0.80764	0.994	T	0.71724	-0.4506	10	0.29301	T	0.29	-10.6882	11.4439	0.50112	0.0:0.0:0.0:1.0	.	612	Q96PF1	TGM7_HUMAN	V	612	ENSP00000389466:I612V	ENSP00000389466:I612V	I	-	1	0	TGM7	41358612	0.987000	0.35691	0.918000	0.36340	0.440000	0.31957	1.643000	0.37217	1.963000	0.57068	0.528000	0.53228	ATT	.	.		0.572	TGM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432489.1	NM_052955	
MAP1A	4130	hgsc.bcm.edu	37	15	43819173	43819173	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:43819173T>A	ENST00000300231.5	+	4	5952	c.5502T>A	c.(5500-5502)acT>acA	p.T1834T	MAP1A_ENST00000382031.1_Silent_p.T2072T|MAP1A_ENST00000399453.1_Silent_p.T1834T			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1834					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	ATGAACCCACTACTCCCTCAT	0.617																																					p.T1834T		Atlas-SNP	.											.	MAP1A	189	.	0			c.T5502A						.						84.0	83.0	84.0					15																	43819173		1964	4162	6126	SO:0001819	synonymous_variant	4130	exon4			ACCCACTACTCCC	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5502T>A	chr15.hg19:g.43819173T>A		145.0	0.0		139.0	8.0	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Silent	SNP	ENST00000300231.5	hg19	CCDS42031.1																																																																																			.	.		0.617	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
USP8	9101	hgsc.bcm.edu	37	15	50782610	50782610	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:50782610A>G	ENST00000396444.3	+	14	2460	c.2122A>G	c.(2122-2124)Agg>Ggg	p.R708G	USP8_ENST00000433963.1_Missense_Mutation_p.R708G|USP8_ENST00000425032.3_Missense_Mutation_p.R602G|USP8_ENST00000307179.4_Missense_Mutation_p.R708G	NM_001128610.1|NM_005154.3	NP_001122082.1|NP_005145.3	P40818	UBP8_HUMAN	ubiquitin specific peptidase 8	708					cell proliferation (GO:0008283)|endosome organization (GO:0007032)|mitotic cytokinesis (GO:0000281)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|Ras protein signal transduction (GO:0007265)|ubiquitin-dependent protein catabolic process (GO:0006511)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|extrinsic component of plasma membrane (GO:0019897)|midbody (GO:0030496)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	35				all cancers(107;0.000225)|GBM - Glioblastoma multiforme(94;0.000771)		TGAGCGGGATAGGGAACCTTC	0.502																																					p.R708G		Atlas-SNP	.											.	USP8	90	.	0			c.A2122G						.						119.0	114.0	116.0					15																	50782610		2196	4294	6490	SO:0001583	missense	9101	exon14			CGGGATAGGGAAC	D29956	CCDS10137.1, CCDS61632.1	15q21.1	2014-03-03	2005-08-08		ENSG00000138592	ENSG00000138592		"""Ubiquitin-specific peptidases"""	12631	protein-coding gene	gene with protein product		603158	"""ubiquitin specific protease 8"""			12838346, 9582025, 24482476	Standard	NM_005154		Approved	HumORF8, KIAA0055, UBPY, SPG59	uc001zyl.4	P40818	OTTHUMG00000131645	ENST00000396444.3:c.2122A>G	chr15.hg19:g.50782610A>G	ENSP00000379721:p.Arg708Gly	137.0	0.0		146.0	43.0	NM_001128610	B4DKA8|Q2TB31|Q7Z3U2|Q86VA0|Q8IWI7	Missense_Mutation	SNP	ENST00000396444.3	hg19	CCDS10137.1	.	.	.	.	.	.	.	.	.	.	A	14.01	2.407400	0.42715	.	.	ENSG00000138592	ENST00000396444;ENST00000433963;ENST00000307179;ENST00000425032	T;T;T;T	0.02446	4.29;4.29;4.29;4.29	5.6	0.0629	0.14346	.	0.213831	0.47455	D	0.000225	T	0.03178	0.0093	L	0.32530	0.975	0.32942	D	0.518504	B;B	0.33583	0.418;0.411	B;B	0.33042	0.157;0.11	T	0.13845	-1.0494	10	0.49607	T	0.09	-9.3646	16.1962	0.82025	0.4289:0.5711:0.0:0.0	.	602;708	B4DKA8;P40818	.;UBP8_HUMAN	G	708;708;708;602	ENSP00000379721:R708G;ENSP00000405537:R708G;ENSP00000302239:R708G;ENSP00000412682:R602G	ENSP00000302239:R708G	R	+	1	2	USP8	48569902	0.968000	0.33430	0.305000	0.25099	0.760000	0.43138	2.451000	0.44952	-0.164000	0.10927	0.528000	0.53228	AGG	.	.		0.502	USP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254541.1	NM_005154	
AP4E1	23431	hgsc.bcm.edu	37	15	51285722	51285722	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:51285722A>T	ENST00000261842.5	+	17	2352	c.2246A>T	c.(2245-2247)gAt>gTt	p.D749V	AP4E1_ENST00000560508.1_Missense_Mutation_p.D674V	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	749					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		ACTAAAAAGGATCAATCTCAA	0.398																																					p.D749V		Atlas-SNP	.											.	AP4E1	78	.	0			c.A2246T						.						111.0	99.0	103.0					15																	51285722		2196	4294	6490	SO:0001583	missense	23431	exon17			AAAAGGATCAATC	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.2246A>T	chr15.hg19:g.51285722A>T	ENSP00000261842:p.Asp749Val	76.0	0.0		95.0	8.0	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	hg19	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	11.73	1.726980	0.30593	.	.	ENSG00000081014	ENST00000261842	T	0.18338	2.22	5.29	4.17	0.49024	.	0.298700	0.37178	N	0.002207	T	0.09774	0.0240	N	0.19112	0.55	0.24216	N	0.995458	B	0.20671	0.047	B	0.19148	0.024	T	0.16482	-1.0401	10	0.34782	T	0.22	-12.0798	6.545	0.22400	0.7445:0.1709:0.0845:0.0	.	749	Q9UPM8	AP4E1_HUMAN	V	749	ENSP00000261842:D749V	ENSP00000261842:D749V	D	+	2	0	AP4E1	49073014	0.971000	0.33674	0.349000	0.25694	0.973000	0.67179	2.456000	0.44997	1.988000	0.58038	0.460000	0.39030	GAT	.	.		0.398	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
LMAN1L	79748	hgsc.bcm.edu	37	15	75115899	75115899	+	Splice_Site	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:75115899G>T	ENST00000309664.5	+	12	1338		c.e12-1		CPLX3_ENST00000395018.4_5'Flank|RP11-414J4.2_ENST00000564823.1_RNA|LMAN1L_ENST00000379709.3_Splice_Site	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like							integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						CCCCCGGTTAGGGATGCAGCT	0.552																																					.		Atlas-SNP	.											.	LMAN1L	43	.	0			c.1200-1G>T						.						79.0	73.0	75.0					15																	75115899		2197	4296	6493	SO:0001630	splice_region_variant	79748	exon12			CGGTTAGGGATGC	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.1200-1G>T	chr15.hg19:g.75115899G>T		81.0	0.0		51.0	7.0	NM_021819	Q6UWN2	Splice_Site	SNP	ENST00000309664.5	hg19	CCDS10270.1	.	.	.	.	.	.	.	.	.	.	G	6.238	0.412061	0.11812	.	.	ENSG00000140506	ENST00000309664;ENST00000379709	.	.	.	5.18	3.31	0.37934	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.1271	0.31005	0.187:0.0:0.813:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LMAN1L	72902952	0.998000	0.40836	0.406000	0.26421	0.135000	0.20990	4.701000	0.61810	0.703000	0.31848	0.561000	0.74099	.	.	.		0.552	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		Intron
LINGO1	84894	hgsc.bcm.edu	37	15	77907675	77907675	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:77907675T>G	ENST00000355300.6	-	2	748	c.574A>C	c.(574-576)Agc>Cgc	p.S192R	LINGO1_ENST00000561030.1_Missense_Mutation_p.S186R	NM_032808.5	NP_116197.4	Q96FE5	LIGO1_HUMAN	leucine rich repeat and Ig domain containing 1	192					central nervous system neuron development (GO:0021954)|negative regulation of axonogenesis (GO:0050771)|negative regulation of oligodendrocyte differentiation (GO:0048715)|neuron projection development (GO:0031175)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein kinase B signaling (GO:0043491)|regulation of axonogenesis (GO:0050770)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31						TGCTCCAGGCTGTTGAGGCCG	0.597																																					p.S192R		Atlas-SNP	.											.	LINGO1	76	.	0			c.A574C						.						119.0	125.0	123.0					15																	77907675		2168	4271	6439	SO:0001583	missense	84894	exon2			CCAGGCTGTTGAG	AK027500	CCDS45313.1, CCDS73766.1	15q24	2013-01-11	2007-02-01	2007-02-01		ENSG00000169783		"""Immunoglobulin superfamily / I-set domain containing"""	21205	protein-coding gene	gene with protein product		609791	"""leucine rich repeat neuronal 6A"""	LRRN6A		14686891	Standard	XM_006720723		Approved	FLJ14594, LERN1	uc002bct.1	Q96FE5		ENST00000355300.6:c.574A>C	chr15.hg19:g.77907675T>G	ENSP00000347451:p.Ser192Arg	133.0	0.0		138.0	57.0	NM_032808	D3DW80|Q6NUK3|Q6UXM3|Q6VVG0|Q6VVG1|Q6VVG2|Q8N3K5|Q96K52	Missense_Mutation	SNP	ENST00000355300.6	hg19	CCDS45313.1	.	.	.	.	.	.	.	.	.	.	T	17.13	3.312077	0.60414	.	.	ENSG00000169783	ENST00000355300	D	0.81659	-1.52	5.29	3.01	0.34805	.	0.079382	0.85682	D	0.000000	T	0.77731	0.4174	L	0.42581	1.335	0.80722	D	1	D	0.60575	0.988	P	0.51777	0.679	T	0.74343	-0.3696	10	0.37606	T	0.19	.	8.9041	0.35512	0.0:0.1513:0.0:0.8487	.	192	Q96FE5	LIGO1_HUMAN	R	192	ENSP00000347451:S192R	ENSP00000347451:S192R	S	-	1	0	LINGO1	75694730	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.256000	0.58810	0.863000	0.35553	0.459000	0.35465	AGC	.	.		0.597	LINGO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419546.1	NM_032808	
ALPK3	57538	hgsc.bcm.edu	37	15	85401062	85401062	+	Silent	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr15:85401062G>T	ENST00000258888.5	+	6	3866	c.3699G>T	c.(3697-3699)ctG>ctT	p.L1233L		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1233					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGACCCTGCTGCTGAGCCCCT	0.682																																					p.L1233L		Atlas-SNP	.											.	ALPK3	289	.	0			c.G3699T						.						59.0	40.0	47.0					15																	85401062		2203	4299	6502	SO:0001819	synonymous_variant	57538	exon6			CCTGCTGCTGAGC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3699G>T	chr15.hg19:g.85401062G>T		32.0	0.0		24.0	7.0	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	hg19	CCDS10333.1																																																																																			.	.		0.682	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
TPSD1	23430	hgsc.bcm.edu	37	16	1308140	1308140	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:1308140A>T	ENST00000211076.3	+	4	749	c.601A>T	c.(601-603)Acc>Tcc	p.T201S	RP11-616M22.5_ENST00000566997.1_RNA|TPSD1_ENST00000397534.2_Missense_Mutation_p.T194S|PRSS29P_ENST00000568091.1_lincRNA	NM_012217.2	NP_036349.1	Q9BZJ3	TRYD_HUMAN	tryptase delta 1	201	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	20		Hepatocellular(780;0.00369)				GGAATATCACACCGGCCTCCA	0.637																																					p.T201S		Atlas-SNP	.											.	TPSD1	47	.	0			c.A601T						.						52.0	51.0	51.0					16																	1308140		2194	4299	6493	SO:0001583	missense	23430	exon4			TATCACACCGGCC	AF206664	CCDS10432.1	16p13.3	2008-07-29			ENSG00000095917	ENSG00000095917	3.4.21.59		14118	protein-coding gene	gene with protein product	"""mMCP-7-like II"", ""mMCP-7-like I"", ""MMCP-7-LIKE-2"""	609272				9920877	Standard	NM_012217		Approved		uc002clb.1	Q9BZJ3	OTTHUMG00000128511	ENST00000211076.3:c.601A>T	chr16.hg19:g.1308140A>T	ENSP00000211076:p.Thr201Ser	244.0	0.0		275.0	14.0	NM_012217	O95824|Q8TDI6|Q96L36|Q96RZ5|Q9H2Y6|Q9UQI8	Missense_Mutation	SNP	ENST00000211076.3	hg19	CCDS10432.1	.	.	.	.	.	.	.	.	.	.	N	2.623	-0.288029	0.05605	.	.	ENSG00000095917	ENST00000397534;ENST00000211076	D;D	0.88664	-2.41;-2.41	3.31	-4.99	0.03010	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	1.254980	0.05769	N	0.606319	T	0.65585	0.2705	N	0.02697	-0.525	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.21360	0.034;0.034	T	0.60949	-0.7161	10	0.08599	T	0.76	.	0.3843	0.00400	0.2046:0.2921:0.2158:0.2875	.	185;201	C9JJL5;Q9BZJ3	.;TRYD_HUMAN	S	194;201	ENSP00000380668:T194S;ENSP00000211076:T201S	ENSP00000211076:T201S	T	+	1	0	TPSD1	1248141	0.019000	0.18553	0.001000	0.08648	0.002000	0.02628	0.552000	0.23376	-0.557000	0.06126	-0.622000	0.04023	ACC	.	.		0.637	TPSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250320.2		
CLCN7	1186	hgsc.bcm.edu	37	16	1510832	1510832	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:1510832T>A	ENST00000382745.4	-	5	1074	c.469A>T	c.(469-471)Agg>Tgg	p.R157W	CLCN7_ENST00000262318.8_Missense_Mutation_p.R133W|CLCN7_ENST00000448525.1_Missense_Mutation_p.R133W	NM_001287.5	NP_001278.1	P51798	CLCN7_HUMAN	chloride channel, voltage-sensitive 7	157					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|response to pH (GO:0009268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			breast(2)|central_nervous_system(3)|endometrium(3)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|skin(2)	24		Hepatocellular(780;0.0893)				TTGATGACCCTGTACTTGAGG	0.642																																					p.R157W		Atlas-SNP	.											.	CLCN7	53	.	0			c.A469T						.						93.0	79.0	84.0					16																	1510832		2199	4300	6499	SO:0001583	missense	1186	exon5			TGACCCTGTACTT	Z67743	CCDS32361.1, CCDS45378.1	16p13	2012-09-26	2012-02-23		ENSG00000103249	ENSG00000103249		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ion channels / Chloride channels : Voltage-sensitive"""	2025	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 63"""	602727	"""chloride channel 7"""			8543009	Standard	NM_001114331		Approved	CLC-7, OPTA2, CLC7, ClC-7, PPP1R63	uc002clv.3	P51798	OTTHUMG00000044467	ENST00000382745.4:c.469A>T	chr16.hg19:g.1510832T>A	ENSP00000372193:p.Arg157Trp	169.0	0.0		156.0	13.0	NM_001287	A6NEJ7|A8K5T9|A8K7X1|B3KPN3|E9PDB9|Q9NYX5	Missense_Mutation	SNP	ENST00000382745.4	hg19	CCDS32361.1	.	.	.	.	.	.	.	.	.	.	T	16.30	3.084302	0.55861	.	.	ENSG00000103249	ENST00000448525;ENST00000262318;ENST00000382745;ENST00000428756	D;D	0.84873	-1.91;-1.91	4.7	-4.2	0.03823	Chloride channel, core (2);	0.650704	0.15751	N	0.246406	T	0.72724	0.3496	N	0.24115	0.695	0.30683	N	0.752097	B;P	0.36712	0.001;0.566	B;B	0.32393	0.008;0.145	T	0.64909	-0.6296	10	0.54805	T	0.06	-21.6841	17.2688	0.87095	0.0:0.0:0.7037:0.2963	.	133;157	E9PDB9;P51798	.;CLCN7_HUMAN	W	133;110;157;99	ENSP00000410907:R133W;ENSP00000372193:R157W	ENSP00000262318:R110W	R	-	1	2	CLCN7	1450833	0.016000	0.18221	0.779000	0.31741	0.948000	0.59901	-0.084000	0.11268	-0.489000	0.06716	-0.438000	0.05819	AGG	.	.		0.642	CLCN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103598.2	NM_001287	
PGP	283871	hgsc.bcm.edu	37	16	2263817	2263817	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:2263817T>A	ENST00000333503.7	-	2	907	c.878A>T	c.(877-879)cAg>cTg	p.Q293L	BRICD5_ENST00000562360.1_5'Flank|RP11-304L19.8_ENST00000561544.1_lincRNA|BRICD5_ENST00000566018.1_5'Flank|BRICD5_ENST00000328540.3_5'Flank	NM_001042371.2	NP_001035830.1	A6NDG6	PGP_HUMAN	phosphoglycolate phosphatase	293					carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|peptidyl-tyrosine dephosphorylation (GO:0035335)		magnesium ion binding (GO:0000287)|nucleotide phosphatase activity, acting on free nucleotides (GO:0098519)|phosphoglycolate phosphatase activity (GO:0008967)|protein tyrosine phosphatase activity (GO:0004725)			skin(1)	1						GTCACTTTCCTGATTATTCTT	0.517																																					p.Q293L	GBM(63;906 1080 2092 17773 18795)	Atlas-SNP	.											.	PGP	6	.	0			c.A878T						.						127.0	129.0	128.0					16																	2263817		1975	4166	6141	SO:0001583	missense	283871	exon2			CTTTCCTGATTAT	BC035985	CCDS42104.1	16p13.3	2012-10-02				ENSG00000184207	3.1.3.18		8909	protein-coding gene	gene with protein product		172280					Standard	NM_001042371		Approved		uc002cpk.1	A6NDG6		ENST00000333503.7:c.878A>T	chr16.hg19:g.2263817T>A	ENSP00000330918:p.Gln293Leu	201.0	0.0		273.0	15.0	NM_001042371		Missense_Mutation	SNP	ENST00000333503.7	hg19	CCDS42104.1	.	.	.	.	.	.	.	.	.	.	T	11.51	1.660391	0.29515	.	.	ENSG00000184207	ENST00000333503	T	0.31769	1.48	4.76	4.76	0.60689	HAD-like domain (2);	0.186034	0.48286	D	0.000184	T	0.23886	0.0578	L	0.33093	0.98	0.80722	D	1	B	0.09022	0.002	B	0.15052	0.012	T	0.04333	-1.0959	10	0.25751	T	0.34	-24.7375	13.2447	0.60016	0.0:0.0:0.0:1.0	.	293	A6NDG6	PGP_HUMAN	L	293	ENSP00000330918:Q293L	ENSP00000330918:Q293L	Q	-	2	0	PGP	2203818	1.000000	0.71417	1.000000	0.80357	0.904000	0.53231	1.300000	0.33436	1.991000	0.58162	0.533000	0.62120	CAG	.	.		0.517	PGP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435095.1	NM_024118	
VWA3A	146177	hgsc.bcm.edu	37	16	22126671	22126671	+	Silent	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:22126671C>T	ENST00000389398.5	+	9	789	c.693C>T	c.(691-693)ctC>ctT	p.L231L	VWA3A_ENST00000389397.4_5'UTR	NM_173615.3	NP_775886.3	A6NCI4	VWA3A_HUMAN	von Willebrand factor A domain containing 3A	231						extracellular region (GO:0005576)				haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)|skin(1)	7				GBM - Glioblastoma multiforme(48;0.0439)		CTCCCAGCCTCCAGGAACTTA	0.443																																					p.L231L		Atlas-SNP	.											.	VWA3A	115	.	0			c.C693T						.						33.0	34.0	34.0					16																	22126671		1863	4111	5974	SO:0001819	synonymous_variant	146177	exon9			CAGCCTCCAGGAA	AK128606, AK098260	CCDS45441.1	16p12.1	2008-02-05				ENSG00000175267			27088	protein-coding gene	gene with protein product						12477932	Standard	XM_006721021		Approved	FLJ46765, FLJ40941	uc010vbq.2	A6NCI4		ENST00000389398.5:c.693C>T	chr16.hg19:g.22126671C>T		116.0	0.0		173.0	36.0	NM_173615	A4QMU8|A6NNC0|Q6UTX4|Q6ZQZ9|Q8IUY6|Q8N9W1	Silent	SNP	ENST00000389398.5	hg19	CCDS45441.1																																																																																			.	.		0.443	VWA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430052.1		
ZNF629	23361	hgsc.bcm.edu	37	16	30793613	30793613	+	Missense_Mutation	SNP	T	T	A	rs200655215		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:30793613T>A	ENST00000262525.4	-	3	2243	c.2036A>T	c.(2035-2037)cAg>cTg	p.Q679L	RP11-2C24.6_ENST00000575562.1_RNA	NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	679					regulation of transcription, DNA-templated (GO:0006355)|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)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GAGCTGATGCTGGAGGAGCAC	0.592																																					p.Q679L		Atlas-SNP	.											.	ZNF629	44	.	0			c.A2036T						.						24.0	25.0	25.0					16																	30793613		2045	4204	6249	SO:0001583	missense	23361	exon3			TGATGCTGGAGGA	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.2036A>T	chr16.hg19:g.30793613T>A	ENSP00000262525:p.Gln679Leu	140.0	0.0		186.0	13.0	NM_001080417	Q15938	Missense_Mutation	SNP	ENST00000262525.4	hg19	CCDS45463.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226046	0.39300	.	.	ENSG00000102870	ENST00000262525	T	0.51325	0.71	5.89	5.89	0.94794	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.42053	D	0.000772	T	0.38453	0.1041	N	0.19112	0.55	0.21652	N	0.999607	P	0.38922	0.651	B	0.42163	0.378	T	0.30208	-0.9986	10	0.26408	T	0.33	-24.1685	15.2948	0.73894	0.0:0.0:0.0:1.0	.	679	Q9UEG4	ZN629_HUMAN	L	679	ENSP00000262525:Q679L	ENSP00000262525:Q679L	Q	-	2	0	ZNF629	30701114	0.000000	0.05858	0.935000	0.37517	0.994000	0.84299	0.243000	0.18106	2.254000	0.74563	0.459000	0.35465	CAG	.	T|1.000;C|0.000		0.592	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
NIP7	51388	hgsc.bcm.edu	37	16	69375171	69375171	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr16:69375171A>G	ENST00000254940.5	+	4	771	c.371A>G	c.(370-372)aAt>aGt	p.N124S	COG8_ENST00000306875.4_5'Flank|COG8_ENST00000562081.1_5'Flank|RP11-343C2.7_ENST00000564737.1_Intron|RP11-343C2.9_ENST00000563634.1_Intron|NIP7_ENST00000254941.6_Intron	NM_016101.4	NP_057185.1	Q9Y221	NIP7_HUMAN	NIP7, nucleolar pre-rRNA processing protein	124	C-terminal domain.|PUA. {ECO:0000255|PROSITE- ProRule:PRU00161}.				ribosome assembly (GO:0042255)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)	6		Ovarian(137;0.101)				ATCACTGAAAATACTTCTCAG	0.443																																					p.N124S		Atlas-SNP	.											.	NIP7	20	.	0			c.A371G						.						112.0	103.0	106.0					16																	69375171		2198	4300	6498	SO:0001583	missense	51388	exon4			CTGAAAATACTTC	AB112439	CCDS10877.1, CCDS56003.1	16q22.1	2013-03-04	2013-03-04		ENSG00000132603	ENSG00000132603			24328	protein-coding gene	gene with protein product			"""nuclear import 7 homolog (S. cerevisiae)"""			14660641, 22195017	Standard	NM_016101		Approved	CGI-37, FLJ10296, HSPC031, KD93	uc002exa.3	Q9Y221	OTTHUMG00000137568	ENST00000254940.5:c.371A>G	chr16.hg19:g.69375171A>G	ENSP00000254940:p.Asn124Ser	208.0	0.0		136.0	73.0	NM_016101	B2RD04|Q9NZZ0	Missense_Mutation	SNP	ENST00000254940.5	hg19	CCDS10877.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399639	0.42512	.	.	ENSG00000132603	ENST00000254940	.	.	.	5.53	5.53	0.82687	Pseudouridine synthase/archaeosine transglycosylase (2);PUA-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53061	0.1773	L	0.42245	1.32	0.80722	D	1	B	0.12013	0.005	B	0.17433	0.018	T	0.49978	-0.8881	9	0.35671	T	0.21	-23.6487	10.8189	0.46593	0.9264:0.0:0.0736:0.0	.	124	Q9Y221	NIP7_HUMAN	S	124	.	ENSP00000254940:N124S	N	+	2	0	NIP7	67932672	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.466000	0.53071	2.101000	0.63845	0.459000	0.35465	AAT	.	.		0.443	NIP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268947.2	NM_016101	
TP53	7157	hgsc.bcm.edu	37	17	7578190	7578190	+	Missense_Mutation	SNP	T	T	C	rs121912666		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:7578190T>C	ENST00000269305.4	-	6	848	c.659A>G	c.(658-660)tAt>tGt	p.Y220C	TP53_ENST00000413465.2_Missense_Mutation_p.Y220C|TP53_ENST00000420246.2_Missense_Mutation_p.Y220C|TP53_ENST00000455263.2_Missense_Mutation_p.Y220C|TP53_ENST00000445888.2_Missense_Mutation_p.Y220C|TP53_ENST00000359597.4_Missense_Mutation_p.Y220C|TP53_ENST00000574684.1_Intron	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	220	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		Y -> C (in LFS; germline mutation and in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:7682763, ECO:0000269|PubMed:9450901}.|Y -> D (in sporadic cancers; somatic mutation).|Y -> F (in a sporadic cancer; somatic mutation).|Y -> H (in sporadic cancers; somatic mutation).|Y -> N (in sporadic cancers; somatic mutation).|Y -> S (in a brain tumor with no family history; germline mutation and in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Y220C(278)|p.Y127C(24)|p.Y220S(12)|p.?(11)|p.0?(8)|p.D208fs*1(1)|p.Y220_P223delYEPP(1)|p.V218_E224delVPYEPPE(1)|p.V218_E221delVPYE(1)|p.Y127S(1)|p.V218_Y220delVPY(1)|p.Y220fs*25(1)|p.V216_Y220delVVVPY(1)|p.Y220fs*2(1)|p.V218fs*26(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	AGGCGGCTCATAGGGCACCAC	0.557		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.Y220C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,0,1	TP53	33396	.	343	Substitution - Missense(315)|Unknown(11)|Whole gene deletion(8)|Deletion - In frame(5)|Deletion - Frameshift(3)|Insertion - Frameshift(1)	ovary(55)|breast(54)|lung(37)|upper_aerodigestive_tract(35)|urinary_tract(19)|oesophagus(19)|large_intestine(17)|liver(17)|central_nervous_system(16)|stomach(15)|haematopoietic_and_lymphoid_tissue(15)|endometrium(14)|soft_tissue(8)|biliary_tract(6)|bone(5)|pancreas(4)|prostate(4)|peritoneum(2)|small_intestine(1)	c.A659G	GRCh37	CM015378|CM951227	TP53	M	rs121912666	.						102.0	94.0	97.0					17																	7578190		2203	4300	6503	SO:0001583	missense	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	GGCTCATAGGGCA	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.659A>G	chr17.hg19:g.7578190T>C	ENSP00000269305:p.Tyr220Cys	212.0	0.0		158.0	75.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.248510	0.80024	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99840	-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08;-7.08	5.28	5.28	0.74379	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.99822	0.9921	M	0.89287	3.02	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.998;0.996;1.0;0.999;0.998;1.0	D	0.96735	0.9542	10	0.87932	D	0	-1.87	13.4753	0.61306	0.0:0.0:0.0:1.0	.	181;220;220;127;220;220;220	B4E095;P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;.;P53_HUMAN;.;.	C	220;220;220;220;220;220;209;127;88;127	ENSP00000410739:Y220C;ENSP00000352610:Y220C;ENSP00000269305:Y220C;ENSP00000398846:Y220C;ENSP00000391127:Y220C;ENSP00000391478:Y220C;ENSP00000425104:Y88C;ENSP00000423862:Y127C	ENSP00000269305:Y220C	Y	-	2	0	TP53	7518915	1.000000	0.71417	0.585000	0.28666	0.993000	0.82548	6.232000	0.72313	2.128000	0.65567	0.460000	0.39030	TAT	.	.		0.557	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
MYH8	4626	hgsc.bcm.edu	37	17	10317595	10317595	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:10317595T>A	ENST00000403437.2	-	11	1016	c.922A>T	c.(922-924)Acc>Tcc	p.T308S	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	308	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TATGGGTTGGTGGTGATCAGG	0.388									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.T308S		Atlas-SNP	.											.	MYH8	346	.	0			c.A922T						.						232.0	221.0	224.0					17																	10317595		2203	4300	6503	SO:0001583	missense	4626	exon11	Familial Cancer Database	Carney Complex Variant	GGTTGGTGGTGAT		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.922A>T	chr17.hg19:g.10317595T>A	ENSP00000384330:p.Thr308Ser	332.0	0.0		257.0	26.0	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	T	16.15	3.042154	0.55003	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	T	0.70749	-0.51	4.83	4.83	0.62350	Myosin head, motor domain (2);	0.000000	0.42964	U	0.000637	T	0.61874	0.2382	L	0.35414	1.06	0.47094	D	0.999317	B	0.12013	0.005	B	0.21917	0.037	T	0.59537	-0.7436	10	0.44086	T	0.13	.	14.5571	0.68109	0.0:0.0:0.0:1.0	.	308	P13535	MYH8_HUMAN	S	308	ENSP00000384330:T308S	ENSP00000252173:T308S	T	-	1	0	MYH8	10258320	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.939000	0.63526	2.036000	0.60181	0.533000	0.62120	ACC	.	.		0.388	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
COPS3	8533	hgsc.bcm.edu	37	17	17179373	17179373	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:17179373T>A	ENST00000268717.5	-	2	267	c.161A>T	c.(160-162)cAc>cTc	p.H54L	COPS3_ENST00000439936.2_Missense_Mutation_p.H34L|COPS3_ENST00000539941.2_Missense_Mutation_p.H34L	NM_003653.3	NP_003644.2	Q9UNS2	CSN3_HUMAN	COP9 signalosome subunit 3	54					cullin deneddylation (GO:0010388)|in utero embryonic development (GO:0001701)|response to light stimulus (GO:0009416)|signal transduction (GO:0007165)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)				NS(1)|large_intestine(3)|lung(6)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	13						GCCCAAGGAGTGTTCTTGTAC	0.438																																					p.H54L		Atlas-SNP	.											.	COPS3	41	.	0			c.A161T						.						121.0	107.0	112.0					17																	17179373		2203	4300	6503	SO:0001583	missense	8533	exon2			AAGGAGTGTTCTT	AF031647	CCDS11183.1, CCDS56022.1	17p11.2	2013-03-14	2013-03-14		ENSG00000141030	ENSG00000141030			2239	protein-coding gene	gene with protein product		604665	"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 3"", ""COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)"""			9535219, 10191102	Standard	NM_003653		Approved	SGN3, CSN3	uc002grd.3	Q9UNS2	OTTHUMG00000059281	ENST00000268717.5:c.161A>T	chr17.hg19:g.17179373T>A	ENSP00000268717:p.His54Leu	164.0	0.0		126.0	14.0	NM_003653	B2R683|B4DY81|O43191|Q7LDR6	Missense_Mutation	SNP	ENST00000268717.5	hg19	CCDS11183.1	.	.	.	.	.	.	.	.	.	.	T	26.8	4.774654	0.90108	.	.	ENSG00000141030	ENST00000268717;ENST00000539941;ENST00000417352;ENST00000439936	T;T;T	0.46819	0.86;0.86;0.86	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	T	0.71634	0.3363	M	0.86502	2.82	0.80722	D	1	D	0.76494	0.999	D	0.72625	0.978	T	0.77466	-0.2577	10	0.66056	D	0.02	-22.038	14.2848	0.66240	0.0:0.0:0.0:1.0	.	54	Q9UNS2	CSN3_HUMAN	L	54;34;54;78	ENSP00000268717:H54L;ENSP00000437606:H34L;ENSP00000409028:H54L	ENSP00000268717:H54L	H	-	2	0	COPS3	17120098	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.801000	0.85960	2.023000	0.59567	0.454000	0.30748	CAC	.	.		0.438	COPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131603.2		
CCR7	1236	hgsc.bcm.edu	37	17	38711882	38711882	+	Silent	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:38711882A>G	ENST00000246657.2	-	3	311	c.249T>C	c.(247-249)taT>taC	p.Y83Y	CCR7_ENST00000579344.1_Silent_p.Y77Y	NM_001838.3	NP_001829.1	P32248	CCR7_HUMAN	chemokine (C-C motif) receptor 7	83					activation of Rho GTPase activity (GO:0032862)|cellular response to cytokine stimulus (GO:0071345)|chemokine (C-C motif) ligand 19 signaling pathway (GO:0038115)|chemokine (C-C motif) ligand 21 signaling pathway (GO:0038116)|chemokine-mediated signaling pathway (GO:0070098)|dendritic cell chemotaxis (GO:0002407)|establishment of T cell polarity (GO:0001768)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|interleukin-12 secretion (GO:0072610)|lymphocyte migration into lymph node (GO:0097022)|mature dendritic cell differentiation (GO:0097029)|myeloid dendritic cell chemotaxis (GO:0002408)|negative regulation of leukocyte apoptotic process (GO:2000107)|negative thymic T cell selection (GO:0045060)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell motility (GO:2000147)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation (GO:2000526)|positive regulation of humoral immune response (GO:0002922)|positive regulation of hypersensitivity (GO:0002885)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immunological synapse formation (GO:2000522)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of T cell costimulation (GO:2000525)|positive regulation of T cell receptor signaling pathway (GO:0050862)|regulation of dendritic cell dendrite assembly (GO:2000547)|regulation of interferon-gamma production (GO:0032649)|regulation of interleukin-1 beta secretion (GO:0050706)|release of sequestered calcium ion into cytosol (GO:0051209)|response to lipopolysaccharide (GO:0032496)|response to nitric oxide (GO:0071731)|response to prostaglandin E (GO:0034695)|ruffle organization (GO:0031529)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|C-C motif chemokine 19 receptor activity (GO:0038117)|C-C motif chemokine 21 receptor activity (GO:0038121)|chemokine (C-C motif) ligand 19 binding (GO:0035757)|chemokine (C-C motif) ligand 21 binding (GO:0035758)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		Breast(137;0.000496)				TGAAATAGATATAGGTCAACA	0.522																																					p.Y83Y		Atlas-SNP	.											.	CCR7	31	.	0			c.T249C						.						103.0	98.0	99.0					17																	38711882		2203	4300	6503	SO:0001819	synonymous_variant	1236	exon3			ATAGATATAGGTC		CCDS11369.1	17q12-q21.2	2012-08-08			ENSG00000126353	ENSG00000126353		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1608	protein-coding gene	gene with protein product		600242		CMKBR7, EBI1		8383238	Standard	NM_001838		Approved	BLR2, CDw197, CD197	uc002huw.3	P32248	OTTHUMG00000133375	ENST00000246657.2:c.249T>C	chr17.hg19:g.38711882A>G		150.0	0.0		173.0	23.0	NM_001838		Silent	SNP	ENST00000246657.2	hg19	CCDS11369.1																																																																																			.	.		0.522	CCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257222.1		
KRT40	125115	hgsc.bcm.edu	37	17	39135187	39135187	+	Silent	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:39135187C>T	ENST00000398486.2	-	8	1225	c.1065G>A	c.(1063-1065)gaG>gaA	p.E355E	KRT40_ENST00000377755.4_Silent_p.E355E	NM_182497.3	NP_872303.2	Q6A162	K1C40_HUMAN	keratin 40	355	Coil 2.|Rod.					intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			endometrium(1)|large_intestine(2)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	9		Breast(137;0.00043)				CCAGCTGGTTCTCCAGGTTAT	0.597																																					p.E355E		Atlas-SNP	.											.	KRT40	27	.	0			c.G1065A						.						89.0	98.0	95.0					17																	39135187		2202	4295	6497	SO:0001819	synonymous_variant	125115	exon8			CTGGTTCTCCAGG	AK093919	CCDS42320.1	17q21.2	2013-01-16			ENSG00000204889	ENSG00000204889		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	26707	protein-coding gene	gene with protein product						16831889	Standard	NM_182497		Approved	FLJ36600, KA36	uc010cxh.1	Q6A162	OTTHUMG00000133596	ENST00000398486.2:c.1065G>A	chr17.hg19:g.39135187C>T		176.0	0.0		152.0	49.0	NM_182497	Q6IFU5	Silent	SNP	ENST00000398486.2	hg19	CCDS42320.1																																																																																			.	.		0.597	KRT40-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257701.3	NM_182497	
STAT3	6774	hgsc.bcm.edu	37	17	40474482	40474482	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:40474482T>A	ENST00000264657.5	-	21	2231	c.1919A>T	c.(1918-1920)tAc>tTc	p.Y640F	STAT3_ENST00000389272.3_Missense_Mutation_p.Y542F|STAT3_ENST00000588969.1_Missense_Mutation_p.Y640F|STAT3_ENST00000404395.3_Missense_Mutation_p.Y640F|STAT3_ENST00000585517.1_Missense_Mutation_p.Y640F	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	640	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		CTGCTTTGTGTATGGTTCCAC	0.463									Hyperimmunoglobulin E Recurrent Infection Syndrome																												p.Y640F		Atlas-SNP	.											STAT3,NS,lymphoid_neoplasm,0,46	STAT3	268	.	0			c.A1919T						.						243.0	213.0	223.0					17																	40474482		2203	4300	6503	SO:0001583	missense	6774	exon21	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	TTTGTGTATGGTT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"""SH2 domain containing"""	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.1919A>T	chr17.hg19:g.40474482T>A	ENSP00000264657:p.Tyr640Phe	343.0	0.0		390.0	22.0	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Missense_Mutation	SNP	ENST00000264657.5	hg19	CCDS32656.1	.	.	.	.	.	.	.	.	.	.	T	19.36	3.813449	0.70912	.	.	ENSG00000168610	ENST00000264657;ENST00000389272;ENST00000404395	D;D;D	0.89196	-2.48;-2.48;-2.48	4.64	4.64	0.57946	SH2 motif (4);	0.000000	0.85682	D	0.000000	D	0.87120	0.6098	N	0.16016	0.355	0.80722	D	1	D;D;D	0.59357	0.982;0.985;0.985	D;D;D	0.78314	0.984;0.991;0.991	T	0.82589	-0.0382	10	0.06891	T	0.86	-37.3581	14.2314	0.65895	0.0:0.0:0.0:1.0	.	640;640;640	P40763-2;P40763;B5BTZ6	.;STAT3_HUMAN;.	F	640;542;640	ENSP00000264657:Y640F;ENSP00000373923:Y542F;ENSP00000384943:Y640F	ENSP00000264657:Y640F	Y	-	2	0	STAT3	37728008	1.000000	0.71417	0.964000	0.40570	0.715000	0.41141	7.868000	0.87116	1.953000	0.56701	0.460000	0.39030	TAC	.	.		0.463	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
SLC25A39	51629	hgsc.bcm.edu	37	17	42398495	42398495	+	Missense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:42398495C>T	ENST00000377095.5	-	8	741	c.622G>A	c.(622-624)Gct>Act	p.A208T	SLC25A39_ENST00000225308.8_Missense_Mutation_p.A200T|SLC25A39_ENST00000586016.1_Missense_Mutation_p.A76T|SLC25A39_ENST00000590194.1_Missense_Mutation_p.A200T|SLC25A39_ENST00000537904.2_Missense_Mutation_p.A185T	NM_001143780.1	NP_001137252.1	Q9BZJ4	S2539_HUMAN	solute carrier family 25, member 39	208					heme biosynthetic process (GO:0006783)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)		p.A200T(1)		endometrium(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	7		Prostate(33;0.0233)		BRCA - Breast invasive adenocarcinoma(366;0.189)		CCACCCTGAGCCACTGCAGTT	0.642																																					p.A208T		Atlas-SNP	.											SLC25A39,NS,carcinoma,0,1	SLC25A39	24	.	1	Substitution - Missense(1)	lung(1)	c.G622A						.						31.0	28.0	29.0					17																	42398495		2202	4299	6501	SO:0001583	missense	51629	exon8			CCTGAGCCACTGC	BC096819	CCDS11482.1, CCDS45700.1	17q12	2013-05-22			ENSG00000013306	ENSG00000013306		"""Solute carriers"""	24279	protein-coding gene	gene with protein product		610820				16949250	Standard	NM_001143780		Approved	FLJ22407, CGI-69	uc002ign.2	Q9BZJ4	OTTHUMG00000132628	ENST00000377095.5:c.622G>A	chr17.hg19:g.42398495C>T	ENSP00000366299:p.Ala208Thr	119.0	0.0		86.0	23.0	NM_001143780	A8JZZ2|D3DX51|D3DX54|Q4V9M1|Q9P182|Q9UF66|Q9Y379	Missense_Mutation	SNP	ENST00000377095.5	hg19	CCDS45700.1	.	.	.	.	.	.	.	.	.	.	C	14.76	2.631520	0.46944	.	.	ENSG00000013306	ENST00000225308;ENST00000377095;ENST00000537904	T;T;T	0.79141	-1.24;-1.24;-1.24	5.31	1.99	0.26369	Mitochondrial carrier domain (2);	0.256023	0.38164	N	0.001790	T	0.67353	0.2884	L	0.41492	1.28	0.38462	D	0.947234	B;B;B	0.18166	0.002;0.026;0.005	B;B;B	0.29077	0.009;0.098;0.012	T	0.61865	-0.6975	10	0.36615	T	0.2	-0.5426	7.7893	0.29110	0.1909:0.6602:0.0:0.1489	.	185;208;200	B4DFG5;Q9BZJ4;Q9BZJ4-2	.;S2539_HUMAN;.	T	200;208;185	ENSP00000225308:A200T;ENSP00000366299:A208T;ENSP00000444540:A185T	ENSP00000225308:A200T	A	-	1	0	SLC25A39	39754021	0.995000	0.38212	1.000000	0.80357	0.860000	0.49131	1.445000	0.35079	0.791000	0.33826	0.655000	0.94253	GCT	.	.		0.642	SLC25A39-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457745.1	NM_016016	
CACNA1G	8913	hgsc.bcm.edu	37	17	48668930	48668930	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:48668930A>G	ENST00000359106.5	+	11	2588	c.2588A>G	c.(2587-2589)gAc>gGc	p.D863G	CACNA1G_ENST00000513964.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000503485.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000507336.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000502264.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000352832.5_Missense_Mutation_p.D863G|CACNA1G_ENST00000354983.4_Missense_Mutation_p.D863G|CACNA1G_ENST00000507510.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000416767.4_Missense_Mutation_p.D863G|CACNA1G_ENST00000512389.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000360761.4_Missense_Mutation_p.D863G|CACNA1G_ENST00000510366.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000515165.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000515765.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000429973.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000507609.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000510115.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000513689.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000358244.5_Missense_Mutation_p.D863G|CACNA1G_ENST00000515411.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000514079.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000514181.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000505165.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000514717.1_Missense_Mutation_p.D863G|CACNA1G_ENST00000442258.2_Missense_Mutation_p.D863G|CACNA1G_ENST00000507896.1_Missense_Mutation_p.D863G	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	863					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AAGACCATGGACAACGTGGCC	0.632																																					p.D863G		Atlas-SNP	.											.	CACNA1G	659	.	0			c.A2588G						.						54.0	58.0	57.0					17																	48668930		2200	4285	6485	SO:0001583	missense	8913	exon11			CCATGGACAACGT	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.2588A>G	chr17.hg19:g.48668930A>G	ENSP00000352011:p.Asp863Gly	128.0	0.0		99.0	32.0	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	hg19	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	a	27.4	4.825215	0.90955	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37;-4.37	5.55	5.55	0.83447	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.96525	0.8866	N	0.25890	0.77	0.80722	D	1	D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;1.0;0.999;0.999;1.0;0.999;0.999;1.0;0.999;0.763;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97110	0.996;1.0;0.999;0.998;0.999;0.999;0.998;1.0;0.998;0.852;1.0;1.0;1.0;1.0;0.998;1.0;1.0;0.999;1.0;1.0;0.999;1.0;1.0;1.0;0.999;0.999	D	0.94741	0.7919	10	0.11794	T	0.64	.	15.6931	0.77469	1.0:0.0:0.0:0.0	.	863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863;863	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	G	863	ENSP00000353990:D863G;ENSP00000339302:D863G;ENSP00000392390:D863G;ENSP00000347078:D863G;ENSP00000409759:D863G;ENSP00000425522:D863G;ENSP00000426261:D863G;ENSP00000425451:D863G;ENSP00000422407:D863G;ENSP00000426814:D863G;ENSP00000427238:D863G;ENSP00000423112:D863G;ENSP00000420918:D863G;ENSP00000426172:D863G;ENSP00000423045:D863G;ENSP00000427173:D863G;ENSP00000426098:D863G;ENSP00000425698:D863G;ENSP00000426232:D863G;ENSP00000423317:D863G;ENSP00000350979:D863G;ENSP00000352011:D863G;ENSP00000414388:D863G;ENSP00000423155:D863G;ENSP00000422268:D863G;ENSP00000421518:D863G	ENSP00000339302:D863G	D	+	2	0	CACNA1G	46023929	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.334000	0.96470	2.119000	0.64992	0.379000	0.24179	GAC	.	.		0.632	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
STXBP4	252983	hgsc.bcm.edu	37	17	53077023	53077023	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:53077023A>T	ENST00000376352.2	+	6	525	c.318A>T	c.(316-318)atA>atT	p.I106I	STXBP4_ENST00000434978.2_Silent_p.I106I|STXBP4_ENST00000299341.4_Silent_p.I31I|STXBP4_ENST00000398391.2_Silent_p.I31I|STXBP4_ENST00000405898.1_Silent_p.I106I	NM_178509.5	NP_848604.3	Q6ZWJ1	STXB4_HUMAN	syntaxin binding protein 4	106					cellular response to DNA damage stimulus (GO:0006974)|glucose transport (GO:0015758)|insulin receptor signaling pathway (GO:0008286)|positive regulation of cell cycle G1/S phase transition (GO:1902808)|positive regulation of keratinocyte proliferation (GO:0010838)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(4)|ovary(1)|upper_aerodigestive_tract(2)	19						TAGCATTCATAAGACAAAAAT	0.343																																					p.I106I		Atlas-SNP	.											.	STXBP4	41	.	0			c.A318T						.						68.0	66.0	66.0					17																	53077023		2203	4300	6503	SO:0001819	synonymous_variant	252983	exon6			ATTCATAAGACAA	BC041485	CCDS11584.2	17q22	2008-02-05			ENSG00000166263	ENSG00000166263			19694	protein-coding gene	gene with protein product		610415				12855681	Standard	XM_005257187		Approved	Synip, MGC50337	uc002iuf.1	Q6ZWJ1	OTTHUMG00000074043	ENST00000376352.2:c.318A>T	chr17.hg19:g.53077023A>T		125.0	0.0		144.0	8.0	NM_178509	Q8IVZ5	Silent	SNP	ENST00000376352.2	hg19	CCDS11584.2																																																																																			.	.		0.343	STXBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157184.1	NM_178509	
RNF43	54894	hgsc.bcm.edu	37	17	56435407	56435407	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:56435407T>A	ENST00000584437.1	-	8	3685	c.1730A>T	c.(1729-1731)cAg>cTg	p.Q577L	RNF43_ENST00000500597.2_Missense_Mutation_p.Q536L|RNF43_ENST00000583753.1_Missense_Mutation_p.Q536L|RNF43_ENST00000407977.2_Missense_Mutation_p.Q577L|RNF43_ENST00000581868.1_Missense_Mutation_p.Q450L|RNF43_ENST00000577625.1_Missense_Mutation_p.Q450L|BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.Q577L			Q68DV7	RNF43_HUMAN	ring finger protein 43	577	Pro-rich.				negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AGGCCTGGACTGGGGGACTCC	0.622																																					p.Q577L		Atlas-SNP	.											.	RNF43	157	.	0			c.A1730T						.						65.0	76.0	73.0					17																	56435407		2202	4300	6502	SO:0001583	missense	54894	exon9			CTGGACTGGGGGA		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.1730A>T	chr17.hg19:g.56435407T>A	ENSP00000463069:p.Gln577Leu	125.0	0.0		121.0	14.0	NM_017763	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	hg19	CCDS11607.1	.	.	.	.	.	.	.	.	.	.	T	4.514	0.095399	0.08681	.	.	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.21543	2.0;2.0	5.3	0.145	0.14829	.	1.080280	0.07039	N	0.829808	T	0.12646	0.0307	N	0.24115	0.695	0.09310	N	1	B;B;B	0.09022	0.0;0.002;0.0	B;B;B	0.09377	0.002;0.004;0.0	T	0.40365	-0.9567	10	0.10377	T	0.69	-19.7098	8.0507	0.30577	0.121:0.0:0.3768:0.5021	.	536;577;577	Q68DV7-2;Q68DV7-4;Q68DV7	.;.;RNF43_HUMAN	L	577;536	ENSP00000385328:Q577L;ENSP00000441969:Q536L	ENSP00000385328:Q577L	Q	-	2	0	RNF43	53790406	0.862000	0.29867	0.058000	0.19502	0.020000	0.10135	-0.171000	0.09883	-0.666000	0.05310	-1.203000	0.01651	CAG	.	.		0.622	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
BCAS3	54828	hgsc.bcm.edu	37	17	59155891	59155891	+	Splice_Site	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:59155891G>A	ENST00000390652.5	+	22	2403		c.e22+1		BCAS3_ENST00000408905.3_Splice_Site|BCAS3_ENST00000588874.1_Splice_Site|BCAS3_ENST00000407086.3_Splice_Site|BCAS3_ENST00000589222.1_Splice_Site|BCAS3_ENST00000588462.1_Splice_Site|BCAS3_ENST00000585744.1_Splice_Site	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3											NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ACAGTCTCAGGTAGGAAATGA	0.403																																					.		Atlas-SNP	.											.	BCAS3	90	.	0			c.2372+1G>A						.						65.0	58.0	60.0					17																	59155891		1925	4142	6067	SO:0001630	splice_region_variant	54828	exon22			TCTCAGGTAGGAA	AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.2372+1G>A	chr17.hg19:g.59155891G>A		138.0	0.0		154.0	44.0	NM_001099432		Splice_Site	SNP	ENST00000390652.5	hg19	CCDS45749.1	.	.	.	.	.	.	.	.	.	.	G	32	5.179424	0.94846	.	.	ENSG00000141376	ENST00000390652;ENST00000407086;ENST00000408905	.	.	.	5.31	5.31	0.75309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.3441	0.94356	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	BCAS3	56510673	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.567000	0.98161	2.658000	0.90341	0.585000	0.79938	.	.	.		0.403	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1	NM_017679	Intron
BPTF	2186	hgsc.bcm.edu	37	17	65920668	65920668	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:65920668A>G	ENST00000321892.4	+	17	6153	c.6092A>G	c.(6091-6093)gAg>gGg	p.E2031G	BPTF_ENST00000424123.3_Missense_Mutation_p.E1892G|BPTF_ENST00000335221.5_Missense_Mutation_p.E2031G|BPTF_ENST00000306378.6_Missense_Mutation_p.E1905G			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2031					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			TGCAGAGTGGAGAAAGAAAAG	0.413																																					p.E2031G		Atlas-SNP	.											.	BPTF	415	.	0			c.A6092G						.						85.0	81.0	82.0					17																	65920668		2203	4300	6503	SO:0001583	missense	2186	exon17			GAGTGGAGAAAGA	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6092A>G	chr17.hg19:g.65920668A>G	ENSP00000315454:p.Glu2031Gly	261.0	0.0		293.0	105.0	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Missense_Mutation	SNP	ENST00000321892.4	hg19		.	.	.	.	.	.	.	.	.	.	A	18.60	3.658798	0.67586	.	.	ENSG00000171634	ENST00000306378;ENST00000335221;ENST00000321892	T;T;T	0.15718	2.4;2.4;2.4	5.12	5.12	0.69794	.	.	.	.	.	T	0.32882	0.0844	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.83275	0.996;0.994	T	0.06427	-1.0827	9	0.87932	D	0	.	15.2325	0.73401	1.0:0.0:0.0:0.0	.	1905;2031	Q12830-2;Q12830-4	.;.	G	1905;2031;2031	ENSP00000307208:E1905G;ENSP00000334351:E2031G;ENSP00000315454:E2031G	ENSP00000307208:E1905G	E	+	2	0	BPTF	63351130	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.073000	0.93992	2.054000	0.61138	0.528000	0.53228	GAG	.	.		0.413	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
KIF19	124602	hgsc.bcm.edu	37	17	72349367	72349367	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:72349367G>T	ENST00000389916.4	+	16	2285	c.2147G>T	c.(2146-2148)gGg>gTg	p.G716V	AC103809.2_ENST00000599136.1_5'Flank	NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	716					ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						GCTGGTACTGGGGCCTGGCAG	0.627																																					p.G716V		Atlas-SNP	.											.	KIF19	102	.	0			c.G2147T						.						32.0	38.0	36.0					17																	72349367		2054	4193	6247	SO:0001583	missense	124602	exon16			GTACTGGGGCCTG	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.2147G>T	chr17.hg19:g.72349367G>T	ENSP00000374566:p.Gly716Val	201.0	0.0		192.0	88.0	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Missense_Mutation	SNP	ENST00000389916.4	hg19	CCDS32718.2	.	.	.	.	.	.	.	.	.	.	G	9.346	1.064263	0.20067	.	.	ENSG00000196169	ENST00000389916	T	0.69306	-0.39	5.14	4.17	0.49024	.	.	.	.	.	T	0.45397	0.1340	N	0.08118	0	0.36603	D	0.874798	B	0.21381	0.055	B	0.17722	0.019	T	0.48747	-0.9008	9	0.44086	T	0.13	.	10.8457	0.46741	0.0897:0.0:0.9103:0.0	.	716	Q2TAC6	KIF19_HUMAN	V	716	ENSP00000374566:G716V	ENSP00000374566:G716V	G	+	2	0	KIF19	69860962	0.959000	0.32827	0.253000	0.24343	0.023000	0.10783	3.731000	0.55013	1.169000	0.42739	0.456000	0.33151	GGG	.	.		0.627	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
LAMA1	284217	hgsc.bcm.edu	37	18	7013887	7013887	+	Missense_Mutation	SNP	G	G	T	rs377575918		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr18:7013887G>T	ENST00000389658.3	-	23	3383	c.3290C>A	c.(3289-3291)aCg>aAg	p.T1097K		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1097	Laminin EGF-like 13. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				GTCCCCCGACGTCCCCCTCAG	0.582																																					p.T1097K		Atlas-SNP	.											.	LAMA1	458	.	0			c.C3290A						.																																			SO:0001583	missense	284217	exon23			CCCGACGTCCCCC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3290C>A	chr18.hg19:g.7013887G>T	ENSP00000374309:p.Thr1097Lys	259.0	0.0		196.0	88.0	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	hg19	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.166549	0.78339	.	.	ENSG00000101680	ENST00000389658	T	0.61980	0.06	5.9	5.9	0.94986	EGF-like, laminin (3);	0.000000	0.85682	D	0.000000	D	0.84238	0.5428	M	0.93420	3.415	0.49213	D	0.999763	D	0.89917	1.0	D	0.73708	0.981	D	0.87579	0.2483	10	0.72032	D	0.01	.	16.5088	0.84279	0.0:0.1306:0.8694:0.0	.	1097	P25391	LAMA1_HUMAN	K	1097	ENSP00000374309:T1097K	ENSP00000374309:T1097K	T	-	2	0	LAMA1	7003887	1.000000	0.71417	0.957000	0.39632	0.486000	0.33341	7.048000	0.76606	2.783000	0.95769	0.637000	0.83480	ACG	.	.		0.582	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
MATK	4145	hgsc.bcm.edu	37	19	3779601	3779601	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:3779601T>A	ENST00000310132.6	-	10	1255	c.857A>T	c.(856-858)gAg>gTg	p.E286V	MATK_ENST00000395040.2_Missense_Mutation_p.E245V|MATK_ENST00000585778.1_Missense_Mutation_p.E286V|MATK_ENST00000395045.2_Missense_Mutation_p.E287V	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	286	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		CACCAGGTTCTCGTGTTGCAT	0.706																																					p.E287V		Atlas-SNP	.											.	MATK	108	.	0			c.A860T						.						21.0	21.0	21.0					19																	3779601		2201	4298	6499	SO:0001583	missense	4145	exon10			AGGTTCTCGTGTT	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.857A>T	chr19.hg19:g.3779601T>A	ENSP00000308734:p.Glu286Val	55.0	0.0		34.0	7.0	NM_002378	B3KNZ9|Q9NST8	Missense_Mutation	SNP	ENST00000310132.6	hg19	CCDS12114.1	.	.	.	.	.	.	.	.	.	.	T	12.59	1.984240	0.35036	.	.	ENSG00000007264	ENST00000395045;ENST00000310132;ENST00000395040	T;T;T	0.62639	0.01;0.01;0.01	3.93	1.43	0.22495	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.148199	0.40222	U	0.001150	T	0.48370	0.1496	L	0.43757	1.38	0.25262	N	0.989585	B;B;B	0.12630	0.002;0.006;0.002	B;B;B	0.16289	0.015;0.004;0.015	T	0.42413	-0.9453	10	0.59425	D	0.04	-17.8713	5.9103	0.19025	0.0:0.3304:0.0:0.6696	.	286;287;286	F1T0G6;B3KNZ9;P42679	.;.;MATK_HUMAN	V	287;286;245	ENSP00000378485:E287V;ENSP00000308734:E286V;ENSP00000378481:E245V	ENSP00000308734:E286V	E	-	2	0	MATK	3730601	1.000000	0.71417	0.813000	0.32504	0.759000	0.43091	2.220000	0.42908	0.045000	0.15804	0.246000	0.17985	GAG	.	.		0.706	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
DNMT1	1786	hgsc.bcm.edu	37	19	10251564	10251564	+	Missense_Mutation	SNP	T	T	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:10251564T>G	ENST00000340748.4	-	31	3603	c.3368A>C	c.(3367-3369)cAa>cCa	p.Q1123P	DNMT1_ENST00000359526.4_Missense_Mutation_p.Q1139P|DNMT1_ENST00000589538.1_5'UTR|DNMT1_ENST00000540357.1_Missense_Mutation_p.Q1123P			P26358	DNMT1_HUMAN	DNA (cytosine-5-)-methyltransferase 1	1123	Interaction with the PRC2/EED-EZH2 complex. {ECO:0000250}.				cellular response to amino acid stimulus (GO:0071230)|chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|gene silencing (GO:0016458)|maintenance of DNA methylation (GO:0010216)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|regulation of cell proliferation (GO:0042127)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|replication fork (GO:0005657)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|DNA-methyltransferase activity (GO:0009008)|methyl-CpG binding (GO:0008327)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(5)|endometrium(8)|kidney(5)|large_intestine(21)|lung(11)|ovary(2)|pancreas(1)|prostate(10)|skin(5)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(20;1.59e-09)|Epithelial(33;2.86e-06)|all cancers(31;6.68e-06)		Azacitidine(DB00928)|Decitabine(DB01262)|Flucytosine(DB01099)|Procainamide(DB01035)	CTCACAGGCTTGGGACTTGGG	0.597																																					p.Q1139P		Atlas-SNP	.											.	DNMT1	148	.	0			c.A3416C						.						76.0	69.0	72.0					19																	10251564		2203	4300	6503	SO:0001583	missense	1786	exon32			CAGGCTTGGGACT	X63692	CCDS12228.1, CCDS45958.1	19p13.2	2014-09-17				ENSG00000130816	2.1.1.37		2976	protein-coding gene	gene with protein product		126375		DNMT		1594447	Standard	NM_001379		Approved	MCMT, CXXC9	uc010xlc.2	P26358		ENST00000340748.4:c.3368A>C	chr19.hg19:g.10251564T>G	ENSP00000345739:p.Gln1123Pro	60.0	0.0		65.0	27.0	NM_001130823	A0AV63|B7ZLW6|Q9UHG5|Q9ULA2|Q9UMZ6	Missense_Mutation	SNP	ENST00000340748.4	hg19	CCDS12228.1	.	.	.	.	.	.	.	.	.	.	T	11.01	1.513982	0.27123	.	.	ENSG00000130816	ENST00000359526;ENST00000540357;ENST00000340748;ENST00000541266	T;T;T	0.24538	1.85;1.85;1.85	5.6	-2.64	0.06114	.	0.505328	0.21369	N	0.075678	T	0.18841	0.0452	L	0.44542	1.39	0.09310	N	1	B;B;B	0.15141	0.012;0.012;0.004	B;B;B	0.12156	0.007;0.007;0.003	T	0.24404	-1.0161	10	0.40728	T	0.16	.	11.6486	0.51275	0.1045:0.0:0.5741:0.3214	.	1123;1139;1123	F5GX68;P26358-2;P26358	.;.;DNMT1_HUMAN	P	1139;1123;1123;991	ENSP00000352516:Q1139P;ENSP00000440457:Q1123P;ENSP00000345739:Q1123P	ENSP00000345739:Q1123P	Q	-	2	0	DNMT1	10112564	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.050000	0.11904	-0.219000	0.10003	-0.313000	0.08912	CAA	.	.		0.597	DNMT1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451166.1	NM_001379	
DNM2	1785	hgsc.bcm.edu	37	19	10906053	10906053	+	Missense_Mutation	SNP	G	G	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:10906053G>C	ENST00000355667.6	+	9	1214	c.1134G>C	c.(1132-1134)gaG>gaC	p.E378D	DNM2_ENST00000408974.4_Missense_Mutation_p.E378D|DNM2_ENST00000314646.5_Missense_Mutation_p.E378D|DNM2_ENST00000585892.1_Missense_Mutation_p.E378D|DNM2_ENST00000389253.4_Missense_Mutation_p.E378D|DNM2_ENST00000359692.6_Missense_Mutation_p.E378D	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	378					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			CTCAGATGGAGTTTGACGAGA	0.562			"""F, N, Splice, Mis, O"""		ETP ALL																																p.E378D		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.G1134C						.						172.0	129.0	143.0					19																	10906053		2203	4300	6503	SO:0001583	missense	1785	exon9			GATGGAGTTTGAC		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.1134G>C	chr19.hg19:g.10906053G>C	ENSP00000347890:p.Glu378Asp	110.0	0.0		131.0	42.0	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	hg19	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	G	11.42	1.633801	0.29068	.	.	ENSG00000079805	ENST00000389252;ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646	T;T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68;-0.68	5.29	3.03	0.35002	Dynamin central domain (1);	0.441600	0.25938	N	0.027333	T	0.47507	0.1449	N	0.16066	0.365	0.49389	D	0.999787	B;B;B;B;P	0.39576	0.31;0.004;0.002;0.024;0.679	B;B;B;B;B	0.40066	0.248;0.029;0.012;0.033;0.318	T	0.37384	-0.9708	10	0.09590	T	0.72	-6.6102	6.9382	0.24478	0.327:0.0:0.673:0.0	.	111;378;378;378;378	B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;DYN2_HUMAN;.	D	367;378;378;378;378;378	ENSP00000386192:E378D;ENSP00000347890:E378D;ENSP00000352721:E378D;ENSP00000373905:E378D;ENSP00000313164:E378D	ENSP00000313164:E378D	E	+	3	2	DNM2	10767053	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	2.032000	0.41127	1.249000	0.43950	-0.140000	0.14226	GAG	.	.		0.562	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
UPF1	5976	hgsc.bcm.edu	37	19	18967008	18967008	+	Nonsense_Mutation	SNP	C	C	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:18967008C>T	ENST00000599848.1	+	13	1965	c.1756C>T	c.(1756-1758)Cag>Tag	p.Q586*	UPF1_ENST00000262803.5_Nonsense_Mutation_p.Q575*			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	586					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GCCTGAGCTGCAGAAGCTGCA	0.602																																					p.Q575X		Atlas-SNP	.											.	UPF1	88	.	0			c.C1723T						.						50.0	49.0	49.0					19																	18967008		2203	4300	6503	SO:0001587	stop_gained	5976	exon13			GAGCTGCAGAAGC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.1756C>T	chr19.hg19:g.18967008C>T	ENSP00000470142:p.Gln586*	120.0	0.0		130.0	8.0	NM_002911	O00239|O43343|Q86Z25|Q92842	Nonsense_Mutation	SNP	ENST00000599848.1	hg19		.	.	.	.	.	.	.	.	.	.	C	42	9.541753	0.99199	.	.	ENSG00000005007	ENST00000262803	.	.	.	4.29	4.29	0.51040	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-34.5199	16.0865	0.81056	0.0:1.0:0.0:0.0	.	.	.	.	X	575	.	ENSP00000262803:Q575X	Q	+	1	0	UPF1	18828008	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.245000	0.78237	2.102000	0.63906	0.655000	0.94253	CAG	.	.		0.602	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
CILP2	148113	hgsc.bcm.edu	37	19	19656087	19656087	+	Silent	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:19656087G>A	ENST00000291495.5	+	8	2818	c.2733G>A	c.(2731-2733)gtG>gtA	p.V911V	CILP2_ENST00000586018.1_Silent_p.V917V	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	911						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						AGTACAACGTGGTCCCCTTCC	0.667																																					p.V911V		Atlas-SNP	.											.	CILP2	84	.	0			c.G2733A						.						40.0	30.0	33.0					19																	19656087		2203	4300	6503	SO:0001819	synonymous_variant	148113	exon8			CAACGTGGTCCCC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.2733G>A	chr19.hg19:g.19656087G>A		142.0	0.0		115.0	26.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	hg19	CCDS12405.1																																																																																			.	.		0.667	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
ZNF85	7639	hgsc.bcm.edu	37	19	21132284	21132284	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:21132284G>T	ENST00000328178.8	+	4	1077	c.964G>T	c.(964-966)Gcc>Tcc	p.A322S	ZNF85_ENST00000601023.1_Missense_Mutation_p.A263S|ZNF85_ENST00000345030.6_Missense_Mutation_p.A289S	NM_001256173.1|NM_003429.4	NP_001243102.1|NP_003420.2	Q03923	ZNF85_HUMAN	zinc finger protein 85	322					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)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(2)	20						ATGTGGCAAAGCCTTTAAGCA	0.363																																					p.A352S		Atlas-SNP	.											.	ZNF85	72	.	0			c.G1054T						.						44.0	48.0	47.0					19																	21132284		2201	4299	6500	SO:0001583	missense	7639	exon5			GGCAAAGCCTTTA	U35376	CCDS32977.1, CCDS58657.1	19p12	2013-01-08	2006-05-12			ENSG00000105750		"""Zinc fingers, C2H2-type"", ""-"""	13160	protein-coding gene	gene with protein product		603899	"""zinc finger protein 85 (HPF4, HTF1)"""			2505992	Standard	NM_003429		Approved	HPF4, HTF1	uc031rjx.1	Q03923		ENST00000328178.8:c.964G>T	chr19.hg19:g.21132284G>T	ENSP00000329793:p.Ala322Ser	32.0	0.0		18.0	12.0	NM_001256171	B9ZVP4|Q6NVI0	Missense_Mutation	SNP	ENST00000328178.8	hg19	CCDS32977.1	.	.	.	.	.	.	.	.	.	.	.	11.36	1.616013	0.28801	.	.	ENSG00000105750	ENST00000328178;ENST00000345030;ENST00000421385	T;T	0.35973	1.28;1.28	1.35	-0.224	0.13115	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.27063	0.0663	N	0.01454	-0.855	0.09310	N	0.999996	D;D;P	0.69078	0.97;0.997;0.951	P;D;P	0.79108	0.779;0.992;0.899	T	0.24083	-1.0170	9	0.66056	D	0.02	.	6.601	0.22701	0.0:0.0:0.3319:0.668	.	289;263;322	Q03923-2;Q49A12;Q03923	.;.;ZNF85_HUMAN	S	322;289;197	ENSP00000329793:A322S;ENSP00000342340:A289S	ENSP00000329793:A322S	A	+	1	0	ZNF85	20924124	0.000000	0.05858	0.337000	0.25536	0.718000	0.41266	-0.776000	0.04674	-0.240000	0.09696	0.462000	0.41574	GCC	.	.		0.363	ZNF85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463430.1	NM_003429	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768845	31768845	+	Silent	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:31768845A>T	ENST00000240587.4	-	2	2181	c.1854T>A	c.(1852-1854)acT>acA	p.T618T		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	618					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)					CAACTTTCTCAGTGACCTTTT	0.582																																					p.T618T		Atlas-SNP	.											.	TSHZ3	549	.	0			c.T1854A						.						70.0	77.0	74.0					19																	31768845		2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			TTTCTCAGTGACC	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.1854T>A	chr19.hg19:g.31768845A>T		169.0	0.0		192.0	14.0	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	hg19	CCDS12421.2																																																																																			.	.		0.582	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
ZNF585B	92285	hgsc.bcm.edu	37	19	37677114	37677114	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:37677114T>A	ENST00000532828.2	-	5	1576	c.1325A>T	c.(1324-1326)cAc>cTc	p.H442L	ZNF585B_ENST00000527838.1_3'UTR|ZNF585B_ENST00000312908.5_Missense_Mutation_p.H30L|ZNF585B_ENST00000531805.1_Missense_Mutation_p.H387L|CTC-454I21.3_ENST00000585860.2_Intron	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	442					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TTTCCCACAGTGACCACATTT	0.393																																					p.H442L	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A1325T						.						109.0	109.0	109.0					19																	37677114		2203	4300	6503	SO:0001583	missense	92285	exon5			CCACAGTGACCAC	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.1325A>T	chr19.hg19:g.37677114T>A	ENSP00000433773:p.His442Leu	139.0	0.0		128.0	11.0	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	hg19	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	7.252	0.603380	0.14002	.	.	ENSG00000245680	ENST00000531805;ENST00000532828;ENST00000312908	T;T;T	0.34667	1.35;3.4;3.4	2.35	2.35	0.29111	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.400480	0.18380	N	0.142995	T	0.18173	0.0436	N	0.05487	-0.04	0.09310	N	1	B;B	0.25441	0.03;0.126	B;B	0.24701	0.055;0.046	T	0.18366	-1.0339	10	0.66056	D	0.02	.	7.821	0.29288	0.0:0.0:0.0:1.0	.	387;442	E9PQH3;Q52M93	.;Z585B_HUMAN	L	387;442;30	ENSP00000436774:H387L;ENSP00000433773:H442L;ENSP00000442139:H30L	ENSP00000442139:H30L	H	-	2	0	ZNF585B	42368954	0.000000	0.05858	0.782000	0.31804	0.710000	0.40934	0.580000	0.23803	1.063000	0.40649	0.254000	0.18369	CAC	.	.		0.393	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
KCNK6	9424	hgsc.bcm.edu	37	19	38817261	38817261	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:38817261T>A	ENST00000263372.3	+	2	458	c.351T>A	c.(349-351)gaT>gaA	p.D117E		NM_004823.1	NP_004814.1	Q9Y257	KCNK6_HUMAN	potassium channel, subfamily K, member 6	117					negative regulation of systemic arterial blood pressure (GO:0003085)|potassium ion transport (GO:0006813)|regulation of resting membrane potential (GO:0060075)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(3)	17	all_cancers(60;5.83e-07)		Lung(45;0.00047)|LUSC - Lung squamous cell carcinoma(53;0.000613)		Ibutilide(DB00308)|Quinidine(DB00908)	CACTGACTGATGCGGGCAAGG	0.577																																					p.D117E		Atlas-SNP	.											.	KCNK6	37	.	0			c.T351A						.						101.0	99.0	100.0					19																	38817261		2203	4299	6502	SO:0001583	missense	9424	exon2			GACTGATGCGGGC	AF117708	CCDS12513.1	19q13.1	2012-03-07				ENSG00000099337		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6281	protein-coding gene	gene with protein product		603939				10075682, 10393428, 16382106	Standard	NM_004823		Approved	K2p6.1, TWIK-2	uc002oic.3	Q9Y257		ENST00000263372.3:c.351T>A	chr19.hg19:g.38817261T>A	ENSP00000263372:p.Asp117Glu	56.0	0.0		58.0	4.0	NM_004823	Q9HB47	Missense_Mutation	SNP	ENST00000263372.3	hg19	CCDS12513.1	.	.	.	.	.	.	.	.	.	.	T	14.89	2.670890	0.47781	.	.	ENSG00000099337	ENST00000263372	T	0.24151	1.87	4.74	-6.88	0.01665	Ion transport 2 (1);	0.103141	0.64402	D	0.000006	T	0.20007	0.0481	L	0.42686	1.345	0.25253	N	0.989658	P	0.42123	0.771	P	0.47528	0.549	T	0.34054	-0.9844	10	0.07175	T	0.84	.	13.6951	0.62572	0.0:0.3003:0.0:0.6997	.	117	Q9Y257	KCNK6_HUMAN	E	117	ENSP00000263372:D117E	ENSP00000263372:D117E	D	+	3	2	KCNK6	43509101	0.000000	0.05858	0.001000	0.08648	0.553000	0.35397	-0.757000	0.04772	-1.059000	0.03193	-2.060000	0.00399	GAT	.	.		0.577	KCNK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460524.1	NM_004823	
LRFN1	57622	hgsc.bcm.edu	37	19	39805513	39805513	+	Missense_Mutation	SNP	G	G	A	rs201576239		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:39805513G>A	ENST00000248668.4	-	1	463	c.464C>T	c.(463-465)gCg>gTg	p.A155V	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	155						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			GTCAAAGGCCGCCGACTCCAC	0.667																																					p.A155V		Atlas-SNP	.											LRFN1,NS,carcinoma,0,1	LRFN1	59	.	0			c.C464T						.	G	VAL/ALA	1,3979		0,1,1989	16.0	19.0	18.0		464	3.1	0.7	19		18	1,8303		0,1,4151	yes	missense	LRFN1	NM_020862.1	64	0,2,6140	AA,AG,GG		0.012,0.0251,0.0163	benign	155/772	39805513	2,12282	1990	4152	6142	SO:0001583	missense	57622	exon1			AAGGCCGCCGACT	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.464C>T	chr19.hg19:g.39805513G>A	ENSP00000248668:p.Ala155Val	87.0	0.0		72.0	5.0	NM_020862	Q8TBS9	Missense_Mutation	SNP	ENST00000248668.4	hg19	CCDS46071.1	.	.	.	.	.	.	.	.	.	.	G	11.59	1.682719	0.29872	2.51E-4	1.2E-4	ENSG00000128011	ENST00000248668	T	0.52526	0.66	4.22	3.14	0.36123	.	0.000000	0.39687	N	0.001296	T	0.36771	0.0979	L	0.58810	1.83	0.29475	N	0.856736	B	0.31351	0.32	B	0.21360	0.034	T	0.25222	-1.0138	10	0.16420	T	0.52	.	10.3862	0.44140	0.0:0.3893:0.6107:0.0	.	155	Q9P244	LRFN1_HUMAN	V	155	ENSP00000248668:A155V	ENSP00000248668:A155V	A	-	2	0	LRFN1	44497353	0.399000	0.25287	0.701000	0.30321	0.753000	0.42808	3.042000	0.49815	0.941000	0.37499	0.555000	0.69702	GCG	.	.		0.667	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
ZNF613	79898	hgsc.bcm.edu	37	19	52448896	52448896	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:52448896A>T	ENST00000293471.6	+	6	2439	c.1760A>T	c.(1759-1761)aAc>aTc	p.N587I	ZNF613_ENST00000391794.4_Missense_Mutation_p.N551I|ZNF613_ENST00000601794.1_Intron	NM_001031721.3	NP_001026891.2	Q6PF04	ZN613_HUMAN	zinc finger protein 613	587					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	19		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.0183)		TCATTAACTAACAGTGCGTTC	0.443																																					p.N587I		Atlas-SNP	.											.	ZNF613	62	.	0			c.A1760T						.						84.0	71.0	76.0					19																	52448896		2203	4300	6503	SO:0001583	missense	79898	exon6			TAACTAACAGTGC	AK027565	CCDS12844.1, CCDS33089.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	25827	protein-coding gene	gene with protein product						12477932	Standard	NM_001031721		Approved	FLJ13590	uc002pxz.2	Q6PF04		ENST00000293471.6:c.1760A>T	chr19.hg19:g.52448896A>T	ENSP00000293471:p.Asn587Ile	165.0	0.0		226.0	80.0	NM_001031721	Q96SS9	Missense_Mutation	SNP	ENST00000293471.6	hg19	CCDS33089.1	.	.	.	.	.	.	.	.	.	.	A	4.035	0.004091	0.07866	.	.	ENSG00000176024	ENST00000293471;ENST00000391794;ENST00000535279	T;T	0.05513	3.52;3.43	2.93	-0.467	0.12150	.	.	.	.	.	T	0.02888	0.0086	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43065	-0.9414	9	0.45353	T	0.12	.	3.1906	0.06615	0.2797:0.0:0.3769:0.3434	.	587	Q6PF04	ZN613_HUMAN	I	587;551;261	ENSP00000293471:N587I;ENSP00000375671:N551I	ENSP00000293471:N587I	N	+	2	0	ZNF613	57140708	0.000000	0.05858	0.000000	0.03702	0.052000	0.14988	-1.597000	0.02089	-0.182000	0.10602	0.482000	0.46254	AAC	.	.		0.443	ZNF613-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461104.2	NM_024840	
LENG8	114823	hgsc.bcm.edu	37	19	54962528	54962528	+	Missense_Mutation	SNP	G	G	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:54962528G>A	ENST00000326764.5	+	2	486	c.7G>A	c.(7-9)Gcc>Acc	p.A3T	LENG8-AS1_ENST00000416022.1_RNA|LENG8_ENST00000376514.2_Missense_Mutation_p.A3T|LENG8-AS1_ENST00000429922.1_RNA|LENG8-AS1_ENST00000448978.1_RNA	NM_052925.2	NP_443157.1	Q96PV6	LENG8_HUMAN	leukocyte receptor cluster (LRC) member 8	0										breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(6)|lung(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	30	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.139)		CCAGATGGCGGCCAACGTGGG	0.552																																					p.A3T		Atlas-SNP	.											.	LENG8	73	.	0			c.G7A						.						97.0	85.0	89.0					19																	54962528		2203	4300	6503	SO:0001583	missense	114823	exon2			ATGGCGGCCAACG	AF211975	CCDS12894.1	19q13.4	2008-02-05			ENSG00000167615	ENSG00000167615			15500	protein-coding gene	gene with protein product						10941842	Standard	XM_005278248		Approved	KIAA1932, MGC40108, pp13842	uc002qfw.2	Q96PV6	OTTHUMG00000065548	ENST00000326764.5:c.7G>A	chr19.hg19:g.54962528G>A	ENSP00000318374:p.Ala3Thr	179.0	0.0		188.0	65.0	NM_052925	B0VJY9|Q8IZ27|Q8NCX6	Missense_Mutation	SNP	ENST00000326764.5	hg19	CCDS12894.1	.	.	.	.	.	.	.	.	.	.	G	17.35	3.366444	0.61513	.	.	ENSG00000167615	ENST00000326764;ENST00000301196;ENST00000439657;ENST00000376514;ENST00000376526;ENST00000443957;ENST00000431846	T;T;T;T	0.52526	1.28;0.66;1.06;1.14	4.92	3.88	0.44766	.	0.134765	0.49305	N	0.000158	T	0.38214	0.1032	L	0.43152	1.355	0.34148	D	0.66717	B;B	0.26602	0.154;0.015	B;B	0.23716	0.048;0.019	T	0.52011	-0.8632	10	0.51188	T	0.08	-24.64	9.9603	0.41693	0.0964:0.0:0.9036:0.0	.	3;3	Q96PV6-2;F8W9Q9	.;.	T	3	ENSP00000318374:A3T;ENSP00000399507:A3T;ENSP00000365709:A3T;ENSP00000388053:A3T	ENSP00000301196:A3T	A	+	1	0	LENG8	59654340	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.603000	0.61105	1.386000	0.46466	0.462000	0.41574	GCC	.	.		0.552	LENG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140523.2	NM_052925	
ZNF547	284306	hgsc.bcm.edu	37	19	57889239	57889239	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:57889239A>T	ENST00000282282.3	+	4	1045	c.895A>T	c.(895-897)Agt>Tgt	p.S299C	AC003002.4_ENST00000597658.1_Intron	NM_173631.2	NP_775902.2	Q8IVP9	ZN547_HUMAN	zinc finger protein 547	299					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TTATGGTTGCAGTGAATGTGG	0.408																																					p.S299C		Atlas-SNP	.											.	ZNF547	45	.	0			c.A895T						.						119.0	118.0	118.0					19																	57889239		2203	4300	6503	SO:0001583	missense	284306	exon4			GGTTGCAGTGAAT	AK055662	CCDS33131.1	19q13.43	2013-01-08				ENSG00000152433		"""Zinc fingers, C2H2-type"", ""-"""	26432	protein-coding gene	gene with protein product							Standard	NM_173631		Approved	FLJ31100	uc002qol.3	Q8IVP9		ENST00000282282.3:c.895A>T	chr19.hg19:g.57889239A>T	ENSP00000282282:p.Ser299Cys	117.0	0.0		130.0	9.0	NM_173631	A8K5Z9|Q96NC4	Missense_Mutation	SNP	ENST00000282282.3	hg19	CCDS33131.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.065261	0.55432	.	.	ENSG00000152433	ENST00000391704;ENST00000282282	T	0.16897	2.31	1.87	1.87	0.25490	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.35998	0.0951	M	0.77486	2.375	0.09310	N	1	D;D;D	0.76494	0.997;0.999;0.997	P;D;P	0.67900	0.753;0.954;0.907	T	0.05733	-1.0867	9	0.56958	D	0.05	.	6.3787	0.21521	0.7503:0.2496:0.0:0.0	.	299;299;299	Q8IVP9-2;C9JTQ3;Q8IVP9	.;.;ZN547_HUMAN	C	299	ENSP00000282282:S299C	ENSP00000282282:S299C	S	+	1	0	ZNF547	62581051	0.000000	0.05858	0.010000	0.14722	0.938000	0.57974	-1.061000	0.03472	1.126000	0.42016	0.402000	0.26972	AGT	.	.		0.408	ZNF547-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465787.1	NM_173631	
ZNF211	10520	hgsc.bcm.edu	37	19	58152706	58152706	+	Silent	SNP	T	T	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr19:58152706T>G	ENST00000347302.3	+	3	1031	c.852T>G	c.(850-852)ccT>ccG	p.P284P	ZNF211_ENST00000544273.1_Silent_p.P296P|ZNF211_ENST00000240731.4_Silent_p.P297P|ZNF211_ENST00000541801.1_Silent_p.P275P|ZNF211_ENST00000391703.3_Silent_p.P223P|ZNF211_ENST00000420680.1_Silent_p.P288P|ZNF211_ENST00000299871.5_Silent_p.P349P|ZNF211_ENST00000254182.7_Silent_p.P275P	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	284					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAGAAAGGCCTTATGAATGCA	0.413																																					p.P349P		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1047G						.						115.0	108.0	110.0					19																	58152706		2203	4300	6503	SO:0001819	synonymous_variant	10520	exon5			AAGGCCTTATGAA	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.852T>G	chr19.hg19:g.58152706T>G		94.0	0.0		77.0	23.0	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Silent	SNP	ENST00000347302.3	hg19	CCDS12957.1	.	.	.	.	.	.	.	.	.	.	T	9.043	0.990163	0.18966	.	.	ENSG00000121417	ENST00000407202	.	.	.	3.51	3.51	0.40186	.	.	.	.	.	T	0.55273	0.1910	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52162	-0.8612	4	.	.	.	.	6.3576	0.21410	0.3538:0.0:0.0:0.6462	.	.	.	.	V	288	.	.	L	+	1	2	ZNF211	62844518	0.000000	0.05858	0.476000	0.27291	0.993000	0.82548	-1.016000	0.03633	1.605000	0.50152	0.472000	0.43445	TTA	.	.		0.413	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
MYH7B	57644	hgsc.bcm.edu	37	20	33582028	33582028	+	Missense_Mutation	SNP	A	A	G			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr20:33582028A>G	ENST00000262873.7	+	25	2742	c.2650A>G	c.(2650-2652)Aag>Gag	p.K884E		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	842						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GCTCTTTTTCAAGATGAAGCC	0.647																																					p.K884E		Atlas-SNP	.											.	MYH7B	145	.	0			c.A2650G						.						92.0	104.0	100.0					20																	33582028		2076	4235	6311	SO:0001583	missense	57644	exon27			TTTTTCAAGATGA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.2650A>G	chr20.hg19:g.33582028A>G	ENSP00000262873:p.Lys884Glu	285.0	0.0		320.0	116.0	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	hg19	CCDS42869.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848416	0.71603	.	.	ENSG00000078814	ENST00000262873	D	0.93488	-3.23	4.33	4.33	0.51752	.	0.000000	0.39615	N	0.001304	D	0.97043	0.9034	M	0.91300	3.195	0.50632	D	0.999884	D	0.56746	0.977	D	0.71656	0.974	D	0.97755	1.0217	10	0.66056	D	0.02	.	13.9525	0.64126	1.0:0.0:0.0:0.0	.	842	A7E2Y1	MYH7B_HUMAN	E	884	ENSP00000262873:K884E	ENSP00000262873:K884E	K	+	1	0	MYH7B	33045689	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	9.135000	0.94478	1.943000	0.56356	0.459000	0.35465	AAG	.	.		0.647	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
AURKA	6790	hgsc.bcm.edu	37	20	54961584	54961584	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr20:54961584T>A	ENST00000347343.2	-	3	315	c.48A>T	c.(46-48)acA>acT	p.T16T	AURKA_ENST00000395913.3_Silent_p.T16T|AURKA_ENST00000395909.4_Silent_p.T16T|AURKA_ENST00000395911.1_Silent_p.T16T|AURKA_ENST00000312783.6_Silent_p.T16T|AURKA_ENST00000371356.2_Silent_p.T16T|AURKA_ENST00000395914.1_Silent_p.T16T|AURKA_ENST00000395907.1_Silent_p.T16T|AURKA_ENST00000395915.3_Silent_p.T16T	NM_003600.2	NP_003591.2	O14965	AURKA_HUMAN	aurora kinase A	16					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|anterior/posterior axis specification (GO:0009948)|centrosome localization (GO:0051642)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein binding (GO:0032091)|negative regulation of spindle checkpoint (GO:0090233)|neuron projection extension (GO:1990138)|positive regulation of mitosis (GO:0045840)|positive regulation of oocyte maturation (GO:1900195)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|protein autophosphorylation (GO:0046777)|protein localization to centrosome (GO:0071539)|protein phosphorylation (GO:0006468)|regulation of centrosome cycle (GO:0046605)|regulation of protein stability (GO:0031647)|spindle assembly involved in female meiosis I (GO:0007057)|spindle stabilization (GO:0043146)	axon hillock (GO:0043203)|centrosome (GO:0005813)|cytosol (GO:0005829)|germinal vesicle (GO:0042585)|meiotic spindle (GO:0072687)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|histone serine kinase activity (GO:0035174)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(2)|cervix(1)|endometrium(1)|large_intestine(4)|lung(9)|ovary(2)|prostate(1)|skin(2)	22			Colorectal(105;0.202)			CAACTGGAGCTGTAGCCTAGA	0.403																																					p.T16T	Melanoma(34;439 1292 51416 52695)|GBM(144;1525 2517 48902 51835)|Esophageal Squamous(191;569 2880 14195 30540)	Atlas-SNP	.											.	AURKA	42	.	0			c.A48T						.						54.0	54.0	54.0					20																	54961584		2203	4300	6503	SO:0001819	synonymous_variant	6790	exon3			TGGAGCTGTAGCC	BC001280	CCDS13451.1	20q13	2012-07-23	2003-07-21	2003-07-23	ENSG00000087586	ENSG00000087586		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	11393	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 47"", ""Aurora-A kinase"""	603072	"""serine/threonine kinase 15"", "" serine/threonine kinase 6"""	STK15, STK6		9174055, 9771714	Standard	NM_003600		Approved	BTAK, AurA, STK7, ARK1, PPP1R47, AIK	uc002xxi.1	O14965	OTTHUMG00000032796	ENST00000347343.2:c.48A>T	chr20.hg19:g.54961584T>A		99.0	0.0		126.0	7.0	NM_198437	E1P5F9|O60445|O75873|Q9BQD6|Q9UPG5	Silent	SNP	ENST00000347343.2	hg19	CCDS13451.1																																																																																			.	.		0.403	AURKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079804.3	NM_003600	
DNAJC5	80331	hgsc.bcm.edu	37	20	62562355	62562355	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr20:62562355A>T	ENST00000360864.4	+	4	626	c.473A>T	c.(472-474)cAg>cTg	p.Q158L	DNAJC5_ENST00000369911.2_Missense_Mutation_p.Q158L	NM_025219.2	NP_079495.1	Q9H3Z4	DNJC5_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 5	158					cell death (GO:0008219)|exocytosis (GO:0006887)|negative regulation of neuron apoptotic process (GO:0043524)|neurotransmitter secretion (GO:0007269)|regulated secretory pathway (GO:0045055)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)				cervix(1)|endometrium(1)|lung(1)|pancreas(1)|upper_aerodigestive_tract(1)	5	all_cancers(38;2.14e-11)|all_epithelial(29;3.41e-13)|Lung NSC(23;3.41e-09)|all_lung(23;1.06e-08)					CTGGAGGCACAGCTGCAGTCT	0.627																																					p.Q158L		Atlas-SNP	.											.	DNAJC5	16	.	0			c.A473T						.						101.0	80.0	87.0					20																	62562355		2203	4300	6503	SO:0001583	missense	80331	exon4			AGGCACAGCTGCA		CCDS13546.1	20q13.33	2014-09-17			ENSG00000101152	ENSG00000101152		"""Heat shock proteins / DNAJ (HSP40)"""	16235	protein-coding gene	gene with protein product		611203	"""ceroid-lipofuscinosis, neuronal 4 (Kufs disease)"""	CLN4			Standard	NM_025219		Approved	FLJ00118, FLJ13070, DNAJC5A	uc002yhf.3	Q9H3Z4	OTTHUMG00000033007	ENST00000360864.4:c.473A>T	chr20.hg19:g.62562355A>T	ENSP00000354111:p.Gln158Leu	155.0	0.0		143.0	10.0	NM_025219	A8K0M0|B3KY68|E1P5G8|Q9H3Z5|Q9H7H2	Missense_Mutation	SNP	ENST00000360864.4	hg19	CCDS13546.1	.	.	.	.	.	.	.	.	.	.	A	32	5.154334	0.94686	.	.	ENSG00000101152	ENST00000369911;ENST00000360864	T;T	0.71579	-0.55;-0.58	5.91	5.91	0.95273	.	0.064025	0.64402	D	0.000004	T	0.81931	0.4927	M	0.86953	2.85	0.80722	D	1	P;P	0.42735	0.734;0.788	P;B	0.50490	0.642;0.218	T	0.82744	-0.0306	10	0.40728	T	0.16	.	16.3512	0.83208	1.0:0.0:0.0:0.0	.	158;158	Q9H3Z4-2;Q9H3Z4	.;DNJC5_HUMAN	L	158	ENSP00000358927:Q158L;ENSP00000354111:Q158L	ENSP00000354111:Q158L	Q	+	2	0	DNAJC5	62032799	1.000000	0.71417	0.998000	0.56505	0.877000	0.50540	8.520000	0.90566	2.266000	0.75297	0.533000	0.62120	CAG	.	.		0.627	DNAJC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080244.1	NM_025219	
DSCAM	1826	hgsc.bcm.edu	37	21	41384983	41384984	+	Missense_Mutation	DNP	GC	GC	AG	rs200591095		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr21:41384983_41384984GC>AG	ENST00000400454.1	-	33	6493_6494	c.6016_6017GC>CT	c.(6016-6018)GCa>CTa	p.A2006L		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	2006				HRPGDLIHLPPYLRMDFLLNRGGPGTSRDLSLGQACLEPQK SRTLKRPTVLEPIPMEAASSASSTREGQSWQPGAVATLPQR EGAELGQAAKMSSSQESLLDSRGHLKGNNPYAKSYTLV -> IGQVTSYICLHTLEWTFC (in Ref. 1; AAC17966). {ECO:0000305}.	cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				GTAAGATTTTGCGTAAGGATTG	0.46																																					p.A2006V|p.A2006P	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.|DSCAM,colon,carcinoma,0,1	DSCAM	347	.	0			c.C6017T|c.G6016C						.																																			SO:0001583	missense	1826	exon33			GATTTTGCGTAAG|ATTTTGCGTAAGG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.6016_6017delinsAG	chr21.hg19:g.41384983_41384984delinsAG	ENSP00000383303:p.Ala2006Leu	172.0|173.0	0.0		134.0|136.0	26.0	NM_001389	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1																																																																																			.	G|1.000;C|0.000|.		0.460	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
HMOX1	3162	hgsc.bcm.edu	37	22	35789564	35789564	+	Silent	SNP	A	A	T	rs140740892	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:35789564A>T	ENST00000216117.8	+	5	1179	c.840A>T	c.(838-840)acA>acT	p.T280T		NM_002133.2	NP_002124.1	P09601	HMOX1_HUMAN	heme oxygenase (decycling) 1	280					angiogenesis (GO:0001525)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to cadmium ion (GO:0071276)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient (GO:0031670)|endothelial cell proliferation (GO:0001935)|erythrocyte homeostasis (GO:0034101)|excretion (GO:0007588)|heme catabolic process (GO:0042167)|heme oxidation (GO:0006788)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|iron ion homeostasis (GO:0055072)|low-density lipoprotein particle clearance (GO:0034383)|negative regulation of DNA binding (GO:0043392)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of mast cell cytokine production (GO:0032764)|negative regulation of mast cell degranulation (GO:0043305)|negative regulation of muscle cell apoptotic process (GO:0010656)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smooth muscle cell proliferation (GO:0048662)|porphyrin-containing compound metabolic process (GO:0006778)|positive regulation of angiogenesis (GO:0045766)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of vasodilation (GO:0045909)|protein homooligomerization (GO:0051260)|regulation of angiogenesis (GO:0045765)|regulation of blood pressure (GO:0008217)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0043619)|response to estrogen (GO:0043627)|response to hydrogen peroxide (GO:0042542)|response to nicotine (GO:0035094)|response to oxidative stress (GO:0006979)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|smooth muscle hyperplasia (GO:0014806)|transmembrane transport (GO:0055085)|wound healing involved in inflammatory response (GO:0002246)	caveola (GO:0005901)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	enzyme binding (GO:0019899)|heme binding (GO:0020037)|heme oxygenase (decyclizing) activity (GO:0004392)|metal ion binding (GO:0046872)|phospholipase D activity (GO:0004630)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16					Vitamin E(DB00163)	TGGTGGCGACAGTTGCTGTAG	0.587																																					p.T280T		Atlas-SNP	.											.	HMOX1	32	.	0			c.A840T						.						142.0	135.0	137.0					22																	35789564		2203	4300	6503	SO:0001819	synonymous_variant	3162	exon5			GGCGACAGTTGCT		CCDS13914.1	22q12	2003-10-13			ENSG00000100292	ENSG00000100292	1.14.99.3		5013	protein-coding gene	gene with protein product		141250				10591208	Standard	NM_002133		Approved	bK286B10, HO-1	uc003ant.2	P09601	OTTHUMG00000150960	ENST00000216117.8:c.840A>T	chr22.hg19:g.35789564A>T		179.0	0.0		141.0	8.0	NM_002133		Silent	SNP	ENST00000216117.8	hg19	CCDS13914.1																																																																																			.	A|0.997;G|0.003		0.587	HMOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320657.1		
EIF3D	8664	hgsc.bcm.edu	37	22	36919311	36919311	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:36919311T>A	ENST00000216190.8	-	6	780	c.410A>T	c.(409-411)cAg>cTg	p.Q137L	EIF3D_ENST00000541106.1_Missense_Mutation_p.Q88L|EIF3D_ENST00000405442.1_Missense_Mutation_p.Q137L	NM_003753.3	NP_003744.1			eukaryotic translation initiation factor 3, subunit D											cervix(1)|endometrium(2)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	15						GAACTTTTTCTGCAGTCGAAT	0.423																																					p.Q137L		Atlas-SNP	.											.	EIF3D	37	.	0			c.A410T						.						176.0	176.0	176.0					22																	36919311		2203	4300	6503	SO:0001583	missense	8664	exon6			TTTTTCTGCAGTC	U54558	CCDS13930.1	22q13.1	2007-07-27	2007-07-27	2007-07-27	ENSG00000100353	ENSG00000100353			3278	protein-coding gene	gene with protein product		603915	"""eukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDa"""	EIF3S7		9341143	Standard	NM_003753		Approved	eIF3-p66, eIF3-zeta, eIF3d	uc003apr.3	O15371	OTTHUMG00000150599	ENST00000216190.8:c.410A>T	chr22.hg19:g.36919311T>A	ENSP00000216190:p.Gln137Leu	102.0	0.0		115.0	9.0	NM_003753		Missense_Mutation	SNP	ENST00000216190.8	hg19	CCDS13930.1	.	.	.	.	.	.	.	.	.	.	T	16.16	3.043136	0.55003	.	.	ENSG00000100353	ENST00000216190;ENST00000397177;ENST00000541106;ENST00000405442;ENST00000455547;ENST00000457241;ENST00000432675	.	.	.	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.54515	0.1863	L	0.39898	1.24	0.80722	D	1	P;P	0.41947	0.766;0.475	B;B	0.44044	0.277;0.439	T	0.51092	-0.8749	9	0.28530	T	0.3	-11.3341	16.0098	0.80391	0.0:0.0:0.0:1.0	.	88;137	B4DVY1;O15371	.;EIF3D_HUMAN	L	137;137;88;137;137;137;137	.	ENSP00000216190:Q137L	Q	-	2	0	EIF3D	35249257	1.000000	0.71417	1.000000	0.80357	0.845000	0.48019	7.132000	0.77251	2.254000	0.74563	0.533000	0.62120	CAG	.	.		0.423	EIF3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319026.1		
ACO2	50	hgsc.bcm.edu	37	22	41911430	41911430	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:41911430A>T	ENST00000216254.4	+	5	597	c.575A>T	c.(574-576)gAc>gTc	p.D192V	ACO2_ENST00000396512.3_Missense_Mutation_p.D192V	NM_001098.2	NP_001089.1	Q99798	ACON_HUMAN	aconitase 2, mitochondrial	192	Substrate binding. {ECO:0000250}.				cell death (GO:0008219)|cellular metabolic process (GO:0044237)|citrate metabolic process (GO:0006101)|generation of precursor metabolites and energy (GO:0006091)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron ion binding (GO:0005506)			breast(3)|endometrium(5)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	23						ATTGGCACTGACTCCCACACC	0.517																																					p.D192V		Atlas-SNP	.											.	ACO2	58	.	0			c.A575T						.						85.0	87.0	86.0					22																	41911430		2203	4300	6503	SO:0001583	missense	50	exon5			GCACTGACTCCCA	AH006514	CCDS14017.1	22q13.2	2013-05-21			ENSG00000100412	ENSG00000100412	4.2.1.3		118	protein-coding gene	gene with protein product	"""aconitate hydratase, mitochondrial"""	100850				10591208	Standard	NM_001098		Approved	ACONM	uc003bac.3	Q99798	OTTHUMG00000030544	ENST00000216254.4:c.575A>T	chr22.hg19:g.41911430A>T	ENSP00000216254:p.Asp192Val	133.0	0.0		158.0	16.0	NM_001098	O75809|Q5JZ41|Q6FHX0|Q8TAQ6	Missense_Mutation	SNP	ENST00000216254.4	hg19	CCDS14017.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.698931	0.88830	.	.	ENSG00000100412	ENST00000544234;ENST00000216254;ENST00000396512	D;D	0.97232	-4.3;-4.3	5.46	5.46	0.80206	Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 (1);Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha (3);	0.000000	0.85682	D	0.000000	D	0.99360	0.9775	H	0.99959	5.06	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.97903	1.0304	10	0.87932	D	0	.	15.5309	0.75960	1.0:0.0:0.0:0.0	.	192;192	A2A274;Q99798	.;ACON_HUMAN	V	173;192;192	ENSP00000216254:D192V;ENSP00000379769:D192V	ENSP00000216254:D192V	D	+	2	0	ACO2	40241376	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.962000	0.93254	2.063000	0.61619	0.533000	0.62120	GAC	.	.		0.517	ACO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259151.1	NM_001098	
MEI1	150365	hgsc.bcm.edu	37	22	42099396	42099396	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:42099396T>A	ENST00000401548.3	+	2	276	c.236T>A	c.(235-237)cTg>cAg	p.L79Q	MEI1_ENST00000540833.1_5'UTR|MEI1_ENST00000400107.1_5'UTR|MEI1_ENST00000300398.4_5'UTR	NM_152513.3	NP_689726.3			meiosis inhibitor 1											breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	30						CATACCTCCCTGGTCACGCAA	0.428																																					p.L79Q		Atlas-SNP	.											.	MEI1	87	.	0			c.T236A						.						77.0	73.0	74.0					22																	42099396		1963	4142	6105	SO:0001583	missense	150365	exon2			CCTCCCTGGTCAC	AK092934	CCDS46718.1	22q13.2	2013-10-11			ENSG00000167077	ENSG00000167077			28613	protein-coding gene	gene with protein product	"""spermatogenesis associated 38"""	608797				16683055	Standard	XM_006724154		Approved	MGC40042, SPATA38	uc003baz.1	Q5TIA1	OTTHUMG00000030083	ENST00000401548.3:c.236T>A	chr22.hg19:g.42099396T>A	ENSP00000384115:p.Leu79Gln	123.0	0.0		106.0	7.0	NM_152513		Missense_Mutation	SNP	ENST00000401548.3	hg19	CCDS46718.1	.	.	.	.	.	.	.	.	.	.	T	11.32	1.605379	0.28623	.	.	ENSG00000167077	ENST00000401548	T	0.20069	2.1	5.22	1.28	0.21552	.	0.979204	0.08343	N	0.960514	T	0.17066	0.0410	L	0.47716	1.5	0.09310	N	0.999998	P;P	0.46220	0.874;0.571	B;B	0.41088	0.347;0.252	T	0.20338	-1.0278	10	0.36615	T	0.2	-5.5299	3.4015	0.07325	0.1705:0.2671:0.0:0.5624	.	79;79	Q5TIA1;Q5TIA1-4	MEI1_HUMAN;.	Q	79	ENSP00000384115:L79Q	ENSP00000384115:L79Q	L	+	2	0	MEI1	40429342	0.081000	0.21417	0.900000	0.35374	0.495000	0.33615	0.721000	0.25911	0.846000	0.35142	0.397000	0.26171	CTG	.	.		0.428	MEI1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000074937.3	NM_152513	
NLGN4X	57502	hgsc.bcm.edu	37	X	6069270	6069270	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:6069270A>T	ENST00000381095.3	-	2	865	c.238T>A	c.(238-240)Tca>Aca	p.S80T	NLGN4X_ENST00000381093.2_Missense_Mutation_p.S80T|NLGN4X_ENST00000381092.1_Missense_Mutation_p.S80T|NLGN4X_ENST00000469740.1_5'UTR|NLGN4X_ENST00000275857.6_Missense_Mutation_p.S80T|NLGN4X_ENST00000538097.1_Missense_Mutation_p.S80T	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	80					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						GTGGGGGGTGAGGCATAGGGG	0.557																																					p.S80T		Atlas-SNP	.											.	NLGN4X	191	.	0			c.T238A						.						75.0	69.0	71.0					X																	6069270		2203	4300	6503	SO:0001583	missense	57502	exon2			GGGGTGAGGCATA	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.238T>A	chrX.hg19:g.6069270A>T	ENSP00000370485:p.Ser80Thr	156.0	0.0		368.0	26.0	NM_181332	Q6UX10|Q9ULG0	Missense_Mutation	SNP	ENST00000381095.3	hg19	CCDS14126.1	.	.	.	.	.	.	.	.	.	.	A	8.100	0.776351	0.16051	.	.	ENSG00000146938	ENST00000381095;ENST00000381093;ENST00000275857;ENST00000381092;ENST00000538097	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	4.2	4.2	0.49525	Carboxylesterase, type B (1);	.	.	.	.	T	0.25457	0.0619	N	0.02334	-0.595	0.25812	N	0.984382	B;B;B	0.11235	0.004;0.0;0.002	B;B;B	0.14023	0.01;0.002;0.004	T	0.09930	-1.0652	9	0.08837	T	0.75	.	11.9007	0.52682	1.0:0.0:0.0:0.0	.	80;80;80	A6NMU8;Q8N0W4;Q8N0W4-2	.;NLGNX_HUMAN;.	T	80	ENSP00000370485:S80T;ENSP00000370483:S80T;ENSP00000275857:S80T;ENSP00000370482:S80T;ENSP00000439203:S80T	ENSP00000275857:S80T	S	-	1	0	NLGN4X	6079270	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	1.890000	0.39728	1.388000	0.46506	0.486000	0.48141	TCA	.	.		0.557	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
ZNF41	7592	hgsc.bcm.edu	37	X	47307358	47307358	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:47307358T>C	ENST00000377065.4	-	5	2450	c.1811A>G	c.(1810-1812)gAg>gGg	p.E604G	ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000313116.7_Missense_Mutation_p.E604G|ZNF41_ENST00000397050.2_Missense_Mutation_p.E614G	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	646					regulation of transcription, DNA-templated (GO:0006355)|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)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				GTACGGTTTCTCTCCTGTATG	0.448																																					p.E604G		Atlas-SNP	.											.	ZNF41	71	.	0			c.A1811G						.						90.0	71.0	77.0					X																	47307358		2203	4300	6503	SO:0001583	missense	7592	exon5			GGTTTCTCTCCTG	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.1811A>G	chrX.hg19:g.47307358T>C	ENSP00000366265:p.Glu604Gly	103.0	0.0		236.0	202.0	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	hg19	CCDS14279.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.969907	0.74246	.	.	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.27557	1.66;1.66;1.66	3.98	3.98	0.46160	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.35677	N	0.003051	T	0.49508	0.1561	M	0.64404	1.975	0.35516	D	0.801006	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.998;0.999;0.999	T	0.62627	-0.6814	10	0.87932	D	0	.	10.3222	0.43773	0.0:0.0:0.0:1.0	.	604;606;614;638;646	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	G	604;604;614	ENSP00000315173:E604G;ENSP00000366265:E604G;ENSP00000380243:E614G	ENSP00000315173:E604G	E	-	2	0	ZNF41	47192302	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.227000	0.65305	1.798000	0.52647	0.486000	0.48141	GAG	.	.		0.448	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380	
HUWE1	10075	hgsc.bcm.edu	37	X	53672381	53672381	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:53672381T>A	ENST00000342160.3	-	6	843	c.386A>T	c.(385-387)cAa>cTa	p.Q129L	HUWE1_ENST00000262854.6_Missense_Mutation_p.Q129L|HUWE1_ENST00000218328.8_Missense_Mutation_p.Q129L			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	129					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						CAGCACCACTTGCATATCAGA	0.438																																					p.Q129L		Atlas-SNP	.											.	HUWE1	724	.	0			c.A386T						.						81.0	64.0	70.0					X																	53672381		2203	4300	6503	SO:0001583	missense	10075	exon7			ACCACTTGCATAT	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.386A>T	chrX.hg19:g.53672381T>A	ENSP00000340648:p.Gln129Leu	53.0	0.0		127.0	7.0	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	T	16.20	3.055444	0.55325	.	.	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000432528	T;T;T	0.66815	-0.08;-0.08;-0.23	5.47	5.47	0.80525	Armadillo-like helical (1);E3 ubiquitin ligase, domain of unknown function DUF908 (1);Armadillo-type fold (1);	0.079709	0.51477	D	0.000089	T	0.51500	0.1678	N	0.19112	0.55	0.58432	D	0.999995	B	0.27013	0.166	B	0.26310	0.068	T	0.49103	-0.8974	10	0.30078	T	0.28	.	13.4813	0.61336	0.0:0.0:0.0:1.0	.	129	Q7Z6Z7	HUWE1_HUMAN	L	129	ENSP00000340648:Q129L;ENSP00000262854:Q129L;ENSP00000218328:Q129L	ENSP00000218328:Q129L	Q	-	2	0	HUWE1	53689106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.040000	0.76551	1.826000	0.53198	0.486000	0.48141	CAA	.	.		0.438	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
HNRNPH2	3188	hgsc.bcm.edu	37	X	100667970	100667970	+	Missense_Mutation	SNP	G	G	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:100667970G>T	ENST00000316594.5	+	2	1072	c.994G>T	c.(994-996)Gat>Tat	p.D332Y		NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	332	2 X 16 AA Gly-rich approximate repeats.|RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|large_intestine(2)|lung(6)|skin(1)	12						CGGTGAGGCAGATGTTGAATT	0.408																																					p.D332Y		Atlas-SNP	.											.	HNRNPH2	50	.	0			c.G994T						.						119.0	104.0	109.0					X																	100667970		2203	4300	6503	SO:0001583	missense	3188	exon2			GAGGCAGATGTTG	U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"""RNA binding motif (RRM) containing"""	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.994G>T	chrX.hg19:g.100667970G>T	ENSP00000361927:p.Asp332Tyr	140.0	0.0		265.0	197.0	NM_001032393	A1L400|Q9HHA7	Missense_Mutation	SNP	ENST00000316594.5	hg19	CCDS14485.1	.	.	.	.	.	.	.	.	.	.	G	15.82	2.945270	0.53079	.	.	ENSG00000126945	ENST00000457902;ENST00000316594	T	0.06142	3.34	4.62	4.62	0.57501	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.13884	0.0336	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.04165	-1.0972	10	0.72032	D	0.01	-21.913	14.0571	0.64776	0.0:0.0:1.0:0.0	.	332	P55795	HNRH2_HUMAN	Y	287;332	ENSP00000361927:D332Y	ENSP00000361927:D332Y	D	+	1	0	HNRNPH2	100554626	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.562000	0.98145	2.281000	0.76405	0.513000	0.50165	GAT	.	.		0.408	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597	
IRS4	8471	hgsc.bcm.edu	37	X	107977707	107977707	+	Missense_Mutation	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:107977707T>A	ENST00000372129.2	-	1	1944	c.1868A>T	c.(1867-1869)aAg>aTg	p.K623M	RP6-24A23.6_ENST00000563887.1_5'Flank|RP6-24A23.3_ENST00000608811.1_RNA|RP6-24A23.3_ENST00000436013.1_RNA	NM_003604.2	NP_003595.1	O14654	IRS4_HUMAN	insulin receptor substrate 4	623					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(30)|ovary(5)|pancreas(2)|prostate(1)|skin(1)	78						TTGCTGTTGCTTGCTTTGAGT	0.502																																					p.K623M		Atlas-SNP	.											.	IRS4	253	.	0			c.A1868T						.						215.0	213.0	214.0					X																	107977707		2203	4300	6503	SO:0001583	missense	8471	exon1			TGTTGCTTGCTTT	AF007567	CCDS14544.1	Xq22.3	2008-08-01			ENSG00000133124	ENSG00000133124			6128	protein-coding gene	gene with protein product		300904				9261155, 9553137	Standard	NM_003604		Approved	PY160, IRS-4	uc004eoc.2	O14654	OTTHUMG00000022181	ENST00000372129.2:c.1868A>T	chrX.hg19:g.107977707T>A	ENSP00000361202:p.Lys623Met	32.0	0.0		79.0	4.0	NM_003604		Missense_Mutation	SNP	ENST00000372129.2	hg19	CCDS14544.1	.	.	.	.	.	.	.	.	.	.	T	14.10	2.434515	0.43224	.	.	ENSG00000133124	ENST00000372129	T	0.38722	1.12	4.9	2.47	0.30058	.	3.127220	0.00678	N	0.000660	T	0.41903	0.1179	L	0.54323	1.7	0.26051	N	0.981479	B	0.26081	0.141	B	0.29942	0.109	T	0.38457	-0.9660	10	0.52906	T	0.07	-8.8109	4.4981	0.11851	0.4376:0.0:0.1407:0.4217	.	623	O14654	IRS4_HUMAN	M	623	ENSP00000361202:K623M	ENSP00000361202:K623M	K	-	2	0	IRS4	107864363	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	1.366000	0.34193	1.807000	0.52817	0.486000	0.48141	AAG	.	.		0.502	IRS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057879.1	NM_003604	
TKTL1	8277	hgsc.bcm.edu	37	X	153558006	153558006	+	Missense_Mutation	SNP	A	A	T			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:153558006A>T	ENST00000369915.3	+	13	1948	c.1759A>T	c.(1759-1761)Ata>Tta	p.I587L	TKTL1_ENST00000369912.2_Missense_Mutation_p.I531L|TKTL1_ENST00000217905.7_Missense_Mutation_p.I327L	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	587					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CAGACATATCATAGTGGCCGT	0.448																																					p.I587L		Atlas-SNP	.											.	TKTL1	61	.	0			c.A1759T						.						226.0	202.0	210.0					X																	153558006		2203	4300	6503	SO:0001583	missense	8277	exon13			CATATCATAGTGG	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.1759A>T	chrX.hg19:g.153558006A>T	ENSP00000358931:p.Ile587Leu	97.0	0.0		222.0	16.0	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Missense_Mutation	SNP	ENST00000369915.3	hg19	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	A	13.88	2.368715	0.42003	.	.	ENSG00000007350	ENST00000369915;ENST00000441970;ENST00000217905;ENST00000369912	T;T;T	0.75589	-0.95;-0.95;-0.95	5.53	-4.18	0.03846	Transketolase, C-terminal/Pyruvate-ferredoxin oxidoreductase, domain II (1);Transketolase-like, C-terminal (1);	0.780183	0.12326	N	0.478801	T	0.72961	0.3526	M	0.81341	2.54	0.09310	N	1	B;B;B	0.21821	0.0;0.061;0.061	B;B;B	0.22601	0.002;0.04;0.04	T	0.62353	-0.6872	10	0.49607	T	0.09	-0.2941	14.6864	0.69052	0.4062:0.0:0.5938:0.0	.	327;581;587	B7Z7M4;B7Z7I0;P51854	.;.;TKTL1_HUMAN	L	587;548;327;531	ENSP00000358931:I587L;ENSP00000217905:I327L;ENSP00000358928:I531L	ENSP00000217905:I327L	I	+	1	0	TKTL1	153211200	0.001000	0.12720	0.000000	0.03702	0.046000	0.14306	0.006000	0.13152	-0.996000	0.03455	-0.662000	0.03851	ATA	.	.		0.448	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253	
F8	2157	hgsc.bcm.edu	37	X	154158501	154158501	+	Silent	SNP	T	T	A			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrX:154158501T>A	ENST00000360256.4	-	14	3764	c.3564A>T	c.(3562-3564)ccA>ccT	p.P1188P		NM_000132.3	NP_000123.1	P00451	FA8_HUMAN	coagulation factor VIII, procoagulant component	1188	B.				acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	copper ion binding (GO:0005507)|oxidoreductase activity (GO:0016491)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(27)|liver(1)|lung(47)|ovary(5)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(5)|urinary_tract(2)	120	all_cancers(53;7.19e-17)|all_epithelial(53;9.83e-11)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)				Coagulation Factor IX(DB00100)|Drotrecogin alfa(DB00055)	TTCTGCTGCTTGGAAAAACCA	0.328																																					p.P1188P		Atlas-SNP	.											.	F8	646	.	0			c.A3564T						.						48.0	49.0	48.0					X																	154158501		2203	4297	6500	SO:0001819	synonymous_variant	2157	exon14			GCTGCTTGGAAAA	M90707	CCDS35457.1, CCDS44026.1	Xq28	2014-09-17	2008-07-29		ENSG00000185010	ENSG00000185010			3546	protein-coding gene	gene with protein product	"""Factor VIIIF8B"", ""hemophilia A"""	300841		F8C		6438528, 3935400	Standard	NM_000132		Approved	FVIII, DXS1253E, HEMA	uc004fmt.3	P00451	OTTHUMG00000022688	ENST00000360256.4:c.3564A>T	chrX.hg19:g.154158501T>A		68.0	0.0		134.0	7.0	NM_000132	Q14286|Q5HY69	Silent	SNP	ENST00000360256.4	hg19	CCDS35457.1																																																																																			.	.		0.328	F8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058869.4		
MT-ND4	4538	hgsc.bcm.edu	37	M	11940	11940	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrM:11940T>C	ENST00000361381.2	+	1	1181	c.1181T>C	c.(1180-1182)cTa>cCa	p.L394P	MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	394					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)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TATCACTCTCCTACTTACAGG	0.458																																					p.L394P		Atlas-SNP	.											.	.	.	.	0			c.T1181C						.																																			SO:0001583	missense	0	exon1			CTCTCCTACTTAC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1181T>C	chrM.hg19:g.11940T>C	ENSP00000354961:p.Leu394Pro	14.0	0.0		47.0	23.0	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	hg19																																																																																				.	.		0.458	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
MT-ND6	4541	hgsc.bcm.edu	37	M	14649	14649	+	Missense_Mutation	SNP	T	T	C			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chrM:14649T>C	ENST00000361681.2	-	1	24	c.25A>G	c.(25-27)Agt>Ggt	p.S9G	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	9					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						TAAACCCACACTCAACAGAAA	0.408																																					p.S9G		Atlas-SNP	.											.	.	.	.	0			c.A25G						.																																			SO:0001583	missense	0	exon1			CCACACTCAACAG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.25A>G	chrM.hg19:g.14649T>C	ENSP00000354665:p.Ser9Gly	36.0	0.0		140.0	130.0	ENST00000361681	Q34774|Q8HG30	Missense_Mutation	SNP	ENST00000361681.2	hg19																																																																																				.	.		0.408	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
IL6ST	3572	hgsc.bcm.edu	37	5	55259982	55259990	+	In_Frame_Del	DEL	ACAGGATCA	ACAGGATCA	-	rs183743555		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	ACAGGATCA	ACAGGATCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr5:55259982_55259990delACAGGATCA	ENST00000381298.2	-	6	954_962	c.642_650delTGATCCTGT	c.(640-651)tttgatcctgta>tta	p.214_217FDPV>L	IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000502326.3_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000381287.4_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000381294.3_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000536319.1_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000522633.2_In_Frame_Del_p.214_217FDPV>L|IL6ST_ENST00000577363.1_5'Flank|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000336909.5_In_Frame_Del_p.214_217FDPV>L	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	214	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				ACCTTTATATACAGGATCAAAATTGATAT	0.301			O		hepatocellular ca																																p.215_217del		Atlas-Indel,Pindel	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.643_651del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.642_650delTGATCCTGT	chr5.hg19:g.55259982_55259990delACAGGATCA	ENSP00000370698:p.Phe214_Val217delinsLeu	121.0	0.0		101.0	18.0	NM_001190981	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.301	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
TSKU	25987	hgsc.bcm.edu	37	11	76506948	76506950	+	In_Frame_Del	DEL	CAC	CAC	-	rs542831459		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:76506948_76506950delCAC	ENST00000527881.1	+	2	1314_1316	c.288_290delCAC	c.(286-291)ctcacc>ctc	p.T97del	TSKU_ENST00000333090.4_In_Frame_Del_p.T97del			Q8WUA8	TSK_HUMAN	tsukushi, small leucine rich proteoglycan	97					anterior commissure morphogenesis (GO:0021960)|ciliary body morphogenesis (GO:0061073)|corpus callosum morphogenesis (GO:0021540)|lateral ventricle development (GO:0021670)|negative regulation of Wnt signaling pathway (GO:0030178)|regulation of gene expression (GO:0010468)	extracellular space (GO:0005615)				NS(1)|large_intestine(4)|lung(6)|urinary_tract(1)	12	Ovarian(111;0.112)					ACAACCTGCTCACCAGCATCTCA	0.631																																					p.96_97del		Atlas-Indel,Pindel	.											.	TSKU	26	.	0			c.287_289del						.																																			SO:0001651	inframe_deletion	25987	exon2			.	AK075476	CCDS8246.1	11q13.5	2012-12-05	2012-12-05	2006-11-21	ENSG00000182704	ENSG00000182704			28850	protein-coding gene	gene with protein product		608015	"""leucine rich repeat containing 54"", ""tsukushin"", ""tsukushi small leucine rich proteoglycan homolog (Xenopus laevis)"""	LRRC54		11085516, 19710929, 22880013	Standard	NM_001258210		Approved	E2IG4, TSK	uc031qcw.1	Q8WUA8		ENST00000527881.1:c.288_290delCAC	chr11.hg19:g.76506948_76506950delCAC	ENSP00000434847:p.Thr97del	212.0	0.0		211.0	22.0	NM_001258210	B3KQT7|Q6UXK1|Q9UG10|Q9UJX9	In_Frame_Del	DEL	ENST00000527881.1	hg19	CCDS8246.1																																																																																			.	.		0.631	TSKU-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382871.1	NM_015516	
SAA1	6288	hgsc.bcm.edu	37	11	18291314	18291315	+	Frame_Shift_Ins	INS	-	-	A	rs11545465|rs150951768		TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr11:18291314_18291315insA	ENST00000405158.2	+	4	465_466	c.281_282insA	c.(280-285)tcgctgfs	p.L95fs	SAA1_ENST00000356524.4_Frame_Shift_Ins_p.L95fs|SAA1_ENST00000532858.1_Frame_Shift_Ins_p.L95fs	NM_000331.4	NP_000322	P0DJI8	SAA1_HUMAN	serum amyloid A1	95					acute-phase response (GO:0006953)|innate immune response (GO:0045087)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of inflammatory response (GO:0050728)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of interleukin-1 secretion (GO:0050716)|regulation of protein secretion (GO:0050708)	endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)	G-protein coupled receptor binding (GO:0001664)|heparin binding (GO:0008201)			endometrium(1)|large_intestine(3)|lung(2)|stomach(3)	9					Human Serum Albumin(DB00062)|Serum albumin iodonated(DB00064)	GCGGAGGACTCGCTGGCTGATC	0.525																																					p.S94fs		Atlas-INDEL	.											.	SAA1	14	.	0			c.281_282insA						.																																			SO:0001589	frameshift_variant	6288	exon4			.	M10906	CCDS7835.1	11p15.1	2014-01-30			ENSG00000173432	ENSG00000173432		"""Endogenous ligands"""	10513	protein-coding gene	gene with protein product		104750		SAA		2595451, 9305847	Standard	NM_199161		Approved	PIG4, TP53I4	uc021qeo.1	P0DJI8	OTTHUMG00000166147	Exception_encountered	chr11.hg19:g.18291314_18291315insA	ENSP00000384906:p.Leu95fs	257.0	0.0		290.0	97.0	NM_199161	P02735|P02736|P02737|Q16730|Q16834|Q16835|Q16879|Q3KRB3|Q6FG67|Q96QN0|Q9UCK9|Q9UCL0	Frame_Shift_Ins	INS	ENST00000405158.2	hg19	CCDS7835.1																																																																																			.	.		0.525	SAA1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395864.1	NM_199161	
ZBED4	9889	hgsc.bcm.edu	37	22	50278080	50278104	+	Frame_Shift_Del	DEL	ACCTCCCTGCTCTCCATTACGATGA	ACCTCCCTGCTCTCCATTACGATGA	-			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	ACCTCCCTGCTCTCCATTACGATGA	ACCTCCCTGCTCTCCATTACGATGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:50278080_50278104delACCTCCCTGCTCTCCATTACGATGA	ENST00000216268.5	+	2	1247_1271	c.770_794delACCTCCCTGCTCTCCATTACGATGA	c.(769-795)cacctccctgctctccattacgatgaafs	p.HLPALHYDE257fs		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	257						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		TCGTCTCCCCACCTCCCTGCTCTCCATTACGATGAACCTGCAGAG	0.547																																					p.257_265del		Atlas-Indel,Pindel	.											.	ZBED4	102	.	0			c.769_793del						.																																			SO:0001589	frameshift_variant	9889	exon2			.	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.770_794delACCTCCCTGCTCTCCATTACGATGA	chr22.hg19:g.50278080_50278104delACCTCCCTGCTCTCCATTACGATGA	ENSP00000216268:p.His257fs	164.0	0.0		136.0	25.0	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Frame_Shift_Del	DEL	ENST00000216268.5	hg19	CCDS33677.1																																																																																			.	.		0.547	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
SUPT6H	6830	hgsc.bcm.edu	37	17	27017195	27017196	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr17:27017195_27017196delAG	ENST00000314616.6	+	26	3721_3722	c.3438_3439delAG	c.(3436-3441)acagagfs	p.E1148fs	SUPT6H_ENST00000347486.4_Frame_Shift_Del_p.E1148fs	NM_003170.3	NP_003161.2	Q7KZ85	SPT6H_HUMAN	suppressor of Ty 6 homolog (S. cerevisiae)	1148	Interaction with KDM6A. {ECO:0000250}.				chromatin remodeling (GO:0006338)|mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|negative regulation of histone H3-K27 methylation (GO:0061086)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|regulation of isotype switching (GO:0045191)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of muscle cell differentiation (GO:0051147)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|hydrolase activity, acting on ester bonds (GO:0016788)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(15)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	Lung NSC(42;0.00431)					CTCCCAACACAGAGGAGATCTT	0.48																																					p.1146_1146del		Atlas-Indel,Pindel	.											.	SUPT6H	165	.	0			c.3437_3438del						.																																			SO:0001589	frameshift_variant	6830	exon26			.	U38658	CCDS32596.1	17q11.2	2013-02-14	2001-11-28			ENSG00000109111		"""SH2 domain containing"""	11470	protein-coding gene	gene with protein product		601333	"""suppressor of Ty (S.cerevisiae) 6 homolog"""			8786132	Standard	XM_005258026		Approved	KIAA0162, SPT6H	uc002hby.3	Q7KZ85		ENST00000314616.6:c.3438_3439delAG	chr17.hg19:g.27017197_27017198delAG	ENSP00000319104:p.Glu1148fs	267.0	0.0		277.0	80.0	NM_003170	A7E2B4|Q15737|Q6GMQ4|Q7KYW9|Q7LDK4|Q8N526|Q92775|Q96AH3|Q9BTH9|Q9BTI2	Frame_Shift_Del	DEL	ENST00000314616.6	hg19	CCDS32596.1																																																																																			.	.		0.480	SUPT6H-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446422.2	NM_003170	
NEFH	4744	hgsc.bcm.edu	37	22	29885288	29885292	+	Frame_Shift_Del	DEL	AGCAA	AGCAA	-	rs544011483|rs575224034	byFrequency	TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	AGCAA	AGCAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr22:29885288_29885292delAGCAA	ENST00000310624.6	+	4	1692_1696	c.1659_1663delAGCAA	c.(1657-1665)ccagcaaagfs	p.AK554fs		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	554	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)	p.A554A(1)		cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCAAGTCTCCAGCAAAGGAAGAGGC	0.571																																					p.553_554del		Atlas-Indel,Pindel	.											.	NEFH	178	.	1	Substitution - coding silent(1)	skin(1)	c.1658_1662del						.																																			SO:0001589	frameshift_variant	4744	exon4			.		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1659_1663delAGCAA	chr22.hg19:g.29885288_29885292delAGCAA	ENSP00000311997:p.Ala554fs	325.0	0.0		220.0	66.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Frame_Shift_Del	DEL	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.571	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
FBXO42	54455	hgsc.bcm.edu	37	1	16578144	16578145	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-ED-A459-01A-11D-A25V-10	TCGA-ED-A459-10A-01D-A25V-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7fc7b316-f3d3-4e71-9417-423fe334e6bc	ba12fec9-e575-4fff-9119-8989b3cf1d18	g.chr1:16578144_16578145delTG	ENST00000375592.3	-	10	1390_1391	c.1174_1175delCA	c.(1174-1176)cagfs	p.Q392fs		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	392										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		TACTGGAGACTGAGAGCGGTAC	0.569																																					p.392_392del		Atlas-Indel,Pindel	.											.	FBXO42	53	.	0			c.1175_1176del						.																																			SO:0001589	frameshift_variant	54455	exon10			.	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1174_1175delCA	chr1.hg19:g.16578144_16578145delTG	ENSP00000364742:p.Gln392fs	201.0	0.0		239.0	29.0	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Frame_Shift_Del	DEL	ENST00000375592.3	hg19	CCDS30613.1																																																																																			.	.		0.569	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
