#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
KCNA3	3738	hgsc.bcm.edu	37	1	111217151	111217151	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:111217151G>T	ENST00000369769.2	-	1	504	c.281C>A	c.(280-282)cCg>cAg	p.P94Q		NM_002232.3	NP_002223.3	P22001	KCNA3_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 3	94					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	membrane raft (GO:0045121)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|voltage-gated ion channel activity (GO:0005244)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(7)|ovary(4)|pancreas(1)|prostate(3)|skin(1)	38		all_cancers(81;3.92e-06)|all_epithelial(167;1.28e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000398)		Lung(183;0.0235)|Colorectal(144;0.0306)|all cancers(265;0.0752)|Epithelial(280;0.0821)|COAD - Colon adenocarcinoma(174;0.132)|LUSC - Lung squamous cell carcinoma(189;0.133)	Dalfampridine(DB06637)	GCCCGCGGCCGGCAGTGAGGG	0.726																																					p.P94Q		Atlas-SNP	.											.	KCNA3	91	.	0			c.C281A						.						9.0	11.0	10.0					1																	111217151		2126	4234	6360	SO:0001583	missense	3738	exon1			GCGGCCGGCAGTG	L23499	CCDS828.2	1p13.3	2012-07-05			ENSG00000177272	ENSG00000177272		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6221	protein-coding gene	gene with protein product		176263				2251283, 16382104	Standard	NM_002232		Approved	Kv1.3, MK3, HLK3, HPCN3	uc001dzv.1	P22001	OTTHUMG00000034493	ENST00000369769.2:c.281C>A	chr1.hg19:g.111217151G>T	ENSP00000358784:p.Pro94Gln	103.0	0.0		99.0	4.0	NM_002232	Q5VWN2	Missense_Mutation	SNP	ENST00000369769.2	hg19	CCDS828.2	.	.	.	.	.	.	.	.	.	.	G	5.372	0.253877	0.10185	.	.	ENSG00000177272	ENST00000369769	D	0.96885	-4.16	3.71	1.45	0.22620	.	.	.	.	.	D	0.82935	0.5145	N	0.14661	0.345	0.26823	N	0.968758	B	0.16802	0.019	B	0.09377	0.004	T	0.73867	-0.3847	9	0.17369	T	0.5	.	10.6977	0.45909	0.0:0.3182:0.6818:0.0	.	94	P22001	KCNA3_HUMAN	Q	94	ENSP00000358784:P94Q	ENSP00000358784:P94Q	P	-	2	0	KCNA3	111018674	0.667000	0.27484	0.999000	0.59377	0.212000	0.24457	0.082000	0.14847	1.613000	0.50231	0.462000	0.41574	CCG	.	.		0.726	KCNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083391.1	NM_002232	
TCHH	7062	hgsc.bcm.edu	37	1	152084323	152084323	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:152084323C>A	ENST00000368804.1	-	2	1369	c.1370G>T	c.(1369-1371)tGg>tTg	p.W457L		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	457	9 X 28 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			gcgcttcagccaatcgcgcct	0.672																																					p.W457L		Atlas-SNP	.											.	TCHH	275	.	0			c.G1370T						.						49.0	55.0	53.0					1																	152084323		2111	4227	6338	SO:0001583	missense	7062	exon3			TTCAGCCAATCGC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.1370G>T	chr1.hg19:g.152084323C>A	ENSP00000357794:p.Trp457Leu	44.0	0.0		56.0	10.0	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	hg19	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	c	3.094	-0.186236	0.06340	.	.	ENSG00000159450	ENST00000368804	T	0.05081	3.5	1.75	-3.51	0.04696	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47573	-0.9107	9	0.14252	T	0.57	.	2.9757	0.05936	0.2017:0.4955:0.0:0.3028	.	457	Q07283	TRHY_HUMAN	L	457	ENSP00000357794:W457L	ENSP00000357794:W457L	W	-	2	0	TCHH	150350947	0.001000	0.12720	0.000000	0.03702	0.009000	0.06853	-0.019000	0.12546	-1.042000	0.03262	-1.149000	0.01842	TGG	.	.		0.672	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
DCST1	149095	hgsc.bcm.edu	37	1	155011941	155011941	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:155011941C>T	ENST00000295542.1	+	5	421	c.325C>T	c.(325-327)Ccc>Tcc	p.P109S	DCST1_ENST00000423025.2_Missense_Mutation_p.P84S|DCST1_ENST00000392480.1_Missense_Mutation_p.P109S|DCST1_ENST00000368419.2_Missense_Mutation_p.P109S	NM_152494.3	NP_689707.2	Q5T197	DCST1_HUMAN	DC-STAMP domain containing 1	109						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(2)|endometrium(4)|kidney(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	27	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)			CCTACTAGTACCCAAGATGCT	0.602																																					p.P109S		Atlas-SNP	.											.	DCST1	69	.	0			c.C325T						.						120.0	112.0	115.0					1																	155011941		2203	4300	6503	SO:0001583	missense	149095	exon5			CTAGTACCCAAGA	AK057347	CCDS1083.1, CCDS44235.1	1q22	2008-02-05			ENSG00000163357	ENSG00000163357			26539	protein-coding gene	gene with protein product							Standard	NM_152494		Approved	FLJ32785	uc001fgn.2	Q5T197	OTTHUMG00000041314	ENST00000295542.1:c.325C>T	chr1.hg19:g.155011941C>T	ENSP00000295542:p.Pro109Ser	70.0	0.0		111.0	6.0	NM_152494	B4DXA0|E9PHV3|Q5T198|Q6P1W6|Q71S70|Q96M70	Missense_Mutation	SNP	ENST00000295542.1	hg19	CCDS1083.1	.	.	.	.	.	.	.	.	.	.	C	23.9	4.475054	0.84640	.	.	ENSG00000163357	ENST00000295542;ENST00000392480;ENST00000423025;ENST00000368419	T;T;T;T	0.57273	0.41;0.41;0.41;0.41	5.26	5.26	0.73747	.	0.276731	0.34156	N	0.004212	T	0.65069	0.2656	M	0.72894	2.215	0.46396	D	0.999024	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77004	0.989;0.983;0.989	T	0.69000	-0.5261	10	0.72032	D	0.01	-28.1907	14.3669	0.66812	0.0:1.0:0.0:0.0	.	84;134;109	E9PHV3;E9PJX3;Q5T197	.;.;DCST1_HUMAN	S	109;109;84;109	ENSP00000295542:P109S;ENSP00000376271:P109S;ENSP00000387369:P84S;ENSP00000357404:P109S	ENSP00000295542:P109S	P	+	1	0	DCST1	153278565	0.998000	0.40836	0.928000	0.36995	0.984000	0.73092	5.030000	0.64128	2.472000	0.83506	0.585000	0.79938	CCC	.	.		0.602	DCST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099006.1	NM_152494	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161018501	161018501	+	Silent	SNP	C	C	T	rs377370667		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:161018501C>T	ENST00000368013.3	-	12	2630	c.2310G>A	c.(2308-2310)gaG>gaA	p.E770E	USF1_ENST00000368021.3_5'Flank|ARHGAP30_ENST00000368016.3_Intron|ARHGAP30_ENST00000368015.1_Silent_p.E593E|USF1_ENST00000435396.1_5'Flank	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	770	Glu-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			GGGCCCCTTGCTCTAGGTCCC	0.488																																					p.E770E		Atlas-SNP	.											.	ARHGAP30	105	.	0			c.G2310A						.						207.0	206.0	207.0					1																	161018501		2203	4300	6503	SO:0001819	synonymous_variant	257106	exon12			CCCTTGCTCTAGG	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.2310G>A	chr1.hg19:g.161018501C>T		122.0	0.0		189.0	135.0	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Silent	SNP	ENST00000368013.3	hg19	CCDS30918.1																																																																																			.	.		0.488	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
SLC30A1	7779	hgsc.bcm.edu	37	1	211751728	211751728	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:211751728C>A	ENST00000367001.4	-	1	356	c.227G>T	c.(226-228)cGa>cTa	p.R76L		NM_021194.2	NP_067017.2	Q9Y6M5	ZNT1_HUMAN	solute carrier family 30 (zinc transporter), member 1	76					cadmium ion transmembrane transport (GO:0070574)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|cellular zinc ion homeostasis (GO:0006882)|detoxification of cadmium ion (GO:0071585)|in utero embryonic development (GO:0001701)|negative regulation of calcium ion import (GO:0090281)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of zinc ion transmembrane import (GO:0071584)|transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	calcium channel inhibitor activity (GO:0019855)|zinc ion transmembrane transporter activity (GO:0005385)	p.R76L(1)		central_nervous_system(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(1)|ovary(3)|prostate(1)	11				OV - Ovarian serous cystadenocarcinoma(81;0.00535)|GBM - Glioblastoma multiforme(131;0.051)|all cancers(67;0.0604)|Epithelial(68;0.0978)		TACCTCGGCTCGGATCCAGCC	0.662																																					p.R76L		Atlas-SNP	.											SLC30A1,NS,carcinoma,0,1	SLC30A1	27	.	1	Substitution - Missense(1)	ovary(1)	c.G227T						.						36.0	45.0	42.0					1																	211751728		2203	4300	6503	SO:0001583	missense	7779	exon1			TCGGCTCGGATCC	AF323590	CCDS1499.1	1q32.3	2013-05-22			ENSG00000170385	ENSG00000170385		"""Solute carriers"""	11012	protein-coding gene	gene with protein product		609521		ZNT1			Standard	NM_021194		Approved	ZRC1	uc001hio.1	Q9Y6M5	OTTHUMG00000036995	ENST00000367001.4:c.227G>T	chr1.hg19:g.211751728C>A	ENSP00000355968:p.Arg76Leu	167.0	0.0		212.0	148.0	NM_021194	Q0VAK9|Q9BZF6	Missense_Mutation	SNP	ENST00000367001.4	hg19	CCDS1499.1	.	.	.	.	.	.	.	.	.	.	C	31	5.070240	0.93950	.	.	ENSG00000170385	ENST00000367001	T	0.73789	-0.78	3.68	3.68	0.42216	.	0.000000	0.85682	D	0.000000	D	0.91327	0.7265	H	0.98446	4.235	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.94905	0.8060	10	0.87932	D	0	-8.1932	15.5717	0.76345	0.0:1.0:0.0:0.0	.	76	Q9Y6M5	ZNT1_HUMAN	L	76	ENSP00000355968:R76L	ENSP00000355968:R76L	R	-	2	0	SLC30A1	209818351	1.000000	0.71417	1.000000	0.80357	0.863000	0.49368	6.787000	0.75099	1.881000	0.54492	0.400000	0.26472	CGA	.	.		0.662	SLC30A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104738.2		
RAB3GAP2	25782	hgsc.bcm.edu	37	1	220340743	220340743	+	Splice_Site	SNP	T	T	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:220340743T>C	ENST00000358951.2	-	26	3097		c.e26-2			NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)						establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		GCAGTAAGTCTGAAAGTCAGA	0.388																																					.		Atlas-SNP	.											.	RAB3GAP2	120	.	0			c.2981-2A>G						.						121.0	115.0	117.0					1																	220340743		2203	4300	6503	SO:0001630	splice_region_variant	25782	exon27			TAAGTCTGAAAGT	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.2981-2A>G	chr1.hg19:g.220340743T>C		183.0	1.0		267.0	183.0	NM_012414	A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Splice_Site	SNP	ENST00000358951.2	hg19	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	T	16.40	3.111694	0.56398	.	.	ENSG00000118873	ENST00000358951	.	.	.	6.02	6.02	0.97574	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.5446	0.84426	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAB3GAP2	218407366	1.000000	0.71417	0.988000	0.46212	0.322000	0.28314	8.040000	0.89188	2.311000	0.77944	0.533000	0.62120	.	.	.		0.388	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414	Intron
HIST3H2A	92815	hgsc.bcm.edu	37	1	228645397	228645397	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:228645397G>A	ENST00000366695.2	-	1	163	c.122C>T	c.(121-123)tCg>tTg	p.S41L	HIST3H2BB_ENST00000369160.2_5'Flank	NM_033445.2	NP_254280.1	Q7L7L0	H2A3_HUMAN	histone cluster 3, H2a	41					nucleosome disassembly (GO:0006337)|UV-damage excision repair (GO:0070914)	extracellular vesicular exosome (GO:0070062)|nuclear nucleosome (GO:0000788)	DNA binding (GO:0003677)			endometrium(1)|lung(3)|ovary(1)	5		Prostate(94;0.183)				CACGCGCTCCGAATAGTTGCC	0.716																																					p.S41L		Atlas-SNP	.											.	HIST3H2A	13	.	0			c.C122T						.						16.0	20.0	19.0					1																	228645397		2196	4295	6491	SO:0001583	missense	92815	exon1			CGCTCCGAATAGT	AY131974	CCDS1573.1	1q42.13	2011-01-27	2006-10-11		ENSG00000181218	ENSG00000181218		"""Histones / Replication-dependent"""	20507	protein-coding gene	gene with protein product		615015	"""histone 3, H2a"""			12408966	Standard	NM_033445		Approved	MGC3165	uc001hsy.3	Q7L7L0	OTTHUMG00000040046	ENST00000366695.2:c.122C>T	chr1.hg19:g.228645397G>A	ENSP00000355656:p.Ser41Leu	175.0	0.0		324.0	18.0	NM_033445	B2R4S4	Missense_Mutation	SNP	ENST00000366695.2	hg19	CCDS1573.1	.	.	.	.	.	.	.	.	.	.	.	13.21	2.169766	0.38315	.	.	ENSG00000181218	ENST00000366695	T	0.69040	-0.37	4.07	3.13	0.36017	Histone-fold (2);Histone core (1);Histone H2A (1);	0.176181	0.27500	N	0.019083	T	0.74928	0.3781	M	0.80746	2.51	0.22591	N	0.998952	D	0.56746	0.977	P	0.52793	0.709	T	0.68957	-0.5272	10	0.87932	D	0	.	11.8956	0.52654	0.0:0.1781:0.8219:0.0	.	41	Q7L7L0	H2A3_HUMAN	L	41	ENSP00000355656:S41L	ENSP00000355656:S41L	S	-	2	0	HIST3H2A	226712020	1.000000	0.71417	0.028000	0.17463	0.132000	0.20833	5.869000	0.69613	1.253000	0.44018	0.655000	0.94253	TCG	.	.		0.716	HIST3H2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096598.1	NM_033445	
CEP170	9859	hgsc.bcm.edu	37	1	243354614	243354614	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:243354614T>A	ENST00000366542.1	-	8	865	c.814A>T	c.(814-816)Ata>Tta	p.I272L	CEP170_ENST00000366544.1_Missense_Mutation_p.I272L|CEP170_ENST00000366543.1_Missense_Mutation_p.I272L	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	272						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)			GCACCTGTTATATGGGAACTT	0.383																																					p.I272L		Atlas-SNP	.											.	CEP170	153	.	0			c.A814T						.						94.0	83.0	86.0					1																	243354614		1863	4091	5954	SO:0001583	missense	9859	exon8			CTGTTATATGGGA	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.814A>T	chr1.hg19:g.243354614T>A	ENSP00000355500:p.Ile272Leu	117.0	0.0		167.0	108.0	NM_001042405	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Missense_Mutation	SNP	ENST00000366542.1	hg19	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	T	13.15	2.150789	0.37923	.	.	ENSG00000143702	ENST00000366542;ENST00000366544;ENST00000366543;ENST00000424081	T;T;T	0.28666	1.6;1.6;1.6	4.71	3.58	0.41010	.	0.419377	0.24388	N	0.038957	T	0.12433	0.0302	N	0.03608	-0.345	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.13407	0.007;0.009;0.003	T	0.07424	-1.0773	10	0.34782	T	0.22	-5.953	6.5992	0.22691	0.0:0.2795:0.0:0.7205	.	272;272;272	Q5SW79-3;Q5SW79-2;Q5SW79	.;.;CE170_HUMAN	L	272;272;272;170	ENSP00000355500:I272L;ENSP00000355502:I272L;ENSP00000355501:I272L	ENSP00000355500:I272L	I	-	1	0	CEP170	241421237	0.988000	0.35896	0.987000	0.45799	0.984000	0.73092	0.914000	0.28624	1.767000	0.52121	0.374000	0.22700	ATA	.	.		0.383	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
RPS27A	6233	hgsc.bcm.edu	37	2	55460543	55460543	+	Silent	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:55460543G>A	ENST00000272317.6	+	3	417	c.93G>A	c.(91-93)caG>caA	p.Q31Q	RPS27A_ENST00000404735.1_Silent_p.Q31Q|CLHC1_ENST00000406437.2_5'Flank|CLHC1_ENST00000406076.1_5'Flank|CLHC1_ENST00000407122.1_5'Flank|CLHC1_ENST00000401408.1_5'Flank|CLHC1_ENST00000494539.1_5'Flank|RPS27A_ENST00000402285.3_Silent_p.Q31Q	NM_002954.5	NP_002945.1	P62979	RS27A_HUMAN	ribosomal protein S27a	31	Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|viral transcription (GO:0019083)|virion assembly (GO:0019068)	cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|small ribosomal subunit (GO:0015935)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			cervix(1)|ovary(1)|urinary_tract(1)	3						CCAAGATCCAGGATAAGGAAG	0.433																																					p.Q31Q		Atlas-SNP	.											.	RPS27A	12	.	0			c.G93A						.						84.0	79.0	81.0					2																	55460543		2203	4300	6503	SO:0001819	synonymous_variant	6233	exon3			GATCCAGGATAAG	AB007163	CCDS33202.1	2p16	2011-04-06			ENSG00000143947	ENSG00000143947		"""S ribosomal proteins"""	10417	protein-coding gene	gene with protein product	"""ubiquitin carboxyl extension protein 80"""	191343				9582194	Standard	NM_001135592		Approved	UBCEP80, Uba80, S27A	uc010yow.2	P62979	OTTHUMG00000151919	ENST00000272317.6:c.93G>A	chr2.hg19:g.55460543G>A		99.0	0.0		92.0	4.0	NM_001135592	P02248|P02249|P02250|P14798|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BQ77|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000272317.6	hg19	CCDS33202.1																																																																																			.	.		0.433	RPS27A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324423.15		
ALMS1	7840	hgsc.bcm.edu	37	2	73613036	73613036	+	Missense_Mutation	SNP	G	G	C	rs61156725|rs72319667|rs3074417	byFrequency	TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:73613036G>C	ENST00000264448.6	+	1	151	c.40G>C	c.(40-42)Gag>Cag	p.E14Q	ALMS1_ENST00000377715.1_Missense_Mutation_p.E14Q|ALMS1_ENST00000409009.1_Missense_Mutation_p.E14Q	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	14	Glu-rich.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)		p.E27_E28delEE(1)		breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CGAGCTggaggaggaggagga	0.692																																					p.E14Q		Atlas-SNP	.											.	ALMS1	384	.	1	Deletion - In frame(1)	ovary(1)	c.G40C						.						3.0	4.0	4.0					2																	73613036		1509	3234	4743	SO:0001583	missense	7840	exon1			CTGGAGGAGGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.40G>C	chr2.hg19:g.73613036G>C	ENSP00000264448:p.Glu14Gln	186.0	0.0		263.0	19.0	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.731519	0.48939	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.26373	2.4;2.61;1.74	3.19	3.19	0.36642	.	0.259523	0.20097	U	0.099311	T	0.32436	0.0829	N	0.19112	0.55	0.22317	N	0.999202	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.03493	-1.1031	10	0.87932	D	0	.	10.1262	0.42652	0.0:0.0:1.0:0.0	.	14;14	B8ZZJ3;Q8TCU4	.;ALMS1_HUMAN	Q	14	ENSP00000386627:E14Q;ENSP00000264448:E14Q;ENSP00000366944:E14Q	ENSP00000264448:E14Q	E	+	1	0	ALMS1	73466544	1.000000	0.71417	1.000000	0.80357	0.826000	0.46750	2.034000	0.41145	2.070000	0.61991	0.484000	0.47621	GAG	.	.		0.692	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SLC9A2	6549	hgsc.bcm.edu	37	2	103236548	103236548	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:103236548C>A	ENST00000233969.2	+	1	383	c.241C>A	c.(241-243)Ccc>Acc	p.P81T		NM_003048.3	NP_003039.2	Q9UBY0	SL9A2_HUMAN	solute carrier family 9, subfamily A (NHE2, cation proton antiporter 2), member 2	81					ion transport (GO:0006811)|protein localization (GO:0008104)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			breast(5)|central_nervous_system(3)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42						CGTGCAGATCCCCTTCGAGAT	0.642																																					p.P81T		Atlas-SNP	.											.	SLC9A2	112	.	0			c.C241A						.						59.0	51.0	54.0					2																	103236548		2203	4300	6503	SO:0001583	missense	6549	exon1			CAGATCCCCTTCG		CCDS2062.1	2q11.2	2013-05-22	2012-03-22		ENSG00000115616	ENSG00000115616		"""Solute carriers"""	11072	protein-coding gene	gene with protein product		600530	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 2"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 2"""	NHE2			Standard	NM_003048		Approved		uc002tca.3	Q9UBY0	OTTHUMG00000130778	ENST00000233969.2:c.241C>A	chr2.hg19:g.103236548C>A	ENSP00000233969:p.Pro81Thr	196.0	0.0		211.0	67.0	NM_003048	B2RMS2	Missense_Mutation	SNP	ENST00000233969.2	hg19	CCDS2062.1	.	.	.	.	.	.	.	.	.	.	C	25.8	4.677163	0.88445	.	.	ENSG00000115616	ENST00000233969	D	0.83837	-1.77	5.15	5.15	0.70609	.	0.058224	0.64402	D	0.000001	T	0.76744	0.4030	L	0.29908	0.895	0.80722	D	1	P	0.45126	0.851	B	0.40165	0.321	T	0.81123	-0.1076	10	0.72032	D	0.01	.	17.3902	0.87428	0.0:1.0:0.0:0.0	.	81	Q9UBY0	SL9A2_HUMAN	T	81	ENSP00000233969:P81T	ENSP00000233969:P81T	P	+	1	0	SLC9A2	102602980	1.000000	0.71417	1.000000	0.80357	0.808000	0.45660	6.700000	0.74619	2.401000	0.81631	0.555000	0.69702	CCC	.	.		0.642	SLC9A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253292.2		
PSD4	23550	hgsc.bcm.edu	37	2	113940649	113940649	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:113940649C>T	ENST00000245796.6	+	2	811	c.616C>T	c.(616-618)Cct>Tct	p.P206S	PSD4_ENST00000441564.3_Missense_Mutation_p.P206S	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	206					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTCCAGCCCACCTGAGAATGA	0.647																																					p.P206S		Atlas-SNP	.											.	PSD4	74	.	0			c.C616T						.						58.0	62.0	61.0					2																	113940649		2203	4300	6503	SO:0001583	missense	23550	exon2			AGCCCACCTGAGA	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.616C>T	chr2.hg19:g.113940649C>T	ENSP00000245796:p.Pro206Ser	78.0	0.0		72.0	5.0	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	hg19	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	C	13.94	2.386696	0.42308	.	.	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.12255	2.7;2.73	5.59	3.74	0.42951	.	2.786630	0.00871	N	0.002024	T	0.20170	0.0485	L	0.29908	0.895	0.09310	N	0.99999	D;P	0.53462	0.96;0.933	P;P	0.52217	0.693;0.497	T	0.15093	-1.0449	9	.	.	.	.	8.038	0.30504	0.0:0.7535:0.159:0.0875	.	206;206	Q8NDX1-2;Q8NDX1	.;PSD4_HUMAN	S	206	ENSP00000245796:P206S;ENSP00000413997:P206S	.	P	+	1	0	PSD4	113657120	0.000000	0.05858	0.032000	0.17829	0.009000	0.06853	0.573000	0.23699	1.321000	0.45227	0.561000	0.74099	CCT	.	.		0.647	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	
COL4A4	1286	hgsc.bcm.edu	37	2	227919329	227919329	+	Silent	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:227919329C>A	ENST00000396625.3	-	31	3048	c.2841G>T	c.(2839-2841)cgG>cgT	p.R947R	COL4A4_ENST00000329662.7_Silent_p.R947R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	947	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CTCTCAGTCCCCGGTCTCCAG	0.483																																					p.R947R		Atlas-SNP	.											.	COL4A4	215	.	0			c.G2841T						.						104.0	110.0	108.0					2																	227919329		1910	4121	6031	SO:0001819	synonymous_variant	1286	exon31			CAGTCCCCGGTCT		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2841G>T	chr2.hg19:g.227919329C>A		123.0	0.0		152.0	9.0	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	hg19	CCDS42828.1																																																																																			.	.		0.483	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
NEU2	4759	hgsc.bcm.edu	37	2	233897434	233897434	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr2:233897434A>T	ENST00000233840.3	+	1	53	c.53A>T	c.(52-54)cAt>cTt	p.H18L		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	18					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	TCGGGAGCCCATGCCTACAGA	0.627																																					p.H18L		Atlas-SNP	.											.	NEU2	42	.	0			c.A53T						.						131.0	111.0	118.0					2																	233897434		2203	4300	6503	SO:0001583	missense	4759	exon1			GAGCCCATGCCTA	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.53A>T	chr2.hg19:g.233897434A>T	ENSP00000233840:p.His18Leu	128.0	0.0		125.0	30.0	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	hg19	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.490103	0.26686	.	.	ENSG00000115488	ENST00000233840	T	0.08807	3.05	5.48	3.17	0.36434	Neuraminidase (2);	1.082620	0.07117	N	0.843272	T	0.07683	0.0193	L	0.46157	1.445	0.09310	N	1	B	0.22480	0.07	B	0.15484	0.013	T	0.46428	-0.9192	10	0.10111	T	0.7	-8.6775	5.4599	0.16612	0.7188:0.0:0.2812:0.0	.	18	Q9Y3R4	NEUR2_HUMAN	L	18	ENSP00000233840:H18L	ENSP00000233840:H18L	H	+	2	0	NEU2	233605678	0.000000	0.05858	0.008000	0.14137	0.651000	0.38670	1.141000	0.31528	0.918000	0.36919	0.533000	0.62120	CAT	.	.		0.627	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
MYH15	22989	hgsc.bcm.edu	37	3	108179187	108179187	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr3:108179187T>A	ENST00000273353.3	-	18	2008	c.1952A>T	c.(1951-1953)aAg>aTg	p.K651M	MYH15_ENST00000495753.2_5'UTR	NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	651	Myosin motor.					cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						AGCTCCTTTCTTTCGTTTCTT	0.313																																					p.K651M		Atlas-SNP	.											.	MYH15	223	.	0			c.A1952T						.						59.0	57.0	57.0					3																	108179187		1821	4067	5888	SO:0001583	missense	22989	exon18			CCTTTCTTTCGTT	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.1952A>T	chr3.hg19:g.108179187T>A	ENSP00000273353:p.Lys651Met	269.0	0.0		283.0	20.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	T	15.40	2.823054	0.50739	.	.	ENSG00000144821	ENST00000273353	D	0.88046	-2.33	4.39	1.94	0.25998	Myosin head, motor domain (2);	.	.	.	.	D	0.93569	0.7947	M	0.93763	3.455	0.44728	D	0.997722	D	0.76494	0.999	D	0.80764	0.994	D	0.91559	0.5263	9	0.87932	D	0	.	6.6819	0.23125	0.1369:0.0761:0.0:0.7871	.	651	Q9Y2K3	MYH15_HUMAN	M	651	ENSP00000273353:K651M	ENSP00000273353:K651M	K	-	2	0	MYH15	109661877	1.000000	0.71417	0.642000	0.29436	0.480000	0.33159	3.373000	0.52394	0.424000	0.26061	0.459000	0.35465	AAG	.	.		0.313	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
ALG3	10195	hgsc.bcm.edu	37	3	183959046	183959046	+	IGR	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr3:183959046G>A	ENST00000397676.3	-	0	1528				VWA5B2_ENST00000426955.2_Missense_Mutation_p.D1012N|ALG3_ENST00000463495.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|MIR1224_ENST00000408193.1_RNA|VWA5B2_ENST00000273794.5_Missense_Mutation_p.D794N	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TGCTTTGGGGGACCCTGCCAC	0.662																																					p.D1012N		Atlas-SNP	.											.	VWA5B2	47	.	0			c.G3034A						.						25.0	36.0	32.0					3																	183959046		692	1591	2283	SO:0001628	intergenic_variant	90113	exon18			TTGGGGGACCCTG	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823		chr3.hg19:g.183959046G>A		166.0	0.0		178.0	16.0	NM_138345	A8JZZ6|Q9BT71	Missense_Mutation	SNP	ENST00000397676.3	hg19	CCDS46968.1	.	.	.	.	.	.	.	.	.	.	G	11.32	1.604699	0.28623	.	.	ENSG00000145198	ENST00000426955;ENST00000273794	T;T	0.17370	2.97;2.28	4.54	3.66	0.41972	.	1.753950	0.03383	N	0.200726	T	0.11665	0.0284	N	0.14661	0.345	0.09310	N	1	B;B;B	0.27498	0.037;0.18;0.079	B;B;B	0.24848	0.023;0.056;0.048	T	0.26916	-1.0089	10	0.17832	T	0.49	-4.024	8.3313	0.32189	0.1069:0.0:0.8931:0.0	.	794;1012;1023	E9PF42;B9EGN7;Q8N398	.;.;VW5B2_HUMAN	N	1012;794	ENSP00000398688:D1012N;ENSP00000273794:D794N	ENSP00000273794:D794N	D	+	1	0	VWA5B2	185441740	0.000000	0.05858	0.056000	0.19401	0.100000	0.18952	0.569000	0.23638	1.265000	0.44215	0.462000	0.41574	GAC	.	.		0.662	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
ACOX3	8310	hgsc.bcm.edu	37	4	8418225	8418225	+	Silent	SNP	G	G	A	rs146635266		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:8418225G>A	ENST00000356406.5	-	2	101	c.24C>T	c.(22-24)ggC>ggT	p.G8G	ACOX3_ENST00000413009.2_Silent_p.G8G|ACOX3_ENST00000503233.1_Silent_p.G8G	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	8					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						GAGCTGTGTCGCCTCCTTCCA	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16330	0.0		0.0	False		,,,				2504	0.0				p.G8G		Atlas-SNP	.											.	ACOX3	70	.	0			c.C24T						.	G	,	1,4405	2.1+/-5.4	0,1,2202	65.0	64.0	64.0		24,24	-5.3	0.0	4	dbSNP_134	64	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ACOX3	NM_001101667.1,NM_003501.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	8/625,8/701	8418225	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8310	exon2			TGTGTCGCCTCCT	Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.24C>T	chr4.hg19:g.8418225G>A		80.0	0.0		112.0	32.0	NM_001101667	Q96AJ8	Silent	SNP	ENST00000356406.5	hg19	CCDS3401.1																																																																																			.	G|1.000;A|0.000		0.582	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4		
MMRN1	22915	hgsc.bcm.edu	37	4	90856570	90856570	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:90856570C>A	ENST00000394980.1	+	7	2058	c.1739C>A	c.(1738-1740)tCt>tAt	p.S580Y	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000264790.2_Missense_Mutation_p.S580Y|MMRN1_ENST00000508372.1_Missense_Mutation_p.S322Y			Q13201	MMRN1_HUMAN	multimerin 1	580					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		CTCACCGTCTCTTTGGAGATG	0.343																																					p.S580Y		Atlas-SNP	.											.	MMRN1	174	.	0			c.C1739A						.						56.0	58.0	57.0					4																	90856570		2203	4297	6500	SO:0001583	missense	22915	exon6			CCGTCTCTTTGGA	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.1739C>A	chr4.hg19:g.90856570C>A	ENSP00000378431:p.Ser580Tyr	215.0	0.0		193.0	45.0	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	hg19	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	C	3.869	-0.028322	0.07589	.	.	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.65732	0.18;0.18;-0.17	5.12	0.973	0.19710	.	1.347860	0.04935	N	0.457576	T	0.31638	0.0803	N	0.08118	0	0.09310	N	1	P	0.48162	0.906	B	0.35413	0.202	T	0.20240	-1.0281	10	0.09084	T	0.74	.	3.8393	0.08908	0.1212:0.5764:0.1482:0.1542	.	580	Q13201	MMRN1_HUMAN	Y	580;580;322	ENSP00000378431:S580Y;ENSP00000264790:S580Y;ENSP00000426461:S322Y	ENSP00000264790:S580Y	S	+	2	0	MMRN1	91075593	0.003000	0.15002	0.075000	0.20258	0.071000	0.16799	-0.020000	0.12525	0.325000	0.23359	0.591000	0.81541	TCT	.	.		0.343	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
KIAA1109	84162	hgsc.bcm.edu	37	4	123260512	123260512	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:123260512A>G	ENST00000264501.4	+	72	12674	c.12301A>G	c.(12301-12303)Aat>Gat	p.N4101D	KIAA1109_ENST00000388738.3_Missense_Mutation_p.N4101D			Q2LD37	K1109_HUMAN	KIAA1109	4101					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CCCTGGAGGTAATGCTACTCA	0.403																																					p.N4101D		Atlas-SNP	.											.	KIAA1109	424	.	0			c.A12301G						.						88.0	80.0	82.0					4																	123260512		1826	4082	5908	SO:0001583	missense	84162	exon70			GGAGGTAATGCTA	AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.12301A>G	chr4.hg19:g.123260512A>G	ENSP00000264501:p.Asn4101Asp	157.0	0.0		162.0	46.0	NM_015312	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	ENST00000264501.4	hg19	CCDS43267.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.747415	0.30955	.	.	ENSG00000138688	ENST00000264501;ENST00000388738;ENST00000438707	T;T;T	0.29917	2.5;2.5;1.55	5.68	-0.0957	0.13640	.	1.143810	0.06229	N	0.688359	T	0.14141	0.0342	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.25082	-1.0142	10	0.36615	T	0.2	.	2.6803	0.05091	0.5475:0.2039:0.1452:0.1033	.	4100;4101	Q2LD37-4;Q2LD37	.;K1109_HUMAN	D	4101;4101;770	ENSP00000264501:N4101D;ENSP00000373390:N4101D;ENSP00000410874:N770D	ENSP00000264501:N4101D	N	+	1	0	KIAA1109	123479962	0.009000	0.17119	0.005000	0.12908	0.997000	0.91878	0.908000	0.28545	0.089000	0.17243	0.460000	0.39030	AAT	.	.		0.403	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316415.1	NM_020797	
ARHGAP10	79658	hgsc.bcm.edu	37	4	148743969	148743969	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr4:148743969C>G	ENST00000336498.3	+	2	485	c.246C>G	c.(244-246)tgC>tgG	p.C82W		NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		ATGAACGATGCATAGGTAATT	0.398																																					p.C82W		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.C246G						.						179.0	167.0	171.0					4																	148743969		2203	4300	6503	SO:0001583	missense	79658	exon2			ACGATGCATAGGT	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.246C>G	chr4.hg19:g.148743969C>G	ENSP00000336923:p.Cys82Trp	156.0	0.0		203.0	38.0	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	C	10.79	1.448903	0.26074	.	.	ENSG00000071205	ENST00000336498	T	0.29142	1.58	5.95	2.66	0.31614	IRSp53/MIM homology domain (IMD) (1);	0.043983	0.85682	D	0.000000	T	0.29817	0.0745	M	0.68317	2.08	0.80722	D	1	P	0.49358	0.923	B	0.40702	0.338	T	0.05053	-1.0909	10	0.38643	T	0.18	.	10.1317	0.42682	0.0:0.6328:0.0:0.3672	.	82	A1A4S6	RHG10_HUMAN	W	82	ENSP00000336923:C82W	ENSP00000336923:C82W	C	+	3	2	ARHGAP10	148963419	0.999000	0.42202	0.995000	0.50966	0.076000	0.17211	0.548000	0.23314	0.370000	0.24538	-0.142000	0.14014	TGC	.	.		0.398	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	
MAST4	375449	hgsc.bcm.edu	37	5	66460639	66460639	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:66460639C>T	ENST00000403625.2	+	29	5927	c.5632C>T	c.(5632-5634)Ccc>Tcc	p.P1878S	MAST4_ENST00000403666.1_Missense_Mutation_p.P1689S|MAST4_ENST00000404260.3_Missense_Mutation_p.P1881S|MAST4_ENST00000261569.7_Missense_Mutation_p.P1684S|MAST4_ENST00000405643.1_Missense_Mutation_p.P1699S	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	1881						cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)	p.S1883fs*59(1)		breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		TTGGTTCCTGCCCCCCAGCCG	0.547																																					p.P1878S		Atlas-SNP	.											.,1	MAST4	218	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.C5632T						.						47.0	52.0	50.0					5																	66460639		1901	4108	6009	SO:0001583	missense	375449	exon29			TTCCTGCCCCCCA	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.5632C>T	chr5.hg19:g.66460639C>T	ENSP00000385727:p.Pro1878Ser	86.0	0.0		103.0	19.0	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Missense_Mutation	SNP	ENST00000403625.2	hg19	CCDS54861.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	7.994|7.994	0.753982|0.753982	0.15778|0.15778	.|.	.|.	ENSG00000069020|ENSG00000069020	ENST00000443808|ENST00000404260;ENST00000403625;ENST00000403666;ENST00000405643;ENST00000380908;ENST00000261569	.|T;T;T;T;T	.|0.65916	.|-0.16;-0.16;-0.18;-0.18;-0.15	4.66|4.66	3.78|3.78	0.43462|0.43462	.|.	.|0.422637	.|0.20823	.|N	.|0.085036	T|T	0.43144|0.43144	0.1234|0.1234	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	1|1	.|B;B	.|0.32829	.|0.267;0.386	.|B;B	.|0.31101	.|0.058;0.124	T|T	0.18461|0.18461	-1.0336|-1.0336	5|10	.|0.16896	.|T	.|0.51	-13.0751|-13.0751	5.6869|5.6869	0.17807|0.17807	0.1963:0.7057:0.0:0.0981|0.1963:0.7057:0.0:0.0981	.|.	.|1881;1689	.|O15021;O15021-3	.|MAST4_HUMAN;.	V|S	934|1881;1878;1689;1699;1699;1684	.|ENSP00000385048:P1881S;ENSP00000385727:P1878S;ENSP00000384313:P1689S;ENSP00000384099:P1699S;ENSP00000261569:P1684S	.|ENSP00000261569:P1684S	A|P	+|+	2|1	0|0	MAST4|MAST4	66496395|66496395	0.024000|0.024000	0.19004|0.19004	0.741000|0.741000	0.31004|0.31004	0.227000|0.227000	0.25037|0.25037	1.647000|1.647000	0.37260|0.37260	1.135000|1.135000	0.42183|0.42183	-0.309000|-0.309000	0.09137|0.09137	GCC|CCC	.	.		0.547	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
LVRN	206338	hgsc.bcm.edu	37	5	115327845	115327845	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:115327845C>A	ENST00000357872.4	+	5	1255	c.1131C>A	c.(1129-1131)gaC>gaA	p.D377E	AQPEP_ENST00000395528.2_5'UTR	NM_173800.4	NP_776161.3	Q6Q4G3	AMPQ_HUMAN		377						integral component of membrane (GO:0016021)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)										CTAGTTTTGACAACCATGCAA	0.318																																					p.D377E		Atlas-SNP	.											.	.	.	.	0			c.C1131A						.						112.0	118.0	116.0					5																	115327845		2202	4300	6502	SO:0001583	missense	0	exon5			TTTTGACAACCAT																												ENST00000357872.4:c.1131C>A	chr5.hg19:g.115327845C>A	ENSP00000350541:p.Asp377Glu	109.0	0.0		114.0	23.0	NM_173800	A8K6J0|C9JGD2|Q32MR1|Q4G0I9|Q4G0V2|Q86XA3|Q8NBZ2	Missense_Mutation	SNP	ENST00000357872.4	hg19	CCDS4124.1	.	.	.	.	.	.	.	.	.	.	C	13.73	2.325778	0.41197	.	.	ENSG00000172901	ENST00000357872;ENST00000379578	T	0.02395	4.31	5.81	2.94	0.34122	Peptidase M1, membrane alanine aminopeptidase, N-terminal (2);	0.472937	0.21269	N	0.077347	T	0.02380	0.0073	L	0.31207	0.915	0.23076	N	0.998339	B	0.23249	0.082	B	0.26864	0.074	T	0.43130	-0.9410	10	0.41790	T	0.15	.	3.5656	0.07899	0.1673:0.5103:0.0:0.3224	.	377	Q6Q4G3	AMPQ_HUMAN	E	377;366	ENSP00000350541:D377E	ENSP00000350541:D377E	D	+	3	2	AC010282.1	115355744	0.712000	0.27916	0.637000	0.29366	0.951000	0.60555	0.108000	0.15396	0.805000	0.34159	0.655000	0.94253	GAC	.	.		0.318	AQPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250852.1		
RAPGEF6	51735	hgsc.bcm.edu	37	5	130797637	130797637	+	Silent	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:130797637C>T	ENST00000509018.1	-	19	2830	c.2625G>A	c.(2623-2625)ttG>ttA	p.L875L	RAPGEF6_ENST00000307984.5_Silent_p.L880L|RAPGEF6_ENST00000512052.1_Silent_p.L590L|RAPGEF6_ENST00000507093.1_Silent_p.L875L|CTC-432M15.3_ENST00000514667.1_Silent_p.L925L|RAPGEF6_ENST00000296859.6_Silent_p.L875L|RAPGEF6_ENST00000308008.6_Silent_p.L875L	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	875	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		TATTACGAAACAAATCAAAGT	0.408																																					p.L880L	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.G2640A						.						102.0	99.0	100.0					5																	130797637		2203	4300	6503	SO:0001819	synonymous_variant	51735	exon20			ACGAAACAAATCA	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.2625G>A	chr5.hg19:g.130797637C>T		124.0	0.0		146.0	46.0	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Silent	SNP	ENST00000509018.1	hg19	CCDS34225.1																																																																																			.	.		0.408	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340	
KLHL3	26249	hgsc.bcm.edu	37	5	136974747	136974747	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:136974747C>G	ENST00000309755.4	-	10	1557	c.1114G>C	c.(1114-1116)Gac>Cac	p.D372H	KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506491.1_Missense_Mutation_p.D290H|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000508657.1_Missense_Mutation_p.D340H	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	372					distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GTCCACTGGTCCTTCACGCCG	0.607																																					p.D372H		Atlas-SNP	.											.	KLHL3	54	.	0			c.G1114C						.						99.0	72.0	82.0					5																	136974747		2203	4300	6503	SO:0001583	missense	26249	exon10			ACTGGTCCTTCAC	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.1114G>C	chr5.hg19:g.136974747C>G	ENSP00000312397:p.Asp372His	77.0	0.0		87.0	7.0	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Missense_Mutation	SNP	ENST00000309755.4	hg19	CCDS4192.1	.	.	.	.	.	.	.	.	.	.	C	31	5.086053	0.94100	.	.	ENSG00000146021	ENST00000506491;ENST00000508657;ENST00000309755;ENST00000505853	T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25	4.69	4.69	0.59074	Galactose oxidase, beta-propeller (1);	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	M	0.90309	3.105	0.80722	D	1	D;D;D;D	0.76494	0.999;0.996;0.998;0.999	D;P;P;D	0.72075	0.976;0.906;0.894;0.959	D	0.91941	0.5563	10	0.66056	D	0.02	.	18.1398	0.89636	0.0:1.0:0.0:0.0	.	141;332;340;372	B7Z6E2;D6RH21;Q9UH77-2;Q9UH77	.;.;.;KLHL3_HUMAN	H	290;340;372;332	ENSP00000424828:D290H;ENSP00000422099:D340H;ENSP00000312397:D372H;ENSP00000426173:D332H	ENSP00000312397:D372H	D	-	1	0	KLHL3	137002646	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.869000	0.69613	2.581000	0.87130	0.561000	0.74099	GAC	.	.		0.607	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
HBEGF	1839	hgsc.bcm.edu	37	5	139714267	139714267	+	Silent	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:139714267G>A	ENST00000230990.6	-	5	923	c.621C>T	c.(619-621)tcC>tcT	p.S207S	HBEGF_ENST00000507104.1_Silent_p.S207S	NM_001945.2	NP_001936.1	Q99075	HBEGF_HUMAN	heparin-binding EGF-like growth factor	207					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|muscle organ development (GO:0007517)|negative regulation of elastin biosynthetic process (GO:0051545)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of keratinocyte migration (GO:0051549)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of wound healing (GO:0090303)|regulation of heart contraction (GO:0008016)|signal transduction (GO:0007165)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|heparin binding (GO:0008201)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|stomach(1)	7			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCTCTCAGTGGGAATTAGTCA	0.468																																					p.S207S		Atlas-SNP	.											.	HBEGF	12	.	0			c.C621T						.						346.0	300.0	316.0					5																	139714267		2203	4300	6503	SO:0001819	synonymous_variant	1839	exon5			TCAGTGGGAATTA		CCDS4223.1	5q23	2012-10-02	2005-01-14	2005-01-14	ENSG00000113070	ENSG00000113070			3059	protein-coding gene	gene with protein product	"""Diphtheria toxin receptor (heparin-binding EGF-like growth factor)"", ""heparin-binding epidermal growth factor"""	126150	"""diphtheria toxin receptor (heparin-binding epidermal growth factor-like growth factor)"""	HEGFL, DTS, DTR		7590736, 12163414	Standard	NM_001945		Approved		uc003lfi.3	Q99075	OTTHUMG00000129496	ENST00000230990.6:c.621C>T	chr5.hg19:g.139714267G>A		99.0	0.0		108.0	5.0	NM_001945	B2R821	Silent	SNP	ENST00000230990.6	hg19	CCDS4223.1																																																																																			.	.		0.468	HBEGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251665.2	NM_001945	
ARAP3	64411	hgsc.bcm.edu	37	5	141034964	141034964	+	Nonsense_Mutation	SNP	G	G	A	rs372420144		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:141034964G>A	ENST00000239440.4	-	32	4179	c.4114C>T	c.(4114-4116)Cga>Tga	p.R1372*	ARAP3_ENST00000513878.1_Intron|ARAP3_ENST00000508305.1_Nonsense_Mutation_p.R1203*|ARAP3_ENST00000512390.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1372					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						TTGTGTAGTCGCCGCTGGACA	0.567																																					p.R1372X		Atlas-SNP	.											.	ARAP3	139	.	0			c.C4114T						.	G	stop/ARG	1,4393		0,1,2196	61.0	48.0	52.0		4114	5.1	1.0	5		52	1,8595		0,1,4297	no	stop-gained	ARAP3	NM_022481.5		0,2,6493	AA,AG,GG		0.0116,0.0228,0.0154		1372/1545	141034964	2,12988	2197	4298	6495	SO:0001587	stop_gained	64411	exon32			GTAGTCGCCGCTG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.4114C>T	chr5.hg19:g.141034964G>A	ENSP00000239440:p.Arg1372*	172.0	0.0		197.0	55.0	NM_022481	B4DIT1|D3DQE3	Nonsense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	41	8.589286	0.98875	2.28E-4	1.16E-4	ENSG00000120318	ENST00000508305;ENST00000239440	.	.	.	5.12	5.12	0.69794	.	0.253727	0.34879	N	0.003616	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.3501	0.90336	0.0:0.0:1.0:0.0	.	.	.	.	X	1203;1372	.	ENSP00000239440:R1372X	R	-	1	2	ARAP3	141015148	1.000000	0.71417	1.000000	0.80357	0.482000	0.33219	6.059000	0.71133	2.662000	0.90505	0.655000	0.94253	CGA	.	.		0.567	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
PTTG1	9232	hgsc.bcm.edu	37	5	159855662	159855662	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:159855662C>A	ENST00000393964.1	+	5	986	c.583C>A	c.(583-585)Cct>Act	p.P195T	PTTG1_ENST00000519287.1_3'UTR|PTTG1_ENST00000520452.1_Missense_Mutation_p.P195T|PTTG1_ENST00000352433.5_Missense_Mutation_p.P195T	NM_001282382.1	NP_001269311.1	O95997	PTTG1_HUMAN	pituitary tumor-transforming 1	195					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|chromosome organization (GO:0051276)|chromosome segregation (GO:0007059)|DNA repair (GO:0006281)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of endopeptidase activity (GO:0010951)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|large_intestine(1)|lung(4)	6	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.00219)|Epithelial(171;0.00348)|all cancers(165;0.0104)		TGAATTGCCACCTGTTTGCTG	0.348																																					p.P195T		Atlas-SNP	.											.	PTTG1	15	.	0			c.C583A						.						220.0	215.0	217.0					5																	159855662		2203	4300	6503	SO:0001583	missense	9232	exon6			TTGCCACCTGTTT	AF062649	CCDS4353.1	5q35.1	2014-08-04			ENSG00000164611	ENSG00000164611			9690	protein-coding gene	gene with protein product	"""ESP1-associated protein 1"", ""tumor-transforming protein 1"""	604147		TUTR1		9811450, 9892021	Standard	NM_004219		Approved	PTTG, HPTTG, EAP1, securin	uc003lyj.3	O95997	OTTHUMG00000130328	ENST00000393964.1:c.583C>A	chr5.hg19:g.159855662C>A	ENSP00000377536:p.Pro195Thr	66.0	0.0		75.0	10.0	NM_004219		Missense_Mutation	SNP	ENST00000393964.1	hg19	CCDS4353.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.054733	0.75960	.	.	ENSG00000164611	ENST00000352433;ENST00000520452;ENST00000393964	T;T;T	0.60920	0.15;0.15;0.15	5.51	5.51	0.81932	.	0.000000	0.85682	D	0.000000	T	0.68229	0.2978	M	0.77616	2.38	0.47659	D	0.999483	P	0.52463	0.953	P	0.51170	0.661	T	0.70702	-0.4799	9	.	.	.	-16.6492	14.9156	0.70795	0.0:1.0:0.0:0.0	.	195	O95997	PTTG1_HUMAN	T	195	ENSP00000344936:P195T;ENSP00000430642:P195T;ENSP00000377536:P195T	.	P	+	1	0	PTTG1	159788240	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.946000	0.56644	2.589000	0.87451	0.561000	0.74099	CCT	.	.		0.348	PTTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252677.1	NM_004219	
FARS2	10667	hgsc.bcm.edu	37	6	5369227	5369227	+	Missense_Mutation	SNP	G	G	A	rs145555213		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:5369227G>A	ENST00000324331.6	+	2	760	c.424G>A	c.(424-426)Gac>Aac	p.D142N	FARS2_ENST00000274680.4_Missense_Mutation_p.D142N			O95363	SYFM_HUMAN	phenylalanyl-tRNA synthetase 2, mitochondrial	142					gene expression (GO:0010467)|phenylalanyl-tRNA aminoacylation (GO:0006432)|tRNA aminoacylation for protein translation (GO:0006418)|tRNA processing (GO:0008033)	mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|phenylalanine-tRNA ligase activity (GO:0004826)|tRNA binding (GO:0000049)			endometrium(3)|kidney(1)|large_intestine(5)|lung(3)|prostate(1)|stomach(2)	15	Ovarian(93;0.11)	all_hematologic(90;0.0104)			L-Phenylalanine(DB00120)	GAAGAAGGGGGACAACTATTA	0.572																																					p.D142N		Atlas-SNP	.											.	FARS2	33	.	0			c.G424A						.	G	ASN/ASP	0,4406		0,0,2203	99.0	88.0	92.0		424	4.5	1.0	6	dbSNP_134	92	1,8599	1.2+/-3.3	0,1,4299	no	missense	FARS2	NM_006567.3	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	142/452	5369227	1,13005	2203	4300	6503	SO:0001583	missense	10667	exon2			AAGGGGGACAACT	AF097441	CCDS4494.1	6p25.1	2011-07-01	2007-02-23	2004-12-03	ENSG00000145982	ENSG00000145982	6.1.1.20	"""Aminoacyl tRNA synthetases / Class II"""	21062	protein-coding gene	gene with protein product	"""phenylalanine tRNA ligase 2, mitochondrial"""	611592	"""phenylalanine-tRNA synthetase 1 (mitochondrial)"""	FARS1		10329163	Standard	NM_006567		Approved	dJ236A3.1	uc003mwr.2	O95363	OTTHUMG00000014178	ENST00000324331.6:c.424G>A	chr6.hg19:g.5369227G>A	ENSP00000316335:p.Asp142Asn	752.0	1.0		763.0	183.0	NM_006567	B2R664|Q53F66|Q5TCS3|Q6FG29|Q9NPY7|Q9P062	Missense_Mutation	SNP	ENST00000324331.6	hg19	CCDS4494.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.806963	0.90623	0.0	1.16E-4	ENSG00000145982	ENST00000274680;ENST00000324331	T;T	0.73469	-0.75;-0.75	5.38	4.49	0.54785	Phenylalanyl-tRNA synthetase (1);	0.096626	0.64402	D	0.000001	D	0.88706	0.6509	H	0.97103	3.94	0.58432	D	0.999995	D	0.89917	1.0	D	0.70487	0.969	D	0.92698	0.6172	10	0.87932	D	0	-8.6428	15.2621	0.73631	0.0:0.1409:0.8591:0.0	.	142	O95363	SYFM_HUMAN	N	142	ENSP00000274680:D142N;ENSP00000316335:D142N	ENSP00000274680:D142N	D	+	1	0	FARS2	5314226	1.000000	0.71417	0.993000	0.49108	0.999000	0.98932	9.489000	0.97949	1.329000	0.45376	0.655000	0.94253	GAC	.	G|1.000;A|0.000		0.572	FARS2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467790.1	NM_006567	
HSD17B8	7923	hgsc.bcm.edu	37	6	33172866	33172866	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:33172866G>T	ENST00000374662.3	+	2	267	c.240G>T	c.(238-240)agG>agT	p.R80S	HSD17B8_ENST00000469186.1_3'UTR|MIR219-1_ENST00000362166.1_RNA	NM_014234.4	NP_055049.1	Q92506	DHB8_HUMAN	hydroxysteroid (17-beta) dehydrogenase 8	80					androgen metabolic process (GO:0008209)|estrogen biosynthetic process (GO:0006703)|fatty acid biosynthetic process (GO:0006633)	mitochondrial envelope (GO:0005740)|mitochondrial matrix (GO:0005759)|plasma membrane (GO:0005886)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone dehydrogenase (NAD+) activity (GO:0047035)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|urinary_tract(2)	9						CTGAGGCCAGGGCCGCCAGGT	0.662																																					p.R80S		Atlas-SNP	.											.	HSD17B8	20	.	0			c.G240T						.						15.0	17.0	16.0					6																	33172866		1508	2709	4217	SO:0001583	missense	7923	exon2			GGCCAGGGCCGCC	D82061	CCDS4769.1	6p21.3	2011-09-14	2002-02-19	2002-02-22	ENSG00000204228	ENSG00000204228	1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	3554	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 30C, member 1"""	601417	"""FabG (beta-ketoacyl-[acyl-carrier-protein] reductase, E coli) like (E. coli)"""	FABGL		8812499, 19027726	Standard	NM_014234		Approved	HKE6, D6S2245E, RING2, KE6, H2-KE6, SDR30C1	uc003odi.2	Q92506	OTTHUMG00000031117	ENST00000374662.3:c.240G>T	chr6.hg19:g.33172866G>T	ENSP00000363794:p.Arg80Ser	57.0	0.0		68.0	20.0	NM_014234	A6NLX7|Q5STP7|Q9UIQ1	Missense_Mutation	SNP	ENST00000374662.3	hg19	CCDS4769.1	.	.	.	.	.	.	.	.	.	.	G	0.274	-0.990706	0.02162	.	.	ENSG00000204228	ENST00000374662	T	0.20463	2.07	4.39	0.26	0.15588	NAD(P)-binding domain (1);	0.590685	0.16822	N	0.198124	T	0.01387	0.0045	N	0.00783	-1.19	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45352	-0.9267	10	0.34782	T	0.22	.	3.1484	0.06479	0.1816:0.1419:0.5401:0.1363	.	80	Q92506	DHB8_HUMAN	S	80	ENSP00000363794:R80S	ENSP00000363794:R80S	R	+	3	2	HSD17B8	33280844	0.149000	0.22717	0.017000	0.16124	0.256000	0.26092	0.168000	0.16622	-0.092000	0.12417	-2.830000	0.00107	AGG	.	.		0.662	HSD17B8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076196.1	NM_014234	
ARMC12	221481	hgsc.bcm.edu	37	6	35715163	35715163	+	Silent	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:35715163G>T	ENST00000373866.3	+	4	592	c.570G>T	c.(568-570)gtG>gtT	p.V190V	ARMC12_ENST00000373869.3_Silent_p.V190V|ARMC12_ENST00000288065.2_Silent_p.V217V			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	190						nucleus (GO:0005634)											TGCGACGGGTGATGCCTGCCT	0.592																																					p.V217V		Atlas-SNP	.											.	.	.	.	0			c.G651T						.						105.0	93.0	97.0					6																	35715163		2203	4300	6503	SO:0001819	synonymous_variant	221481	exon4			ACGGGTGATGCCT	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"""Armadillo repeat containing"""	21099	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 81"""	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.570G>T	chr6.hg19:g.35715163G>T		72.0	0.0		87.0	25.0	NM_145028	Q8NEB2|Q96LL8	Silent	SNP	ENST00000373866.3	hg19																																																																																				.	.		0.592	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028	
SENP6	26054	hgsc.bcm.edu	37	6	76344460	76344460	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:76344460G>T	ENST00000447266.2	+	5	869	c.391G>T	c.(391-393)Gta>Tta	p.V131L	SENP6_ENST00000370010.2_Missense_Mutation_p.V131L|SENP6_ENST00000327284.8_Missense_Mutation_p.V131L|SENP6_ENST00000370014.3_Missense_Mutation_p.V131L	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	131					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TTCTGGAACTGTAGTTCATGG	0.318																																					p.V131L		Atlas-SNP	.											.	SENP6	189	.	0			c.G391T						.						115.0	105.0	108.0					6																	76344460		1870	4112	5982	SO:0001583	missense	26054	exon5			GGAACTGTAGTTC		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.391G>T	chr6.hg19:g.76344460G>T	ENSP00000402527:p.Val131Leu	84.0	0.0		122.0	29.0	NM_001100409	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Missense_Mutation	SNP	ENST00000447266.2	hg19	CCDS47454.1	.	.	.	.	.	.	.	.	.	.	G	15.98	2.991363	0.54041	.	.	ENSG00000112701	ENST00000370010;ENST00000370014;ENST00000538088;ENST00000327284;ENST00000447266;ENST00000483859;ENST00000424947	T;T;T;T;T;T	0.50813	0.73;0.73;0.73;0.73;0.73;0.73	5.83	0.511	0.16989	.	0.284063	0.33753	N	0.004597	T	0.28532	0.0706	M	0.62723	1.935	0.80722	D	1	B;B;B	0.26744	0.158;0.098;0.158	B;B;B	0.30029	0.11;0.051;0.11	T	0.28073	-1.0055	10	0.72032	D	0.01	-7.9296	10.8136	0.46562	0.4266:0.0:0.5734:0.0	.	131;131;131	Q9GZR1-2;Q9GZR1;F8W6D9	.;SENP6_HUMAN;.	L	131;131;131;131;131;22;21	ENSP00000359027:V131L;ENSP00000359031:V131L;ENSP00000321820:V131L;ENSP00000402527:V131L;ENSP00000426480:V22L;ENSP00000391426:V21L	ENSP00000321820:V131L	V	+	1	0	SENP6	76401180	0.986000	0.35501	0.997000	0.53966	0.945000	0.59286	0.637000	0.24659	0.130000	0.18549	-0.237000	0.12165	GTA	.	.		0.318	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
MDN1	23195	hgsc.bcm.edu	37	6	90460121	90460121	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr6:90460121T>C	ENST00000369393.3	-	24	3473	c.3358A>G	c.(3358-3360)Att>Gtt	p.I1120V	MDN1_ENST00000428876.1_Missense_Mutation_p.I1120V			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1120					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)		TAACAACCAATGTACTCCTGA	0.443																																					p.I1120V		Atlas-SNP	.											.	MDN1	478	.	0			c.A3358G						.						233.0	199.0	211.0					6																	90460121		2203	4300	6503	SO:0001583	missense	23195	exon24			AACCAATGTACTC	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.3358A>G	chr6.hg19:g.90460121T>C	ENSP00000358400:p.Ile1120Val	121.0	0.0		122.0	39.0	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	14.49	2.549947	0.45383	.	.	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.42131	0.98;0.98;0.98	5.59	5.59	0.84812	ATPase, AAA+ type, core (1);ATPase, dynein-related, AAA domain (1);	0.104322	0.64402	D	0.000005	T	0.26195	0.0639	N	0.26130	0.795	0.52501	D	0.999955	P	0.37207	0.587	B	0.44224	0.444	T	0.08722	-1.0708	10	0.34782	T	0.22	.	15.7669	0.78135	0.0:0.0:0.0:1.0	.	1120	Q9NU22	MDN1_HUMAN	V	1120;1120;1047	ENSP00000358400:I1120V;ENSP00000413970:I1120V;ENSP00000409664:I1047V	ENSP00000358400:I1120V	I	-	1	0	MDN1	90516842	1.000000	0.71417	0.997000	0.53966	0.362000	0.29581	7.364000	0.79526	2.130000	0.65690	0.402000	0.26972	ATT	.	.		0.443	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
FSCN1	6624	hgsc.bcm.edu	37	7	5633032	5633032	+	Silent	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:5633032G>A	ENST00000382361.3	+	1	579	c.465G>A	c.(463-465)ctG>ctA	p.L155L	FSCN1_ENST00000340250.6_Silent_p.L134L	NM_003088.3	NP_003079.1	Q16658	FSCN1_HUMAN	fascin actin-bundling protein 1	155					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|cell migration (GO:0016477)|cell motility (GO:0048870)|cell proliferation (GO:0008283)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|invadopodium (GO:0071437)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|drug binding (GO:0008144)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|kidney(3)|large_intestine(1)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	9		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;1.21e-13)		ACGCGCACCTGAGCGCGCGGC	0.687																																					p.L155L		Atlas-SNP	.											.	FSCN1	29	.	0			c.G465A						.						31.0	26.0	28.0					7																	5633032		2193	4290	6483	SO:0001819	synonymous_variant	6624	exon1			GCACCTGAGCGCG	U03057	CCDS5342.1	7p22	2014-02-03	2014-02-03	2002-09-20	ENSG00000075618	ENSG00000075618		"""Fascins"""	11148	protein-coding gene	gene with protein product	"""Singed, drosophila, homolog-like"", ""actin bundling protein"""	602689	"""singed (Drosophila)-like (sea urchin fascin homolog like)"", ""fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus)"""	SNL		8068206, 10783262	Standard	NM_003088		Approved	p55, FLJ38511	uc003sou.3	Q16658	OTTHUMG00000090599	ENST00000382361.3:c.465G>A	chr7.hg19:g.5633032G>A		200.0	0.0		244.0	74.0	NM_003088	A6NI89|B2RE97|Q96IC5|Q96IH1|Q9BRF1	Silent	SNP	ENST00000382361.3	hg19	CCDS5342.1																																																																																			.	.		0.687	FSCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207153.3	NM_003088	
SEMA3C	10512	hgsc.bcm.edu	37	7	80374511	80374511	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:80374511T>C	ENST00000265361.3	-	18	2516	c.1955A>G	c.(1954-1956)cAg>cGg	p.Q652R	SEMA3C_ENST00000419255.2_Missense_Mutation_p.Q652R|SEMA3C_ENST00000544525.1_Missense_Mutation_p.Q670R	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	652	Ig-like C2-type.				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						GGCTATGGTCTGCTTGAAACT	0.473																																					p.Q652R		Atlas-SNP	.											.	SEMA3C	106	.	0			c.A1955G						.						83.0	79.0	80.0					7																	80374511		2203	4300	6503	SO:0001583	missense	10512	exon18			ATGGTCTGCTTGA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.1955A>G	chr7.hg19:g.80374511T>C	ENSP00000265361:p.Gln652Arg	126.0	0.0		116.0	24.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	T	13.40	2.226688	0.39300	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.67865	-0.29;-0.29;-0.29	5.56	5.56	0.83823	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.051625	0.85682	D	0.000000	T	0.50086	0.1595	N	0.11870	0.19	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.11329	0.003;0.006	T	0.43442	-0.9391	10	0.30854	T	0.27	.	15.7177	0.77681	0.0:0.0:0.0:1.0	.	670;652	F5H1Z7;Q99985	.;SEM3C_HUMAN	R	652;652;670	ENSP00000265361:Q652R;ENSP00000411193:Q652R;ENSP00000445649:Q670R	ENSP00000265361:Q652R	Q	-	2	0	SEMA3C	80212447	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.628000	0.67791	2.130000	0.65690	0.528000	0.53228	CAG	.	.		0.473	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
SEMA3A	10371	hgsc.bcm.edu	37	7	83610774	83610774	+	Silent	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:83610774T>A	ENST00000265362.4	-	14	1829	c.1515A>T	c.(1513-1515)tcA>tcT	p.S505S	SEMA3A_ENST00000436949.1_Silent_p.S505S	NM_006080.2	NP_006071.1	Q14563	SEM3A_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3A	505	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|dendrite morphogenesis (GO:0048813)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of epithelial cell migration (GO:0010633)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neural crest cell migration involved in sympathetic nervous system development (GO:1903045)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of male gonad development (GO:2000020)|positive regulation of neuron migration (GO:2001224)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of heart rate (GO:0002027)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|sensory system development (GO:0048880)|sympathetic ganglion development (GO:0061549)|sympathetic nervous system development (GO:0048485)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular region (GO:0005576)|membrane (GO:0016020)	chemorepellent activity (GO:0045499)|neuropilin binding (GO:0038191)|receptor activity (GO:0004872)			breast(3)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|liver(1)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53						CCCCAGCCGTTGAACCAATAT	0.433																																					p.S505S		Atlas-SNP	.											.	SEMA3A	121	.	0			c.A1515T						.						55.0	56.0	55.0					7																	83610774		2203	4300	6503	SO:0001819	synonymous_variant	10371	exon14			AGCCGTTGAACCA	L26081	CCDS5599.1	7p12.1	2013-01-11			ENSG00000075213	ENSG00000075213		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10723	protein-coding gene	gene with protein product	"""sema III"""	603961		SEMAD		8269517, 7748561	Standard	NM_006080		Approved	SEMA1, SemD, coll-1, Hsema-I	uc003uhz.3	Q14563	OTTHUMG00000023443	ENST00000265362.4:c.1515A>T	chr7.hg19:g.83610774T>A		135.0	0.0		161.0	33.0	NM_006080		Silent	SNP	ENST00000265362.4	hg19	CCDS5599.1																																																																																			.	.		0.433	SEMA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253355.2	NM_006080	
PODXL	5420	hgsc.bcm.edu	37	7	131241029	131241029	+	Silent	SNP	G	G	C	rs11277659|rs547816245|rs532078953|rs79759078|rs571821675	byFrequency	TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:131241029G>C	ENST00000378555.3	-	1	337	c.90C>G	c.(88-90)ccC>ccG	p.P30P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Silent_p.P30P|PODXL_ENST00000322985.9_Silent_p.P30P|PODXL_ENST00000541194.1_Silent_p.P30P			O00592	PODXL_HUMAN	podocalyxin-like	30					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					CATTCTGGGAGggcgacggcg	0.751																																					p.P30P		Atlas-SNP	.											.	PODXL	53	.	0			c.C90G						.						5.0	7.0	6.0					7																	131241029		1981	3946	5927	SO:0001819	synonymous_variant	5420	exon1			CTGGGAGGGCGAC		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.90C>G	chr7.hg19:g.131241029G>C		92.0	0.0		127.0	10.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Silent	SNP	ENST00000378555.3	hg19	CCDS34755.1																																																																																			.	.		0.751	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
PODXL	5420	hgsc.bcm.edu	37	7	131241055	131241055	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr7:131241055A>G	ENST00000378555.3	-	1	311	c.64T>C	c.(64-66)Tcg>Ccg	p.S22P	PODXL_ENST00000465001.1_Intron|PODXL_ENST00000537928.1_Missense_Mutation_p.S22P|PODXL_ENST00000322985.9_Missense_Mutation_p.S22P|PODXL_ENST00000541194.1_Missense_Mutation_p.S22P			O00592	PODXL_HUMAN	podocalyxin-like	22					cell adhesion (GO:0007155)|cell migration (GO:0016477)|epithelial tube formation (GO:0072175)|glomerular visceral epithelial cell development (GO:0072015)|leukocyte migration (GO:0050900)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-cell adhesion (GO:0022408)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|regulation of microvillus assembly (GO:0032534)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|slit diaphragm (GO:0036057)				NS(1)|breast(3)|endometrium(3)|kidney(3)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24	Melanoma(18;0.162)					gacggcgacgacggcagcagc	0.741																																					p.S22P		Atlas-SNP	.											.	PODXL	53	.	0			c.T64C						.						5.0	8.0	7.0					7																	131241055		1914	3836	5750	SO:0001583	missense	5420	exon1			GCGACGACGGCAG		CCDS34755.1, CCDS47714.1	7q32-q33	2008-07-18			ENSG00000128567	ENSG00000128567			9171	protein-coding gene	gene with protein product		602632					Standard	NM_001018111		Approved	PCLP, Gp200, PC	uc003vqx.4	O00592	OTTHUMG00000154918	ENST00000378555.3:c.64T>C	chr7.hg19:g.131241055A>G	ENSP00000367817:p.Ser22Pro	101.0	0.0		130.0	9.0	NM_001018111	A6NHX8|Q52LZ7|Q53ER6	Missense_Mutation	SNP	ENST00000378555.3	hg19	CCDS34755.1	.	.	.	.	.	.	.	.	.	.	A	10.93	1.488975	0.26686	.	.	ENSG00000128567	ENST00000541194;ENST00000537928;ENST00000378555;ENST00000322985	T;T;T;T	0.12774	2.82;2.65;2.82;2.85	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.08670	0.0215	N	0.14661	0.345	0.09310	N	0.999994	.	.	.	.	.	.	T	0.24728	-1.0152	6	0.29301	T	0.29	.	.	.	.	.	22;22	O00592-2;O00592	.;PODXL_HUMAN	P	22	ENSP00000440518:S22P;ENSP00000442655:S22P;ENSP00000367817:S22P;ENSP00000319782:S22P	ENSP00000319782:S22P	S	-	1	0	PODXL	130891595	0.001000	0.12720	0.027000	0.17364	0.027000	0.11550	0.743000	0.26231	0.056000	0.16144	0.055000	0.15244	TCG	.	.		0.741	PODXL-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000337627.2	NM_001018111	
BNIP3L	665	hgsc.bcm.edu	37	8	26265768	26265768	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr8:26265768C>T	ENST00000380629.2	+	5	720	c.487C>T	c.(487-489)Cgt>Tgt	p.R163C	BNIP3L_ENST00000518611.1_Missense_Mutation_p.R123C|BNIP3L_ENST00000521254.1_3'UTR|BNIP3L_ENST00000520409.1_Missense_Mutation_p.R123C|BNIP3L_ENST00000523515.1_Missense_Mutation_p.R123C	NM_004331.2	NP_004322.1	O60238	BNI3L_HUMAN	BCL2/adenovirus E1B 19kDa interacting protein 3-like	163					defense response to virus (GO:0051607)|mitochondrial outer membrane permeabilization (GO:0097345)|mitochondrial protein catabolic process (GO:0035694)|negative regulation of apoptotic process (GO:0043066)|positive regulation of apoptotic process (GO:0043065)|viral process (GO:0016032)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)	identical protein binding (GO:0042802)|lamin binding (GO:0005521)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			large_intestine(3)|lung(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0019)|Epithelial(17;1.59e-12)|all cancers(2;3.75e-11)|OV - Ovarian serous cystadenocarcinoma(2;2.57e-08)|Colorectal(74;0.135)		ACACCCTAAACGTTCTGTGTC	0.448																																					p.R163C		Atlas-SNP	.											.	BNIP3L	7	.	0			c.C487T						.						86.0	83.0	84.0					8																	26265768		2203	4300	6503	SO:0001583	missense	665	exon5			CCTAAACGTTCTG	AB004788	CCDS6050.1	8p21	2014-05-13	2002-08-29		ENSG00000104765	ENSG00000104765			1085	protein-coding gene	gene with protein product		605368	"""BCL2/adenovirus E1B 19kD-interacting protein 3-like"""			9523198, 9973195	Standard	NM_004331		Approved	Nix, BNIP3a	uc003xex.1	O60238	OTTHUMG00000099433	ENST00000380629.2:c.487C>T	chr8.hg19:g.26265768C>T	ENSP00000370003:p.Arg163Cys	139.0	0.0		127.0	38.0	NM_004331	B0AZS9|Q5JW63|Q8NF87	Missense_Mutation	SNP	ENST00000380629.2	hg19	CCDS6050.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.494572	0.85069	.	.	ENSG00000104765	ENST00000380629;ENST00000221209;ENST00000523949;ENST00000523515;ENST00000520409;ENST00000518611	.	.	.	6.16	5.28	0.74379	.	0.000000	0.85682	D	0.000000	T	0.79015	0.4375	M	0.84326	2.69	0.80722	D	1	D;D	0.76494	0.999;0.999	P;D	0.63597	0.877;0.916	T	0.82752	-0.0302	9	0.87932	D	0	.	14.5092	0.67772	0.2672:0.7328:0.0:0.0	.	123;163	B0AZS9;O60238	.;BNI3L_HUMAN	C	163;163;141;123;123;123	.	ENSP00000221209:R163C	R	+	1	0	BNIP3L	26321685	1.000000	0.71417	0.762000	0.31397	0.986000	0.74619	5.618000	0.67722	1.598000	0.50083	0.650000	0.86243	CGT	.	.		0.448	BNIP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216895.1	NM_004331	
RIMS2	9699	hgsc.bcm.edu	37	8	104778484	104778484	+	Silent	SNP	A	A	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr8:104778484A>G	ENST00000406091.3	+	3	417	c.417A>G	c.(415-417)aaA>aaG	p.K139K		NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	170	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cAMP-mediated signaling (GO:0019933)|insulin secretion (GO:0030073)|intracellular protein transport (GO:0006886)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	metal ion binding (GO:0046872)			NS(1)|breast(4)|central_nervous_system(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(22)|liver(1)|lung(68)|ovary(6)|pancreas(2)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(10)|urinary_tract(1)	144			OV - Ovarian serous cystadenocarcinoma(57;7.7e-07)|STAD - Stomach adenocarcinoma(118;0.229)			TGTGCCGAAAACAACAAGAAA	0.358										HNSCC(12;0.0054)																											p.K139K		Atlas-SNP	.											.	RIMS2	1357	.	0			c.A417G						.						78.0	73.0	74.0					8																	104778484		1860	4096	5956	SO:0001819	synonymous_variant	9699	exon3			CCGAAAACAACAA	AB018294	CCDS43761.1, CCDS64948.1, CCDS64949.1	8q22.3	2008-08-08	2002-06-12	2002-06-14					17283	protein-coding gene	gene with protein product		606630	"""RAB3 interacting protein 3"""	RAB3IP3		9872452, 12578829	Standard	NM_014677		Approved	KIAA0751, RIM2, OBOE	uc003ylp.3	Q9UQ26		ENST00000406091.3:c.417A>G	chr8.hg19:g.104778484A>G		132.0	0.0		199.0	30.0	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	hg19	CCDS55269.1																																																																																			.	.		0.358	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117	
HAUS6	54801	hgsc.bcm.edu	37	9	19102558	19102558	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:19102558G>A	ENST00000380502.3	-	1	559	c.92C>T	c.(91-93)gCc>gTc	p.A31V		NM_001270890.1|NM_017645.4	NP_001257819.1|NP_060115.3	Q7Z4H7	HAUS6_HUMAN	HAUS augmin-like complex, subunit 6	31					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						CTTTCCGCAGGCAATGGTTGC	0.682																																					p.A31V		Atlas-SNP	.											.	HAUS6	66	.	0			c.C92T						.						34.0	37.0	36.0					9																	19102558		2203	4299	6502	SO:0001583	missense	54801	exon1			CCGCAGGCAATGG	AL832495	CCDS6489.1	9p22.1	2011-10-24	2009-04-20	2009-04-20	ENSG00000147874	ENSG00000147874		"""HAUS augmin-like complex subunits"""	25948	protein-coding gene	gene with protein product		613433	"""family with sequence similarity 29, member A"""	FAM29A		10997877, 19427217	Standard	NM_001270890		Approved	FLJ20060, KIAA1574, dgt6	uc003znk.4	Q7Z4H7	OTTHUMG00000019622	ENST00000380502.3:c.92C>T	chr9.hg19:g.19102558G>A	ENSP00000369871:p.Ala31Val	204.0	0.0		218.0	59.0	NM_017645	B3KPK4|B4DX82|Q05CG1|Q14CB6|Q14CD9|Q2TA91|Q6IQ10|Q6NZX5|Q8IZQ4|Q96FN0|Q9H950|Q9H998|Q9HCJ8|Q9NXT8	Missense_Mutation	SNP	ENST00000380502.3	hg19	CCDS6489.1	.	.	.	.	.	.	.	.	.	.	G	9.349	1.064996	0.20067	.	.	ENSG00000147874	ENST00000380502	T	0.22945	1.93	5.52	2.13	0.27403	.	0.626539	0.17585	N	0.168973	T	0.20007	0.0481	L	0.57536	1.79	0.18873	N	0.999984	B	0.25955	0.138	B	0.28465	0.09	T	0.18935	-1.0321	10	0.33141	T	0.24	1.4026	1.1407	0.01765	0.1911:0.151:0.4312:0.2268	.	31	Q7Z4H7	HAUS6_HUMAN	V	31	ENSP00000369871:A31V	ENSP00000369871:A31V	A	-	2	0	HAUS6	19092558	0.140000	0.22579	0.010000	0.14722	0.138000	0.21146	1.141000	0.31528	0.770000	0.33336	-0.175000	0.13238	GCC	.	.		0.682	HAUS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051825.1	NM_017645	
CDKN2A	1029	hgsc.bcm.edu	37	9	21971101	21971101	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:21971101G>T	ENST00000304494.5	-	2	527	c.257C>A	c.(256-258)gCc>gAc	p.A86D	CDKN2A_ENST00000579755.1_Nonsense_Mutation_p.C100*|RP11-145E5.5_ENST00000404796.2_Intron|CDKN2A_ENST00000361570.3_Nonsense_Mutation_p.C141*|CDKN2A_ENST00000498124.1_Missense_Mutation_p.A86D|CDKN2A_ENST00000530628.2_Nonsense_Mutation_p.C100*|CDKN2A_ENST00000578845.2_Missense_Mutation_p.A35D|CDKN2A_ENST00000497750.1_Missense_Mutation_p.A35D|CDKN2A_ENST00000479692.2_Missense_Mutation_p.A35D|CDKN2A_ENST00000498628.2_Missense_Mutation_p.A35D|CDKN2A_ENST00000494262.1_Missense_Mutation_p.A35D|CDKN2A_ENST00000579122.1_Missense_Mutation_p.A86D|CDKN2A_ENST00000446177.1_Missense_Mutation_p.A86D	NM_000077.4	NP_000068.1	P42771	CD2A1_HUMAN	cyclin-dependent kinase inhibitor 2A	86					cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular senescence (GO:2000774)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|Ras protein signal transduction (GO:0007265)|replicative senescence (GO:0090399)|senescence-associated heterochromatin focus assembly (GO:0035986)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|senescence-associated heterochromatin focus (GO:0035985)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)	p.0?(1315)|p.?(44)|p.H83fs*2(2)|p.D84_F90del(1)|p.0(1)|p.V82_G89>G(1)|p.E61_L94del(1)|p.R137fs*48(1)|p.A68fs*3(1)|p.A86fs*34(1)|p.V82_E88del(1)|p.A86V(1)		NS(28)|adrenal_gland(6)|autonomic_ganglia(11)|biliary_tract(74)|bone(84)|breast(46)|central_nervous_system(522)|cervix(23)|endometrium(14)|eye(4)|genital_tract(15)|haematopoietic_and_lymphoid_tissue(698)|kidney(39)|large_intestine(11)|liver(92)|lung(365)|meninges(18)|oesophagus(239)|ovary(98)|pancreas(263)|pleura(94)|prostate(13)|salivary_gland(10)|skin(541)|small_intestine(1)|soft_tissue(93)|stomach(48)|thymus(4)|thyroid(24)|upper_aerodigestive_tract(436)|urinary_tract(283)|vulva(2)	4199		all_cancers(5;0)|Acute lymphoblastic leukemia(3;0)|all_hematologic(3;0)|all_epithelial(2;2.37e-290)|Lung NSC(2;1.26e-139)|all_lung(2;4.48e-131)|Glioma(2;3.26e-60)|all_neural(2;2.1e-52)|Renal(3;1.07e-46)|Esophageal squamous(3;3.83e-46)|Melanoma(2;2.74e-34)|Breast(3;1.14e-11)|Ovarian(3;0.000128)|Hepatocellular(5;0.00162)|Colorectal(97;0.172)		all cancers(2;0)|GBM - Glioblastoma multiforme(3;0)|Lung(2;4.07e-74)|Epithelial(2;1.08e-61)|LUSC - Lung squamous cell carcinoma(2;3.82e-48)|LUAD - Lung adenocarcinoma(2;4.56e-26)|OV - Ovarian serous cystadenocarcinoma(39;7.64e-10)|BRCA - Breast invasive adenocarcinoma(2;5.01e-09)|STAD - Stomach adenocarcinoma(4;4.63e-07)|Kidney(2;5.79e-07)|KIRC - Kidney renal clear cell carcinoma(2;7.27e-07)|COAD - Colon adenocarcinoma(8;5.15e-05)		GCCCTCCCGGGCAGCGTCGTG	0.746		17								HNSCC(2;<9.43e_08)|TSP Lung(5;3.83e-07)																											p.C100X		Atlas-SNP	.											CDKN2A,NS,carcinoma,0,1	CDKN2A	4810	.	1370	Whole gene deletion(1316)|Unknown(44)|Deletion - Frameshift(4)|Deletion - In frame(3)|Insertion - Frameshift(1)|Complex - deletion inframe(1)|Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(283)|skin(175)|central_nervous_system(167)|lung(148)|urinary_tract(91)|bone(74)|soft_tissue(57)|oesophagus(52)|pleura(51)|upper_aerodigestive_tract(50)|ovary(36)|kidney(32)|breast(32)|pancreas(31)|thyroid(13)|NS(12)|biliary_tract(12)|stomach(12)|autonomic_ganglia(9)|meninges(7)|large_intestine(6)|liver(6)|salivary_gland(4)|thymus(4)|vulva(2)|endometrium(2)|prostate(2)	c.C300A						.						12.0	15.0	14.0					9																	21971101		2171	4256	6427	SO:0001583	missense	1029	exon2			TCCCGGGCAGCGT	L27211	CCDS6510.1, CCDS6511.1, CCDS6511.2, CCDS56565.1	9p21	2014-09-17	2012-03-08		ENSG00000147889	ENSG00000147889			1787	protein-coding gene	gene with protein product		600160	"""cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4)"""	CDKN2, MLM		8152487, 7606716	Standard	NM_058195		Approved	CDK4I, p16, INK4a, MTS1, CMM2, ARF, p19, p14, INK4, p16INK4a, p19Arf	uc003zpk.3	P42771	OTTHUMG00000019686	ENST00000304494.5:c.257C>A	chr9.hg19:g.21971101G>T	ENSP00000307101:p.Ala86Asp	139.0	0.0		133.0	43.0	NM_058195	A5X2G7|D3DRK1|O95440|Q15191|Q5VVJ5|Q96B52|Q9NP05	Nonsense_Mutation	SNP	ENST00000304494.5	hg19	CCDS6510.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	40|40	8.491908|8.491908	0.98834|0.98834	.|.	.|.	ENSG00000147889|ENSG00000147889	ENST00000304494;ENST00000446177|ENST00000361570;ENST00000530628	T;T|.	0.72615|.	-0.67;-0.67|.	5.93|5.93	5.93|5.93	0.95920|0.95920	Ankyrin repeat-containing domain (4);|.	.|1.401910	.|0.04941	.|N	.|0.458690	T|.	0.74824|.	0.3767|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	D|.	0.76494|.	0.999|.	P|.	0.60173|.	0.87|.	T|.	0.68534|.	-0.5383|.	7|.	0.87932|0.72032	D|D	0|0.01	-12.7152|-12.7152	19.1221|19.1221	0.93367|0.93367	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	86|.	P42771|.	CD2A1_HUMAN|.	D|X	86|141;100	ENSP00000307101:A86D;ENSP00000394932:A86D|.	ENSP00000307101:A86D|ENSP00000355153:C141X	A|C	-|-	2|3	0|2	CDKN2A|CDKN2A	21961101|21961101	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.959000|0.959000	0.62525|0.62525	8.665000|8.665000	0.91144|0.91144	2.808000|2.808000	0.96608|0.96608	0.655000|0.655000	0.94253|0.94253	GCC|TGC	.	.		0.746	CDKN2A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000051915.1	NM_000077	
FGD3	89846	hgsc.bcm.edu	37	9	95780428	95780428	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:95780428T>A	ENST00000375482.3	+	11	1782	c.1286T>A	c.(1285-1287)aTc>aAc	p.I429N	FGD3_ENST00000538555.1_Missense_Mutation_p.I32N|FGD3_ENST00000337352.6_Missense_Mutation_p.I429N|FGD3_ENST00000416701.2_Missense_Mutation_p.I429N	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	429	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						GTGCAGGATATCGTCAAGCCA	0.463																																					p.I429N		Atlas-SNP	.											.	FGD3	116	.	0			c.T1286A						.						124.0	124.0	124.0					9																	95780428		1966	4166	6132	SO:0001583	missense	89846	exon11			AGGATATCGTCAA	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.1286T>A	chr9.hg19:g.95780428T>A	ENSP00000364631:p.Ile429Asn	80.0	0.0		65.0	19.0	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Missense_Mutation	SNP	ENST00000375482.3	hg19	CCDS43849.1	.	.	.	.	.	.	.	.	.	.	T	1.998	-0.430075	0.04701	.	.	ENSG00000127084	ENST00000375482;ENST00000416701;ENST00000337352;ENST00000538555	D;D;D;D	0.88046	-2.33;-2.33;-2.33;-2.33	4.7	-2.41	0.06562	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.679389	0.12147	N	0.495305	T	0.72415	0.3457	N	0.17474	0.49	0.18873	N	0.999984	B;B;B	0.11235	0.003;0.004;0.001	B;B;B	0.13407	0.005;0.009;0.009	T	0.58295	-0.7661	10	0.41790	T	0.15	.	5.645	0.17584	0.0:0.3628:0.2595:0.3777	.	429;429;429	Q5JSP0-2;F8W7P2;Q5JSP0	.;.;FGD3_HUMAN	N	429;429;429;32	ENSP00000364631:I429N;ENSP00000413833:I429N;ENSP00000336914:I429N;ENSP00000442560:I32N	ENSP00000336914:I429N	I	+	2	0	FGD3	94820249	0.077000	0.21312	0.006000	0.13384	0.029000	0.11900	-0.428000	0.06991	-0.265000	0.09352	-0.411000	0.06167	ATC	.	.		0.463	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
FKBP15	23307	hgsc.bcm.edu	37	9	115959216	115959216	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr9:115959216C>A	ENST00000238256.3	-	9	977	c.860G>T	c.(859-861)aGg>aTg	p.R287M		NM_015258.1	NP_056073.1	Q5T1M5	FKB15_HUMAN	FK506 binding protein 15, 133kDa	287	PPIase FKBP-type. {ECO:0000255|PROSITE- ProRule:PRU00277}.				endocytosis (GO:0006897)|negative regulation of phosphatase activity (GO:0010923)|protein folding (GO:0006457)	actin filament (GO:0005884)|axon (GO:0030424)|endosome (GO:0005768)|growth cone (GO:0030426)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(9)|ovary(3)|urinary_tract(1)	26						ACTCACCCGCCTAACCTCCAC	0.463																																					p.R287M		Atlas-SNP	.											.	FKBP15	128	.	0			c.G860T						.						82.0	82.0	82.0					9																	115959216		1967	4137	6104	SO:0001583	missense	23307	exon9			ACCCGCCTAACCT	AB014574	CCDS48007.1	9q33.1	2014-05-09	2006-10-31	2006-10-31	ENSG00000119321	ENSG00000119321		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23397	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 76"", ""WASP and FKBP-like protein"""		"""KIAA0674"""	KIAA0674		16756961, 20376207	Standard	NM_015258		Approved	PPP1R76, FKBP133, WAFL	uc004bgs.2	Q5T1M5	OTTHUMG00000020518	ENST00000238256.3:c.860G>T	chr9.hg19:g.115959216C>A	ENSP00000238256:p.Arg287Met	103.0	0.0		120.0	19.0	NM_015258	Q05DK8|Q5T1M2|Q6DD85|Q9Y4D0	Missense_Mutation	SNP	ENST00000238256.3	hg19	CCDS48007.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.069615	0.55539	.	.	ENSG00000119321	ENST00000446284;ENST00000238256;ENST00000414250	T;T;T	0.42131	0.98;0.98;0.98	5.33	-0.433	0.12287	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	.	.	.	.	T	0.38799	0.1054	L	0.27053	0.805	0.31269	N	0.692028	P;P;D	0.53462	0.951;0.895;0.96	P;P;P	0.56514	0.698;0.532;0.8	T	0.46205	-0.9208	9	0.72032	D	0.01	-3.7993	5.5401	0.17033	0.0:0.4308:0.1415:0.4278	.	287;287;287	Q5T1M5-2;Q5T1M5-3;Q5T1M5	.;.;FKB15_HUMAN	M	312;287;312	ENSP00000416158:R312M;ENSP00000238256:R287M;ENSP00000415733:R312M	ENSP00000238256:R287M	R	-	2	0	FKBP15	114999037	0.729000	0.28090	0.987000	0.45799	0.563000	0.35712	0.675000	0.25232	0.003000	0.14656	-0.136000	0.14681	AGG	.	.		0.463	FKBP15-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015258	
CCDC7	79741	hgsc.bcm.edu	37	10	32833205	32833205	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr10:32833205A>G	ENST00000362006.5	+	14	1653	c.1110A>G	c.(1108-1110)atA>atG	p.I370M	C10orf68_ENST00000572165.1_3'UTR|CCDC7_ENST00000277657.6_Missense_Mutation_p.I370M	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	370										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				AGTTTAAAATAAAAGAAGATT	0.303																																					p.I370M		Atlas-SNP	.											CCDC7,parotid,carcinoma,0,1	CCDC7	47	.	0			c.A1110G						.						80.0	83.0	82.0					10																	32833205		2203	4286	6489	SO:0001583	missense	221016	exon14			TAAAATAAAAGAA	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 68"""	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.1110A>G	chr10.hg19:g.32833205A>G	ENSP00000355078:p.Ile370Met	396.0	0.0		417.0	127.0	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	hg19	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	A	9.396	1.076804	0.20227	.	.	ENSG00000216937	ENST00000277657;ENST00000362006;ENST00000435402	T;T;T	0.55930	1.34;1.34;0.49	3.19	-0.791	0.10929	.	.	.	.	.	T	0.29588	0.0738	N	0.19112	0.55	0.09310	N	0.999997	B	0.14012	0.009	B	0.14023	0.01	T	0.20207	-1.0282	9	0.46703	T	0.11	-38.2876	0.5368	0.00638	0.4384:0.2199:0.1286:0.2132	.	370	Q96M83	CCDC7_HUMAN	M	370;370;39	ENSP00000277657:I370M;ENSP00000355078:I370M;ENSP00000401923:I39M	ENSP00000277657:I370M	I	+	3	3	CCDC7	32873211	0.000000	0.05858	0.064000	0.19789	0.308000	0.27856	-0.035000	0.12205	-0.154000	0.11118	0.528000	0.53228	ATA	.	.		0.303	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
DENND5A	23258	hgsc.bcm.edu	37	11	9225351	9225351	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:9225351T>C	ENST00000328194.3	-	4	1125	c.805A>G	c.(805-807)Ata>Gta	p.I269V	DENND5A_ENST00000530044.1_Missense_Mutation_p.I269V	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	269	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				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						TGGCAGATTATTGGCCCATAG	0.507																																					p.I269V		Atlas-SNP	.											.	DENND5A	84	.	0			c.A805G						.						66.0	71.0	69.0					11																	9225351		2201	4296	6497	SO:0001583	missense	23258	exon4			AGATTATTGGCCC	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.805A>G	chr11.hg19:g.9225351T>C	ENSP00000328524:p.Ile269Val	163.0	0.0		198.0	43.0	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Missense_Mutation	SNP	ENST00000328194.3	hg19	CCDS31423.1	.	.	.	.	.	.	.	.	.	.	T	7.933	0.741139	0.15642	.	.	ENSG00000184014	ENST00000328194;ENST00000530044	T;T	0.12039	2.72;2.72	5.31	1.64	0.23874	DENN (3);	0.259259	0.44688	N	0.000440	T	0.10551	0.0258	L	0.41906	1.305	0.80722	D	1	B;B	0.14805	0.011;0.003	B;B	0.22880	0.042;0.024	T	0.20472	-1.0274	10	0.23302	T	0.38	.	8.4273	0.32735	0.0:0.2402:0.0:0.7598	.	269;269	E9PS91;Q6IQ26	.;DEN5A_HUMAN	V	269	ENSP00000328524:I269V;ENSP00000435866:I269V	ENSP00000328524:I269V	I	-	1	0	DENND5A	9181927	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.629000	0.37071	0.027000	0.15297	0.528000	0.53228	ATA	.	.		0.507	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
ABCC8	6833	hgsc.bcm.edu	37	11	17496563	17496563	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:17496563G>A	ENST00000389817.3	-	2	228	c.160C>T	c.(160-162)Cag>Tag	p.Q54*	ABCC8_ENST00000302539.4_Nonsense_Mutation_p.Q54*			Q09428	ABCC8_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 8	54					carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|ion channel binding (GO:0044325)|potassium ion transmembrane transporter activity (GO:0015079)|sulfonylurea receptor activity (GO:0008281)			NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(38)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	67				READ - Rectum adenocarcinoma(2;0.0325)|Colorectal(2;0.1)	Adenosine triphosphate(DB00171)|Chlorpropamide(DB00672)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Gliquidone(DB01251)|Glyburide(DB01016)|Glycodiazine(DB01382)|Mitiglinide(DB01252)|Nateglinide(DB00731)|Repaglinide(DB00912)|Tolbutamide(DB01124)	TTGGAGCTCTGACTTCCCCAT	0.582																																					p.Q54X		Atlas-SNP	.											.	ABCC8	170	.	0			c.C160T	GRCh37	CM086731	ABCC8	M		.						176.0	110.0	132.0					11																	17496563		2200	4293	6493	SO:0001587	stop_gained	6833	exon2			AGCTCTGACTTCC	L78207	CCDS31437.1, CCDS73264.1	11p15.1	2014-09-17			ENSG00000006071	ENSG00000006071		"""ATP binding cassette transporters / subfamily C"""	59	protein-coding gene	gene with protein product	"""sulfonylurea receptor (hyperinsulinemia)"""	600509		SUR, HRINS		7920639, 7716548	Standard	NM_000352		Approved	HI, PHHI, SUR1, MRP8, ABC36, HHF1, TNDM2	uc001mnc.3	Q09428	OTTHUMG00000166316	ENST00000389817.3:c.160C>T	chr11.hg19:g.17496563G>A	ENSP00000374467:p.Gln54*	92.0	0.0		114.0	22.0	NM_000352	A6NMX8|E3UYX6|O75948|Q16583	Nonsense_Mutation	SNP	ENST00000389817.3	hg19	CCDS31437.1	.	.	.	.	.	.	.	.	.	.	G	38	6.795783	0.97845	.	.	ENSG00000006071	ENST00000389817;ENST00000302539;ENST00000379493	.	.	.	5.19	5.19	0.71726	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19590	T	0.45	.	18.7138	0.91668	0.0:0.0:1.0:0.0	.	.	.	.	X	54;54;68	.	ENSP00000303960:Q54X	Q	-	1	0	ABCC8	17453139	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.854000	0.99522	2.414000	0.81942	0.585000	0.79938	CAG	.	.		0.582	ABCC8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389093.1	NM_000352	
CHST1	8534	hgsc.bcm.edu	37	11	45672282	45672282	+	Silent	SNP	G	G	A	rs200379237		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:45672282G>A	ENST00000308064.2	-	4	862	c.192C>T	c.(190-192)ctC>ctT	p.L64L	CHST1_ENST00000533673.1_5'Flank|RP11-495O11.1_ENST00000525563.1_RNA	NM_003654.5	NP_003645.1	O43916	CHST1_HUMAN	carbohydrate (keratan sulfate Gal-6) sulfotransferase 1	64					carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)|glycosaminoglycan metabolic process (GO:0030203)|inflammatory response (GO:0006954)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|polysaccharide metabolic process (GO:0005976)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	keratan sulfotransferase activity (GO:0045130)|sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(10)|lung(17)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	42				GBM - Glioblastoma multiforme(35;3e-06)|BRCA - Breast invasive adenocarcinoma(625;0.0781)		TGGCCAGGATGAGGATGTGGG	0.647																																					p.L64L		Atlas-SNP	.											.	CHST1	81	.	0			c.C192T						.						83.0	80.0	81.0					11																	45672282		2203	4299	6502	SO:0001819	synonymous_variant	8534	exon4			CAGGATGAGGATG	U65637	CCDS7913.1	11p11.2	2010-04-29			ENSG00000175264	ENSG00000175264		"""Sulfotransferases, membrane-bound"""	1969	protein-coding gene	gene with protein product		603797				9405439, 9639683	Standard	NM_003654		Approved	C6ST, KSGal6ST	uc001mys.2	O43916		ENST00000308064.2:c.192C>T	chr11.hg19:g.45672282G>A		113.0	0.0		132.0	6.0	NM_003654	D3DQP2	Silent	SNP	ENST00000308064.2	hg19	CCDS7913.1																																																																																			.	G|0.999;A|0.001		0.647	CHST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390127.1	NM_003654	
OR5L2	26338	hgsc.bcm.edu	37	11	55594822	55594822	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:55594822T>A	ENST00000378397.1	+	1	128	c.128T>A	c.(127-129)cTg>cAg	p.L43Q		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	43						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				TTAGCCAATCTGGGCATGACT	0.493										HNSCC(27;0.073)																											p.L43Q		Atlas-SNP	.											.	OR5L2	135	.	0			c.T128A						.						324.0	283.0	297.0					11																	55594822		2200	4296	6496	SO:0001583	missense	26338	exon1			CCAATCTGGGCAT	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.128T>A	chr11.hg19:g.55594822T>A	ENSP00000367650:p.Leu43Gln	102.0	0.0		94.0	23.0	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	hg19	CCDS31511.1	.	.	.	.	.	.	.	.	.	.	.	12.63	1.996585	0.35226	.	.	ENSG00000205030	ENST00000378397	T	0.00433	7.43	5.31	5.31	0.75309	GPCR, rhodopsin-like superfamily (1);	0.000000	0.38663	N	0.001608	T	0.02156	0.0067	H	0.97186	3.955	0.09310	N	1	D	0.89917	1.0	D	0.70487	0.969	T	0.15752	-1.0426	10	0.87932	D	0	-12.0656	14.5472	0.68041	0.0:0.0:0.0:1.0	.	43	Q8NGL0	OR5L2_HUMAN	Q	43	ENSP00000367650:L43Q	ENSP00000367650:L43Q	L	+	2	0	OR5L2	55351398	0.001000	0.12720	0.965000	0.40720	0.160000	0.22226	1.202000	0.32271	2.173000	0.68751	0.509000	0.49947	CTG	.	.		0.493	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
DCUN1D5	84259	hgsc.bcm.edu	37	11	102935046	102935046	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:102935046T>A	ENST00000260247.5	-	7	958	c.616A>T	c.(616-618)Aca>Tca	p.T206S	DCUN1D5_ENST00000531543.1_Missense_Mutation_p.T121S	NM_032299.3	NP_115675.1	Q9BTE7	DCNL5_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 5	206	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.									NS(1)|central_nervous_system(1)|endometrium(2)	4		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.00032)|Epithelial(105;0.0689)|all cancers(92;0.186)		GCATGGACTGTTCTGCTGAAT	0.269																																					p.T206S		Atlas-SNP	.											.	DCUN1D5	11	.	0			c.A616T						.						135.0	130.0	131.0					11																	102935046		2202	4294	6496	SO:0001583	missense	84259	exon7			GGACTGTTCTGCT		CCDS8325.1	11q22.3	2013-06-10	2013-06-10		ENSG00000137692	ENSG00000137692			28409	protein-coding gene	gene with protein product			"""DCN1, defective in cullin neddylation 1, domain containing 5 (S. cerevisiae)"""			15988528	Standard	NM_032299		Approved	MGC2714, FLJ32431	uc001phm.3	Q9BTE7	OTTHUMG00000165822	ENST00000260247.5:c.616A>T	chr11.hg19:g.102935046T>A	ENSP00000260247:p.Thr206Ser	55.0	0.0		74.0	20.0	NM_032299	Q3ZTT2	Missense_Mutation	SNP	ENST00000260247.5	hg19	CCDS8325.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846962	0.71603	.	.	ENSG00000137692	ENST00000260247;ENST00000531543	T	0.21734	1.99	5.91	5.91	0.95273	Domain of unknown function DUF298 (2);	0.000000	0.85682	D	0.000000	T	0.21509	0.0518	L	0.38953	1.18	0.80722	D	1	B	0.26672	0.156	B	0.33799	0.17	T	0.05566	-1.0877	10	0.20519	T	0.43	-12.7153	16.35	0.83199	0.0:0.0:0.0:1.0	.	206	Q9BTE7	DCNL5_HUMAN	S	206;121	ENSP00000260247:T206S	ENSP00000260247:T206S	T	-	1	0	DCUN1D5	102440256	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	8.040000	0.89188	2.270000	0.75569	0.528000	0.53228	ACA	.	.		0.269	DCUN1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386382.2	NM_032299	
OR8D4	338662	hgsc.bcm.edu	37	11	123777473	123777473	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr11:123777473G>A	ENST00000321355.2	+	1	365	c.335G>A	c.(334-336)tGc>tAc	p.C112Y		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		ATTTCTGAATGCTACATGCTG	0.478																																					p.C112Y		Atlas-SNP	.											.	OR8D4	62	.	0			c.G335A						.						200.0	195.0	197.0					11																	123777473		2202	4299	6501	SO:0001583	missense	338662	exon1			CTGAATGCTACAT	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.335G>A	chr11.hg19:g.123777473G>A	ENSP00000325381:p.Cys112Tyr	86.0	0.0		79.0	19.0	NM_001005197	Q6IFE9	Missense_Mutation	SNP	ENST00000321355.2	hg19	CCDS31698.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747228	0.49257	.	.	ENSG00000181518	ENST00000321355	T	0.00463	7.25	5.68	4.77	0.60923	GPCR, rhodopsin-like superfamily (1);	0.129861	0.35677	N	0.003052	T	0.00754	0.0025	M	0.80847	2.515	0.32616	N	0.523972	P	0.45986	0.87	P	0.46320	0.512	T	0.41680	-0.9495	10	0.52906	T	0.07	.	9.758	0.40515	0.0774:0.1416:0.781:0.0	.	112	Q8NGM9	OR8D4_HUMAN	Y	112	ENSP00000325381:C112Y	ENSP00000325381:C112Y	C	+	2	0	OR8D4	123282683	0.055000	0.20627	0.989000	0.46669	0.819000	0.46315	0.496000	0.22499	1.405000	0.46838	0.561000	0.74099	TGC	.	.		0.478	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
AMHR2	269	hgsc.bcm.edu	37	12	53825147	53825147	+	Missense_Mutation	SNP	G	G	T	rs116281343		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr12:53825147G>T	ENST00000257863.4	+	11	1692	c.1612G>T	c.(1612-1614)Gcc>Tcc	p.A538S	AMHR2_ENST00000379791.3_Missense_Mutation_p.A443S|AMHR2_ENST00000550311.1_3'UTR	NM_001164690.1|NM_020547.2	NP_001158162.1|NP_065434.1	Q16671	AMHR2_HUMAN	anti-Mullerian hormone receptor, type II	538					Mullerian duct regression (GO:0001880)|negative regulation of anti-Mullerian hormone signaling pathway (GO:1902613)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)	integral component of plasma membrane (GO:0005887)	anti-Mullerian hormone receptor activity (GO:1990272)|ATP binding (GO:0005524)|hormone binding (GO:0042562)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor activity, type II (GO:0005026)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|skin(2)	34					Adenosine triphosphate(DB00171)	TTCAATTCCTGCCCCTACCAT	0.602																																					p.A538S		Atlas-SNP	.											.	AMHR2	61	.	0			c.G1612T						.						122.0	103.0	110.0					12																	53825147		2203	4300	6503	SO:0001583	missense	269	exon11			ATTCCTGCCCCTA	AF172932	CCDS8858.1, CCDS53798.1, CCDS55829.1	12q13	2013-03-14							465	protein-coding gene	gene with protein product	"""Muellerian inhibiting substance type II receptor"""	600956				7493017	Standard	NM_001164690		Approved	MISR2, MISRII	uc001scx.2	Q16671	OTTHUMG00000170048	ENST00000257863.4:c.1612G>T	chr12.hg19:g.53825147G>T	ENSP00000257863:p.Ala538Ser	86.0	0.0		85.0	22.0	NM_020547	A0AVE1|B9EGB7|E9PGD2|F8W1D2|Q13762|Q647K2	Missense_Mutation	SNP	ENST00000257863.4	hg19	CCDS8858.1	.	.	.	.	.	.	.	.	.	.	G	9.890	1.203978	0.22205	.	.	ENSG00000135409	ENST00000257863;ENST00000379791	D;D	0.93659	-3.14;-3.26	4.86	1.91	0.25777	.	0.209202	0.24245	N	0.040237	T	0.82079	0.4959	N	0.12182	0.205	0.21020	N	0.99981	B	0.13594	0.008	B	0.06405	0.002	T	0.67389	-0.5683	10	0.22109	T	0.4	.	4.7842	0.13217	0.2333:0.2907:0.4761:0.0	.	538	Q16671	AMHR2_HUMAN	S	538;443	ENSP00000257863:A538S;ENSP00000369117:A443S	ENSP00000257863:A538S	A	+	1	0	AMHR2	52111414	0.003000	0.15002	0.269000	0.24586	0.764000	0.43329	0.244000	0.18124	0.301000	0.22738	0.563000	0.77884	GCC	.	G|0.999;A|0.001		0.602	AMHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407048.1	NM_020547	
HECTD4	283450	hgsc.bcm.edu	37	12	112721009	112721009	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr12:112721009A>G	ENST00000430131.2	-	8	1396	c.251T>C	c.(250-252)cTa>cCa	p.L84P	HECTD4_ENST00000550722.1_Missense_Mutation_p.L334P|HECTD4_ENST00000377560.5_Missense_Mutation_p.L334P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	84					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										AAGTCTACTTAGAAGCATCTC	0.458																																					p.L334P		Atlas-SNP	.											.	.	.	.	0			c.T1001C						.						112.0	102.0	105.0					12																	112721009		1906	4133	6039	SO:0001583	missense	283450	exon8			CTACTTAGAAGCA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.251T>C	chr12.hg19:g.112721009A>G	ENSP00000404379:p.Leu84Pro	154.0	0.0		174.0	43.0	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	hg19		.	.	.	.	.	.	.	.	.	.	A	31	5.079173	0.94050	.	.	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.63913	0.01;-0.07;-0.05	5.62	5.62	0.85841	.	.	.	.	.	T	0.66167	0.2762	N	0.14661	0.345	0.80722	D	1	D	0.65815	0.995	D	0.75484	0.986	T	0.72757	-0.4197	9	0.87932	D	0	.	15.8154	0.78595	1.0:0.0:0.0:0.0	.	84	Q9Y4D8	K0614_HUMAN	P	334;84;334	ENSP00000366783:L334P;ENSP00000404379:L84P;ENSP00000449784:L334P	ENSP00000366783:L334P	L	-	2	0	C12orf51	111205392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	8.923000	0.92808	2.152000	0.67230	0.459000	0.35465	CTA	.	.		0.458	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
TMEM132D	121256	hgsc.bcm.edu	37	12	130185090	130185090	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr12:130185090C>T	ENST00000422113.2	-	2	559	c.233G>A	c.(232-234)cGg>cAg	p.R78Q	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	78					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGACTCCACCCGGGACTGCAG	0.547																																					p.R78Q		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G233A						.						60.0	56.0	58.0					12																	130185090		2203	4300	6503	SO:0001583	missense	121256	exon2			TCCACCCGGGACT	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.233G>A	chr12.hg19:g.130185090C>T	ENSP00000408581:p.Arg78Gln	156.0	0.0		144.0	36.0	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	hg19	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.919068	0.92249	.	.	ENSG00000151952	ENST00000422113	T	0.16897	2.31	5.33	5.33	0.75918	.	0.000000	0.56097	D	0.000030	T	0.44498	0.1296	M	0.75884	2.315	0.36095	D	0.84371	D	0.89917	1.0	D	0.77557	0.99	T	0.52026	-0.8630	9	.	.	.	-42.2379	19.0288	0.92946	0.0:1.0:0.0:0.0	.	78	Q14C87	T132D_HUMAN	Q	78	ENSP00000408581:R78Q	.	R	-	2	0	TMEM132D	128751043	0.999000	0.42202	0.931000	0.37212	0.983000	0.72400	5.910000	0.69931	2.472000	0.83506	0.555000	0.69702	CGG	.	.		0.547	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
OR4N2	390429	hgsc.bcm.edu	37	14	20296452	20296452	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr14:20296452T>C	ENST00000315947.1	+	1	845	c.845T>C	c.(844-846)tTg>tCg	p.L282S	OR4N2_ENST00000568211.1_3'UTR	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	282						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTTCCTTTGTTGAATCCTGTC	0.433																																					p.L282S		Atlas-SNP	.											.	OR4N2	125	.	0			c.T845C						.						66.0	68.0	68.0					14																	20296452		2203	4300	6503	SO:0001583	missense	390429	exon1			CTTTGTTGAATCC		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.845T>C	chr14.hg19:g.20296452T>C	ENSP00000319601:p.Leu282Ser	125.0	0.0		152.0	32.0	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	hg19	CCDS32022.1	.	.	.	.	.	.	.	.	.	.	.	18.00	3.524762	0.64747	.	.	ENSG00000176294	ENST00000315947	T	0.48836	0.8	4.57	4.57	0.56435	GPCR, rhodopsin-like superfamily (1);	0.184888	0.26146	N	0.026063	T	0.66086	0.2754	H	0.96208	3.785	0.31464	N	0.669204	P	0.45428	0.858	P	0.45794	0.493	T	0.79564	-0.1751	10	0.87932	D	0	-4.6361	12.161	0.54103	0.0:0.0:0.0:1.0	.	282	Q8NGD1	OR4N2_HUMAN	S	282	ENSP00000319601:L282S	ENSP00000319601:L282S	L	+	2	0	OR4N2	19366292	0.997000	0.39634	0.991000	0.47740	0.888000	0.51559	7.022000	0.76431	2.037000	0.60232	0.482000	0.46254	TTG	.	.		0.433	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
ITPK1	3705	hgsc.bcm.edu	37	14	93408041	93408041	+	Silent	SNP	C	C	T	rs532039520		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr14:93408041C>T	ENST00000267615.6	-	11	1283	c.1110G>A	c.(1108-1110)gcG>gcA	p.A370A	ITPK1_ENST00000354313.3_Intron|ITPK1_ENST00000555495.1_Silent_p.A251A|ITPK1_ENST00000556603.2_Silent_p.A370A			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	370					blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		CCTTCCAGGGCGCGTCCTGGC	0.731													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13516	0.0		0.0	False		,,,				2504	0.0				p.A370A		Atlas-SNP	.											.	ITPK1	53	.	0			c.G1110A						.						3.0	4.0	4.0					14																	93408041		1857	3656	5513	SO:0001819	synonymous_variant	3705	exon11			CCAGGGCGCGTCC	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"""inositol 1,3,4-triphosphate 5/6 kinase"""			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.1110G>A	chr14.hg19:g.93408041C>T		29.0	0.0		45.0	10.0	NM_001142593	Q9BTL6|Q9H2E7	Silent	SNP	ENST00000267615.6	hg19	CCDS9907.1																																																																																			.	.		0.731	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216	
NEO1	4756	hgsc.bcm.edu	37	15	73552722	73552722	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr15:73552722G>A	ENST00000339362.5	+	16	2761	c.2314G>A	c.(2314-2316)Gcc>Acc	p.A772T	NEO1_ENST00000558964.1_Missense_Mutation_p.A772T|NEO1_ENST00000560262.1_Missense_Mutation_p.A772T|NEO1_ENST00000261908.6_Missense_Mutation_p.A772T			Q92859	NEO1_HUMAN	neogenin 1	772	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|iron ion homeostasis (GO:0055072)|muscle cell differentiation (GO:0042692)|myoblast fusion (GO:0007520)|positive regulation of muscle cell differentiation (GO:0051149)|regulation of transcription, DNA-templated (GO:0006355)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(9)|lung(26)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	57						CAGAGGTTACGCCATTGGTTA	0.483																																					p.A772T		Atlas-SNP	.											.	NEO1	102	.	0			c.G2314A						.						124.0	104.0	111.0					15																	73552722		2198	4297	6495	SO:0001583	missense	4756	exon15			GGTTACGCCATTG	U61262	CCDS10247.1, CCDS53957.1, CCDS58378.1	15q22.3-q23	2014-06-20	2010-06-24		ENSG00000067141	ENSG00000067141		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7754	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 2"""	601907	"""neogenin (chicken) homolog 1"""			9121761	Standard	NM_002499		Approved	NGN, HsT17534, IGDCC2, NTN1R2	uc002avm.4	Q92859	OTTHUMG00000133509	ENST00000339362.5:c.2314G>A	chr15.hg19:g.73552722G>A	ENSP00000341198:p.Ala772Thr	129.0	0.0		150.0	12.0	NM_001172623	B7ZKM9|B7ZKN0|O00340|Q17RX1	Missense_Mutation	SNP	ENST00000339362.5	hg19	CCDS10247.1	.	.	.	.	.	.	.	.	.	.	G	9.537	1.112265	0.20795	.	.	ENSG00000067141	ENST00000339362;ENST00000379842;ENST00000261908	T;T	0.56275	0.47;0.47	5.2	5.2	0.72013	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.192709	0.56097	D	0.000040	T	0.22166	0.0534	N	0.00468	-1.46	0.58432	D	0.99999	B;B;B;B	0.28233	0.204;0.023;0.014;0.099	B;B;B;B	0.29716	0.106;0.024;0.015;0.078	T	0.36601	-0.9741	10	0.09338	T	0.73	-16.963	19.1117	0.93318	0.0:0.0:1.0:0.0	.	772;772;510;772	B7ZKM9;B7ZKN0;E7EUX3;Q92859	.;.;.;NEO1_HUMAN	T	772;510;772	ENSP00000341198:A772T;ENSP00000261908:A772T	ENSP00000261908:A772T	A	+	1	0	NEO1	71339775	1.000000	0.71417	0.996000	0.52242	0.982000	0.71751	5.003000	0.63959	2.593000	0.87608	0.655000	0.94253	GCC	.	.		0.483	NEO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257472.2	NM_002499	
UNC45A	55898	hgsc.bcm.edu	37	15	91493443	91493443	+	Silent	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr15:91493443C>T	ENST00000418476.2	+	16	2173	c.2133C>T	c.(2131-2133)gcC>gcT	p.A711A	UNC45A_ENST00000394275.2_Silent_p.A696A|AC068831.6_ENST00000553321.1_RNA	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	711					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CAGCCCAGGCCCTTGCCAAGC	0.642																																					p.A711A		Atlas-SNP	.											.	UNC45A	57	.	0			c.C2133T						.						88.0	74.0	79.0					15																	91493443		1989	3817	5806	SO:0001819	synonymous_variant	55898	exon16			CCAGGCCCTTGCC		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.2133C>T	chr15.hg19:g.91493443C>T		97.0	0.0		134.0	10.0	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Silent	SNP	ENST00000418476.2	hg19	CCDS10367.1																																																																																			.	.		0.642	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
ABCC6	368	hgsc.bcm.edu	37	16	16248587	16248587	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr16:16248587T>G	ENST00000205557.7	-	29	4135	c.4106A>C	c.(4105-4107)gAg>gCg	p.E1369A		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1369	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCAGATAGCCTCGTCCGAGTG	0.677																																					p.E1369A		Atlas-SNP	.											.	ABCC6	110	.	0			c.A4106C						.						33.0	28.0	30.0					16																	16248587		2197	4300	6497	SO:0001583	missense	368	exon29			ATAGCCTCGTCCG	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.4106A>C	chr16.hg19:g.16248587T>G	ENSP00000205557:p.Glu1369Ala	148.0	0.0		137.0	47.0	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	hg19	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	T	8.125	0.781884	0.16189	.	.	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.91295	-2.82	4.59	3.5	0.40072	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.697795	0.12253	U	0.485469	T	0.81959	0.4933	N	0.12637	0.245	0.80722	D	1	P;P	0.42827	0.791;0.791	B;B	0.43155	0.41;0.41	T	0.78797	-0.2063	10	0.46703	T	0.11	.	6.3997	0.21632	0.0:0.0874:0.1596:0.753	.	1369;1369	O95255;A8Y988	MRP6_HUMAN;.	A	1369;307	ENSP00000205557:E1369A	ENSP00000205557:E1369A	E	-	2	0	ABCC6	16156088	0.318000	0.24598	0.175000	0.22980	0.104000	0.19210	2.229000	0.42990	1.708000	0.51301	0.381000	0.24937	GAG	.	.		0.677	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
FAM57B	83723	hgsc.bcm.edu	37	16	30041827	30041827	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr16:30041827C>A	ENST00000380495.4	-	1	753	c.22G>T	c.(22-24)Ggg>Tgg	p.G8W	FAM57B_ENST00000567037.1_5'Flank|FAM57B_ENST00000279389.4_5'Flank|FAM57B_ENST00000564806.1_5'Flank	NM_031478.4	NP_113666.2	Q71RH2	FA57B_HUMAN	family with sequence similarity 57, member B	8					ceramide biosynthetic process (GO:0046513)|negative regulation of fat cell differentiation (GO:0045599)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sphingosine N-acyltransferase activity (GO:0050291)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(5)|upper_aerodigestive_tract(1)	14						ACCACCCCCCCGGCCACCATC	0.677																																					p.G8W		Atlas-SNP	.											.	FAM57B	26	.	0			c.G22T						.						13.0	16.0	15.0					16																	30041827		1866	4081	5947	SO:0001583	missense	83723	exon1			CCCCCCCGGCCAC	AF370365	CCDS10667.2	16p11.2	2013-02-19			ENSG00000149926	ENSG00000149926			25295	protein-coding gene	gene with protein product		615175				11230166, 23275342	Standard	NM_031478		Approved	DKFZP434I2117	uc002dvt.3	Q71RH2	OTTHUMG00000132105	ENST00000380495.4:c.22G>T	chr16.hg19:g.30041827C>A	ENSP00000369863:p.Gly8Trp	143.0	0.0		156.0	41.0	NM_031478	Q9H0J1	Missense_Mutation	SNP	ENST00000380495.4	hg19	CCDS10667.2	.	.	.	.	.	.	.	.	.	.	C	26.6	4.756147	0.89843	.	.	ENSG00000149926	ENST00000380495	.	.	.	4.68	4.68	0.58851	.	0.203505	0.41097	D	0.000943	T	0.77631	0.4159	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80632	-0.1296	9	0.87932	D	0	0.0637	14.8742	0.70483	0.0:1.0:0.0:0.0	.	8	Q71RH2	FA57B_HUMAN	W	8	.	ENSP00000369863:G8W	G	-	1	0	FAM57B	29949328	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.043000	0.71004	2.320000	0.78422	0.561000	0.74099	GGG	.	.		0.677	FAM57B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255142.2	NM_031478	
NFATC3	4775	hgsc.bcm.edu	37	16	68160388	68160388	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr16:68160388G>T	ENST00000346183.3	+	3	1300	c.1276G>T	c.(1276-1278)Gct>Tct	p.A426S	NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.A426S|NFATC3_ENST00000329524.4_Missense_Mutation_p.A426S|NFATC3_ENST00000349223.5_Missense_Mutation_p.A426S	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	426	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.				cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GCCTTTACCAGCTCATTTTGG	0.408																																					p.A426S		Atlas-SNP	.											.	NFATC3	190	.	0			c.G1276T						.						146.0	113.0	124.0					16																	68160388		2198	4300	6498	SO:0001583	missense	4775	exon3			TTACCAGCTCATT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.1276G>T	chr16.hg19:g.68160388G>T	ENSP00000300659:p.Ala426Ser	122.0	0.0		143.0	39.0	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	hg19	CCDS10860.1	.	.	.	.	.	.	.	.	.	.	G	5.647	0.303946	0.10678	.	.	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524	T;T;T	0.38240	1.15;1.15;1.15	5.48	0.75	0.18387	Rel homology (2);p53-like transcription factor, DNA-binding (1);	0.128661	0.64402	D	0.000001	T	0.04815	0.0130	N	0.00062	-2.325	0.25068	N	0.991016	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.001;0.002;0.001;0.001	T	0.41106	-0.9527	10	0.02654	T	1	-3.0191	4.7376	0.12995	0.6508:0.0:0.22:0.1292	.	426;426;426;426	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	S	426	ENSP00000264008:A426S;ENSP00000300659:A426S;ENSP00000331324:A426S	ENSP00000331324:A426S	A	+	1	0	NFATC3	66717889	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	4.268000	0.58883	0.065000	0.16485	-0.378000	0.06908	GCT	.	.		0.408	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
PELP1	27043	hgsc.bcm.edu	37	17	4580066	4580066	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:4580066C>A	ENST00000574876.1	-	6	701	c.684G>T	c.(682-684)ttG>ttT	p.L228F	PELP1_ENST00000301396.4_Missense_Mutation_p.L228F|PELP1_ENST00000572293.1_Missense_Mutation_p.L278F|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000436683.2_Missense_Mutation_p.L81F|PELP1_ENST00000269230.7_Missense_Mutation_p.L228F			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	228					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GCTGAGGGCTCAAGGCATCCA	0.557																																					p.L228F		Atlas-SNP	.											.	PELP1	102	.	0			c.G684T						.						45.0	44.0	44.0					17																	4580066		1954	4131	6085	SO:0001583	missense	27043	exon6			AGGGCTCAAGGCA		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.684G>T	chr17.hg19:g.4580066C>A	ENSP00000461625:p.Leu228Phe	186.0	0.0		196.0	28.0	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	hg19	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	15.78	2.934795	0.52866	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.68479	-0.3;-0.18;-0.33	5.31	5.31	0.75309	.	0.626193	0.15140	N	0.278359	T	0.73590	0.3606	L	0.44542	1.39	0.34133	D	0.66551	D;D	0.62365	0.991;0.983	P;P	0.60949	0.881;0.799	T	0.77938	-0.2400	10	0.49607	T	0.09	-1.0784	14.3972	0.67020	0.0:1.0:0.0:0.0	.	81;228	E7EV54;Q8IZL8	.;PELP1_HUMAN	F	228;228;81	ENSP00000301396:L228F;ENSP00000269230:L228F;ENSP00000416231:L81F	ENSP00000269230:L228F	L	-	3	2	AC091153.1	4526815	1.000000	0.71417	0.999000	0.59377	0.776000	0.43924	1.708000	0.37899	2.774000	0.95407	0.650000	0.86243	TTG	.	.		0.557	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33806550	33806550	+	Missense_Mutation	SNP	A	A	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:33806550A>C	ENST00000260908.7	-	2	796	c.679T>G	c.(679-681)Ttc>Gtc	p.F227V	RP11-686D22.9_ENST00000587076.1_RNA|SLFN12L_ENST00000449046.1_Missense_Mutation_p.F258V|SLFN12L_ENST00000361112.4_Missense_Mutation_p.F256V	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	227						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						TCAGTCGAGAAGTTTTTTATT	0.338																																					p.F227V		Atlas-SNP	.											.	SLFN12L	140	.	0			c.T679G						.						103.0	83.0	89.0					17																	33806550		692	1591	2283	SO:0001583	missense	100506736	exon2			TCGAGAAGTTTTT	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.679T>G	chr17.hg19:g.33806550A>C	ENSP00000437635:p.Phe227Val	93.0	0.0		119.0	19.0	NM_001195790	F5H6G3	Missense_Mutation	SNP	ENST00000260908.7	hg19	CCDS56026.1	.	.	.	.	.	.	.	.	.	.	A	12.43	1.936605	0.34189	.	.	ENSG00000205045	ENST00000260908;ENST00000361112;ENST00000449046	T;T;T	0.28666	1.6;1.6;1.6	2.62	1.46	0.22682	.	.	.	.	.	T	0.39306	0.1073	L	0.45051	1.395	0.09310	N	1	D	0.71674	0.998	D	0.66847	0.947	T	0.13845	-1.0494	9	0.49607	T	0.09	.	4.7657	0.13130	0.7221:0.0:0.0:0.2779	.	256	Q6IEE8-2	.	V	227;256;258	ENSP00000437635:F227V;ENSP00000354412:F256V;ENSP00000389348:F258V	ENSP00000437635:F227V	F	-	1	0	SLFN12L	30830663	0.022000	0.18835	0.000000	0.03702	0.009000	0.06853	2.261000	0.43276	0.209000	0.20645	0.338000	0.21704	TTC	.	.		0.338	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
HOXB4	3214	hgsc.bcm.edu	37	17	46655393	46655393	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:46655393G>A	ENST00000332503.5	-	1	2080	c.289C>T	c.(289-291)Cca>Tca	p.P97S	MIR10A_ENST00000385043.1_RNA|HOXB3_ENST00000498678.1_Intron|HOXB3_ENST00000485909.2_5'Flank|HOXB3_ENST00000489475.1_Intron|HOXB-AS3_ENST00000465846.2_RNA|HOXB3_ENST00000465120.3_Intron|HOXB3_ENST00000472863.1_Intron|HOXB3_ENST00000552000.2_Intron|HOXB3_ENST00000460160.1_Intron|HOXB3_ENST00000476342.1_Intron	NM_024015.4	NP_076920.1	P17483	HXB4_HUMAN	homeobox B4	97	Pro-rich (part of the transcriptional activation domain).				anterior/posterior pattern specification (GO:0009952)|bone marrow development (GO:0048539)|cell proliferation (GO:0008283)|definitive hemopoiesis (GO:0060216)|embryonic skeletal system morphogenesis (GO:0048704)|hematopoietic stem cell differentiation (GO:0060218)|morphogenesis of an epithelial sheet (GO:0002011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of stem cell differentiation (GO:2000738)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatic stem cell division (GO:0048103)|spleen development (GO:0048536)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	9						CCGGCGGGTGGCGGCGCAGGA	0.831																																					p.P97S		Atlas-SNP	.											.	HOXB4	16	.	0			c.C289T						.						3.0	3.0	3.0					17																	46655393		990	2253	3243	SO:0001583	missense	3214	exon1			CGGGTGGCGGCGC		CCDS11529.1	17q21.32	2011-06-20	2005-12-22		ENSG00000182742	ENSG00000182742		"""Homeoboxes / ANTP class : HOXL subclass"""	5115	protein-coding gene	gene with protein product		142965	"""homeo box B4"""	HOX2, HOX2F		1973146, 1358459	Standard	NM_024015		Approved		uc002inp.3	P17483	OTTHUMG00000159920	ENST00000332503.5:c.289C>T	chr17.hg19:g.46655393G>A	ENSP00000328928:p.Pro97Ser	17.0	0.0		30.0	7.0	NM_024015	Q9NTA0	Missense_Mutation	SNP	ENST00000332503.5	hg19	CCDS11529.1	.	.	.	.	.	.	.	.	.	.	G	6.741	0.505545	0.12822	.	.	ENSG00000182742	ENST00000332503	T	0.50277	0.75	3.38	1.25	0.21368	.	0.399441	0.24422	N	0.038663	T	0.31327	0.0793	L	0.40543	1.245	0.31863	N	0.620736	B	0.02656	0.0	B	0.01281	0.0	T	0.35126	-0.9801	10	0.10377	T	0.69	.	8.2615	0.31788	0.2141:0.0:0.7859:0.0	.	97	P17483	HXB4_HUMAN	S	97	ENSP00000328928:P97S	ENSP00000328928:P97S	P	-	1	0	HOXB4	44010392	0.821000	0.29204	0.065000	0.19835	0.423000	0.31445	1.967000	0.40491	-0.004000	0.14419	0.313000	0.20887	CCA	.	.		0.831	HOXB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358259.2		
DCXR	51181	hgsc.bcm.edu	37	17	79995521	79995521	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:79995521G>A	ENST00000306869.2	-	1	87	c.38C>T	c.(37-39)aCc>aTc	p.T13I	DCXR_ENST00000584318.1_5'Flank|RP13-650J16.1_ENST00000584705.1_RNA|RP13-650J16.1_ENST00000582558.1_RNA	NM_001195218.1|NM_016286.3	NP_001182147.1|NP_057370.1	Q7Z4W1	DCXR_HUMAN	dicarbonyl/L-xylulose reductase	13					D-xylose metabolic process (GO:0042732)|glucose metabolic process (GO:0006006)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|xylulose metabolic process (GO:0005997)	brush border (GO:0005903)|cytoplasmic microtubule (GO:0005881)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)	L-xylulose reductase (NADP+) activity (GO:0050038)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)			kidney(1)|lung(3)	4	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GCCTGCCCCGGTGACCAGCAC	0.726																																					p.T13I		Atlas-SNP	.											.	DCXR	10	.	0			c.C38T						.						5.0	6.0	6.0					17																	79995521		1987	4035	6022	SO:0001583	missense	51181	exon1			GCCCCGGTGACCA	AB013846	CCDS11799.1	17q25.3	2011-09-14				ENSG00000169738	1.1.1.10	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 20C, member 1"""	608347				11882650, 19027726	Standard	NM_016286		Approved	KIDCR, DCR, SDR20C1	uc002kdg.3	Q7Z4W1		ENST00000306869.2:c.38C>T	chr17.hg19:g.79995521G>A	ENSP00000303356:p.Thr13Ile	78.0	0.0		94.0	18.0	NM_001195218	Q9BTZ3|Q9UHY9	Missense_Mutation	SNP	ENST00000306869.2	hg19	CCDS11799.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.697988	0.48307	.	.	ENSG00000169738	ENST00000306869	T	0.38401	1.14	3.85	3.85	0.44370	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.61751	0.2372	M	0.82056	2.57	0.80722	D	1	D	0.71674	0.998	D	0.83275	0.996	T	0.67738	-0.5593	9	.	.	.	.	15.9235	0.79592	0.0:0.0:1.0:0.0	.	13	Q7Z4W1	DCXR_HUMAN	I	13	ENSP00000303356:T13I	.	T	-	2	0	DCXR	77588810	1.000000	0.71417	0.994000	0.49952	0.830000	0.47004	5.009000	0.63998	1.969000	0.57287	0.491000	0.48974	ACC	.	.		0.726	DCXR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442153.2		
FASN	2194	hgsc.bcm.edu	37	17	80051184	80051184	+	Missense_Mutation	SNP	T	T	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr17:80051184T>G	ENST00000306749.2	-	5	784	c.566A>C	c.(565-567)aAt>aCt	p.N189T		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	189	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CAGCAGGACATTGATGCCCCC	0.657																																					p.N189T	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.A566C						.						43.0	31.0	35.0					17																	80051184		2182	4285	6467	SO:0001583	missense	2194	exon5			AGGACATTGATGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.566A>C	chr17.hg19:g.80051184T>G	ENSP00000304592:p.Asn189Thr	155.0	0.0		191.0	68.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	T	13.92	2.380592	0.42207	.	.	ENSG00000169710	ENST00000306749	T	0.32988	1.43	4.77	4.77	0.60923	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.000000	0.85682	D	0.000000	T	0.34600	0.0903	L	0.59436	1.845	0.58432	D	0.999997	P	0.40619	0.724	P	0.45232	0.474	T	0.08827	-1.0703	10	0.37606	T	0.19	-55.651	9.664	0.39972	0.1554:0.0:0.0:0.8446	.	189	P49327	FAS_HUMAN	T	189	ENSP00000304592:N189T	ENSP00000304592:N189T	N	-	2	0	FASN	77644473	1.000000	0.71417	0.849000	0.33467	0.109000	0.19521	4.982000	0.63825	1.783000	0.52377	0.379000	0.24179	AAT	.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
CDH7	1005	hgsc.bcm.edu	37	18	63481780	63481780	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr18:63481780G>A	ENST00000397968.2	+	4	991	c.565G>A	c.(565-567)Gcc>Acc	p.A189T	CDH7_ENST00000323011.3_Missense_Mutation_p.A189T|CDH7_ENST00000536984.2_Missense_Mutation_p.A189T	NM_004361.2	NP_004352.2	Q9ULB5	CADH7_HUMAN	cadherin 7, type 2	189	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(43)|ovary(3)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(2)	80		Esophageal squamous(42;0.129)				TGGCAACAGTGCCAGAGTGGT	0.433																																					p.A189T		Atlas-SNP	.											.	CDH7	362	.	0			c.G565A						.						179.0	159.0	166.0					18																	63481780		2203	4300	6503	SO:0001583	missense	1005	exon4			AACAGTGCCAGAG	AB035301	CCDS11993.1	18q22.1	2010-01-26			ENSG00000081138	ENSG00000081138		"""Cadherins / Major cadherins"""	1766	protein-coding gene	gene with protein product		605806				9615235	Standard	NM_033646		Approved		uc002ljz.3	Q9ULB5	OTTHUMG00000132800	ENST00000397968.2:c.565G>A	chr18.hg19:g.63481780G>A	ENSP00000381058:p.Ala189Thr	109.0	0.0		130.0	39.0	NM_004361	Q9H157	Missense_Mutation	SNP	ENST00000397968.2	hg19	CCDS11993.1	.	.	.	.	.	.	.	.	.	.	G	36	5.652508	0.96724	.	.	ENSG00000081138	ENST00000323011;ENST00000536984;ENST00000397966;ENST00000397968	T;T;T	0.60797	0.16;0.16;0.16	5.75	5.75	0.90469	Cadherin (4);Cadherin-like (1);	0.126750	0.52532	D	0.000066	T	0.77198	0.4095	M	0.72353	2.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.996;0.998	T	0.78321	-0.2249	10	0.87932	D	0	.	19.9478	0.97189	0.0:0.0:1.0:0.0	.	189;189	F5H5X9;Q9ULB5	.;CADH7_HUMAN	T	189	ENSP00000319166:A189T;ENSP00000443030:A189T;ENSP00000381058:A189T	ENSP00000319166:A189T	A	+	1	0	CDH7	61632760	1.000000	0.71417	0.965000	0.40720	0.975000	0.68041	9.325000	0.96381	2.712000	0.92718	0.591000	0.81541	GCC	.	.		0.433	CDH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256217.2	NM_033646	
MISP	126353	hgsc.bcm.edu	37	19	758004	758004	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:758004G>A	ENST00000215582.6	+	2	1161	c.1058G>A	c.(1057-1059)cGg>cAg	p.R353Q		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	353					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											TACGTGCAGCGGGACATAGTA	0.687																																					p.R353Q		Atlas-SNP	.											.	C19orf21	56	.	0			c.G1058A						.						16.0	19.0	18.0					19																	758004		2196	4292	6488	SO:0001583	missense	126353	exon2			TGCAGCGGGACAT	BC052236	CCDS12042.1	19p13.3	2014-06-25	2013-05-03	2013-05-03	ENSG00000099812	ENSG00000099812			27000	protein-coding gene	gene with protein product	"""mitotic interactor and substrate of Plk1"""	615289	"""chromosome 19 open reading frame 21"""	C19orf21		23574715, 23509069, 24475924	Standard	NM_173481		Approved	DKFZp686H18209, Caprice		Q8IVT2	OTTHUMG00000181786	ENST00000215582.6:c.1058G>A	chr19.hg19:g.758004G>A	ENSP00000215582:p.Arg353Gln	38.0	0.0		37.0	8.0	NM_173481		Missense_Mutation	SNP	ENST00000215582.6	hg19	CCDS12042.1	.	.	.	.	.	.	.	.	.	.	G	19.54	3.847148	0.71603	.	.	ENSG00000099812	ENST00000215582	T	0.46063	0.88	4.13	4.13	0.48395	.	0.376195	0.23760	N	0.044825	T	0.60547	0.2277	M	0.64997	1.995	0.43588	D	0.995935	D	0.89917	1.0	D	0.79784	0.993	T	0.65071	-0.6257	10	0.87932	D	0	-25.5125	13.9053	0.63831	0.0:0.0:1.0:0.0	.	353	Q8IVT2	CS021_HUMAN	Q	353	ENSP00000215582:R353Q	ENSP00000215582:R353Q	R	+	2	0	C19orf21	709004	0.998000	0.40836	0.997000	0.53966	0.153000	0.21895	3.558000	0.53749	2.036000	0.60181	0.491000	0.48974	CGG	.	.		0.687	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
NFIC	4782	hgsc.bcm.edu	37	19	3452573	3452573	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:3452573C>T	ENST00000443272.2	+	8	1229	c.1178C>T	c.(1177-1179)gCc>gTc	p.A393V	NFIC_ENST00000589123.1_Missense_Mutation_p.A384V|NFIC_ENST00000395111.3_Missense_Mutation_p.A384V|NFIC_ENST00000346156.5_Missense_Mutation_p.A360V|NFIC_ENST00000341919.3_Missense_Mutation_p.A393V|NFIC_ENST00000590282.1_Missense_Mutation_p.A393V|NFIC_ENST00000586919.1_Missense_Mutation_p.A360V	NM_001245002.1	NP_001231931.1	P08651	NFIC_HUMAN	nuclear factor I/C (CCAAT-binding transcription factor)	393					DNA replication (GO:0006260)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleolus (GO:0005730)|nucleus (GO:0005634)	core promoter proximal region DNA binding (GO:0001159)|double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;7.8e-05)|Epithelial(107;2.94e-108)|BRCA - Breast invasive adenocarcinoma(158;0.00154)|STAD - Stomach adenocarcinoma(1328;0.191)		CCCCACACGGCCATCCGCTAC	0.652																																					p.A393V		Atlas-SNP	.											NFIC,colon,carcinoma,0,1	NFIC	36	.	0			c.C1178T						.						187.0	159.0	168.0					19																	3452573		2203	4300	6503	SO:0001583	missense	4782	exon8			ACACGGCCATCCG	X12492	CCDS12107.1, CCDS45914.1, CCDS58640.1, CCDS59330.1, CCDS59331.1	19p13.3	2008-02-05				ENSG00000141905			7786	protein-coding gene	gene with protein product		600729		NFI		3398920, 7590749	Standard	NM_205843		Approved	CTF, NF-I, CTF5	uc010xhi.2	P08651		ENST00000443272.2:c.1178C>T	chr19.hg19:g.3452573C>T	ENSP00000396843:p.Ala393Val	74.0	0.0		79.0	9.0	NM_001245004	A8K1H0|B7Z4U5|B7Z9C3|K7EMU1|P08652|Q14932|Q9UPJ3|Q9UPJ9|Q9UPK0|Q9UPK1	Missense_Mutation	SNP	ENST00000443272.2	hg19	CCDS59330.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.890863	0.91889	.	.	ENSG00000141905	ENST00000443272;ENST00000395111;ENST00000346156;ENST00000341919;ENST00000343825;ENST00000269778	T;T;T	0.53640	0.61;0.61;0.61	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.66117	0.2757	M	0.65498	2.005	0.52501	D	0.999953	D;D;D;D;D	0.76494	0.999;0.999;0.998;0.972;0.998	D;D;D;P;D	0.83275	0.996;0.996;0.994;0.592;0.994	T	0.69614	-0.5098	10	0.54805	T	0.06	.	15.0657	0.71992	0.0:1.0:0.0:0.0	.	393;393;384;393;384	B7Z4U5;P08651;P08651-3;P08651-5;P08651-2	.;NFIC_HUMAN;.;.;.	V	384;384;360;393;393;393	ENSP00000378543:A384V;ENSP00000301935:A360V;ENSP00000342194:A393V	ENSP00000269778:A393V	A	+	2	0	NFIC	3403573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.240000	0.78192	1.874000	0.54306	0.555000	0.69702	GCC	.	.		0.652	NFIC-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452834.1	NM_005597	
ZNF99	7652	hgsc.bcm.edu	37	19	22941303	22941303	+	Missense_Mutation	SNP	T	T	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:22941303T>C	ENST00000596209.1	-	4	1498	c.1408A>G	c.(1408-1410)Aaa>Gaa	p.K470E	ZNF99_ENST00000397104.3_Missense_Mutation_p.K379E	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	470					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(20)|lung(55)|ovary(2)|prostate(10)|skin(5)|stomach(9)|upper_aerodigestive_tract(2)|urinary_tract(3)	124		Lung NSC(12;0.0207)|all_lung(12;0.0214)|all_epithelial(12;0.102)				ATCTCATGTTTTCTAAGGGCT	0.348																																					p.K470E		Atlas-SNP	.											.	ZNF99	273	.	0			c.A1408G						.						68.0	70.0	69.0					19																	22941303		2005	4209	6214	SO:0001583	missense	7652	exon4			CATGTTTTCTAAG	BC021822	CCDS59369.1	19p12	2013-01-08	2006-01-17		ENSG00000213973	ENSG00000213973		"""Zinc fingers, C2H2-type"", ""-"""	13175	protein-coding gene	gene with protein product		603981	"""zinc finger protein 99 (F8281)"", ""chromosome 19 open reading frame 9"""	C19orf9			Standard	NM_001080409		Approved	MGC24986	uc021urt.1	A8MXY4		ENST00000596209.1:c.1408A>G	chr19.hg19:g.22941303T>C	ENSP00000472969:p.Lys470Glu	67.0	0.0		105.0	29.0	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	N	0.004	-2.247202	0.00271	.	.	ENSG00000213973	ENST00000397104	T	0.06687	3.27	1.28	0.17	0.15021	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04815	0.0130	N	0.20530	0.585	0.09310	N	1	P	0.40534	0.72	P	0.45474	0.482	T	0.18085	-1.0348	9	0.02654	T	1	.	2.2405	0.04018	0.2521:0.1924:0.0:0.5554	.	379	A8MXY4	ZNF99_HUMAN	E	379	ENSP00000380293:K379E	ENSP00000380293:K379E	K	-	1	0	ZNF99	22733143	0.000000	0.05858	0.001000	0.08648	0.021000	0.10359	-3.434000	0.00472	0.566000	0.29273	0.325000	0.21440	AAA	.	.		0.348	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
FCGBP	8857	hgsc.bcm.edu	37	19	40434029	40434029	+	Silent	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:40434029G>T	ENST00000221347.6	-	2	247	c.240C>A	c.(238-240)gtC>gtA	p.V80V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	80	IgGFc-binding.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GCCTCACTGTGACCTTCTTTG	0.567																																					p.V80V		Atlas-SNP	.											.	FCGBP	416	.	0			c.C240A						.						123.0	106.0	112.0					19																	40434029		2203	4300	6503	SO:0001819	synonymous_variant	8857	exon2			CACTGTGACCTTC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.240C>A	chr19.hg19:g.40434029G>T		131.0	0.0		146.0	34.0	NM_003890	O95784	Silent	SNP	ENST00000221347.6	hg19	CCDS12546.1																																																																																			.	.		0.567	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
HAS1	3036	hgsc.bcm.edu	37	19	52220241	52220241	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:52220241G>A	ENST00000222115.1	-	3	942	c.908C>T	c.(907-909)tCc>tTc	p.S303F	HAS1_ENST00000594621.1_Missense_Mutation_p.S157F|HAS1_ENST00000601714.1_Missense_Mutation_p.S310F|HAS1_ENST00000540069.2_Missense_Mutation_p.S302F	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	303					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GCTGATGCAGGATACACAGTG	0.577																																					p.S303F	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.C908T						.						108.0	103.0	104.0					19																	52220241		2203	4300	6503	SO:0001583	missense	3036	exon3			ATGCAGGATACAC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.908C>T	chr19.hg19:g.52220241G>A	ENSP00000222115:p.Ser303Phe	67.0	0.0		83.0	19.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	g	19.12	3.764912	0.69878	.	.	ENSG00000105509	ENST00000540069;ENST00000222115;ENST00000376737;ENST00000376738	T;T	0.43294	0.95;0.95	3.96	3.96	0.45880	.	0.070349	0.64402	U	0.000017	T	0.61160	0.2325	M	0.66506	2.035	0.80722	D	1	D;D;D	0.76494	0.997;0.999;0.999	D;D;D	0.75484	0.964;0.986;0.986	T	0.65882	-0.6060	10	0.66056	D	0.02	-25.9268	13.9492	0.64106	0.0:0.0:1.0:0.0	.	302;303;302	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	F	302;303;160;157	ENSP00000445021:S302F;ENSP00000222115:S303F	ENSP00000222115:S303F	S	-	2	0	HAS1	56912053	1.000000	0.71417	1.000000	0.80357	0.739000	0.42172	4.454000	0.60068	1.947000	0.56498	0.489000	0.48404	TCC	.	.		0.577	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
LILRB5	10990	hgsc.bcm.edu	37	19	54757883	54757883	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:54757883C>A	ENST00000316219.5	-	8	1459	c.1352G>T	c.(1351-1353)aGt>aTt	p.S451I	LILRB5_ENST00000345866.6_Missense_Mutation_p.S352I|LILRB5_ENST00000450632.1_Missense_Mutation_p.S443I|LILRB5_ENST00000449561.2_Missense_Mutation_p.S452I	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	451					cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TCACTCACCACTCTGGGGATC	0.672																																					p.S452I		Atlas-SNP	.											.	LILRB5	176	.	0			c.G1355T						.						24.0	24.0	24.0					19																	54757883		2194	4295	6489	SO:0001583	missense	10990	exon8			TCACCACTCTGGG	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.1352G>T	chr19.hg19:g.54757883C>A	ENSP00000320390:p.Ser451Ile	210.0	0.0		212.0	9.0	NM_001081442	Q8N760	Missense_Mutation	SNP	ENST00000316219.5	hg19	CCDS12885.1	.	.	.	.	.	.	.	.	.	.	C	6.471	0.454991	0.12283	.	.	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.00490	7.05;7.03;7.05;7.05	1.53	-3.05	0.05396	.	7739.210000	0.00166	N	0.000000	T	0.00356	0.0011	L	0.42581	1.335	0.09310	N	1	P;B;B;B	0.41265	0.744;0.022;0.261;0.0	B;B;B;B	0.32864	0.154;0.037;0.076;0.0	T	0.43426	-0.9392	10	0.66056	D	0.02	.	3.7018	0.08386	0.0:0.2555:0.4111:0.3334	.	443;352;452;451	C9JMK7;O75023-2;O75023-3;O75023	.;.;.;LIRB5_HUMAN	I	451;443;452;352	ENSP00000320390:S451I;ENSP00000414225:S443I;ENSP00000406478:S452I;ENSP00000263430:S352I	ENSP00000320390:S451I	S	-	2	0	LILRB5	59449695	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-1.309000	0.02728	-1.453000	0.01928	0.430000	0.28490	AGT	.	.		0.672	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
ZNF787	126208	hgsc.bcm.edu	37	19	56600216	56600216	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:56600216G>C	ENST00000270459.3	-	3	443	c.325C>G	c.(325-327)Ctg>Gtg	p.L109V		NM_001002836.2	NP_001002836	Q6DD87	ZN787_HUMAN	zinc finger protein 787	109					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(1)|lung(2)|pancreas(1)	5		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0559)		TGCTGCACCAGGTGCGAGCTC	0.682																																					p.L109V		Atlas-SNP	.											.	ZNF787	20	.	0			c.C325G						.						21.0	23.0	23.0					19																	56600216		2203	4299	6502	SO:0001583	missense	126208	exon3			GCACCAGGTGCGA	BC077728, AF000560	CCDS42634.1	19q13.42	2013-01-08				ENSG00000142409		"""Zinc fingers, C2H2-type"""	26998	protein-coding gene	gene with protein product							Standard	NM_001002836		Approved		uc010eth.1	Q6DD87		ENST00000270459.3:c.325C>G	chr19.hg19:g.56600216G>C	ENSP00000270459:p.Leu109Val	80.0	0.0		90.0	20.0	NM_001002836	O00455	Missense_Mutation	SNP	ENST00000270459.3	hg19	CCDS42634.1	.	.	.	.	.	.	.	.	.	.	G	16.39	3.111009	0.56398	.	.	ENSG00000142409	ENST00000270459	T	0.52983	0.64	3.46	2.36	0.29203	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.58991	0.2161	L	0.60845	1.875	0.80722	D	1	D	0.69078	0.997	D	0.67725	0.953	T	0.58747	-0.7582	9	0.62326	D	0.03	-21.1662	9.1854	0.37168	0.1163:0.0:0.8836:0.0	.	109	Q6DD87	ZN787_HUMAN	V	109	ENSP00000270459:L109V	ENSP00000270459:L109V	L	-	1	2	ZNF787	61292028	0.859000	0.29813	1.000000	0.80357	0.914000	0.54420	0.892000	0.28322	0.748000	0.32831	0.462000	0.41574	CTG	.	.		0.682	ZNF787-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457498.1	NM_001002836	
DDX27	55661	hgsc.bcm.edu	37	20	47855523	47855523	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr20:47855523G>T	ENST00000371764.4	+	15	1827	c.1818G>T	c.(1816-1818)atG>atT	p.M606I	ZNFX1_ENST00000469991.1_5'UTR|ZNFX1_ENST00000371754.4_Silent_p.S1247S|DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	606						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)	p.M606I(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TTGAGAAAATGGAGAAAGATG	0.478																																					p.M606I		Atlas-SNP	.											DDX27,NS,carcinoma,0,1	DDX27	74	.	1	Substitution - Missense(1)	lung(1)	c.G1818T						.						64.0	59.0	61.0					20																	47855523		2203	4300	6503	SO:0001583	missense	55661	exon15			GAAAATGGAGAAA	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.1818G>T	chr20.hg19:g.47855523G>T	ENSP00000360828:p.Met606Ile	64.0	0.0		106.0	5.0	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	hg19	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	G	15.11	2.736757	0.49045	.	.	ENSG00000124228	ENST00000371764	T	0.01430	4.9	5.23	5.23	0.72850	.	0.169570	0.53938	D	0.000045	T	0.02193	0.0068	L	0.43923	1.385	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.56860	-0.7909	10	0.45353	T;T	0.12;0.12	-27.0788	16.3221	0.82954	0.0:0.0:1.0:0.0	.	606	Q96GQ7	DDX27_HUMAN	I	606	ENSP00000360828:M606I	ENSP00000360828:M606I;ENSP00000360828:M606I	M	+	3	0	DDX27	47288930	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.260000	0.65490	2.438000	0.82558	0.655000	0.94253	ATG	.	.		0.478	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
CTCFL	140690	hgsc.bcm.edu	37	20	56090848	56090848	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr20:56090848G>T	ENST00000608263.1	-	5	1763	c.1102C>A	c.(1102-1104)Cgc>Agc	p.R368S	CTCFL_ENST00000422869.2_Missense_Mutation_p.R368S|CTCFL_ENST00000502686.2_Missense_Mutation_p.R106S|CTCFL_ENST00000608858.1_5'UTR|CTCFL_ENST00000243914.3_Missense_Mutation_p.R368S|CTCFL_ENST00000423479.3_Missense_Mutation_p.R368S|CTCFL_ENST00000539382.1_Missense_Mutation_p.R163S|CTCFL_ENST00000609232.1_Missense_Mutation_p.R368S|CTCFL_ENST00000608440.1_Missense_Mutation_p.R368S|CTCFL_ENST00000432255.2_Intron|CTCFL_ENST00000433949.3_Missense_Mutation_p.R163S|CTCFL_ENST00000608425.1_Missense_Mutation_p.R368S|CTCFL_ENST00000371196.2_Missense_Mutation_p.R368S|CTCFL_ENST00000608903.1_Missense_Mutation_p.R106S|CTCFL_ENST00000429804.3_Missense_Mutation_p.R368S	NM_001269041.1	NP_001255970.1	Q8NI51	CTCFL_HUMAN	CCCTC-binding factor (zinc finger protein)-like	368					cell cycle (GO:0007049)|DNA methylation involved in gamete generation (GO:0043046)|histone methylation (GO:0016571)|positive regulation of gene expression (GO:0010628)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of histone H3-K4 methylation (GO:0051569)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(28)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58	Lung NSC(12;0.00132)|all_lung(29;0.00433)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;3.95e-12)|Epithelial(14;3.41e-08)|all cancers(14;2.09e-07)			TGAAAGGGGCGCTCCCCAGTG	0.478																																					p.R368S		Atlas-SNP	.											.	CTCFL	97	.	0			c.C1102A						.						163.0	156.0	159.0					20																	56090848		2203	4300	6503	SO:0001583	missense	140690	exon5			AGGGGCGCTCCCC		CCDS13459.1, CCDS58776.1, CCDS58777.1, CCDS58778.1, CCDS58779.1, CCDS58780.1, CCDS58781.1, CCDS58782.1, CCDS68161.1, CCDS68162.1, CCDS68163.1, CCDS68164.1	20q13.31	2013-01-08			ENSG00000124092	ENSG00000124092		"""Zinc fingers, C2H2-type"""	16234	protein-coding gene	gene with protein product	"""cancer/testis antigen 27"""	607022					Standard	NM_001269040		Approved	dJ579F20.2, BORIS, CT27	uc010giw.1	Q8NI51	OTTHUMG00000032829	ENST00000608263.1:c.1102C>A	chr20.hg19:g.56090848G>T	ENSP00000476783:p.Arg368Ser	65.0	0.0		61.0	14.0	NM_001269044	A0S6W1|A1L4C6|A6XGL8|A6XGM2|A6XGM3|A6XGM8|A6XGN0|A6XGN1|A6XGN2|A6XGN3|A6XGN4|E7EQ27|E7EUE3|E9PBA9|Q5JUG4|Q9BZ30|Q9NQJ3	Missense_Mutation	SNP	ENST00000608263.1	hg19	CCDS13459.1	.	.	.	.	.	.	.	.	.	.	G	32	5.108533	0.94292	.	.	ENSG00000124092	ENST00000423479;ENST00000243914;ENST00000371196;ENST00000429804;ENST00000433949;ENST00000502686;ENST00000422109;ENST00000426658;ENST00000539382;ENST00000422869	T;T;T;T;T;T;T;T;T;T	0.19250	2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16;2.16	5.24	5.24	0.73138	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.44902	D	0.000406	T	0.49983	0.1589	M	0.78344	2.41	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.999;1.0;1.0;1.0	T	0.53287	-0.8460	10	0.87932	D	0	-44.5807	17.9607	0.89084	0.0:0.0:1.0:0.0	.	368;368;368;368;368	A6XGM9;A6XGM2;E7EUE3;A6XGL8;Q8NI51	.;.;.;.;CTCFL_HUMAN	S	368;368;368;368;368;106;368;368;163;368	ENSP00000415579:R368S;ENSP00000243914:R368S;ENSP00000360239:R368S;ENSP00000415329:R368S;ENSP00000392034:R368S;ENSP00000437999:R106S;ENSP00000413713:R368S;ENSP00000403369:R368S;ENSP00000439998:R163S;ENSP00000399061:R368S	ENSP00000243914:R368S	R	-	1	0	CTCFL	55524254	1.000000	0.71417	0.972000	0.41901	0.782000	0.44232	6.387000	0.73191	2.608000	0.88229	0.650000	0.86243	CGC	.	.		0.478	CTCFL-019	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472040.1	NM_080618	
KAL1	3730	hgsc.bcm.edu	37	X	8503661	8503661	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:8503661T>A	ENST00000262648.3	-	12	1962	c.1813A>T	c.(1813-1815)Att>Ttt	p.I605F	KAL1_ENST00000481896.1_5'UTR	NM_000216.2	NP_000207.2	P23352	KALM_HUMAN	Kallmann syndrome 1 sequence	605	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)	extracellular space (GO:0005615)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.I605F(1)		breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|liver(1)|lung(6)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(1)	32						TGTGAAATAATGCTGTTGGGT	0.493																																					p.I605F		Atlas-SNP	.											.	KAL1	78	.	1	Substitution - Missense(1)	lung(1)	c.A1813T						.						171.0	127.0	142.0					X																	8503661		2203	4300	6503	SO:0001583	missense	3730	exon12			AAATAATGCTGTT		CCDS14130.1	Xp22.32	2013-02-11			ENSG00000011201	ENSG00000011201		"""WAP four-disulfide core domain containing"", ""Fibronectin type III domain containing"""	6211	protein-coding gene	gene with protein product	"""anosmin-1"", ""WAP four-disulfide core domain 19"""	300836		KAL, ADMLX		11463336	Standard	NM_000216		Approved	KALIG-1, WFDC19	uc004csf.3	P23352	OTTHUMG00000021107	ENST00000262648.3:c.1813A>T	chrX.hg19:g.8503661T>A	ENSP00000262648:p.Ile605Phe	186.0	0.0		196.0	106.0	NM_000216	B2RPF8	Missense_Mutation	SNP	ENST00000262648.3	hg19	CCDS14130.1	.	.	.	.	.	.	.	.	.	.	T	13.42	2.233337	0.39498	.	.	ENSG00000011201	ENST00000262648	T	0.78707	-1.2	4.43	1.81	0.25067	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055572	0.64402	D	0.000001	T	0.81088	0.4750	L	0.44542	1.39	0.43841	D	0.996423	D	0.69078	0.997	D	0.74348	0.983	T	0.78585	-0.2147	10	0.72032	D	0.01	-22.6232	9.7523	0.40483	0.0:0.0:0.3297:0.6703	.	605	P23352	KALM_HUMAN	F	605	ENSP00000262648:I605F	ENSP00000262648:I605F	I	-	1	0	KAL1	8463661	1.000000	0.71417	0.966000	0.40874	0.112000	0.19704	3.081000	0.50120	-0.004000	0.14419	0.486000	0.48141	ATT	.	.		0.493	KAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055692.1	NM_000216	
PHEX	5251	hgsc.bcm.edu	37	X	22263484	22263484	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:22263484G>A	ENST00000379374.4	+	21	2670	c.2105G>A	c.(2104-2106)cGa>cAa	p.R702Q	PHEX_ENST00000535894.1_Missense_Mutation_p.R605Q|PHEX_ENST00000537599.1_Intron|PHEX_ENST00000418858.3_Missense_Mutation_p.R405Q	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	702					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						GAAGCTGCCCGAGAACAAGTC	0.458																																					p.R702Q		Atlas-SNP	.											.	PHEX	95	.	0			c.G2105A						.						169.0	154.0	159.0					X																	22263484		2203	4300	6503	SO:0001583	missense	5251	exon21			CTGCCCGAGAACA	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"""phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"""	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.2105G>A	chrX.hg19:g.22263484G>A	ENSP00000368682:p.Arg702Gln	106.0	0.0		107.0	11.0	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Missense_Mutation	SNP	ENST00000379374.4	hg19	CCDS14204.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.017292	0.93404	.	.	ENSG00000102174	ENST00000379374;ENST00000535894;ENST00000418858	D;D;D	0.90004	-2.6;-2.6;-2.6	5.82	5.82	0.92795	Peptidase M13, neprilysin, C-terminal (1);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.83257	0.5215	L	0.35793	1.09	0.47862	D	0.999536	P	0.39903	0.694	B	0.33620	0.167	T	0.82432	-0.0460	10	0.28530	T	0.3	-19.6123	17.2568	0.87059	0.0:0.0:1.0:0.0	.	702	P78562	PHEX_HUMAN	Q	702;605;405	ENSP00000368682:R702Q;ENSP00000439418:R605Q;ENSP00000443531:R405Q	ENSP00000368682:R702Q	R	+	2	0	PHEX	22173405	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.354000	0.79424	2.457000	0.83068	0.544000	0.68410	CGA	.	.		0.458	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444	
KCND1	3750	hgsc.bcm.edu	37	X	48823176	48823176	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:48823176C>T	ENST00000218176.3	-	3	2657	c.1360G>A	c.(1360-1362)Ggc>Agc	p.G454S	KCND1_ENST00000376477.1_Missense_Mutation_p.G77S	NM_004979.4	NP_004970.3	Q9NSA2	KCND1_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 1	454					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)	24					Dalfampridine(DB06637)	ACCTCAAGGCCCCCATTCTGC	0.577																																					p.G454S		Atlas-SNP	.											.	KCND1	63	.	0			c.G1360A						.						93.0	79.0	84.0					X																	48823176		2203	4300	6503	SO:0001583	missense	3750	exon3			CAAGGCCCCCATT	AF166003	CCDS14314.1	Xp11.23	2012-07-05			ENSG00000102057	ENSG00000102057		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6237	protein-coding gene	gene with protein product		300281				10729221, 16382104	Standard	NM_004979		Approved	Kv4.1	uc004dlx.1	Q9NSA2	OTTHUMG00000024127	ENST00000218176.3:c.1360G>A	chrX.hg19:g.48823176C>T	ENSP00000218176:p.Gly454Ser	26.0	0.0		28.0	10.0	NM_004979	A6NEF1|B2RCG0|O75671	Missense_Mutation	SNP	ENST00000218176.3	hg19	CCDS14314.1	.	.	.	.	.	.	.	.	.	.	C	9.057	0.993445	0.19043	.	.	ENSG00000102057	ENST00000376477;ENST00000218176	D;D	0.81821	-1.54;-1.54	5.7	4.84	0.62591	Potassium channel, voltage dependent, Kv4, C-terminal (1);	0.195954	0.40640	N	0.001050	T	0.68348	0.2991	L	0.31294	0.92	0.45194	D	0.998201	B	0.14012	0.009	B	0.18263	0.021	T	0.60161	-0.7317	10	0.09338	T	0.73	.	12.7154	0.57111	0.0:0.9172:0.0:0.0828	.	454	Q9NSA2	KCND1_HUMAN	S	77;454	ENSP00000365660:G77S;ENSP00000218176:G454S	ENSP00000218176:G454S	G	-	1	0	KCND1	48708120	0.969000	0.33509	0.989000	0.46669	0.762000	0.43233	1.830000	0.39131	1.157000	0.42530	0.594000	0.82650	GGC	.	.		0.577	KCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060774.1	NM_004979	
ATP7A	538	hgsc.bcm.edu	37	X	77245380	77245380	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:77245380A>G	ENST00000341514.6	+	4	1417	c.1262A>G	c.(1261-1263)tAt>tGt	p.Y421C	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Missense_Mutation_p.Y421C	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	421	HMA 4. {ECO:0000255|PROSITE- ProRule:PRU00280}.				blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ACTGTTGAGTATGATCCTCTA	0.398																																					p.Y421C		Atlas-SNP	.											.	ATP7A	248	.	0			c.A1262G						.						91.0	83.0	86.0					X																	77245380		2203	4296	6499	SO:0001583	missense	538	exon4			TTGAGTATGATCC	L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.1262A>G	chrX.hg19:g.77245380A>G	ENSP00000345728:p.Tyr421Cys	284.0	0.0		258.0	138.0	NM_000052	B1AT72|O00227|O00745|Q9BYY8	Missense_Mutation	SNP	ENST00000341514.6	hg19	CCDS35339.1	.	.	.	.	.	.	.	.	.	.	A	15.32	2.797715	0.50208	.	.	ENSG00000165240	ENST00000343533;ENST00000341514;ENST00000355691	D;D	0.86497	-2.13;-2.13	5.77	3.19	0.36642	Heavy metal-associated domain, HMA (3);Heavy metal-associated domain, copper ion-binding (1);	0.202249	0.44285	D	0.000467	D	0.94248	0.8153	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.97110	0.969;1.0	D	0.93978	0.7255	10	0.87932	D	0	-0.7507	10.2368	0.43288	0.7332:0.0:0.0:0.2668	.	421;431	Q04656;Q59HD1	ATP7A_HUMAN;.	C	421;421;431	ENSP00000343026:Y421C;ENSP00000345728:Y421C	ENSP00000345728:Y421C	Y	+	2	0	ATP7A	77132036	1.000000	0.71417	0.996000	0.52242	0.954000	0.61252	4.210000	0.58500	0.780000	0.33566	0.481000	0.45027	TAT	.	.		0.398	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1	NM_000052	
CXorf57	55086	hgsc.bcm.edu	37	X	105879772	105879772	+	Splice_Site	SNP	G	G	T			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chrX:105879772G>T	ENST00000372548.4	+	7	1412		c.e7-1		CXorf57_ENST00000372544.2_Splice_Site	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57								poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						TTGTTCTCTAGTGGCATATTT	0.343																																					.		Atlas-SNP	.											.	CXorf57	107	.	0			c.1304-1G>T						.						146.0	131.0	136.0					X																	105879772		2203	4299	6502	SO:0001630	splice_region_variant	55086	exon7			TCTCTAGTGGCAT	AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.1304-1G>T	chrX.hg19:g.105879772G>T		64.0	0.0		74.0	39.0	NM_001184782	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Splice_Site	SNP	ENST00000372548.4	hg19	CCDS14519.1	.	.	.	.	.	.	.	.	.	.	g	10.31	1.314334	0.23908	.	.	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	.	.	.	4.33	4.33	0.51752	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.3433	0.60557	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CXorf57	105766428	1.000000	0.71417	0.725000	0.30721	0.210000	0.24377	5.358000	0.66064	2.083000	0.62718	0.425000	0.28330	.	.	.		0.343	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015	Intron
RPP14	11102	hgsc.bcm.edu	37	3	58303188	58303189	+	Frame_Shift_Del	DEL	TT	TT	-			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr3:58303188_58303189delTT	ENST00000445193.3	+	6	751_752	c.340_341delTT	c.(340-342)ttafs	p.L114fs	RPP14_ENST00000466547.1_Frame_Shift_Del_p.L114fs|RPP14_ENST00000295959.5_Frame_Shift_Del_p.L114fs|RPP14_ENST00000477305.1_3'UTR|RPP14_ENST00000528153.1_5'Flank	NM_001098783.2	NP_001092253.1	O95059	RPP14_HUMAN	ribonuclease P/MRP 14kDa subunit	114					tRNA processing (GO:0008033)	nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)|RNA binding (GO:0003723)			large_intestine(2)|lung(1)	3				BRCA - Breast invasive adenocarcinoma(55;0.000187)|KIRC - Kidney renal clear cell carcinoma(10;0.0102)|Kidney(10;0.0118)|OV - Ovarian serous cystadenocarcinoma(275;0.191)		TCTTCTTGCATTATCTGGTAAT	0.391																																					p.113_114del		Atlas-Indel,Pindel	.											.	RPP14	6	.	0			c.339_340del						.																																			SO:0001589	frameshift_variant	11102	exon6			.	AF001175	CCDS2888.1	3p21.2	2012-05-21	2007-06-26		ENSG00000163684	ENSG00000163684			30327	protein-coding gene	gene with protein product		606112	"""ribonuclease P 14kDa subunit"""			10024167, 11929972	Standard	NM_001098783		Approved	P14	uc031sah.1	O95059	OTTHUMG00000159152	ENST00000445193.3:c.340_341delTT	chr3.hg19:g.58303188_58303189delTT	ENSP00000412894:p.Leu114fs	57.0	0.0		89.0	20.0	NM_007042	Q53X97	Frame_Shift_Del	DEL	ENST00000445193.3	hg19	CCDS2888.1																																																																																			.	.		0.391	RPP14-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353527.2	NM_007042	
NEFH	4744	hgsc.bcm.edu	37	22	29885585	29885586	+	In_Frame_Ins	INS	-	-	AAGTCCCCTGAGAAGGCC	rs200984527|rs267607533		TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr22:29885585_29885586insAAGTCCCCTGAGAAGGCC	ENST00000310624.6	+	4	1989_1990	c.1956_1957insAAGTCCCCTGAGAAGGCC	c.(1957-1959)aag>AAGTCCCCTGAGAAGGCCaag	p.653_653K>KSPEKAK		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	659	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)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CTGAGAAGGCCAAGTCCCCAGA	0.564																																					p.A652delinsAKSPEKA		Atlas-INDEL	.											.,1	NEFH	178	.	0			c.1956_1957insAAGTCCCCTGAGAAGGCC						.																																			SO:0001652	inframe_insertion	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.1939_1956dupAAGTCCCCTGAGAAGGCC	chr22.hg19:g.29885585_29885586insAAGTCCCCTGAGAAGGCC	ENSP00000311997:p.SerProGluLysAlaLys653dup	247.0	0.0		274.0	136.0	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	hg19	CCDS13858.1																																																																																			.	.		0.564	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
AFF4	27125	hgsc.bcm.edu	37	5	132216770	132216771	+	Frame_Shift_Ins	INS	-	-	C			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:132216770_132216771insC	ENST00000265343.5	-	21	3851_3852	c.3472_3473insG	c.(3472-3474)gatfs	p.D1158fs		NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	1158					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			CAACTTGGCATCCTGGCGAAGC	0.46																																					p.D1158fs	Ovarian(126;889 1733 2942 10745 11605)	Atlas-Indel,Pindel	.											.	AFF4	120	.	0			c.3473_3474insG						.																																			SO:0001589	frameshift_variant	27125	exon21			.	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.3473dupG	chr5.hg19:g.132216772_132216772dupC	ENSP00000265343:p.Asp1158fs	190.0	0.0		212.0	47.0	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Frame_Shift_Ins	INS	ENST00000265343.5	hg19	CCDS4164.1																																																																																			.	.		0.460	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
PCDHB14	56122	hgsc.bcm.edu	37	5	140603901	140603910	+	Frame_Shift_Del	DEL	GAAAAATATC	GAAAAATATC	-			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	GAAAAATATC	GAAAAATATC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr5:140603901_140603910delGAAAAATATC	ENST00000239449.4	+	1	824_833	c.824_833delGAAAAATATC	c.(823-834)ggaaaaatatctfs	p.GKIS275fs	PCDHB14_ENST00000515856.2_Frame_Shift_Del_p.GKIS122fs	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	275	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAAACTATGGAAAAATATCTTACACATTT	0.414																																					p.275_278del	Ovarian(141;50 1831 27899 33809 37648)	Atlas-Indel,Pindel	.											.	PCDHB14	132	.	0			c.823_832del						.																																			SO:0001589	frameshift_variant	56122	exon1			.	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.824_833delGAAAAATATC	chr5.hg19:g.140603901_140603910delGAAAAATATC	ENSP00000239449:p.Gly275fs	102.0	0.0		87.0	17.0	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Frame_Shift_Del	DEL	ENST00000239449.4	hg19	CCDS4256.1																																																																																			.	.		0.414	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
USH2A	7399	hgsc.bcm.edu	37	1	216595468	216595469	+	In_Frame_Ins	INS	-	-	AGA			TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr1:216595468_216595469insAGA	ENST00000307340.3	-	2	596_597	c.210_211insTCT	c.(208-213)tctgct>tctTCTgct	p.70_71insS	USH2A_ENST00000366942.3_In_Frame_Ins_p.70_71insS|USH2A_ENST00000366943.2_In_Frame_Ins_p.70_71insS	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	70					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)		TCAGCAGCAGCAGAGCTGTGAC	0.5										HNSCC(13;0.011)																											p.A71delinsSA		Atlas-Indel,Pindel	.											.	USH2A	1168	.	0			c.211_212insTCT						.																																			SO:0001652	inframe_insertion	7399	exon2			.	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.208_210dupTCT	chr1.hg19:g.216595469_216595471dupAGA	ENSP00000305941:p.Ser70_Ser70dup	142.0	0.0		244.0	109.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	In_Frame_Ins	INS	ENST00000307340.3	hg19	CCDS31025.1																																																																																			.	.		0.500	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
ZNF626	199777	hgsc.bcm.edu	37	19	20807134	20807300	+	Frame_Shift_Del	DEL	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	-	rs200411264|rs4808252|rs4808251|rs190319020|rs4809071|rs4809072|rs547337333|rs76605719|rs10408597|rs71332197|rs549423118|rs78715171|rs4808250|rs376295094|rs78217174|rs375690494|rs35575803|rs71174721	byFrequency	TCGA-DD-AAC9-01A-11D-A40R-10	TCGA-DD-AAC9-10A-01D-A40U-10	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	GCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	4211b22d-de83-4dba-b4f6-846ab2aeba13	c2e6366d-0283-4200-b9eb-0f2a11942592	g.chr19:20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENST00000601440.1	-	4	1529_1695	c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	c.(1381-1551)gcttttaagtgctcctctaaccttactacacataagaaaattcatactggagagagaccctacaaatgtgaagaatgtggcaaagccttcaaccagtcctcaatccttactacacatgagagaatcatactggagagaaattctacaaatgtgaagaatgtggcaaagcctfs	p.FKCSSNLTTHKKIHTGERPYKCEECGKAFNQSSILTTHERIILERNSTNVKNVAKP462fs	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	462					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.K473R(2)|p.E484K(1)|p.I502F(1)		breast(1)|endometrium(1)|lung(3)|skin(1)	6						CCGCTTGAAGGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAAGCTTTGCCAC	0.384																																					p.462_517del		Pindel	.											.	ZNF626	121	.	4	Substitution - Missense(4)	lung(3)|central_nervous_system(1)	c.1384_1550del						.																																			SO:0001589	frameshift_variant	199777	exon4			.	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.1383_1549delTTTTAAGTGCTCCTCTAACCTTACTACACATAAGAAAATTCATACTGGAGAGAGACCCTACAAATGTGAAGAATGTGGCAAAGCCTTCAACCAGTCCTCAATCCTTACTACACATGAGAGAATCATACTGGAGAGAAATTCTACAAATGTGAAGAATGTGGCAAAGC	chr19.hg19:g.20807134_20807300delGCTTTGCCACATTCTTCACATTTGTAGAATTTCTCTCCAGTATGATTCTCTCATGTGTAGTAAGGATTGAGGACTGGTTGAAGGCTTTGCCACATTCTTCACATTTGTAGGGTCTCTCTCCAGTATGAATTTTCTTATGTGTAGTAAGGTTAGAGGAGCACTTAAAA	ENSP00000469958:p.Phe462fs	29.0	0.0		23.0	10.0	NM_001076675	Q8N8T4|Q96QM1	Frame_Shift_Del	DEL	ENST00000601440.1	hg19	CCDS42535.1																																																																																			.	.		0.384	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
