#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_Confidence	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_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	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_dbSNP_PopFreq	i_dbSNP_Strength	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
MFN2	9927	hgsc.bcm.edu	37	1	12052714	12052714	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:12052714C>T	ENST00000235329.5	+	4	600	c.278C>T	c.(277-279)gCt>gTt	p.A93V	MFN2_ENST00000444836.1_Missense_Mutation_p.A93V	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	93	Dynamin-type G.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		GAGGTGCTGGCTCGGAGGCAC	0.527																																					p.A93V		Atlas-SNP	.											.	MFN2	83	.	0			c.C278T						PASS	.						242.0	220.0	228.0					1																	12052714		2203	4300	6503	SO:0001583	missense	9927	exon4			TGCTGGCTCGGAG	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.278C>T	chr1.hg19:g.12052714C>T	ENSP00000235329:p.Ala93Val	169.0	0.0	.		153.0	29.0	.	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Missense_Mutation	SNP	ENST00000235329.5	hg19	CCDS30587.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.498702	0.64298	.	.	ENSG00000116688	ENST00000444836;ENST00000235329;ENST00000412236	D;D;D	0.95482	-3.72;-3.72;-3.63	5.5	5.5	0.81552	.	0.106729	0.64402	D	0.000006	D	0.93452	0.7911	L	0.50333	1.59	0.80722	D	1	B	0.20671	0.047	B	0.16289	0.015	D	0.90115	0.4195	10	0.32370	T	0.25	-25.6319	18.3893	0.90477	0.0:1.0:0.0:0.0	.	93	O95140	MFN2_HUMAN	V	93	ENSP00000416338:A93V;ENSP00000235329:A93V;ENSP00000412023:A93V	ENSP00000235329:A93V	A	+	2	0	MFN2	11975301	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.487000	0.81328	2.588000	0.87417	0.561000	0.74099	GCT	.	.	.	none		0.527	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874	
SRSF4	6429	hgsc.bcm.edu	37	1	29486974	29486974	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:29486974G>C	ENST00000373795.4	-	2	397	c.163C>G	c.(163-165)Ctg>Gtg	p.L55V	SRSF4_ENST00000546138.1_Missense_Mutation_p.L55V|SRSF4_ENST00000466448.1_5'UTR	NM_005626.4	NP_005617.2	Q08170	SRSF4_HUMAN	serine/arginine-rich splicing factor 4	55	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(1)	27						TTGCCATTCAGTTCATAAACA	0.458																																					p.L55V		Atlas-SNP	.											.	SRSF4	44	.	0			c.C163G						PASS	.						191.0	166.0	175.0					1																	29486974		2203	4300	6503	SO:0001583	missense	6429	exon2			CATTCAGTTCATA	BC002781	CCDS333.1	1p35.3	2013-02-12	2010-06-22	2010-06-22	ENSG00000116350	ENSG00000116350		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10786	protein-coding gene	gene with protein product	"""SR splicing factor 4"""	601940	"""splicing factor, arginine/serine-rich 4"""	SFRS4		8321209, 20516191	Standard	NM_005626		Approved	SRP75	uc001bro.3	Q08170	OTTHUMG00000003663	ENST00000373795.4:c.163C>G	chr1.hg19:g.29486974G>C	ENSP00000362900:p.Leu55Val	184.0	0.0	.		205.0	33.0	.	NM_005626	Q5VXP1|Q9BUA4|Q9UEB5	Missense_Mutation	SNP	ENST00000373795.4	hg19	CCDS333.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678755	0.47886	.	.	ENSG00000116350	ENST00000373795;ENST00000434636;ENST00000546138	T;T	0.80653	1.82;-1.4	5.23	3.34	0.38264	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.070031	0.64402	D	0.000017	D	0.86318	0.5904	M	0.74258	2.255	0.54753	D	0.999987	D;D	0.67145	0.995;0.996	D;D	0.72982	0.947;0.979	D	0.85670	0.1294	10	0.87932	D	0	.	6.2158	0.20653	0.1568:0.0:0.6966:0.1466	.	55;55	F6T1J1;Q08170	.;SRSF4_HUMAN	V	55	ENSP00000362900:L55V;ENSP00000444600:L55V	ENSP00000362900:L55V	L	-	1	2	SRSF4	29359561	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.066000	0.50002	1.203000	0.43233	0.561000	0.74099	CTG	.	.	.	none		0.458	SRSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010392.1	NM_005626	
FAM151A	338094	hgsc.bcm.edu	37	1	55080373	55080373	+	Splice_Site	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:55080373T>C	ENST00000302250.2	-	4	735	c.575A>G	c.(574-576)cAg>cGg	p.Q192R	ACOT11_ENST00000371316.3_Intron|FAM151A_ENST00000371304.2_Splice_Site_p.Q192R	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	192						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						GAACACTCACTGTGTGGCATT	0.542																																					p.Q192R		Atlas-SNP	.											.	FAM151A	58	.	0			c.A575G						PASS	.						129.0	100.0	110.0					1																	55080373		2203	4300	6503	SO:0001630	splice_region_variant	338094	exon4			ACTCACTGTGTGG	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.575+1A>G	chr1.hg19:g.55080373T>C		136.0	0.0	.		127.0	24.0	.	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Missense_Mutation	SNP	ENST00000302250.2	hg19	CCDS594.1	.	.	.	.	.	.	.	.	.	.	T	5.034	0.191930	0.09547	.	.	ENSG00000162391	ENST00000302250;ENST00000371304;ENST00000294370	T;T	0.10960	2.82;2.82	3.7	-0.227	0.13102	.	0.539876	0.18021	N	0.154258	T	0.05044	0.0135	N	0.12663	0.25	0.58432	D	0.999999	B	0.15141	0.012	B	0.18561	0.022	T	0.43376	-0.9395	9	.	.	.	-4.4951	8.1077	0.30896	0.0:0.4413:0.0:0.5587	.	192	Q8WW52	F151A_HUMAN	R	192	ENSP00000306888:Q192R;ENSP00000360353:Q192R	.	Q	-	2	0	FAM151A	54852961	0.001000	0.12720	0.846000	0.33378	0.520000	0.34377	-0.605000	0.05661	-0.116000	0.11893	0.379000	0.24179	CAG	.	.	.	none		0.542	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	Missense_Mutation
SLC44A5	204962	hgsc.bcm.edu	37	1	75669452	75669452	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:75669452T>A	ENST00000370859.3	-	24	2259	c.2114A>T	c.(2113-2115)aAg>aTg	p.K705M		NM_001130058.1	NP_001123530.1	Q8NCS7	CTL5_HUMAN	solute carrier family 44, member 5	705					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				kidney(1)|large_intestine(13)|lung(35)|ovary(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61						CTGGAAAATCTTCAGCAAAGG	0.408																																					p.K705M		Atlas-SNP	.											.	SLC44A5	231	.	0			c.A2114T						PASS	.						203.0	201.0	202.0					1																	75669452		692	1591	2283	SO:0001583	missense	204962	exon24			AAAATCTTCAGCA	BC034580	CCDS667.1, CCDS44164.1	1p31.1	2013-05-22			ENSG00000137968	ENSG00000137968		"""Solute carriers"""	28524	protein-coding gene	gene with protein product						15715662	Standard	NM_152697		Approved	MGC34032, CTL5	uc001dgu.3	Q8NCS7	OTTHUMG00000009721	ENST00000370859.3:c.2114A>T	chr1.hg19:g.75669452T>A	ENSP00000359896:p.Lys705Met	82.0	0.0	.		89.0	15.0	.	NM_001130058	B5MCU3|Q4G0K0|Q8NA44|Q8NB86	Missense_Mutation	SNP	ENST00000370859.3	hg19	CCDS44164.1	.	.	.	.	.	.	.	.	.	.	T	14.64	2.595748	0.46318	.	.	ENSG00000137968	ENST00000370859;ENST00000536707	T	0.12255	2.7	5.53	5.53	0.82687	.	.	.	.	.	T	0.28034	0.0691	M	0.77616	2.38	0.80722	D	1	D;P;D	0.60160	0.987;0.868;0.984	P;P;P	0.62649	0.806;0.729;0.905	T	0.03278	-1.1053	9	0.59425	D	0.04	.	15.9488	0.79817	0.0:0.0:0.0:1.0	.	744;705;744	B7Z470;Q8NCS7-2;F5GYS0	.;.;.	M	705;744	ENSP00000359896:K705M	ENSP00000359896:K705M	K	-	2	0	SLC44A5	75442040	0.843000	0.29541	0.999000	0.59377	0.388000	0.30384	1.986000	0.40677	2.227000	0.72691	0.533000	0.62120	AAG	.	.	.	none		0.408	SLC44A5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000026823.3	NM_152697	
HENMT1	113802	hgsc.bcm.edu	37	1	109192980	109192980	+	Silent	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:109192980G>A	ENST00000370032.5	-	7	1029	c.609C>T	c.(607-609)taC>taT	p.Y203Y	HENMT1_ENST00000402983.1_Silent_p.Y203Y|HENMT1_ENST00000493676.1_5'UTR|HENMT1_ENST00000370031.1_Silent_p.Y203Y	NM_144584.2	NP_653185.2	Q5T8I9	HENMT_HUMAN	HEN1 methyltransferase homolog 1 (Arabidopsis)	203					gene silencing by RNA (GO:0031047)|piRNA metabolic process (GO:0034587)|RNA methylation (GO:0001510)	P granule (GO:0043186)	metal ion binding (GO:0046872)|O-methyltransferase activity (GO:0008171)|RNA binding (GO:0003723)|RNA methyltransferase activity (GO:0008173)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(2)|stomach(1)	16						ACTCCACAGAGTAATCATAGC	0.423																																					p.Y203Y		Atlas-SNP	.											.	HENMT1	38	.	0			c.C609T						PASS	.						91.0	85.0	87.0					1																	109192980		2203	4300	6503	SO:0001819	synonymous_variant	113802	exon7			CACAGAGTAATCA		CCDS787.1	1p13.3	2011-01-28	2011-01-28	2011-01-28	ENSG00000162639	ENSG00000162639			26400	protein-coding gene	gene with protein product	"""HEN1 methyltransferase homolog (Arabidopsis)"""	612178	"""chromosome 1 open reading frame 59"""	C1orf59			Standard	NM_144584		Approved	FLJ30525, HEN1	uc001dvt.4	Q5T8I9	OTTHUMG00000011123	ENST00000370032.5:c.609C>T	chr1.hg19:g.109192980G>A		84.0	0.0	.		85.0	15.0	.	NM_144584	A8MRR6|B1AM16|B1AM17|Q96EJ7|Q96NN0	Silent	SNP	ENST00000370032.5	hg19	CCDS787.1																																																																																			.	.	.	none		0.423	HENMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030592.1	NM_144584	
ASH1L	55870	hgsc.bcm.edu	37	1	155449729	155449729	+	Silent	SNP	A	A	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:155449729A>G	ENST00000368346.3	-	3	3571	c.2932T>C	c.(2932-2934)Tta>Cta	p.L978L	ASH1L_ENST00000392403.3_Silent_p.L978L			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	978					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			GTTTTCATTAATTGTCCATTG	0.323																																					p.L978L		Atlas-SNP	.											.	ASH1L	279	.	0			c.T2932C						PASS	.						62.0	64.0	63.0					1																	155449729		2202	4300	6502	SO:0001819	synonymous_variant	55870	exon3			TCATTAATTGTCC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.2932T>C	chr1.hg19:g.155449729A>G		55.0	0.0	.		57.0	12.0	.	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Silent	SNP	ENST00000368346.3	hg19																																																																																				.	.	.	none		0.323	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
LMNA	4000	hgsc.bcm.edu	37	1	156105104	156105104	+	Splice_Site	SNP	G	G	A	rs267607588		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:156105104G>A	ENST00000368300.4	+	5	1148		c.e5+1		LMNA_ENST00000448611.2_Splice_Site|LMNA_ENST00000392353.3_Splice_Site|LMNA_ENST00000368297.1_Splice_Site|LMNA_ENST00000368301.2_Splice_Site|LMNA_ENST00000368299.3_Splice_Site|LMNA_ENST00000361308.4_Splice_Site|LMNA_ENST00000496738.1_Splice_Site|LMNA_ENST00000473598.2_Splice_Site|LMNA_ENST00000347559.2_Splice_Site	NM_170707.3	NP_733821.1	P02545	LMNA_HUMAN	lamin A/C						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular protein metabolic process (GO:0044267)|cellular response to hypoxia (GO:0071456)|endoplasmic reticulum unfolded protein response (GO:0030968)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic nuclear envelope reassembly (GO:0007084)|muscle organ development (GO:0007517)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|positive regulation of cell aging (GO:0090343)|protein localization to nucleus (GO:0034504)|regulation of cell migration (GO:0030334)|regulation of protein localization to nucleus (GO:1900180)|sterol regulatory element binding protein import into nucleus (GO:0035105)|ventricular cardiac muscle cell development (GO:0055015)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|lamin filament (GO:0005638)|nuclear envelope (GO:0005635)|nuclear lamina (GO:0005652)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|lung(3)|ovary(4)	10	Hepatocellular(266;0.158)					CCAGAAGCAGGTGATACCCCA	0.672									Werner syndrome;Hutchinson-Gilford Progeria Syndrome																												.		Atlas-SNP	.											.	LMNA	31	.	0			c.936+1G>A						PASS	.						22.0	25.0	24.0					1																	156105104		2202	4299	6501	SO:0001630	splice_region_variant	4000	exon5	Familial Cancer Database	WS, Adult Progeria;HGPS, Progeria	AAGCAGGTGATAC	BC014507	CCDS1129.1, CCDS1131.1, CCDS58038.1, CCDS72941.1, CCDS72942.1	1q22	2014-09-17			ENSG00000160789	ENSG00000160789		"""Intermediate filaments type V, lamins"""	6636	protein-coding gene	gene with protein product		150330	"""cardiomyopathy, dilated 1A (autosomal dominant)"", ""limb girdle muscular dystrophy 1B (autosomal dominant)"", ""progeria 1 (Hutchinson-Gilford type)"", ""lamin A/C-like 1"""	LMN1, CMD1A, LGMD1B, PRO1, LMNL1		8511676, 8838815, 12702809	Standard	NM_005572		Approved	HGPS	uc001fni.3	P02545	OTTHUMG00000013961	ENST00000368300.4:c.936+1G>A	chr1.hg19:g.156105104G>A		147.0	0.0	.		165.0	34.0	.	NM_170707	B4DI32|D3DVB0|D6RAQ3|E7EUI9|P02546|Q5I6Y4|Q5I6Y6|Q5TCJ2|Q5TCJ3|Q6UYC3|Q969I8|Q96JA2	Splice_Site	SNP	ENST00000368300.4	hg19	CCDS1129.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186744	0.78789	.	.	ENSG00000160789	ENST00000368301;ENST00000347559;ENST00000361308;ENST00000368300;ENST00000368299;ENST00000292302;ENST00000392355;ENST00000448611;ENST00000368297;ENST00000473598;ENST00000392353	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.1117	0.86676	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	LMNA	154371728	1.000000	0.71417	0.999000	0.59377	0.821000	0.46438	9.781000	0.99029	2.653000	0.90120	0.563000	0.77884	.	.	.	.	alt		0.672	LMNA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039200.2	NM_170707	Intron
IQGAP3	128239	hgsc.bcm.edu	37	1	156510499	156510499	+	Splice_Site	SNP	C	C	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:156510499C>A	ENST00000361170.2	-	23	2750		c.e23+1		IQGAP3_ENST00000498755.1_5'Flank	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3						activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGGCCCCATACCTGCAGAGTG	0.512																																					.		Atlas-SNP	.											.	IQGAP3	146	.	0			c.2739+1G>T						PASS	.						149.0	101.0	117.0					1																	156510499		2203	4300	6503	SO:0001630	splice_region_variant	128239	exon24			CCCATACCTGCAG	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.2739+1G>T	chr1.hg19:g.156510499C>A		86.0	0.0	.		64.0	10.0	.	NM_178229	Q5T3H8	Splice_Site	SNP	ENST00000361170.2	hg19	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	C	17.08	3.297384	0.60086	.	.	ENSG00000183856	ENST00000361170	.	.	.	4.71	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.1956	0.73084	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	IQGAP3	154777123	1.000000	0.71417	1.000000	0.80357	0.555000	0.35460	7.633000	0.83260	2.435000	0.82474	0.591000	0.81541	.	.	.	.	none		0.512	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	Intron
DNAH14	127602	hgsc.bcm.edu	37	1	225267022	225267022	+	Silent	SNP	A	A	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:225267022A>G	ENST00000445597.2	+	14	2340	c.2340A>G	c.(2338-2340)aaA>aaG	p.K780K	DNAH14_ENST00000439375.2_Silent_p.K846K|DNAH14_ENST00000430092.1_Silent_p.K846K			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	780					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AATTAGAAAAAGAGTTCTTAA	0.333																																					p.K846K		Atlas-SNP	.											DNAH14_ENST00000430092,NS,carcinoma,0,2	DNAH14	300	.	0			c.A2538G						PASS	.						73.0	61.0	65.0					1																	225267022		692	1590	2282	SO:0001819	synonymous_variant	127602	exon18			AGAAAAAGAGTTC	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.2340A>G	chr1.hg19:g.225267022A>G		281.0	0.0	.		293.0	51.0	.	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Silent	SNP	ENST00000445597.2	hg19																																																																																				.	.	.	none		0.333	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
RSAD2	91543	hgsc.bcm.edu	37	2	7035978	7035978	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:7035978G>A	ENST00000382040.3	+	6	1127	c.991G>A	c.(991-993)Gaa>Aaa	p.E331K	RSAD2_ENST00000541728.1_Missense_Mutation_p.E224K	NM_080657.4	NP_542388.2			radical S-adenosyl methionine domain containing 2											endometrium(1)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(1)	20	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			OV - Ovarian serous cystadenocarcinoma(76;0.191)		TGGTGTAGAAGAAGCTATAAA	0.413																																					p.E331K		Atlas-SNP	.											.	RSAD2	38	.	0			c.G991A						PASS	.						86.0	83.0	84.0					2																	7035978		2203	4300	6503	SO:0001583	missense	91543	exon6			GTAGAAGAAGCTA	AF442151	CCDS1656.1	2p25.2	2008-02-05			ENSG00000134321	ENSG00000134321			30908	protein-coding gene	gene with protein product		607810				11752458	Standard	NM_080657		Approved	cig5, viperin, vig1	uc002qyp.1	Q8WXG1	OTTHUMG00000090352	ENST00000382040.3:c.991G>A	chr2.hg19:g.7035978G>A	ENSP00000371471:p.Glu331Lys	113.0	0.0	.		96.0	19.0	.	NM_080657		Missense_Mutation	SNP	ENST00000382040.3	hg19	CCDS1656.1	.	.	.	.	.	.	.	.	.	.	G	11.75	1.730833	0.30684	.	.	ENSG00000134321	ENST00000382040;ENST00000541728	T	0.29397	1.57	5.57	4.67	0.58626	.	0.234163	0.49916	N	0.000122	T	0.17662	0.0424	N	0.19112	0.55	0.40643	D	0.981964	B	0.06786	0.001	B	0.08055	0.003	T	0.08330	-1.0727	10	0.13108	T	0.6	-20.1755	10.0238	0.42059	0.0715:0.1391:0.7894:0.0	.	331	Q8WXG1	RSAD2_HUMAN	K	331;224	ENSP00000371471:E331K	ENSP00000371471:E331K	E	+	1	0	RSAD2	6953429	0.982000	0.34865	0.642000	0.29436	0.977000	0.68977	1.644000	0.37228	1.459000	0.47892	0.655000	0.94253	GAA	.	.	.	none		0.413	RSAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206724.2	NM_080657	
SRSF7	6432	hgsc.bcm.edu	37	2	38977271	38977271	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:38977271T>C	ENST00000313117.6	-	2	331	c.94A>G	c.(94-96)Agt>Ggt	p.S32G	SRSF7_ENST00000409276.1_Missense_Mutation_p.S32G|SRSF7_ENST00000446327.2_Missense_Mutation_p.S32G|GEMIN6_ENST00000409011.1_5'Flank	NM_001031684.2|NM_001195446.1	NP_001026854.1|NP_001182375.1	Q16629	SRSF7_HUMAN	serine/arginine-rich splicing factor 7	32	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						CCATAATAACTGAAAGCCCTT	0.428																																					p.S32G		Atlas-SNP	.											SRSF7,NS,carcinoma,0,1	SRSF7	29	.	0			c.A94G						PASS	.						117.0	114.0	115.0					2																	38977271		2203	4300	6503	SO:0001583	missense	6432	exon2			AATAACTGAAAGC	L41887	CCDS33183.1, CCDS56115.1	2p22.1	2013-02-12	2010-06-22	2010-06-22	ENSG00000115875	ENSG00000115875		"""Zinc fingers, CCHC domain containing"", ""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10789	protein-coding gene	gene with protein product	"""SR splicing factor 7"""	600572	"""splicing factor, arginine/serine-rich 7 (35kD)"", ""splicing factor, arginine/serine-rich 7, 35kDa"""	SFRS7		8013463, 20516191	Standard	NM_001031684		Approved	9G8, ZCRB2, HSSG1, AAG3, RBM37, ZCCHC20	uc002rqz.3	Q16629	OTTHUMG00000102076	ENST00000313117.6:c.94A>G	chr2.hg19:g.38977271T>C	ENSP00000325905:p.Ser32Gly	127.0	2.0	.		114.0	15.0	.	NM_001195446	B4DLU6|G5E9M3|Q564D3	Missense_Mutation	SNP	ENST00000313117.6	hg19	CCDS33183.1	.	.	.	.	.	.	.	.	.	.	T	6.752	0.507676	0.12883	.	.	ENSG00000115875	ENST00000313117;ENST00000446327;ENST00000409276	T;T;T	0.17854	2.25;2.25;2.25	6.07	6.07	0.98685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	T	0.10937	0.0267	N	0.05158	-0.105	0.80722	D	1	B;B	0.14438	0.008;0.01	B;B	0.20184	0.017;0.028	T	0.19745	-1.0296	10	0.36615	T	0.2	.	16.6407	0.85098	0.0:0.0:0.0:1.0	.	32;32	G5E9M3;Q16629	.;SRSF7_HUMAN	G	32	ENSP00000325905:S32G;ENSP00000402264:S32G;ENSP00000386806:S32G	ENSP00000325905:S32G	S	-	1	0	SRSF7	38830775	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.754000	0.47532	2.326000	0.78906	0.533000	0.62120	AGT	.	.	.	none		0.428	SRSF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219889.2	NM_001031684	
SLC8A1	6546	hgsc.bcm.edu	37	2	40657412	40657412	+	Silent	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:40657412G>A	ENST00000403092.1	-	2	42	c.9C>T	c.(7-9)aaC>aaT	p.N3N	SLC8A1_ENST00000402441.1_Silent_p.N3N|SLC8A1_ENST00000405269.1_Silent_p.N3N|SLC8A1_ENST00000542024.1_Silent_p.N3N|SLC8A1_ENST00000406785.2_Silent_p.N3N|SLC8A1_ENST00000332839.4_Silent_p.N3N|SLC8A1_ENST00000406391.2_Silent_p.N3N|SLC8A1_ENST00000405901.3_Silent_p.N3N|SLC8A1_ENST00000542756.1_Silent_p.N3N|SLC8A1_ENST00000408028.2_Silent_p.N3N			P32418	NAC1_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 1	3					blood coagulation (GO:0007596)|calcium ion export (GO:1901660)|calcium ion homeostasis (GO:0055074)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|cardiac muscle cell development (GO:0055013)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to caffeine (GO:0071313)|cellular response to reactive oxygen species (GO:0034614)|cellular sodium ion homeostasis (GO:0006883)|cytosolic calcium ion transport (GO:0060401)|embryonic heart tube development (GO:0035050)|embryonic placenta development (GO:0001892)|heart morphogenesis (GO:0003007)|ion transport (GO:0006811)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|muscle contraction (GO:0006936)|muscle fiber development (GO:0048747)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|post-embryonic development (GO:0009791)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|relaxation of smooth muscle (GO:0044557)|sodium ion export (GO:0071436)|sodium ion import (GO:0097369)|transmembrane transport (GO:0055085)|vascular smooth muscle contraction (GO:0014829)	basolateral plasma membrane (GO:0016323)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|calcium:sodium antiporter activity (GO:0005432)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|liver(1)|lung(57)|ovary(2)|pancreas(1)|skin(7)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(2)	100					Alpha-Linolenic Acid(DB00132)|Icosapent(DB00159)	ATCGCCGCATGTTGTACATGA	0.418																																					p.N3N		Atlas-SNP	.											.	SLC8A1	221	.	0			c.C9T						PASS	.						60.0	56.0	58.0					2																	40657412		2203	4300	6503	SO:0001819	synonymous_variant	6546	exon1			CCGCATGTTGTAC		CCDS1806.1, CCDS46264.1, CCDS46265.1, CCDS59430.1	2p22.1	2013-07-15			ENSG00000183023	ENSG00000183023		"""Solute carriers"""	11068	protein-coding gene	gene with protein product	"""Na+/Ca++ exchanger"""	182305		NCX1		1559714	Standard	NM_021097		Approved		uc002rrx.3	P32418	OTTHUMG00000102183	ENST00000403092.1:c.9C>T	chr2.hg19:g.40657412G>A		66.0	0.0	.		66.0	18.0	.	NM_001252624	A8K6N1|D6W595|O95849|Q4QQG6|Q587I6|Q59GN4|Q9UBL8|Q9UD55|Q9UDN1|Q9UDN2|Q9UKX6	Silent	SNP	ENST00000403092.1	hg19	CCDS1806.1																																																																																			.	.	.	none		0.418	SLC8A1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326065.1	NM_021097	
THNSL2	55258	hgsc.bcm.edu	37	2	88474889	88474889	+	Silent	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:88474889G>A	ENST00000324166.5	+	3	2231	c.540G>A	c.(538-540)acG>acA	p.T180T	THNSL2_ENST00000402102.1_Silent_p.T180T|THNSL2_ENST00000343544.4_Silent_p.T180T|THNSL2_ENST00000449349.1_Silent_p.T148T|THNSL2_ENST00000358591.2_Silent_p.T180T|THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000377254.3_Silent_p.T180T	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	180					2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)			breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						AGATGACAACGGTGCTGAAGC	0.517																																					p.T180T		Atlas-SNP	.											.	THNSL2	66	.	0			c.G540A						PASS	.						154.0	112.0	126.0					2																	88474889		2203	4300	6503	SO:0001819	synonymous_variant	55258	exon3			GACAACGGTGCTG		CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.540G>A	chr2.hg19:g.88474889G>A		189.0	0.0	.		187.0	28.0	.	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Silent	SNP	ENST00000324166.5	hg19	CCDS2002.2																																																																																			.	.	.	none		0.517	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271	
AFF3	3899	hgsc.bcm.edu	37	2	100266104	100266104	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:100266104G>C	ENST00000409236.2	-	11	1280	c.1168C>G	c.(1168-1170)Cgc>Ggc	p.R390G	AFF3_ENST00000409579.1_Missense_Mutation_p.R415G|AFF3_ENST00000356421.2_Missense_Mutation_p.R415G|AFF3_ENST00000317233.4_Missense_Mutation_p.R390G			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	390					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)	p.R415C(2)		NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GAGAGAGCGCGGAGAGCCGTT	0.363																																					p.R415G		Atlas-SNP	.											AFF3,scalp,carcinoma,0,2	AFF3	164	.	2	Substitution - Missense(2)	endometrium(1)|skin(1)	c.C1243G						PASS	.						87.0	101.0	96.0					2																	100266104		2203	4300	6503	SO:0001583	missense	3899	exon12			GAGCGCGGAGAGC	U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.1168C>G	chr2.hg19:g.100266104G>C	ENSP00000387207:p.Arg390Gly	372.0	0.0	.		359.0	85.0	.	NM_001025108	B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Missense_Mutation	SNP	ENST00000409236.2	hg19	CCDS42723.1	.	.	.	.	.	.	.	.	.	.	G	14.60	2.585306	0.46110	.	.	ENSG00000144218	ENST00000317233;ENST00000356421;ENST00000409579;ENST00000409236;ENST00000433370;ENST00000444786;ENST00000432288	T;T;T;T	0.70516	-0.49;-0.49;-0.49;-0.49	6.08	6.08	0.98989	.	0.160493	0.29594	N	0.011704	T	0.70219	0.3199	L	0.36672	1.1	0.40959	D	0.984609	P;P;P	0.44946	0.846;0.549;0.493	P;B;B	0.48304	0.573;0.282;0.119	T	0.65948	-0.6044	10	0.27785	T	0.31	.	18.844	0.92196	0.0:0.0:1.0:0.0	.	543;390;415	B7Z4I6;P51826;P51826-2	.;AFF3_HUMAN;.	G	390;415;415;390;390;543;415	ENSP00000317421:R390G;ENSP00000348793:R415G;ENSP00000386834:R415G;ENSP00000387207:R390G	ENSP00000317421:R390G	R	-	1	0	AFF3	99632536	1.000000	0.71417	1.000000	0.80357	0.918000	0.54935	4.444000	0.60001	2.894000	0.99253	0.655000	0.94253	CGC	.	.	.	none		0.363	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3	NM_002285	
CCDC115	84317	hgsc.bcm.edu	37	2	131096793	131096793	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:131096793G>T	ENST00000259229.2	-	5	666	c.443C>A	c.(442-444)gCc>gAc	p.A148D	CCDC115_ENST00000437688.2_3'UTR|CCDC115_ENST00000409127.1_Missense_Mutation_p.A143D	NM_032357.2	NP_115733.2	Q96NT0	CC115_HUMAN	coiled-coil domain containing 115	148						endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	7	Colorectal(110;0.1)					TATGTCTGCGGCCAGCTGCAG	0.577																																					p.A148D		Atlas-SNP	.											.	CCDC115	19	.	0			c.C443A						PASS	.						44.0	42.0	43.0					2																	131096793		2203	4300	6503	SO:0001583	missense	84317	exon5			TCTGCGGCCAGCT	AK054693	CCDS2159.1	2q21.1	2010-12-24			ENSG00000136710	ENSG00000136710			28178	protein-coding gene	gene with protein product		613734				21118521	Standard	XM_005263825		Approved	MGC12981, FLJ30131, ccp1	uc002tqy.1	Q96NT0	OTTHUMG00000131631	ENST00000259229.2:c.443C>A	chr2.hg19:g.131096793G>T	ENSP00000259229:p.Ala148Asp	49.0	0.0	.		42.0	5.0	.	NM_032357	B4DJ47|Q9BR88	Missense_Mutation	SNP	ENST00000259229.2	hg19	CCDS2159.1	.	.	.	.	.	.	.	.	.	.	G	20.1	3.937236	0.73557	.	.	ENSG00000136710	ENST00000259229;ENST00000409127	D;D	0.96802	-4.13;-4.13	4.0	4.0	0.46444	.	0.067301	0.64402	D	0.000010	D	0.97595	0.9212	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.97354	0.9965	10	0.66056	D	0.02	.	11.8974	0.52663	0.0:0.0:1.0:0.0	.	148;143	Q96NT0;B8ZZ99	CC115_HUMAN;.	D	148;143	ENSP00000259229:A148D;ENSP00000387301:A143D	ENSP00000259229:A148D	A	-	2	0	CCDC115	130813263	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	3.833000	0.55790	2.520000	0.84964	0.591000	0.81541	GCC	.	.	.	none		0.577	CCDC115-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254524.2	NM_032357	
LRP1B	53353	hgsc.bcm.edu	37	2	141641491	141641491	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:141641491T>A	ENST00000389484.3	-	25	5035	c.4064A>T	c.(4063-4065)aAt>aTt	p.N1355I		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	1355					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		TTGGTCCAGATTGCTGTCTAT	0.512										TSP Lung(27;0.18)																											p.N1355I	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.A4064T						PASS	.						184.0	175.0	178.0					2																	141641491		2203	4300	6503	SO:0001583	missense	53353	exon25			TCCAGATTGCTGT	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.4064A>T	chr2.hg19:g.141641491T>A	ENSP00000374135:p.Asn1355Ile	81.0	0.0	.		115.0	17.0	.	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	hg19	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.859686	0.91433	.	.	ENSG00000168702	ENST00000389484;ENST00000544579;ENST00000434794	D;D	0.84298	-1.83;-1.83	5.64	5.64	0.86602	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	D	0.89522	0.6739	L	0.45051	1.395	0.80722	D	1	D;D	0.89917	0.989;1.0	D;D	0.91635	0.965;0.999	D	0.89616	0.3845	10	0.49607	T	0.09	.	16.1404	0.81517	0.0:0.0:0.0:1.0	.	538;1355	Q96NT6;Q9NZR2	.;LRP1B_HUMAN	I	1355;1293;500	ENSP00000374135:N1355I;ENSP00000413239:N500I	ENSP00000374135:N1355I	N	-	2	0	LRP1B	141357961	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.926000	0.87569	2.261000	0.74972	0.533000	0.62120	AAT	.	.	.	none		0.512	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
COL5A2	1290	hgsc.bcm.edu	37	2	189916160	189916160	+	Silent	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:189916160T>A	ENST00000374866.3	-	42	3091	c.2817A>T	c.(2815-2817)ggA>ggT	p.G939G		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	939					axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			GACCTGGAGGTCCCTCCTTCC	0.612																																					p.G939G		Atlas-SNP	.											.	COL5A2	230	.	0			c.A2817T						PASS	.						48.0	50.0	49.0					2																	189916160		2203	4300	6503	SO:0001819	synonymous_variant	1290	exon42			TGGAGGTCCCTCC	Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.2817A>T	chr2.hg19:g.189916160T>A		90.0	0.0	.		120.0	26.0	.	NM_000393	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	ENST00000374866.3	hg19	CCDS33350.1																																																																																			.	.	.	none		0.612	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313523.1	NM_000393	
DNAH7	56171	hgsc.bcm.edu	37	2	196915964	196915964	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:196915964C>T	ENST00000312428.6	-	3	188	c.88G>A	c.(88-90)Gcc>Acc	p.A30T	DNAH7_ENST00000410072.1_Missense_Mutation_p.A30T	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	30	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TCTTTGCTGGCTAATTTCTCC	0.328																																					p.A30T		Atlas-SNP	.											.	DNAH7	512	.	0			c.G88A						PASS	.						167.0	163.0	164.0					2																	196915964		1817	4070	5887	SO:0001583	missense	56171	exon3			TGCTGGCTAATTT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.88G>A	chr2.hg19:g.196915964C>T	ENSP00000311273:p.Ala30Thr	87.0	0.0	.		76.0	18.0	.	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	2.570	-0.299741	0.05532	.	.	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446;ENST00000427816	T;T	0.21734	1.99;2.89	4.13	-2.63	0.06133	.	1.029540	0.07754	N	0.949060	T	0.07954	0.0199	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39623	-0.9605	10	0.09843	T	0.71	.	5.1125	0.14817	0.5731:0.2462:0.0:0.1807	.	30	Q8WXX0	DYH7_HUMAN	T	30;30;30;5	ENSP00000311273:A30T;ENSP00000386260:A30T	ENSP00000311273:A30T	A	-	1	0	DNAH7	196624209	0.000000	0.05858	0.002000	0.10522	0.009000	0.06853	-3.248000	0.00541	-0.544000	0.06232	-0.314000	0.08810	GCC	.	.	.	none		0.328	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
PARD3B	117583	hgsc.bcm.edu	37	2	206110541	206110541	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:206110541A>T	ENST00000406610.2	+	16	2387	c.2180A>T	c.(2179-2181)aAa>aTa	p.K727I	PARD3B_ENST00000351153.1_Missense_Mutation_p.K727I|PARD3B_ENST00000462231.1_Missense_Mutation_p.K727I|PARD3B_ENST00000358768.2_Missense_Mutation_p.K665I|PARD3B_ENST00000349953.3_Missense_Mutation_p.K727I	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta	727					cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		GCTGGACAAAAATCGGGTAAG	0.403																																					p.K727I		Atlas-SNP	.											.	PARD3B	314	.	0			c.A2180T						PASS	.						155.0	147.0	149.0					2																	206110541		1830	4086	5916	SO:0001583	missense	117583	exon16			GACAAAAATCGGG	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.2180A>T	chr2.hg19:g.206110541A>T	ENSP00000385848:p.Lys727Ile	164.0	0.0	.		173.0	41.0	.	NM_205863	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Missense_Mutation	SNP	ENST00000406610.2	hg19		.	.	.	.	.	.	.	.	.	.	A	16.30	3.083825	0.55861	.	.	ENSG00000116117	ENST00000406610;ENST00000358768;ENST00000351153;ENST00000349953	T;T;T;T	0.30981	1.63;1.63;1.51;1.63	5.85	1.19	0.21007	.	0.449872	0.21999	N	0.066026	T	0.29588	0.0738	L	0.29908	0.895	0.23376	N	0.99781	P;P;P;P;P	0.47604	0.898;0.836;0.604;0.579;0.828	P;B;P;B;P	0.51355	0.667;0.368;0.52;0.43;0.555	T	0.09840	-1.0656	10	0.72032	D	0.01	.	9.4325	0.38620	0.5621:0.0:0.4379:0.0	.	727;727;727;665;727	Q8TEW8-3;Q8TEW8;E9PE87;Q8TEW8-2;Q8TEW8-5	.;PAR3L_HUMAN;.;.;.	I	727;665;727;727	ENSP00000385848:K727I;ENSP00000351618:K665I;ENSP00000317261:K727I;ENSP00000340280:K727I	ENSP00000340280:K727I	K	+	2	0	PARD3B	205818786	0.977000	0.34250	0.991000	0.47740	0.724000	0.41520	0.829000	0.27449	0.532000	0.28657	0.533000	0.62120	AAA	.	.	.	none		0.403	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	
ACADL	33	hgsc.bcm.edu	37	2	211057576	211057576	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:211057576A>G	ENST00000233710.3	-	10	1378	c.1151T>C	c.(1150-1152)gTa>gCa	p.V384A	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	384					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		ATGGAGCTGTACACAGTCGTA	0.373																																					p.V384A		Atlas-SNP	.											.	ACADL	38	.	0			c.T1151C						PASS	.						96.0	87.0	90.0					2																	211057576		2203	4300	6503	SO:0001583	missense	33	exon10			AGCTGTACACAGT	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.1151T>C	chr2.hg19:g.211057576A>G	ENSP00000233710:p.Val384Ala	87.0	0.0	.		92.0	15.0	.	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	hg19	CCDS2389.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.048038	0.75846	.	.	ENSG00000115361	ENST00000233710	D	0.96522	-4.04	6.03	6.03	0.97812	Acyl-CoA dehydrogenase/oxidase C-terminal (2);Acyl-CoA oxidase/dehydrogenase, type 1 (1);	0.189851	0.46442	D	0.000297	D	0.96457	0.8844	M	0.83774	2.66	0.52099	D	0.999949	B	0.20368	0.044	B	0.28305	0.088	D	0.94543	0.7747	10	0.87932	D	0	.	16.2316	0.82347	1.0:0.0:0.0:0.0	.	384	P28330	ACADL_HUMAN	A	384	ENSP00000233710:V384A	ENSP00000233710:V384A	V	-	2	0	ACADL	210765821	1.000000	0.71417	0.627000	0.29227	0.960000	0.62799	6.551000	0.73909	2.308000	0.77769	0.533000	0.62120	GTA	.	.	.	none		0.373	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
ARMC9	80210	hgsc.bcm.edu	37	2	232081381	232081381	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr2:232081381T>C	ENST00000349938.4	+	5	573	c.379T>C	c.(379-381)Tac>Cac	p.Y127H	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	127						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		AAAGATTTCCTACTTCAAAAC	0.483																																					p.Y127H		Atlas-SNP	.											.	ARMC9	129	.	0			c.T379C						PASS	.						185.0	169.0	174.0					2																	232081381		2203	4300	6503	SO:0001583	missense	80210	exon5			ATTTCCTACTTCA	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.379T>C	chr2.hg19:g.232081381T>C	ENSP00000258417:p.Tyr127His	118.0	0.0	.		143.0	33.0	.	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	hg19	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	T	7.414	0.635408	0.14322	.	.	ENSG00000135931	ENST00000349938;ENST00000359743;ENST00000440107	T;T	0.18174	2.23;2.23	5.5	4.31	0.51392	.	0.480617	0.21657	N	0.071085	T	0.08268	0.0206	N	0.11560	0.145	0.09310	N	1	B	0.06786	0.001	B	0.09377	0.004	T	0.37103	-0.9720	10	0.15952	T	0.53	-6.7602	8.7057	0.34354	0.0:0.2153:0.0:0.7847	.	127	Q7Z3E5	ARMC9_HUMAN	H	127	ENSP00000258417:Y127H;ENSP00000387391:Y127H	ENSP00000258417:Y127H	Y	+	1	0	ARMC9	231789625	0.006000	0.16342	0.432000	0.26747	0.931000	0.56810	1.657000	0.37366	0.880000	0.35969	0.533000	0.62120	TAC	.	.	.	none		0.483	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
ZNF619	285267	hgsc.bcm.edu	37	3	40523745	40523745	+	Intron	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:40523745T>A	ENST00000314686.5	+	3	485				ZNF619_ENST00000447116.2_Missense_Mutation_p.L68Q|ZNF619_ENST00000521353.1_Missense_Mutation_p.L68Q|ZNF619_ENST00000520737.1_Intron|ZNF619_ENST00000432264.2_Intron|ZNF619_ENST00000522736.1_Intron|ZNF619_ENST00000456778.1_Intron|ZNF619_ENST00000429348.2_Intron			Q8N2I2	ZN619_HUMAN	zinc finger protein 619						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0525)|Kidney(284;0.0661)		GGCTTTCCTCTGGATACAGAG	0.502																																					p.L68Q		Atlas-SNP	.											.	ZNF619	57	.	0			c.T203A						PASS	.						72.0	70.0	71.0					3																	40523745		692	1591	2283	SO:0001627	intron_variant	285267	exon4			TTCCTCTGGATAC	AK075245	CCDS46801.1, CCDS46802.1, CCDS46803.1	3p21.33	2013-01-08			ENSG00000177873	ENSG00000177873		"""Zinc fingers, C2H2-type"", ""-"""	26910	protein-coding gene	gene with protein product							Standard	NM_001145083		Approved	FLJ90764	uc011azb.2	Q8N2I2	OTTHUMG00000131391	ENST00000314686.5:c.80+238T>A	chr3.hg19:g.40523745T>A		48.0	0.0	.		83.0	24.0	.	NM_001145082	B4E271|C9JRN5|D4PHA2|E9PCD9	Missense_Mutation	SNP	ENST00000314686.5	hg19		.	.	.	.	.	.	.	.	.	.	T	12.37	1.917530	0.33815	.	.	ENSG00000177873	ENST00000447116;ENST00000521353	T;T	0.07114	3.22;3.22	3.52	3.52	0.40303	.	.	.	.	.	T	0.11196	0.0273	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.32375	-0.9909	9	0.39692	T	0.17	.	10.3183	0.43751	0.0:0.0:0.0:1.0	.	68	E9PCD9	.	Q	68	ENSP00000411132:L68Q;ENSP00000430705:L68Q	ENSP00000411132:L68Q	L	+	2	0	ZNF619	40498749	0.000000	0.05858	0.065000	0.19835	0.018000	0.09664	-0.630000	0.05502	1.366000	0.46076	0.460000	0.39030	CTG	.	.	.	none		0.502	ZNF619-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000254180.2	NM_173656	
ROBO1	6091	hgsc.bcm.edu	37	3	78710202	78710202	+	Silent	SNP	C	C	T	rs536774102		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:78710202C>T	ENST00000464233.1	-	16	2411	c.2298G>A	c.(2296-2298)aaG>aaA	p.K766K	ROBO1_ENST00000467549.1_Silent_p.K730K|ROBO1_ENST00000436010.2_Silent_p.K727K|ROBO1_ENST00000495273.1_Silent_p.K730K	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	766	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TTTTGGCAAACTTGATTTCAC	0.343																																					p.K766K		Atlas-SNP	.											.	ROBO1	833	.	0			c.G2298A						PASS	.						95.0	89.0	91.0					3																	78710202		1834	4091	5925	SO:0001819	synonymous_variant	6091	exon16			GGCAAACTTGATT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2298G>A	chr3.hg19:g.78710202C>T		99.0	0.0	.		112.0	30.0	.	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	hg19	CCDS54611.1																																																																																			.	.	.	none		0.343	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
NMD3	51068	hgsc.bcm.edu	37	3	160967299	160967299	+	Silent	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:160967299T>C	ENST00000460469.1	+	13	1716	c.1261T>C	c.(1261-1263)Ttg>Ctg	p.L421L	NMD3_ENST00000472947.1_Silent_p.L421L|NMD3_ENST00000351193.2_Silent_p.L421L			Q96D46	NMD3_HUMAN	NMD3 ribosome export adaptor	421					protein transport (GO:0015031)|ribosomal large subunit export from nucleus (GO:0000055)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|ribosomal large subunit binding (GO:0043023)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(10)|ovary(1)|skin(1)|urinary_tract(2)	25			Lung(72;0.00111)|LUSC - Lung squamous cell carcinoma(72;0.00156)			AAACTGGAAATTGAAAGAGCT	0.353																																					p.L421L		Atlas-SNP	.											.	NMD3	49	.	0			c.T1261C						PASS	.						76.0	75.0	75.0					3																	160967299		2203	4300	6503	SO:0001819	synonymous_variant	51068	exon14			TGGAAATTGAAAG	BC013317	CCDS3194.1	3q26.1	2013-08-06	2013-08-06		ENSG00000169251	ENSG00000169251			24250	protein-coding gene	gene with protein product		611021	"""NMD3 homolog (S. cerevisiae)"""			10810093, 23782956, 12773398	Standard	NM_015938		Approved	CGI-07	uc003feb.1	Q96D46	OTTHUMG00000159063	ENST00000460469.1:c.1261T>C	chr3.hg19:g.160967299T>C		304.0	0.0	.		337.0	57.0	.	NM_015938	D3DNM7|Q9Y2Z6	Silent	SNP	ENST00000460469.1	hg19	CCDS3194.1																																																																																			.	.	.	none		0.353	NMD3-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353114.1	NM_015938	
ALG3	10195	hgsc.bcm.edu	37	3	183963295	183963295	+	Silent	SNP	G	G	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:183963295G>C	ENST00000397676.3	-	3	435	c.405C>G	c.(403-405)acC>acG	p.T135T	ALG3_ENST00000455059.1_Silent_p.T95T|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000445626.2_Silent_p.T87T|EIF2B5_ENST00000444495.1_Intron|ALG3_ENST00000418734.2_Silent_p.T79T	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	135					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)			CAAGCAGCAAGGTAGCCAGGT	0.567																																					p.T135T		Atlas-SNP	.											.	ALG3	48	.	0			c.C405G						PASS	.						62.0	64.0	64.0					3																	183963295		2121	4233	6354	SO:0001819	synonymous_variant	10195	exon3			CAGCAAGGTAGCC	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	ENST00000397676.3:c.405C>G	chr3.hg19:g.183963295G>C		146.0	0.0	.		159.0	45.0	.	NM_005787	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	hg19	CCDS46968.1																																																																																			.	.	.	none		0.567	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
SENP5	205564	hgsc.bcm.edu	37	3	196613001	196613001	+	Nonsense_Mutation	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:196613001A>T	ENST00000323460.5	+	2	1198	c.949A>T	c.(949-951)Aag>Tag	p.K317*	SENP5_ENST00000419026.1_Intron|SENP5_ENST00000445299.2_Nonsense_Mutation_p.K317*	NM_152699.4	NP_689912.2	Q96HI0	SENP5_HUMAN	SUMO1/sentrin specific peptidase 5	317					cell cycle (GO:0007049)|cell division (GO:0051301)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein sumoylation (GO:0016925)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(9)|lung(14)|skin(1)	32	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;3.14e-24)|all cancers(36;2.1e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.004)		TGCTGTGGTGAAGGGGACGAA	0.512																																					p.K317X	Ovarian(47;891 1095 11174 13858 51271)	Atlas-SNP	.											.	SENP5	68	.	0			c.A949T						PASS	.						107.0	94.0	98.0					3																	196613001		2203	4300	6503	SO:0001587	stop_gained	205564	exon2			GTGGTGAAGGGGA	BC030705	CCDS3322.1	3q29	2005-08-17	2005-08-17		ENSG00000119231	ENSG00000119231			28407	protein-coding gene	gene with protein product		612845	"""SUMO1/sentrin specific protease 5"""			12477932	Standard	NM_152699		Approved	MGC27076	uc003fwz.4	Q96HI0	OTTHUMG00000155527	ENST00000323460.5:c.949A>T	chr3.hg19:g.196613001A>T	ENSP00000327197:p.Lys317*	53.0	0.0	.		75.0	28.0	.	NM_152699	B4DY82|Q96SA5	Nonsense_Mutation	SNP	ENST00000323460.5	hg19	CCDS3322.1	.	.	.	.	.	.	.	.	.	.	A	38	6.956467	0.97964	.	.	ENSG00000119231	ENST00000323460;ENST00000445299	.	.	.	5.37	4.22	0.49857	.	0.349524	0.27429	N	0.019408	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-7.1768	9.6073	0.39641	0.9168:0.0:0.0832:0.0	.	.	.	.	X	317	.	ENSP00000327197:K317X	K	+	1	0	SENP5	198097398	0.999000	0.42202	0.999000	0.59377	0.954000	0.61252	3.305000	0.51873	0.992000	0.38840	0.533000	0.62120	AAG	.	.	.	none		0.512	SENP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340524.1	NM_152699	
SPON2	10417	hgsc.bcm.edu	37	4	1165650	1165650	+	Silent	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:1165650A>T	ENST00000290902.5	-	2	542	c.210T>A	c.(208-210)tcT>tcA	p.S70S	SPON2_ENST00000431380.1_Silent_p.S70S	NM_012445.3	NP_036577	Q9BUD6	SPON2_HUMAN	spondin 2, extracellular matrix protein	70	Spondin. {ECO:0000255|PROSITE- ProRule:PRU00364}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|innate immune response (GO:0045087)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|pancreas(1)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(23;0.00805)	UCEC - Uterine corpus endometrioid carcinoma (64;0.139)|Colorectal(103;0.19)		CCAGCAGCGAAGACCACTGCG	0.687																																					p.S70S		Atlas-SNP	.											.	SPON2	22	.	0			c.T210A						PASS	.						47.0	65.0	59.0					4																	1165650		2192	4292	6484	SO:0001819	synonymous_variant	10417	exon2			CAGCGAAGACCAC	AB027466	CCDS3347.1	4p16.3	2008-07-29			ENSG00000159674	ENSG00000159674			11253	protein-coding gene	gene with protein product	"""Mindin"", ""M-spondin"""	605918				10512675, 15094111	Standard	NM_012445		Approved	DIL1	uc003gco.4	Q9BUD6	OTTHUMG00000089002	ENST00000290902.5:c.210T>A	chr4.hg19:g.1165650A>T		120.0	0.0	.		76.0	18.0	.	NM_012445	D3DVN9|Q4W5N4|Q9ULW1	Silent	SNP	ENST00000290902.5	hg19	CCDS3347.1																																																																																			.	.	.	none		0.687	SPON2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202080.2		
MAN2B2	23324	hgsc.bcm.edu	37	4	6576972	6576972	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:6576972C>A	ENST00000285599.3	+	1	71	c.35C>A	c.(34-36)cCg>cAg	p.P12Q	MAN2B2_ENST00000504248.1_Missense_Mutation_p.P12Q	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	12					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CTGCTGGCACCGCTCCTGTTG	0.746																																					p.P12Q		Atlas-SNP	.											.	MAN2B2	80	.	0			c.C35A						PASS	.						4.0	5.0	5.0					4																	6576972		1999	3945	5944	SO:0001583	missense	23324	exon1			TGGCACCGCTCCT	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.35C>A	chr4.hg19:g.6576972C>A	ENSP00000285599:p.Pro12Gln	63.0	0.0	.		76.0	18.0	.	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	hg19	CCDS33951.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	1.365|1.365	-0.587738|-0.587738	0.03799|0.03799	.|.	.|.	ENSG00000013288|ENSG00000013288	ENST00000285599;ENST00000504248|ENST00000505907	T;D|.	0.83673|.	-1.31;-1.75|.	2.46|2.46	-4.92|-4.92	0.03075|0.03075	.|.	2.051680|.	0.02792|.	N|.	0.122182|.	T|T	0.08403|0.08403	0.0209|0.0209	N|N	0.02142|0.02142	-0.665|-0.665	0.09310|0.09310	N|N	1|1	B;B;B|.	0.06786|.	0.0;0.0;0.001|.	B;B;B|.	0.06405|.	0.001;0.001;0.002|.	T|T	0.09357|0.09357	-1.0678|-1.0678	10|5	0.13108|.	T|.	0.6|.	.|.	3.8561|3.8561	0.08976|0.08976	0.3608:0.3061:0.0:0.3331|0.3608:0.3061:0.0:0.3331	.|.	12;12;12|.	E9PCD7;Q9Y2E5;Q9Y2E5-2|.	.;MA2B2_HUMAN;.|.	Q|S	12|11	ENSP00000285599:P12Q;ENSP00000423129:P12Q|.	ENSP00000285599:P12Q|.	P|R	+|+	2|1	0|0	MAN2B2|MAN2B2	6627873|6627873	0.003000|0.003000	0.15002|0.15002	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.090000|0.090000	0.15025|0.15025	-3.717000|-3.717000	0.00116|0.00116	-2.834000|-2.834000	0.00106|0.00106	CCG|CGC	.	.	.	none		0.746	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
SEC31A	22872	hgsc.bcm.edu	37	4	83748748	83748748	+	Nonsense_Mutation	SNP	G	G	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:83748748G>T	ENST00000395310.2	-	24	3247	c.3065C>A	c.(3064-3066)tCa>tAa	p.S1022*	SEC31A_ENST00000509142.1_Nonsense_Mutation_p.S908*|SEC31A_ENST00000505472.1_Nonsense_Mutation_p.S1053*|SEC31A_ENST00000432794.1_Nonsense_Mutation_p.S1035*|SEC31A_ENST00000505984.1_Nonsense_Mutation_p.S968*|SEC31A_ENST00000348405.4_Nonsense_Mutation_p.S983*|SEC31A_ENST00000326950.5_Nonsense_Mutation_p.S983*|SEC31A_ENST00000355196.2_Nonsense_Mutation_p.S1022*|SEC31A_ENST00000443462.2_Nonsense_Mutation_p.S1002*|SEC31A_ENST00000513858.1_Nonsense_Mutation_p.S869*|SEC31A_ENST00000311785.7_Nonsense_Mutation_p.S908*|SEC31A_ENST00000500777.2_Nonsense_Mutation_p.S869*|SEC31A_ENST00000264405.5_Nonsense_Mutation_p.S771*|SEC31A_ENST00000508502.1_Nonsense_Mutation_p.S1007*|SEC31A_ENST00000448323.1_Nonsense_Mutation_p.S1022*	NM_001077207.2|NM_001077208.2|NM_014933.3	NP_001070675.1|NP_001070676.1|NP_055748.2	O94979	SC31A_HUMAN	SEC31 homolog A (S. cerevisiae)	1022	Interaction with PDCD6.|Pro-rich.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|response to calcium ion (GO:0051592)	COPII vesicle coat (GO:0030127)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum exit site (GO:0070971)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|vesicle coat (GO:0030120)	calcium-dependent protein binding (GO:0048306)		SEC31A/ALK(3)|SEC31A/JAK2(4)	breast(1)	1		Hepatocellular(203;0.114)				CATGATTGGTGATGTGATGGG	0.458																																					p.S1022X		Atlas-SNP	.											.	SEC31A	227	.	0			c.C3065A						PASS	.						171.0	165.0	167.0					4																	83748748		2203	4300	6503	SO:0001587	stop_gained	22872	exon24			ATTGGTGATGTGA	AB018358	CCDS3596.1, CCDS3597.1, CCDS43244.1, CCDS47088.1, CCDS54773.1, CCDS75155.1, CCDS75156.1	4q21.3	2013-01-10	2006-10-05	2006-09-07	ENSG00000138674	ENSG00000138674		"""WD repeat domain containing"""	17052	protein-coding gene	gene with protein product		610257	"""SEC31-like 1 (S. cerevisiae)"", ""Sec31 homolog A (S. cerevisiae)"""	SEC31L1		10048485, 10788476	Standard	NM_001077206		Approved	KIAA0905, ABP125, ABP130	uc003hnh.3	O94979	OTTHUMG00000130297	ENST00000395310.2:c.3065C>A	chr4.hg19:g.83748748G>T	ENSP00000378721:p.Ser1022*	143.0	0.0	.		155.0	28.0	.	NM_001077207	B4DIW6|B7ZKZ7|B7ZL00|H7C2W3|Q17RR5|Q5H9P6|Q5XG74|Q659G7|Q6ZU90|Q7LCX9|Q86TJ0|Q8IZH4|Q9P048|Q9P0A6|Q9UM05|Q9UM06	Nonsense_Mutation	SNP	ENST00000395310.2	hg19	CCDS3596.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.07|15.07	2.725353|2.725353	0.48833|0.48833	.|.	.|.	ENSG00000138674|ENSG00000138674	ENST00000503937|ENST00000348405;ENST00000513858;ENST00000395310;ENST00000443462;ENST00000509142;ENST00000432794;ENST00000448323;ENST00000326950;ENST00000311785;ENST00000505472;ENST00000500777;ENST00000508502;ENST00000355196;ENST00000264405;ENST00000505984	.|.	.|.	.|.	5.77|5.77	4.9|4.9	0.64082|0.64082	.|.	.|0.201050	.|0.44097	.|D	.|0.000483	T|.	0.54287|.	0.1849|.	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.54450|.	-0.8292|.	3|.	.|0.12766	.|T	.|0.61	-2.6138|-2.6138	15.9381|15.9381	0.79734|0.79734	0.0:0.0:0.8639:0.1361|0.0:0.0:0.8639:0.1361	.|.	.|.	.|.	.|.	N|X	185|983;869;1022;1002;908;1035;1022;983;908;1053;869;1007;1022;771;968	.|.	.|ENSP00000264405:S771X	H|S	-|-	1|2	0|0	SEC31A|SEC31A	83967772|83967772	1.000000|1.000000	0.71417|0.71417	0.652000|0.652000	0.29579|0.29579	0.106000|0.106000	0.19336|0.19336	7.795000|7.795000	0.85887|0.85887	1.377000|1.377000	0.46286|0.46286	0.655000|0.655000	0.94253|0.94253	CAC|TCA	.	.	.	none		0.458	SEC31A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252640.1	NM_016211	
USP53	54532	hgsc.bcm.edu	37	4	120190931	120190931	+	Silent	SNP	A	A	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:120190931A>G	ENST00000274030.6	+	15	2553	c.1374A>G	c.(1372-1374)ttA>ttG	p.L458L	USP53_ENST00000450251.1_Silent_p.L458L	NM_019050.2	NP_061923.2			ubiquitin specific peptidase 53											breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(5)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	27						AGAAAAACTTACTTTCTTCAC	0.318																																					p.L458L		Atlas-SNP	.											.	USP53	69	.	0			c.A1374G						PASS	.						98.0	100.0	99.0					4																	120190931		1802	4058	5860	SO:0001819	synonymous_variant	54532	exon14			AAACTTACTTTCT	BC017382	CCDS43265.1	4q26	2010-05-12	2005-08-08		ENSG00000145390	ENSG00000145390		"""Ubiquitin-specific peptidases"""	29255	protein-coding gene	gene with protein product			"""ubiquitin specific protease 53"""			10718198, 14715245	Standard	NM_019050		Approved	KIAA1350	uc003ics.4	Q70EK8	OTTHUMG00000161331	ENST00000274030.6:c.1374A>G	chr4.hg19:g.120190931A>G		489.0	0.0	.		524.0	54.0	.	NM_019050		Silent	SNP	ENST00000274030.6	hg19	CCDS43265.1																																																																																			.	.	.	none		0.318	USP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364564.2	XM_052597	
DROSHA	29102	hgsc.bcm.edu	37	5	31526232	31526232	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:31526232C>A	ENST00000511367.2	-	4	1052	c.808G>T	c.(808-810)Gac>Tac	p.D270Y	DROSHA_ENST00000513349.1_Missense_Mutation_p.D270Y|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000344624.3_Missense_Mutation_p.D270Y|DROSHA_ENST00000442743.1_Missense_Mutation_p.D270Y	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	270	Arg-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						CTCCCTCGGTCATAATCAGAT	0.587																																					p.D270Y		Atlas-SNP	.											.	DROSHA	130	.	0			c.G808T						PASS	.						101.0	104.0	103.0					5																	31526232		2082	4213	6295	SO:0001583	missense	29102	exon4			CTCGGTCATAATC	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.808G>T	chr5.hg19:g.31526232C>A	ENSP00000425979:p.Asp270Tyr	82.0	0.0	.		78.0	17.0	.	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	hg19	CCDS47195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.56|10.56	1.384535|1.384535	0.25031|0.25031	.|.	.|.	ENSG00000113360|ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000512302|ENST00000512076	T;T;T;T;T|.	0.51574|.	0.7;0.7;0.7;0.7;0.97|.	4.55|4.55	4.55|4.55	0.56014|0.56014	.|.	0.187574|.	0.43919|.	D|.	0.000519|.	T|.	0.49457|.	0.1558|.	N|N	0.24115|0.24115	0.695|0.695	0.58432|0.58432	D|D	0.999992|0.999992	P;B;B|.	0.48503|.	0.911;0.38;0.38|.	P;B;B|.	0.47705|.	0.555;0.125;0.125|.	T|.	0.42050|.	-0.9474|.	10|.	0.21540|.	T|.	0.41|.	-5.2075|-5.2075	12.0196|12.0196	0.53336|0.53336	0.0:0.9169:0.0:0.083|0.0:0.9169:0.0:0.083	.|.	270;270;270|.	Q9NRR4-2;E7EMP9;Q9NRR4|.	.;.;RNC_HUMAN|.	Y|L	270;270;270;270;263;263;68|99	ENSP00000425979:D270Y;ENSP00000339845:D270Y;ENSP00000409335:D270Y;ENSP00000424161:D270Y;ENSP00000428782:D68Y|.	ENSP00000265075:D263Y|.	D|X	-|-	1|2	0|2	DROSHA|DROSHA	31561989|31561989	0.998000|0.998000	0.40836|0.40836	0.449000|0.449000	0.26957|0.26957	0.080000|0.080000	0.17528|0.17528	4.622000|4.622000	0.61240|0.61240	2.348000|2.348000	0.79779|0.79779	0.650000|0.650000	0.86243|0.86243	GAC|TGA	.	.	.	none		0.587	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
WDR41	55255	hgsc.bcm.edu	37	5	76758982	76758982	+	Silent	SNP	A	A	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:76758982A>G	ENST00000296679.4	-	4	661	c.286T>C	c.(286-288)Ttg>Ctg	p.L96L	WDR41_ENST00000507029.1_Silent_p.L41L|WDR41_ENST00000414719.2_5'UTR	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	96						lysosomal membrane (GO:0005765)		p.L96V(1)		NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		CAAGATTCCAAGGAAGGAAAT	0.343																																					p.L96L		Atlas-SNP	.											WDR41,colon,carcinoma,0,1	WDR41	29	.	1	Substitution - Missense(1)	large_intestine(1)	c.T286C						PASS	.						120.0	122.0	121.0					5																	76758982		2203	4300	6503	SO:0001819	synonymous_variant	55255	exon4			ATTCCAAGGAAGG	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.286T>C	chr5.hg19:g.76758982A>G		118.0	0.0	.		97.0	17.0	.	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	hg19	CCDS4038.1																																																																																			.	.	.	none		0.343	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
WDR36	134430	hgsc.bcm.edu	37	5	110448824	110448824	+	Missense_Mutation	SNP	A	A	T	rs562223310		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:110448824A>T	ENST00000513710.2	+	16	1940	c.1936A>T	c.(1936-1938)Att>Ttt	p.I646F	WDR36_ENST00000506538.2_Missense_Mutation_p.I646F			Q8NI36	WDR36_HUMAN	WD repeat domain 36	646					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		GGATTGCTCTATTAGGACTTG	0.289																																					p.I646F		Atlas-SNP	.											.	WDR36	111	.	0			c.A1936T						PASS	.						150.0	151.0	150.0					5																	110448824		2202	4300	6502	SO:0001583	missense	134430	exon16			TGCTCTATTAGGA	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"""WD repeat domain containing"""	30696	protein-coding gene	gene with protein product		609669	"""glaucoma 1, open angle, G"""	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.1936A>T	chr5.hg19:g.110448824A>T	ENSP00000424628:p.Ile646Phe	97.0	0.0	.		90.0	21.0	.	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Missense_Mutation	SNP	ENST00000513710.2	hg19	CCDS4102.1	.	.	.	.	.	.	.	.	.	.	A	18.13	3.555751	0.65425	.	.	ENSG00000134987	ENST00000506538;ENST00000513710	T;T	0.70045	-0.45;-0.45	6.06	-9.14	0.00701	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.194328	0.56097	D	0.000029	T	0.72145	0.3424	M	0.91140	3.18	0.80722	D	1	P	0.43885	0.82	P	0.45474	0.482	T	0.81883	-0.0728	10	0.87932	D	0	-5.945	17.9341	0.89007	0.4286:0.0:0.5714:0.0	.	646	Q8NI36	WDR36_HUMAN	F	646	ENSP00000423067:I646F;ENSP00000424628:I646F	ENSP00000423067:I646F	I	+	1	0	WDR36	110476723	0.102000	0.21896	0.359000	0.25824	0.804000	0.45430	0.737000	0.26144	-1.830000	0.01199	-1.986000	0.00452	ATT	.	.	.	none		0.289	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140857767	140857767	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:140857767T>G	ENST00000308177.3	+	1	2188	c.2084T>G	c.(2083-2085)cTt>cGt	p.L695R	PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA9_ENST00000573521.1_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB3_ENST00000576222.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	695					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTTATCTACTTCTTTCTCTA	0.483											OREG0016865	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L695R		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.T2084G						PASS	.						159.0	198.0	185.0					5																	140857767		2203	4300	6503	SO:0001583	missense	5098	exon1			ATCTACTTCTTTC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.2084T>G	chr5.hg19:g.140857767T>G	ENSP00000312070:p.Leu695Arg	80.0	0.0	.	1659	86.0	18.0	.	NM_032402	O60622|Q08192|Q9Y5C4	Missense_Mutation	SNP	ENST00000308177.3	hg19	CCDS4261.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.433275	0.83776	.	.	ENSG00000240184	ENST00000308177	T	0.51574	0.7	5.55	5.55	0.83447	.	.	.	.	.	T	0.56171	0.1967	L	0.29908	0.895	0.32577	N	0.529007	D;D	0.76494	0.996;0.999	P;D	0.67548	0.823;0.952	T	0.66044	-0.6021	9	0.87932	D	0	.	14.0843	0.64944	0.0:0.0:0.0:1.0	.	695;695	Q9UN70;Q9UN70-2	PCDGK_HUMAN;.	R	695	ENSP00000312070:L695R	ENSP00000312070:L695R	L	+	2	0	PCDHGC3	140837951	0.992000	0.36948	1.000000	0.80357	0.989000	0.77384	4.297000	0.59061	2.326000	0.78906	0.533000	0.62120	CTT	.	.	.	none		0.483	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
MTCH1	23787	hgsc.bcm.edu	37	6	36936732	36936732	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:36936732A>C	ENST00000373627.5	-	12	1241	c.1117T>G	c.(1117-1119)Tcc>Gcc	p.S373A	MTCH1_ENST00000373616.5_Missense_Mutation_p.S356A|MTCH1_ENST00000471737.1_5'UTR	NM_001271641.1	NP_001258570.1	Q9NZJ7	MTCH1_HUMAN	mitochondrial carrier 1	373					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|neuronal ion channel clustering (GO:0045161)|positive regulation of apoptotic process (GO:0043065)|regulation of signal transduction (GO:0009966)|transport (GO:0006810)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AGCAGGCTGGAGCCTCGGAAG	0.562																																					p.S373A		Atlas-SNP	.											.	MTCH1	24	.	0			c.T1117G						PASS	.						78.0	70.0	73.0					6																	36936732		2203	4300	6503	SO:0001583	missense	23787	exon12			GGCTGGAGCCTCG	AF151822	CCDS4828.1, CCDS64411.1	6p21.2	2013-05-22	2011-05-19		ENSG00000137409	ENSG00000137409		"""Solute carriers"""	17586	protein-coding gene	gene with protein product	"""solute carrier family 25, member 49"""	610449	"""mitochondrial carrier homolog 1 (C. elegans)"""			12377771	Standard	NM_014341		Approved	CGI-64, PSAP, SLC25A49	uc003ond.2	Q9NZJ7	OTTHUMG00000014614	ENST00000373627.5:c.1117T>G	chr6.hg19:g.36936732A>C	ENSP00000362730:p.Ser373Ala	91.0	0.0	.		69.0	16.0	.	NM_001271641	A8KAX5|B2RCE3|Q6PK60|Q6UX45|Q7L465|Q9BW23|Q9NZR6|Q9UJZ5	Missense_Mutation	SNP	ENST00000373627.5	hg19		.	.	.	.	.	.	.	.	.	.	A	17.75	3.465220	0.63513	.	.	ENSG00000137409	ENST00000373616;ENST00000373627;ENST00000337855	T;T	0.77229	-1.08;-1.08	5.16	5.16	0.70880	Mitochondrial carrier domain (2);	2.951400	0.01758	N	0.030350	T	0.79233	0.4411	L	0.44542	1.39	0.80722	D	1	D;D	0.56521	0.976;0.974	P;D	0.67725	0.86;0.953	T	0.67146	-0.5744	10	0.20046	T	0.44	.	13.5751	0.61868	1.0:0.0:0.0:0.0	.	373;356	Q9NZJ7;Q9NZJ7-2	MTCH1_HUMAN;.	A	356;373;292	ENSP00000362718:S356A;ENSP00000362730:S373A	ENSP00000338712:S292A	S	-	1	0	MTCH1	37044710	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.964000	0.76061	1.955000	0.56771	0.533000	0.62120	TCC	.	.	.	none		0.562	MTCH1-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040396.1	NM_014341	
CYP39A1	51302	hgsc.bcm.edu	37	6	46604152	46604152	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:46604152A>C	ENST00000275016.2	-	5	909	c.706T>G	c.(706-708)Tgt>Ggt	p.C236G		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	236					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						GCAGATTTACATGCTTTTATA	0.254																																					p.C236G		Atlas-SNP	.											.	CYP39A1	41	.	0			c.T706G						PASS	.						48.0	49.0	49.0					6																	46604152		2201	4291	6492	SO:0001583	missense	51302	exon5			ATTTACATGCTTT	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.706T>G	chr6.hg19:g.46604152A>C	ENSP00000275016:p.Cys236Gly	163.0	0.0	.		155.0	27.0	.	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	hg19	CCDS4916.1	.	.	.	.	.	.	.	.	.	.	A	6.429	0.447325	0.12223	.	.	ENSG00000146233	ENST00000275016	T	0.67698	-0.28	6.04	-4.27	0.03744	.	1.033410	0.07651	N	0.931975	T	0.13841	0.0335	N	0.08118	0	0.09310	N	1	B;B	0.13145	0.003;0.007	B;B	0.11329	0.004;0.006	T	0.09885	-1.0654	10	0.15066	T	0.55	1.0091	1.0259	0.01527	0.2813:0.1006:0.277:0.3411	.	216;236	B7Z786;Q9NYL5	.;CP39A_HUMAN	G	236	ENSP00000275016:C236G	ENSP00000275016:C236G	C	-	1	0	CYP39A1	46712111	0.000000	0.05858	0.000000	0.03702	0.575000	0.36095	-0.191000	0.09601	-0.304000	0.08843	0.459000	0.35465	TGT	.	.	.	none		0.254	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
MDN1	23195	hgsc.bcm.edu	37	6	90405588	90405588	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:90405588G>T	ENST00000369393.3	-	61	9622	c.9507C>A	c.(9505-9507)agC>agA	p.S3169R	MDN1_ENST00000428876.1_Missense_Mutation_p.S3169R			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	3169					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)		AGGCCTGGCTGCTCCCAAGCA	0.642																																					p.S3169R		Atlas-SNP	.											.	MDN1	478	.	0			c.C9507A						PASS	.						39.0	41.0	41.0					6																	90405588		2203	4300	6503	SO:0001583	missense	23195	exon61			CTGGCTGCTCCCA	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.9507C>A	chr6.hg19:g.90405588G>T	ENSP00000358400:p.Ser3169Arg	104.0	0.0	.		111.0	23.0	.	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	hg19	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	G	6.555	0.470722	0.12461	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03124	4.04;4.04	5.19	0.217	0.15264	.	0.622155	0.16894	N	0.195186	T	0.00468	0.0015	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43988	-0.9357	10	0.19147	T	0.46	.	2.3682	0.04324	0.2946:0.148:0.4511:0.1064	.	3169	Q9NU22	MDN1_HUMAN	R	3169	ENSP00000358400:S3169R;ENSP00000413970:S3169R	ENSP00000358400:S3169R	S	-	3	2	MDN1	90462309	0.940000	0.31905	0.015000	0.15790	0.809000	0.45718	0.326000	0.19646	-0.277000	0.09193	-0.140000	0.14226	AGC	.	.	.	none		0.642	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
AK9	221264	hgsc.bcm.edu	37	6	109954291	109954291	+	Silent	SNP	G	G	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:109954291G>T	ENST00000424296.2	-	12	1165	c.1089C>A	c.(1087-1089)atC>atA	p.I363I	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000285397.5_Silent_p.I363I|AK9_ENST00000368948.2_Silent_p.I363I	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	363					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										AAAGACAGTAGATTTTACCTA	0.338																																					p.I363I		Atlas-SNP	.											.	AKD1	223	.	0			c.C1089A						PASS	.						82.0	77.0	79.0					6																	109954291		2203	4300	6503	SO:0001819	synonymous_variant	221264	exon12			ACAGTAGATTTTA	AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.1089C>A	chr6.hg19:g.109954291G>T		77.0	0.0	.		103.0	33.0	.	NM_145025	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Silent	SNP	ENST00000424296.2	hg19	CCDS55048.1																																																																																			.	.	.	none		0.338	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001145128	
KATNA1	11104	hgsc.bcm.edu	37	6	149944285	149944285	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:149944285A>T	ENST00000335647.5	-	3	499	c.455T>A	c.(454-456)gTt>gAt	p.V152D	KATNA1_ENST00000494504.1_5'Flank|KATNA1_ENST00000367411.2_Missense_Mutation_p.V152D|KATNA1_ENST00000335643.8_Missense_Mutation_p.V152D					katanin p60 (ATPase containing) subunit A 1											endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	12		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;2.95e-12)|GBM - Glioblastoma multiforme(68;0.173)		ACGACAACGAACAGCTTTCCC	0.358																																					p.V152D		Atlas-SNP	.											.	KATNA1	34	.	0			c.T455A						PASS	.						176.0	141.0	153.0					6																	149944285		2203	4300	6503	SO:0001583	missense	11104	exon4			CAACGAACAGCTT	AF056022	CCDS5217.1, CCDS56456.1	6q24.3	2011-01-25	2011-01-25		ENSG00000186625	ENSG00000186625		"""ATPases / AAA-type"""	6216	protein-coding gene	gene with protein product		606696	"""katanin p60 (ATPase-containing) subunit A 1"""			9658175	Standard	NM_007044		Approved		uc003qms.3	O75449	OTTHUMG00000015787	ENST00000335647.5:c.455T>A	chr6.hg19:g.149944285A>T	ENSP00000335106:p.Val152Asp	93.0	0.0	.		92.0	12.0	.	NM_007044		Missense_Mutation	SNP	ENST00000335647.5	hg19	CCDS5217.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.324241	0.41197	.	.	ENSG00000186625	ENST00000335647;ENST00000335643;ENST00000367411;ENST00000444282;ENST00000420200	D;D;D;D	0.95853	-3.39;-3.52;-3.39;-3.83	5.88	4.72	0.59763	.	0.523100	0.21943	N	0.066860	D	0.86707	0.5997	L	0.33485	1.01	0.58432	D	0.999999	B;P;B	0.35656	0.025;0.514;0.012	B;B;B	0.34242	0.028;0.178;0.028	D	0.84247	0.0475	9	.	.	.	.	12.0234	0.53356	0.9325:0.0:0.0675:0.0	.	152;152;152	A8K7S5;O75449-2;O75449	.;.;KTNA1_HUMAN	D	152	ENSP00000335106:V152D;ENSP00000335180:V152D;ENSP00000356381:V152D;ENSP00000390322:V152D	.	V	-	2	0	KATNA1	149985978	1.000000	0.71417	0.889000	0.34880	0.996000	0.88848	5.934000	0.70138	1.044000	0.40200	0.482000	0.46254	GTT	.	.	.	none		0.358	KATNA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042641.2	NM_007044	
ZNF479	90827	hgsc.bcm.edu	37	7	57187920	57187920	+	Missense_Mutation	SNP	C	C	G	rs572783904		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:57187920C>G	ENST00000331162.4	-	5	1472	c.1202G>C	c.(1201-1203)aGa>aCa	p.R401T		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	401					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.R401I(1)		NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			AGTATGAATTCTCTTGTGGAT	0.438																																					p.R401T		Atlas-SNP	.											ZNF479,colon,carcinoma,0,1	ZNF479	193	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1202C						PASS	.						14.0	12.0	13.0					7																	57187920		1821	3902	5723	SO:0001583	missense	90827	exon5			TGAATTCTCTTGT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1202G>C	chr7.hg19:g.57187920C>G	ENSP00000333776:p.Arg401Thr	241.0	1.0	.		307.0	80.0	.	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	hg19	CCDS43590.1	.	.	.	.	.	.	.	.	.	.	c	8.487	0.861161	0.17178	.	.	ENSG00000185177	ENST00000331162	T	0.02421	4.3	0.946	-0.375	0.12509	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03136	0.0092	L	0.56340	1.77	0.24060	N	0.996018	P	0.50066	0.931	B	0.41088	0.347	T	0.33471	-0.9867	9	0.66056	D	0.02	.	2.1182	0.03719	0.2948:0.4775:0.0:0.2278	.	401	Q96JC4	ZN479_HUMAN	T	401	ENSP00000333776:R401T	ENSP00000333776:R401T	R	-	2	0	ZNF479	57191862	0.001000	0.12720	0.012000	0.15200	0.012000	0.07955	1.404000	0.34623	-1.303000	0.02332	-1.323000	0.01288	AGA	.	.	.	none		0.438	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
GTF2IRD1	9569	hgsc.bcm.edu	37	7	73953047	73953047	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:73953047A>T	ENST00000265755.3	+	13	1878	c.1485A>T	c.(1483-1485)aaA>aaT	p.K495N	GTF2IRD1_ENST00000489094.1_3'UTR|GTF2IRD1_ENST00000455841.2_Missense_Mutation_p.K527N|GTF2IRD1_ENST00000476977.1_Missense_Mutation_p.K495N|GTF2IRD1_ENST00000424337.2_Missense_Mutation_p.K495N	NM_005685.3|NM_016328.2	NP_005676.3|NP_057412.1	Q9UHL9	GT2D1_HUMAN	GTF2I repeat domain containing 1	495					multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|transition between slow and fast fiber (GO:0014886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(19)|ovary(6)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						GGCCGATCAAAATTGAGCCAG	0.592																																					p.K527N		Atlas-SNP	.											.	GTF2IRD1	91	.	0			c.A1581T						PASS	.						70.0	70.0	70.0					7																	73953047		2203	4300	6503	SO:0001583	missense	9569	exon13			GATCAAAATTGAG	AF151354	CCDS5571.1, CCDS47613.1, CCDS56492.1	7q11.23	2008-04-18	2002-01-14		ENSG00000006704	ENSG00000006704			4661	protein-coding gene	gene with protein product	"""binding factor for early enhancer"""	604318	"""GTF2I repeat domain-containing 1"""	WBSCR11		9774679, 10198167	Standard	NM_016328		Approved	MusTRD1, RBAP2, GTF3, WBSCR12, BEN, Cream1	uc010lbq.3	Q9UHL9	OTTHUMG00000023782	ENST00000265755.3:c.1485A>T	chr7.hg19:g.73953047A>T	ENSP00000265755:p.Lys495Asn	72.0	0.0	.		49.0	8.0	.	NM_001199207	O95444|Q6DSU6|Q75MX7|Q86UM3|Q8WVC4|Q9UHK8|Q9UI91	Missense_Mutation	SNP	ENST00000265755.3	hg19	CCDS5571.1	.	.	.	.	.	.	.	.	.	.	A	22.7	4.323217	0.81580	.	.	ENSG00000006704	ENST00000265755;ENST00000455841;ENST00000424337;ENST00000476977	T;T;T;T	0.52754	0.68;0.67;0.71;0.65	4.8	2.34	0.29019	.	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	M	0.65498	2.005	0.50632	D	0.999881	D;P;D;D	0.71674	0.998;0.792;0.967;0.98	D;B;P;P	0.78314	0.991;0.255;0.662;0.818	T	0.60702	-0.7211	10	0.87932	D	0	-14.944	7.1506	0.25608	0.7434:0.0:0.2566:0.0	.	527;495;495;495	Q6DSU6;E9PFE2;Q9UHL9;Q9UHL9-2	.;.;GT2D1_HUMAN;.	N	495;527;495;495	ENSP00000265755:K495N;ENSP00000397566:K527N;ENSP00000408477:K495N;ENSP00000418383:K495N	ENSP00000265755:K495N	K	+	3	2	GTF2IRD1	73590983	1.000000	0.71417	0.998000	0.56505	0.921000	0.55340	1.323000	0.33701	0.762000	0.33152	0.459000	0.35465	AAA	.	.	.	none		0.592	GTF2IRD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252654.2	NM_016328	
MUC17	140453	hgsc.bcm.edu	37	7	100683876	100683876	+	Missense_Mutation	SNP	T	T	G	rs145514577		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:100683876T>G	ENST00000306151.4	+	3	9243	c.9179T>G	c.(9178-9180)aTt>aGt	p.I3060S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3060	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CCAGTGGCCATTCCTGAGGCT	0.493													G|||	1	0.000199681	0.0	0.0	5008	,	,		25521	0.0		0.001	False		,,,				2504	0.0				p.I3060S		Atlas-SNP	.											MUC17,NS,carcinoma,0,1	MUC17	804	.	0			c.T9179G						PASS	.						275.0	283.0	280.0					7																	100683876		2203	4300	6503	SO:0001583	missense	140453	exon3			TGGCCATTCCTGA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.9179T>G	chr7.hg19:g.100683876T>G	ENSP00000302716:p.Ile3060Ser	42.0	2.0	.		57.0	5.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	N	0.327	-0.958208	0.02267	.	.	ENSG00000169876	ENST00000306151	T	0.02197	4.4	0.814	-0.258	0.12975	.	.	.	.	.	T	0.00998	0.0033	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.48681	-0.9014	9	0.17369	T	0.5	.	3.7091	0.08413	0.0:0.5408:0.2591:0.2001	.	3060	Q685J3	MUC17_HUMAN	S	3060	ENSP00000302716:I3060S	ENSP00000302716:I3060S	I	+	2	0	MUC17	100470596	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-4.610000	0.00209	-0.661000	0.05345	-2.058000	0.00401	ATT	.	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MOGAT3	346606	hgsc.bcm.edu	37	7	100844043	100844043	+	Silent	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:100844043G>A	ENST00000223114.4	-	1	259	c.93C>T	c.(91-93)ctC>ctT	p.L31L	MOGAT3_ENST00000379423.3_Silent_p.L31L|MOGAT3_ENST00000440203.2_Silent_p.L31L	NM_178176.2	NP_835470.1	Q86VF5	MOGT3_HUMAN	monoacylglycerol O-acyltransferase 3	31					glycerol metabolic process (GO:0006071)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|diacylglycerol O-acyltransferase activity (GO:0004144)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(10)|ovary(3)	22	Lung NSC(181;0.168)|all_lung(186;0.215)					AGAGGAAAGTGAGCACATATT	0.592																																					p.L31L		Atlas-SNP	.											.	MOGAT3	72	.	0			c.C93T						PASS	.						93.0	72.0	79.0					7																	100844043		2203	4300	6503	SO:0001819	synonymous_variant	346606	exon1			GAAAGTGAGCACA	AY229854	CCDS5714.1, CCDS75643.1	7q22	2012-09-06			ENSG00000106384	ENSG00000106384	2.3.1.20, 2.3.1.22		23249	protein-coding gene	gene with protein product		610184				12618427, 14970677	Standard	XM_005250309		Approved	DC7, MGAT3	uc003uyc.3	Q86VF5	OTTHUMG00000023328	ENST00000223114.4:c.93C>T	chr7.hg19:g.100844043G>A		89.0	0.0	.		78.0	13.0	.	NM_178176	Q496A6|Q496A7|Q496A8|Q9UDW7	Silent	SNP	ENST00000223114.4	hg19	CCDS5714.1																																																																																			.	.	.	none		0.592	MOGAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059649.3	NM_178176	
RINT1	60561	hgsc.bcm.edu	37	7	105187490	105187490	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:105187490G>A	ENST00000257700.2	+	5	880	c.649G>A	c.(649-651)Gtt>Att	p.V217I		NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	217					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GAGAGCCACAGTTAAATTCTG	0.403																																					p.V217I		Atlas-SNP	.											.	RINT1	65	.	0			c.G649A						PASS	.						108.0	98.0	102.0					7																	105187490		2203	4300	6503	SO:0001583	missense	60561	exon5			GCCACAGTTAAAT	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.649G>A	chr7.hg19:g.105187490G>A	ENSP00000257700:p.Val217Ile	147.0	0.0	.		184.0	54.0	.	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Missense_Mutation	SNP	ENST00000257700.2	hg19	CCDS34726.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650241	0.47362	.	.	ENSG00000135249	ENST00000257700	T	0.22336	1.96	5.26	4.38	0.52667	.	0.189193	0.46442	N	0.000290	T	0.19644	0.0472	L	0.48362	1.52	0.49687	D	0.999815	B	0.22346	0.068	B	0.13407	0.009	T	0.02567	-1.1140	10	0.30078	T	0.28	-10.9031	13.7518	0.62912	0.0749:0.0:0.9251:0.0	.	217	Q6NUQ1	RINT1_HUMAN	I	217	ENSP00000257700:V217I	ENSP00000257700:V217I	V	+	1	0	RINT1	104974726	1.000000	0.71417	0.884000	0.34674	0.970000	0.65996	4.771000	0.62318	1.205000	0.43262	0.563000	0.77884	GTT	.	.	.	none		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	
NAA38	84316	hgsc.bcm.edu	37	7	117828344	117828344	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:117828344G>A	ENST00000249299.2	+	3	277	c.85G>A	c.(85-87)Ggt>Agt	p.G29S	NAA38_ENST00000422760.1_Missense_Mutation_p.G8S|NAA38_ENST00000424702.1_Missense_Mutation_p.G29S	NM_016200.4	NP_057284.1	Q9BRA0	LSMD1_HUMAN	N(alpha)-acetyltransferase 38, NatC auxiliary subunit	69					negative regulation of apoptotic process (GO:0043066)	cytoplasm (GO:0005737)|NatC complex (GO:0031417)|nucleus (GO:0005634)		p.G29S(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	8						AACACTGAAAGGTTTTGACCA	0.363																																					p.G29S		Atlas-SNP	.											NAA38,mouth,carcinoma,0,1	NAA38	16	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.G85A						PASS	.						83.0	85.0	84.0					7																	117828344		2203	4300	6503	SO:0001583	missense	51691	exon3			CTGAAAGGTTTTG		CCDS11122.1	17p13.1	2014-01-21	2014-01-21	2014-01-21		ENSG00000183011		"""N(alpha)-acetyltransferase subunits"""	28212	protein-coding gene	gene with protein product			"""LSM domain containing 1"""	LSMD1		16484612, 19398576	Standard	NM_032356		Approved	MGC14151, PFAAP2	uc002gja.3	Q9BRA0		ENST00000249299.2:c.85G>A	chr7.hg19:g.117828344G>A	ENSP00000249299:p.Gly29Ser	68.0	0.0	.		86.0	28.0	.	NM_016200	Q8N4M0	Missense_Mutation	SNP	ENST00000249299.2	hg19	CCDS5775.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.916546	0.92249	.	.	ENSG00000128534	ENST00000249299;ENST00000424702;ENST00000422760;ENST00000411938	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.69	4.78	0.61160	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	T	0.61850	0.2380	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.79108	0.992	T	0.57670	-0.7771	9	0.32370	T	0.25	-19.584	16.7642	0.85520	0.0:0.1285:0.8715:0.0	.	29	O95777	NAA38_HUMAN	S	29;29;8;40	ENSP00000249299:G29S;ENSP00000395263:G29S;ENSP00000403811:G8S;ENSP00000408267:G40S	ENSP00000249299:G29S	G	+	1	0	NAA38	117615580	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.359000	0.79477	2.687000	0.91594	0.650000	0.86243	GGT	.	.	.	none		0.363	NAA38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346774.2	NM_032356	
MGAM	8972	hgsc.bcm.edu	37	7	141720863	141720863	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:141720863T>A	ENST00000549489.2	+	5	633	c.538T>A	c.(538-540)Tct>Act	p.S180T	MGAM_ENST00000475668.2_Missense_Mutation_p.S180T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	180					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	ATATCAGACATCTAATCGTTT	0.348																																					p.S180T		Atlas-SNP	.											.	MGAM	767	.	0			c.T538A						PASS	.						99.0	89.0	92.0					7																	141720863		1829	4082	5911	SO:0001583	missense	8972	exon5			CAGACATCTAATC	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.538T>A	chr7.hg19:g.141720863T>A	ENSP00000447378:p.Ser180Thr	86.0	0.0	.		123.0	17.0	.	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	hg19	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	T	11.14	1.550895	0.27739	.	.	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000475668;ENST00000548812	T;D	0.85702	-0.79;-2.02	5.22	2.71	0.32032	Glycoside hydrolase-type carbohydrate-binding (1);	0.138996	0.33875	N	0.004470	T	0.76814	0.4040	L	0.49640	1.575	0.09310	N	1	B	0.10296	0.003	B	0.11329	0.006	T	0.59273	-0.7485	10	0.21014	T	0.42	.	6.3621	0.21435	0.1454:0.0:0.3461:0.5085	.	180	O43451	MGA_HUMAN	T	180;180;180;57	ENSP00000419372:S180T;ENSP00000447378:S180T	ENSP00000316431:S57T	S	+	1	0	MGAM	141367332	0.000000	0.05858	0.748000	0.31131	0.979000	0.70002	-1.353000	0.02617	0.985000	0.38656	0.460000	0.39030	TCT	.	.	.	none		0.348	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
ZNF786	136051	hgsc.bcm.edu	37	7	148767517	148767517	+	Nonstop_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:148767517A>C	ENST00000491431.1	-	4	2411	c.2347T>G	c.(2347-2349)Tga>Gga	p.*783G	ZNF786_ENST00000451334.3_Nonstop_Mutation_p.*746G|ZNF786_ENST00000316286.9_Nonstop_Mutation_p.*697G	NM_152411.3	NP_689624.2	Q8N393	ZN786_HUMAN	zinc finger protein 786	0					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|cervix(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(2)|skin(2)|soft_tissue(1)|urinary_tract(2)	26	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			ACTCTGCCTCAACTCCAATCG	0.498																																					p.X783G		Atlas-SNP	.											.	ZNF786	69	.	0			c.T2347G						PASS	.						270.0	264.0	266.0					7																	148767517		2011	4186	6197	SO:0001578	stop_lost	136051	exon4			TGCCTCAACTCCA	AK095701, AL834510	CCDS47738.1	7q36.1	2013-01-08			ENSG00000197362	ENSG00000197362		"""Zinc fingers, C2H2-type"", ""-"""	21806	protein-coding gene	gene with protein product							Standard	NM_152411		Approved	DKFZp762I137	uc003wfh.2	Q8N393	OTTHUMG00000158975	ENST00000491431.1:c.2347T>G	chr7.hg19:g.148767517A>C	ENSP00000417470:p.*783Argext*9	67.0	0.0	.		91.0	34.0	.	NM_152411	A1A568|B4DMI1	Missense_Mutation	SNP	ENST00000491431.1	hg19	CCDS47738.1	.	.	.	.	.	.	.	.	.	.	A	13.42	2.232594	0.39498	.	.	ENSG00000197362	ENST00000316286;ENST00000491431;ENST00000451334	.	.	.	4.62	4.62	0.57501	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.3575	0.43974	1.0:0.0:0.0:0.0	.	.	.	.	G	697;783;746	.	.	X	-	1	0	ZNF786	148398450	0.027000	0.19231	0.997000	0.53966	0.787000	0.44495	1.219000	0.32479	1.954000	0.56735	0.482000	0.46254	TGA	.	.	.	none		0.498	ZNF786-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352751.1	NM_152411	
AOC1	26	hgsc.bcm.edu	37	7	150554944	150554944	+	Silent	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:150554944T>C	ENST00000493429.1	+	4	1970	c.1386T>C	c.(1384-1386)gaT>gaC	p.D462D	AOC1_ENST00000467291.1_Silent_p.D462D|AOC1_ENST00000360937.4_Silent_p.D462D|AOC1_ENST00000416793.2_Silent_p.D462D			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	462					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	ACAATTATGATTACATTTGGG	0.527																																					p.D462D		Atlas-SNP	.											.	ABP1	92	.	0			c.T1386C						PASS	.						71.0	78.0	76.0					7																	150554944		2077	4222	6299	SO:0001819	synonymous_variant	26	exon2			TTATGATTACATT	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.1386T>C	chr7.hg19:g.150554944T>C		51.0	0.0	.		63.0	23.0	.	NM_001091	C9J690|Q16683|Q16684|Q56II4|Q6GU42	Silent	SNP	ENST00000493429.1	hg19	CCDS43679.1																																																																																			.	.	.	none		0.527	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
TNFRSF10D	8793	hgsc.bcm.edu	37	8	23012460	23012460	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr8:23012460C>A	ENST00000312584.3	-	2	277	c.183G>T	c.(181-183)caG>caT	p.Q61H		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	61					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAACTTCGTCCTGCCGGGGGA	0.582																																					p.Q61H		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.G183T						PASS	.						55.0	49.0	51.0					8																	23012460		2203	4300	6503	SO:0001583	missense	8793	exon2			TTCGTCCTGCCGG	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.183G>T	chr8.hg19:g.23012460C>A	ENSP00000310263:p.Gln61His	73.0	0.0	.		78.0	13.0	.	NM_003840	B2R8W0|Q9Y6Q4	Missense_Mutation	SNP	ENST00000312584.3	hg19	CCDS6038.1	.	.	.	.	.	.	.	.	.	.	c	5.149	0.213132	0.09757	.	.	ENSG00000173530	ENST00000312584	D	0.83755	-1.76	1.72	0.824	0.18818	.	11.086800	0.00691	U	0.000727	T	0.77592	0.4153	L	0.52573	1.65	0.09310	N	1	B	0.21381	0.055	B	0.18263	0.021	T	0.53954	-0.8365	10	0.30078	T	0.28	.	4.0905	0.09967	0.0:0.7771:0.0:0.2229	.	61	Q9UBN6	TR10D_HUMAN	H	61	ENSP00000310263:Q61H	ENSP00000310263:Q61H	Q	-	3	2	TNFRSF10D	23068405	0.000000	0.05858	0.003000	0.11579	0.004000	0.04260	-1.049000	0.03514	0.303000	0.22785	0.313000	0.20887	CAG	.	.	.	none		0.582	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
TG	7038	hgsc.bcm.edu	37	8	133953675	133953675	+	Silent	SNP	C	C	A	rs142766592		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr8:133953675C>A	ENST00000220616.4	+	26	5161	c.5121C>A	c.(5119-5121)ccC>ccA	p.P1707P	TG_ENST00000377869.1_Silent_p.P1650P|TG_ENST00000542445.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1707					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		TGTACAACCCCATTGTGTTCT	0.502																																					p.P1707P		Atlas-SNP	.											.	TG	416	.	0			c.C5121A						PASS	.						171.0	144.0	153.0					8																	133953675		2203	4300	6503	SO:0001819	synonymous_variant	7038	exon26			CAACCCCATTGTG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5121C>A	chr8.hg19:g.133953675C>A		113.0	0.0	.		111.0	23.0	.	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	hg19	CCDS34944.1																																																																																			.	C|1.000;T|0.000	.	alt		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
PLEC	5339	hgsc.bcm.edu	37	8	144999275	144999275	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr8:144999275C>T	ENST00000322810.4	-	31	5402	c.5233G>A	c.(5233-5235)Gag>Aag	p.E1745K	PLEC_ENST00000354589.3_Missense_Mutation_p.E1608K|PLEC_ENST00000527096.1_Missense_Mutation_p.E1631K|PLEC_ENST00000356346.3_Missense_Mutation_p.E1594K|PLEC_ENST00000357649.2_Missense_Mutation_p.E1612K|PLEC_ENST00000345136.3_Missense_Mutation_p.E1608K|PLEC_ENST00000436759.2_Missense_Mutation_p.E1635K|PLEC_ENST00000354958.2_Missense_Mutation_p.E1586K|PLEC_ENST00000398774.2_Missense_Mutation_p.E1576K	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	1745	Central fibrous rod domain.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TCAGCCTCCTCCCGCAGCTGT	0.711																																					p.E1745K		Atlas-SNP	.											.	PLEC	1144	.	0			c.G5233A						PASS	.						3.0	3.0	3.0					8																	144999275		1885	3799	5684	SO:0001583	missense	5339	exon31			CCTCCTCCCGCAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.5233G>A	chr8.hg19:g.144999275C>T	ENSP00000323856:p.Glu1745Lys	204.0	0.0	.		197.0	42.0	.	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	hg19	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.946650	0.73672	.	.	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.77877	-1.09;-1.08;-1.13;-1.13;-1.07;-1.09;-1.08;-1.09;-1.08	4.71	4.71	0.59529	.	0.187621	0.31010	U	0.008426	D	0.86389	0.5921	M	0.72894	2.215	0.48288	D	0.999622	P;P;P;P;P;P;D;P	0.71674	0.908;0.908;0.908;0.851;0.908;0.908;0.998;0.908	P;P;P;B;P;P;D;P	0.67900	0.492;0.492;0.492;0.297;0.492;0.492;0.954;0.492	D	0.86228	0.1635	10	0.39692	T	0.17	.	17.273	0.87107	0.0:1.0:0.0:0.0	.	1635;1594;1586;1745;1576;1608;1612;1608	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	K	1608;1612;1608;1576;1745;1586;1594;1635;1631	ENSP00000344848:E1608K;ENSP00000350277:E1612K;ENSP00000346602:E1608K;ENSP00000381756:E1576K;ENSP00000323856:E1745K;ENSP00000347044:E1586K;ENSP00000348702:E1594K;ENSP00000388180:E1635K;ENSP00000434583:E1631K	ENSP00000323856:E1745K	E	-	1	0	PLEC	145071263	0.980000	0.34600	0.989000	0.46669	0.959000	0.62525	3.143000	0.50608	2.166000	0.68216	0.542000	0.68232	GAG	.	.	.	none		0.711	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PTPRD	5789	hgsc.bcm.edu	37	9	8341183	8341183	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:8341183A>C	ENST00000381196.4	-	38	5576	c.5033T>G	c.(5032-5034)aTt>aGt	p.I1678S	PTPRD_ENST00000397617.3_Missense_Mutation_p.I1271S|PTPRD_ENST00000358503.5_Missense_Mutation_p.I1656S|PTPRD_ENST00000397611.3_Missense_Mutation_p.I1268S|PTPRD_ENST00000537002.1_Missense_Mutation_p.I1268S|PTPRD_ENST00000540109.1_Missense_Mutation_p.I1678S|PTPRD_ENST00000397606.3_Missense_Mutation_p.I1271S|PTPRD_ENST00000355233.5_Missense_Mutation_p.I1272S|PTPRD_ENST00000356435.5_Missense_Mutation_p.I1678S|PTPRD_ENST00000360074.4_Missense_Mutation_p.I1665S|PTPRD_ENST00000486161.1_Missense_Mutation_p.I1271S	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1678	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		ATATGGCATAATATTAACAAG	0.398										TSP Lung(15;0.13)																											p.I1678S		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T5033G						PASS	.						195.0	206.0	202.0					9																	8341183		2203	4300	6503	SO:0001583	missense	5789	exon41			GGCATAATATTAA	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.5033T>G	chr9.hg19:g.8341183A>C	ENSP00000370593:p.Ile1678Ser	152.0	0.0	.		141.0	30.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Missense_Mutation	SNP	ENST00000381196.4	hg19	CCDS43786.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.030464	0.75504	.	.	ENSG00000153707	ENST00000381196;ENST00000356435;ENST00000360074;ENST00000358503;ENST00000355233;ENST00000397617;ENST00000397611;ENST00000537002;ENST00000346816;ENST00000540109;ENST00000486161;ENST00000397606	D;D;D;D;D;D;D;D;D;D;D	0.85629	-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01;-2.01	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.049513	0.85682	D	0.000000	D	0.95417	0.8512	H	0.97365	3.99	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	0.994;0.994;0.994;0.994;1.0;0.992;1.0;0.996;0.999	D;D;D;D;D;D;D;D;D	0.97110	0.988;0.988;0.988;0.988;1.0;0.979;0.999;0.994;0.999	D	0.96950	0.9694	9	.	.	.	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1271;1262;1271;1272;1268;1268;1665;1678;1678	Q3KPJ2;Q3KPI9;Q3KPJ0;Q3KPJ1;F5GWT7;F5GWY7;G3XAE2;Q2HXI4;P23468	.;.;.;.;.;.;.;.;PTPRD_HUMAN	S	1678;1678;1665;1656;1272;1271;1268;1268;1149;1678;1271;1271	ENSP00000370593:I1678S;ENSP00000348812:I1678S;ENSP00000353187:I1665S;ENSP00000351293:I1656S;ENSP00000347373:I1272S;ENSP00000380741:I1271S;ENSP00000380735:I1268S;ENSP00000440515:I1268S;ENSP00000438164:I1678S;ENSP00000417093:I1271S;ENSP00000380731:I1271S	.	I	-	2	0	PTPRD	8331183	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.287000	0.95975	2.326000	0.78906	0.533000	0.62120	ATT	.	.	.	none		0.398	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
PSIP1	11168	hgsc.bcm.edu	37	9	15472713	15472713	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:15472713G>T	ENST00000380733.4	-	10	1237	c.894C>A	c.(892-894)caC>caA	p.H298Q	PSIP1_ENST00000380716.4_Missense_Mutation_p.H298Q|PSIP1_ENST00000380715.1_Missense_Mutation_p.H298Q|PSIP1_ENST00000397519.2_Missense_Mutation_p.H298Q|PSIP1_ENST00000380738.4_Missense_Mutation_p.H298Q			O75475	PSIP1_HUMAN	PC4 and SFRS1 interacting protein 1	298					establishment of integrated proviral latency (GO:0075713)|mRNA 5'-splice site recognition (GO:0000395)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to heat (GO:0009408)|response to oxidative stress (GO:0006979)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription coactivator activity (GO:0001105)|supercoiled DNA binding (GO:0097100)			breast(2)|endometrium(2)|kidney(1)|lung(3)|prostate(1)	9				GBM - Glioblastoma multiforme(50;2.38e-06)		TATTCCTTCTGTGAGCAGTCT	0.368																																					p.H298Q		Atlas-SNP	.											.	PSIP1	93	.	0			c.C894A						PASS	.						185.0	163.0	170.0					9																	15472713		2203	4300	6503	SO:0001583	missense	11168	exon9			CCTTCTGTGAGCA	AF098482	CCDS6479.1, CCDS6480.1	9p22.2	2008-02-05	2004-02-24		ENSG00000164985	ENSG00000164985			9527	protein-coding gene	gene with protein product		603620	"""PC4 and SFRS1 interacting protein 2"""	PSIP2		9822615, 9885563	Standard	NM_033222		Approved	p52, LEDGF, p75	uc003zlw.4	O75475	OTTHUMG00000021021	ENST00000380733.4:c.894C>A	chr9.hg19:g.15472713G>T	ENSP00000370109:p.His298Gln	70.0	0.0	.		64.0	6.0	.	NM_021144	D3DRI9|O00256|O95368|Q6P391|Q86YB9|Q9NZI3|Q9UER6	Missense_Mutation	SNP	ENST00000380733.4	hg19	CCDS6479.1	.	.	.	.	.	.	.	.	.	.	G	16.21	3.058992	0.55325	.	.	ENSG00000164985	ENST00000380733;ENST00000380738;ENST00000380715;ENST00000380716;ENST00000397519	T;T;T;T;T	0.42131	1.0;1.0;0.99;0.98;0.98	6.07	0.269	0.15631	.	0.271857	0.42420	N	0.000704	T	0.26774	0.0655	L	0.35723	1.085	0.28008	N	0.935038	B;B	0.12013	0.005;0.003	B;B	0.10450	0.005;0.001	T	0.16394	-1.0404	10	0.23302	T	0.38	.	7.352	0.26697	0.3068:0.1518:0.5415:0.0	.	298;298	O75475-2;O75475	.;PSIP1_HUMAN	Q	298	ENSP00000370109:H298Q;ENSP00000370114:H298Q;ENSP00000370091:H298Q;ENSP00000370092:H298Q;ENSP00000380653:H298Q	ENSP00000370091:H298Q	H	-	3	2	PSIP1	15462713	1.000000	0.71417	0.990000	0.47175	0.971000	0.66376	1.086000	0.30853	-0.146000	0.11274	0.585000	0.79938	CAC	.	.	.	none		0.368	PSIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055445.1	NM_033222	
MAPKAP1	79109	hgsc.bcm.edu	37	9	128347834	128347834	+	Splice_Site	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:128347834T>C	ENST00000373498.1	-	4	739	c.671A>G	c.(670-672)aAt>aGt	p.N224S	MAPKAP1_ENST00000394063.1_Splice_Site_p.N32S|MAPKAP1_ENST00000373503.3_Splice_Site_p.N32S|MAPKAP1_ENST00000265960.3_Splice_Site_p.N224S|MAPKAP1_ENST00000350766.3_Splice_Site_p.N224S|MAPKAP1_ENST00000373497.5_Splice_Site_p.K32R|MAPKAP1_ENST00000373511.2_Splice_Site_p.N224S|MAPKAP1_ENST00000394060.3_Splice_Site_p.N224S			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	224	Interaction with NBN.				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)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						AATGGATTACTTGAGCTTCGG	0.537																																					p.N224S		Atlas-SNP	.											.	MAPKAP1	68	.	0			c.A671G						PASS	.						108.0	94.0	98.0					9																	128347834		2203	4300	6503	SO:0001630	splice_region_variant	79109	exon5			GATTACTTGAGCT	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.671+1A>G	chr9.hg19:g.128347834T>C		74.0	0.0	.		55.0	11.0	.	NM_001006618	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Missense_Mutation	SNP	ENST00000373498.1	hg19	CCDS35140.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.98|16.98	3.270351|3.270351	0.59540|0.59540	.|.	.|.	ENSG00000119487|ENSG00000119487	ENST00000373497|ENST00000373511;ENST00000350766;ENST00000373503;ENST00000373498;ENST00000265960;ENST00000394063;ENST00000420643;ENST00000394060;ENST00000427078;ENST00000468896	.|.	.|.	.|.	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.040219	.|0.85682	.|D	.|0.000000	T|T	0.43809|0.43809	0.1264|0.1264	L|L	0.48362|0.48362	1.52|1.52	0.26792|0.26792	N|N	0.969376|0.969376	P|B;B;B;B;B	0.38711|0.28933	0.643|0.228;0.228;0.034;0.169;0.074	B|B;B;B;B;B	0.36567|0.30855	0.228|0.121;0.085;0.062;0.115;0.08	T|T	0.35699|0.35699	-0.9778|-0.9778	7|8	.|.	.|.	.|.	-7.1874|-7.1874	15.448|15.448	0.75248|0.75248	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	32|224;224;224;224;224	B7Z5E5|Q9BPZ7-6;Q9BPZ7-5;Q9BPZ7-3;Q9BPZ7-2;Q9BPZ7	.|.;.;.;.;SIN1_HUMAN	R|S	32|224;224;32;224;224;32;32;224;32;125	.|.	.|.	K|N	-|-	2|2	0|0	MAPKAP1|MAPKAP1	127387655|127387655	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	4.118000|4.118000	0.57884|0.57884	2.240000|2.240000	0.73641|0.73641	0.533000|0.533000	0.62120|0.62120	AAA|AAT	.	.	.	none		0.537	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		Missense_Mutation
RPL7A	6130	hgsc.bcm.edu	37	9	136215842	136215842	+	Silent	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:136215842G>A	ENST00000323345.6	+	2	99	c.69G>A	c.(67-69)gaG>gaA	p.E23E	MED22_ENST00000344469.5_5'Flank|SURF1_ENST00000495952.1_5'Flank|RPL7A_ENST00000463740.1_3'UTR|RPL7A_ENST00000315731.4_5'UTR|SNORD36B_ENST00000363961.1_RNA|MED22_ENST00000343730.5_5'Flank|MED22_ENST00000371999.1_5'Flank|SNORD24_ENST00000383884.1_RNA|MED22_ENST00000471524.1_5'Flank|SNORD36C_ENST00000516733.1_RNA|MED22_ENST00000476080.1_5'Flank|MED22_ENST00000491289.1_5'Flank|SNORD36A_ENST00000362874.1_RNA	NM_000972.2	NP_000963.1	P62424	RL7A_HUMAN	ribosomal protein L7a	23					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(1)|lung(3)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(145;4.93e-07)|Epithelial(140;4.09e-06)|all cancers(34;3.78e-05)		AGAAGCAGGAGGCTAAGAAAG	0.483																																					p.E23E		Atlas-SNP	.											.	RPL7A	9	.	0			c.G69A						PASS	.						51.0	55.0	54.0					9																	136215842		2203	4296	6499	SO:0001819	synonymous_variant	6130	exon2			GCAGGAGGCTAAG	BC005128	CCDS6965.1	9q34	2011-04-06			ENSG00000148303	ENSG00000148303		"""L ribosomal proteins"""	10364	protein-coding gene	gene with protein product	"""surfeit 3"", ""PLA-X polypeptide"", ""surfeit locus protein 3"", ""60S ribosomal protein L7a"", "";"", ""thyroid hormone receptor uncoupling protein"""	185640				2403926, 2966065	Standard	NM_000972		Approved	SURF3, TRUP, L7A	uc004cde.1	P62424	OTTHUMG00000020864	ENST00000323345.6:c.69G>A	chr9.hg19:g.136215842G>A		54.0	0.0	.		50.0	9.0	.	NM_000972	P11518|Q5T8U4	Silent	SNP	ENST00000323345.6	hg19	CCDS6965.1																																																																																			.	.	.	none		0.483	RPL7A-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054869.1	NM_000972	
SNAPC4	6621	hgsc.bcm.edu	37	9	139292750	139292751	+	Splice_Site	DNP	CC	CC	AA	rs7031489	byFrequency	TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:139292750_139292751CC>AA	ENST00000298532.2	-	1	498_499	c.130_131GG>TT	c.(130-132)GGt>TTt	p.G44F		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		AAGGGGCTTACCTGCTTCAGAA	0.554																																					.|p.D44Y		Atlas-SNP	.											SNAPC4,NS,malignant_melanoma,0,1|.	SNAPC4	82	.	0			c.130+1G>T|c.G130T						PASS	.																																			SO:0001630	splice_region_variant	6621	exon2|exon1			GGCTTACCTGCTT|GCTTACCTGCTTC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.130_131delinsAA	chr9.hg19:g.139292750_139292751delinsAA		74.0|73.0	0.0	.		55.0|59.0	14.0	.	NM_003086		Splice_Site|Missense_Mutation	SNP	ENST00000298532.2	hg19	CCDS6998.1																																																																																			.	.|C|0.991;T|0.009	.	none|alt		0.554	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Missense_Mutation
PIP4K2A	5305	hgsc.bcm.edu	37	10	22862322	22862322	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:22862322A>G	ENST00000376573.4	-	5	785	c.557T>C	c.(556-558)gTt>gCt	p.V186A	PIP4K2A_ENST00000545335.1_Missense_Mutation_p.V127A|PIP4K2A_ENST00000323883.7_Missense_Mutation_p.V32A|PIP4K2A_ENST00000422321.1_5'UTR	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	186	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						AACTCCATCAACATTAAGCCG	0.388																																					p.V186A		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.T557C						PASS	.						116.0	99.0	105.0					10																	22862322		2203	4300	6503	SO:0001583	missense	5305	exon5			CCATCAACATTAA	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.557T>C	chr10.hg19:g.22862322A>G	ENSP00000365757:p.Val186Ala	122.0	0.0	.		128.0	19.0	.	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Missense_Mutation	SNP	ENST00000376573.4	hg19	CCDS7141.1	.	.	.	.	.	.	.	.	.	.	A	26.3	4.723888	0.89298	.	.	ENSG00000150867	ENST00000376573;ENST00000323883;ENST00000545335;ENST00000422321;ENST00000376565	T;T;T	0.31510	1.49;1.49;1.49	5.5	5.5	0.81552	Phosphatidylinositol-4-phosphate 5-kinase, core (2);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.52125	0.1715	M	0.72479	2.2	0.80722	D	1	B;P	0.45240	0.261;0.854	B;P	0.59012	0.42;0.85	T	0.47971	-0.9075	10	0.39692	T	0.17	-29.164	15.9002	0.79369	1.0:0.0:0.0:0.0	.	32;186	B4DH09;P48426	.;PI42A_HUMAN	A	186;32;127;138;145	ENSP00000365757:V186A;ENSP00000326294:V32A;ENSP00000442098:V127A	ENSP00000326294:V32A	V	-	2	0	PIP4K2A	22902328	1.000000	0.71417	0.928000	0.36995	0.962000	0.63368	8.865000	0.92300	2.219000	0.72066	0.533000	0.62120	GTT	.	.	.	none		0.388	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
JMJD1C	221037	hgsc.bcm.edu	37	10	64976992	64976992	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:64976992C>T	ENST00000399262.2	-	5	871	c.653G>A	c.(652-654)cGc>cAc	p.R218H	JMJD1C_ENST00000489372.2_5'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.R36H|JMJD1C_ENST00000402544.1_5'UTR|JMJD1C_ENST00000399251.1_5'UTR	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	218					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					GATCATGGTGCGGGTGAAGAG	0.373																																					p.R218H		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G653A						PASS	.						113.0	109.0	110.0					10																	64976992		1848	4104	5952	SO:0001583	missense	221037	exon5			ATGGTGCGGGTGA	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.653G>A	chr10.hg19:g.64976992C>T	ENSP00000382204:p.Arg218His	65.0	0.0	.		72.0	10.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	C	18.19	3.569375	0.65765	.	.	ENSG00000171988	ENST00000399262;ENST00000542921	T;T	0.13657	2.57;2.57	5.74	4.83	0.62350	.	0.255682	0.32578	U	0.005909	T	0.14013	0.0339	L	0.44542	1.39	0.80722	D	1	B	0.22541	0.071	B	0.14578	0.011	T	0.02519	-1.1147	10	0.49607	T	0.09	-5.1461	15.0302	0.71701	0.0:0.9309:0.0:0.0691	.	218	Q15652	JHD2C_HUMAN	H	218;36	ENSP00000382204:R218H;ENSP00000444682:R36H	ENSP00000382204:R218H	R	-	2	0	JMJD1C	64646998	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.696000	0.61774	2.707000	0.92482	0.557000	0.71058	CGC	.	.	.	none		0.373	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
DDX21	9188	hgsc.bcm.edu	37	10	70734488	70734488	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:70734488A>C	ENST00000354185.4	+	11	1829	c.1731A>C	c.(1729-1731)aaA>aaC	p.K577N		NM_001256910.1|NM_004728.3	NP_001243839.1|NP_004719.2	Q9NR30	DDX21_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 21	577					ATP catabolic process (GO:0006200)|osteoblast differentiation (GO:0001649)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	20						CTTCCAGCAAAGATGCCATCA	0.368																																					p.K577N		Atlas-SNP	.											.	DDX21	57	.	0			c.A1731C						PASS	.						86.0	80.0	82.0					10																	70734488		2203	4300	6503	SO:0001583	missense	9188	exon11			CAGCAAAGATGCC	U41387	CCDS31211.1, CCDS73144.1	10q21	2013-05-13	2012-02-23		ENSG00000165732	ENSG00000165732		"""DEAD-boxes"""	2744	protein-coding gene	gene with protein product		606357	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 21"""			8614622, 18180292	Standard	NM_004728		Approved	RH-II/GU, GURDB	uc001jov.2	Q9NR30	OTTHUMG00000018366	ENST00000354185.4:c.1731A>C	chr10.hg19:g.70734488A>C	ENSP00000346120:p.Lys577Asn	91.0	0.0	.		101.0	24.0	.	NM_004728	B2RDL0|Q13436|Q5VX41|Q68D35	Missense_Mutation	SNP	ENST00000354185.4	hg19	CCDS31211.1	.	.	.	.	.	.	.	.	.	.	A	11.31	1.600031	0.28534	.	.	ENSG00000165732	ENST00000354185	T	0.18502	2.21	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.12860	0.0312	L	0.33293	1	0.48511	D	0.999665	B	0.24823	0.112	B	0.15870	0.014	T	0.09185	-1.0686	10	0.33141	T	0.24	-11.3454	10.2563	0.43399	0.7547:0.0:0.0:0.2453	.	577	Q9NR30	DDX21_HUMAN	N	577	ENSP00000346120:K577N	ENSP00000346120:K577N	K	+	3	2	DDX21	70404494	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.750000	0.38329	2.171000	0.68590	0.533000	0.62120	AAA	.	.	.	none		0.368	DDX21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048374.1	NM_004728	
DNAJB12	54788	hgsc.bcm.edu	37	10	74114543	74114543	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:74114543T>C	ENST00000444643.2	-	1	445	c.113A>G	c.(112-114)tAt>tGt	p.Y38C	DNAJB12_ENST00000461919.1_5'Flank|DNAJB12_ENST00000338820.3_Missense_Mutation_p.Y72C|DNAJB12_ENST00000394903.2_Missense_Mutation_p.Y72C			Q9NXW2	DJB12_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 12	38						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|skin(1)	4						CGGCGTCGGATACAGCCGCTG	0.632																																					p.Y72C		Atlas-SNP	.											.	DNAJB12	22	.	0			c.A215G						PASS	.						34.0	36.0	35.0					10																	74114543		2203	4300	6503	SO:0001583	missense	54788	exon1			GTCGGATACAGCC	AK000034	CCDS7316.2	10q22	2011-09-02			ENSG00000148719	ENSG00000148719		"""Heat shock proteins / DNAJ (HSP40)"""	14891	protein-coding gene	gene with protein product		608376				11147971	Standard	NM_001002762		Approved	DJ10, FLJ20027	uc001jta.2	Q9NXW2	OTTHUMG00000018436	ENST00000444643.2:c.113A>G	chr10.hg19:g.74114543T>C	ENSP00000403313:p.Tyr38Cys	44.0	0.0	.		38.0	9.0	.	NM_017626	B7Z7I3|Q9H6H0	Missense_Mutation	SNP	ENST00000444643.2	hg19		.	.	.	.	.	.	.	.	.	.	T	23.4	4.405711	0.83230	.	.	ENSG00000148719	ENST00000338820;ENST00000394903;ENST00000444643	T;T;T	0.19394	2.15;2.15;2.15	5.58	5.58	0.84498	.	0.058186	0.64402	D	0.000002	T	0.40473	0.1118	M	0.77103	2.36	0.43777	D	0.9963	D;D	0.60575	0.988;0.98	P;P	0.57548	0.823;0.671	T	0.35822	-0.9773	10	0.62326	D	0.03	-30.1516	10.6161	0.45451	0.1435:0.0:0.0:0.8565	.	38;38	Q9NXW2-2;Q9NXW2	.;DJB12_HUMAN	C	72;72;38	ENSP00000345575:Y72C;ENSP00000378363:Y72C;ENSP00000403313:Y38C	ENSP00000345575:Y72C	Y	-	2	0	DNAJB12	73784549	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	3.330000	0.52068	2.111000	0.64477	0.459000	0.35465	TAT	.	.	.	none		0.632	DNAJB12-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048581.2		
CPN1	1369	hgsc.bcm.edu	37	10	101802229	101802229	+	Silent	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:101802229T>C	ENST00000370418.3	-	9	1583	c.1332A>G	c.(1330-1332)agA>agG	p.R444R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	444					response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		TTTCTTTCTTTCTGGCTTGGG	0.542																																					p.R444R		Atlas-SNP	.											.	CPN1	62	.	0			c.A1332G						PASS	.						96.0	84.0	88.0					10																	101802229		2203	4300	6503	SO:0001819	synonymous_variant	1369	exon9			TTTCTTTCTGGCT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.1332A>G	chr10.hg19:g.101802229T>C		59.0	0.0	.		61.0	7.0	.	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	hg19	CCDS7486.1																																																																																			.	.	.	none		0.542	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
GPAM	57678	hgsc.bcm.edu	37	10	113924282	113924282	+	Splice_Site	SNP	C	C	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr10:113924282C>A	ENST00000348367.4	-	13	1505		c.e13+1		GPAM_ENST00000423155.1_Splice_Site|GPAM_ENST00000369425.1_Splice_Site			Q9HCL2	GPAT1_HUMAN	glycerol-3-phosphate acyltransferase, mitochondrial						acyl-CoA metabolic process (GO:0006637)|CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|defense response to virus (GO:0051607)|fatty acid homeostasis (GO:0055089)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|interleukin-2 secretion (GO:0070970)|negative regulation of activation-induced cell death of T cells (GO:0070236)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of multicellular organism growth (GO:0040018)|regulation of cytokine secretion (GO:0050707)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	glycerol-3-phosphate O-acyltransferase activity (GO:0004366)			breast(2)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31				Epithelial(162;0.0306)|all cancers(201;0.123)		ACAAATTTTACCTTGAAGGAA	0.348																																					.	Ovarian(161;1017 2606 18293 52943)	Atlas-SNP	.											.	GPAM	68	.	0			c.1307+1G>T						PASS	.						56.0	57.0	57.0					10																	113924282		2203	4300	6503	SO:0001630	splice_region_variant	57678	exon14			ATTTTACCTTGAA	AL832464	CCDS7570.1	10q25.3	2009-07-15			ENSG00000119927	ENSG00000119927			24865	protein-coding gene	gene with protein product	"""glycerol-3-phosphate acyltransferase 1, mitochondrial"""	602395				10997877, 8369314	Standard	NM_020918		Approved	KIAA1560, MGC26846, GPAT1	uc001kzp.3	Q9HCL2	OTTHUMG00000019055	ENST00000348367.4:c.1307+1G>T	chr10.hg19:g.113924282C>A		82.0	0.0	.		90.0	22.0	.	NM_020918	Q5VW51|Q86TA3	Splice_Site	SNP	ENST00000348367.4	hg19	CCDS7570.1	.	.	.	.	.	.	.	.	.	.	C	20.6	4.025850	0.75390	.	.	ENSG00000119927	ENST00000348367;ENST00000423155;ENST00000369425	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0238	0.86440	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GPAM	113914272	1.000000	0.71417	0.989000	0.46669	0.866000	0.49608	5.794000	0.69067	2.432000	0.82394	0.643000	0.83706	.	.	.	.	none		0.348	GPAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050377.1	NM_020918	Intron
PIK3C2A	5286	hgsc.bcm.edu	37	11	17113603	17113603	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr11:17113603A>C	ENST00000265970.7	-	29	4581	c.4582T>G	c.(4582-4584)Tgt>Ggt	p.C1528G	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Missense_Mutation_p.C1148G	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1528	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						AAGAAAGTACAAACAAGATCA	0.318																																					p.C1528G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4582G						PASS	.						90.0	93.0	92.0					11																	17113603		2200	4294	6494	SO:0001583	missense	5286	exon29			AAGTACAAACAAG	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.4582T>G	chr11.hg19:g.17113603A>C	ENSP00000265970:p.Cys1528Gly	173.0	0.0	.		139.0	20.0	.	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Missense_Mutation	SNP	ENST00000265970.7	hg19	CCDS7824.1	.	.	.	.	.	.	.	.	.	.	A	18.03	3.532468	0.64972	.	.	ENSG00000011405	ENST00000265970;ENST00000540361	T;T	0.38722	1.12;1.12	5.85	5.85	0.93711	Phox homologous domain (5);	0.048833	0.85682	D	0.000000	T	0.30230	0.0758	N	0.08118	0	0.44890	D	0.9979	B;P	0.42584	0.214;0.784	B;B	0.42522	0.253;0.39	T	0.27872	-1.0061	10	0.59425	D	0.04	-5.6727	16.2473	0.82450	1.0:0.0:0.0:0.0	.	1148;1528	F5H2B0;O00443	.;P3C2A_HUMAN	G	1528;1148	ENSP00000265970:C1528G;ENSP00000438687:C1148G	ENSP00000265970:C1528G	C	-	1	0	PIK3C2A	17070179	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.854000	0.92228	2.238000	0.73509	0.533000	0.62120	TGT	.	.	.	none		0.318	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
FNBP4	23360	hgsc.bcm.edu	37	11	47745677	47745677	+	Silent	SNP	T	T	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr11:47745677T>G	ENST00000263773.5	-	14	2379	c.2367A>C	c.(2365-2367)atA>atC	p.I789I	Y_RNA_ENST00000363220.1_RNA	NM_015308.2	NP_056123.2	Q8N3X1	FNBP4_HUMAN	formin binding protein 4	789						nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	44						CTTTCCTCTTTATTCCTTTAG	0.428																																					p.I789I		Atlas-SNP	.											.	FNBP4	99	.	0			c.A2367C						PASS	.						126.0	126.0	126.0					11																	47745677		1874	4119	5993	SO:0001819	synonymous_variant	23360	exon14			CCTCTTTATTCCT	BC037404	CCDS41644.1	11q12.1	2008-02-05			ENSG00000109920	ENSG00000109920			19752	protein-coding gene	gene with protein product		615265				10231032	Standard	NM_015308		Approved	KIAA1014	uc009ylv.3	Q8N3X1	OTTHUMG00000166533	ENST00000263773.5:c.2367A>C	chr11.hg19:g.47745677T>G		72.0	0.0	.		79.0	15.0	.	NM_015308	Q9H985|Q9NT81|Q9Y2L7	Silent	SNP	ENST00000263773.5	hg19	CCDS41644.1																																																																																			.	.	.	none		0.428	FNBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390237.3		
WNK1	65125	hgsc.bcm.edu	37	12	1017829	1017829	+	Silent	SNP	G	G	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:1017829G>C	ENST00000315939.6	+	28	7663	c.7020G>C	c.(7018-7020)acG>acC	p.T2340T	WNK1_ENST00000537687.1_Silent_p.T2600T|WNK1_ENST00000535572.1_Silent_p.T2092T|WNK1_ENST00000530271.2_Silent_p.T2838T|WNK1_ENST00000340908.4_Silent_p.T1933T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	2340					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GGAGTGGGACGGGTGGCCCAG	0.542																																					p.T2600T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.G7800C						PASS	.						68.0	64.0	65.0					12																	1017829		2203	4300	6503	SO:0001819	synonymous_variant	65125	exon28			TGGGACGGGTGGC	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.7020G>C	chr12.hg19:g.1017829G>C		107.0	0.0	.		110.0	19.0	.	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Silent	SNP	ENST00000315939.6	hg19	CCDS8506.1																																																																																			.	.	.	none		0.542	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
CS	1431	hgsc.bcm.edu	37	12	56669848	56669848	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:56669848G>T	ENST00000351328.3	-	7	910	c.720C>A	c.(718-720)ttC>ttA	p.F240L	CS_ENST00000548567.1_Missense_Mutation_p.F174L|CS_ENST00000542324.2_Missense_Mutation_p.F227L	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	240					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		ACATGTTGGTGAAATTGTGAG	0.498																																					p.F240L		Atlas-SNP	.											.	CS	44	.	0			c.C720A						PASS	.						161.0	133.0	143.0					12																	56669848		2203	4300	6503	SO:0001583	missense	1431	exon7			GTTGGTGAAATTG		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.720C>A	chr12.hg19:g.56669848G>T	ENSP00000342056:p.Phe240Leu	105.0	0.0	.		146.0	28.0	.	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Missense_Mutation	SNP	ENST00000351328.3	hg19	CCDS8913.1	.	.	.	.	.	.	.	.	.	.	G	19.75	3.886371	0.72410	.	.	ENSG00000062485	ENST00000548567;ENST00000351328;ENST00000542324	.	.	.	5.41	3.56	0.40772	Citrate synthase-like, large alpha subdomain (1);Citrate synthase-like, core (1);	0.000000	0.85682	D	0.000000	T	0.41236	0.1150	L	0.41573	1.285	0.58432	D	0.999999	P;B;B;B	0.36144	0.539;0.034;0.058;0.034	B;B;B;B	0.37508	0.252;0.074;0.106;0.06	T	0.14587	-1.0467	9	0.30854	T	0.27	-16.2635	8.3037	0.32029	0.2519:0.0:0.7481:0.0	.	174;227;195;240	B7Z1E1;B4DJV2;B3KTN4;O75390	.;.;.;CISY_HUMAN	L	174;240;227	.	ENSP00000342056:F240L	F	-	3	2	CS	54956115	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.240000	0.51368	0.753000	0.32945	0.555000	0.69702	TTC	.	.	.	none		0.498	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
TMTC2	160335	hgsc.bcm.edu	37	12	83251151	83251151	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:83251151T>C	ENST00000321196.3	+	2	1153	c.446T>C	c.(445-447)cTc>cCc	p.L149P	TMTC2_ENST00000549919.1_Missense_Mutation_p.L143P|TMTC2_ENST00000548305.1_Missense_Mutation_p.L149P	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	149					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						CTCTTCTTTCTCCTCTCCTTG	0.557																																					p.L149P		Atlas-SNP	.											.	TMTC2	100	.	0			c.T446C						PASS	.						123.0	99.0	107.0					12																	83251151		2203	4300	6503	SO:0001583	missense	160335	exon2			TCTTTCTCCTCTC	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.446T>C	chr12.hg19:g.83251151T>C	ENSP00000322300:p.Leu149Pro	59.0	0.0	.		95.0	16.0	.	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	hg19	CCDS9025.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.008826	0.75046	.	.	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919	T;T;T	0.71698	0.03;-0.59;-0.05	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000001	D	0.88603	0.6481	H	0.95260	3.645	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.91786	0.5439	10	0.87932	D	0	-14.0917	14.6569	0.68838	0.0:0.0:0.0:1.0	.	149;149	Q8N394;F8VSH2	TMTC2_HUMAN;.	P	149;149;143	ENSP00000322300:L149P;ENSP00000448292:L149P;ENSP00000447609:L143P	ENSP00000322300:L149P	L	+	2	0	TMTC2	81775282	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.456000	0.80751	2.251000	0.74343	0.528000	0.53228	CTC	.	.	.	none		0.557	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	
TBC1D4	9882	hgsc.bcm.edu	37	13	75898483	75898483	+	Silent	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr13:75898483A>T	ENST00000377636.3	-	11	2434	c.2088T>A	c.(2086-2088)ctT>ctA	p.L696L	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Intron|TBC1D4_ENST00000431480.2_Silent_p.L696L	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	696	Ser-rich.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GAAGACTTGGAAGACTGGAGG	0.418																																					p.L696L		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T2088A						PASS	.						129.0	136.0	134.0					13																	75898483		1900	4112	6012	SO:0001819	synonymous_variant	9882	exon11			ACTTGGAAGACTG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.2088T>A	chr13.hg19:g.75898483A>T		133.0	0.0	.		135.0	26.0	.	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	hg19	CCDS41901.1																																																																																			.	.	.	none		0.418	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
IRS2	8660	hgsc.bcm.edu	37	13	110437628	110437628	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr13:110437628T>A	ENST00000375856.3	-	1	1287	c.773A>T	c.(772-774)gAg>gTg	p.E258V		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	258	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			GCGGCCCACCTCGATGAAGAA	0.652																																					p.E258V	Melanoma(100;613 2409 40847)	Atlas-SNP	.											.	IRS2	44	.	0			c.A773T						PASS	.						11.0	12.0	12.0					13																	110437628		2186	4283	6469	SO:0001583	missense	8660	exon1			CCCACCTCGATGA	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.773A>T	chr13.hg19:g.110437628T>A	ENSP00000365016:p.Glu258Val	72.0	0.0	.		68.0	14.0	.	NM_003749	Q96RR2|Q9BZG0|Q9Y6I5	Missense_Mutation	SNP	ENST00000375856.3	hg19	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.270350	0.80469	.	.	ENSG00000185950	ENST00000375856	T	0.71579	-0.58	3.61	3.61	0.41365	Pleckstrin homology-type (1);Insulin receptor substrate-1, PTB (4);	0.064380	0.64402	U	0.000013	D	0.82742	0.5103	M	0.81341	2.54	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	D	0.84437	0.0580	10	0.62326	D	0.03	-13.1799	11.3514	0.49589	0.0:0.0:0.0:1.0	.	258	Q9Y4H2	IRS2_HUMAN	V	258	ENSP00000365016:E258V	ENSP00000365016:E258V	E	-	2	0	IRS2	109235629	1.000000	0.71417	1.000000	0.80357	0.943000	0.58893	6.999000	0.76283	1.527000	0.49086	0.408000	0.27601	GAG	.	.	.	none		0.652	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045755.1	NM_003749	
METTL3	56339	hgsc.bcm.edu	37	14	21969115	21969115	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:21969115C>G	ENST00000298717.4	-	5	1207	c.1056G>C	c.(1054-1056)gaG>gaC	p.E352D		NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	352					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		TAAGAGCAAGCTCCTGGCTTG	0.507																																					p.E352D		Atlas-SNP	.											.	METTL3	48	.	0			c.G1056C						PASS	.						67.0	61.0	63.0					14																	21969115		2203	4300	6503	SO:0001583	missense	56339	exon5			AGCAAGCTCCTGG	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.1056G>C	chr14.hg19:g.21969115C>G	ENSP00000298717:p.Glu352Asp	130.0	0.0	.		126.0	30.0	.	NM_019852	O14736|Q86V05|Q9HB32	Missense_Mutation	SNP	ENST00000298717.4	hg19	CCDS32044.1	.	.	.	.	.	.	.	.	.	.	C	12.20	1.867899	0.32977	.	.	ENSG00000165819	ENST00000298717	.	.	.	5.5	0.761	0.18448	.	0.047580	0.85682	D	0.000000	T	0.27419	0.0673	N	0.17082	0.46	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.03761	-1.1006	9	0.16896	T	0.51	-19.8692	4.8131	0.13353	0.0:0.3033:0.1686:0.5281	.	352	Q86U44	MTA70_HUMAN	D	352	.	ENSP00000298717:E352D	E	-	3	2	METTL3	21038955	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	0.640000	0.24705	0.251000	0.21505	0.655000	0.94253	GAG	.	.	.	none		0.507	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
SGPP1	81537	hgsc.bcm.edu	37	14	64194241	64194241	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:64194241T>A	ENST00000247225.6	-	1	516	c.422A>T	c.(421-423)gAa>gTa	p.E141V		NM_030791.2	NP_110418.1	Q9BX95	SGPP1_HUMAN	sphingosine-1-phosphate phosphatase 1	141					extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway (GO:0097193)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate metabolic process (GO:0006668)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	sphingosine-1-phosphate phosphatase activity (GO:0042392)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(4)|skin(2)	10				OV - Ovarian serous cystadenocarcinoma(108;0.0056)|all cancers(60;0.0141)|BRCA - Breast invasive adenocarcinoma(234;0.103)		GTAGAAGAGTTCGTTGCCCAG	0.642																																					p.E141V		Atlas-SNP	.											.	SGPP1	29	.	0			c.A422T						PASS	.						55.0	63.0	60.0					14																	64194241		2203	4300	6503	SO:0001583	missense	81537	exon1			AAGAGTTCGTTGC	AJ293294	CCDS9760.1	14q23.1	2003-09-17			ENSG00000126821	ENSG00000126821			17720	protein-coding gene	gene with protein product		612826				10859351	Standard	NM_030791		Approved		uc001xgj.3	Q9BX95	OTTHUMG00000029080	ENST00000247225.6:c.422A>T	chr14.hg19:g.64194241T>A	ENSP00000247225:p.Glu141Val	60.0	0.0	.		51.0	9.0	.	NM_030791	B2RAH0|Q9H189	Missense_Mutation	SNP	ENST00000247225.6	hg19	CCDS9760.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.637752	0.87760	.	.	ENSG00000126821	ENST00000247225	T	0.39056	1.1	4.67	3.49	0.39957	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.60011	0.2236	M	0.75447	2.3	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.57481	-0.7804	10	0.36615	T	0.2	4.0704	11.2511	0.49026	0.0:0.0:0.1538:0.8462	.	141	Q9BX95	SGPP1_HUMAN	V	141	ENSP00000247225:E141V	ENSP00000247225:E141V	E	-	2	0	SGPP1	63263994	1.000000	0.71417	0.972000	0.41901	0.986000	0.74619	7.914000	0.87478	0.601000	0.29879	0.379000	0.24179	GAA	.	.	.	none		0.642	SGPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072626.3	NM_030791	
PCNX	22990	hgsc.bcm.edu	37	14	71518644	71518644	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:71518644T>A	ENST00000304743.2	+	24	4938	c.4492T>A	c.(4492-4494)Tct>Act	p.S1498T	PCNX_ENST00000439984.3_Missense_Mutation_p.S1387T|PCNX_ENST00000238570.5_Missense_Mutation_p.S1498T	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1498						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		GGCCTTCTTCTCTACTCCACT	0.428																																					p.S1498T		Atlas-SNP	.											.	PCNX	198	.	0			c.T4492A						PASS	.						198.0	188.0	191.0					14																	71518644		2203	4300	6503	SO:0001583	missense	22990	exon24			TTCTTCTCTACTC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4492T>A	chr14.hg19:g.71518644T>A	ENSP00000304192:p.Ser1498Thr	74.0	0.0	.		77.0	19.0	.	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	hg19	CCDS9806.1	.	.	.	.	.	.	.	.	.	.	T	17.92	3.507607	0.64410	.	.	ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984	T;T;T	0.13420	2.96;2.72;2.59	5.84	4.66	0.58398	.	0.049858	0.85682	D	0.000000	T	0.32376	0.0827	M	0.89095	3.005	0.58432	D	0.999999	P;D;P	0.62365	0.675;0.991;0.546	B;P;B	0.58331	0.13;0.837;0.097	T	0.52786	-0.8529	10	0.02654	T	1	.	13.0601	0.59002	0.0:0.0:0.1343:0.8657	.	1498;1387;1498	Q96RV3-3;B2RTR6;Q96RV3	.;.;PCX1_HUMAN	T	1498;1498;1387	ENSP00000304192:S1498T;ENSP00000238570:S1498T;ENSP00000396617:S1387T	ENSP00000238570:S1498T	S	+	1	0	PCNX	70588397	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.907000	0.69908	0.993000	0.38866	0.455000	0.32223	TCT	.	.	.	none		0.428	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
DDX24	57062	hgsc.bcm.edu	37	14	94527306	94527306	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:94527306T>G	ENST00000330836.5	-	4	1481	c.1350A>C	c.(1348-1350)gaA>gaC	p.E450D	DDX24_ENST00000544005.1_Missense_Mutation_p.E200D|DDX24_ENST00000555054.1_Missense_Mutation_p.E407D	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	450	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		CTTTAATTAATTCCCACAGCC	0.468																																					p.E450D		Atlas-SNP	.											.	DDX24	82	.	0			c.A1350C						PASS	.						95.0	94.0	94.0					14																	94527306		2203	4300	6503	SO:0001583	missense	57062	exon4			AATTAATTCCCAC	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"""DEAD-boxes"""	13266	protein-coding gene	gene with protein product		606181	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"""			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.1350A>C	chr14.hg19:g.94527306T>G	ENSP00000328690:p.Glu450Asp	115.0	0.0	.		118.0	19.0	.	NM_020414	E7EMJ4|Q4V9L5	Missense_Mutation	SNP	ENST00000330836.5	hg19	CCDS9918.1	.	.	.	.	.	.	.	.	.	.	T	13.13	2.144094	0.37825	.	.	ENSG00000089737	ENST00000330836;ENST00000544005;ENST00000440370;ENST00000543787;ENST00000555054;ENST00000542247	T;T;T	0.03801	3.8;3.8;3.8	5.03	0.632	0.17705	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.049652	0.85682	D	0.000000	T	0.02649	0.0080	N	0.03084	-0.415	0.40889	D	0.984059	B	0.27264	0.173	B	0.35688	0.208	T	0.54609	-0.8268	10	0.29301	T	0.29	-2.3005	9.5849	0.39510	0.0:0.7044:0.0:0.2956	.	450	Q9GZR7	DDX24_HUMAN	D	450;200;395;76;407;407	ENSP00000328690:E450D;ENSP00000440623:E200D;ENSP00000452145:E407D	ENSP00000328690:E450D	E	-	3	2	DDX24	93597059	0.874000	0.30092	0.800000	0.32199	0.273000	0.26683	0.054000	0.14205	0.170000	0.19704	-0.993000	0.02533	GAA	.	.	.	none		0.468	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414	
ADCY7	113	hgsc.bcm.edu	37	16	50325746	50325746	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr16:50325746C>T	ENST00000394697.2	+	4	815	c.475C>T	c.(475-477)Ctc>Ttc	p.L159F	ADCY7_ENST00000564044.1_Intron|ADCY7_ENST00000537579.1_Missense_Mutation_p.L159F|ADCY7_ENST00000566433.2_Missense_Mutation_p.L159F|ADCY7_ENST00000538642.1_Missense_Mutation_p.L159F|ADCY7_ENST00000254235.3_Missense_Mutation_p.L159F			P51828	ADCY7_HUMAN	adenylate cyclase 7	159					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		TGCCTCCCACCTCCTGGTGCT	0.622																																					p.L159F		Atlas-SNP	.											.	ADCY7	90	.	0			c.C475T						PASS	.						86.0	78.0	81.0					16																	50325746		2198	4300	6498	SO:0001583	missense	113	exon3			TCCCACCTCCTGG	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"""Adenylate cyclases"""	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.475C>T	chr16.hg19:g.50325746C>T	ENSP00000378187:p.Leu159Phe	52.0	0.0	.		44.0	11.0	.	NM_001114	A0AVA6	Missense_Mutation	SNP	ENST00000394697.2	hg19	CCDS10741.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632511	0.67015	.	.	ENSG00000121281	ENST00000538642;ENST00000394697;ENST00000537579;ENST00000254235	T;D;T;D	0.83591	-1.23;-1.74;-1.23;-1.74	4.03	4.03	0.46877	.	0.221259	0.22600	U	0.057965	T	0.79233	0.4411	L	0.54323	1.7	0.37366	D	0.911421	B;B	0.23058	0.005;0.079	B;B	0.29176	0.009;0.099	T	0.80013	-0.1560	10	0.52906	T	0.07	.	10.0746	0.42353	0.3531:0.6469:0.0:0.0	.	159;159	P51828;F5H4D1	ADCY7_HUMAN;.	F	159	ENSP00000445046:L159F;ENSP00000378187:L159F;ENSP00000437788:L159F;ENSP00000254235:L159F	ENSP00000254235:L159F	L	+	1	0	ADCY7	48883247	0.989000	0.36119	1.000000	0.80357	0.648000	0.38561	3.071000	0.50041	2.231000	0.72958	0.561000	0.74099	CTC	.	.	.	none		0.622	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3		
ASGR2	433	hgsc.bcm.edu	37	17	7011820	7011820	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:7011820A>T	ENST00000380952.2	-	4	577	c.313T>A	c.(313-315)Tcg>Acg	p.S105T	ASGR2_ENST00000446679.2_Missense_Mutation_p.S86T|ASGR2_ENST00000254850.7_Missense_Mutation_p.S81T|ASGR2_ENST00000355035.5_Missense_Mutation_p.S105T	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	105					bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	AGGGTGCTCGAGGAGAAGTTG	0.622																																					p.S105T		Atlas-SNP	.											.	ASGR2	38	.	0			c.T313A						PASS	.						68.0	56.0	60.0					17																	7011820		2203	4300	6503	SO:0001583	missense	433	exon4			TGCTCGAGGAGAA	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.313T>A	chr17.hg19:g.7011820A>T	ENSP00000370339:p.Ser105Thr	63.0	0.0	.		64.0	9.0	.	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Missense_Mutation	SNP	ENST00000380952.2	hg19	CCDS32544.1	.	.	.	.	.	.	.	.	.	.	A	12.58	1.979766	0.34942	.	.	ENSG00000161944	ENST00000355035;ENST00000254850;ENST00000380952;ENST00000446679;ENST00000450034	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	2.9	-1.2	0.09554	Hepatic lectin, N-terminal (1);	1.161450	0.06753	N	0.780358	T	0.15955	0.0384	L	0.32530	0.975	0.09310	N	1	P;B;P;B;B;P	0.35307	0.476;0.041;0.494;0.314;0.439;0.494	B;B;B;B;B;B	0.39935	0.145;0.011;0.314;0.248;0.209;0.314	T	0.33828	-0.9853	10	0.25106	T	0.35	.	4.3131	0.10979	0.3967:0.4057:0.0:0.1976	.	81;81;105;100;86;105	B4E1D2;P07307-3;P07307;Q7Z4G9;P07307-2;D3DTN0	.;.;ASGR2_HUMAN;.;.;.	T	105;81;105;86;81	ENSP00000347140:S105T;ENSP00000254850:S81T;ENSP00000370339:S105T;ENSP00000405844:S86T	ENSP00000254850:S81T	S	-	1	0	ASGR2	6952544	0.003000	0.15002	0.065000	0.19835	0.437000	0.31866	-0.242000	0.08928	-0.275000	0.09219	0.438000	0.28831	TCG	.	.	.	none		0.622	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	
TMEM97	27346	hgsc.bcm.edu	37	17	26646334	26646334	+	Silent	SNP	C	C	A	rs369813368		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:26646334C>A	ENST00000226230.6	+	1	214	c.69C>A	c.(67-69)ccC>ccA	p.P23P	TMEM97_ENST00000582113.1_Silent_p.P23P|TMEM97_ENST00000336687.6_5'Flank|TMEM97_ENST00000583381.1_Intron	NM_014573.2	NP_055388.2	Q5BJF2	TMM97_HUMAN	transmembrane protein 97	23					cholesterol homeostasis (GO:0042632)|regulation of cell growth (GO:0001558)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|rough endoplasmic reticulum (GO:0005791)				endometrium(1)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	6	all_lung(13;0.000238)|Lung NSC(42;0.000789)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)		GCCACATCCCCATCACCCTGT	0.677																																					p.P23P		Atlas-SNP	.											.	TMEM97	27	.	0			c.C69A						PASS	.						27.0	34.0	31.0					17																	26646334		2045	4160	6205	SO:0001819	synonymous_variant	27346	exon1			CATCCCCATCACC	BC091504	CCDS11226.2	17q11.2	2014-01-28			ENSG00000109084	ENSG00000109084			28106	protein-coding gene	gene with protein product		612912				7694637, 15375745	Standard	NM_014573		Approved	MAC30	uc002hat.3	Q5BJF2	OTTHUMG00000132497	ENST00000226230.6:c.69C>A	chr17.hg19:g.26646334C>A		109.0	0.0	.		130.0	22.0	.	NM_014573	B4DS02|Q07823	Silent	SNP	ENST00000226230.6	hg19	CCDS11226.2																																																																																			.	.	.	alt		0.677	TMEM97-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255675.2	NM_014573	
EXOC7	23265	hgsc.bcm.edu	37	17	74090635	74090635	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:74090635C>T	ENST00000335146.7	-	6	721	c.668G>A	c.(667-669)cGc>cAc	p.R223H	EXOC7_ENST00000405575.4_Missense_Mutation_p.R223H|EXOC7_ENST00000607838.1_Missense_Mutation_p.R223H|EXOC7_ENST00000589210.1_Missense_Mutation_p.R223H|EXOC7_ENST00000411744.2_Missense_Mutation_p.R223H|EXOC7_ENST00000467929.2_Missense_Mutation_p.R182H|EXOC7_ENST00000332065.5_Missense_Mutation_p.R223H			Q9UPT5	EXOC7_HUMAN	exocyst complex component 7	223					cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	centriolar satellite (GO:0034451)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)				NS(1)|breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	14			LUSC - Lung squamous cell carcinoma(166;0.187)			CTGGCTGGAGCGTATCTGGTA	0.547																																					p.R223H		Atlas-SNP	.											.	EXOC7	47	.	0			c.G668A						PASS	.						125.0	120.0	121.0					17																	74090635		2203	4300	6503	SO:0001583	missense	23265	exon6			CTGGAGCGTATCT	BC029432	CCDS11741.1, CCDS32738.1, CCDS45781.1, CCDS45782.1, CCDS45784.1, CCDS74164.1	17q25.3	2013-01-22			ENSG00000182473	ENSG00000182473			23214	protein-coding gene	gene with protein product		608163				12477932	Standard	NM_001013839		Approved	EXO70, KIAA1067, YJL085W, Exo70p	uc010wsw.2	Q9UPT5	OTTHUMG00000150720	ENST00000335146.7:c.668G>A	chr17.hg19:g.74090635C>T	ENSP00000334100:p.Arg223His	92.0	0.0	.		119.0	7.0	.	NM_001145298	B5MC69|B8XXP2|Q8ND93|Q8WV91|Q96FF0|Q9H8C3|Q9H9X3|Q9HA32	Missense_Mutation	SNP	ENST00000335146.7	hg19	CCDS45782.1	.	.	.	.	.	.	.	.	.	.	C	35	5.431701	0.96150	.	.	ENSG00000182473	ENST00000332065;ENST00000351709;ENST00000405575;ENST00000335146;ENST00000357231;ENST00000425372;ENST00000411744;ENST00000405068;ENST00000420116	.	.	.	4.84	4.84	0.62591	Cullin repeat-like-containing domain (1);	0.054405	0.64402	D	0.000001	T	0.68035	0.2957	L	0.36672	1.1	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.97110	0.999;1.0;0.993;0.998;1.0;0.999;1.0;1.0	T	0.71424	-0.4597	9	0.87932	D	0	-17.4317	16.2936	0.82761	0.0:1.0:0.0:0.0	.	223;223;182;182;223;223;223;223	Q9UPT5-5;Q9UPT5-6;B4DJ07;F5H1P1;Q9UPT5-4;Q9UPT5;Q9UPT5-2;Q9UPT5-1	.;.;.;.;.;EXOC7_HUMAN;.;.	H	223;143;223;223;223;182;223;223;108	.	ENSP00000333806:R223H	R	-	2	0	EXOC7	71602230	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.284000	0.78650	2.508000	0.84585	0.557000	0.71058	CGC	.	.	.	none		0.547	EXOC7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000319768.2	NM_015219	
AFG3L2	10939	hgsc.bcm.edu	37	18	12329586	12329586	+	Missense_Mutation	SNP	G	G	A	rs372136184		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr18:12329586G>A	ENST00000269143.3	-	17	2603	c.2372C>T	c.(2371-2373)cCg>cTg	p.P791L	TUBB6_ENST00000590967.1_Intron|TUBB6_ENST00000591909.1_3'UTR	NM_006796.2	NP_006787.2	Q9Y4W6	AFG32_HUMAN	AFG3-like AAA ATPase 2	791					axonogenesis (GO:0007409)|cell death (GO:0008219)|cristae formation (GO:0042407)|mitochondrial fusion (GO:0008053)|mitochondrial protein processing (GO:0034982)|muscle fiber development (GO:0048747)|myelination (GO:0042552)|nerve development (GO:0021675)|neuromuscular junction development (GO:0007528)|regulation of multicellular organism growth (GO:0040014)|righting reflex (GO:0060013)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(12)|prostate(3)|skin(1)|stomach(3)|urinary_tract(1)	27					Adenosine triphosphate(DB00171)	TTTCTCACCCGGGGGCTCCTC	0.532																																					p.P791L		Atlas-SNP	.											.	AFG3L2	60	.	0			c.C2372T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	73.0	83.0	80.0		2372	1.8	0.0	18		80	1,8599	1.2+/-3.3	0,1,4299	no	missense	AFG3L2	NM_006796.2	98	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	791/798	12329586	1,13005	2203	4300	6503	SO:0001583	missense	10939	exon17			TCACCCGGGGGCT	Y18314	CCDS11859.1	18p11.21	2014-09-17	2013-10-17		ENSG00000141385	ENSG00000141385		"""ATPases / AAA-type"""	315	protein-coding gene	gene with protein product		604581	"""AFG3 (ATPase family gene 3, yeast)-like 2"", ""spinocerebellar ataxia 28"", ""AFG3 ATPase family gene 3-like 2 (yeast)"", ""AFG3 ATPase family gene 3-like 2 (S. cerevisiae)"", ""AFG3 ATPase family member 3-like 2 (S. cerevisiae)"""	SCA28		10395799, 18769991	Standard	NM_006796		Approved	SPAX5	uc002kqz.2	Q9Y4W6	OTTHUMG00000131695	ENST00000269143.3:c.2372C>T	chr18.hg19:g.12329586G>A	ENSP00000269143:p.Pro791Leu	108.0	0.0	.		98.0	17.0	.	NM_006796	Q6P1L0	Missense_Mutation	SNP	ENST00000269143.3	hg19	CCDS11859.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.172684	0.57584	0.0	1.16E-4	ENSG00000141385	ENST00000269143;ENST00000537174	D	0.92595	-3.07	5.56	1.75	0.24633	.	2.193060	0.01444	N	0.015203	D	0.87442	0.6178	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.71537	-0.4563	10	0.44086	T	0.13	1.1635	4.8492	0.13528	0.1341:0.1195:0.6226:0.1238	.	791	Q9Y4W6	AFG32_HUMAN	L	791;806	ENSP00000269143:P791L	ENSP00000269143:P791L	P	-	2	0	AFG3L2	12319586	0.000000	0.05858	0.000000	0.03702	0.924000	0.55760	0.652000	0.24888	0.100000	0.17581	0.655000	0.94253	CCG	.	.	.	weak		0.532	AFG3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254603.2	NM_006796	
ILVBL	10994	hgsc.bcm.edu	37	19	15226999	15226999	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:15226999C>G	ENST00000263383.3	-	12	1574	c.1435G>C	c.(1435-1437)Gta>Cta	p.V479L	ILVBL_ENST00000534378.1_Missense_Mutation_p.V372L	NM_006844.3	NP_006835.2	A1L0T0	ILVBL_HUMAN	ilvB (bacterial acetolactate synthase)-like	479	Thiamine pyrophosphate binding. {ECO:0000250}.					integral component of membrane (GO:0016021)|membrane (GO:0016020)	magnesium ion binding (GO:0000287)|thiamine pyrophosphate binding (GO:0030976)|transferase activity (GO:0016740)			NS(3)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|skin(1)	26						CGGGGCTGTACCAGATGGGCA	0.652																																					p.V479L		Atlas-SNP	.											.	ILVBL	54	.	0			c.G1435C						PASS	.						81.0	71.0	74.0					19																	15226999		2203	4300	6503	SO:0001583	missense	10994	exon12			GCTGTACCAGATG	U61263	CCDS12325.1	19p13.1	2008-07-16			ENSG00000105135	ENSG00000105135			6041	protein-coding gene	gene with protein product	"""acetolactate synthase homolog"""	605770				8954801	Standard	NM_006844		Approved	209L8, AHAS, ILV2H, MGC1269, FLJ39061, MGC19535	uc002nam.3	A1L0T0	OTTHUMG00000165630	ENST00000263383.3:c.1435G>C	chr19.hg19:g.15226999C>G	ENSP00000263383:p.Val479Leu	51.0	0.0	.		59.0	11.0	.	NM_006844	O43341|Q96F08|Q99651|Q9BWN5|Q9UEB2	Missense_Mutation	SNP	ENST00000263383.3	hg19	CCDS12325.1	.	.	.	.	.	.	.	.	.	.	C	3.360	-0.130703	0.06753	.	.	ENSG00000105135	ENST00000263383	T	0.36340	1.26	5.22	4.19	0.49359	Thiamine pyrophosphate enzyme, C-terminal TPP-binding (1);	0.252402	0.42294	D	0.000726	T	0.20007	0.0481	N	0.12422	0.21	0.40211	D	0.977625	B	0.20671	0.047	B	0.26094	0.066	T	0.07290	-1.0780	10	0.16896	T	0.51	-17.1147	9.8081	0.40805	0.0:0.9045:0.0:0.0955	.	479	A1L0T0	ILVBL_HUMAN	L	479	ENSP00000263383:V479L	ENSP00000263383:V479L	V	-	1	0	ILVBL	15087999	1.000000	0.71417	0.998000	0.56505	0.072000	0.16883	1.307000	0.33516	1.209000	0.43321	-0.258000	0.10820	GTA	.	.	.	none		0.652	ILVBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385439.1	NM_006844	
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587251	15587251	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:15587251T>A	ENST00000340880.4	-	2	710	c.230A>T	c.(229-231)aAt>aTt	p.N77I	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.N77I	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	77					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CTCTGTAGCATTGAGGCTCCA	0.582																																					p.N77I		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.A230T						PASS	.						108.0	78.0	89.0					19																	15587251		2203	4300	6503	SO:0001583	missense	114770	exon2			GTAGCATTGAGGC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.230A>T	chr19.hg19:g.15587251T>A	ENSP00000345968:p.Asn77Ile	91.0	0.0	.		81.0	14.0	.	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	hg19	CCDS12330.2	.	.	.	.	.	.	.	.	.	.	T	11.16	1.555531	0.27739	.	.	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.05081	3.53;3.5	5.27	0.412	0.16397	.	3.618340	0.00864	N	0.001941	T	0.06234	0.0161	L	0.44542	1.39	0.09310	N	1	P;B	0.44946	0.846;0.412	B;B	0.37888	0.26;0.053	T	0.26052	-1.0114	10	0.66056	D	0.02	-8.1911	0.6612	0.00843	0.1668:0.1881:0.1728:0.4723	.	77;77	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	I	77	ENSP00000345968:N77I;ENSP00000292609:N77I	ENSP00000292609:N77I	N	-	2	0	PGLYRP2	15448251	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.187000	0.16998	0.006000	0.14734	-0.376000	0.06991	AAT	.	.	.	none		0.582	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
NR2F6	2063	hgsc.bcm.edu	37	19	17343235	17343235	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:17343235G>A	ENST00000291442.3	-	4	1860	c.1141C>T	c.(1141-1143)Ccc>Tcc	p.P381S		NM_005234.3	NP_005225.2	P10588	NR2F6_HUMAN	nuclear receptor subfamily 2, group F, member 6	381	Important for dimerization. {ECO:0000250}.|Ligand-binding. {ECO:0000250}.				detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|entrainment of circadian clock by photoperiod (GO:0043153)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron development (GO:0048666)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|thyroid hormone receptor activity (GO:0004887)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)	5						GTCTCAATGGGCGTCTTCCCC	0.667																																					p.P381S		Atlas-SNP	.											.	NR2F6	18	.	0			c.C1141T						PASS	.						70.0	62.0	65.0					19																	17343235		2203	4300	6503	SO:0001583	missense	2063	exon4			CAATGGGCGTCTT	X12794	CCDS12352.1	19p13.11	2013-09-20			ENSG00000160113	ENSG00000160113		"""Nuclear hormone receptors"""	7977	protein-coding gene	gene with protein product		132880		ERBAL2		2905047	Standard	NM_005234		Approved	EAR-2	uc002nfq.3	P10588	OTTHUMG00000182728	ENST00000291442.3:c.1141C>T	chr19.hg19:g.17343235G>A	ENSP00000291442:p.Pro381Ser	108.0	0.0	.		102.0	18.0	.	NM_005234	B2RC68|Q5XGA0|Q6P586|Q9BUE8	Missense_Mutation	SNP	ENST00000291442.3	hg19	CCDS12352.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.536811	0.85812	.	.	ENSG00000160113	ENST00000291442;ENST00000536940	T	0.52983	0.64	4.71	4.71	0.59529	Nuclear hormone receptor, ligand-binding (2);	0.000000	0.85682	D	0.000000	T	0.64136	0.2571	L	0.55213	1.73	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.67845	-0.5565	10	0.87932	D	0	.	15.175	0.72903	0.0:0.0:1.0:0.0	.	381	P10588	NR2F6_HUMAN	S	381;354	ENSP00000291442:P381S	ENSP00000291442:P381S	P	-	1	0	NR2F6	17204235	1.000000	0.71417	0.999000	0.59377	0.865000	0.49528	9.658000	0.98594	2.168000	0.68352	0.555000	0.69702	CCC	.	.	.	none		0.667	NR2F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463325.1		
ZNF99	7652	hgsc.bcm.edu	37	19	22940373	22940373	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:22940373T>C	ENST00000596209.1	-	4	2428	c.2338A>G	c.(2338-2340)Aag>Gag	p.K780E	ZNF99_ENST00000397104.3_Missense_Mutation_p.K689E|CTC-451A6.4_ENST00000442497.2_lincRNA	NM_001080409.2	NP_001073878.2	A8MXY4	ZNF99_HUMAN	zinc finger protein 99	780					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.K689E(3)		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)				TGAATTATCTTATGTTTTCTA	0.343																																					p.K780E		Atlas-SNP	.											ZNF99,NS,carcinoma,0,4	ZNF99	273	.	3	Substitution - Missense(3)	prostate(1)|lung(1)|kidney(1)	c.A2338G						PASS	.						32.0	34.0	34.0					19																	22940373		1947	4138	6085	SO:0001583	missense	7652	exon4			TTATCTTATGTTT	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.2338A>G	chr19.hg19:g.22940373T>C	ENSP00000472969:p.Lys780Glu	21.0	0.0	.		30.0	2.0	.	NM_001080409	M0R335	Missense_Mutation	SNP	ENST00000596209.1	hg19	CCDS59369.1	.	.	.	.	.	.	.	.	.	.	t	9.727	1.161345	0.21538	.	.	ENSG00000213973	ENST00000397104	T	0.18016	2.24	1.26	-2.52	0.06346	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20495	0.0493	L	0.28400	0.85	0.09310	N	1	D	0.65815	0.995	D	0.65233	0.933	T	0.12837	-1.0532	9	0.54805	T	0.06	.	4.187	0.10402	0.1821:0.0:0.5141:0.3038	.	689	A8MXY4	ZNF99_HUMAN	E	689	ENSP00000380293:K689E	ENSP00000380293:K689E	K	-	1	0	ZNF99	22732213	0.000000	0.05858	0.002000	0.10522	0.007000	0.05969	-0.737000	0.04877	-0.939000	0.03709	0.313000	0.20887	AAG	.	.	.	none		0.343	ZNF99-001	NOVEL	not_best_in_genome_evidence|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000464591.1	XM_065124	
ZNF91	7644	hgsc.bcm.edu	37	19	23544826	23544826	+	Missense_Mutation	SNP	C	C	G			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:23544826C>G	ENST00000300619.7	-	4	1160	c.955G>C	c.(955-957)Gag>Cag	p.E319Q	ZNF91_ENST00000397082.2_Missense_Mutation_p.E287Q|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	319					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TAGGGTTTCTCTCCAGTATGA	0.398																																					p.E319Q		Atlas-SNP	.											.	ZNF91	349	.	0			c.G955C						PASS	.						66.0	70.0	69.0					19																	23544826		2141	4273	6414	SO:0001583	missense	7644	exon4			GTTTCTCTCCAGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.955G>C	chr19.hg19:g.23544826C>G	ENSP00000300619:p.Glu319Gln	79.0	0.0	.		77.0	15.0	.	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	hg19	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	C	14.48	2.548805	0.45383	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.25912	1.77;1.77	1.97	0.778	0.18543	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25121	0.0610	L	0.49571	1.57	0.26282	N	0.978262	P;P	0.47409	0.895;0.589	B;B	0.43536	0.423;0.419	T	0.12502	-1.0545	9	0.72032	D	0.01	.	9.033	0.36271	0.0:0.7693:0.2307:0.0	.	287;319	Q05481-2;Q05481	.;ZNF91_HUMAN	Q	319;287	ENSP00000300619:E319Q;ENSP00000380272:E287Q	ENSP00000300619:E319Q	E	-	1	0	ZNF91	23336666	0.003000	0.15002	0.001000	0.08648	0.024000	0.10985	0.998000	0.29744	0.126000	0.18424	0.162000	0.16502	GAG	.	.	.	none		0.398	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
CLASRP	11129	hgsc.bcm.edu	37	19	45555367	45555367	+	Silent	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:45555367A>C	ENST00000221455.3	+	3	236	c.138A>C	c.(136-138)cgA>cgC	p.R46R	CLASRP_ENST00000544944.2_Silent_p.R46R|CLASRP_ENST00000391953.4_Intron	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	46					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						TACATGGCCGAGCTTGCAAGG	0.572																																					p.R46R		Atlas-SNP	.											.	CLASRP	44	.	0			c.A138C						PASS	.						99.0	91.0	94.0					19																	45555367		2203	4300	6503	SO:0001819	synonymous_variant	11129	exon3			TGGCCGAGCTTGC	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"""Clk4 associating SR-related protein"""		"""splicing factor, arginine/serine-rich 16"""	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.138A>C	chr19.hg19:g.45555367A>C		30.0	0.0	.		41.0	10.0	.	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	hg19	CCDS12652.2																																																																																			.	.	.	none		0.572	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	
FTL	2512	hgsc.bcm.edu	37	19	49469662	49469662	+	Splice_Site	SNP	A	A	G	rs17856437		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:49469662A>G	ENST00000331825.6	+	3	581	c.374A>G	c.(373-375)cAt>cGt	p.H125R	CTD-2639E6.9_ENST00000599784.1_lincRNA	NM_000146.3	NP_000137.2	P02792	FRIL_HUMAN	ferritin, light polypeptide	125	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular ferritin complex (GO:0008043)|membrane (GO:0016020)	ferric iron binding (GO:0008199)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)			cervix(1)|kidney(3)|lung(5)	9		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000152)|all cancers(93;0.000435)|GBM - Glioblastoma multiforme(486;0.0171)|Epithelial(262;0.0267)	Iron Dextran(DB00893)	ACGGACCCCCATGTACGTACC	0.557																																					p.H125R		Atlas-SNP	.											.	FTL	19	.	0			c.A374G						PASS	.						46.0	46.0	46.0					19																	49469662		2203	4300	6503	SO:0001630	splice_region_variant	2512	exon3			ACCCCCATGTACG	AY207005	CCDS33070.1	19q13.33	2014-05-19			ENSG00000087086	ENSG00000087086			3999	protein-coding gene	gene with protein product	"""ferritin light polypeptide-like 3"", ""L apoferritin"", ""ferritin L subunit"", ""ferritin light chain"", ""ferritin L-chain"", ""neurodegeneration with brain iron accumulation 3"""	134790				3000916, 9526618	Standard	NM_000146		Approved	MGC71996, NBIA3	uc002plo.3	P02792		ENST00000331825.6:c.375+1A>G	chr19.hg19:g.49469662A>G		85.0	0.0	.		119.0	8.0	.	NM_000146	B2R4B9|Q6IBT7|Q7Z2W1|Q86WI9|Q8WU07|Q96AU9|Q96CU0|Q9BTZ8	Missense_Mutation	SNP	ENST00000331825.6	hg19	CCDS33070.1	.	.	.	.	.	.	.	.	.	.	A	17.57	3.422947	0.62733	.	.	ENSG00000087086	ENST00000331825;ENST00000397259	T	0.64803	-0.12	4.46	4.46	0.54185	Ferritin/ribonucleotide reductase-like (1);Ferritin, conserved site (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.000000	0.85682	D	0.000000	T	0.70561	0.3238	M	0.65498	2.005	0.45183	D	0.998191	P	0.44380	0.834	P	0.53401	0.725	T	0.74334	-0.3699	10	0.72032	D	0.01	.	12.021	0.53344	1.0:0.0:0.0:0.0	rs17856437	125	P02792	FRIL_HUMAN	R	125	ENSP00000366525:H125R	ENSP00000366525:H125R	H	+	2	0	FTL	54161474	1.000000	0.71417	1.000000	0.80357	0.311000	0.27955	8.334000	0.90028	2.011000	0.59026	0.460000	0.39030	CAT	.	.	.	weak		0.557	FTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466233.1	NM_000146	Missense_Mutation
ZNF628	89887	hgsc.bcm.edu	37	19	55992961	55992961	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:55992961A>T	ENST00000598519.1	+	3	954	c.401A>T	c.(400-402)cAc>cTc	p.H134L	ZNF628_ENST00000391718.2_Missense_Mutation_p.H130L			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	134					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TGGTCGTCCCACTACCAGTAC	0.662																																					p.H134L		Atlas-SNP	.											.	ZNF628	75	.	0			c.A401T						PASS	.						40.0	40.0	40.0					19																	55992961		2203	4299	6502	SO:0001583	missense	89887	exon3			CGTCCCACTACCA	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.401A>T	chr19.hg19:g.55992961A>T	ENSP00000469591:p.His134Leu	101.0	0.0	.		93.0	15.0	.	NM_033113	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	hg19	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	15.79	2.936377	0.52972	.	.	ENSG00000197483	ENST00000391718	T	0.13089	2.62	3.62	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.48767	U	0.000162	T	0.14614	0.0353	N	0.16130	0.375	0.44531	D	0.997482	D	0.76494	0.999	D	0.68353	0.957	T	0.07385	-1.0775	10	0.06625	T	0.88	-16.2924	10.5074	0.44842	1.0:0.0:0.0:0.0	.	130	Q5EBL2	ZN628_HUMAN	L	130	ENSP00000375598:H130L	ENSP00000375598:H130L	H	+	2	0	ZNF628	60684773	0.714000	0.27936	0.971000	0.41717	0.613000	0.37349	2.323000	0.43823	1.654000	0.50703	0.397000	0.26171	CAC	.	.	.	none		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
C21orf62	56245	hgsc.bcm.edu	37	21	34166443	34166443	+	Missense_Mutation	SNP	G	G	A	rs377322005		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr21:34166443G>A	ENST00000536776.1	-	2	430	c.290C>T	c.(289-291)aCg>aTg	p.T97M	C21orf49_ENST00000453404.1_Intron|C21orf62_ENST00000487113.1_Missense_Mutation_p.T97M|C21orf49_ENST00000477513.1_Intron|C21orf62_ENST00000490358.1_Missense_Mutation_p.T97M|C21orf62_ENST00000479548.1_Missense_Mutation_p.T97M|C21orf49_ENST00000382377.3_Intron|C21orf49_ENST00000382375.4_Intron|C21orf49_ENST00000382378.1_Intron	NM_001162495.2|NM_001162496.2|NM_019596.5	NP_001155967.2|NP_001155968.2|NP_062542.5	Q9NYP8	CU062_HUMAN	chromosome 21 open reading frame 62	97										endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	6		Myeloproliferative disorder(46;0.0255)				TTGGACCAGCGTGAAGTTCAG	0.552																																					p.T97M		Atlas-SNP	.											.	C21orf62	26	.	0			c.C290T						PASS	.	G	MET/THR,MET/THR,MET/THR	1,4195		0,1,2097	94.0	94.0	94.0		290,290,290	5.4	1.0	21		94	0,8456		0,0,4228	no	missense,missense,missense	C21orf62	NM_001162495.2,NM_001162496.2,NM_019596.5	81,81,81	0,1,6325	AA,AG,GG		0.0,0.0238,0.0079	probably-damaging,probably-damaging,probably-damaging	97/220,97/220,97/220	34166443	1,12651	2098	4228	6326	SO:0001583	missense	56245	exon4			ACCAGCGTGAAGT	AF231922	CCDS42919.1, CCDS42919.2	21q22.1	2011-02-24			ENSG00000205929	ENSG00000205929			1305	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 120"""	C21orf120			Standard	NM_001162495		Approved	B37, PRED81	uc011adu.2	Q9NYP8	OTTHUMG00000163477	ENST00000536776.1:c.290C>T	chr21.hg19:g.34166443G>A	ENSP00000444950:p.Thr97Met	93.0	0.0	.		89.0	20.0	.	NM_001162495	A8K4L8	Missense_Mutation	SNP	ENST00000536776.1	hg19	CCDS42919.2	.	.	.	.	.	.	.	.	.	.	G	16.02	3.005005	0.54254	2.38E-4	0.0	ENSG00000205929	ENST00000536776;ENST00000490358;ENST00000487113;ENST00000382373;ENST00000479548	.	.	.	5.37	5.37	0.77165	.	0.090322	0.43416	U	0.000561	T	0.79482	0.4453	M	0.70275	2.135	0.51012	D	0.999905	D	0.89917	1.0	D	0.91635	0.999	T	0.81473	-0.0917	9	0.87932	D	0	-7.2789	18.7116	0.91659	0.0:0.0:1.0:0.0	.	97	Q9NYP8	CU062_HUMAN	M	97;97;97;144;97	.	ENSP00000371810:T144M	T	-	2	0	C21orf62	33088313	1.000000	0.71417	0.957000	0.39632	0.150000	0.21749	4.250000	0.58772	2.519000	0.84933	0.462000	0.41574	ACG	.	.	.	weak		0.552	C21orf62-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139598.5	NM_019596	
CCDC116	164592	hgsc.bcm.edu	37	22	21990901	21990901	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr22:21990901G>C	ENST00000292779.3	+	5	1545	c.1384G>C	c.(1384-1386)Ggc>Cgc	p.G462R		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	462										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					TAAGCAGCTGGGCTTCTTCTC	0.582																																					p.G462R		Atlas-SNP	.											CCDC116,lower_third,carcinoma,0,1	CCDC116	56	.	0			c.G1384C						PASS	.						97.0	78.0	84.0					22																	21990901		2203	4300	6503	SO:0001583	missense	164592	exon5			CAGCTGGGCTTCT	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.1384G>C	chr22.hg19:g.21990901G>C	ENSP00000292779:p.Gly462Arg	74.0	0.0	.		76.0	13.0	.	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	hg19	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.534618	0.64972	.	.	ENSG00000161180	ENST00000292779	T	0.33216	1.42	4.78	4.78	0.61160	.	0.000000	0.45361	D	0.000368	T	0.45875	0.1364	L	0.39898	1.24	0.33807	D	0.627382	D	0.89917	1.0	D	0.97110	1.0	T	0.57653	-0.7774	10	0.87932	D	0	-29.332	13.5001	0.61449	0.0:0.0:1.0:0.0	.	462	Q8IYX3-2	.	R	462	ENSP00000292779:G462R	ENSP00000292779:G462R	G	+	1	0	CCDC116	20320901	1.000000	0.71417	0.998000	0.56505	0.460000	0.32559	4.725000	0.61979	2.655000	0.90218	0.585000	0.79938	GGC	.	.	.	none		0.582	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
MN1	4330	hgsc.bcm.edu	37	22	28194894	28194894	+	Silent	SNP	C	C	T	rs202212250		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr22:28194894C>T	ENST00000302326.4	-	1	2592	c.1638G>A	c.(1636-1638)caG>caA	p.Q546Q		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	546	Poly-Gln.				intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						gctgctgctgctgctgttgct	0.642			T	ETV6	"""AML, meningioma"""																																p.Q546Q		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	.	MN1	122	.	0			c.G1638A						PASS	.						4.0	5.0	5.0					22																	28194894		1986	4018	6004	SO:0001819	synonymous_variant	4330	exon1			CTGCTGCTGCTGT	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.1638G>A	chr22.hg19:g.28194894C>T		62.0	0.0	.		53.0	6.0	.	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	hg19	CCDS42998.1																																																																																			.	.	.	none		0.642	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
MAP3K15	389840	hgsc.bcm.edu	37	X	19389154	19389154	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chrX:19389154A>C	ENST00000338883.4	-	24	3322	c.3323T>G	c.(3322-3324)aTt>aGt	p.I1108S	MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000469203.2_Missense_Mutation_p.I940S|MAP3K15_ENST00000359173.3_Missense_Mutation_p.I543S	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1108							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					GTGGGGCCTAATTAAGTGGTT	0.433																																					p.I1108S		Atlas-SNP	.											.	MAP3K15	108	.	0			c.T3323G						PASS	.						44.0	44.0	44.0					X																	19389154		2203	4300	6503	SO:0001583	missense	389840	exon24			GGCCTAATTAAGT	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3323T>G	chrX.hg19:g.19389154A>C	ENSP00000345629:p.Ile1108Ser	202.0	0.0	.		191.0	78.0	.	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	hg19		.	.	.	.	.	.	.	.	.	.	A	16.69	3.192878	0.58017	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	D;D;D	0.82893	-1.63;-1.66;-1.59	5.25	4.05	0.47172	.	0.045663	0.85682	D	0.000000	D	0.89230	0.6656	M	0.87180	2.865	0.80722	D	1	D;P	0.56035	0.974;0.736	P;B	0.55871	0.786;0.221	D	0.89322	0.3641	10	0.87932	D	0	.	10.8165	0.46580	0.8561:0.0:0.0:0.1439	.	583;1108	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	S	1108;543;940	ENSP00000345629:I1108S;ENSP00000352093:I543S;ENSP00000428356:I940S	ENSP00000345629:I1108S	I	-	2	0	MAP3K15	19299075	1.000000	0.71417	0.987000	0.45799	0.992000	0.81027	6.988000	0.76212	0.705000	0.31890	0.451000	0.29950	ATT	.	.	.	none		0.433	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671	
MT-CO3	4514	hgsc.bcm.edu	37	M	9242	9242	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chrM:9242A>C	ENST00000362079.2	+	1	36	c.36A>C	c.(34-36)aaA>aaC	p.K12N	MT-TR_ENST00000387439.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	12					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						CATATAGTAAAACCCAGCCCA	0.493																																					p.K12N		Atlas-SNP	.											.	.	.	.	0			c.A36C						PASS	.																																			SO:0001583	missense	5742	exon1			AGTAAAACCCAGC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.36A>C	chrM.hg19:g.9242A>C	ENSP00000354982:p.Lys12Asn	30.0	0.0	.		82.0	5.0	.	ENST00000362079	Q14Y83	Missense_Mutation	SNP	ENST00000362079.2	hg19																																																																																				.	.	.	none		0.493	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
MT-ND4	4538	hgsc.bcm.edu	37	M	11126	11126	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chrM:11126G>A	ENST00000361381.2	+	1	367	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	MT-TR_ENST00000387439.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	123					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATATCTTCTTCGAAACCACAC	0.413																																					p.E123K		Atlas-SNP	.											.	.	.	.	0			c.G367A						PASS	.																																			SO:0001583	missense	0	exon1			TTCTTCGAAACCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.367G>A	chrM.hg19:g.11126G>A	ENSP00000354961:p.Glu123Lys	28.0	0.0	.		81.0	9.0	.	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	hg19																																																																																				.	.	.	none		0.413	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
MT-CYB	4519	hgsc.bcm.edu	37	M	15786	15786	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chrM:15786T>C	ENST00000361789.2	+	1	1040	c.1040T>C	c.(1039-1041)tTt>tCt	p.F347S	MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	347					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						AAGCTACCCTTTTACCATCAT	0.408																																					p.F347S		Atlas-SNP	.											.	.	.	.	0			c.T1040C						PASS	.																																			SO:0001583	missense	0	exon1			ACCCTTTTACCAT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.1040T>C	chrM.hg19:g.15786T>C	ENSP00000354554:p.Phe347Ser	22.0	0.0	.		76.0	11.0	.	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	T|0.999;C|0.001	0.001	weak		0.408	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
ADCY6	112	hgsc.bcm.edu	37	12	49171962	49171964	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	GCT	GCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr12:49171962_49171964delGCT	ENST00000307885.4	-	2	1635_1637	c.941_943delAGC	c.(940-945)cagcgc>cgc	p.Q314del	ADCY6_ENST00000552090.1_5'Flank|ADCY6_ENST00000357869.3_In_Frame_Del_p.Q314del|ADCY6_ENST00000550422.1_In_Frame_Del_p.Q314del	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	314					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|negative regulation of neuron projection development (GO:0010977)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						AAGGCCTGGCGCTGAGACACCTC	0.631																																					p.314_315del		Atlas-Indel,Pindel	.											.	ADCY6	81	.	0			c.942_944del						PASS	.																																			SO:0001651	inframe_deletion	112	exon2			.		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.941_943delAGC	chr12.hg19:g.49171962_49171964delGCT	ENSP00000311405:p.Gln314del	137.0	0.0	0		159.0	61.0	0.383648	NM_015270	Q9NR75|Q9UDB0	In_Frame_Del	DEL	ENST00000307885.4	hg19	CCDS8767.1																																																																																			.	.	.	none		0.631	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
DIDO1	11083	hgsc.bcm.edu	37	20	61527694	61527695	+	Frame_Shift_Ins	INS	-	-	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr20:61527694_61527695insT	ENST00000266070.4	-	8	2429_2430	c.2104_2105insA	c.(2104-2106)attfs	p.I702fs	DIDO1_ENST00000395340.1_Frame_Shift_Ins_p.I702fs|DIDO1_ENST00000395343.1_Frame_Shift_Ins_p.I702fs|DIDO1_ENST00000395335.2_Frame_Shift_Ins_p.I702fs	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	702	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.I702V(1)		NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					ATGGAGGGCAATTTTTCCTACT	0.356																																					p.I702fs	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-Indel,Pindel	.											.	DIDO1	321	.	1	Substitution - Missense(1)	lung(1)	c.2105_2106insA						PASS	.																																			SO:0001589	frameshift_variant	11083	exon8			.	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2105dupA	chr20.hg19:g.61527699_61527699dupT	ENSP00000266070:p.Ile702fs	128.0	0.0	0		118.0	30.0	0.254237	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Frame_Shift_Ins	INS	ENST00000266070.4	hg19	CCDS33506.1																																																																																			.	.	.	none		0.356	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
ARHGAP24	83478	hgsc.bcm.edu	37	4	86916509	86916510	+	Frame_Shift_Ins	INS	-	-	C			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:86916509_86916510insC	ENST00000395184.1	+	9	2168_2169	c.1702_1703insC	c.(1702-1704)tccfs	p.S568fs	ARHGAP24_ENST00000264343.4_Frame_Shift_Ins_p.S475fs|ARHGAP24_ENST00000395183.2_Frame_Shift_Ins_p.S473fs	NM_001025616.2	NP_001020787.2	Q8N264	RHG24_HUMAN	Rho GTPase activating protein 24	568					activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of ruffle assembly (GO:1900028)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|wound healing, spreading of epidermal cells (GO:0035313)	cell projection (GO:0042995)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)	Rac GTPase activator activity (GO:0030675)			breast(3)|cervix(1)|endometrium(3)|large_intestine(4)|lung(10)|skin(1)|stomach(1)|urinary_tract(1)	24		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000571)		CCCTGAGAACTCCAACTCCTGT	0.53																																					p.S568fs		Atlas-INDEL	.											.,2	ARHGAP24	116	.	0			c.1702_1703insC						PASS	.																																			SO:0001589	frameshift_variant	83478	exon9			.	AK091196	CCDS3611.1, CCDS34025.1, CCDS43246.1	4q22.1	2013-01-10			ENSG00000138639	ENSG00000138639		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	25361	protein-coding gene	gene with protein product		610586				11230166, 15254788	Standard	NM_001042669		Approved	DKFZP564B1162, FLJ33877, FilGAP	uc003hpk.3	Q8N264	OTTHUMG00000130427	ENST00000395184.1:c.1704dupC	chr4.hg19:g.86916511_86916511dupC	ENSP00000378611:p.Ser568fs	112.0	0.0	0		101.0	14.0	0.138614	NM_001025616	Q4KMG1|Q6ZNV3|Q86TI5|Q86WE4|Q9H0T6	Frame_Shift_Ins	INS	ENST00000395184.1	hg19	CCDS34025.1																																																																																			.	.	.	none		0.530	ARHGAP24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252815.2	NM_031305	
SIMC1	375484	hgsc.bcm.edu	37	5	175772284	175772294	+	Frame_Shift_Del	DEL	GAGAAGCAGAT	GAGAAGCAGAT	-	rs116804795		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	GAGAAGCAGAT	GAGAAGCAGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr5:175772284_175772294delGAGAAGCAGAT	ENST00000443967.1	+	12	2862_2872	c.2455_2465delGAGAAGCAGAT	c.(2455-2466)gagaagcagattfs	p.EKQI819fs	KIAA1191_ENST00000393728.2_5'Flank|SIMC1_ENST00000332772.4_Frame_Shift_Del_p.EKQI280fs|RP11-843P14.2_ENST00000508187.1_RNA|SIMC1_ENST00000430704.2_Frame_Shift_Del_p.EKQI404fs|SIMC1_ENST00000341199.6_Frame_Shift_Del_p.EKQI404fs			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	819							SUMO polymer binding (GO:0032184)										GGTAGACGTAGAGAAGCAGATTGAGGCCTTC	0.502																																					p.403_407del		Atlas-Indel,Pindel	.											.	.	.	.	0			c.1209_1219del						PASS	.																																			SO:0001589	frameshift_variant	375484	exon9			.	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.2455_2465delGAGAAGCAGAT	chr5.hg19:g.175772284_175772294delGAGAAGCAGAT	ENSP00000406571:p.Glu819fs	187.0	0.0	0		182.0	25.0	0.137363	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Frame_Shift_Del	DEL	ENST00000443967.1	hg19																																																																																				.	.	.	none		0.502	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
EYS	346007	hgsc.bcm.edu	37	6	64574111	64574111	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr6:64574111delG	ENST00000370621.3	-	36	7722	c.7196delC	c.(7195-7197)ccafs	p.P2399fs	EYS_ENST00000370616.2_Frame_Shift_Del_p.P2399fs|EYS_ENST00000503581.1_Frame_Shift_Del_p.P2399fs			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2399	EGF-like 23. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCTCCCATATGGGCAGAGGCA	0.468																																					p.P2399fs		Atlas-Indel,Pindel	.											.	EYS	527	.	0			c.7197delA						PASS	.						112.0	94.0	99.0					6																	64574111		692	1591	2283	SO:0001589	frameshift_variant	346007	exon36			.		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7196delC	chr6.hg19:g.64574111delG	ENSP00000359655:p.Pro2399fs	77.0	0.0	0		93.0	19.0	0.204301	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Frame_Shift_Del	DEL	ENST00000370621.3	hg19																																																																																				.	.	.	none		0.468	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
KSR1	8844	hgsc.bcm.edu	37	17	25919630	25919630	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:25919630delT	ENST00000319524.6	+	9	1277	c.1277delT	c.(1276-1278)ctcfs	p.L426fs	KSR1_ENST00000581975.1_3'UTR|KSR1_ENST00000398988.3_Frame_Shift_Del_p.L289fs|KSR1_ENST00000268763.6_Frame_Shift_Del_p.L289fs|KSR1_ENST00000509603.2_Frame_Shift_Del_p.L426fs			Q8IVT5	KSR1_HUMAN	kinase suppressor of ras 1	426					Ras protein signal transduction (GO:0007265)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(12)|prostate(2)|urinary_tract(1)	28	Lung NSC(42;0.00836)		BRCA - Breast invasive adenocarcinoma(3;0.00122)	UCEC - Uterine corpus endometrioid carcinoma (53;0.168)		TTTGGAACCCTCCCCAAAGCA	0.562																																					p.L289fs	Esophageal Squamous(88;1120 1336 6324 10502 16832)	Atlas-Indel,Pindel	.											.	KSR1	151	.	0			c.865delC						PASS	.						69.0	69.0	69.0					17																	25919630		1911	4122	6033	SO:0001589	frameshift_variant	8844	exon9			.	U43586	CCDS58532.1	17q11.2	2012-05-23	2005-12-14	2005-12-14	ENSG00000141068	ENSG00000141068			6465	protein-coding gene	gene with protein product		601132	"""kinase suppressor of ras"""	KSR		8521512	Standard	XM_006722151		Approved	RSU2	uc031qzj.1	Q8IVT5	OTTHUMG00000132051	ENST00000319524.6:c.1277delT	chr17.hg19:g.25919630delT	ENSP00000323178:p.Leu426fs	50.0	0.0	0		78.0	20.0	0.25641	NM_014238	F8WEA9|H7BYU0|Q13476	Frame_Shift_Del	DEL	ENST00000319524.6	hg19																																																																																				.	.	.	none		0.562	KSR1-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_014238	
FAT1	2195	hgsc.bcm.edu	37	4	187629592	187629593	+	Frame_Shift_Ins	INS	-	-	A			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:187629592_187629593insA	ENST00000441802.2	-	2	1598_1599	c.1389_1390insT	c.(1387-1392)tttaccfs	p.T464fs		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	464	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GCTGTCTGGGTAAATTCAGGGG	0.48										HNSCC(5;0.00058)																											p.T464fs	Colon(197;1040 2055 4143 4984 49344)	Atlas-Indel,Pindel	.											.	FAT1	500	.	0			c.1390_1391insT						PASS	.																																			SO:0001589	frameshift_variant	2195	exon2			.	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.1390dupT	chr4.hg19:g.187629595_187629595dupA	ENSP00000406229:p.Thr464fs	109.0	0.0	0		103.0	25.0	0.242718	NM_005245		Frame_Shift_Ins	INS	ENST00000441802.2	hg19	CCDS47177.1																																																																																			.	.	.	none		0.480	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
TLR1	7096	hgsc.bcm.edu	37	4	38800432	38800432	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr4:38800432delA	ENST00000502213.2	-	3	250	c.21delT	c.(19-21)tttfs	p.F7fs	TLR1_ENST00000308979.2_Frame_Shift_Del_p.F7fs			Q15399	TLR1_HUMAN	toll-like receptor 1	7					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AGATAATGGCAAAATGGAAGA	0.328																																					p.A8fs	GBM(5;216 373 40795 46382)	Atlas-Indel,Pindel	.											.	TLR1	70	.	0			c.22delG						PASS	.						33.0	36.0	35.0					4																	38800432		2194	4292	6486	SO:0001589	frameshift_variant	7096	exon4			.	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.21delT	chr4.hg19:g.38800432delA	ENSP00000421259:p.Phe7fs	285.0	0.0	0		317.0	70.0	0.22082	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Frame_Shift_Del	DEL	ENST00000502213.2	hg19	CCDS33973.1																																																																																			.	.	.	none		0.328	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
KMT2C	58508	hgsc.bcm.edu	37	7	151856014	151856014	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr7:151856014delC	ENST00000262189.6	-	44	11822	c.11604delG	c.(11602-11604)aggfs	p.R3868fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.R3868fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3868					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										CGTCCTTTTTCCTTTTCTTTG	0.463																																					p.K3869fs		Atlas-Indel,Pindel	.											.	MLL3	1564	.	0			c.11605delA						PASS	.						356.0	320.0	332.0					7																	151856014		2203	4300	6503	SO:0001589	frameshift_variant	58508	exon44			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11604delG	chr7.hg19:g.151856014delC	ENSP00000262189:p.Arg3868fs	63.0	0.0	0		98.0	14.0	0.142857	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.	.	none		0.463	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
ZNF627	199692	hgsc.bcm.edu	37	19	11728063	11728063	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:11728063delA	ENST00000361113.5	+	4	953	c.745delA	c.(745-747)aaafs	p.K249fs	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	249					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						CACTGGAGATAAACCCTATGA	0.418																																					p.D248fs	Melanoma(112;173 1614 10731 17751 23322)	Atlas-Indel,Pindel	.											.	ZNF627	43	.	0			c.744delT						PASS	.						56.0	59.0	58.0					19																	11728063		2203	4299	6502	SO:0001589	frameshift_variant	199692	exon4			.	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"""Zinc fingers, C2H2-type"", ""-"""	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.745delA	chr19.hg19:g.11728063delA	ENSP00000354414:p.Lys249fs	138.0	0.0	0		132.0	21.0	0.159091	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Frame_Shift_Del	DEL	ENST00000361113.5	hg19	CCDS42502.1																																																																																			.	.	.	none		0.418	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295	
POMT1	10585	hgsc.bcm.edu	37	9	134394275	134394276	+	Frame_Shift_Del	DEL	GG	GG	-	rs376882399		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	GG	GG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr9:134394275_134394276delGG	ENST00000372228.3	+	15	1662_1663	c.1483_1484delGG	c.(1483-1485)gggfs	p.G495fs	POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000423007.1_Frame_Shift_Del_p.G473fs|POMT1_ENST00000541219.1_Frame_Shift_Del_p.G251fs|POMT1_ENST00000354713.4_Frame_Shift_Del_p.G443fs|POMT1_ENST00000341012.7_Frame_Shift_Del_p.G419fs|POMT1_ENST00000404875.2_Frame_Shift_Del_p.G356fs|POMT1_ENST00000402686.3_Frame_Shift_Del_p.G473fs|POMT1_ENST00000419118.2_Frame_Shift_Del_p.G321fs|RP11-334J6.6_ENST00000415423.1_RNA	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	495	MIR 3. {ECO:0000255|PROSITE- ProRule:PRU00131}.				carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		GGAGATCGTCGGGGAGAAGCTG	0.673																																					p.494_495del		Atlas-Indel,Pindel	.											.	POMT1	59	.	0			c.1482_1483del						PASS	.																																			SO:0001589	frameshift_variant	10585	exon15			.	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.1483_1484delGG	chr9.hg19:g.134394277_134394278delGG	ENSP00000361302:p.Gly495fs	124.0	0.0	0		110.0	17.0	0.154545	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Frame_Shift_Del	DEL	ENST00000372228.3	hg19	CCDS6943.1																																																																																			.	.	.	none		0.673	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
ZNF628	89887	hgsc.bcm.edu	37	19	55992958	55992958	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:55992958delC	ENST00000598519.1	+	3	951	c.398delC	c.(397-399)tccfs	p.S133fs	ZNF628_ENST00000391718.2_Frame_Shift_Del_p.S129fs			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	133					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		AAGTGGTCGTCCCACTACCAG	0.662																																					p.S133fs		Atlas-INDEL	.											.	ZNF628	75	.	0			c.397delT						PASS	.						40.0	40.0	40.0					19																	55992958		2203	4299	6502	SO:0001589	frameshift_variant	89887	exon3			.	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.398delC	chr19.hg19:g.55992958delC	ENSP00000469591:p.Ser133fs	98.0	0.0	0		90.0	15.0	0.166667	NM_033113	Q86X34	Frame_Shift_Del	DEL	ENST00000598519.1	hg19	CCDS33116.3																																																																																			.	.	.	none		0.662	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
HTR3D	200909	hgsc.bcm.edu	37	3	183756708	183756709	+	Frame_Shift_Ins	INS	-	-	T			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:183756708_183756709insT	ENST00000382489.3	+	8	1310_1311	c.1310_1311insT	c.(1309-1314)tacctgfs	p.L438fs	HTR3D_ENST00000428798.2_Frame_Shift_Ins_p.L388fs|HTR3D_ENST00000453435.1_Frame_Shift_Ins_p.L217fs|HTR3D_ENST00000334128.2_Frame_Shift_Ins_p.L263fs	NM_001163646.1	NP_001157118.1	Q70Z44	5HT3D_HUMAN	5-hydroxytryptamine (serotonin) receptor 3D, ionotropic	438					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(2)	10	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;6.23e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)		Ergoloid mesylate(DB01049)	TTCCGCCTCTACCTGCTCTTCA	0.589																																					p.Y437fs		Atlas-Indel,Pindel	.											.	HTR3D	65	.	0			c.1310_1311insT						PASS	.																																			SO:0001589	frameshift_variant	200909	exon8			.	AY159812	CCDS3249.1, CCDS46966.1, CCDS54685.1	3q27	2012-05-22	2012-02-03		ENSG00000186090	ENSG00000186090		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24004	protein-coding gene	gene with protein product		610122	"""5-hydroxytryptamine (serotonin) receptor 3 family member D"""			12801637	Standard	NM_001145143		Approved		uc011bqv.2	Q70Z44	OTTHUMG00000156858	Exception_encountered	chr3.hg19:g.183756708_183756709insT	ENSP00000371929:p.Leu438fs	139.0	0.0	0		140.0	33.0	0.235714	NM_001163646	C9J2I6|J3QT78|Q495N5|Q495N6|Q7Z6B3	Frame_Shift_Ins	INS	ENST00000382489.3	hg19	CCDS54685.1																																																																																			.	.	.	none		0.589	HTR3D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346289.1	NM_182537	
FOXJ1	2302	hgsc.bcm.edu	37	17	74136299	74136299	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:74136299delG	ENST00000322957.6	-	2	532	c.178delC	c.(178-180)cacfs	p.H60fs	RNF157_ENST00000589912.1_5'Flank|RNF157-AS1_ENST00000586627.1_RNA|RNF157-AS1_ENST00000585542.1_RNA|RNF157-AS1_ENST00000590137.1_RNA	NM_001454.3	NP_001445.2	Q92949	FOXJ1_HUMAN	forkhead box J1	60					actin cytoskeleton organization (GO:0030036)|activation of Rho GTPase activity (GO:0032862)|brain development (GO:0007420)|central tolerance induction (GO:0002508)|cilium assembly (GO:0042384)|epithelium development (GO:0060429)|establishment of apical/basal cell polarity (GO:0035089)|glomerular parietal epithelial cell development (GO:0072016)|humoral immune response (GO:0006959)|left/right pattern formation (GO:0060972)|leukocyte migration (GO:0050900)|lung epithelium development (GO:0060428)|metanephric part of ureteric bud development (GO:0035502)|negative regulation of B cell activation (GO:0050869)|negative regulation of germinal center formation (GO:0002635)|negative regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002924)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of T cell proliferation (GO:0042130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pattern specification process (GO:0007389)|positive regulation of central B cell tolerance induction (GO:0002897)|positive regulation of lung ciliated cell differentiation (GO:1901248)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			large_intestine(1)|liver(1)|pancreas(1)|skin(1)	4			LUSC - Lung squamous cell carcinoma(166;0.187)			TGGTAGCCGTGGGGGTCGGTG	0.736																																					p.H60fs		Atlas-Indel,Pindel	.											.	FOXJ1	11	.	0			c.179delA						PASS	.						3.0	5.0	4.0					17																	74136299		1712	3354	5066	SO:0001589	frameshift_variant	2302	exon2			.	X99349	CCDS32739.1	17q25.1	2008-05-14				ENSG00000129654		"""Forkhead boxes"""	3816	protein-coding gene	gene with protein product		602291		FKHL13		9073514, 16518568	Standard	NM_001454		Approved	HFH-4, HFH4	uc002jqx.3	Q92949		ENST00000322957.6:c.178delC	chr17.hg19:g.74136299delG	ENSP00000323880:p.His60fs	60.0	0.0	0		45.0	18.0	0.4	NM_001454	O00630	Frame_Shift_Del	DEL	ENST00000322957.6	hg19	CCDS32739.1																																																																																			.	.	.	none		0.736	FOXJ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449856.1	NM_001454	
CROCC	9696	hgsc.bcm.edu	37	1	17256398	17256398	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr1:17256398delC	ENST00000375541.5	+	4	478	c.409delC	c.(409-411)ctgfs	p.L137fs	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		GCCCAGGGGGCTGGTACGGCA	0.711																																					p.G136fs		Atlas-INDEL	.											.	CROCC	185	.	0			c.408delG						PASS	.						9.0	11.0	10.0					1																	17256398		2172	4244	6416	SO:0001589	frameshift_variant	9696	exon4			.	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.409delC	chr1.hg19:g.17256398delC	ENSP00000364691:p.Leu137fs	54.0	0.0	0		54.0	10.0	0.185185	NM_014675		Frame_Shift_Del	DEL	ENST00000375541.5	hg19	CCDS30616.1																																																																																			.	.	.	none		0.711	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
TRIP11	9321	hgsc.bcm.edu	37	14	92469868	92469876	+	In_Frame_Del	DEL	CTCTTGTAA	CTCTTGTAA	-	rs528054481		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	CTCTTGTAA	CTCTTGTAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr14:92469868_92469876delCTCTTGTAA	ENST00000267622.4	-	11	4817_4825	c.4444_4452delTTACAAGAG	c.(4444-4452)ttacaagagdel	p.LQE1482del		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1482					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TCATGTTAGTCTCTTGTAACGCTTGATAT	0.368			T	PDGFRB	AML																																p.1482_1485del	Ovarian(84;609 1888 9852 42686)	Atlas-Indel,Pindel	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.4445_4453del						PASS	.																																			SO:0001651	inframe_deletion	9321	exon11			.	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.4444_4452delTTACAAGAG	chr14.hg19:g.92469868_92469876delCTCTTGTAA	ENSP00000267622:p.Leu1482_Glu1484del	83.0	0.0	0		99.0	13.0	0.131313	NM_004239	B2RUT2|O14689|O15154|O95949	In_Frame_Del	DEL	ENST00000267622.4	hg19	CCDS9899.1																																																																																			.	.	.	none		0.368	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
C3orf22	152065	hgsc.bcm.edu	37	3	126270916	126270916	+	Frame_Shift_Del	DEL	C	C	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr3:126270916delC	ENST00000318225.2	-	3	517	c.139delG	c.(139-141)gtcfs	p.V47fs		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	47										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		TCGTTTGTGACCTCCCAGGGC	0.617																																					p.V47fs		Atlas-Indel,Pindel	.											.	C3orf22	17	.	0			c.140delT						PASS	.						94.0	83.0	87.0					3																	126270916		2203	4300	6503	SO:0001589	frameshift_variant	152065	exon3			.		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.139delG	chr3.hg19:g.126270916delC	ENSP00000316644:p.Val47fs	45.0	0.0	0		61.0	18.0	0.295082	NM_152533	B3KUS9	Frame_Shift_Del	DEL	ENST00000318225.2	hg19	CCDS3040.1																																																																																			.	.	.	none		0.617	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
TSR1	55720	hgsc.bcm.edu	37	17	2238104	2238110	+	Frame_Shift_Del	DEL	AGCGCTT	AGCGCTT	-	rs139020440|rs140750763		TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	AGCGCTT	AGCGCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr17:2238104_2238110delAGCGCTT	ENST00000301364.5	-	5	1716_1722	c.637_643delAAGCGCT	c.(637-645)aagcgctttfs	p.KRF213fs	SGSM2_ENST00000268989.3_5'Flank|TSR1_ENST00000576112.2_Frame_Shift_Del_p.KRF197fs|SGSM2_ENST00000426855.2_5'Flank|SGSM2_ENST00000574563.1_5'Flank	NM_018128.4	NP_060598.3	Q2NL82	TSR1_HUMAN	TSR1, 20S rRNA accumulation, homolog (S. cerevisiae)	213	Bms1-type G.				ribosome assembly (GO:0042255)	nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|urinary_tract(1)	20						TCATGCGGAAAGCGCTTCTCCACTGCT	0.478																																					p.213_215del		Atlas-Indel,Pindel	.											.	TSR1	57	.	0			c.638_644del						PASS	.																																			SO:0001589	frameshift_variant	55720	exon5			.	AK026565	CCDS32525.1	17p13.3	2006-04-20	2006-04-20			ENSG00000167721			25542	protein-coding gene	gene with protein product		611214	"""TSR1, 20S rRNA accumulation, homolog (yeast)"""			10718198	Standard	NM_018128		Approved	FLJ10534	uc002fuj.3	Q2NL82		ENST00000301364.5:c.637_643delAAGCGCT	chr17.hg19:g.2238104_2238110delAGCGCTT	ENSP00000301364:p.Lys213fs	86.0	0.0	0		92.0	23.0	0.25	NM_018128	Q8WUY5|Q9NVT0|Q9P2E6	Frame_Shift_Del	DEL	ENST00000301364.5	hg19	CCDS32525.1																																																																																			.	.	.	none		0.478	TSR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438180.2	NM_018128	
ZNF628	89887	hgsc.bcm.edu	37	19	55992960	55992961	+	Frame_Shift_Del	DEL	CA	CA	-			TCGA-GL-A9DD-01A-11D-A36X-10	TCGA-GL-A9DD-10A-01D-A370-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	7bd84624-b7e4-417d-aff5-1b303bb9d686	62afbca2-3422-4619-8efb-351ae7a8221a	g.chr19:55992960_55992961delCA	ENST00000598519.1	+	3	953_954	c.400_401delCA	c.(400-402)cacfs	p.H134fs	ZNF628_ENST00000391718.2_Frame_Shift_Del_p.H130fs			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	134					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		GTGGTCGTCCCACTACCAGTAC	0.663																																					p.133_134del		Pindel	.											.	ZNF628	75	.	0			c.399_400del						PASS	.																																			SO:0001589	frameshift_variant	89887	exon3			.	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.400_401delCA	chr19.hg19:g.55992960_55992961delCA	ENSP00000469591:p.His134fs	100.0	0.0	.		93.0	12.0	0.129	NM_033113	Q86X34	Frame_Shift_Del	DEL	ENST00000598519.1	hg19	CCDS33116.3																																																																																			.	.	.	none		0.663	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
