#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_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_IGV	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	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_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_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
CROCCP2	84809	broad.mit.edu	37	1	16956611	16956611	+	lincRNA	SNP	G	G	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr1:16956611G>C	ENST00000412962.1	-	0	294							Q86T23	CROL1_HUMAN	ciliary rootlet coiled-coil, rootletin pseudogene 2						centrosome organization (GO:0051297)	ciliary rootlet (GO:0035253)											GCAGGTCCTGGCTTGCCTCAT	0.652																																					.													.	.			0			.																																											0	.			GTCCTGGCTTGCC	AK090414		1p36.13	2010-07-08	2010-07-08	2010-07-08	ENSG00000215908	ENSG00000215908			28170	pseudogene	pseudogene			"""ciliary rootlet coiled-coil, rootletin-like 1"""	CROCCL1		12477932	Standard	NR_026752		Approved	MGC12760	uc001azf.3	Q86T23	OTTHUMG00000037884		1.37:g.16956611G>C			64	0	0		96	0.03	3	.	0		0	Q8NF65|Q96FR5|Q9BRE8	RNA	SNP	ENST00000412962.1	37																																																																																						0.652	CROCCP2-003	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000092784.1		NR_026752.1	
AHDC1	27245	broad.mit.edu	37	1	27878527	27878528	+	Frame_Shift_Ins	INS	-	-	GG			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr1:27878527_27878528insGG	ENST00000247087.5	-	5	695_696	c.99_100insCC	c.(97-102)cccaccfs	p.T34fs	AHDC1_ENST00000374011.2_Frame_Shift_Ins_p.T34fs			Q5TGY3	AHDC1_HUMAN	AT hook, DNA binding motif, containing 1	34	Pro-rich.						DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	42		all_lung(284;1.06e-05)|Lung NSC(340;1.86e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.00503)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0434)|OV - Ovarian serous cystadenocarcinoma(117;8.48e-25)|Colorectal(126;9.17e-09)|COAD - Colon adenocarcinoma(152;1.84e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00192)|BRCA - Breast invasive adenocarcinoma(304;0.00259)|STAD - Stomach adenocarcinoma(196;0.00311)|READ - Rectum adenocarcinoma(331;0.0291)		ggccggggggtgggggggccgc	0.708																																					p.T34fs													.	AHDC1	98		0			c.100_101insCC																																									SO:0001589	frameshift_variant	27245	exon6			GGGGGGTGGGGGG	AK125431	CCDS30652.1	1p36.13	2008-02-05			ENSG00000126705	ENSG00000126705			25230	protein-coding gene	gene with protein product		615790				8619474, 9110174	Standard	XM_005245848		Approved	DJ159A19.3, RP1-159A19.1	uc009vsy.3	Q5TGY3	OTTHUMG00000003398	ENST00000247087.5:c.98_99dupCC	1.37:g.27878532_27878533dupGG	ENSP00000247087:p.Thr34fs		35	0	0		47	0.19	9	NM_001029882	3	0.00	0	Q5TGY4|Q6PJK1|Q6ZUQ6|Q99769|Q9NUF5	Frame_Shift_Ins	INS	ENST00000247087.5	37	CCDS30652.1																																																																																					0.708	AHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000009523.3			
NLRP3	114548	mdanderson.org	37	1	247582355	247582355	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr1:247582355G>T	ENST00000336119.3	+	1	1005	c.259G>T	c.(259-261)Gca>Tca	p.A87S	NLRP3_ENST00000366496.2_Missense_Mutation_p.A87S|NLRP3_ENST00000391827.2_Missense_Mutation_p.A87S|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000348069.2_Missense_Mutation_p.A87S|NLRP3_ENST00000391828.3_Missense_Mutation_p.A87S|NLRP3_ENST00000366497.2_Missense_Mutation_p.A87S	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	87	DAPIN. {ECO:0000255|PROSITE- ProRule:PRU00061}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TTATGAGAAAGCAAAAAGAGA	0.448																																					p.A87S													.	.			0			c.G259T												61.0	58.0	59.0					1																	247582355		2203	4300	6503	SO:0001583	missense	114548	exon1			GAGAAAGCAAAAA	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.259G>T	1.37:g.247582355G>T	ENSP00000337383:p.Ala87Ser		17	0	0		19	0.11	2	NM_004895	1	0.00	0	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	37	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	G	15.58	2.876137	0.51801	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	T;T;T;T;T;T	0.52295	0.67;0.67;0.67;0.67;0.67;0.67	4.49	4.49	0.54785	Pyrin (2);DEATH-like (2);	0.000000	0.51477	D	0.000099	T	0.67154	0.2863	M	0.79123	2.44	0.24858	N	0.992366	D;B;D;P;D	0.56521	0.976;0.025;0.969;0.871;0.969	D;B;D;D;D	0.74674	0.975;0.295;0.977;0.914;0.984	T	0.60167	-0.7316	10	0.56958	D	0.05	.	12.8787	0.58003	0.0:0.0:1.0:0.0	.	87;87;87;87;87	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	S	87	ENSP00000375704:A87S;ENSP00000355453:A87S;ENSP00000337383:A87S;ENSP00000294752:A87S;ENSP00000355452:A87S;ENSP00000375703:A87S	ENSP00000337383:A87S	A	+	1	0	NLRP3	245648978	0.596000	0.26866	0.317000	0.25265	0.470000	0.32858	1.746000	0.38288	2.498000	0.84270	0.561000	0.74099	GCA			0.448	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000097740.1		NM_004895	
TBATA	219793	broad.mit.edu	37	10	72541683	72541683	+	Missense_Mutation	SNP	G	G	A	rs199669673		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:72541683G>A	ENST00000299290.1	-	4	540	c.151C>T	c.(151-153)Cgg>Tgg	p.R51W	TBATA_ENST00000456372.2_Missense_Mutation_p.R51W|TBATA_ENST00000545575.1_Missense_Mutation_p.R41W	NM_152710.2	NP_689923	Q96M53	TBATA_HUMAN	thymus, brain and testes associated	51					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|nucleus (GO:0005634)		p.R51R(2)									CGGCGGATCCGCTCGAAATCC	0.597																																					p.R51W													C10orf27,colon,carcinoma,0,2	.		2	2	Substitution - coding silent(2)	lung(2)	c.C151T							G	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	125.0	121.0	122.0		151	2.3	0.0	10		122	0,8600		0,0,4300	no	missense	C10orf27	NM_152710.2	101	0,3,6500	AA,AG,GG		0.0,0.0681,0.0231	possibly-damaging	51/352	72541683	3,13003	2203	4300	6503	SO:0001583	missense	219793	exon4			GGATCCGCTCGAA	AK057382	CCDS7308.1	10q22.2	2012-05-23	2012-05-23	2012-05-23	ENSG00000166220	ENSG00000166220			23511	protein-coding gene	gene with protein product		612640	"""chromosome 10 open reading frame 27"""	C10orf27		20937703	Standard	NM_152710		Approved	FLJ32820, spatial	uc001jrj.1	Q96M53	OTTHUMG00000018413	ENST00000299290.1:c.151C>T	10.37:g.72541683G>A	ENSP00000299290:p.Arg51Trp		134	0	0		136	0.03	4	NM_152710	0		0	A4QPA8|B2RPQ2|Q5T4G2	Missense_Mutation	SNP	ENST00000299290.1	37	CCDS7308.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466959	0.43839	6.81E-4	0.0	ENSG00000166220	ENST00000299290;ENST00000536955;ENST00000456372;ENST00000545575	T	0.44482	0.92	5.39	2.33	0.28932	.	1.641390	0.03486	N	0.215824	T	0.50463	0.1617	N	0.22421	0.69	0.09310	N	1	D;D;D;P;D;P	0.76494	0.995;0.999;0.971;0.924;0.982;0.924	P;D;P;B;P;B	0.65233	0.533;0.933;0.471;0.292;0.533;0.292	T	0.42799	-0.9430	10	0.66056	D	0.02	0.0	8.9934	0.36037	0.0:0.3388:0.5093:0.152	.	40;40;51;51;41;51	B7Z8D7;B7Z8G0;B7ZMN4;B7ZMN5;B7Z8I8;Q96M53	.;.;.;.;.;SPATL_HUMAN	W	51;38;51;41	ENSP00000299290:R51W	ENSP00000299290:R51W	R	-	1	2	C10orf27	72211689	0.021000	0.18746	0.008000	0.14137	0.117000	0.20001	0.698000	0.25571	0.263000	0.21812	0.591000	0.81541	CGG			0.597	TBATA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000048519.1		NM_152710	
FAM149B1	317662	hgsc.bcm.edu	37	10	74937685	74937685	+	Silent	SNP	C	C	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:74937685C>A	ENST00000242505.6	+	3	408	c.234C>A	c.(232-234)ggC>ggA	p.G78G		NM_173348.1	NP_775483.1	Q96BN6	F149B_HUMAN	family with sequence similarity 149, member B1	78										breast(2)|endometrium(1)|kidney(1)|stomach(3)	7						GTTATACAGGCGCAGGGATAT	0.443																																					p.G78G													FAM149B1,NS,carcinoma,0,2	FAM149B1	0	2	0			c.C234A												153.0	121.0	131.0					10																	74937685		692	1591	2283	SO:0001819	synonymous_variant	317662	exon3			TACAGGCGCAGGG	AB023191	CCDS44435.1	10q22.2	2008-10-27	2007-11-14	2007-11-14	ENSG00000138286	ENSG00000138286			29162	protein-coding gene	gene with protein product			"""KIAA0974"""	KIAA0974		10231032	Standard	NM_173348		Approved		uc009xqz.3	Q96BN6	OTTHUMG00000067794	ENST00000242505.6:c.234C>A	10.37:g.74937685C>A			58	0	0		66	0.06	4	NM_173348	11	0.00	0	Q9Y2I0	Silent	SNP	ENST00000242505.6	37	CCDS44435.1	.	.	.	.	.	.	.	.	.	.	C	8.762	0.923843	0.18056	.	.	ENSG00000138286	ENST00000372955	.	.	.	5.16	3.22	0.36961	.	.	.	.	.	T	0.38558	0.1045	.	.	.	0.80722	D	1	B	0.20780	0.048	B	0.18561	0.022	T	0.13791	-1.0496	6	.	.	.	-8.8823	6.8167	0.23835	0.1779:0.7268:0.0:0.0953	.	57	B4E0M2	.	E	19	.	.	A	+	2	0	FAM149B1	74607691	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	0.415000	0.21181	1.259000	0.44117	0.591000	0.81541	GCG			0.443	FAM149B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000145438.1		NM_173348	
IFIT3	3437	mdanderson.org	37	10	91099835	91099835	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:91099835G>A	ENST00000371818.4	+	2	1603	c.1423G>A	c.(1423-1425)Gtc>Atc	p.V475I	LIPA_ENST00000371837.1_Intron|IFIT3_ENST00000371811.4_Missense_Mutation_p.V475I|LIPA_ENST00000487618.1_Intron	NM_001549.4	NP_001540.2	O14879	IFIT3_HUMAN	interferon-induced protein with tetratricopeptide repeats 3	475					cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)			breast(1)|central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(3)|skin(2)|urinary_tract(1)	15						CCAGGGCGCAGTCAGCTCCAG	0.552																																					p.V475I													.	.			0			c.G1423A												61.0	65.0	64.0					10																	91099835		2203	4300	6503	SO:0001583	missense	3437	exon2			GGCGCAGTCAGCT	U52513	CCDS7402.1, CCDS31241.1	10q23.31	2014-05-22	2004-07-16	2004-07-16	ENSG00000119917	ENSG00000119917		"""Tetratricopeptide (TTC) repeat domain containing"""	5411	protein-coding gene	gene with protein product		604650	"""interferon-induced protein with tetratricopeptide repeats 4"""	IFIT4		9828129, 9391139	Standard	NM_001031683		Approved	ISG60, RIG-G, CIG-49, IFI60, GARG-49, IRG2	uc001kgg.3	O14879	OTTHUMG00000018708	ENST00000371818.4:c.1423G>A	10.37:g.91099835G>A	ENSP00000360883:p.Val475Ile		48	0	0		42	0.07	3	NM_001031683	98	0.00	0	Q99634|Q9BSK7	Missense_Mutation	SNP	ENST00000371818.4	37	CCDS7402.1	.	.	.	.	.	.	.	.	.	.	G	11.48	1.651366	0.29336	.	.	ENSG00000119917	ENST00000371818;ENST00000371811;ENST00000543062	T;T	0.11821	2.74;2.74	4.75	-1.85	0.07784	.	1.078650	0.07297	N	0.873453	T	0.06416	0.0165	N	0.14661	0.345	0.09310	N	1	B	0.22604	0.072	B	0.16289	0.015	T	0.41840	-0.9486	10	0.22109	T	0.4	0.104	3.9742	0.09467	0.0824:0.124:0.2789:0.5147	.	475	O14879	IFIT3_HUMAN	I	475;475;296	ENSP00000360883:V475I;ENSP00000360876:V475I	ENSP00000360876:V475I	V	+	1	0	IFIT3	91089815	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.490000	0.06482	-0.305000	0.08831	0.655000	0.94253	GTC			0.552	IFIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049294.1		NM_001549	
RRP12	23223	hgsc.bcm.edu;bcgsc.ca;mdanderson.org	37	10	99126540	99126540	+	Silent	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:99126540C>T	ENST00000370992.4	-	27	3285	c.3174G>A	c.(3172-3174)gaG>gaA	p.E1058E	RRP12_ENST00000536831.1_Silent_p.E776E|RRP12_ENST00000414986.1_Silent_p.E997E|RRP12_ENST00000315563.6_Silent_p.E958E|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1058	Glu-rich.					integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		cctcctcctcctcttcttcct	0.662																																					p.E1058E													.	.			0			c.G3174A												94.0	108.0	103.0					10																	99126540		2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			CTCCTCCTCTTCT		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3174G>A	10.37:g.99126540C>T			45	0	0		57	0.11	6	NM_015179	20	0.00	0	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																					0.662	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000049699.4		NM_015179	
PKD2L1	9033	mdanderson.org	37	10	102059351	102059351	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:102059351C>A	ENST00000318222.3	-	3	856	c.474G>T	c.(472-474)tgG>tgT	p.W158C	PKD2L1_ENST00000353274.3_Missense_Mutation_p.W158C|PKD2L1_ENST00000338519.3_Missense_Mutation_p.W158C	NM_001253837.1|NM_016112.2	NP_001240766.1|NP_057196.2	Q9P0L9	PK2L1_HUMAN	polycystic kidney disease 2-like 1	158					cation transport (GO:0006812)|cellular response to acidic pH (GO:0071468)|detection of chemical stimulus involved in sensory perception of sour taste (GO:0001581)|detection of mechanical stimulus (GO:0050982)|potassium ion transmembrane transport (GO:0071805)|protein homotrimerization (GO:0070207)|sensory perception of sour taste (GO:0050915)|smoothened signaling pathway (GO:0007224)|sodium ion transmembrane transport (GO:0035725)	calcium channel complex (GO:0034704)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	alpha-actinin binding (GO:0051393)|calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-activated potassium channel activity (GO:0015269)|cation channel activity (GO:0005261)|cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|sodium channel activity (GO:0005272)|sour taste receptor activity (GO:0033040)			NS(2)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	43		Colorectal(252;0.117)		Epithelial(162;6.15e-10)|all cancers(201;5.14e-08)		TACTCACATCCCAGAAGTCCG	0.478																																					p.W158C													.	.			0			c.G474T												96.0	89.0	92.0					10																	102059351		2203	4300	6503	SO:0001583	missense	9033	exon3			CACATCCCAGAAG	AF094827	CCDS7492.1	10q24.31	2011-12-16			ENSG00000107593	ENSG00000107593		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9011	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 3"""	604532		PKD2L, PKDL		9878261, 9748274	Standard	NM_016112		Approved	PCL, TRPP3	uc001kqx.1	Q9P0L9	OTTHUMG00000018910	ENST00000318222.3:c.474G>T	10.37:g.102059351C>A	ENSP00000325296:p.Trp158Cys		56	0	0		37	0.08	3	NM_016112	0		0	O75972|Q5W039|Q9UP35|Q9UPA2	Missense_Mutation	SNP	ENST00000318222.3	37	CCDS7492.1	.	.	.	.	.	.	.	.	.	.	C	23.8	4.463764	0.84425	.	.	ENSG00000107593	ENST00000338519;ENST00000353274;ENST00000318222;ENST00000339977	T;T;T	0.73258	-0.73;-0.73;-0.73	5.31	5.31	0.75309	Polycystin cation channel, PKD1/PKD2 (1);	0.058088	0.85682	D	0.000000	D	0.86973	0.6062	M	0.89095	3.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.995;0.999	D	0.89390	0.3688	10	0.87932	D	0	-17.1173	17.9675	0.89103	0.0:1.0:0.0:0.0	.	111;158	Q1L4F0;Q9P0L9	.;PK2L1_HUMAN	C	158	ENSP00000345068:W158C;ENSP00000266049:W158C;ENSP00000325296:W158C	ENSP00000325296:W158C	W	-	3	0	PKD2L1	102049341	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.739000	0.68622	2.480000	0.83734	0.555000	0.69702	TGG			0.478	PKD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000049863.2		NM_016112	
NFKB2	4791	mdanderson.org	37	10	104159451	104159451	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:104159451C>T	ENST00000369966.3	+	14	1695	c.1445C>T	c.(1444-1446)aCg>aTg	p.T482M	NFKB2_ENST00000189444.6_Missense_Mutation_p.T482M|NFKB2_ENST00000428099.1_Missense_Mutation_p.T482M|NFKB2_ENST00000336486.5_3'UTR	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	482					extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	CACCTGCTGACGGCGCAGGAC	0.741			T	IGH@	B-NHL																																p.T482M				Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	.			0			c.C1445T												4.0	6.0	6.0					10																	104159451		1647	3329	4976	SO:0001583	missense	4791	exon13			TGCTGACGGCGCA	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"""Ankyrin repeat domain containing"""	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.1445C>T	10.37:g.104159451C>T	ENSP00000358983:p.Thr482Met		14	0	0		22	0.09	2	NM_001261403	44	0.00	0	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Missense_Mutation	SNP	ENST00000369966.3	37	CCDS41564.1	.	.	.	.	.	.	.	.	.	.	C	12.76	2.035724	0.35893	.	.	ENSG00000077150	ENST00000428099;ENST00000369966;ENST00000336486;ENST00000189444	T;T;T	0.39787	1.06;1.06;1.06	4.24	1.07	0.20283	Ankyrin repeat-containing domain (1);	0.437109	0.23768	N	0.044746	T	0.13457	0.0326	N	0.00926	-1.1	0.09310	N	1	B;B	0.11235	0.004;0.004	B;B	0.04013	0.001;0.001	T	0.22521	-1.0214	10	0.45353	T	0.12	.	6.9399	0.24486	0.0:0.6789:0.1457:0.1754	.	482;482	Q00653;A8K9D9	NFKB2_HUMAN;.	M	482	ENSP00000410256:T482M;ENSP00000358983:T482M;ENSP00000189444:T482M	ENSP00000189444:T482M	T	+	2	0	NFKB2	104149441	0.797000	0.28877	0.563000	0.28383	0.979000	0.70002	1.236000	0.32683	0.530000	0.28619	0.511000	0.50034	ACG			0.741	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000050080.2			
CYP17A1	1586	mdanderson.org	37	10	104591290	104591290	+	Nonsense_Mutation	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:104591290C>T	ENST00000369887.3	-	7	1389	c.1218G>A	c.(1216-1218)tgG>tgA	p.W406*	CYP17A1_ENST00000489268.1_5'Flank|CYP17A1-AS1_ENST00000369884.4_RNA	NM_000102.3	NP_000093.1	P05093	CP17A_HUMAN	cytochrome P450, family 17, subfamily A, polypeptide 1	406			W -> R (in AH5). {ECO:0000269|PubMed:14671162}.		adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|biphenyl metabolic process (GO:0018879)|cellular response to antibiotic (GO:0071236)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to lipopolysaccharide (GO:0071222)|dibenzo-p-dioxin metabolic process (GO:0018894)|glucocorticoid biosynthetic process (GO:0006704)|hippocampus development (GO:0021766)|hormone biosynthetic process (GO:0042446)|Leydig cell differentiation (GO:0033327)|ovulation (GO:0030728)|phenol-containing compound metabolic process (GO:0018958)|phthalate metabolic process (GO:0018963)|positive regulation of steroid hormone biosynthetic process (GO:0090031)|progesterone metabolic process (GO:0042448)|response to acetate (GO:0010034)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to fungicide (GO:0060992)|response to herbicide (GO:0009635)|response to insecticide (GO:0017085)|response to ionizing radiation (GO:0010212)|response to methylmercury (GO:0051597)|response to nutrient levels (GO:0031667)|response to retinoic acid (GO:0032526)|response to steroid hormone (GO:0048545)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	axon (GO:0030424)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)	17-alpha-hydroxyprogesterone aldolase activity (GO:0047442)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|steroid 17-alpha-monooxygenase activity (GO:0004508)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.122)|all_hematologic(284;0.152)		Epithelial(162;3.93e-09)|all cancers(201;1.02e-07)|BRCA - Breast invasive adenocarcinoma(275;0.215)	Abiraterone(DB05812)|Aminophenazone(DB01424)|Dexamethasone(DB01234)|Metoclopramide(DB01233)|Progesterone(DB00396)	CCGGCTGGTGCCACTCCTTCT	0.577																																					p.W406X													.	.			0			c.G1218A												137.0	99.0	112.0					10																	104591290		2203	4300	6503	SO:0001587	stop_gained	1586	exon7			CTGGTGCCACTCC	M19489	CCDS7541.1	10q24.3	2010-05-04	2003-02-14	2003-02-28	ENSG00000148795	ENSG00000148795	1.14.99.9	"""Cytochrome P450s"""	2593	protein-coding gene	gene with protein product	"""Steroid 17-alpha-monooxygenase"""	609300	"""cytochrome P450, subfamily XVII (steroid 17-alpha-hydroxylase), adrenal hyperplasia"""	CYP17		1347802	Standard	NM_000102		Approved	P450C17, CPT7, S17AH	uc001kwg.3	P05093	OTTHUMG00000018969	ENST00000369887.3:c.1218G>A	10.37:g.104591290C>T	ENSP00000358903:p.Trp406*		65	0	0		45	0.07	3	NM_000102	108	0.00	0	Q5TZV7	Nonsense_Mutation	SNP	ENST00000369887.3	37	CCDS7541.1	.	.	.	.	.	.	.	.	.	.	C	36	5.852426	0.97030	.	.	ENSG00000148795	ENST00000369887	.	.	.	5.02	5.02	0.67125	.	0.058609	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.2957	0.90145	0.0:1.0:0.0:0.0	.	.	.	.	X	406	.	ENSP00000358903:W406X	W	-	3	0	CYP17A1	104581280	1.000000	0.71417	0.932000	0.37286	0.500000	0.33767	6.975000	0.76128	2.487000	0.83934	0.484000	0.47621	TGG			0.577	CYP17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050101.1		NM_000102	
PLEKHS1	79949	mdanderson.org	37	10	115528592	115528592	+	Missense_Mutation	SNP	G	G	T	rs559395228		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr10:115528592G>T	ENST00000369310.3	+	5	922	c.360G>T	c.(358-360)tgG>tgT	p.W120C	PLEKHS1_ENST00000369309.1_5'Flank|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.W38C|PLEKHS1_ENST00000361048.1_Missense_Mutation_p.W126C	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	120	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.																TTAAAGACTGGGTCTCCTTCA	0.403																																					p.W126C													.	.			0			c.G378T												127.0	118.0	121.0					10																	115528592		2203	4300	6503	SO:0001583	missense	79949	exon6			AGACTGGGTCTCC	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.360G>T	10.37:g.115528592G>T	ENSP00000358316:p.Trp120Cys		33	0	0		46	0.07	3	NM_024889	0		0	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	G	19.08	3.758854	0.69763	.	.	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310	T;T;T	0.31247	1.5;1.5;1.5	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.64170	0.2574	M	0.90595	3.13	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.70850	-0.4760	10	0.87932	D	0	-13.7519	16.7398	0.85456	0.0:0.0:1.0:0.0	.	120;120;126	Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	.;.;.	C	126;38;120	ENSP00000354332:W126C;ENSP00000358318:W38C;ENSP00000358316:W120C	ENSP00000354332:W126C	W	+	3	0	C10orf81	115518582	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.294000	0.65687	2.791000	0.96007	0.655000	0.94253	TGG			0.403	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000050432.1		NM_024889	
MUC2	4583	mdanderson.org	37	11	1092900	1092900	+	Silent	SNP	A	A	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr11:1092900A>T	ENST00000441003.2	+	30	4746	c.4719A>T	c.(4717-4719)ccA>ccT	p.P1573P	MUC2_ENST00000359061.5_Silent_p.P1574P|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccccaaccccaacacccaccg	0.637																																					p.P1573P													.	.			0			c.A4719T												104.0	146.0	131.0					11																	1092900		1954	3639	5593	SO:0001819	synonymous_variant	4583	exon30			AACCCCAACACCC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.4719A>T	11.37:g.1092900A>T			29	0.0344827586	1		30	0.17	5	NM_002457	0		0	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																						0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000345894.2		NM_002457	
ARL14EP	120534	mdanderson.org	37	11	30354428	30354428	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr11:30354428G>T	ENST00000282032.3	+	3	657	c.442G>T	c.(442-444)Gct>Tct	p.A148S	ARL14EP_ENST00000533457.1_3'UTR	NM_152316.1	NP_689529.1	Q8N8R7	AL14E_HUMAN	ADP-ribosylation factor-like 14 effector protein	148						cytoplasm (GO:0005737)											AACTGCTAAAGCTTTGAGGTC	0.343																																					p.A148S													.	.			0			c.G442T												72.0	73.0	73.0					11																	30354428		2202	4299	6501	SO:0001583	missense	120534	exon3			GCTAAAGCTTTGA	AK096287	CCDS7869.1	11p14.1	2014-09-17	2012-07-09	2012-07-09	ENSG00000152219	ENSG00000152219			26798	protein-coding gene	gene with protein product		612295	"""chromosome 11 open reading frame 46"""	C11orf46		21458045	Standard	XM_005252792		Approved	FLJ38968, ARF7EP	uc001mso.1	Q8N8R7	OTTHUMG00000166154	ENST00000282032.3:c.442G>T	11.37:g.30354428G>T	ENSP00000282032:p.Ala148Ser		48	0	0		36	0.08	3	NM_152316	74	0.01	1	Q5HYH9	Missense_Mutation	SNP	ENST00000282032.3	37	CCDS7869.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.973919	0.74246	.	.	ENSG00000152219	ENST00000282032;ENST00000530909	T	0.62498	0.02	5.38	5.38	0.77491	.	0.197691	0.42294	D	0.000738	T	0.72244	0.3436	L	0.46157	1.445	0.48571	D	0.99967	D	0.61697	0.99	D	0.70935	0.971	T	0.63945	-0.6522	10	0.12103	T	0.63	-26.1873	19.4956	0.95070	0.0:0.0:1.0:0.0	.	148	Q8N8R7	CK046_HUMAN	S	148	ENSP00000282032:A148S	ENSP00000282032:A148S	A	+	1	0	C11orf46	30311004	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.336000	0.72954	2.693000	0.91896	0.655000	0.94253	GCT			0.343	ARL14EP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000388129.1		NM_152316	
MAP3K11	4296	broad.mit.edu	37	11	65375896	65375896	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr11:65375896T>C	ENST00000309100.3	-	2	1248	c.763A>G	c.(763-765)Agt>Ggt	p.S255G	MAP3K11_ENST00000534432.1_5'Flank|MAP3K11_ENST00000530153.1_5'UTR|MAP3K11_ENST00000532507.1_5'Flank	NM_002419.3	NP_002410.1			mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						ATGTCGTCACTCTCAATGGGC	0.567																																					p.S255G													.	MAP3K11	67		0			c.A763G												76.0	62.0	67.0					11																	65375896		2201	4297	6498	SO:0001583	missense	4296	exon2			CGTCACTCTCAAT		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000309100.3:c.763A>G	11.37:g.65375896T>C	ENSP00000309597:p.Ser255Gly		139	0	0		133	0.03	4	NM_002419	107	0.00	0		Missense_Mutation	SNP	ENST00000309100.3	37	CCDS8107.1	.	.	.	.	.	.	.	.	.	.	C	9.511	1.105677	0.20632	.	.	ENSG00000173327	ENST00000309100;ENST00000526293	D;T	0.93426	-3.22;-1.4	4.75	4.75	0.60458	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.128650	0.53938	N	0.000053	D	0.83857	0.5345	N	0.12182	0.205	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.76160	-0.3061	10	0.23891	T	0.37	.	7.3497	0.26684	0.0:0.8079:0.0:0.1921	.	255	Q16584	M3K11_HUMAN	G	255;5	ENSP00000309597:S255G;ENSP00000435970:S5G	ENSP00000309597:S255G	S	-	1	0	MAP3K11	65132472	0.561000	0.26578	0.982000	0.44146	0.974000	0.67602	1.144000	0.31565	1.251000	0.43983	-0.215000	0.12644	AGT			0.567	MAP3K11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000390209.3			
RIN1	9610	mdanderson.org	37	11	66100214	66100214	+	Silent	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr11:66100214G>T	ENST00000311320.4	-	10	2011	c.1885C>A	c.(1885-1887)Cga>Aga	p.R629R	RIN1_ENST00000530056.1_Silent_p.R463R|RIN1_ENST00000524804.1_5'UTR|RP11-867G23.12_ENST00000526655.1_RNA|RIN1_ENST00000424433.2_Silent_p.R524R	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	629	Ras and 14-3-3 protein binding region.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						TAGGCTACTCGGAGGAGGTGC	0.587																																					p.R629R													RIN1,bladder,carcinoma,+1,1	RIN1	1	1	0			c.C1885A												65.0	72.0	69.0					11																	66100214		2192	4265	6457	SO:0001819	synonymous_variant	9610	exon10			CTACTCGGAGGAG	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.1885C>A	11.37:g.66100214G>T			20	0	0		18	0.11	2	NM_004292	50	0.00	0	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																					0.587	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000392980.2		NM_004292	
POLD3	10714	mdanderson.org	37	11	74322571	74322571	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr11:74322571G>T	ENST00000263681.2	+	4	376	c.247G>T	c.(247-249)Gat>Tat	p.D83Y	POLD3_ENST00000527458.1_Missense_Mutation_p.D44Y|POLD3_ENST00000532497.1_5'UTR	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	83					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					AGTGAGAGAAGATAAATTGGA	0.348																																					p.D83Y													.	.			0			c.G247T												163.0	171.0	168.0					11																	74322571		2200	4293	6493	SO:0001583	missense	10714	exon4			AGAGAAGATAAAT	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.247G>T	11.37:g.74322571G>T	ENSP00000263681:p.Asp83Tyr		49	0	0		45	0.07	3	NM_006591	7	0.00	0	B7ZAI6|Q32MZ9|Q32N00	Missense_Mutation	SNP	ENST00000263681.2	37	CCDS8233.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325528	0.81580	.	.	ENSG00000077514	ENST00000528481;ENST00000263681;ENST00000527458;ENST00000538052;ENST00000530511;ENST00000531615	.	.	.	6.07	6.07	0.98685	.	0.154299	0.56097	D	0.000022	T	0.79387	0.4437	M	0.76328	2.33	0.80722	D	1	D	0.76494	0.999	D	0.72075	0.976	T	0.78061	-0.2351	9	0.48119	T	0.1	-25.2324	18.1531	0.89682	0.0:0.0:1.0:0.0	.	83	Q15054	DPOD3_HUMAN	Y	44;83;44;83;44;44	.	ENSP00000263681:D83Y	D	+	1	0	POLD3	74000219	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.741000	0.91583	2.885000	0.99019	0.655000	0.94253	GAT			0.348	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000385376.1		NM_006591	
ZNF384	171017	mdanderson.org	37	12	6777083	6777083	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr12:6777083G>A	ENST00000396801.3	-	11	1738	c.1531C>T	c.(1531-1533)Cag>Tag	p.Q511*	RP4-761J14.8_ENST00000589924.1_RNA|RP4-761J14.8_ENST00000586338.1_RNA|ZNF384_ENST00000396795.1_Nonsense_Mutation_p.Q450*|ZNF384_ENST00000361959.3_Nonsense_Mutation_p.Q511*|ZNF384_ENST00000355772.4_Nonsense_Mutation_p.Q395*|ZNF384_ENST00000319770.3_Nonsense_Mutation_p.Q434*|ZNF384_ENST00000396799.2_Nonsense_Mutation_p.Q450*	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	511	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)		EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						tgctgctgctgctgctgctgc	0.677			T	"""EWSR1, TAF15 """	ALL																																p.Q511X				Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	.	.			0			c.C1531T												14.0	18.0	17.0					12																	6777083		2198	4288	6486	SO:0001587	stop_gained	171017	exon11			GCTGCTGCTGCTG	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"""Zinc fingers, C2H2-type"""	11955	protein-coding gene	gene with protein product		609951	"""trinucleotide repeat containing 1"""	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1531C>T	12.37:g.6777083G>A	ENSP00000380019:p.Gln511*		44	0	0		49	0.06	3	NM_001135734	76	0.04	3	O15407|Q7Z722|Q8N938	Nonsense_Mutation	SNP	ENST00000396801.3	37	CCDS44817.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.435217	0.83885	.	.	ENSG00000126746	ENST00000319770;ENST00000396795;ENST00000396801;ENST00000361959;ENST00000355772;ENST00000396799	.	.	.	3.35	3.35	0.38373	.	0.423027	0.21610	N	0.071814	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.42905	T	0.14	-2.0395	12.1303	0.53940	0.0:0.0:1.0:0.0	.	.	.	.	X	434;450;511;511;395;450	.	ENSP00000321650:Q434X	Q	-	1	0	ZNF384	6647344	1.000000	0.71417	0.978000	0.43139	0.395000	0.30598	3.710000	0.54860	1.622000	0.50330	0.579000	0.79373	CAG			0.677	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000400712.1			
KMT2D	8085	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	49420275	49420275	+	Silent	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr12:49420275C>T	ENST00000301067.7	-	48	15473	c.15474G>A	c.(15472-15474)gaG>gaA	p.E5158E		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	5158					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										CCTCGTCCCGCTCAATGTAGA	0.562																																					p.E5158E													.	.			0			c.G15474A												62.0	63.0	63.0					12																	49420275		2089	4201	6290	SO:0001819	synonymous_variant	8085	exon48			GTCCCGCTCAATG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.15474G>A	12.37:g.49420275C>T			55	0	0		65	0.22	14	NM_003482	30	0.03	1	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																					0.562	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000390183.2			
DNAJC14	85406	broad.mit.edu	37	12	56226581	56226581	+	5'Flank	SNP	G	G	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr12:56226581G>C	ENST00000357606.3	-	0	0				DNAJC14_ENST00000317287.5_5'Flank|TMEM198B_ENST00000478241.1_RNA			Q6Y2X3	DJC14_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 14						protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(2)|kidney(1)|large_intestine(8)|lung(7)|ovary(3)|prostate(1)|skin(1)	23						GCCCCCCCCCGACCCTAAGCG	0.532																																					.													.	.			0			.																																									SO:0001631	upstream_gene_variant	0	.			CCCCCCGACCCTA	AF141342	CCDS8894.1	12q12	2011-09-02				ENSG00000135392		"""Heat shock proteins / DNAJ (HSP40)"""	24581	protein-coding gene	gene with protein product		606092				11331877, 11984006	Standard	NM_032364		Approved	DNAJ, DRIP78, HDJ3, LIP6, FLJ32792	uc001shu.2	Q6Y2X3			12.37:g.56226581G>C	Exception_encountered		39	0.1794871795	7		65	0.23	15	.	8	0.00	0	A5YM67|Q17RY2|Q66K17|Q96N59|Q96T63	RNA	SNP	ENST00000357606.3	37	CCDS8894.1																																																																																					0.532	DNAJC14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000409095.1		NM_032364	
LRP1	4035	mdanderson.org	37	12	57567646	57567646	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr12:57567646G>T	ENST00000243077.3	+	22	3896	c.3430G>T	c.(3430-3432)Gcc>Tcc	p.A1144S		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1144	LDL-receptor class A 10. {ECO:0000255|PROSITE-ProRule:PRU00124}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CGAGTCCCTGGCCTGCAGGCC	0.607																																					p.A1144S													.	.			0			c.G3430T												190.0	141.0	158.0					12																	57567646		2203	4300	6503	SO:0001583	missense	4035	exon22			TCCCTGGCCTGCA	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.3430G>T	12.37:g.57567646G>T	ENSP00000243077:p.Ala1144Ser		61	0	0		77	0.05	4	NM_002332	30	0.00	0	Q2PP12|Q86SW0|Q8IVG8	Missense_Mutation	SNP	ENST00000243077.3	37	CCDS8932.1	.	.	.	.	.	.	.	.	.	.	G	23.3	4.404708	0.83230	.	.	ENSG00000123384	ENST00000243077	D	0.95412	-3.7	5.03	5.03	0.67393	.	0.190213	0.31821	N	0.007006	D	0.89894	0.6847	N	0.16862	0.45	0.80722	D	1	B	0.27625	0.183	B	0.28385	0.089	D	0.86724	0.1944	10	0.08599	T	0.76	.	17.2939	0.87164	0.0:0.0:1.0:0.0	.	1144	Q07954	LRP1_HUMAN	S	1144	ENSP00000243077:A1144S	ENSP00000243077:A1144S	A	+	1	0	LRP1	55853913	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.138000	0.50570	2.619000	0.88677	0.491000	0.48974	GCC			0.607	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000412772.2		NM_002332	
TMTC3	160418	mdanderson.org	37	12	88568462	88568462	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr12:88568462G>T	ENST00000266712.6	+	9	1498	c.1278G>T	c.(1276-1278)tgG>tgT	p.W426C		NM_181783.3	NP_861448.2	Q6ZXV5	TMTC3_HUMAN	transmembrane and tetratricopeptide repeat containing 3	426					bud outgrowth involved in lung branching (GO:0060447)|lung alveolus development (GO:0048286)|muscle fiber development (GO:0048747)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|endometrium(1)|kidney(4)|large_intestine(5)|liver(1)|lung(12)|prostate(4)|skin(1)	31						ACAGAAATTGGGATTGGGAGT	0.343																																					p.W426C													.	.			0			c.G1278T												130.0	118.0	122.0					12																	88568462		2203	4299	6502	SO:0001583	missense	160418	exon9			AAATTGGGATTGG		CCDS9032.1	12q21.32	2014-09-04			ENSG00000139324	ENSG00000139324		"""Tetratricopeptide (TTC) repeat domain containing"""	26899	protein-coding gene	gene with protein product							Standard	NM_181783		Approved	FLJ90492, SMILE	uc001tau.3	Q6ZXV5	OTTHUMG00000169887	ENST00000266712.6:c.1278G>T	12.37:g.88568462G>T	ENSP00000266712:p.Trp426Cys		52	0	0		116	0.04	5	NM_181783	2	0.00	0	Q5CZ86|Q5H9T6|Q68DQ6|Q68DX0|Q7Z332|Q8NC50	Missense_Mutation	SNP	ENST00000266712.6	37	CCDS9032.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.064851	0.76187	.	.	ENSG00000139324	ENST00000266712	T	0.40225	1.04	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.61850	0.2380	M	0.62723	1.935	0.80722	D	1	D	0.71674	0.998	D	0.63793	0.918	T	0.57225	-0.7848	10	0.39692	T	0.17	-4.545	19.8576	0.96767	0.0:0.0:1.0:0.0	.	426	Q6ZXV5-2	.	C	426	ENSP00000266712:W426C	ENSP00000266712:W426C	W	+	3	0	TMTC3	87092593	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.297000	0.96120	2.696000	0.92011	0.655000	0.94253	TGG			0.343	TMTC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000406421.1		NM_181783	
CHFR	55743	broad.mit.edu	37	12	133435706	133435707	+	In_Frame_Ins	INS	-	-	CAT			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr12:133435706_133435707insCAT	ENST00000432561.2	-	8	967_968	c.894_895insATG	c.(892-897)atggag>atgATGgag	p.298_299insM	CHFR_ENST00000315585.7_In_Frame_Ins_p.257_258insM|CHFR_ENST00000266880.7_In_Frame_Ins_p.298_299insM|CHFR_ENST00000537522.1_5'Flank|CHFR_ENST00000541837.2_De_novo_Start_OutOfFrame|CHFR_ENST00000443047.2_In_Frame_Ins_p.206_207insM|CHFR_ENST00000450056.2_In_Frame_Ins_p.286_287insM			Q96EP1	CHFR_HUMAN	checkpoint with forkhead and ring finger domains, E3 ubiquitin protein ligase	298					mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|modification-dependent protein catabolic process (GO:0019941)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)|PML body (GO:0016605)	ligase activity (GO:0016874)|nucleotide binding (GO:0000166)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.00552)|all_epithelial(31;0.226)		OV - Ovarian serous cystadenocarcinoma(86;2.59e-08)|Epithelial(86;6.38e-07)|all cancers(50;1.56e-05)		AGCGTCTCCTCCATCTTGTCTG	0.594																																					p.E299delinsME													.	CHFR	83		0			c.895_896insATG																																									SO:0001652	inframe_insertion	0	exon8			TCTCCTCCATCTT	AK001658	CCDS31937.1, CCDS53847.1, CCDS53848.1, CCDS53849.1	12q24.33	2012-02-23	2012-02-23			ENSG00000072609		"""RING-type (C3HC4) zinc fingers"""	20455	protein-coding gene	gene with protein product		605209	"""checkpoint with forkhead and ring finger domains"""			10935642, 11807090	Standard	NM_001161344		Approved	FLJ10796, RNF196	uc001ulf.2	Q96EP1		ENST00000432561.2:c.892_894dupATG	12.37:g.133435707_133435709dupCAT	ENSP00000392395:p.Met298_Met298dup		65	0	0		103	0.07	7	NM_001161345	31	0.00	0	A6NEN5|B4DZ77|B4E2L6|Q96SL3|Q9NRT4|Q9NT32|Q9NVD5	Translation_Start_Site	INS	ENST00000432561.2	37	CCDS53849.1																																																																																					0.594	CHFR-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000397130.2			
APEX1	328	broad.mit.edu	37	14	20923824	20923824	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr14:20923824A>G	ENST00000216714.3	+	2	288	c.20A>G	c.(19-21)aAg>aGg	p.K7R	OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000557365.1_Intron|APEX1_ENST00000555414.1_Missense_Mutation_p.K7R|APEX1_ENST00000398030.4_Missense_Mutation_p.K7R|OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557054.1_Missense_Mutation_p.K7R	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	7	Necessary for interaction with YBX1, binding to RNA, NPM1-dependent association with rRNA, endoribonuclease activity on abasic RNA and localization in the nucleoli.				aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)			breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	CGTGGGAAAAAGGGAGCGGTG	0.562								Other BER factors																													p.K7R													.	APEX1	23		0			c.A20G												112.0	102.0	105.0					14																	20923824		2203	4300	6503	SO:0001583	missense	328	exon2			GGAAAAAGGGAGC	X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"""APEX nuclease (multifunctional DNA repair enzyme)"""	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.20A>G	14.37:g.20923824A>G	ENSP00000216714:p.Lys7Arg		97	0.0103092784	1		106	0.04	4	NM_080648	274	0.00	1	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	37	CCDS9550.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.266405	0.80358	.	.	ENSG00000100823	ENST00000555414;ENST00000216714;ENST00000553681;ENST00000557344;ENST00000398030;ENST00000557181;ENST00000555839;ENST00000556054	T;T;T;T;T;T;T;T	0.69435	-0.4;-0.4;0.31;-0.16;-0.4;0.38;-0.15;0.28	5.89	5.89	0.94794	.	0.048492	0.85682	N	0.000000	T	0.56920	0.2018	L	0.38175	1.15	0.80722	D	1	P	0.47762	0.9	B	0.40677	0.337	T	0.60094	-0.7330	10	0.44086	T	0.13	.	12.6954	0.57001	1.0:0.0:0.0:0.0	.	7	P27695	APEX1_HUMAN	R	7	ENSP00000451979:K7R;ENSP00000216714:K7R;ENSP00000451327:K7R;ENSP00000452137:K7R;ENSP00000381111:K7R;ENSP00000452304:K7R;ENSP00000452460:K7R;ENSP00000451170:K7R	ENSP00000216714:K7R	K	+	2	0	APEX1	19993664	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.007000	0.49536	2.251000	0.74343	0.533000	0.62120	AAG			0.562	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000073641.3		NM_001641	
C14orf23	387978	hgsc.bcm.edu;bcgsc.ca	37	14	29242602	29242602	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr14:29242602A>G	ENST00000399387.4	+	2	189	c.85A>G	c.(85-87)Agg>Ggg	p.R29G	C14orf23_ENST00000548213.1_Missense_Mutation_p.R29G|C14orf23_ENST00000552957.1_Missense_Mutation_p.R29G					chromosome 14 open reading frame 23											central_nervous_system(1)	1						GCCGAGGAAAAGGATATCAGG	0.483																																					.													.	.			0			.																																									SO:0001583	missense	387978	.			AGGAAAAGGATAT			14q11.2	2013-01-15			ENSG00000186960	ENSG00000186960			19828	other	unknown							Standard	NR_026731		Approved		uc001wqf.3	Q86U37	OTTHUMG00000029410	ENST00000399387.4:c.85A>G	14.37:g.29242602A>G	ENSP00000382318:p.Arg29Gly		70	0	0		66	0.06	4	.	0		0		RNA	SNP	ENST00000399387.4	37		.	.	.	.	.	.	.	.	.	.	A	10.54	1.377943	0.24944	.	.	ENSG00000186960	ENST00000399387;ENST00000552957;ENST00000548213	.	.	.	4.94	2.02	0.26589	.	0.522536	0.14133	U	0.339239	T	0.29126	0.0724	.	.	.	0.09310	N	1	B	0.21452	0.056	B	0.20384	0.029	T	0.20338	-1.0278	8	0.48119	T	0.1	.	6.2299	0.20728	0.7377:0.0:0.2623:0.0	.	29	Q86U37	CN023_HUMAN	G	29	.	ENSP00000382318:R29G	R	+	1	2	C14orf23	28312353	0.006000	0.16342	0.002000	0.10522	0.028000	0.11728	0.500000	0.22562	0.183000	0.20059	0.455000	0.32223	AGG			0.483	C14orf23-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		OTTHUMT00000134019.2		NR_026731	
ATP5S	27109	broad.mit.edu	37	14	50798952	50798952	+	Silent	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr14:50798952C>T	ENST00000358473.1	+	5	699	c.699C>T	c.(697-699)ggC>ggT	p.G233G	CDKL1_ENST00000216378.2_3'UTR|CDKL1_ENST00000395834.1_Intron			Q99766	ATP5S_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit s (factor B)	0					ATP biosynthetic process (GO:0006754)|hydrogen ion transmembrane transport (GO:1902600)|proton transport (GO:0015992)	mitochondrial inner membrane (GO:0005743)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(2)|liver(1)|lung(2)|ovary(1)|skin(2)|stomach(1)	12	all_epithelial(31;0.000636)|Breast(41;0.0102)			OV - Ovarian serous cystadenocarcinoma(311;0.0685)		TACCAGGTGGCAGGTAGGAGA	0.458																																					.													.	CDKL1	50		0			.												173.0	168.0	170.0					14																	50798952		2203	4300	6503	SO:0001819	synonymous_variant	27109	.			AGGTGGCAGGTAG	U79253	CCDS32075.1, CCDS32076.1, CCDS45102.1	14q21.3	2011-04-13	2010-06-11			ENSG00000125375			18799	protein-coding gene	gene with protein product			"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B)"""			11744738, 8619474	Standard	NM_015684		Approved	HSU79253, ATPW	uc001wxw.2	Q99766		ENST00000358473.1:c.699C>T	14.37:g.50798952C>T			59	0	0		76	0.05	4	.	6	0.00	0	A8K1U3|D9N156|Q8WWX3|Q96F77	Silent	SNP	ENST00000358473.1	37																																																																																						0.458	ATP5S-011	NOVEL	basic	protein_coding	protein_coding		OTTHUMT00000410765.1		NM_015684	
RP11-666E17.1	0	broad.mit.edu	37	14	82384401	82384402	+	lincRNA	INS	-	-	A	rs199686389		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr14:82384401_82384402insA	ENST00000554814.1	+	0	315																											TTTGGAGCCAGAAAaaaaaatg	0.361																																					.													.	.			0			.																																											0	.			GAGCCAGAAAAAA																													14.37:g.82384410_82384410dupA			4	0	0		6	0.33	2	.	27	0.00	0		RNA	INS	ENST00000554814.1	37																																																																																						0.361	RP11-666E17.1-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000413276.1			
AHNAK2	113146	hgsc.bcm.edu;broad.mit.edu	37	14	105409580	105409580	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr14:105409580delG	ENST00000333244.5	-	7	12327	c.12208delC	c.(12208-12210)cagfs	p.Q4070fs	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	4070						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACATCTATCTGGGGGCCCTTG	0.612																																					p.Q4070fs													.	.			0			c.12209delA												144.0	150.0	148.0					14																	105409580		1828	4073	5901	SO:0001589	frameshift_variant	113146	exon7			CTATCTGGGGGCC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.12208delC	14.37:g.105409580delG	ENSP00000353114:p.Gln4070fs		126	0	0		170	0.06	11	NM_138420	2	0.00	0	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Frame_Shift_Del	DEL	ENST00000333244.5	37	CCDS45177.1																																																																																					0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000410300.1		NM_138420	
GPR176	11245	mdanderson.org	37	15	40093937	40093937	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr15:40093937G>T	ENST00000561100.1	-	3	1809	c.944C>A	c.(943-945)gCa>gAa	p.A315E	GPR176_ENST00000560729.1_5'Flank|GPR176_ENST00000299092.3_Missense_Mutation_p.A314E|RP11-37C7.1_ENST00000558616.1_RNA|GPR176_ENST00000543580.1_Missense_Mutation_p.A270E	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	315					G-protein coupled receptor signaling pathway (GO:0007186)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)	23		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		AACAGGGTTTGCCAGCAGGGA	0.532											OREG0023053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A315E													.	.			0			c.C944A												77.0	74.0	75.0					15																	40093937		2203	4300	6503	SO:0001583	missense	11245	exon3			GGGTTTGCCAGCA	BC067106	CCDS10051.1, CCDS61588.1, CCDS61589.1	15q14-q15.1	2012-08-21			ENSG00000166073	ENSG00000166073		"""GPCR / Class A : Orphans"""	32370	protein-coding gene	gene with protein product		612183				7893747	Standard	NM_007223		Approved	Gm1012	uc010uck.2	Q14439	OTTHUMG00000129873	ENST00000561100.1:c.944C>A	15.37:g.40093937G>T	ENSP00000453076:p.Ala315Glu		43	0	0	890	45	0.07	3	NM_007223	15	0.00	0	Q6NXF6	Missense_Mutation	SNP	ENST00000561100.1	37	CCDS10051.1	.	.	.	.	.	.	.	.	.	.	G	24.5	4.542186	0.85917	.	.	ENSG00000166073	ENST00000299092;ENST00000543580	T	0.38560	1.13	6.08	6.08	0.98989	GPCR, rhodopsin-like superfamily (1);	0.049206	0.85682	D	0.000000	T	0.48804	0.1520	L	0.29908	0.895	0.47547	D	0.999454	P	0.44521	0.837	P	0.52267	0.694	T	0.27706	-1.0066	10	0.44086	T	0.13	-25.0205	20.6634	0.99662	0.0:0.0:1.0:0.0	.	315	Q14439	GP176_HUMAN	E	315;270	ENSP00000439361:A270E	ENSP00000299092:A315E	A	-	2	0	GPR176	37881229	1.000000	0.71417	0.994000	0.49952	0.976000	0.68499	7.827000	0.86722	2.894000	0.99253	0.655000	0.94253	GCA			0.532	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252117.2		NM_007223	
ZNF213	7760	mdanderson.org	37	16	3191187	3191187	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr16:3191187G>A	ENST00000396878.3	+	6	1694	c.1219G>A	c.(1219-1221)Ggc>Agc	p.G407S	ZNF213_ENST00000574902.1_Missense_Mutation_p.G407S|ZNF213_ENST00000576416.1_Missense_Mutation_p.G407S|ZNF213_ENST00000416391.2_Missense_Mutation_p.G249S	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	407				G -> A (in Ref. 1; AAB70531). {ECO:0000305}.	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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						CAGCGACTGCGGCAAGAGCTT	0.652																																					p.G407S													.	.			0			c.G1219A												42.0	42.0	42.0					16																	3191187		2197	4300	6497	SO:0001583	missense	7760	exon6			GACTGCGGCAAGA	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.1219G>A	16.37:g.3191187G>A	ENSP00000380087:p.Gly407Ser		28	0	0		47	0.06	3	NM_001134655	21	0.00	0	A8K1B9|B4DMG6|Q96IS1	Missense_Mutation	SNP	ENST00000396878.3	37	CCDS10495.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899777	0.33535	.	.	ENSG00000085644	ENST00000396878;ENST00000416391	T;T	0.21734	1.99;1.99	5.09	4.11	0.48088	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.154071	0.30492	N	0.009513	T	0.24928	0.0605	M	0.81802	2.56	0.37150	D	0.902114	P	0.37441	0.595	B	0.28784	0.094	T	0.35475	-0.9787	10	0.87932	D	0	.	12.5405	0.56167	0.0:0.0:0.8322:0.1678	.	407	O14771	ZN213_HUMAN	S	407;249	ENSP00000380087:G407S;ENSP00000403892:G249S	ENSP00000380087:G407S	G	+	1	0	ZNF213	3131188	0.998000	0.40836	0.997000	0.53966	0.995000	0.86356	2.737000	0.47393	1.096000	0.41439	0.462000	0.41574	GGC			0.652	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000437334.1		NM_004220	
CD2BP2	10421	mdanderson.org	37	16	30365009	30365009	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr16:30365009T>C	ENST00000305596.3	-	5	663	c.488A>G	c.(487-489)gAg>gGg	p.E163G	CD2BP2_ENST00000569466.1_Missense_Mutation_p.E163G|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	163					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of phosphatase activity (GO:0010923)|RNA splicing (GO:0008380)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	ribonucleoprotein complex binding (GO:0043021)			breast(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	15						CAATAGGAGCTCCAAAAGTCC	0.647																																					p.E163G													.	.			0			c.A488G												15.0	15.0	15.0					16																	30365009		2180	4269	6449	SO:0001583	missense	10421	exon5			AGGAGCTCCAAAA	AF104222	CCDS10675.1	16p11.2	2012-04-17	2006-03-28		ENSG00000169217	ENSG00000169217		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 59"""	604470	"""CD2 antigen (cytoplasmic tail)-binding protein 2"""			9843987	Standard	NM_006110		Approved	LIN1, Snu40, PPP1R59	uc002dxs.3	O95400	OTTHUMG00000132397	ENST00000305596.3:c.488A>G	16.37:g.30365009T>C	ENSP00000304903:p.Glu163Gly		24	0	0		36	0.08	3	NM_006110	148	0.00	0	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	37	CCDS10675.1	.	.	.	.	.	.	.	.	.	.	t	17.39	3.377272	0.61735	.	.	ENSG00000169217	ENST00000305596	T	0.34275	1.37	5.06	5.06	0.68205	.	0.048616	0.85682	D	0.000000	T	0.35451	0.0932	L	0.47716	1.5	0.80722	D	1	P	0.49090	0.919	P	0.45343	0.477	T	0.07385	-1.0775	10	0.21014	T	0.42	0.4157	13.801	0.63199	0.0:0.0:0.0:1.0	.	163	O95400	CD2B2_HUMAN	G	163	ENSP00000304903:E163G	ENSP00000304903:E163G	E	-	2	0	CD2BP2	30272510	1.000000	0.71417	0.972000	0.41901	0.520000	0.34377	4.812000	0.62613	1.893000	0.54813	0.533000	0.62120	GAG			0.647	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000255528.1		NM_006110	
PLLP	51090	mdanderson.org	37	16	57290893	57290893	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr16:57290893T>C	ENST00000219207.5	-	4	627	c.481A>G	c.(481-483)Agc>Ggc	p.S161G	PLLP_ENST00000569059.1_Missense_Mutation_p.S103G	NM_015993.2	NP_057077.1	Q9Y342	PLLP_HUMAN	plasmolipin	161	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				ion transport (GO:0006811)|myelination (GO:0042552)|response to wounding (GO:0009611)	compact myelin (GO:0043218)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)				endometrium(1)|prostate(1)	2						GCCTGGTAGCTGAAGAAGGCA	0.577																																					p.S161G													.	.			0			c.A481G												104.0	88.0	94.0					16																	57290893		2198	4300	6498	SO:0001583	missense	51090	exon4			GGTAGCTGAAGAA	AF137386	CCDS10777.1	16q13	2010-06-24	2010-06-24	2005-03-21	ENSG00000102934	ENSG00000102934			18553	protein-coding gene	gene with protein product	"""plasma membrane proteolipid"""	600340	"""transmembrane 4 superfamily member 11 (plasmolipin)"", ""plasma membrane proteolipid (plasmolipin)"""	TM4SF11		11707781	Standard	NM_015993		Approved	PMLP	uc002elg.2	Q9Y342	OTTHUMG00000133465	ENST00000219207.5:c.481A>G	16.37:g.57290893T>C	ENSP00000219207:p.Ser161Gly		23	0	0		33	0.09	3	NM_015993	64	0.00	0	B2R9T6	Missense_Mutation	SNP	ENST00000219207.5	37	CCDS10777.1	.	.	.	.	.	.	.	.	.	.	T	26.9	4.779859	0.90195	.	.	ENSG00000102934	ENST00000219207	T	0.29397	1.57	5.65	5.65	0.86999	Marvel (1);	0.181999	0.64402	D	0.000014	T	0.39911	0.1096	M	0.67953	2.075	0.58432	D	0.999997	P	0.47762	0.9	P	0.45946	0.498	T	0.20571	-1.0271	10	0.36615	T	0.2	-5.7368	15.8391	0.78831	0.0:0.0:0.0:1.0	.	161	Q9Y342	PLLP_HUMAN	G	161	ENSP00000219207:S161G	ENSP00000219207:S161G	S	-	1	0	PLLP	55848394	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.071000	0.57556	2.279000	0.76181	0.533000	0.62120	AGC			0.577	PLLP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257341.2			
MINK1	50488	broad.mit.edu	37	17	4790982	4790982	+	Missense_Mutation	SNP	A	A	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:4790982A>T	ENST00000355280.6	+	12	1323	c.1127A>T	c.(1126-1128)cAg>cTg	p.Q376L	MINK1_ENST00000347992.7_Missense_Mutation_p.Q376L|MINK1_ENST00000453408.3_Missense_Mutation_p.Q376L	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						cagcagctgcagcagcagcag	0.607																																					p.Q376L													.	MINK1	110		0			c.A1127T												7.0	9.0	8.0					17																	4790982		2021	4168	6189	SO:0001583	missense	50488	exon12			AGCTGCAGCAGCA	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1127A>T	17.37:g.4790982A>T	ENSP00000347427:p.Gln376Leu		70	0.0142857143	1		94	0.04	4	NM_170663	35	0.00	0		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	A	15.33	2.801384	0.50315	.	.	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.21734	1.99;1.99;1.99	4.63	4.63	0.57726	.	0.081959	0.52532	D	0.000073	T	0.08802	0.0218	N	0.02916	-0.46	0.33781	D	0.624279	P;P;P;P	0.50528	0.936;0.936;0.895;0.936	P;P;B;P	0.44477	0.451;0.451;0.264;0.451	T	0.12400	-1.0549	10	0.21540	T	0.41	.	6.8042	0.23768	0.8971:0.0:0.1029:0.0	.	376;376;376;376	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	L	376	ENSP00000347427:Q376L;ENSP00000406487:Q376L;ENSP00000269296:Q376L	ENSP00000269296:Q376L	Q	+	2	0	MINK1	4731765	0.953000	0.32496	1.000000	0.80357	0.835000	0.47333	0.830000	0.27462	1.947000	0.56498	0.374000	0.22700	CAG			0.607	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000439801.1		NM_015716	
KDM6B	23135	broad.mit.edu	37	17	7751771	7751771	+	Missense_Mutation	SNP	A	A	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:7751771A>C	ENST00000448097.2	+	11	2496	c.2165A>C	c.(2164-2166)cAa>cCa	p.Q722P	KDM6B_ENST00000254846.5_Missense_Mutation_p.Q722P			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	722	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						GTGGCCCCCCAACCCCCGCTG	0.592																																					p.Q722P													.	KDM6B	95		0			c.A2165C												79.0	93.0	88.0					17																	7751771		2203	4300	6503	SO:0001583	missense	23135	exon11			CCCCCCAACCCCC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.2165A>C	17.37:g.7751771A>C	ENSP00000412513:p.Gln722Pro		30	0.1	3		38	0.29	11	NM_001080424	16	0.00	0	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		.	.	.	.	.	.	.	.	.	.	C	0.014	-1.573338	0.00887	.	.	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.04502	3.61;3.61	4.52	2.44	0.29823	.	0.353337	0.23442	N	0.048129	T	0.02083	0.0065	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47649	-0.9101	10	0.02654	T	1	-4.2915	12.868	0.57949	0.4243:0.5757:0.0:0.0	.	722;722	O15054;O15054-1	KDM6B_HUMAN;.	P	722	ENSP00000254846:Q722P;ENSP00000412513:Q722P	ENSP00000254846:Q722P	Q	+	2	0	KDM6B	7692496	0.000000	0.05858	0.186000	0.23195	0.203000	0.24098	0.224000	0.17738	0.239000	0.21243	-0.323000	0.08544	CAA			0.592	KDM6B-002	KNOWN	basic	protein_coding	protein_coding		OTTHUMT00000440248.1		XM_043272	
RAB34	83871	mdanderson.org	37	17	27044263	27044263	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:27044263G>A	ENST00000395245.3	-	1	648	c.22C>T	c.(22-24)Cgg>Tgg	p.R8W	RAB34_ENST00000395243.3_Missense_Mutation_p.R8W|RPL23A_ENST00000422514.2_5'Flank|RPL23A_ENST00000394938.4_5'Flank|RAB34_ENST00000450529.1_Missense_Mutation_p.R8W|RAB34_ENST00000415040.2_Missense_Mutation_p.R8W|RAB34_ENST00000447716.1_Missense_Mutation_p.R65W|RAB34_ENST00000453384.3_Missense_Mutation_p.R65W|RAB34_ENST00000395242.2_Missense_Mutation_p.R8W|RPL23A_ENST00000496182.1_5'Flank|RAB34_ENST00000301043.6_Missense_Mutation_p.R8W|RAB34_ENST00000436730.3_Missense_Mutation_p.R8W	NM_001256281.1|NM_031934.5	NP_001243210.1|NP_114140.4	Q9BZG1	RAB34_HUMAN	RAB34, member RAS oncogene family	8					antigen processing and presentation (GO:0019882)|Golgi to plasma membrane protein transport (GO:0043001)|lysosome localization (GO:0032418)|phagosome maturation (GO:0090382)|phagosome-lysosome fusion (GO:0090385)|protein localization to plasma membrane (GO:0072659)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|Golgi stack (GO:0005795)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|phagocytic vesicle (GO:0045335)|vesicle (GO:0031982)	GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(8)|skin(2)	14	Lung NSC(42;0.00431)					CGATCCCTCCGCACGGGTGCC	0.731																																					p.A155V	Pancreas(175;216 2049 29940 32498 41589)												.	.			0			c.C464T												12.0	15.0	14.0					17																	27044263		2194	4295	6489	SO:0001583	missense	0	exon1			CCCTCCGCACGGG	AF322067	CCDS11240.1, CCDS45636.1, CCDS54101.1, CCDS58536.1	17q11.2	2008-07-18			ENSG00000109113	ENSG00000109113		"""RAB, member RAS oncogene"""	16519	protein-coding gene	gene with protein product		610917				12446704	Standard	NM_031934		Approved	RAB39, RAH	uc010was.1	P0DI83	OTTHUMG00000132680	ENST00000395245.3:c.22C>T	17.37:g.27044263G>A	ENSP00000378666:p.Arg8Trp		24	0	0		35	0.09	3	NM_001256281	264	0.00	0	B4E3A0|E9PEJ9|Q5BJE6|Q8NCJ8|Q96AR4	Missense_Mutation	SNP	ENST00000395245.3	37	CCDS11240.1	.	.	.	.	.	.	.	.	.	.	G	26.6	4.752259	0.89753	.	.	ENSG00000109113	ENST00000453384;ENST00000447716;ENST00000301043;ENST00000395243;ENST00000415040;ENST00000450529;ENST00000395242;ENST00000395245;ENST00000436730;ENST00000412625;ENST00000353676	T;T;T;T;T;T;T;T;T	0.71461	-0.49;-0.25;-0.13;-0.57;0.11;-0.13;-0.13;-0.28;-0.28	5.16	5.16	0.70880	.	0.358481	0.29225	N	0.012769	T	0.80253	0.4589	L	0.50333	1.59	0.44862	D	0.997872	D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;1.0;0.999;0.999;1.0	D;P;D;D;D;D;D	0.72625	0.952;0.908;0.978;0.936;0.952;0.952;0.936	T	0.83255	-0.0051	9	0.72032	D	0.01	-3.075	15.7235	0.77732	0.0:0.0:1.0:0.0	.	65;8;8;31;31;8;8	E7ES60;E9PEJ9;Q9BZG1-2;C9JI96;B4DNC0;A8MYQ9;Q9BZG1	.;.;.;.;.;.;RAB34_HUMAN	W	65;65;8;8;8;31;8;8;31;8;8	ENSP00000413156:R65W;ENSP00000410403:R65W;ENSP00000301043:R8W;ENSP00000378664:R8W;ENSP00000410279:R8W;ENSP00000378663:R8W;ENSP00000378666:R8W;ENSP00000398706:R8W;ENSP00000226259:R8W	ENSP00000301043:R8W	R	-	1	2	RAB34	24068390	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.522000	0.35921	2.551000	0.86045	0.561000	0.74099	CGG			0.731	RAB34-018	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000345906.1		NM_031934	
FAM222B	55731	mdanderson.org	37	17	27085505	27085505	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:27085505G>T	ENST00000341217.5	-	3	1687	c.1472C>A	c.(1471-1473)cCc>cAc	p.P491H	FAM222B_ENST00000582266.1_3'UTR|FAM222B_ENST00000452648.3_Missense_Mutation_p.P491H|FAM222B_ENST00000581407.1_Missense_Mutation_p.P491H	NM_018182.2	NP_060652.2	Q8WU58	F222B_HUMAN	family with sequence similarity 222, member B	491																	GTGGGCCCCGGGAGCTGCCGC	0.642																																					p.P491H													.	.			0			c.C1472A												38.0	41.0	40.0					17																	27085505		1968	4137	6105	SO:0001583	missense	55731	exon4			GCCCCGGGAGCTG	AK001562	CCDS45637.1, CCDS74022.1	17q11.2	2012-04-27	2012-04-27	2012-04-27	ENSG00000173065	ENSG00000173065			25563	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 63"""	C17orf63			Standard	NM_001288631		Approved	FLJ10700	uc010way.1	Q8WU58		ENST00000341217.5:c.1472C>A	17.37:g.27085505G>T	ENSP00000343115:p.Pro491His		23	0	0		36	0.08	3	NM_018182	26	0.00	0	Q9H6F3|Q9NVJ4|Q9NXN6	Missense_Mutation	SNP	ENST00000341217.5	37	CCDS45637.1	.	.	.	.	.	.	.	.	.	.	G	14.43	2.533545	0.45073	.	.	ENSG00000173065	ENST00000341217;ENST00000452648	T;T	0.30981	1.51;1.51	4.97	4.97	0.65823	.	0.718532	0.13046	N	0.418086	T	0.32763	0.0840	N	0.22421	0.69	0.43029	D	0.994591	D	0.61697	0.99	P	0.53450	0.726	T	0.01697	-1.1293	10	0.33141	T	0.24	1.7266	13.1614	0.59547	0.0:0.1602:0.8398:0.0	.	491	Q8WU58	CQ063_HUMAN	H	491	ENSP00000343115:P491H;ENSP00000413645:P491H	ENSP00000343115:P491H	P	-	2	0	C17orf63	24109632	1.000000	0.71417	0.997000	0.53966	0.621000	0.37620	6.932000	0.75869	2.567000	0.86603	0.561000	0.74099	CCC			0.642	FAM222B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000446703.1		NM_018182	
TBC1D3	729873	broad.mit.edu	37	17	36357182	36357182	+	5'UTR	SNP	T	T	C	rs532795791		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:36357182T>C	ENST00000537432.1	-	0	132				RP11-1407O15.2_ENST00000544906.1_Silent_p.Q202Q|RP11-1407O15.2_ENST00000312412.4_Silent_p.Q357Q			Q8IZP1	TBC3A_HUMAN	TBC1 domain family, member 3							plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)			breast(1)|large_intestine(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	5	Breast(7;2.97e-12)	Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		TTCCAAACCATTGATGGGCAA	0.358													T|||	1	0.000199681	0.0	0.0	5008	,	,		55478	0.0		0.0	False		,,,				2504	0.001				.													.	.			0			.																																									SO:0001623	5_prime_UTR_variant	0	.			AAACCATTGATGG		CCDS45658.1	17q12	2014-09-16			ENSG00000274611	ENSG00000274419			19031	protein-coding gene	gene with protein product	"""prostate cancer gene 17"""	607741				12604796, 12359748, 16863688	Standard	NM_001123391		Approved	TBC1D3A, DKFZp434P2235, PRC17	uc002hoo.2	Q8IZP1	OTTHUMG00000188487	ENST00000537432.1:c.-357A>G	17.37:g.36357182T>C			632	0	0		783	0.01	9	.	34	0.00	0	A6NGX2|A8K007|Q6DCB4|Q9H0B9|Q9UDD4	Silent	SNP	ENST00000537432.1	37	CCDS45658.1	.	.	.	.	.	.	.	.	.	.	T	6.540	0.467970	0.12402	.	.	ENSG00000174093	ENST00000523089	.	.	.	2.68	1.56	0.23342	.	.	.	.	.	T	0.52008	0.1708	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38693	-0.9649	4	.	.	.	.	5.4042	0.16312	0.0:0.4949:0.0:0.5051	.	.	.	.	V	313	.	.	M	-	1	0	RP11-1407O15.2	33610977	1.000000	0.71417	1.000000	0.80357	0.833000	0.47200	4.787000	0.62432	0.263000	0.21812	0.163000	0.16589	ATG			0.358	TBC1D3-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				NM_001123391	
THRA	7067	broad.mit.edu	37	17	38240101	38240101	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:38240101G>A	ENST00000264637.4	+	5	816	c.236G>A	c.(235-237)cGc>cAc	p.R79H	THRA_ENST00000584985.1_Missense_Mutation_p.R79H|THRA_ENST00000450525.2_Missense_Mutation_p.R79H|THRA_ENST00000546243.1_Missense_Mutation_p.R79H|THRA_ENST00000394121.4_Missense_Mutation_p.R79H	NM_003250.5	NP_003241.2	P10827	THA_HUMAN	thyroid hormone receptor, alpha	79					cartilage condensation (GO:0001502)|cytoplasmic sequestering of transcription factor (GO:0042994)|erythrocyte differentiation (GO:0030218)|female courtship behavior (GO:0008050)|gene expression (GO:0010467)|hormone-mediated signaling pathway (GO:0009755)|learning or memory (GO:0007611)|negative regulation of DNA-templated transcription, initiation (GO:2000143)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of female receptivity (GO:0045925)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of heart contraction (GO:0008016)|regulation of lipid catabolic process (GO:0050994)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cold (GO:0009409)|thyroid gland development (GO:0030878)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Type I pneumocyte differentiation (GO:0060509)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|steroid receptor RNA activator RNA binding (GO:0002153)|TBP-class protein binding (GO:0017025)|thyroid hormone binding (GO:0070324)|thyroid hormone receptor activity (GO:0004887)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.R79H(2)		endometrium(1)|kidney(3)|large_intestine(2)|lung(4)|prostate(1)	11	Colorectal(19;0.000442)	Myeloproliferative disorder(1115;0.0255)			Dextrothyroxine(DB00509)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	TTCTTTCGCCGCACAATCCAG	0.547																																					p.R79H													THRA_ENST00000450525,NS,carcinoma,0,2	THRA	88	2	2	Substitution - Missense(2)	kidney(2)	c.G236A												145.0	129.0	134.0					17																	38240101		2203	4300	6503	SO:0001583	missense	7067	exon5			TTCGCCGCACAAT	J03239	CCDS11360.1, CCDS42316.1, CCDS58546.1	17q21.1	2013-01-16	2011-05-19		ENSG00000126351	ENSG00000126351		"""Nuclear hormone receptors"""	11796	protein-coding gene	gene with protein product		190120	"""thyroid hormone receptor, alpha (avian erythroblastic leukemia viral (v-erb-a) oncogene homolog)"", ""thyroid hormone receptor, alpha (erythroblastic leukemia viral (v-erb-a) oncogene homolog, avian)"""	THRA1, THRA2, ERBA1		6323162, 6589608	Standard	NM_003250		Approved	EAR-7.1/EAR-7.2, THRA3, AR7, ERBA, NR1A1	uc002htw.3	P10827	OTTHUMG00000133332	ENST00000264637.4:c.236G>A	17.37:g.38240101G>A	ENSP00000264637:p.Arg79His		144	0.0069444444	1		169	0.03	5	NM_001190918	92	0.00	0	A8K3B5|P21205|Q8N6A1|Q96H73	Missense_Mutation	SNP	ENST00000264637.4	37	CCDS11360.1	.	.	.	.	.	.	.	.	.	.	G	32	5.125665	0.94429	.	.	ENSG00000126351	ENST00000394121;ENST00000264637;ENST00000450525;ENST00000546243	D;D;D;D	0.98987	-5.3;-5.3;-5.3;-5.3	5.31	4.33	0.51752	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (5);	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	H	0.99475	4.585	0.80722	D	1	D;D;B	0.89917	1.0;1.0;0.007	D;D;B	0.97110	1.0;1.0;0.007	D	0.97246	0.9894	10	0.87932	D	0	.	14.0146	0.64517	0.0753:0.0:0.9247:0.0	.	79;79;79	P10827-3;P10827;Q6FH41	.;THA_HUMAN;.	H	79	ENSP00000377679:R79H;ENSP00000264637:R79H;ENSP00000395641:R79H;ENSP00000443972:R79H	ENSP00000264637:R79H	R	+	2	0	THRA	35493627	0.998000	0.40836	1.000000	0.80357	0.990000	0.78478	7.932000	0.87634	2.477000	0.83638	0.430000	0.28490	CGC			0.547	THRA-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000257160.2			
NPLOC4	55666	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca;mdanderson.org	37	17	79589248	79589248	+	Missense_Mutation	SNP	G	G	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr17:79589248G>C	ENST00000331134.6	-	3	368	c.153C>G	c.(151-153)aaC>aaG	p.N51K	NPLOC4_ENST00000374747.5_Missense_Mutation_p.N51K|NPLOC4_ENST00000539314.1_5'UTR	NM_017921.2	NP_060391.2	Q8TAT6	NPL4_HUMAN	nuclear protein localization 4 homolog (S. cerevisiae)	51					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|Golgi organization (GO:0007030)|membrane fusion (GO:0061025)	endoplasmic reticulum (GO:0005783)|nuclear outer membrane-endoplasmic reticulum membrane network (GO:0042175)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)	11	all_neural(118;0.0878)|Melanoma(429;0.242)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0739)			CTCCGGTCTTGTTTCTATTGA	0.418																																					p.N51K													.	.			0			c.C153G												111.0	106.0	107.0					17																	79589248		1861	4101	5962	SO:0001583	missense	55666	exon3			GGTCTTGTTTCTA	AB040932	CCDS45812.1	17q25.3	2012-09-20			ENSG00000182446	ENSG00000182446			18261	protein-coding gene	gene with protein product		606590				11574150, 10811609	Standard	NM_017921		Approved	NPL4, FLJ20657, KIAA1499	uc002kas.3	Q8TAT6	OTTHUMG00000177990	ENST00000331134.6:c.153C>G	17.37:g.79589248G>C	ENSP00000331487:p.Asn51Lys		68	0	0		75	0.08	6	NM_017921	17	0.24	4	Q8N3J1|Q9H8V2|Q9H964|Q9NWR5|Q9P229	Missense_Mutation	SNP	ENST00000331134.6	37	CCDS45812.1	.	.	.	.	.	.	.	.	.	.	G	16.67	3.188739	0.57909	.	.	ENSG00000182446	ENST00000331134;ENST00000374747	.	.	.	5.21	4.24	0.50183	Nuclear pore localisation protein Npl4, ubiquitin-like domain (1);	0.000000	0.85682	D	0.000000	T	0.65375	0.2685	M	0.65498	2.005	0.80722	D	1	D;D	0.58970	0.984;0.97	P;P	0.59595	0.86;0.801	T	0.62590	-0.6822	9	0.15499	T	0.54	-38.7437	9.9823	0.41821	0.1578:0.0:0.8422:0.0	.	51;51	Q8TAT6-2;Q8TAT6	.;NPL4_HUMAN	K	51;50	.	ENSP00000331487:N51K	N	-	3	2	NPLOC4	77199653	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.645000	0.61404	1.315000	0.45114	0.591000	0.81541	AAC			0.418	NPLOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000440140.1			
MUC16	94025	mdanderson.org	37	19	9033260	9033260	+	Silent	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:9033260G>T	ENST00000397910.4	-	10	36569	c.36366C>A	c.(36364-36366)ctC>ctA	p.L12122L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12124	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGCCTGAATAGAGGTATTCCA	0.527																																					p.L12122L													.	.			0			c.C36366A												66.0	65.0	66.0					19																	9033260		1980	4154	6134	SO:0001819	synonymous_variant	94025	exon10			TGAATAGAGGTAT	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.36366C>A	19.37:g.9033260G>T			57	0	0		68	0.06	4	NM_024690	0		0	Q6ZQW5|Q96RK2	Silent	SNP	ENST00000397910.4	37	CCDS54212.1																																																																																					0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000402806.1		NM_024690	
PPAN	56342	mdanderson.org	37	19	10217274	10217274	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:10217274C>T	ENST00000253107.7	+	2	222	c.116C>T	c.(115-117)aCg>aTg	p.T39M	PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.T39M|PPAN_ENST00000556468.1_Missense_Mutation_p.T39M|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.T39M|PPAN_ENST00000393793.1_5'UTR|SNORD105_ENST00000386910.1_RNA	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	39	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.				RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			CGAGGCTGCACGGGTCGCAAC	0.706																																					p.T39M													.	.			0			c.C116T												7.0	10.0	9.0					19																	10217274		2132	4189	6321	SO:0001583	missense	56342	exon2			GCTGCACGGGTCG	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"""peter pan (Drosophila) homolog"""			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.116C>T	19.37:g.10217274C>T	ENSP00000253107:p.Thr39Met		26	0	0		32	0.09	3	NM_020230	32	0.00	0	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.460908	0.26248	.	.	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696	T;T;T;T	0.22945	1.93;1.93;1.93;1.93	5.45	0.906	0.19314	Brix domain (3);	.	.	.	.	T	0.11836	0.0288	N	0.12182	0.205	0.09310	N	1	P;P;D	0.53151	0.927;0.927;0.958	B;B;B	0.40199	0.286;0.322;0.322	T	0.13791	-1.0496	9	0.51188	T	0.08	-18.6332	4.6138	0.12415	0.0:0.4426:0.3171:0.2403	.	39;39;39	C9J3F9;C9JW41;Q9NQ55	.;.;SSF1_HUMAN	M	39	ENSP00000411918:T39M;ENSP00000377385:T39M;ENSP00000253107:T39M;ENSP00000450710:T39M	ENSP00000253107:T39M	T	+	2	0	PPAN;PPAN-P2RY11	10078274	0.952000	0.32445	0.144000	0.22314	0.003000	0.03518	1.668000	0.37481	0.274000	0.22072	-0.304000	0.09214	ACG			0.706	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000316658.1		NM_020230	
ZNF708	7562	mdanderson.org	37	19	21476897	21476897	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:21476897G>T	ENST00000356929.3	-	4	1068	c.871C>A	c.(871-873)Cag>Aag	p.Q291K		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	227					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(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						TTTGAGGACTGTTTAAAAGCT	0.388																																					p.Q291K													.	.			0			c.C871A												51.0	55.0	54.0					19																	21476897		2201	4299	6500	SO:0001583	missense	7562	exon4			AGGACTGTTTAAA	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.871C>A	19.37:g.21476897G>T	ENSP00000349401:p.Gln291Lys		18	0	0		19	0.11	2	NM_021269	3	0.00	0	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	.	.	.	.	.	.	.	.	.	.	.	0.043	-1.277680	0.01410	.	.	ENSG00000182141	ENST00000356929	T	0.17691	2.26	1.05	-0.883	0.10600	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12944	0.0314	L	0.42581	1.335	0.09310	N	1	B	0.23650	0.089	B	0.20955	0.032	T	0.30416	-0.9979	9	0.34782	T	0.22	.	7.367	0.26779	0.0:0.452:0.548:0.0	.	291	P17019	ZN708_HUMAN	K	291	ENSP00000349401:Q291K	ENSP00000349401:Q291K	Q	-	1	0	ZNF708	21268737	0.000000	0.05858	0.317000	0.25265	0.263000	0.26337	-4.548000	0.00217	0.482000	0.27582	0.485000	0.47835	CAG			0.388	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000463953.1		NM_021269	
FFAR2	2867	mdanderson.org	37	19	35940862	35940862	+	Silent	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:35940862C>T	ENST00000599180.2	+	2	326	c.246C>T	c.(244-246)tgC>tgT	p.C82C	FFAR2_ENST00000246549.2_Silent_p.C82C|FFAR2_ENST00000601590.1_Intron			O15552	FFAR2_HUMAN	free fatty acid receptor 2	82					cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to fatty acid (GO:0071398)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipid storage (GO:0019915)|mucosal immune response (GO:0002385)|positive regulation of acute inflammatory response to non-antigenic stimulus (GO:0002879)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production involved in immune response (GO:0002720)|positive regulation of interleukin-8 secretion (GO:2000484)|regulation of acute inflammatory response (GO:0002673)|regulation of peptide hormone secretion (GO:0090276)	cell projection (GO:0042995)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)	p.C82*(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(6)|skin(1)|urinary_tract(1)	22	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGTCGTCTGCGCCCTCACGA	0.627																																					p.C82C	GBM(40;139 809 9833 23358 48736)												FFAR2,NS,carcinoma,0,1	FFAR2	0	1	1	Substitution - Nonsense(1)	lung(1)	c.C246T												57.0	46.0	49.0					19																	35940862		2203	4300	6503	SO:0001819	synonymous_variant	2867	exon1			CGTCTGCGCCCTC	AF024690	CCDS12461.1	19q13.1	2012-08-08	2006-02-15	2006-02-15		ENSG00000126262		"""GPCR / Class A : Fatty acid receptors"""	4501	protein-coding gene	gene with protein product		603823	"""G protein-coupled receptor 43"""	GPR43		9344866	Standard	NM_005306		Approved	FFA2R	uc010eea.3	O15552		ENST00000599180.2:c.246C>T	19.37:g.35940862C>T			47	0	0		42	0.07	3	NM_005306	0		0	B0M0J9|Q4VAZ3|Q4VAZ5|Q4VBL5	Silent	SNP	ENST00000599180.2	37	CCDS12461.1																																																																																					0.627	FFAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000466120.3		NM_005306	
CATSPERG	57828	hgsc.bcm.edu	37	19	38858705	38858705	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:38858705G>T	ENST00000409235.3	+	26	3063	c.2948G>T	c.(2947-2949)tGg>tTg	p.W983L	CATSPERG_ENST00000410018.1_Missense_Mutation_p.W943L|CATSPERG_ENST00000215069.4_3'UTR	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	983					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						AGCCTTATCTGGACCACGAGG	0.612																																					p.W983L													.	.			0			c.G2948T												264.0	210.0	228.0					19																	38858705		2203	4300	6503	SO:0001583	missense	57828	exon26			TTATCTGGACCAC	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.2948G>T	19.37:g.38858705G>T	ENSP00000386962:p.Trp983Leu		64	0	0		81	0.05	4	NM_021185	1	0.00	0	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	.	.	.	.	.	.	.	.	.	.	G	16.96	3.264947	0.59431	.	.	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410	T;T	0.32023	1.49;1.47	3.35	3.35	0.38373	.	0.000000	0.33895	U	0.004455	T	0.41282	0.1152	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.996	T	0.14254	-1.0479	10	0.42905	T	0.14	-8.3764	10.5005	0.44802	0.0:0.0:1.0:0.0	.	983;943	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	L	943;983;983	ENSP00000387057:W943L;ENSP00000386962:W983L	ENSP00000386962:W983L	W	+	2	0	CATSPERG	43550545	1.000000	0.71417	0.999000	0.59377	0.143000	0.21401	2.409000	0.44583	2.152000	0.67230	0.585000	0.79938	TGG			0.612	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000330204.1		NM_021185	
DYRK1B	9149	mdanderson.org	37	19	40321083	40321083	+	Missense_Mutation	SNP	G	G	T	rs367643250		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:40321083G>T	ENST00000593685.1	-	4	772	c.304C>A	c.(304-306)Cgc>Agc	p.R102S	DYRK1B_ENST00000430012.2_Missense_Mutation_p.R102S|DYRK1B_ENST00000601972.1_Missense_Mutation_p.R102S|DYRK1B_ENST00000597639.1_Missense_Mutation_p.R102S|DYRK1B_ENST00000323039.5_Missense_Mutation_p.R102S|DYRK1B_ENST00000348817.3_Missense_Mutation_p.R102S			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B	102			R -> C (in AOMS3; accumulation of intracellular lipid is significantly greater than with wild-type protein; cells expressing the variant are able to transform into mature adipocytes without requiring adipogenic medium; expression levels of CEBPA, PPARG forms 1 and 2 and PPARGC1A are higher and those of GLI1 and CDKN1B are lower in cells transfected with the mutant protein compared to wild- type; WNT1 signaling activity is lower in mutant cells compared to wild-type). {ECO:0000269|PubMed:24827035}.|R -> H (in dbSNP:rs55687541). {ECO:0000269|PubMed:17344846}.		adipose tissue development (GO:0060612)|myoblast fusion (GO:0007520)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(7)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	24	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)			TCGCCACTGCGCACGATGTAG	0.597																																					p.R102S													.	.			0			c.C304A												146.0	108.0	121.0					19																	40321083		2203	4300	6503	SO:0001583	missense	9149	exon4			CACTGCGCACGAT	Y17999	CCDS12543.1, CCDS12544.1, CCDS46075.1	19q13.2	2012-10-02			ENSG00000105204	ENSG00000105204	2.7.12.1		3092	protein-coding gene	gene with protein product	"""minibrain-related kinase"""	604556				9918863	Standard	XM_005259395		Approved	MIRK	uc002omj.3	Q9Y463		ENST00000593685.1:c.304C>A	19.37:g.40321083G>T	ENSP00000469863:p.Arg102Ser		45	0	0		49	0.06	3	NM_006483	31	0.00	0	O75258|O75788|O75789	Missense_Mutation	SNP	ENST00000593685.1	37	CCDS12543.1	.	.	.	.	.	.	.	.	.	.	G	9.783	1.175921	0.21704	.	.	ENSG00000105204	ENST00000323039;ENST00000348817;ENST00000430012	T;T;T	0.19669	2.13;2.13;2.13	4.44	4.44	0.53790	Protein kinase-like domain (1);	0.072440	0.53938	D	0.000049	T	0.18593	0.0446	L	0.41492	1.28	0.40438	D	0.980012	B;B;B;B	0.24675	0.059;0.049;0.059;0.109	B;B;B;B	0.30646	0.055;0.073;0.033;0.118	T	0.06041	-1.0849	10	0.34782	T	0.22	.	9.9308	0.41521	0.0:0.0:0.7965:0.2035	.	102;102;102;102	B3KQI0;Q9Y463-2;Q9Y463;Q9Y463-3	.;.;DYR1B_HUMAN;.	S	102	ENSP00000312789:R102S;ENSP00000221803:R102S;ENSP00000403182:R102S	ENSP00000312789:R102S	R	-	1	0	DYRK1B	45012923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.689000	0.61723	2.026000	0.59711	0.563000	0.77884	CGC			0.597	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000462874.2		NM_004714	
SHKBP1	92799	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	19	41094564	41094564	+	Silent	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:41094564T>C	ENST00000291842.5	+	14	1420	c.1371T>C	c.(1369-1371)tcT>tcC	p.S457S	SHKBP1_ENST00000600733.1_Silent_p.S432S|SHKBP1_ENST00000597649.1_3'UTR	NM_138392.3	NP_612401.2	Q8TBC3	SHKB1_HUMAN	SH3KBP1 binding protein 1	457					protein homooligomerization (GO:0051260)					breast(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|pancreas(1)|skin(3)|urinary_tract(1)	29			Lung(22;0.000114)|LUSC - Lung squamous cell carcinoma(20;0.000384)			GGACATGGTCTGTGACTCGCT	0.622																																					p.S457S													.	.			0			c.T1371C												172.0	153.0	160.0					19																	41094564		2203	4300	6503	SO:0001819	synonymous_variant	92799	exon14			ATGGTCTGTGACT	AF258553	CCDS12560.1	19q13.2	2013-01-10				ENSG00000160410		"""WD repeat domain containing"""	19214	protein-coding gene	gene with protein product						11152963	Standard	NM_138392		Approved	PP203, Sb1	uc002oob.3	Q8TBC3		ENST00000291842.5:c.1371T>C	19.37:g.41094564T>C			79	0	0		125	0.14	17	NM_138392	160	0.07	11	Q8N2I6|Q8WY93|Q96IB8	Silent	SNP	ENST00000291842.5	37	CCDS12560.1																																																																																					0.622	SHKBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000462613.2		NM_138392	
APOC4	346	mdanderson.org	37	19	45448465	45448465	+	Missense_Mutation	SNP	T	T	A	rs5167	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:45448465T>A	ENST00000592954.1	+	3	327	c.287T>A	c.(286-288)cTc>cAc	p.L96H	APOC2_ENST00000252490.4_5'Flank|APOC2_ENST00000592257.1_5'Flank|APOC4-APOC2_ENST00000589057.1_Intron|APOC4_ENST00000419266.2_Missense_Mutation_p.L96H|APOC2_ENST00000590360.1_5'Flank|APOC2_ENST00000591597.1_5'Flank	NM_001646.2	NP_001637.1	P55056	APOC4_HUMAN	apolipoprotein C-IV	96			L -> R (in dbSNP:rs5167). {ECO:0000269|PubMed:10996355}.		lipid metabolic process (GO:0006629)|positive regulation of sequestering of triglyceride (GO:0010890)|triglyceride homeostasis (GO:0070328)	high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	lipid transporter activity (GO:0005319)			breast(1)|endometrium(1)|lung(2)	4	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00334)|Epithelial(262;0.178)		CTGGGTCCGCTCACCAAGGCC	0.587																																					p.L96H													.	.			0			c.T287A	GRCh37	CM065970	APOC4	M	rs5167							179.0	177.0	177.0					19																	45448465		2203	4300	6503	SO:0001583	missense	346	exon3			GTCCGCTCACCAA	U32576	CCDS12649.1	19q13.2	2013-09-30			ENSG00000267467	ENSG00000267467		"""Apolipoproteins"""	611	protein-coding gene	gene with protein product		600745				8530039	Standard	NM_001646		Approved			P55056	OTTHUMG00000180845	ENST00000592954.1:c.287T>A	19.37:g.45448465T>A	ENSP00000468236:p.Leu96His		50	0	0		60	0.03	2	NM_001646	0		0	B3KWY6|Q53YY8	Missense_Mutation	SNP	ENST00000592954.1	37	CCDS12649.1	.	.	.	.	.	.	.	.	.	.	G	0.017	-1.507085	0.00992	.	.	ENSG00000224916	ENST00000419266;ENST00000436871	T;T	0.23552	1.9;1.9	4.26	2.07	0.26955	.	0.168114	0.28821	N	0.014031	T	0.11196	0.0273	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.06826	-1.0805	9	0.66056	D	0.02	-18.197	4.6363	0.12527	0.195:0.0:0.6327:0.1723	.	96	P55056	APOC4_HUMAN	H	96	ENSP00000406381:L96H;ENSP00000412935:L96H	ENSP00000406381:L96H	L	+	2	0	APOC4	50140305	0.042000	0.20092	0.006000	0.13384	0.060000	0.15804	1.155000	0.31700	0.176000	0.19873	-0.702000	0.03669	CTC			0.587	APOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000453255.1		NM_001646	
RSPH6A	81492	mdanderson.org	37	19	46303719	46303719	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr19:46303719G>T	ENST00000221538.3	-	5	2043	c.1901C>A	c.(1900-1902)gCc>gAc	p.A634D	RSPH6A_ENST00000600188.1_Missense_Mutation_p.A370D|RSPH6A_ENST00000597055.1_Missense_Mutation_p.A634D	NM_030785.3	NP_110412.1	Q9H0K4	RSH6A_HUMAN	radial spoke head 6 homolog A (Chlamydomonas)	634	Glu-rich.					intracellular (GO:0005622)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	32						ACTGGCATAGGCATAGGCCCC	0.642																																					p.A634D													.	.			0			c.C1901A												47.0	45.0	46.0					19																	46303719		2203	4300	6503	SO:0001583	missense	81492	exon5			GCATAGGCATAGG	AL136761	CCDS12675.1	19q13.3	2010-02-17	2009-11-18	2009-11-18	ENSG00000104941	ENSG00000104941			14241	protein-coding gene	gene with protein product		607548	"""radial spokehead-like 1"""	RSHL1		11237735	Standard	NM_030785		Approved	RSP4, RSP6, RSPH4B	uc002pdm.3	Q9H0K4		ENST00000221538.3:c.1901C>A	19.37:g.46303719G>T	ENSP00000221538:p.Ala634Asp		17	0	0		30	0.10	3	NM_030785	0		0	Q53FE2|Q6PEZ9	Missense_Mutation	SNP	ENST00000221538.3	37	CCDS12675.1	.	.	.	.	.	.	.	.	.	.	.	23.3	4.399643	0.83120	.	.	ENSG00000104941	ENST00000221538	T	0.20598	2.06	5.03	5.03	0.67393	.	0.412945	0.28273	N	0.015956	T	0.49983	0.1589	M	0.86502	2.82	0.40059	D	0.975878	D	0.63880	0.993	D	0.68039	0.955	T	0.56836	-0.7913	10	0.72032	D	0.01	-6.3194	14.1299	0.65247	0.0:0.0:1.0:0.0	.	634	Q9H0K4	RSH6A_HUMAN	D	634	ENSP00000221538:A634D	ENSP00000221538:A634D	A	-	2	0	RSPH6A	50995559	1.000000	0.71417	0.522000	0.27862	0.807000	0.45602	8.523000	0.90576	2.804000	0.96469	0.555000	0.69702	GCC			0.642	RSPH6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000461657.1			
KCNS3	3790	broad.mit.edu;mdanderson.org	37	2	18113148	18113148	+	Silent	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr2:18113148C>T	ENST00000403915.1	+	3	1324	c.873C>T	c.(871-873)atC>atT	p.I291I	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Silent_p.I291I	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	291					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGGTCCAGATCCTACGGCTTA	0.488																																					p.I291I													.	KCNS3	85		0			c.C873T												117.0	113.0	115.0					2																	18113148		2203	4300	6503	SO:0001819	synonymous_variant	3790	exon3			CCAGATCCTACGG	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.873C>T	2.37:g.18113148C>T			90	0	0		126	0.04	5	NM_002252	5	0.00	0	D6W520|O43651|Q4ZFY1|Q96B56	Silent	SNP	ENST00000403915.1	37	CCDS1692.1																																																																																					0.488	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000323808.1		NM_002252	
SOS1	6654	hgsc.bcm.edu	37	2	39237743	39237743	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr2:39237743A>G	ENST00000426016.1	-	16	2578	c.2492T>C	c.(2491-2493)cTc>cCc	p.L831P	SOS1_ENST00000402219.2_Missense_Mutation_p.L831P|SOS1_ENST00000395038.2_Missense_Mutation_p.L831P			Q07889	SOS1_HUMAN	son of sevenless homolog 1 (Drosophila)	831	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|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)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|Ras protein signal transduction (GO:0007265)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	DNA binding (GO:0003677)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|liver(1)|lung(29)|ovary(4)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	75		all_hematologic(82;0.21)				CCACAGAGTGAGGTTGGTGGT	0.333									Noonan syndrome																												p.L831P													.	.			0			c.T2492C												135.0	127.0	130.0					2																	39237743		2203	4300	6503	SO:0001583	missense	6654	exon15	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	AGAGTGAGGTTGG	L13857	CCDS1802.1	2p21	2014-09-17	2002-11-05		ENSG00000115904	ENSG00000115904		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11187	protein-coding gene	gene with protein product		182530	"""gingival fibromatosis, hereditary, 1"""	GINGF		8276400, 10995566	Standard	NM_005633		Approved	HGF, GF1	uc002rrk.4	Q07889	OTTHUMG00000102109	ENST00000426016.1:c.2492T>C	2.37:g.39237743A>G	ENSP00000387784:p.Leu831Pro		57	0	0		67	0.06	4	NM_005633	8	0.00	0	A8K2G3|B4DXG2	Missense_Mutation	SNP	ENST00000426016.1	37	CCDS1802.1	.	.	.	.	.	.	.	.	.	.	A	18.88	3.716696	0.68844	.	.	ENSG00000115904	ENST00000426016;ENST00000402219;ENST00000543698;ENST00000395038;ENST00000263879	T;T;T	0.38240	1.15;1.15;1.15	5.65	5.65	0.86999	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.064522	0.64402	D	0.000006	T	0.66117	0.2757	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.73056	-0.4103	10	0.87932	D	0	.	15.9118	0.79477	1.0:0.0:0.0:0.0	.	831	Q07889	SOS1_HUMAN	P	831;831;563;831;831	ENSP00000387784:L831P;ENSP00000384675:L831P;ENSP00000378479:L831P	ENSP00000263879:L831P	L	-	2	0	SOS1	39091247	1.000000	0.71417	1.000000	0.80357	0.662000	0.39071	9.205000	0.95048	2.141000	0.66446	0.524000	0.50904	CTC			0.333	SOS1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000219948.3		NM_005633	
USP34	9736	broad.mit.edu	37	2	61610448	61610448	+	Silent	SNP	G	G	T	rs202087339	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr2:61610448G>T	ENST00000398571.2	-	6	853	c.777C>A	c.(775-777)ccC>ccA	p.P259P		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	259					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.P259P(1)		autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			GCATGACAGCGGGAATATGTA	0.274																																					p.P259P													.	USP34	334		1	Substitution - coding silent(1)	lung(1)	c.C777A												49.0	51.0	50.0					2																	61610448		1823	4078	5901	SO:0001819	synonymous_variant	9736	exon6			GACAGCGGGAATA	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.777C>A	2.37:g.61610448G>T			239	0	0		318	0.01	4	NM_014709	1	0.00	0	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Silent	SNP	ENST00000398571.2	37	CCDS42686.1																																																																																					0.274	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000325650.4			
ACTR1B	10120	broad.mit.edu;mdanderson.org	37	2	98274702	98274702	+	Silent	SNP	G	G	A	rs146624887	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr2:98274702G>A	ENST00000289228.5	-	7	951	c.735C>T	c.(733-735)gaC>gaT	p.D245D		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	245					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						GCGTGCTGCCGTCTGGCAACG	0.642													G|||	2	0.000399361	0.0	0.0014	5008	,	,		20714	0.0		0.001	False		,,,				2504	0.0				p.D245D													.	ACTR1B	34		0			c.C735T							G		2,4404		0,2,2201	98.0	77.0	84.0		735	-8.1	0.0	2	dbSNP_134	84	18,8582		0,18,4282	no	coding-synonymous	ACTR1B	NM_005735.3		0,20,6483	AA,AG,GG		0.2093,0.0454,0.1538		245/377	98274702	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	10120	exon7			GCTGCCGTCTGGC	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"""ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"""	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.735C>T	2.37:g.98274702G>A			44	0	0		62	0.06	4	NM_005735	93	0.02	2	D3DVH2|Q53SK5|Q9BRB7	Silent	SNP	ENST00000289228.5	37	CCDS2033.1																																																																																					0.642	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000252973.1		NM_005735	
KCNJ13	3769	broad.mit.edu	37	2	233635973	233635973	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr2:233635973C>T	ENST00000233826.3	-	2	239	c.100G>A	c.(100-102)Gct>Act	p.A34T	GIGYF2_ENST00000373566.3_Intron|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000409547.1_Intron|GIGYF2_ENST00000409451.3_Intron|KCNJ13_ENST00000409779.1_Missense_Mutation_p.A34T|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000410029.1_Missense_Mutation_p.A34T	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	34					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		CCTCTTTGAGCGCCATCCATT	0.473																																					p.A34T													.	KCNJ13	18		0			c.G100A												152.0	131.0	138.0					2																	233635973		2203	4300	6503	SO:0001583	missense	3769	exon2			TTTGAGCGCCATC	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.100G>A	2.37:g.233635973C>T	ENSP00000233826:p.Ala34Thr		100	0	0		135	0.03	4	NM_001172416	0		0	A0PGH1|O76023|Q53SA1|Q8N3Y4	Missense_Mutation	SNP	ENST00000233826.3	37	CCDS2498.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.29|13.29	2.192743|2.192743	0.38707|0.38707	.|.	.|.	ENSG00000115474|ENSG00000115474	ENST00000233826;ENST00000409779;ENST00000410029|ENST00000444142	D;D;D|.	0.93763|.	-3.28;-3.28;-3.28|.	5.6|5.6	5.6|5.6	0.85130|0.85130	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);|.	0.442058|.	0.26935|.	N|.	0.021742|.	T|T	0.57607|0.57607	0.2065|0.2065	L|L	0.40543|0.40543	1.245|1.245	0.36325|0.36325	D|D	0.858509|0.858509	P;D|.	0.63046|.	0.898;0.992|.	B;P|.	0.47134|.	0.209;0.539|.	T|T	0.61594|0.61594	-0.7031|-0.7031	10|5	0.66056|.	D|.	0.02|.	.|.	12.8928|12.8928	0.58082|0.58082	0.0:0.9257:0.0:0.0743|0.0:0.9257:0.0:0.0743	.|.	34;34|.	O60928;A0PGH1|.	IRK13_HUMAN;.|.	T|H	34|1	ENSP00000233826:A34T;ENSP00000386408:A34T;ENSP00000386251:A34T|.	ENSP00000233826:A34T|.	A|R	-|-	1|2	0|0	KCNJ13|KCNJ13	233344217|233344217	0.958000|0.958000	0.32768|0.32768	0.984000|0.984000	0.44739|0.44739	0.949000|0.949000	0.60115|0.60115	1.061000|1.061000	0.30542|0.30542	2.629000|2.629000	0.89072|0.89072	0.655000|0.655000	0.94253|0.94253	GCT|CGC			0.473	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257036.1		NM_002242	
SCLY	51540	mdanderson.org	37	2	239006909	239006909	+	Silent	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr2:239006909C>T	ENST00000555827.1	+	12	1315	c.1251C>T	c.(1249-1251)agC>agT	p.S417S	ESPNL_ENST00000343063.3_5'Flank|SCLY_ENST00000429612.2_Silent_p.S211S|ESPNL_ENST00000409169.1_5'Flank|SCLY_ENST00000254663.6_Silent_p.S425S|SCLY_ENST00000422984.2_Silent_p.S323S			Q96I15	SCLY_HUMAN	selenocysteine lyase	417					cellular amino acid metabolic process (GO:0006520)	cytosol (GO:0005829)	pyridoxal phosphate binding (GO:0030170)|selenocysteine lyase activity (GO:0009000)|transferase activity (GO:0016740)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(5)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	22		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;1.37e-23)|OV - Ovarian serous cystadenocarcinoma(60;4.6e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;8.25e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000128)|Lung(119;0.0118)|LUSC - Lung squamous cell carcinoma(224;0.0285)		TCCGGCTCAGCGTGGGCCGCA	0.716																																					p.S425S	Melanoma(24;424 891 11947 32582 36034)|Ovarian(46;648 1065 26199 32764 45893)												.	.			0			c.C1275T												31.0	30.0	30.0					2																	239006909		2203	4297	6500	SO:0001819	synonymous_variant	51540	exon12			GCTCAGCGTGGGC	AF175767	CCDS2524.1, CCDS2524.2	2q37.3	2008-02-05			ENSG00000132330	ENSG00000132330			18161	protein-coding gene	gene with protein product	"""putative selenocysteine lyase"""	611056				10692412	Standard	NM_016510		Approved	SCL	uc010fyv.4	Q96I15	OTTHUMG00000133336	ENST00000555827.1:c.1251C>T	2.37:g.239006909C>T			42	0	0		43	0.07	3	NM_016510	10	0.00	0	B9A068|J3KN06|Q53SN1|Q53SN8|Q7L670|Q9NVT7|Q9NZR7	Silent	SNP	ENST00000555827.1	37																																																																																						0.716	SCLY-204	KNOWN	basic|appris_candidate	protein_coding	protein_coding				NM_016510	
FRG1B	284802	bcgsc.ca	37	20	29623214	29623214	+	Missense_Mutation	SNP	C	C	T	rs367590609		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr20:29623214C>T	ENST00000278882.3	+	3	406	c.26C>T	c.(25-27)tCg>tTg	p.S9L	FRG1B_ENST00000358464.4_Missense_Mutation_p.S9L|FRG1B_ENST00000439954.2_Silent_p.L10L			Q9BZ01	FRG1B_HUMAN	FSHD region gene 1 family, member B	9										endometrium(10)|kidney(21)|lung(3)|pancreas(1)|prostate(9)|urinary_tract(9)	53						TACATGCACTCGACAATGGTC	0.393																																					.													.	FRG1B	181		0			.																																									SO:0001583	missense	284802	.			TGCACTCGACAAT			20q11.1	2013-03-18	2007-10-11	2007-10-11	ENSG00000149531	ENSG00000149531			15792	other	unknown			"""chromosome 20 open reading frame 80"""	C20orf80			Standard	NR_003579		Approved	bA348I14.2	uc010ztl.1	Q9BZ01	OTTHUMG00000032157	ENST00000278882.3:c.26C>T	20.37:g.29623214C>T	ENSP00000278882:p.Ser9Leu		220	0.0454545455	10		250	0.11	28	.	54	0.00	0	C4AME5	Missense_Mutation	SNP	ENST00000278882.3	37		.	.	.	.	.	.	.	.	.	.	c	6.225	0.409655	0.11812	.	.	ENSG00000149531	ENST00000278882;ENST00000358464	.	.	.	1.93	-0.799	0.10901	.	0.226615	0.39020	N	0.001481	T	0.26268	0.0641	.	.	.	0.21064	N	0.999793	.	.	.	.	.	.	T	0.21827	-1.0234	6	0.72032	D	0.01	.	0.1722	0.00114	0.2331:0.1666:0.2366:0.3637	.	.	.	.	L	9	.	ENSP00000278882:S9L	S	+	2	0	FRG1B	28236875	0.975000	0.34042	0.996000	0.52242	0.067000	0.16453	-0.074000	0.11450	-0.180000	0.10637	-0.465000	0.05216	TCG			0.393	FRG1B-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000078494.2		NR_003579	
NCOA6	23054	hgsc.bcm.edu	37	20	33345756	33345756	+	Silent	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr20:33345756T>C	ENST00000374796.2	-	8	3365	c.795A>G	c.(793-795)caA>caG	p.Q265Q	NCOA6_ENST00000359003.2_Silent_p.Q265Q			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	265	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q265Q(1)		NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						gttgttgttgttgctgctgct	0.537																																					p.Q265Q													NCOA6,bladder,carcinoma,0,2	NCOA6	0	2	1	Substitution - coding silent(1)	central_nervous_system(1)	c.A795G												62.0	52.0	55.0					20																	33345756		2203	4300	6503	SO:0001819	synonymous_variant	23054	exon7			TTGTTGTTGCTGC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.795A>G	20.37:g.33345756T>C			40	0	0		48	0.04	2	NM_014071	6	0.00	0	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																					0.537	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000078811.2		NM_014071	
LTN1	26046	mdanderson.org	37	21	30304979	30304979	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr21:30304979G>T	ENST00000361371.5	-	28	4962	c.4883C>A	c.(4882-4884)gCt>gAt	p.A1628D	LTN1_ENST00000389194.2_Missense_Mutation_p.A1674D			O94822	LTN1_HUMAN	listerin E3 ubiquitin protein ligase 1	1628					protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(4)|kidney(5)|large_intestine(12)|lung(19)|ovary(5)|pancreas(1)|prostate(2)|skin(6)|stomach(2)|upper_aerodigestive_tract(2)	60						AGTAGCTCGAGCTTTAACCTG	0.338																																					p.A1674D													.	.			0			c.C5021A												86.0	92.0	90.0					21																	30304979		2203	4300	6503	SO:0001583	missense	26046	exon28			GCTCGAGCTTTAA	AK001915	CCDS33527.1, CCDS33527.2	21q21.3	2013-01-09	2010-09-17	2010-09-17	ENSG00000198862	ENSG00000198862		"""RING-type (C3HC4) zinc fingers"""	13082	protein-coding gene	gene with protein product	"""listerin"""	613083	"""chromosome 21 open reading frame 98"", ""zinc finger protein 294"", ""ring finger protein 160"""	C21orf98, C21orf10, ZNF294, RNF160		20835226, 19196968	Standard	NM_015565		Approved	KIAA0714, FLJ11053, LISTERIN	uc002ymr.2	O94822	OTTHUMG00000078803	ENST00000361371.5:c.4883C>A	21.37:g.30304979G>T	ENSP00000354977:p.Ala1628Asp		37	0	0		46	0.07	3	NM_015565	18	0.00	0	A6NL41|A7E2D0|B2RTS0|C9J7U3|J3KPL4|Q05C47|Q9H8M4|Q9NUY5|Q9P0E9	Missense_Mutation	SNP	ENST00000361371.5	37		.	.	.	.	.	.	.	.	.	.	G	28.5	4.923570	0.92319	.	.	ENSG00000198862	ENST00000389194;ENST00000361371	T;T	0.20881	2.04;2.05	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.49304	0.1549	M	0.77820	2.39	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.45160	-0.9280	10	0.49607	T	0.09	.	19.151	0.93488	0.0:0.0:1.0:0.0	.	1628	O94822	LTN1_HUMAN	D	1674;1628	ENSP00000373846:A1674D;ENSP00000354977:A1628D	ENSP00000354977:A1628D	A	-	2	0	LTN1	29226850	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	9.392000	0.97252	2.757000	0.94681	0.563000	0.77884	GCT			0.338	LTN1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000472108.1		NM_015565	
MIRLET7BHG	400931	broad.mit.edu	37	22	46505875	46505875	+	Silent	SNP	A	A	G			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr22:46505875A>G	ENST00000360737.3	+	5	627	c.468A>G	c.(466-468)ggA>ggG	p.G156G	MIRLET7A3_ENST00000362116.1_RNA																							GCCCAGGGGGAGGGCACTTGT	0.612																																					.													.	.			0			.												18.0	19.0	18.0					22																	46505875		692	1591	2283	SO:0001819	synonymous_variant	0	.			AGGGGGAGGGCAC																												ENST00000360737.3:c.468A>G	22.37:g.46505875A>G			60	0.0166666667	1		76	0.04	3	.	0		0		Silent	SNP	ENST00000360737.3	37																																																																																						0.612	FLJ27365-001	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000316781.1			
PKDREJ	10343	hgsc.bcm.edu;broad.mit.edu;mdanderson.org	37	22	46658494	46658494	+	Silent	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr22:46658494G>A	ENST00000253255.5	-	1	725	c.726C>T	c.(724-726)aaC>aaT	p.N242N		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	242	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)	p.N242N(1)		NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		GCACCGAGGCGTTGATGGTGG	0.697																																					p.N242N													PKDREJ,colon,carcinoma,0,1	PKDREJ	0	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C726T												24.0	26.0	26.0					22																	46658494		2203	4299	6502	SO:0001819	synonymous_variant	10343	exon1			CGAGGCGTTGATG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.726C>T	22.37:g.46658494G>A			55	0	0		65	0.12	8	NM_006071	1	0.00	0	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																					0.697	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318466.1		NM_006071	
FANCD2	2177	ucsc.edu	37	3	10091153	10091153	+	Silent	SNP	C	C	T	rs35652360	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic		WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr3:10091153C>T	ENST00000419585.1	+	17	1670	c.1509C>T	c.(1507-1509)aaC>aaT	p.N503N	FANCD2_ENST00000383806.1_Silent_p.N503N|FANCD2_ENST00000287647.3_Silent_p.N503N|FANCD2_ENST00000383807.1_Silent_p.N503N			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	503					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		TAGTGTTAAACCCATCTGCTA	0.408			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.N503N			yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	.	FANCD2	253		0			c.C1509T												237.0	256.0	249.0					3																	10091153		2201	4296	6497	SO:0001819	synonymous_variant	2177	exon17	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GTTAAACCCATCT	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.1509C>T	3.37:g.10091153C>T			86	0.0813953488	7		85	0.16	14	NM_001018115	7	0.57	4	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Silent	SNP	ENST00000419585.1	37	CCDS33696.1																																																																																					0.408	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000339873.1			
OSBPL10	114884	mdanderson.org	37	3	32022535	32022535	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr3:32022535G>T	ENST00000396556.2	-	1	259	c.137C>A	c.(136-138)gCg>gAg	p.A46E	ZNF860_ENST00000360311.4_5'Flank|OSBPL10_ENST00000438237.2_Missense_Mutation_p.A46E	NM_017784.4	NP_060254.2	Q9BXB5	OSB10_HUMAN	oxysterol binding protein-like 10	46					lipid transport (GO:0006869)		cholesterol binding (GO:0015485)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	34				STAD - Stomach adenocarcinoma(1;0.00406)		gagcccggccgccgccgACCG	0.791																																					p.A46E													.	.			0			c.C137A												1.0	1.0	1.0					3																	32022535		358	1100	1458	SO:0001583	missense	114884	exon1			CCGGCCGCCGCCG	AF392451	CCDS2651.1, CCDS54559.1	3p23	2013-01-10			ENSG00000144645	ENSG00000144645		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16395	protein-coding gene	gene with protein product		606738					Standard	NM_001174060		Approved		uc021wuu.1	Q9BXB5	OTTHUMG00000130672	ENST00000396556.2:c.137C>A	3.37:g.32022535G>T	ENSP00000379804:p.Ala46Glu		13	0	0		15	0.13	2	NM_017784	0		0	B4E212|Q9BTU5	Missense_Mutation	SNP	ENST00000396556.2	37	CCDS2651.1	.	.	.	.	.	.	.	.	.	.	G	8.867	0.948433	0.18356	.	.	ENSG00000144645	ENST00000396556;ENST00000438237	T;T	0.23552	1.9;2.19	4.07	1.26	0.21427	.	606.941000	0.00166	N	0.000001	T	0.15955	0.0384	N	0.14661	0.345	0.09310	N	1	B;B	0.18166	0.026;0.026	B;B	0.15052	0.012;0.012	T	0.20638	-1.0269	10	0.12766	T	0.61	1.0E-4	7.8168	0.29265	0.2913:0.0:0.7087:0.0	.	46;46	B4E212;Q9BXB5	.;OSB10_HUMAN	E	46	ENSP00000379804:A46E;ENSP00000406124:A46E	ENSP00000379804:A46E	A	-	2	0	OSBPL10	31997539	0.055000	0.20627	0.023000	0.16930	0.043000	0.13939	0.452000	0.21795	0.139000	0.18822	0.313000	0.20887	GCG			0.791	OSBPL10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000253165.2			
APEH	327	hgsc.bcm.edu	37	3	49723603	49723603	+	IGR	SNP	G	G	A	rs199969873	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr3:49723603G>A	ENST00000296456.5	+	0	3220				MST1_ENST00000494828.2_5'Flank|MST1_ENST00000383728.3_3'UTR|MST1_ENST00000449682.2_Missense_Mutation_p.R347W|AC099668.5_ENST00000563780.1_RNA	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.R333W(5)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		TCGGGGTTCCGGCAGAAGTTC	0.662													G|||	4	0.000798722	0.0008	0.0	5008	,	,		14102	0.001		0.001	False		,,,				2504	0.001				p.R347W													MST1,NS,carcinoma,0,5	MST1	0	5	5	Substitution - Missense(5)	endometrium(4)|skin(1)	c.C1039T																																									SO:0001628	intergenic_variant	4485	exon9			GGTTCCGGCAGAA	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723603G>A			44	0.0227272727	1		68	0.15	10	NM_020998	14	0.00	0	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	11	0.005036630036630037	4	0.008130081300813009	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	28.4	4.921307	0.92249	.	.	ENSG00000173531	ENST00000449682	D	0.93953	-3.32	5.47	2.53	0.30540	.	0.000000	0.38005	N	0.001857	D	0.96321	0.8800	H	0.97186	3.955	0.80722	D	1	D	0.56521	0.976	P	0.60609	0.877	D	0.95291	0.8395	10	0.66056	D	0.02	.	13.6859	0.62515	0.0:0.0:0.4634:0.5366	.	347	G3XAK1	.	W	347	ENSP00000414287:R347W	ENSP00000414287:R347W	R	-	1	2	MST1	49698607	1.000000	0.71417	0.997000	0.53966	0.991000	0.79684	3.194000	0.51005	0.213000	0.20722	0.655000	0.94253	CGG	0.005		0.662	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000346415.2			
LINC00969	440993	broad.mit.edu	37	3	195412514	195412515	+	lincRNA	INS	-	-	C	rs140203535	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr3:195412514_195412515insC	ENST00000445430.1	+	0	3711_3712									long intergenic non-protein coding RNA 969																		tcatttacagtcccctgttgcg	0.376													|||unknown(NO_COVERAGE)	1724	0.344249	0.2526	0.3689	5008	,	,		33784	0.3889		0.3797	False		,,,				2504	0.3681				.													.	.			0			.																																											0	.			TTACAGTCCCCTG	AK128346		3q29	2013-06-07			ENSG00000242086	ENSG00000242086		"""Long non-coding RNAs"""	48729	non-coding RNA	RNA, long non-coding							Standard	XR_427455		Approved				OTTHUMG00000155834		3.37:g.195412518_195412518dupC			7	0.2857142857	2		7	0.43	3	.	13	0.00	0		RNA	INS	ENST00000445430.1	37																																																																																						0.376	LINC00969-038	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000341951.1			
OTOP1	133060	mdanderson.org	37	4	4204288	4204288	+	Nonsense_Mutation	SNP	G	G	T	rs150117288		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr4:4204288G>T	ENST00000296358.4	-	4	641	c.617C>A	c.(616-618)tCg>tAg	p.S206*		NM_177998.1	NP_819056.1	Q7RTM1	OTOP1_HUMAN	otopetrin 1	206					biomineral tissue development (GO:0031214)|detection of gravity (GO:0009590)|inner ear morphogenesis (GO:0042472)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(3)|liver(4)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	34				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		GGTGAACACCGAGTGGATCAC	0.532																																					p.S206X													.	.			0			c.C617A												98.0	89.0	92.0					4																	4204288		2203	4300	6503	SO:0001587	stop_gained	133060	exon4			AACACCGAGTGGA	BK000653	CCDS3372.1	4p16.2	2008-02-05			ENSG00000163982	ENSG00000163982			19656	protein-coding gene	gene with protein product		607806				12651873	Standard	NM_177998		Approved		uc003ghp.1	Q7RTM1	OTTHUMG00000090301	ENST00000296358.4:c.617C>A	4.37:g.4204288G>T	ENSP00000296358:p.Ser206*		29	0	0		36	0.08	3	NM_177998	0		0	A1L476	Nonsense_Mutation	SNP	ENST00000296358.4	37	CCDS3372.1	.	.	.	.	.	.	.	.	.	.	G	37	6.406454	0.97542	.	.	ENSG00000163982	ENST00000296358	.	.	.	5.46	5.46	0.80206	.	0.058264	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-25.5076	19.3021	0.94148	0.0:0.0:1.0:0.0	.	.	.	.	X	206	.	ENSP00000296358:S206X	S	-	2	0	OTOP1	4255189	1.000000	0.71417	0.987000	0.45799	0.904000	0.53231	8.713000	0.91408	2.565000	0.86533	0.603000	0.83216	TCG			0.532	OTOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000206661.2		NM_177998	
FAM149A	25854	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	4	187084616	187084616	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr4:187084616G>A	ENST00000356371.5	+	10	1745	c.1745G>A	c.(1744-1746)gGt>gAt	p.G582D	FAM149A_ENST00000389354.5_Missense_Mutation_p.G291D|FAM149A_ENST00000227065.4_Missense_Mutation_p.G291D|FAM149A_ENST00000502970.1_Missense_Mutation_p.G291D|FAM149A_ENST00000503432.1_Missense_Mutation_p.G291D|FAM149A_ENST00000514153.1_Missense_Mutation_p.G291D			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	582										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		GGAGGGGCAGGTGCTCTCTCC	0.567																																					p.G291D													.	.			0			c.G872A												81.0	75.0	77.0					4																	187084616		2203	4300	6503	SO:0001583	missense	25854	exon9			GGGCAGGTGCTCT	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.1745G>A	4.37:g.187084616G>A	ENSP00000348732:p.Gly582Asp		100	0	0		114	0.11	12	NM_001006655	13	0.08	1	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		.	.	.	.	.	.	.	.	.	.	g	10.15	1.270397	0.23221	.	.	ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354	T;T;T;T;T;T	0.12147	2.77;2.71;2.77;2.77;2.77;2.77	4.99	1.28	0.21552	.	0.879568	0.09926	N	0.737820	T	0.16428	0.0395	L	0.57536	1.79	0.09310	N	1	P;P	0.41848	0.763;0.704	B;B	0.41894	0.369;0.143	T	0.15665	-1.0429	10	0.51188	T	0.08	0.36	8.0209	0.30408	0.1435:0.2031:0.6534:0.0	.	582;582	A5PLN7-3;A5PLN7	.;F149A_HUMAN	D	291;582;291;291;291;291	ENSP00000426835:G291D;ENSP00000348732:G582D;ENSP00000227065:G291D;ENSP00000427155:G291D;ENSP00000424380:G291D;ENSP00000374005:G291D	ENSP00000227065:G291D	G	+	2	0	FAM149A	187321610	0.031000	0.19500	0.000000	0.03702	0.021000	0.10359	2.241000	0.43097	-0.071000	0.12886	0.298000	0.19748	GGT			0.567	FAM149A-201	KNOWN	basic	protein_coding	protein_coding				NM_001006655	
EGFLAM	133584	broad.mit.edu	37	5	38438444	38438444	+	Missense_Mutation	SNP	C	C	T	rs200259259		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:38438444C>T	ENST00000354891.3	+	17	2697	c.2351C>T	c.(2350-2352)gCg>gTg	p.A784V	EGFLAM_ENST00000397202.2_Missense_Mutation_p.A150V|EGFLAM_ENST00000322350.5_Missense_Mutation_p.A784V|EGFLAM_ENST00000336740.6_Missense_Mutation_p.A550V	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	784	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GTGGAGAATGCGGCCCACCCC	0.547																																					p.A784V	Colon(62;485 1295 3347 17454)												.	EGFLAM	302		0			c.C2351T												60.0	62.0	62.0					5																	38438444		2203	4300	6503	SO:0001583	missense	133584	exon17			AGAATGCGGCCCA	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.2351C>T	5.37:g.38438444C>T	ENSP00000346964:p.Ala784Val		158	0	0		188	0.03	6	NM_001205301	28	0.00	0	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Missense_Mutation	SNP	ENST00000354891.3	37	CCDS56363.1	.	.	.	.	.	.	.	.	.	.	C	23.0	4.357047	0.82243	.	.	ENSG00000164318	ENST00000354891;ENST00000322350;ENST00000336740;ENST00000397202;ENST00000339580	T;T;T;D	0.83335	0.85;0.69;-1.25;-1.71	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);Epidermal growth factor-like, type 3 (1);	0.165528	0.52532	D	0.000065	D	0.87916	0.6298	M	0.76170	2.325	0.80722	D	1	D;D;P	0.54964	0.967;0.969;0.936	P;P;B	0.50490	0.642;0.536;0.388	D	0.88263	0.2924	10	0.54805	T	0.06	-9.8195	19.9065	0.97010	0.0:1.0:0.0:0.0	.	550;784;784	Q63HQ2-4;Q63HQ2;Q63HQ2-2	.;EGFLA_HUMAN;.	V	784;784;550;150;550	ENSP00000346964:A784V;ENSP00000313084:A784V;ENSP00000337607:A550V;ENSP00000380385:A150V	ENSP00000313084:A784V	A	+	2	0	EGFLAM	38474201	1.000000	0.71417	0.046000	0.18839	0.986000	0.74619	7.411000	0.80078	2.696000	0.92011	0.655000	0.94253	GCG			0.547	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000367323.1		NM_152403	
GZMK	3003	broad.mit.edu	37	5	54329635	54329635	+	Missense_Mutation	SNP	G	G	A	rs200562138		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:54329635G>A	ENST00000231009.2	+	5	746	c.676G>A	c.(676-678)Gct>Act	p.A226T	CTD-2313F11.1_ENST00000609792.1_RNA|CTD-2313F11.1_ENST00000609699.1_RNA|CTD-2313F11.1_ENST00000595218.1_RNA|CTD-2313F11.1_ENST00000596137.1_RNA	NM_002104.2	NP_002095.1	P49863	GRAK_HUMAN	granzyme K (granzyme 3; tryptase II)	226	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.A226S(1)		autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)	15		Lung NSC(810;4.08e-05)|Breast(144;0.0433)|Prostate(74;0.183)				TGTCTTCCACGCTATAGTCTC	0.453																																					p.A226T													GZMK,NS,carcinoma,0,1	GZMK	39	1	1	Substitution - Missense(1)	lung(1)	c.G676A							G	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	102.0	93.0	96.0		676	5.3	0.7	5		96	1,8599	1.2+/-3.3	0,1,4299	no	missense	GZMK	NM_002104.2	58	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	probably-damaging	226/265	54329635	2,13004	2203	4300	6503	SO:0001583	missense	3003	exon5			TTCCACGCTATAG	BC035802	CCDS3964.1	5q11.2	2008-05-15	2005-08-17		ENSG00000113088	ENSG00000113088			4711	protein-coding gene	gene with protein product		600784	"""granzyme K (serine protease, granzyme 3; tryptase II)"""			7758581	Standard	NM_002104		Approved	TRYP2, PRSS	uc003jpl.1	P49863	OTTHUMG00000097009	ENST00000231009.2:c.676G>A	5.37:g.54329635G>A	ENSP00000231009:p.Ala226Thr		114	0	0		146	0.03	4	NM_002104	35	0.00	0	B2R563	Missense_Mutation	SNP	ENST00000231009.2	37	CCDS3964.1	.	.	.	.	.	.	.	.	.	.	G	36	5.733630	0.96865	2.27E-4	1.16E-4	ENSG00000113088	ENST00000231009	D	0.88975	-2.45	5.28	5.28	0.74379	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.065450	0.64402	D	0.000018	D	0.90494	0.7022	L	0.49778	1.585	0.42889	D	0.994198	D	0.61080	0.989	P	0.53518	0.728	D	0.91543	0.5251	10	0.87932	D	0	.	16.4636	0.84071	0.0:0.0:1.0:0.0	.	226	P49863	GRAK_HUMAN	T	226	ENSP00000231009:A226T	ENSP00000231009:A226T	A	+	1	0	GZMK	54365392	0.998000	0.40836	0.687000	0.30102	0.559000	0.35586	7.069000	0.76755	2.738000	0.93877	0.655000	0.94253	GCT			0.453	GZMK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000214098.1		NM_002104	
NUDT12	83594	mdanderson.org	37	5	102887928	102887928	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:102887928G>T	ENST00000230792.2	-	6	1364	c.1268C>A	c.(1267-1269)aCt>aAt	p.T423N	NUDT12_ENST00000507423.1_Missense_Mutation_p.T405N|NUDT12_ENST00000515407.1_5'Flank	NM_031438.2	NP_113626.1	Q9BQG2	NUD12_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 12	423	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				NAD catabolic process (GO:0019677)|NADP catabolic process (GO:0006742)	nucleus (GO:0005634)|peroxisome (GO:0005777)	metal ion binding (GO:0046872)|NAD+ diphosphatase activity (GO:0000210)|NADH pyrophosphatase activity (GO:0035529)			endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|urinary_tract(1)	12		all_cancers(142;6.38e-08)|all_epithelial(76;1.99e-10)|Prostate(80;0.0138)|Lung NSC(167;0.0212)|Colorectal(57;0.0247)|all_lung(232;0.0283)|Ovarian(225;0.0423)		Epithelial(69;9.3e-13)|COAD - Colon adenocarcinoma(37;0.0221)		CTGTTCTCTAGTGAACCAGCG	0.398																																					p.T423N													.	.			0			c.C1268A												139.0	136.0	137.0					5																	102887928		2202	4300	6502	SO:0001583	missense	83594	exon6			TCTCTAGTGAACC	AL136592	CCDS4096.1, CCDS75284.1	5q15	2013-01-10			ENSG00000112874	ENSG00000112874		"""Nudix motif containing"", ""Ankyrin repeat domain containing"""	18826	protein-coding gene	gene with protein product	"""nucleoside diphosphate linked moiety X-type motif 12"""	609232				11230166	Standard	XM_005272095		Approved	DKFZP761I172	uc003koi.3	Q9BQG2	OTTHUMG00000128739	ENST00000230792.2:c.1268C>A	5.37:g.102887928G>T	ENSP00000230792:p.Thr423Asn		58	0	0		45	0.07	3	NM_031438	7	0.00	0	B3KUW2|Q8TAL7	Missense_Mutation	SNP	ENST00000230792.2	37	CCDS4096.1	.	.	.	.	.	.	.	.	.	.	G	19.78	3.890439	0.72524	.	.	ENSG00000112874	ENST00000230792;ENST00000507423	T;T	0.45276	0.9;0.9	5.46	5.46	0.80206	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.091171	0.85682	D	0.000000	T	0.61135	0.2323	M	0.71296	2.17	0.53688	D	0.999979	D;D	0.63880	0.993;0.98	P;P	0.61477	0.889;0.833	T	0.62020	-0.6942	10	0.54805	T	0.06	-29.1391	15.9762	0.80066	0.0:0.1348:0.8652:0.0	.	405;423	E7EM93;Q9BQG2	.;NUD12_HUMAN	N	423;405	ENSP00000230792:T423N;ENSP00000424521:T405N	ENSP00000230792:T423N	T	-	2	0	NUDT12	102915827	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.501000	0.81600	2.724000	0.93272	0.650000	0.86243	ACT			0.398	NUDT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000250650.1		NM_031438	
CAMK4	814	mdanderson.org	37	5	110814164	110814164	+	Missense_Mutation	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:110814164T>C	ENST00000282356.4	+	9	1185	c.787T>C	c.(787-789)Tcc>Ccc	p.S263P	CAMK4_ENST00000512453.1_Missense_Mutation_p.S263P	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	263	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		TTACTTTATCTCCCCCTGGTG	0.318																																					p.S263P													.	.			0			c.T787C												78.0	82.0	81.0					5																	110814164		2202	4299	6501	SO:0001583	missense	814	exon9			TTTATCTCCCCCT	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"""brain Ca++-calmodulin-dependent protein kinase type IV"", ""calcium/calmodulin-dependent protein kinase type IV catalytic chain"", ""CAM kinase IV"", ""CAM kinase- GR"""	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.787T>C	5.37:g.110814164T>C	ENSP00000282356:p.Ser263Pro		34	0.0294117647	1		44	0.07	3	NM_001744	1	0.00	0	D3DSZ7	Missense_Mutation	SNP	ENST00000282356.4	37	CCDS4103.1	.	.	.	.	.	.	.	.	.	.	T	29.8	5.037645	0.93630	.	.	ENSG00000152495	ENST00000512453;ENST00000282356	T;T	0.66638	-0.22;-0.22	5.9	5.9	0.94986	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.180982	0.50627	N	0.000109	T	0.68421	0.2999	L	0.28115	0.83	0.80722	D	1	P	0.51537	0.946	P	0.55087	0.768	T	0.72656	-0.4227	10	0.87932	D	0	.	16.3232	0.82961	0.0:0.0:0.0:1.0	.	263	Q16566	KCC4_HUMAN	P	263	ENSP00000422634:S263P;ENSP00000282356:S263P	ENSP00000282356:S263P	S	+	1	0	CAMK4	110842063	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.621000	0.83083	2.254000	0.74563	0.482000	0.46254	TCC			0.318	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000250719.2		NM_001744	
CCDC112	153733	mdanderson.org	37	5	114612674	114612674	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:114612674G>T	ENST00000512261.1	-	5	606	c.190C>A	c.(190-192)Cct>Act	p.P64T	CCDC112_ENST00000506442.1_Missense_Mutation_p.P64T|CCDC112_ENST00000503027.1_5'UTR|CCDC112_ENST00000395557.4_Missense_Mutation_p.P64T|CCDC112_ENST00000379611.5_Missense_Mutation_p.P147T			Q8NEF3	CC112_HUMAN	coiled-coil domain containing 112	64										endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|skin(1)	20		all_cancers(142;0.000523)|all_epithelial(76;6.44e-06)|Prostate(80;0.00955)|Ovarian(225;0.0443)|all_lung(232;0.132)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;4.09e-08)|Epithelial(69;5.28e-08)|all cancers(49;7.06e-06)		TCAGGTGTAGGCTTCACATCT	0.299																																					p.P147T													.	.			0			c.C439A												126.0	124.0	125.0					5																	114612674		2201	4298	6499	SO:0001583	missense	153733	exon4			GTGTAGGCTTCAC	BC031242	CCDS4117.1, CCDS34213.1	5q22.3	2009-04-17			ENSG00000164221	ENSG00000164221			28599	protein-coding gene	gene with protein product						12477932	Standard	NM_001040440		Approved	MGC39633	uc003kqz.2	Q8NEF3	OTTHUMG00000128894	ENST00000512261.1:c.190C>A	5.37:g.114612674G>T	ENSP00000423712:p.Pro64Thr		30	0	0		43	0.07	3	NM_001040440	0		0	Q6A334	Missense_Mutation	SNP	ENST00000512261.1	37	CCDS4117.1	.	.	.	.	.	.	.	.	.	.	G	18.84	3.709703	0.68730	.	.	ENSG00000164221	ENST00000379611;ENST00000512261;ENST00000506442;ENST00000395557	T;T;T;T	0.20738	2.05;2.12;2.14;2.12	5.72	4.67	0.58626	.	0.154368	0.64402	D	0.000015	T	0.34337	0.0894	L	0.53249	1.67	0.36697	D	0.879928	D;D;D	0.58620	0.983;0.983;0.983	P;P;P	0.56865	0.808;0.808;0.808	T	0.11421	-1.0588	10	0.25751	T	0.34	-15.6877	15.6018	0.76631	0.0767:0.0:0.9233:0.0	.	64;147;64	D6RF76;Q8NEF3-2;Q8NEF3	.;.;CC112_HUMAN	T	147;64;64;64	ENSP00000368931:P147T;ENSP00000423712:P64T;ENSP00000424876:P64T;ENSP00000378925:P64T	ENSP00000368931:P147T	P	-	1	0	CCDC112	114640573	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.793000	0.69060	2.711000	0.92665	0.655000	0.94253	CCT			0.299	CCDC112-003	PUTATIVE	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000370999.1		NM_152549	
APBB3	10307	mdanderson.org	37	5	139941994	139941994	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:139941994G>T	ENST00000357560.4	-	5	885	c.442C>A	c.(442-444)Cag>Aag	p.Q148K	SLC35A4_ENST00000514199.1_5'Flank|APBB3_ENST00000358580.5_Missense_Mutation_p.Q148K|APBB3_ENST00000508496.2_5'UTR|SLC35A4_ENST00000323146.3_5'Flank|APBB3_ENST00000356738.2_Missense_Mutation_p.Q148K|APBB3_ENST00000511201.2_Missense_Mutation_p.Q148K|APBB3_ENST00000354402.5_Missense_Mutation_p.Q148K|APBB3_ENST00000412920.3_Missense_Mutation_p.Q148K|APBB3_ENST00000507279.1_5'Flank	NM_006051.3|NM_133173.2	NP_006042.3|NP_573419.2	O95704	APBB3_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 3	148	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)	11			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCAGCTGCTGGATACAGTTA	0.612																																					p.Q148K													.	.			0			c.C442A												103.0	111.0	108.0					5																	139941994		2203	4300	6503	SO:0001583	missense	10307	exon5			GCTGCTGGATACA	AB018247	CCDS4227.1, CCDS4228.1, CCDS4229.1, CCDS47279.1	5q31	2008-02-05			ENSG00000113108	ENSG00000113108			20708	protein-coding gene	gene with protein product		602711				9407065	Standard	NM_133172		Approved	FE65L2	uc003lgd.1	O95704	OTTHUMG00000129504	ENST00000357560.4:c.442C>A	5.37:g.139941994G>T	ENSP00000350171:p.Gln148Lys		39	0	0		32	0.09	3	NM_133172	36	0.00	0	B3KQN9|Q08AG4|Q96Q18|Q9BYD4|Q9NYX6|Q9NYX7|Q9NYX8	Missense_Mutation	SNP	ENST00000357560.4	37	CCDS4229.1	.	.	.	.	.	.	.	.	.	.	G	29.4	5.000805	0.93227	.	.	ENSG00000113108	ENST00000358580;ENST00000356738;ENST00000354402;ENST00000357560;ENST00000412920;ENST00000511201	T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;2.19;2.19	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.55130	0.1901	M	0.65975	2.015	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.99	T	0.54655	-0.8261	9	.	.	.	-10.0463	18.213	0.89877	0.0:0.0:1.0:0.0	.	148;148	O95704-2;O95704-3	.;.	K	148	ENSP00000351389:Q148K;ENSP00000349177:Q148K;ENSP00000346378:Q148K;ENSP00000350171:Q148K;ENSP00000402591:Q148K;ENSP00000424317:Q148K	.	Q	-	1	0	APBB3	139922178	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.646000	0.98474	2.303000	0.77524	0.650000	0.86243	CAG			0.612	APBB3-003	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000251677.2		NM_006051	
F12	2161	mdanderson.org	37	5	176831071	176831071	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr5:176831071G>A	ENST00000253496.3	-	10	1087	c.1039C>T	c.(1039-1041)Cag>Tag	p.Q347*	F12_ENST00000514943.1_5'Flank	NM_000505.3	NP_000496.2	P00748	FA12_HUMAN	coagulation factor XII (Hageman factor)	347	Pro-rich.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|plasma kallikrein-kinin cascade (GO:0002353)|positive regulation of blood coagulation (GO:0030194)|positive regulation of fibrinolysis (GO:0051919)|positive regulation of plasminogen activation (GO:0010756)|protein autoprocessing (GO:0016540)|protein processing (GO:0016485)|response to misfolded protein (GO:0051788)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	misfolded protein binding (GO:0051787)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)		Ethanolamine Oleate(DB06689)	GAAGGCGGCTGCTCCCGCTTC	0.721									Hereditary Angioedema		OREG0017088	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Q347X													.	.			0			c.C1039T												10.0	14.0	13.0					5																	176831071		2143	4255	6398	SO:0001587	stop_gained	2161	exon10	Familial Cancer Database	HAE, type I-III, Hereditary Angioneurotic Edema, HANE,	GCGGCTGCTCCCG	M31315	CCDS34302.1	5q35.3	2014-09-17			ENSG00000131187	ENSG00000131187	3.4.21.38		3530	protein-coding gene	gene with protein product		610619					Standard	NM_000505		Approved		uc003mgo.4	P00748	OTTHUMG00000163403	ENST00000253496.3:c.1039C>T	5.37:g.176831071G>A	ENSP00000253496:p.Gln347*		9	0	0	1934	24	0.13	3	NM_000505	4	0.00	0	P78339	Nonsense_Mutation	SNP	ENST00000253496.3	37	CCDS34302.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.564560	0.86439	.	.	ENSG00000131187	ENST00000253496	.	.	.	5.0	0.585	0.17428	.	2.791560	0.01523	N	0.018423	.	.	.	.	.	.	0.19575	N	0.999961	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.1553	0.15031	0.0816:0.3971:0.386:0.1353	.	.	.	.	X	347	.	ENSP00000253496:Q347X	Q	-	1	0	F12	176763677	0.000000	0.05858	0.001000	0.08648	0.113000	0.19764	-0.134000	0.10436	0.174000	0.19809	0.561000	0.74099	CAG			0.721	F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000373217.1			
BTN2A3P	54718	broad.mit.edu	37	6	26422627	26422628	+	RNA	INS	-	-	A	rs3734537|rs34196747	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr6:26422627_26422628insA	ENST00000466808.2	+	0	79							Q96KV6	BT2A3_HUMAN	butyrophilin, subfamily 2, member A3, pseudogene							integral component of membrane (GO:0016021)											gcaaattttccaaaaaaattaa	0.292														729	0.145567	0.1641	0.1801	5008	,	,		17074	0.0308		0.166	False		,,,				2504	0.1933				.													.	.			0			.																																											0	.			ATTTTCCAAAAAA	AL021917		6p22.1	2014-01-14	2011-09-06	2011-09-06	ENSG00000124549	ENSG00000124549		"""Butyrophilins"""	13229	pseudogene	pseudogene		613592	"""butyrophilin, subfamily 2, member A3"""	BTN2A3			Standard	NR_027795		Approved	BTN2.3	uc011dkl.1	Q96KV6	OTTHUMG00000014453		6.37:g.26422634_26422634dupA			8	0	0		9	0.44	4	.	0		0	A6NEF4	RNA	INS	ENST00000466808.2	37																																																																																						0.292	BTN2A3P-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000040118.4		NR_027795	
MUC21	394263	hgsc.bcm.edu	37	6	30954728	30954728	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	A	A					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr6:30954728A>G	ENST00000376296.3	+	2	1017	c.776A>G	c.(775-777)gAg>gGg	p.E259G	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	259	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCAACTCTGAGTCCAGCACG	0.617																																					p.E259G													MUC21,bladder,carcinoma,-1,1	MUC21	-1	1	0			c.A776G												142.0	144.0	143.0					6																	30954728		2203	4300	6503	SO:0001583	missense	394263	exon2			ACTCTGAGTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.776A>G	6.37:g.30954728A>G	ENSP00000365473:p.Glu259Gly		35	0.0285714286	1		70	0.09	6	NM_001010909	0		0	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	11.51	1.659396	0.29515	.	.	ENSG00000204544	ENST00000376296	T	0.01388	4.95	4.28	-0.938	0.10412	.	.	.	.	.	T	0.00328	0.0010	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.42155	-0.9468	8	.	.	.	.	1.8519	0.03171	0.32:0.3592:0.2068:0.114	.	259	Q5SSG8	MUC21_HUMAN	G	259	ENSP00000365473:E259G	.	E	+	2	0	MUC21	31062707	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-2.354000	0.01089	-0.320000	0.08640	-0.655000	0.03904	GAG			0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000128579.3		NM_001010909	
BAG6	7917	mdanderson.org	37	6	31608010	31608010	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr6:31608010G>A	ENST00000375964.6	-	23	3435	c.3122C>T	c.(3121-3123)gCc>gTc	p.A1041V	BAG6_ENST00000439687.2_Missense_Mutation_p.A861V|BAG6_ENST00000470875.1_5'Flank|BAG6_ENST00000404765.2_Missense_Mutation_p.A1071V|BAG6_ENST00000211379.5_Missense_Mutation_p.A1035V|BAG6_ENST00000362049.6_Missense_Mutation_p.A1035V|BAG6_ENST00000375976.4_Missense_Mutation_p.A1035V	NM_004639.3|NM_080703.2	NP_004630.3|NP_542434.1	P46379	BAG6_HUMAN	BCL2-associated athanogene 6	1041					brain development (GO:0007420)|cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|embryo development (GO:0009790)|immune system process (GO:0002376)|internal peptidyl-lysine acetylation (GO:0018393)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|kidney development (GO:0001822)|lung development (GO:0030324)|negative regulation of apoptotic process (GO:0043066)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of proteolysis (GO:0045861)|protein stabilization (GO:0050821)|regulation of cell proliferation (GO:0042127)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)|tail-anchored membrane protein insertion into ER membrane (GO:0071816)|transport (GO:0006810)|ubiquitin-dependent protein catabolic process (GO:0006511)	BAT3 complex (GO:0071818)|cytosol (GO:0005829)|nucleus (GO:0005634)	polyubiquitin binding (GO:0031593)|proteasome binding (GO:0070628)|ribosome binding (GO:0043022)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(18)|ovary(2)|pancreas(2)|skin(3)|urinary_tract(2)	36						ACTGAGGTAGGCATCACTCAG	0.517																																					p.A1041V													.	.			0			c.C3122T												81.0	79.0	80.0					6																	31608010		2203	4300	6503	SO:0001583	missense	7917	exon23			AGGTAGGCATCAC	M31294	CCDS4709.1, CCDS47403.1, CCDS56414.1, CCDS56415.1	6p21.3	2011-06-14	2010-12-09	2010-12-09	ENSG00000204463	ENSG00000204463			13919	protein-coding gene	gene with protein product		142590	"""HLA-B associated transcript 3"""	BAT3		2156268	Standard	NM_004639		Approved	G3, D6S52E	uc003nvf.4	P46379	OTTHUMG00000031171	ENST00000375964.6:c.3122C>T	6.37:g.31608010G>A	ENSP00000365131:p.Ala1041Val		72	0	0		77	0.05	4	NM_004639	611	0.00	1	A2ADJ7|A3KQ42|A3KQ44|A6NGY6|A6PWF7|B0UX84|B4DZ12|B4E3V4|E7EMZ4|F8VXY4|O95874|Q5HYL9|Q5SQ35|Q5SQ36|Q5SQ37|Q5SQ41|Q5SRP8|Q5SRP9|Q5STC1|Q5STX1|Q5STX3|Q96SA6|Q9BCN4	Missense_Mutation	SNP	ENST00000375964.6	37	CCDS47403.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.2|21.2	4.106639|4.106639	0.77096|0.77096	.|.	.|.	ENSG00000204463|ENSG00000204463	ENST00000375976;ENST00000375964;ENST00000211379;ENST00000404765;ENST00000439687;ENST00000362049|ENST00000422948;ENST00000441793	T;T;T;T;T;T|.	0.78595|.	-0.24;-0.3;-0.24;-0.28;-1.19;-0.25|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.63331|0.63331	0.2502|0.2502	L|L	0.50333|0.50333	1.59|1.59	0.80722|0.80722	D|D	1|1	D;P;P;P|.	0.67145|.	0.996;0.51;0.626;0.57|.	P;B;B;B|.	0.61070|.	0.883;0.13;0.123;0.172|.	T|T	0.57100|0.57100	-0.7869|-0.7869	10|5	0.56958|.	D|.	0.05|.	.|.	18.6545|18.6545	0.91445|0.91445	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	861;1035;1041;1035|.	E7EMZ4;F8VXY4;P46379;P46379-2|.	.;.;BAG6_HUMAN;.|.	V|S	1035;1041;1035;1071;861;1035|94;184	ENSP00000365143:A1035V;ENSP00000365131:A1041V;ENSP00000211379:A1035V;ENSP00000384494:A1071V;ENSP00000402856:A861V;ENSP00000354875:A1035V|.	ENSP00000211379:A1035V|.	A|P	-|-	2|1	0|0	BAG6|BAG6	31715989|31715989	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	7.792000|7.792000	0.85828|0.85828	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	GCC|CCT			0.517	BAG6-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				NM_080703	
HLA-DMA	3108	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	6	32917166	32917166	+	Silent	SNP	G	G	A	rs371040586		TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr6:32917166G>A	ENST00000374843.4	-	4	748	c.663C>T	c.(661-663)aaC>aaT	p.N221N	HLA-DMA_ENST00000395303.3_Silent_p.N187N|HLA-DMA_ENST00000464392.1_5'UTR|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395305.3_Silent_p.N126N	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	221	Connecting peptide. {ECO:0000255}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)	p.N221N(1)|p.A222S(1)		kidney(1)|large_intestine(2)|lung(8)	11						AGGGCAGTGCGTTCCGGGGTA	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		19799	0.0		0.0	False		,,,				2504	0.001				p.N221N													HLA-DMA,NS,carcinoma,-1,2	HLA-DMA	-1	2	2	Substitution - Missense(1)|Substitution - coding silent(1)	lung(2)	c.C663T							G		1,4405	2.1+/-5.4	0,1,2202	74.0	69.0	71.0		663	-6.9	0.0	6		71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HLA-DMA	NM_006120.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		221/262	32917166	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3108	exon4			CAGTGCGTTCCGG		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.663C>T	6.37:g.32917166G>A			65	0	0		66	0.17	11	NM_006120	632	0.00	3	Q29639|Q29640	Silent	SNP	ENST00000374843.4	37	CCDS4761.1																																																																																					0.582	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000076325.2		NM_006120	
ORC3	23595	mdanderson.org	37	6	88313102	88313102	+	Splice_Site	SNP	C	C	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr6:88313102C>T	ENST00000392844.3	+	4	226	c.178C>T	c.(178-180)Cga>Tga	p.R60*	ORC3_ENST00000417380.2_Splice_Site_p.R7*|ORC3_ENST00000546266.1_5'UTR|ORC3_ENST00000257789.4_Splice_Site_p.R60*	NM_012381.3|NM_181837.2	NP_036513.2|NP_862820.1	Q9UBD5	ORC3_HUMAN	origin recognition complex, subunit 3	60					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|neural precursor cell proliferation (GO:0061351)	nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|origin recognition complex (GO:0000808)	DNA replication origin binding (GO:0003688)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	28						TTCTTTGTAGCGACTACAAGA	0.313																																					p.R60X													.	.			0			c.C178T												26.0	27.0	27.0					6																	88313102		2201	4298	6499	SO:0001630	splice_region_variant	23595	exon4			TTGTAGCGACTAC	AF093535	CCDS5012.1, CCDS43486.1, CCDS56440.1	6q	2010-10-12	2010-10-12	2010-10-12	ENSG00000135336	ENSG00000135336			8489	protein-coding gene	gene with protein product		604972	"""origin recognition complex, subunit 3 (yeast homolog)-like"", ""origin recognition complex, subunit 3-like (yeast)"", ""origin recognition complex, subunit 3 honolog (yeast)"""	ORC3L		9829972, 10402192	Standard	NM_181837		Approved	IMAGE50150, LATHEO	uc003pmg.3	Q9UBD5	OTTHUMG00000015179	ENST00000392844.3:c.178-1C>T	6.37:g.88313102C>T			40	0	0		41	0.07	3	NM_012381	21	0.00	0	A2A2T5|B4E025|Q13565|Q53GY6|Q5T159|Q6IUY7|Q86TN5|Q9UG44|Q9UNT6	Nonsense_Mutation	SNP	ENST00000392844.3	37	CCDS43486.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.588181	0.46110	.	.	ENSG00000135336	ENST00000392844;ENST00000257789;ENST00000417380	.	.	.	5.52	1.27	0.21489	.	0.642666	0.14921	N	0.290665	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	0.2098	7.1911	0.25826	0.2116:0.6067:0.1159:0.0658	.	.	.	.	X	60;60;7	.	.	R	+	1	2	ORC3	88369821	0.994000	0.37717	0.544000	0.28141	0.172000	0.22775	1.378000	0.34328	0.266000	0.21894	-0.188000	0.12872	CGA			0.313	ORC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000041452.2			Nonsense_Mutation
MCM7	4176	mdanderson.org	37	7	99693551	99693551	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr7:99693551G>T	ENST00000303887.5	-	11	2086	c.1441C>A	c.(1441-1443)Cgc>Agc	p.R481S	MCM7_ENST00000354230.3_Missense_Mutation_p.R305S|MIR106B_ENST00000385301.1_RNA|MIR25_ENST00000384816.1_RNA|MCM7_ENST00000343023.6_Intron|MIR93_ENST00000385024.1_RNA	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7	481	MCM.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of phosphorylation (GO:0042325)|response to drug (GO:0042493)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|MCM complex (GO:0042555)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA helicase activity (GO:0003678)|single-stranded DNA binding (GO:0003697)			endometrium(1)|kidney(5)|large_intestine(5)|lung(4)|ovary(1)|stomach(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					ATGGAGCAGCGGGCATTGAGT	0.632																																					p.R481S													.	.			0			c.C1441A												99.0	86.0	90.0					7																	99693551		2203	4300	6503	SO:0001583	missense	4176	exon11			AGCAGCGGGCATT		CCDS5683.1, CCDS5684.1	7q21.3-q22.1	2014-06-12	2007-04-04		ENSG00000166508	ENSG00000166508			6950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 104"""	600592	"""minichromosome maintenance deficient (S. cerevisiae) 7"", ""MCM7 minichromosome maintenance deficient 7 (S. cerevisiae)"""	MCM2		7842741	Standard	NM_005916		Approved	CDC47, PPP1R104	uc003usw.1	P33993	OTTHUMG00000154671	ENST00000303887.5:c.1441C>A	7.37:g.99693551G>T	ENSP00000307288:p.Arg481Ser		56	0	0		47	0.09	4	NM_005916	309	0.01	2	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Missense_Mutation	SNP	ENST00000303887.5	37	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.028358	0.93518	.	.	ENSG00000166508	ENST00000303887;ENST00000542483;ENST00000362082;ENST00000354230	T;T	0.12039	2.72;2.72	5.28	5.28	0.74379	ATPase, AAA+ type, core (1);	0.059515	0.64402	D	0.000001	T	0.56140	0.1965	H	0.98646	4.29	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.73836	-0.3857	10	0.87932	D	0	-15.6776	16.4558	0.84012	0.0:0.0:1.0:0.0	.	481	P33993	MCM7_HUMAN	S	481;418;374;305	ENSP00000307288:R481S;ENSP00000346171:R305S	ENSP00000307288:R481S	R	-	1	0	MCM7	99531487	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	9.595000	0.98260	2.738000	0.93877	0.655000	0.94253	CGC			0.632	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000336534.3			
SSPO	23145	broad.mit.edu;mdanderson.org	37	7	149510874	149510874	+	RNA	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr7:149510874G>T	ENST00000378016.2	+	0	10159							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AAGGCCTGACGGCTGCAACCA	0.667																																					p.G3387C													.	.			0			c.G10159T												24.0	28.0	27.0					7																	149510874		2016	4170	6186			23145	exon71			CCTGACGGCTGCA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149510874G>T			28	0	0		36	0.08	3	NM_198455	1	0.00	0	Q76B61	RNA	SNP	ENST00000378016.2	37																																																																																						0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript					
CTSV	1515	broad.mit.edu	37	9	99797977	99797977	+	Splice_Site	SNP	T	T	C			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr9:99797977T>C	ENST00000259470.5	-	6	871		c.e6-2		CTSV_ENST00000479932.1_5'Flank|CTSV_ENST00000538255.1_Splice_Site	NM_001333.3	NP_001324.2	O60911	CATL2_HUMAN	cathepsin V						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic cell death (GO:0048102)|catagen (GO:0042637)|cellular response to starvation (GO:0009267)|decidualization (GO:0046697)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|multicellular organismal aging (GO:0010259)|negative regulation of keratinocyte proliferation (GO:0010839)|nerve development (GO:0021675)|protein autoprocessing (GO:0016540)|regulation of actin cytoskeleton reorganization (GO:2000249)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to gonadotropin (GO:0034698)|Sertoli cell differentiation (GO:0060008)|spermatogenesis (GO:0007283)	cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|microvillus (GO:0005902)|neuron projection (GO:0043005)|nucleolus (GO:0005730)|perikaryon (GO:0043204)	aminopeptidase activity (GO:0004177)|cysteine-type carboxypeptidase activity (GO:0016807)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|peptide binding (GO:0042277)										GATTTCATCCTTTTAAAGTTA	0.448																																					.													.	CTSL2	40		0			c.622-2A>G												48.0	44.0	46.0					9																	99797977		2203	4300	6503	SO:0001630	splice_region_variant	1515	exon7			TCATCCTTTTAAA	Y14734	CCDS6723.1	9q22.33	2013-06-27	2013-06-27	2013-06-27	ENSG00000136943	ENSG00000136943		"""Cathepsins"""	2538	protein-coding gene	gene with protein product		603308	"""cathepsin L2"""	CTSL2		9563472, 10029531	Standard	NM_001201575		Approved	CTSU	uc004awt.3	O60911	OTTHUMG00000020314	ENST00000259470.5:c.622-2A>G	9.37:g.99797977T>C			60	0	0		66	0.05	3	NM_001333	0		0	O60233|Q2TB86|Q5T1U0	Splice_Site	SNP	ENST00000259470.5	37	CCDS6723.1	.	.	.	.	.	.	.	.	.	.	t	15.69	2.908800	0.52439	.	.	ENSG00000136943	ENST00000259470;ENST00000538255	.	.	.	3.65	3.65	0.41850	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.8908	0.46994	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	CTSL2	98837798	1.000000	0.71417	0.989000	0.46669	0.270000	0.26580	3.962000	0.56766	1.920000	0.55613	0.459000	0.35465	.			0.448	CTSV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000053301.2		NM_001333	Intron
GRIN3A	116443	mdanderson.org	37	9	104432598	104432598	+	Missense_Mutation	SNP	C	C	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr9:104432598C>A	ENST00000361820.3	-	3	2696	c.2096G>T	c.(2095-2097)aGt>aTt	p.S699I		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	699					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	ACCAAATGGACTCTTCCATTC	0.478																																					p.S699I													.	.			0			c.G2096T												126.0	132.0	130.0					9																	104432598		2203	4300	6503	SO:0001583	missense	116443	exon3			AATGGACTCTTCC		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2096G>T	9.37:g.104432598C>A	ENSP00000355155:p.Ser699Ile		50	0	0		49	0.06	3	NM_133445	1	0.00	0	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	37	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	18.39	3.614304	0.66672	.	.	ENSG00000198785	ENST00000361820	T	0.51574	0.7	5.39	5.39	0.77823	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.000000	0.85682	D	0.000000	T	0.76169	0.3950	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80999	-0.1131	10	0.87932	D	0	.	19.5908	0.95509	0.0:1.0:0.0:0.0	.	699	Q8TCU5	NMD3A_HUMAN	I	699	ENSP00000355155:S699I	ENSP00000355155:S699I	S	-	2	0	GRIN3A	103472419	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	5.956000	0.70315	2.714000	0.92807	0.580000	0.79431	AGT			0.478	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000053453.1			
KIAA0368	23392	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	9	114134001	114134001	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	.	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr9:114134001G>A	ENST00000338205.5	-	42	4856	c.4637C>T	c.(4636-4638)gCa>gTa	p.A1546V	KIAA0368_ENST00000259335.4_Missense_Mutation_p.A1724V|KIAA0368_ENST00000465499.1_5'Flank|KIAA0368_ENST00000374378.3_Missense_Mutation_p.A10V			Q5VYK3	ECM29_HUMAN	KIAA0368	1552					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	centrosome (GO:0005813)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle (GO:0030134)|late endosome (GO:0005770)|membrane (GO:0016020)|multivesicular body (GO:0005771)|nucleus (GO:0005634)|proteasome complex (GO:0000502)				NS(2)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(23)|prostate(3)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	65						TGCAATTGATGCCATGGCAAT	0.483																																					p.A1724V													.	.			0			c.C5171T												171.0	162.0	165.0					9																	114134001		1889	4112	6001	SO:0001583	missense	23392	exon44			ATTGATGCCATGG	AK025689	CCDS48006.1	9q32	2012-11-29	2006-11-23	2006-11-23	ENSG00000136813	ENSG00000136813			29020	protein-coding gene	gene with protein product	"""ECM29 homolog (S. cerevisiae)"""					9205841, 15496406, 20682791	Standard	NM_001080398		Approved	FLJ22036, ECM29	uc004bfe.1	Q5VYK3	OTTHUMG00000020489	ENST00000338205.5:c.4637C>T	9.37:g.114134001G>A	ENSP00000339889:p.Ala1546Val		110	0	0		93	0.06	6	NM_001080398	96	0.22	21	O15074|Q8WU82	Missense_Mutation	SNP	ENST00000338205.5	37		.	.	.	.	.	.	.	.	.	.	G	19.79	3.892316	0.72524	.	.	ENSG00000136813	ENST00000338205;ENST00000259335;ENST00000374383;ENST00000543827;ENST00000374378	T;T	0.67171	-0.25;-0.25	5.73	4.83	0.62350	.	0.056173	0.64402	D	0.000001	T	0.65491	0.2696	M	0.64997	1.995	0.48511	D	0.999667	B	0.21753	0.06	B	0.23150	0.044	T	0.62435	-0.6855	10	0.38643	T	0.18	.	16.212	0.82168	0.0:0.0:0.866:0.134	.	1021	B3KXF2	.	V	1546;1724;10;1021;10	ENSP00000259335:A1724V;ENSP00000363499:A10V	ENSP00000259335:A1724V	A	-	2	0	KIAA0368	113173822	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.476000	0.97823	1.398000	0.46701	0.655000	0.94253	GCA			0.483	KIAA0368-001	NOVEL	basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000053637.2		NM_014686	
NELFB	25920	broad.mit.edu;bcgsc.ca;mdanderson.org	37	9	140150039	140150039	+	Silent	SNP	G	G	A	rs201291926	byFrequency	TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chr9:140150039G>A	ENST00000343053.4	+	1	415	c.78G>A	c.(76-78)ccG>ccA	p.P26P		NM_015456.3	NP_056271.2	Q8WX92	NELFB_HUMAN	negative elongation factor complex member B	26					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)											GCACGGAGCCGCTCAAGGCCA	0.756																																					p.P26P													.	.			0			c.G78A												15.0	14.0	14.0					9																	140150039		2043	4024	6067	SO:0001819	synonymous_variant	25920	exon1			GGAGCCGCTCAAG	AF464935	CCDS7040.1	9q34	2013-01-31	2013-01-31	2013-01-31	ENSG00000188986	ENSG00000188986			24324	protein-coding gene	gene with protein product		611180	"""cofactor of BRCA1"""	COBRA1		11230166, 10574461, 17910036, 17659869	Standard	NM_015456		Approved	KIAA1182, NELF-B	uc004cmm.4	Q8WX92	OTTHUMG00000131778	ENST00000343053.4:c.78G>A	9.37:g.140150039G>A			75	0	0		57	0.09	5	NM_015456	106	0.00	0	A2BFA3|Q96EW5|Q9H9R4|Q9ULN8|Q9Y3W0	Silent	SNP	ENST00000343053.4	37	CCDS7040.1																																																																																					0.756	NELFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000254710.1		NM_015456	
CCDC120	90060	mdanderson.org	37	X	48922190	48922190	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chrX:48922190G>T	ENST00000376396.3	+	6	833	c.614G>T	c.(613-615)aGc>aTc	p.S205I	CCDC120_ENST00000536628.2_Missense_Mutation_p.S193I|CCDC120_ENST00000496529.2_Missense_Mutation_p.S205I|CCDC120_ENST00000422185.2_Missense_Mutation_p.S205I|CCDC120_ENST00000597275.1_Missense_Mutation_p.S205I|CCDC120_ENST00000603986.1_Missense_Mutation_p.S240I	NM_001271835.1|NM_001271836.1|NM_033626.2	NP_001258764.1|NP_001258765.1|NP_296375.1	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	205										breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14						GCTCAGCTCAGCCAAGGTGAG	0.647																																					p.S240I													.	.			0			c.G719T												24.0	21.0	22.0					X																	48922190		2198	4289	6487	SO:0001583	missense	90060	exon6			AGCTCAGCCAAGG	BC008769	CCDS14316.1, CCDS55413.1, CCDS55414.1, CCDS55414.2	Xp11.23	2008-02-05			ENSG00000147144	ENSG00000147144			28910	protein-coding gene	gene with protein product						12477932	Standard	NM_033626		Approved	JM11	uc011mmr.3	Q96HB5	OTTHUMG00000021509	ENST00000376396.3:c.614G>T	X.37:g.48922190G>T	ENSP00000365577:p.Ser205Ile		26	0	0		42	0.07	3	NM_001163321	1	0.00	0	B4DFC1|B4DTU2|F5GZU4	Missense_Mutation	SNP	ENST00000376396.3	37	CCDS14316.1	.	.	.	.	.	.	.	.	.	.	G	16.91	3.253732	0.59212	.	.	ENSG00000147144	ENST00000376396;ENST00000422185;ENST00000536628	.	.	.	4.35	4.35	0.52113	.	0.152029	0.40222	N	0.001147	T	0.39118	0.1066	N	0.11313	0.125	0.36249	D	0.853809	D;D;D;D	0.61080	0.978;0.989;0.978;0.978	P;P;P;P	0.53912	0.601;0.737;0.601;0.601	T	0.49986	-0.8880	9	0.38643	T	0.18	-9.9057	11.5478	0.50702	0.0:0.0:1.0:0.0	.	193;240;193;205	B4DTU2;B4DFC1;B4DF24;Q96HB5	.;.;.;CC120_HUMAN	I	205;205;193	.	ENSP00000365577:S205I	S	+	2	0	CCDC120	48809134	1.000000	0.71417	1.000000	0.80357	0.610000	0.37248	4.376000	0.59556	1.756000	0.51951	0.292000	0.19580	AGC			0.647	CCDC120-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000056528.1		NM_033626	
SHROOM4	57477	bcgsc.ca;mdanderson.org	37	X	50438918	50438918	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_1	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chrX:50438918G>T	ENST00000289292.7	-	2	420	c.137C>A	c.(136-138)gCa>gAa	p.A46E	SHROOM4_ENST00000376020.2_Missense_Mutation_p.A46E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	46	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					GGACAAAGCTGCCTTGCCTCC	0.473																																					p.A46E													.	SHROOM4	171		0			c.C137A												92.0	78.0	82.0					X																	50438918		2203	4300	6503	SO:0001583	missense	57477	exon2			AAAGCTGCCTTGC	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.137C>A	X.37:g.50438918G>T	ENSP00000289292:p.Ala46Glu		46	0	0		62	0.10	6	NM_020717	0		0	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	17.92	3.507038	0.64410	.	.	ENSG00000158352	ENST00000289292;ENST00000376020	T;T	0.38077	1.16;1.16	5.4	5.4	0.78164	PDZ/DHR/GLGF (4);	0.183522	0.32640	N	0.005824	T	0.73791	0.3632	H	0.97465	4.01	0.58432	D	0.999998	D	0.89917	1.0	D	0.91635	0.999	D	0.83854	0.0264	10	0.87932	D	0	.	15.7052	0.77573	0.0:0.0:1.0:0.0	.	46	Q9ULL8	SHRM4_HUMAN	E	46	ENSP00000289292:A46E;ENSP00000365188:A46E	ENSP00000289292:A46E	A	-	2	0	SHROOM4	50455658	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.881000	0.92415	2.394000	0.81467	0.544000	0.68410	GCA			0.473	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000056564.4		NM_020717	
GAB3	139716	mdanderson.org	37	X	153928305	153928305	+	Nonsense_Mutation	SNP	G	G	A			TCGA-2G-AALZ-01A-11D-A42Y-10	TCGA-2G-AALZ-10A-01D-A433-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	20764d97-a509-4c5a-8ab1-fc15b82c0958	b79135a4-1369-4dd1-892e-f72cbed6242b	g.chrX:153928305G>A	ENST00000369575.3	-	5	1127	c.1096C>T	c.(1096-1098)Cga>Tga	p.R366*	GAB3_ENST00000424127.2_Nonsense_Mutation_p.R367*|GAB3_ENST00000496390.1_5'UTR	NM_001081573.1|NM_080612.2	NP_001075042.1|NP_542179.1	Q8WWW8	GAB3_HUMAN	GRB2-associated binding protein 3	366					macrophage differentiation (GO:0030225)			p.R366*(1)		NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)	25	all_cancers(53;8.15e-17)|all_epithelial(53;1.1e-10)|all_lung(58;6.63e-07)|Lung NSC(58;2.08e-06)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)|Renal(33;0.214)					CGCTTGTCTCGGTGTCTTAAG	0.393																																					p.R367X													.	.			1	Substitution - Nonsense(1)	large_intestine(1)	c.C1099T												159.0	142.0	148.0					X																	153928305		2203	4300	6503	SO:0001587	stop_gained	139716	exon5			TGTCTCGGTGTCT	AY057989	CCDS14760.1, CCDS48198.1, CCDS65357.1	Xq28	2013-01-10			ENSG00000160219	ENSG00000160219		"""Pleckstrin homology (PH) domain containing"""	17515	protein-coding gene	gene with protein product	"""DOS/Gab family member 3"", ""Gab3 scaffolding protein"""	300482				11739737	Standard	XM_005274648		Approved		uc004fmk.1	Q8WWW8	OTTHUMG00000024245	ENST00000369575.3:c.1096C>T	X.37:g.153928305G>A	ENSP00000358588:p.Arg366*		47	0	0		52	0.06	3	NM_001081573	2	0.00	0	A6NHF8|E9PB44	Nonsense_Mutation	SNP	ENST00000369575.3	37	CCDS14760.1	.	.	.	.	.	.	.	.	.	.	G	37	6.374336	0.97515	.	.	ENSG00000160219	ENST00000369575;ENST00000369568;ENST00000424127	.	.	.	5.76	4.87	0.63330	.	0.871922	0.09643	N	0.774794	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15066	T	0.55	-7.1472	10.7036	0.45942	0.0:0.0:0.6542:0.3458	.	.	.	.	X	366;367;367	.	ENSP00000358581:R367X	R	-	1	2	GAB3	153581499	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	1.916000	0.39986	1.147000	0.42369	0.468000	0.43344	CGA			0.393	GAB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000061192.2		NM_001081573	
