#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
EXTL1	2134	hgsc.bcm.edu	37	1	26349593	26349593	+	Silent	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:26349593A>G	ENST00000374280.3	+	1	1323	c.456A>G	c.(454-456)caA>caG	p.Q152Q		NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	152					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCTCTGCAATGGAACAGGG	0.647																																					p.Q152Q		Atlas-SNP	.											.	EXTL1	61	.	0			c.A456G						.						55.0	54.0	54.0					1																	26349593		2203	4300	6503	SO:0001819	synonymous_variant	2134	exon1			TCTGCAATGGAAC	U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.456A>G	chr1.hg19:g.26349593A>G		132.0	0.0		94.0	36.0	NM_004455	Q6GSC1	Silent	SNP	ENST00000374280.3	hg19	CCDS271.1																																																																																			.	.		0.647	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
HECTD3	79654	hgsc.bcm.edu	37	1	45469948	45469948	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:45469948C>T	ENST00000372172.4	-	17	2315	c.2244G>A	c.(2242-2244)gaG>gaA	p.E748E	HECTD3_ENST00000486132.1_5'UTR|HECTD3_ENST00000372168.3_Silent_p.E358E	NM_024602.5	NP_078878.3	Q5T447	HECD3_HUMAN	HECT domain containing E3 ubiquitin protein ligase 3	748	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|stomach(1)	28	Acute lymphoblastic leukemia(166;0.155)					CCACAGTGACCTCTGGATCCC	0.602																																					p.E748E		Atlas-SNP	.											.	HECTD3	158	.	0			c.G2244A						.						96.0	99.0	98.0					1																	45469948		2128	4262	6390	SO:0001819	synonymous_variant	79654	exon17			AGTGACCTCTGGA	BC019105	CCDS41318.1	1p34.1	2012-02-23	2012-02-23		ENSG00000126107	ENSG00000126107			26117	protein-coding gene	gene with protein product			"""HECT domain containing 3"""			12477932	Standard	NM_024602		Approved	FLJ21156	uc009vxk.3	Q5T447	OTTHUMG00000008587	ENST00000372172.4:c.2244G>A	chr1.hg19:g.45469948C>T		103.0	0.0		79.0	37.0	NM_024602	B3KPV7|B3KRH4|Q5T448|Q9H783	Silent	SNP	ENST00000372172.4	hg19	CCDS41318.1																																																																																			.	.		0.602	HECTD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023734.1	NM_024602	
POMGNT1	55624	hgsc.bcm.edu	37	1	46654596	46654596	+	3'UTR	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:46654596G>T	ENST00000371984.3	-	0	2486				POMGNT1_ENST00000371992.1_Missense_Mutation_p.P681Q|POMGNT1_ENST00000535522.1_3'UTR|POMGNT1_ENST00000485714.1_5'Flank|POMGNT1_ENST00000371986.3_Missense_Mutation_p.P681Q|POMGNT1_ENST00000396420.3_3'UTR	NM_017739.3	NP_060209	Q8WZA1	PMGT1_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 1 (beta 1,2-)						protein O-linked glycosylation (GO:0006493)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,3-N-acetylglucosaminyltransferase activity (GO:0047223)			breast(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(166;0.155)					CTCCAGGTTCGGCCTGTTTTC	0.547																																					p.P681Q		Atlas-SNP	.											.	POMGNT1	96	.	0			c.C2042A						.						64.0	63.0	63.0					1																	46654596		876	1991	2867	SO:0001624	3_prime_UTR_variant	55624	exon23			AGGTTCGGCCTGT		CCDS531.1, CCDS57995.1	1p34.1	2014-09-17	2013-07-31		ENSG00000085998	ENSG00000085998	2.4.1.-	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	19139	protein-coding gene	gene with protein product	"""protein O-mannose beta-1,2-N-acetylglucosaminyltransferase"""	606822	"""muscle-eye-brain disease"", ""protein O-linked mannose beta1,2-N-acetylglucosaminyltransferase"""	MEB		11742540, 12788071	Standard	NM_017739		Approved	FLJ20277, MGAT1.2, LGMD2O	uc001cpg.3	Q8WZA1	OTTHUMG00000007604	ENST00000371984.3:c.*346C>A	chr1.hg19:g.46654596G>T		103.0	0.0		90.0	36.0	NM_001243766	D3DQ16|Q5VST2|Q5VST3|Q9BV55|Q9H9L8|Q9NXF9|Q9NYF7	Missense_Mutation	SNP	ENST00000371984.3	hg19	CCDS531.1	.	.	.	.	.	.	.	.	.	.	G	11.44	1.639815	0.29157	.	.	ENSG00000085998	ENST00000371992;ENST00000371986	T;T	0.37584	1.19;1.19	3.93	-2.0	0.07433	.	1.011550	0.07962	N	0.982524	T	0.19685	0.0473	.	.	.	0.09310	N	0.999997	B	0.02656	0.0	B	0.01281	0.0	T	0.23511	-1.0186	9	0.30078	T	0.28	3.4947	3.5172	0.07728	0.1295:0.5203:0.2013:0.1489	.	681	Q5VST3	.	Q	681	ENSP00000361060:P681Q;ENSP00000361054:P681Q	ENSP00000361054:P681Q	P	-	2	0	POMGNT1	46427183	0.001000	0.12720	0.008000	0.14137	0.914000	0.54420	-0.264000	0.08658	-0.347000	0.08299	-0.257000	0.10917	CCG	.	.		0.547	POMGNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020146.1	NM_017739	
NDC1	55706	hgsc.bcm.edu	37	1	54238115	54238115	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:54238115G>A	ENST00000371429.3	-	17	2446	c.1848C>T	c.(1846-1848)ccC>ccT	p.P616P	NDC1_ENST00000540001.1_3'UTR|NDC1_ENST00000234725.8_Silent_p.P501P|NDC1_ENST00000537333.1_Silent_p.P281P|SNORA58_ENST00000364133.1_RNA	NM_001168551.1|NM_018087.4	NP_001162023.1|NP_060557.3	Q9BTX1	NDC1_HUMAN	NDC1 transmembrane nucleoporin	616					mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|nuclear pore distribution (GO:0031081)|protein transport (GO:0015031)|spermatogenesis (GO:0007283)|synapsis (GO:0007129)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)										CTGAAATCCGGGGTGGTTTAC	0.388																																					p.P616P		Atlas-SNP	.											.	TMEM48	47	.	0			c.C1848T						.						116.0	115.0	116.0					1																	54238115		2203	4300	6503	SO:0001819	synonymous_variant	55706	exon17			AATCCGGGGTGGT	AL354613	CCDS583.1	1p32.3	2014-01-28	2013-05-23	2013-05-23	ENSG00000058804	ENSG00000058804			25525	protein-coding gene	gene with protein product	"""nuclear division cycle 1 homolog (S. cerevisiae)"""	610115	"""transmembrane protein 48"""	TMEM48		16779818, 12958361	Standard	NR_033142		Approved	FLJ10407, NET3		Q9BTX1	OTTHUMG00000008073	ENST00000371429.3:c.1848C>T	chr1.hg19:g.54238115G>A		157.0	0.0		155.0	58.0	NM_018087	B4DHA3|B4DQQ5|G3XA81|Q8NB76|Q9H9T6|Q9NSG3|Q9NSG4|Q9NVZ7	Silent	SNP	ENST00000371429.3	hg19	CCDS583.1																																																																																			.	.		0.388	NDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022101.1	NM_018087	
PKN2	5586	hgsc.bcm.edu	37	1	89251817	89251817	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:89251817A>G	ENST00000370521.3	+	8	1561	c.1202A>G	c.(1201-1203)aAt>aGt	p.N401S	PKN2_ENST00000370505.3_Missense_Mutation_p.N244S|PKN2_ENST00000370513.5_Missense_Mutation_p.N401S|PKN2_ENST00000316005.7_Missense_Mutation_p.N401S|PKN2_ENST00000544045.1_Missense_Mutation_p.N75S	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	401	C2.|Necessary to rescue apical junction formation. {ECO:0000250}.				apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		AAGCTCGATAATACTGTGGTT	0.368																																					p.N401S		Atlas-SNP	.											.	PKN2	109	.	0			c.A1202G						.						100.0	94.0	96.0					1																	89251817		1843	4094	5937	SO:0001583	missense	5586	exon8			TCGATAATACTGT	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1202A>G	chr1.hg19:g.89251817A>G	ENSP00000359552:p.Asn401Ser	126.0	0.0		132.0	51.0	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	hg19	CCDS714.1	.	.	.	.	.	.	.	.	.	.	A	22.8	4.340161	0.81911	.	.	ENSG00000065243	ENST00000370521;ENST00000316005;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T;T	0.21932	2.93;2.93;2.93;1.98;2.93	5.48	5.48	0.80851	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.47852	U	0.000210	T	0.40670	0.1126	M	0.80028	2.48	0.58432	D	0.999999	P;P;D;D	0.76494	0.952;0.952;0.997;0.999	P;P;D;P	0.75020	0.831;0.831;0.985;0.867	T	0.44314	-0.9336	10	0.66056	D	0.02	.	15.5726	0.76352	1.0:0.0:0.0:0.0	.	385;401;401;401	B4DTP5;E7ESL7;Q16513;B1AL79	.;.;PKN2_HUMAN;.	S	401;401;244;401;75	ENSP00000359552:N401S;ENSP00000317851:N401S;ENSP00000359536:N244S;ENSP00000359544:N401S;ENSP00000439643:N75S	ENSP00000317851:N401S	N	+	2	0	PKN2	89024405	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	8.962000	0.93254	2.080000	0.62538	0.455000	0.32223	AAT	.	.		0.368	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
SETDB1	9869	hgsc.bcm.edu	37	1	150936503	150936503	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:150936503T>G	ENST00000271640.5	+	21	3892	c.3702T>G	c.(3700-3702)aaT>aaG	p.N1234K	RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000561294.1_3'UTR|RP11-316M1.12_ENST00000561111.1_RNA|SETDB1_ENST00000368969.4_Missense_Mutation_p.N1234K|CERS2_ENST00000345896.4_5'Flank	NM_001145415.1|NM_012432.3	NP_001138887.1|NP_036564.3	Q15047	SETB1_HUMAN	SET domain, bifurcated 1	1234	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				bone development (GO:0060348)|histone H3-K9 trimethylation (GO:0036124)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(5)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12	all_lung(15;9e-35)|Lung NSC(24;3.45e-31)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.108)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|BRCA - Breast invasive adenocarcinoma(12;0.0152)|LUSC - Lung squamous cell carcinoma(543;0.211)			TTGTCCAGAATGTCTTCGTGG	0.527																																					p.N1234K		Atlas-SNP	.											.	SETDB1	204	.	0			c.T3702G						.						143.0	128.0	133.0					1																	150936503		2203	4300	6503	SO:0001583	missense	9869	exon21			CCAGAATGTCTTC	D31891	CCDS972.1, CCDS44217.1, CCDS58026.1	1q21	2013-01-23			ENSG00000143379	ENSG00000143379		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Tudor domain containing"""	10761	protein-coding gene	gene with protein product	"""tudor domain containing 21"""	604396				10343109	Standard	NM_001145415		Approved	KG1T, KIAA0067, ESET, KMT1E, TDRD21	uc001evu.2	Q15047	OTTHUMG00000035003	ENST00000271640.5:c.3702T>G	chr1.hg19:g.150936503T>G	ENSP00000271640:p.Asn1234Lys	154.0	0.0		129.0	54.0	NM_012432	A6NEW2|Q5SZD8|Q5SZD9|Q5SZE0|Q5SZE7|Q96GM9	Missense_Mutation	SNP	ENST00000271640.5	hg19	CCDS44217.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.238181	0.79800	.	.	ENSG00000143379	ENST00000271640;ENST00000368969	D;D	0.81579	-1.51;-1.51	5.65	2.08	0.27032	SET domain (3);	0.000000	0.85682	D	0.000000	T	0.63105	0.2483	N	0.02266	-0.62	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.87578	0.972;0.998	T	0.72656	-0.4227	10	0.87932	D	0	.	7.8288	0.29330	0.0:0.2964:0.0:0.7036	.	1234;1234	Q15047-3;Q15047	.;SETB1_HUMAN	K	1234	ENSP00000271640:N1234K;ENSP00000357965:N1234K	ENSP00000271640:N1234K	N	+	3	2	SETDB1	149203127	0.886000	0.30341	1.000000	0.80357	0.992000	0.81027	-0.081000	0.11321	0.934000	0.37316	0.379000	0.24179	AAT	.	.		0.527	SETDB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084717.2		
FLG	2312	hgsc.bcm.edu	37	1	152285059	152285059	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:152285059G>T	ENST00000368799.1	-	3	2338	c.2303C>A	c.(2302-2304)gCt>gAt	p.A768D	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA|FLG-AS1_ENST00000420707.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	768	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			ATGGTGACCAGCCTGTCCATG	0.562									Ichthyosis																												p.A768D		Atlas-SNP	.											.	FLG	900	.	0			c.C2303A						.						361.0	339.0	347.0					1																	152285059		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGACCAGCCTGTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2303C>A	chr1.hg19:g.152285059G>T	ENSP00000357789:p.Ala768Asp	124.0	0.0		137.0	67.0	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	hg19	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	7.512	0.654832	0.14580	.	.	ENSG00000143631	ENST00000368799	T	0.01767	4.65	2.81	2.81	0.32909	.	.	.	.	.	T	0.00875	0.0029	M	0.78223	2.4	0.09310	N	1	P	0.41232	0.743	B	0.31442	0.13	T	0.46317	-0.9200	9	0.19590	T	0.45	.	8.9131	0.35565	0.0:0.0:1.0:0.0	.	768	P20930	FILA_HUMAN	D	768	ENSP00000357789:A768D	ENSP00000357789:A768D	A	-	2	0	FLG	150551683	0.010000	0.17322	0.002000	0.10522	0.012000	0.07955	1.677000	0.37576	1.418000	0.47098	0.479000	0.44913	GCT	.	.		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204438438	204438438	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:204438438T>C	ENST00000367187.3	-	3	1049	c.493A>G	c.(493-495)Atc>Gtc	p.I165V	PIK3C2B_ENST00000424712.2_Missense_Mutation_p.I165V	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	165	Interaction with GRB2.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			GTATCCCAGATAGAAGCTCGG	0.562																																					p.I165V		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.A493G						.						55.0	65.0	62.0					1																	204438438		2203	4300	6503	SO:0001583	missense	5287	exon3			CCCAGATAGAAGC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.493A>G	chr1.hg19:g.204438438T>C	ENSP00000356155:p.Ile165Val	74.0	0.0		77.0	25.0	NM_002646	O95666|Q5SW99	Missense_Mutation	SNP	ENST00000367187.3	hg19	CCDS1446.1	.	.	.	.	.	.	.	.	.	.	T	14.55	2.570129	0.45798	.	.	ENSG00000133056	ENST00000367187;ENST00000424712	T;T	0.61392	0.11;0.15	5.14	5.14	0.70334	.	0.928229	0.09093	N	0.849583	T	0.51261	0.1664	L	0.29908	0.895	0.27710	N	0.945509	P;P	0.45078	0.85;0.766	P;B	0.46320	0.512;0.314	T	0.23904	-1.0175	10	0.10111	T	0.7	.	13.2033	0.59780	0.0:0.0:0.0:1.0	.	165;165	F5GWN5;O00750	.;P3C2B_HUMAN	V	165	ENSP00000356155:I165V;ENSP00000400561:I165V	ENSP00000356155:I165V	I	-	1	0	PIK3C2B	202705061	1.000000	0.71417	1.000000	0.80357	0.781000	0.44180	0.748000	0.26305	1.932000	0.55993	0.379000	0.24179	ATC	.	.		0.562	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
INTS7	25896	hgsc.bcm.edu	37	1	212193463	212193463	+	Splice_Site	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:212193463C>T	ENST00000366994.3	-	3	476		c.e3+1		INTS7_ENST00000440600.2_Intron|INTS7_ENST00000366993.3_Splice_Site|INTS7_ENST00000366992.3_Splice_Site|INTS7_ENST00000469606.1_Splice_Site	NM_001199811.1|NM_001199812.1|NM_015434.3	NP_001186740.1|NP_001186741.1|NP_056249.1	Q9NVH2	INT7_HUMAN	integrator complex subunit 7						cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|snRNA processing (GO:0016180)	chromosome (GO:0005694)|integrator complex (GO:0032039)				NS(1)|breast(1)|kidney(1)|large_intestine(8)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(81;0.00584)|all cancers(67;0.0318)|Epithelial(68;0.0852)		ACGGTATATACCGGAGGGTGA	0.313																																					.		Atlas-SNP	.											.	INTS7	68	.	0			c.371+1G>A						.						54.0	54.0	54.0					1																	212193463		2203	4298	6501	SO:0001630	splice_region_variant	25896	exon4			TATATACCGGAGG	AK022509	CCDS1501.1, CCDS55684.1, CCDS55683.1, CCDS55685.1	1q32.3	2008-02-05	2006-03-15	2006-03-15	ENSG00000143493	ENSG00000143493			24484	protein-coding gene	gene with protein product		611350	"""chromosome 1 open reading frame 73"""	C1orf73		16239144	Standard	NM_015434		Approved	DKFZP434B168, INT7	uc001hiw.2	Q9NVH2	OTTHUMG00000037119	ENST00000366994.3:c.371+1G>A	chr1.hg19:g.212193463C>T		154.0	0.0		216.0	112.0	NM_001199811	B4DLZ6|B7WNP6|B7WPB6|Q8N4K7|Q8WUH5|Q9H9V3|Q9NVU5|Q9UFC6|Q9UFM3	Splice_Site	SNP	ENST00000366994.3	hg19	CCDS1501.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.642815	0.87859	.	.	ENSG00000143493	ENST00000366994;ENST00000366993;ENST00000366992	.	.	.	5.21	5.21	0.72293	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.7919	0.91976	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	INTS7	210260086	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.459000	0.80802	2.431000	0.82371	0.650000	0.86243	.	.	.		0.313	INTS7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090142.1	NM_015434	Intron
FLVCR1	28982	hgsc.bcm.edu	37	1	213046020	213046020	+	Splice_Site	SNP	C	C	T	rs138069386		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:213046020C>T	ENST00000366971.4	+	3	1082	c.884C>T	c.(883-885)gCc>gTc	p.A295V		NM_014053.3	NP_054772.1	Q9Y5Y0	FLVC1_HUMAN	feline leukemia virus subgroup C cellular receptor 1	295					blood vessel development (GO:0001568)|cell death (GO:0008219)|cellular iron ion homeostasis (GO:0006879)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|erythrocyte differentiation (GO:0030218)|erythrocyte maturation (GO:0043249)|head morphogenesis (GO:0060323)|heme export (GO:0097037)|heme transport (GO:0015886)|in utero embryonic development (GO:0001701)|mitochondrial transport (GO:0006839)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|regulation of organ growth (GO:0046620)|spleen development (GO:0048536)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	heme transporter activity (GO:0015232)|transporter activity (GO:0005215)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(2)	12				OV - Ovarian serous cystadenocarcinoma(81;0.00733)|all cancers(67;0.013)|GBM - Glioblastoma multiforme(131;0.0845)|Epithelial(68;0.11)		ATATTCTCAGCCTTCAAAGAA	0.333																																					p.A295V	Esophageal Squamous(199;2235 2952 19233 26256)	Atlas-SNP	.											.	FLVCR1	31	.	0			c.C884T						.						46.0	49.0	48.0					1																	213046020		2203	4300	6503	SO:0001630	splice_region_variant	28982	exon3			TCTCAGCCTTCAA	AF118637	CCDS1510.1	1q32.3	2014-05-30			ENSG00000162769	ENSG00000162769		"""Solute carriers"""	24682	protein-coding gene	gene with protein product		609144	"""ataxia, posterior column 1, with retinitis pigmentosa"""	AXPC1		10400745, 10648427, 21070897	Standard	NM_014053		Approved	FLVCR, MFSD7B, PCA	uc001hjt.3	Q9Y5Y0	OTTHUMG00000036924	ENST00000366971.4:c.884-1C>T	chr1.hg19:g.213046020C>T		449.0	1.0		481.0	229.0	NM_014053	Q1HE16|Q86XY9|Q9NVR9	Missense_Mutation	SNP	ENST00000366971.4	hg19	CCDS1510.1	.	.	.	.	.	.	.	.	.	.	C	2.446	-0.327410	0.05350	.	.	ENSG00000162769	ENST00000366971	T	0.56776	0.44	5.43	4.52	0.55395	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.055946	0.64402	D	0.000001	T	0.13415	0.0325	N	0.00226	-1.805	0.42382	D	0.992497	B	0.10296	0.003	B	0.14023	0.01	T	0.29852	-0.9998	9	.	.	.	.	5.4954	0.16799	0.0:0.7235:0.0:0.2765	.	295	Q9Y5Y0	FLVC1_HUMAN	V	295	ENSP00000355938:A295V	.	A	+	2	0	FLVCR1	211112643	1.000000	0.71417	0.998000	0.56505	0.351000	0.29236	2.007000	0.40883	2.559000	0.86315	0.655000	0.94253	GCC	.	C|1.000;G|0.000		0.333	FLVCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089678.2	NM_014053	Missense_Mutation
NUP133	55746	hgsc.bcm.edu	37	1	229641905	229641905	+	Splice_Site	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr1:229641905C>T	ENST00000261396.3	-	2	274	c.183G>A	c.(181-183)cgG>cgA	p.R61R	NUP133_ENST00000366678.3_Splice_Site_p.R61R|RP4-613A2.1_ENST00000417605.1_RNA|NUP133_ENST00000537506.1_Splice_Site_p.R45R	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	61				R -> G (in Ref. 1; BAA91829). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TTGGTGTTCCCCTAAAGAAAA	0.338																																					p.R61R		Atlas-SNP	.											.	NUP133	111	.	0			c.G183A						.						152.0	145.0	147.0					1																	229641905		2203	4300	6503	SO:0001630	splice_region_variant	55746	exon2			TGTTCCCCTAAAG		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.183-1G>A	chr1.hg19:g.229641905C>T		77.0	0.0		122.0	45.0	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Silent	SNP	ENST00000261396.3	hg19	CCDS1579.1																																																																																			.	.		0.338	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	Silent
CMPK2	129607	hgsc.bcm.edu	37	2	6990084	6990084	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:6990084C>T	ENST00000256722.5	-	5	1246	c.1247G>A	c.(1246-1248)cGg>cAg	p.R416Q	CMPK2_ENST00000478738.1_5'UTR|CMPK2_ENST00000458098.1_Intron	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	416					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					ATTCTCCATCCGCTGGTAGGA	0.458																																					p.R416Q		Atlas-SNP	.											CMPK2,NS,carcinoma,0,1	CMPK2	30	.	0			c.G1247A						.						70.0	70.0	70.0					2																	6990084		1898	4104	6002	SO:0001583	missense	129607	exon5			TCCATCCGCTGGT		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"""cytidylate kinase 2"""	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.1247G>A	chr2.hg19:g.6990084C>T	ENSP00000256722:p.Arg416Gln	85.0	0.0		134.0	44.0	NM_207315	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	hg19	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.852651	0.91355	.	.	ENSG00000134326	ENST00000256722	T	0.41400	1.0	5.69	3.86	0.44501	.	0.000000	0.85682	D	0.000000	T	0.42359	0.1199	L	0.55990	1.75	0.80722	D	1	P	0.51653	0.947	P	0.45998	0.5	T	0.36792	-0.9733	10	0.62326	D	0.03	-23.9803	10.7854	0.46403	0.1319:0.8005:0.0:0.0676	.	416	Q5EBM0	CMPK2_HUMAN	Q	416	ENSP00000256722:R416Q	ENSP00000256722:R416Q	R	-	2	0	CMPK2	6907535	1.000000	0.71417	0.985000	0.45067	0.804000	0.45430	5.144000	0.64832	0.839000	0.34971	0.655000	0.94253	CGG	.	.		0.458	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315	
APOB	338	hgsc.bcm.edu	37	2	21231070	21231070	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:21231070G>T	ENST00000233242.1	-	26	8797	c.8670C>A	c.(8668-8670)ttC>ttA	p.F2890L		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2890					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCAATTTGTGGAAGTATTTAG	0.423																																					p.F2890L		Atlas-SNP	.											APOB,NS,carcinoma,0,1	APOB	761	.	0			c.C8670A						.						180.0	177.0	178.0					2																	21231070		2203	4299	6502	SO:0001583	missense	338	exon26			TTTGTGGAAGTAT	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.8670C>A	chr2.hg19:g.21231070G>T	ENSP00000233242:p.Phe2890Leu	137.0	0.0		143.0	50.0	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	hg19	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	G	11.36	1.614336	0.28712	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.00686	5.85	5.51	1.68	0.24146	.	0.727572	0.12466	N	0.466471	T	0.01156	0.0038	M	0.72479	2.2	0.80722	D	1	B	0.26318	0.146	B	0.19148	0.024	T	0.52931	-0.8509	10	0.52906	T	0.07	.	5.2808	0.15674	0.4271:0.0:0.4419:0.131	.	2890	P04114	APOB_HUMAN	L	2890	ENSP00000233242:F2890L	ENSP00000233242:F2890L	F	-	3	2	APOB	21084575	0.184000	0.23200	0.953000	0.39169	0.951000	0.60555	-0.299000	0.08254	0.301000	0.22738	-0.266000	0.10368	TTC	.	.		0.423	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
ABCG5	64240	hgsc.bcm.edu	37	2	44051474	44051474	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:44051474A>C	ENST00000260645.1	-	8	1141	c.1002T>G	c.(1000-1002)atT>atG	p.I334M	ABCG5_ENST00000543989.1_Intron|ABCG5_ENST00000405322.1_Missense_Mutation_p.I163M	NM_022436.2	NP_071881.1	Q9H222	ABCG5_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 5	334					ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	TTTTATGACAAATTGCTGATT	0.388																																					p.I334M		Atlas-SNP	.											.	ABCG5	72	.	0			c.T1002G						.						126.0	134.0	131.0					2																	44051474		2203	4300	6503	SO:0001583	missense	64240	exon8			ATGACAAATTGCT	T93792	CCDS1814.1	2p21	2012-03-14	2008-07-31		ENSG00000138075	ENSG00000138075		"""ATP binding cassette transporters / subfamily G"""	13886	protein-coding gene	gene with protein product	"""sterolin 1"""	605459				11099417, 11452359	Standard	NM_022436		Approved	STSL	uc002rtn.3	Q9H222	OTTHUMG00000128758	ENST00000260645.1:c.1002T>G	chr2.hg19:g.44051474A>C	ENSP00000260645:p.Ile334Met	140.0	0.0		174.0	104.0	NM_022436	Q2T9G2|Q96QZ2|Q96QZ3	Missense_Mutation	SNP	ENST00000260645.1	hg19	CCDS1814.1	.	.	.	.	.	.	.	.	.	.	A	10.96	1.499787	0.26861	.	.	ENSG00000138075	ENST00000260645;ENST00000405322	T;T	0.80653	1.79;-1.4	5.45	1.91	0.25777	.	0.867855	0.10025	N	0.725453	T	0.62588	0.2440	N	0.19112	0.55	0.80722	D	1	B;B	0.31485	0.325;0.132	B;B	0.23716	0.037;0.048	T	0.50215	-0.8854	10	0.34782	T	0.22	.	4.9726	0.14123	0.5604:0.16:0.2796:0.0	.	163;334	E7EX35;Q9H222	.;ABCG5_HUMAN	M	334;163	ENSP00000260645:I334M;ENSP00000384513:I163M	ENSP00000260645:I334M	I	-	3	3	ABCG5	43904978	1.000000	0.71417	0.083000	0.20561	0.678000	0.39670	1.711000	0.37930	0.152000	0.19188	0.533000	0.62120	ATT	.	.		0.388	ABCG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250675.1	NM_022436	
STON1	11037	hgsc.bcm.edu	37	2	48809181	48809181	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:48809181A>G	ENST00000406226.1	+	3	1604	c.1409A>G	c.(1408-1410)tAt>tGt	p.Y470C	STON1_ENST00000309835.3_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000402114.2_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000309827.2_Missense_Mutation_p.Y470C|STON1_ENST00000404752.1_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000394754.1_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000405008.1_Missense_Mutation_p.Y470C|STON1-GTF2A1L_ENST00000394751.3_Missense_Mutation_p.Y470C	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	470	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			GATGAATCCTATTATGAGAAG	0.368																																					p.Y470C		Atlas-SNP	.											.	STON1	100	.	0			c.A1409G						.						113.0	118.0	116.0					2																	48809181		2203	4300	6503	SO:0001583	missense	11037	exon3			AATCCTATTATGA	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1409A>G	chr2.hg19:g.48809181A>G	ENSP00000384615:p.Tyr470Cys	129.0	0.0		152.0	79.0	NM_001198595	A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Missense_Mutation	SNP	ENST00000406226.1	hg19	CCDS1841.1	.	.	.	.	.	.	.	.	.	.	A	3.981	-0.006517	0.07773	.	.	ENSG00000243244;ENSG00000243244;ENSG00000243244;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781;ENSG00000068781	ENST00000404752;ENST00000406226;ENST00000309835;ENST00000405008;ENST00000402114;ENST00000394754;ENST00000309827;ENST00000394751	T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.3	2.74	0.32292	Clathrin adaptor, mu subunit, C-terminal (3);	0.182483	0.49916	N	0.000127	T	0.24084	0.0583	M	0.65975	2.015	0.35933	D	0.832659	B;B;B	0.25390	0.003;0.125;0.052	B;B;B	0.27500	0.009;0.073;0.08	T	0.18209	-1.0344	10	0.72032	D	0.01	.	10.6345	0.45556	0.9092:0.0:0.0908:0.0	.	470;470;470	A8MXJ1;Q53S48;Q9Y6Q2	.;.;STON1_HUMAN	C	470	ENSP00000385273:Y470C;ENSP00000384615:Y470C;ENSP00000310969:Y470C;ENSP00000385499:Y470C;ENSP00000385701:Y470C;ENSP00000378236:Y470C;ENSP00000311493:Y470C;ENSP00000378234:Y470C	ENSP00000310969:Y470C	Y	+	2	0	STON1-GTF2A1L;STON1	48662685	1.000000	0.71417	0.228000	0.23943	0.136000	0.21042	4.173000	0.58249	0.387000	0.25024	0.533000	0.62120	TAT	.	.		0.368	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873	
C2orf42	54980	hgsc.bcm.edu	37	2	70392230	70392230	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:70392230G>A	ENST00000264434.2	-	8	1726	c.1347C>T	c.(1345-1347)acC>acT	p.T449T	C2orf42_ENST00000420306.1_Silent_p.T449T	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	449										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						TCACCTCTGGGGTATCTAAGA	0.423																																					p.T449T		Atlas-SNP	.											.	C2orf42	30	.	0			c.C1347T						.						108.0	116.0	113.0					2																	70392230		2203	4300	6503	SO:0001819	synonymous_variant	54980	exon8			CTCTGGGGTATCT	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.1347C>T	chr2.hg19:g.70392230G>A		133.0	0.0		120.0	46.0	NM_017880	D6W5G3|Q9H629	Silent	SNP	ENST00000264434.2	hg19	CCDS1899.1																																																																																			.	.		0.423	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
LRRTM1	347730	hgsc.bcm.edu	37	2	80529936	80529936	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:80529936C>T	ENST00000295057.3	-	2	1665	c.1009G>A	c.(1009-1011)Gat>Aat	p.D337N	CTNNA2_ENST00000540488.1_Intron|LRRTM1_ENST00000409148.1_Missense_Mutation_p.D337N|CTNNA2_ENST00000402739.4_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000496558.1_Intron|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000466387.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	337	LRRCT.				exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						AAGTTGCCATCGTAGCGCCCC	0.657										HNSCC(69;0.2)																											p.D337N		Atlas-SNP	.											.	LRRTM1	251	.	0			c.G1009A						.						29.0	27.0	27.0					2																	80529936		2203	4300	6503	SO:0001583	missense	347730	exon2			TGCCATCGTAGCG	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1009G>A	chr2.hg19:g.80529936C>T	ENSP00000295057:p.Asp337Asn	233.0	0.0		222.0	112.0	NM_178839	A8K397|D6W5K1|Q96DN1	Missense_Mutation	SNP	ENST00000295057.3	hg19	CCDS1966.1	.	.	.	.	.	.	.	.	.	.	C	27.0	4.789431	0.90367	.	.	ENSG00000162951	ENST00000295057;ENST00000409148	T;T	0.42900	0.96;0.96	5.32	5.32	0.75619	.	0.000000	0.85682	U	0.000000	T	0.58694	0.2140	L	0.58428	1.81	0.80722	D	1	D	0.71674	0.998	P	0.60012	0.867	T	0.56165	-0.8024	9	.	.	.	.	18.995	0.92809	0.0:1.0:0.0:0.0	.	337	Q86UE6	LRRT1_HUMAN	N	337	ENSP00000295057:D337N;ENSP00000386646:D337N	.	D	-	1	0	LRRTM1	80383447	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.808000	0.86044	2.452000	0.82932	0.655000	0.94253	GAT	.	.		0.657	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
CNNM4	26504	hgsc.bcm.edu	37	2	97426789	97426789	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:97426789G>T	ENST00000377075.2	+	1	151	c.53G>T	c.(52-54)cGc>cTc	p.R18L		NM_020184.3	NP_064569.3	Q6P4Q7	CNNM4_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 4	18					biomineral tissue development (GO:0031214)|ion transport (GO:0006811)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			breast(2)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)	20						gcccgcgggcgccTCCTCCTG	0.821																																					p.R18L		Atlas-SNP	.											.	CNNM4	48	.	0			c.G53T						.						3.0	4.0	4.0					2																	97426789		1705	3177	4882	SO:0001583	missense	26504	exon1			GCGGGCGCCTCCT	AB046812	CCDS2024.2	2q11.2	2014-08-08	2014-08-07		ENSG00000158158	ENSG00000158158			105	protein-coding gene	gene with protein product		607805	"""cyclin M4"""	ACDP4		21393841, 24194943	Standard	XM_005263914		Approved	KIAA1592	uc002swx.3	Q6P4Q7	OTTHUMG00000130532	ENST00000377075.2:c.53G>T	chr2.hg19:g.97426789G>T	ENSP00000366275:p.Arg18Leu	397.0	0.0		378.0	184.0	NM_020184	B7Z1U0|C7SQM3|C7SQM4|C7SQM5|Q53RE5|Q9H9G3|Q9HCI0|Q9NRN1	Missense_Mutation	SNP	ENST00000377075.2	hg19	CCDS2024.2	.	.	.	.	.	.	.	.	.	.	G	10.47	1.359159	0.24598	.	.	ENSG00000158158	ENST00000377075	T	0.73152	-0.72	3.54	2.62	0.31277	.	4.504510	0.01309	U	0.010559	T	0.63379	0.2506	L	0.34521	1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.52859	-0.8519	10	0.72032	D	0.01	-18.0963	7.3926	0.26919	0.0:0.1855:0.6235:0.1909	.	18	Q6P4Q7	CNNM4_HUMAN	L	18	ENSP00000366275:R18L	ENSP00000366275:R18L	R	+	2	0	CNNM4	96790516	0.998000	0.40836	0.989000	0.46669	0.034000	0.12701	2.038000	0.41184	0.776000	0.33473	0.462000	0.41574	CGC	.	.		0.821	CNNM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252954.1	NM_020184	
CNGA3	1261	hgsc.bcm.edu	37	2	98999859	98999859	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:98999859C>T	ENST00000272602.2	+	4	443	c.404C>T	c.(403-405)cCc>cTc	p.P135L	CNGA3_ENST00000436404.2_Intron|CNGA3_ENST00000393504.1_Missense_Mutation_p.P135L|CNGA3_ENST00000409937.1_Missense_Mutation_p.P139L			Q16281	CNGA3_HUMAN	cyclic nucleotide gated channel alpha 3	135					cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to magnesium ion (GO:0032026)|retinal cone cell development (GO:0046549)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|perikaryon (GO:0043204)|photoreceptor outer segment membrane (GO:0042622)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(17)|ovary(5)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	49						AGCGCCTGGCCCCTGGCCAAA	0.597																																					p.P135L		Atlas-SNP	.											CNGA3,colon,carcinoma,0,1	CNGA3	118	.	0			c.C404T						.						107.0	95.0	99.0					2																	98999859		2203	4300	6503	SO:0001583	missense	1261	exon5			CCTGGCCCCTGGC	S76069	CCDS2034.1, CCDS42719.1	2q11.2	2013-01-08			ENSG00000144191	ENSG00000144191		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2150	protein-coding gene	gene with protein product		600053		CNCG3, ACHM2		7532814, 9517456, 16382102	Standard	NM_001298		Approved	CCNC1, CCNCa, CNG3	uc002syt.3	Q16281	OTTHUMG00000130561	ENST00000272602.2:c.404C>T	chr2.hg19:g.98999859C>T	ENSP00000272602:p.Pro135Leu	107.0	0.0		106.0	43.0	NM_001298	E9PF93|Q4VAP7|Q53RD2|Q6ZNA7|Q9UP64	Missense_Mutation	SNP	ENST00000272602.2	hg19	CCDS2034.1	.	.	.	.	.	.	.	.	.	.	C	16.00	2.999736	0.54147	.	.	ENSG00000144191	ENST00000393504;ENST00000272602;ENST00000409937	D;D;D	0.97620	-4.39;-4.39;-4.46	4.76	4.76	0.60689	.	0.450627	0.22121	N	0.064324	D	0.95268	0.8465	L	0.47716	1.5	0.44523	D	0.997477	D;B	0.54047	0.964;0.001	P;B	0.45310	0.476;0.001	D	0.94006	0.7280	10	0.29301	T	0.29	.	14.7937	0.69863	0.0:1.0:0.0:0.0	.	139;135	E9PF93;Q16281	.;CNGA3_HUMAN	L	135;135;139	ENSP00000377140:P135L;ENSP00000272602:P135L;ENSP00000386761:P139L	ENSP00000272602:P135L	P	+	2	0	CNGA3	98366291	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.449000	0.66619	2.483000	0.83821	0.561000	0.74099	CCC	.	.		0.597	CNGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252986.1	NM_001298	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131801932	131801932	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:131801932G>A	ENST00000326016.5	+	12	2179	c.1660G>A	c.(1660-1662)Gtg>Atg	p.V554M	ARHGEF4_ENST00000409303.1_Missense_Mutation_p.V494M|ARHGEF4_ENST00000355771.3_Missense_Mutation_p.V483M|ARHGEF4_ENST00000392953.3_Missense_Mutation_p.V554M|ARHGEF4_ENST00000525839.1_Missense_Mutation_p.V554M|ARHGEF4_ENST00000428230.2_Intron	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	554	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		CGGCCTGGAGGTGGTGGACCT	0.657																																					p.V554M		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.G1660A						.						67.0	52.0	57.0					2																	131801932		2197	4300	6497	SO:0001583	missense	50649	exon12			CTGGAGGTGGTGG	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1660G>A	chr2.hg19:g.131801932G>A	ENSP00000316845:p.Val554Met	287.0	0.0		233.0	13.0	NM_032995	Q9HDC6|Q9UPP0	Missense_Mutation	SNP	ENST00000326016.5	hg19	CCDS2165.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.69|17.69	3.452100|3.452100	0.63290|0.63290	.|.	.|.	ENSG00000136002|ENSG00000136002	ENST00000532720|ENST00000326016;ENST00000392953;ENST00000525839;ENST00000409303;ENST00000355771	.|D;D;D;D;D	.|0.91068	.|-2.78;-2.78;-2.78;-2.78;-2.78	5.2|5.2	0.445|0.445	0.16597|0.16597	.|Pleckstrin homology-type (1);Pleckstrin homology domain (3);	.|0.254015	.|0.33180	.|N	.|0.005191	D|D	0.91938|0.91938	0.7447|0.7447	M|M	0.80982|0.80982	2.52|2.52	0.43304|0.43304	D|D	0.995301|0.995301	.|P;P;P	.|0.51653	.|0.943;0.947;0.943	.|P;P;P	.|0.58172	.|0.834;0.732;0.834	D|D	0.88392|0.88392	0.3009|0.3009	5|10	.|0.87932	.|D	.|0	.|.	3.3375|3.3375	0.07106|0.07106	0.1082:0.3074:0.4285:0.156|0.1082:0.3074:0.4285:0.156	.|.	.|494;554;554	.|E9PEM0;Q9NR80-4;Q9NR80	.|.;.;ARHG4_HUMAN	D|M	170|554;554;554;494;483	.|ENSP00000316845:V554M;ENSP00000376680:V554M;ENSP00000432267:V554M;ENSP00000387285:V494M;ENSP00000348017:V483M	.|ENSP00000316845:V554M	G|V	+|+	2|1	0|0	ARHGEF4|ARHGEF4	131518402|131518402	1.000000|1.000000	0.71417|0.71417	0.004000|0.004000	0.12327|0.12327	0.829000|0.829000	0.46940|0.46940	2.639000|2.639000	0.46570|0.46570	0.164000|0.164000	0.19529|0.19529	0.561000|0.561000	0.74099|0.74099	GGT|GTG	.	.		0.657	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
MAP3K19	80122	hgsc.bcm.edu	37	2	135741259	135741259	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:135741259C>A	ENST00000375845.3	-	8	3239	c.3209G>T	c.(3208-3210)gGa>gTa	p.G1070V	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.G1087V|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Missense_Mutation_p.G252V|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.G957V	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1070	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										GCCGTAGGCTCCCTTTCCAAG	0.468																																					p.G1070V		Atlas-SNP	.											.	.	.	.	0			c.G3209T						.						91.0	95.0	94.0					2																	135741259		2203	4300	6503	SO:0001583	missense	80122	exon8			TAGGCTCCCTTTC	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3209G>T	chr2.hg19:g.135741259C>A	ENSP00000365005:p.Gly1070Val	182.0	0.0		222.0	37.0	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689516	0.88735	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392915;ENST00000437365	D;D;D;T;D	0.85339	-1.97;-1.97;-1.97;-0.05;-1.97	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.48767	D	0.000172	D	0.96334	0.8804	H	0.99357	4.53	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;1.0	D	0.97543	1.0087	10	0.87932	D	0	.	20.303	0.98618	0.0:1.0:0.0:0.0	.	957;1087;252;1070	Q56UN5-3;A8MWG7;Q56UN5-5;Q56UN5	.;.;.;YSK4_HUMAN	V	1070;957;252;1087;460	ENSP00000365005:G1070V;ENSP00000351140:G957V;ENSP00000365004:G252V;ENSP00000376647:G1087V;ENSP00000392827:G460V	ENSP00000351140:G957V	G	-	2	0	YSK4	135457729	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.101000	0.76997	2.806000	0.96561	0.549000	0.68633	GGA	.	.		0.468	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
MAP3K19	80122	hgsc.bcm.edu	37	2	135741322	135741322	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:135741322G>C	ENST00000375845.3	-	8	3176	c.3146C>G	c.(3145-3147)tCt>tGt	p.S1049C	MAP3K19_ENST00000392918.3_Missense_Mutation_p.S231C|MAP3K19_ENST00000392915.1_Missense_Mutation_p.S1066C|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000375844.3_Missense_Mutation_p.S231C|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.S936C	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	1049							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										ACTATTTTCAGAAAATATCTT	0.388																																					p.S1049C		Atlas-SNP	.											YSK4_ENST00000375845,colon,carcinoma,0,2	.	.	.	0			c.C3146G						.						96.0	98.0	97.0					2																	135741322		2203	4300	6503	SO:0001583	missense	80122	exon8			TTTTCAGAAAATA	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.3146C>G	chr2.hg19:g.135741322G>C	ENSP00000365005:p.Ser1049Cys	168.0	0.0		210.0	39.0	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	hg19	CCDS2176.2	.	.	.	.	.	.	.	.	.	.	G	12.91	2.080809	0.36758	.	.	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000375844;ENST00000392918;ENST00000392915;ENST00000437365	T;T;T;T;T;T	0.74632	-0.75;-0.74;-0.63;-0.24;0.89;-0.86	5.91	5.04	0.67666	Protein kinase-like domain (1);	0.136119	0.34223	N	0.004151	D	0.83723	0.5316	M	0.68952	2.095	0.80722	D	1	D;D;D;P;D	0.89917	0.996;0.969;1.0;0.933;0.988	P;P;D;P;P	0.66497	0.855;0.708;0.944;0.614;0.635	D	0.85364	0.1109	10	0.62326	D	0.03	.	14.9815	0.71313	0.0:0.0:0.8574:0.1426	.	936;231;1066;231;1049	Q56UN5-3;Q56UN5-4;A8MWG7;Q56UN5-5;Q56UN5	.;.;.;.;YSK4_HUMAN	C	1049;936;231;231;1066;439	ENSP00000365005:S1049C;ENSP00000351140:S936C;ENSP00000365004:S231C;ENSP00000376650:S231C;ENSP00000376647:S1066C;ENSP00000392827:S439C	ENSP00000351140:S936C	S	-	2	0	YSK4	135457792	1.000000	0.71417	1.000000	0.80357	0.120000	0.20174	3.272000	0.51616	1.507000	0.48752	-0.287000	0.09952	TCT	.	.		0.388	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
KIF5C	3800	hgsc.bcm.edu	37	2	149864490	149864490	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:149864490A>G	ENST00000435030.1	+	23	2827	c.2459A>G	c.(2458-2460)gAc>gGc	p.D820G	KIF5C_ENST00000414838.2_Missense_Mutation_p.D725G|KIF5C_ENST00000397413.1_Missense_Mutation_p.D588G|KIF5C_ENST00000464066.1_3'UTR			O60282	KIF5C_HUMAN	kinesin family member 5C	820					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		GTGGAGTTGGACAACGATGAT	0.527																																					p.D820G		Atlas-SNP	.											.	KIF5C	166	.	0			c.A2459G						.						70.0	75.0	74.0					2																	149864490		1941	4156	6097	SO:0001583	missense	3800	exon23			AGTTGGACAACGA	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2459A>G	chr2.hg19:g.149864490A>G	ENSP00000393379:p.Asp820Gly	78.0	0.0		75.0	36.0	NM_004522	O95079|Q2YDC5	Missense_Mutation	SNP	ENST00000435030.1	hg19		.	.	.	.	.	.	.	.	.	.	A	21.3	4.124208	0.77436	.	.	ENSG00000168280	ENST00000435030;ENST00000414838;ENST00000334436;ENST00000397413	D;D;D	0.86865	-2.18;-2.18;-2.18	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.81513	0.4838	.	.	.	0.58432	D	0.999998	B;B	0.20368	0.044;0.022	B;B	0.22386	0.039;0.03	T	0.76236	-0.3033	8	.	.	.	.	15.7543	0.78013	1.0:0.0:0.0:0.0	.	820;128	O60282;Q59GB8	KIF5C_HUMAN;.	G	820;725;723;588	ENSP00000393379:D820G;ENSP00000410115:D725G;ENSP00000380560:D588G	.	D	+	2	0	KIF5C	149572736	1.000000	0.71417	1.000000	0.80357	0.657000	0.38888	9.339000	0.96797	2.134000	0.65973	0.460000	0.39030	GAC	.	.		0.527	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
LY75	4065	hgsc.bcm.edu	37	2	160755561	160755561	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:160755561G>T	ENST00000263636.4	-	2	131	c.104C>A	c.(103-105)cCc>cAc	p.P35H	LY75_ENST00000554112.1_Missense_Mutation_p.P35H|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.P35H|LY75_ENST00000553424.1_Missense_Mutation_p.P35H|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.P35H	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	35	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GATGGTGAAGGGGTCATTAGC	0.493																																					p.P35H		Atlas-SNP	.											.	LY75	151	.	0			c.C104A						.						155.0	150.0	152.0					2																	160755561		2203	4300	6503	SO:0001583	missense	4065	exon2			GTGAAGGGGTCAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.104C>A	chr2.hg19:g.160755561G>T	ENSP00000263636:p.Pro35His	61.0	0.0		46.0	31.0	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	19.98	3.927402	0.73327	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	6.02	6.02	0.97574	Ricin B-related lectin (1);Ricin B lectin (2);	0.000000	0.34959	N	0.003556	T	0.63058	0.2479	M	0.72479	2.2	0.33698	D	0.61414	D;D;D	0.69078	0.997;0.991;0.997	P;P;P	0.58970	0.849;0.621;0.847	T	0.70249	-0.4924	10	0.62326	D	0.03	-2.3155	20.5407	0.99260	0.0:0.0:1.0:0.0	.	35;35;35	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	H	35	ENSP00000451511:P35H;ENSP00000451446:P35H;ENSP00000263636:P35H;ENSP00000423463:P35H;ENSP00000421035:P35H	ENSP00000423463:P35H	P	-	2	0	LY75;LY75-CD302	160463807	0.671000	0.27521	0.999000	0.59377	0.679000	0.39708	3.447000	0.52936	2.865000	0.98341	0.655000	0.94253	CCC	.	.		0.493	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
FRZB	2487	hgsc.bcm.edu	37	2	183731006	183731006	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:183731006T>C	ENST00000295113.4	-	1	884	c.275A>G	c.(274-276)tAc>tGc	p.Y92C		NM_001463.3	NP_001454.2	Q92765	SFRP3_HUMAN	frizzled-related protein	92	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|cochlea morphogenesis (GO:0090103)|convergent extension involved in organogenesis (GO:0060029)|epithelium development (GO:0060429)|gonad development (GO:0008406)|mammary gland involution (GO:0060056)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell development (GO:0010721)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of hepatocyte differentiation (GO:0070367)|negative regulation of Wnt signaling pathway (GO:0030178)|neural crest cell differentiation (GO:0014033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of fat cell differentiation (GO:0045600)|skeletal system development (GO:0001501)|somite development (GO:0061053)|vasculature development (GO:0001944)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(117;0.109)|Epithelial(96;0.231)			GATGGGCGCGTACATGGCACA	0.612																																					p.Y92C		Atlas-SNP	.											.	FRZB	42	.	0			c.A275G						.						91.0	80.0	84.0					2																	183731006		2203	4300	6503	SO:0001583	missense	2487	exon1			GGCGCGTACATGG	U24163	CCDS2286.1	2q32.1	2013-09-19			ENSG00000162998	ENSG00000162998		"""Secreted frizzled-related proteins"""	3959	protein-coding gene	gene with protein product		605083				8824257, 9118218	Standard	NM_001463		Approved	FRZB-PEN, FRZB1, SRFP3, FRP-3, SFRP3, FRE, FRITZ, FRZB-1, FZRB, hFIZ	uc002upa.2	Q92765	OTTHUMG00000132597	ENST00000295113.4:c.275A>G	chr2.hg19:g.183731006T>C	ENSP00000295113:p.Tyr92Cys	91.0	0.0		90.0	44.0	NM_001463	O00181|Q99686	Missense_Mutation	SNP	ENST00000295113.4	hg19	CCDS2286.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.332653	0.81801	.	.	ENSG00000162998	ENST00000295113	T	0.76968	-1.06	4.78	4.78	0.61160	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.90913	0.7144	H	0.94771	3.58	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.93403	0.6762	10	0.87932	D	0	.	14.463	0.67465	0.0:0.0:0.0:1.0	.	92	Q92765	SFRP3_HUMAN	C	92	ENSP00000295113:Y92C	ENSP00000295113:Y92C	Y	-	2	0	FRZB	183439251	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.726000	0.84824	1.992000	0.58205	0.379000	0.24179	TAC	.	.		0.612	FRZB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255808.1	NM_001463	
PGAP1	80055	hgsc.bcm.edu	37	2	197761869	197761869	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:197761869C>A	ENST00000354764.4	-	7	1027	c.913G>T	c.(913-915)Gct>Tct	p.A305S	PGAP1_ENST00000409475.1_Missense_Mutation_p.A305S|PGAP1_ENST00000485830.1_5'UTR|PGAP1_ENST00000409188.1_Missense_Mutation_p.A263S	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	305					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TTAGTATCAGCATCAATAAGA	0.249																																					p.A305S		Atlas-SNP	.											.	PGAP1	84	.	0			c.G913T						.						34.0	33.0	33.0					2																	197761869		2190	4279	6469	SO:0001583	missense	80055	exon7			TATCAGCATCAAT		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.913G>T	chr2.hg19:g.197761869C>A	ENSP00000346809:p.Ala305Ser	834.0	0.0		862.0	384.0	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	hg19	CCDS2318.1	.	.	.	.	.	.	.	.	.	.	C	12.57	1.976249	0.34848	.	.	ENSG00000197121	ENST00000422382;ENST00000354764;ENST00000409475;ENST00000409188;ENST00000374738	.	.	.	4.65	4.65	0.58169	.	0.270973	0.38436	N	0.001687	T	0.17619	0.0423	N	0.08118	0	0.27349	N	0.9563	B;B;B	0.32467	0.255;0.372;0.118	B;B;B	0.27796	0.016;0.083;0.054	T	0.07366	-1.0776	9	0.09338	T	0.73	-16.2658	15.8224	0.78667	0.0:1.0:0.0:0.0	.	263;305;305	B4DYY6;Q75T13-3;Q75T13	.;.;PGAP1_HUMAN	S	85;305;305;263;85	.	ENSP00000346809:A305S	A	-	1	0	PGAP1	197470114	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.411000	0.44600	2.576000	0.86940	0.563000	0.77884	GCT	.	.		0.249	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
DNER	92737	hgsc.bcm.edu	37	2	230312120	230312120	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:230312120G>A	ENST00000341772.4	-	8	1532	c.1398C>T	c.(1396-1398)gcC>gcT	p.A466A		NM_139072.3	NP_620711.3	Q8NFT8	DNER_HUMAN	delta/notch-like EGF repeat containing	466	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				central nervous system development (GO:0007417)|endocytosis (GO:0006897)|glial cell differentiation (GO:0010001)|neuron migration (GO:0001764)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|skeletal muscle fiber development (GO:0048741)|synapse assembly (GO:0007416)	dendrite (GO:0030425)|early endosome (GO:0005769)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|clathrin binding (GO:0030276)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	63		all_lung(227;0.00413)|Renal(207;0.0113)|Lung NSC(271;0.0211)|all_hematologic(139;0.105)|Acute lymphoblastic leukemia(138;0.175)		Epithelial(121;1.4e-11)|all cancers(144;7.7e-09)|LUSC - Lung squamous cell carcinoma(224;0.034)|Lung(119;0.0375)		CAATAAGCTGGGCACAGGTCG	0.627																																					p.A466A		Atlas-SNP	.											.	DNER	129	.	0			c.C1398T						.						51.0	47.0	48.0					2																	230312120		2203	4300	6503	SO:0001819	synonymous_variant	92737	exon8			AAGCTGGGCACAG	AY358891	CCDS33390.1	2q36.3	2006-10-26			ENSG00000187957	ENSG00000187957			24456	protein-coding gene	gene with protein product		607299				11950833, 11997712	Standard	NM_139072		Approved	UNQ26, bet	uc002vpv.3	Q8NFT8	OTTHUMG00000153637	ENST00000341772.4:c.1398C>T	chr2.hg19:g.230312120G>A		394.0	0.0		372.0	166.0	NM_139072	A6NP39|Q53R88|Q53TP7|Q53TQ5|Q8IYT0|Q8TB42|Q9NTF1|Q9UDM2	Silent	SNP	ENST00000341772.4	hg19	CCDS33390.1																																																																																			.	.		0.627	DNER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331902.1	NM_139072	
TRPM8	79054	hgsc.bcm.edu	37	2	234846104	234846104	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:234846104C>A	ENST00000324695.4	+	4	339	c.299C>A	c.(298-300)aCc>aAc	p.T100N	TRPM8_ENST00000409625.1_Missense_Mutation_p.T23N|TRPM8_ENST00000433712.2_5'UTR|TRPM8_ENST00000355722.4_Missense_Mutation_p.T50N	NM_024080.4	NP_076985.4	Q7Z2W7	TRPM8_HUMAN	transient receptor potential cation channel, subfamily M, member 8	100					calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|protein homotetramerization (GO:0051289)|protein homotrimerization (GO:0070207)|response to cold (GO:0009409)|thermoception (GO:0050955)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			breast(5)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(2)|lung(27)|prostate(2)|skin(7)|stomach(2)	66		Breast(86;0.00205)|Renal(207;0.00694)|all_lung(227;0.0129)|Lung NSC(271;0.0408)|all_hematologic(139;0.0753)|Acute lymphoblastic leukemia(138;0.224)		Epithelial(121;1.19e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000139)|Lung(119;0.00758)|LUSC - Lung squamous cell carcinoma(224;0.0108)	Menthol(DB00825)	GAATTTCCTACCGACGCCTTT	0.473																																					p.T100N		Atlas-SNP	.											.	TRPM8	146	.	0			c.C299A						.						154.0	150.0	151.0					2																	234846104		2203	4300	6503	SO:0001583	missense	79054	exon4			TTCCTACCGACGC	AC005538	CCDS33407.1	2q37	2011-12-14			ENSG00000144481	ENSG00000144481		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17961	protein-coding gene	gene with protein product		606678				16382100	Standard	NM_024080		Approved		uc002vvh.3	Q7Z2W7	OTTHUMG00000059129	ENST00000324695.4:c.299C>A	chr2.hg19:g.234846104C>A	ENSP00000323926:p.Thr100Asn	152.0	0.0		163.0	73.0	NM_024080	A0AVG2|Q3YFM7|Q6QNH9|Q8TAC3|Q8TDX8|Q9BVK1	Missense_Mutation	SNP	ENST00000324695.4	hg19	CCDS33407.1	.	.	.	.	.	.	.	.	.	.	C	19.53	3.844452	0.71488	.	.	ENSG00000144481	ENST00000324695;ENST00000355722;ENST00000409625	T;T;T	0.70164	-0.46;-0.46;-0.46	5.68	5.68	0.88126	.	0.145975	0.47093	D	0.000247	D	0.86414	0.5927	M	0.92784	3.345	0.80722	D	1	D;D	0.76494	0.987;0.999	D;D	0.80764	0.96;0.994	D	0.89215	0.3567	10	0.87932	D	0	-23.5913	18.3402	0.90303	0.0:1.0:0.0:0.0	.	50;100	Q7Z2W7-2;Q7Z2W7	.;TRPM8_HUMAN	N	100;50;23	ENSP00000323926:T100N;ENSP00000347956:T50N;ENSP00000386771:T23N	ENSP00000323926:T100N	T	+	2	0	TRPM8	234510843	1.000000	0.71417	0.623000	0.29173	0.371000	0.29859	6.749000	0.74883	2.676000	0.91093	0.591000	0.81541	ACC	.	.		0.473	TRPM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131005.4	NM_024080	
CAPN7	23473	hgsc.bcm.edu	37	3	15262371	15262371	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:15262371G>C	ENST00000253693.2	+	5	774	c.521G>C	c.(520-522)aGa>aCa	p.R174T		NM_014296.2	NP_055111.1	Q9Y6W3	CAN7_HUMAN	calpain 7	174					positive regulation of epithelial cell migration (GO:0010634)|self proteolysis (GO:0097264)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|endopeptidase activity (GO:0004175)|MIT domain binding (GO:0090541)			breast(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|skin(2)	22						CCTCCAGTGAGAGCACATTTT	0.468																																					p.R174T		Atlas-SNP	.											.	CAPN7	63	.	0			c.G521C						.						102.0	94.0	97.0					3																	15262371		2203	4300	6503	SO:0001583	missense	23473	exon5			CAGTGAGAGCACA	AB028639	CCDS2624.1	3p24	2008-07-18			ENSG00000131375	ENSG00000131375			1484	protein-coding gene	gene with protein product	"""calpain like protease"", ""homolog of Aspergillus Nidulans PALB"""	606400				8163008, 10051333	Standard	NM_014296		Approved	PalBH	uc003bzn.3	Q9Y6W3	OTTHUMG00000129863	ENST00000253693.2:c.521G>C	chr3.hg19:g.15262371G>C	ENSP00000253693:p.Arg174Thr	317.0	0.0		320.0	72.0	NM_014296		Missense_Mutation	SNP	ENST00000253693.2	hg19	CCDS2624.1	.	.	.	.	.	.	.	.	.	.	G	4.322	0.059138	0.08339	.	.	ENSG00000131375	ENST00000253693	D	0.85955	-2.05	5.79	3.95	0.45737	.	0.526289	0.21304	N	0.076748	T	0.80808	0.4694	M	0.72118	2.19	0.46078	D	0.99885	B	0.13594	0.008	B	0.06405	0.002	T	0.72064	-0.4403	10	0.10636	T	0.68	-17.5957	9.775	0.40614	0.0744:0.1392:0.7864:0.0	.	174	Q9Y6W3	CAN7_HUMAN	T	174	ENSP00000253693:R174T	ENSP00000253693:R174T	R	+	2	0	CAPN7	15237375	1.000000	0.71417	0.755000	0.31263	0.065000	0.16274	3.187000	0.50950	1.470000	0.48102	0.555000	0.69702	AGA	.	.		0.468	CAPN7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252105.2	NM_014296	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266101	41266101	+	Missense_Mutation	SNP	C	C	G	rs121913416|rs121913400		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:41266101C>G	ENST00000349496.5	+	3	378	c.98C>G	c.(97-99)tCt>tGt	p.S33C	CTNNB1_ENST00000453024.1_Missense_Mutation_p.S26C|CTNNB1_ENST00000405570.1_Missense_Mutation_p.S33C|CTNNB1_ENST00000396183.3_Missense_Mutation_p.S33C|CTNNB1_ENST00000396185.3_Missense_Mutation_p.S33C	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	33			Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> F (in PTR, MDB and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:10666372}.|S -> L (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|S -> Y (in colorectal cancer and PTR; enhances transactivation of target genes). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:9065402}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.S33C(168)|p.S33F(97)|p.S33Y(60)|p.A5_A80del(53)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.S33L(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S33N(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.M14_S45del(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.S29_H36del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.S33_S37del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.D32_H36>D(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TACCTGGACTCTGGAATCCAT	0.488	S33C(SKMEL1_SKIN)|S33F(SW1573_LUNG)|S33Y(SW48_LARGE_INTESTINE)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.S33C	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,0,359	CTNNB1	4904	.	468	Substitution - Missense(331)|Deletion - In frame(111)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(165)|central_nervous_system(82)|large_intestine(40)|endometrium(37)|stomach(32)|skin(21)|ovary(20)|pituitary(19)|pancreas(12)|lung(7)|biliary_tract(6)|soft_tissue(4)|bone(4)|breast(3)|prostate(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|parathyroid(2)|small_intestine(2)|thyroid(1)|NS(1)|urinary_tract(1)|adrenal_gland(1)	c.C98G						.						92.0	77.0	82.0					3																	41266101		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	TGGACTCTGGAAT	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.98C>G	chr3.hg19:g.41266101C>G	ENSP00000344456:p.Ser33Cys	160.0	0.0		148.0	71.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.381716	0.82792	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.51071	0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72;0.72	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.72053	0.3413	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74188	-0.3746	10	0.87932	D	0	-10.7796	19.9596	0.97236	0.0:1.0:0.0:0.0	.	33	P35222	CTNB1_HUMAN	C	26;33;33;33;33;26;33;33;33	ENSP00000400508:S26C;ENSP00000385604:S33C;ENSP00000412219:S33C;ENSP00000379486:S33C;ENSP00000344456:S33C;ENSP00000411226:S26C;ENSP00000379488:S33C;ENSP00000409302:S33C;ENSP00000401599:S33C	ENSP00000344456:S33C	S	+	2	0	CTNNB1	41241105	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.726000	0.93360	0.655000	0.94253	TCT	.	.		0.488	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
ROBO1	6091	hgsc.bcm.edu	37	3	78701014	78701014	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:78701014C>T	ENST00000464233.1	-	19	2793	c.2680G>A	c.(2680-2682)Gtg>Atg	p.V894M	ROBO1_ENST00000467549.1_Missense_Mutation_p.V858M|ROBO1_ENST00000495273.1_Missense_Mutation_p.V858M|ROBO1_ENST00000436010.2_Missense_Mutation_p.V855M	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	894					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GGCTGCTTCACCACATCTGAA	0.502																																					p.V894M		Atlas-SNP	.											.	ROBO1	833	.	0			c.G2680A						.						132.0	132.0	132.0					3																	78701014		2044	4192	6236	SO:0001583	missense	6091	exon19			GCTTCACCACATC	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.2680G>A	chr3.hg19:g.78701014C>T	ENSP00000420321:p.Val894Met	130.0	0.0		122.0	47.0	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Missense_Mutation	SNP	ENST00000464233.1	hg19	CCDS54611.1	.	.	.	.	.	.	.	.	.	.	C	18.57	3.652506	0.67472	.	.	ENSG00000169855	ENST00000436010;ENST00000398412;ENST00000464233;ENST00000495273;ENST00000467549;ENST00000398414	T;T;T;T	0.63417	-0.02;-0.04;-0.04;0.03	5.98	5.98	0.97165	.	0.000000	0.85682	D	0.000000	T	0.79873	0.4521	M	0.71036	2.16	0.80722	D	1	D;D;D;D;D	0.89917	0.999;1.0;1.0;1.0;1.0	D;D;D;D;D	0.83275	0.996;0.993;0.979;0.993;0.996	T	0.77183	-0.2681	9	.	.	.	.	20.4434	0.99119	0.0:1.0:0.0:0.0	.	858;894;858;858;855	Q9Y6N7-3;Q9Y6N7;B2RXI1;E9PD49;Q9Y6N7-4	.;ROBO1_HUMAN;.;.;.	M	855;858;894;858;858;898	ENSP00000406043:V855M;ENSP00000420321:V894M;ENSP00000420637:V858M;ENSP00000417992:V858M	.	V	-	1	0	ROBO1	78783704	1.000000	0.71417	0.969000	0.41365	0.004000	0.04260	7.818000	0.86416	2.838000	0.97847	0.655000	0.94253	GTG	.	.		0.502	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
MYH15	22989	hgsc.bcm.edu	37	3	108140007	108140007	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:108140007C>T	ENST00000273353.3	-	29	3873	c.3817G>A	c.(3817-3819)Gca>Aca	p.A1273T		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1273						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						TCTAGCTTTGCAGTTGCTTCA	0.453																																					p.A1273T		Atlas-SNP	.											.	MYH15	223	.	0			c.G3817A						.						232.0	213.0	219.0					3																	108140007		1942	4146	6088	SO:0001583	missense	22989	exon29			GCTTTGCAGTTGC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3817G>A	chr3.hg19:g.108140007C>T	ENSP00000273353:p.Ala1273Thr	39.0	0.0		51.0	23.0	NM_014981		Missense_Mutation	SNP	ENST00000273353.3	hg19	CCDS43127.1	.	.	.	.	.	.	.	.	.	.	C	0.707	-0.788757	0.02884	.	.	ENSG00000144821	ENST00000273353	T	0.77750	-1.12	4.72	1.89	0.25635	Myosin tail (1);	.	.	.	.	T	0.54208	0.1844	N	0.10972	0.075	0.20489	N	0.999891	B	0.06786	0.001	B	0.14023	0.01	T	0.35400	-0.9790	9	0.08599	T	0.76	.	8.0084	0.30338	0.0:0.6028:0.0:0.3972	.	1273	Q9Y2K3	MYH15_HUMAN	T	1273	ENSP00000273353:A1273T	ENSP00000273353:A1273T	A	-	1	0	MYH15	109622697	0.000000	0.05858	0.985000	0.45067	0.612000	0.37316	-0.324000	0.07986	0.609000	0.30018	0.655000	0.94253	GCA	.	.		0.453	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
AMOTL2	51421	hgsc.bcm.edu	37	3	134080568	134080568	+	Missense_Mutation	SNP	C	C	A	rs543579880		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:134080568C>A	ENST00000422605.2	-	6	1527	c.1361G>T	c.(1360-1362)cGt>cTt	p.R454L	AMOTL2_ENST00000249883.5_Missense_Mutation_p.R454L|AMOTL2_ENST00000513145.1_Missense_Mutation_p.R454L|AMOTL2_ENST00000514516.1_Missense_Mutation_p.R512L			Q9Y2J4	AMOL2_HUMAN	angiomotin like 2	454					hippo signaling (GO:0035329)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|tight junction (GO:0005923)				endometrium(8)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	19						CAGCTCGGCACGCCGCCGCTG	0.647																																					p.R454L		Atlas-SNP	.											.	AMOTL2	52	.	0			c.G1361T						.						11.0	12.0	12.0					3																	134080568		2197	4283	6480	SO:0001583	missense	51421	exon6			TCGGCACGCCGCC	AF175966	CCDS33860.1, CCDS63783.1, CCDS63784.1	3q21-q22	2008-07-18			ENSG00000114019	ENSG00000114019			17812	protein-coding gene	gene with protein product	"""Leman coiled-coil protein"", ""angiomotin-like protein 2"""	614658					Standard	NM_016201		Approved	LCCP	uc003eqg.1	Q9Y2J4	OTTHUMG00000159777	ENST00000422605.2:c.1361G>T	chr3.hg19:g.134080568C>A	ENSP00000409999:p.Arg454Leu	68.0	0.0		55.0	27.0	NM_016201	A8K6F1|B7Z5Q1|E9PHW3|Q53EP1|Q96F99|Q9UKB4	Missense_Mutation	SNP	ENST00000422605.2	hg19		.	.	.	.	.	.	.	.	.	.	C	19.79	3.892906	0.72524	.	.	ENSG00000114019	ENST00000249883;ENST00000422605;ENST00000514516;ENST00000513145	T;T;T;T	0.24151	1.87;1.87;1.87;1.87	5.32	4.43	0.53597	.	0.053091	0.85682	D	0.000000	T	0.29749	0.0743	L	0.53249	1.67	0.58432	D	0.99999	P;P;P	0.44690	0.841;0.841;0.753	B;B;B	0.42882	0.401;0.401;0.325	T	0.11372	-1.0590	10	0.66056	D	0.02	-15.3774	14.5284	0.67905	0.0:0.9287:0.0:0.0713	.	454;454;512	Q9Y2J4-3;Q9Y2J4-2;E9PHW3	.;.;.	L	454;454;512;454	ENSP00000249883:R454L;ENSP00000409999:R454L;ENSP00000424765:R512L;ENSP00000425475:R454L	ENSP00000249883:R454L	R	-	2	0	AMOTL2	135563258	0.920000	0.31207	0.854000	0.33618	0.991000	0.79684	1.947000	0.40293	1.447000	0.47661	0.563000	0.77884	CGT	.	.		0.647	AMOTL2-014	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000358149.1	NM_016201	
LSG1	55341	hgsc.bcm.edu	37	3	194369508	194369508	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:194369508A>C	ENST00000265245.5	-	11	1759	c.1445T>G	c.(1444-1446)gTt>gGt	p.V482G	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	482					GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		AGCTTCTAAAACATGTCTTGG	0.463																																					p.V482G		Atlas-SNP	.											.	LSG1	38	.	0			c.T1445G						.						161.0	144.0	149.0					3																	194369508		2203	4300	6503	SO:0001583	missense	55341	exon11			TCTAAAACATGTC		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.1445T>G	chr3.hg19:g.194369508A>C	ENSP00000265245:p.Val482Gly	109.0	0.0		98.0	38.0	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Missense_Mutation	SNP	ENST00000265245.5	hg19	CCDS33922.1	.	.	.	.	.	.	.	.	.	.	A	26.8	4.767811	0.90020	.	.	ENSG00000041802	ENST00000265245	T	0.16897	2.31	5.79	5.79	0.91817	.	0.122706	0.53938	D	0.000044	T	0.42562	0.1208	M	0.85462	2.755	0.80722	D	1	D	0.59357	0.985	D	0.65323	0.934	T	0.44559	-0.9320	10	0.66056	D	0.02	.	10.4659	0.44607	0.9278:0.0:0.0722:0.0	.	482	Q9H089	LSG1_HUMAN	G	482	ENSP00000265245:V482G	ENSP00000265245:V482G	V	-	2	0	LSG1	195850797	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.574000	0.82434	2.215000	0.71742	0.528000	0.53228	GTT	.	.		0.463	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
DLG1	1739	hgsc.bcm.edu	37	3	196867115	196867115	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr3:196867115G>T	ENST00000419354.1	-	9	994	c.708C>A	c.(706-708)ttC>ttA	p.F236L	DLG1_ENST00000452595.1_Missense_Mutation_p.F120L|DLG1_ENST00000448528.2_Missense_Mutation_p.F236L|DLG1_ENST00000357674.4_Missense_Mutation_p.F203L|DLG1_ENST00000443183.1_Missense_Mutation_p.F120L|DLG1_ENST00000346964.2_Missense_Mutation_p.F236L|DLG1_ENST00000314062.3_Missense_Mutation_p.F185L|DLG1_ENST00000422288.1_Missense_Mutation_p.F185L|DLG1_ENST00000450955.1_Missense_Mutation_p.F203L|DLG1_ENST00000392382.2_Missense_Mutation_p.F203L			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	236	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		CTGCAATGCTGAAACCAAGCC	0.418																																					p.F236L		Atlas-SNP	.											.	DLG1	120	.	0			c.C708A						.						133.0	129.0	130.0					3																	196867115		2203	4300	6503	SO:0001583	missense	1739	exon9			AATGCTGAAACCA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.708C>A	chr3.hg19:g.196867115G>T	ENSP00000407531:p.Phe236Leu	114.0	0.0		127.0	57.0	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Missense_Mutation	SNP	ENST00000419354.1	hg19	CCDS43194.1	.	.	.	.	.	.	.	.	.	.	G	19.86	3.904979	0.72868	.	.	ENSG00000075711	ENST00000346964;ENST00000359922;ENST00000357674;ENST00000381807;ENST00000314062;ENST00000419354;ENST00000452595;ENST00000422288;ENST00000448528;ENST00000443183;ENST00000392382;ENST00000450955;ENST00000447466;ENST00000453607	T;T;T;T;T;T;T;T;T;T;T;T	0.18502	2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21;2.21	5.67	2.47	0.30058	PDZ/DHR/GLGF (4);	0.000000	0.85682	D	0.000000	T	0.33147	0.0853	M	0.67625	2.065	0.53688	D	0.99997	D;D;D;D;D;D;D	0.89917	0.987;1.0;1.0;1.0;1.0;0.999;1.0	P;D;D;D;D;D;D	0.91635	0.895;0.991;0.999;0.999;0.999;0.992;0.999	T	0.04413	-1.0953	10	0.66056	D	0.02	.	5.6317	0.17514	0.4577:0.0:0.5423:0.0	.	203;120;120;120;203;236;236	Q12959-4;E9PG21;E7EWL7;B4DGU1;Q12959-3;Q12959;Q12959-2	.;.;.;.;.;DLG1_HUMAN;.	L	236;236;203;236;185;236;120;185;236;120;203;203;45;89	ENSP00000345731:F236L;ENSP00000350303:F203L;ENSP00000321087:F185L;ENSP00000407531:F236L;ENSP00000398939:F120L;ENSP00000413238:F185L;ENSP00000391732:F236L;ENSP00000396658:F120L;ENSP00000376187:F203L;ENSP00000411278:F203L;ENSP00000398702:F45L;ENSP00000412579:F89L	ENSP00000321087:F185L	F	-	3	2	DLG1	198351512	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	0.789000	0.26886	0.878000	0.35920	-0.942000	0.02676	TTC	.	.		0.418	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
FGFRL1	53834	hgsc.bcm.edu	37	4	1017449	1017449	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:1017449G>T	ENST00000398484.2	+	5	953	c.373G>T	c.(373-375)Gag>Tag	p.E125*	FGFRL1_ENST00000510644.1_Nonsense_Mutation_p.E125*|FGFRL1_ENST00000264748.6_Nonsense_Mutation_p.E125*|FGFRL1_ENST00000504138.1_Nonsense_Mutation_p.E125*			Q8N441	FGRL1_HUMAN	fibroblast growth factor receptor-like 1	125					diaphragm development (GO:0060539)|heart valve morphogenesis (GO:0003179)|negative regulation of cell proliferation (GO:0008285)|skeletal system development (GO:0001501)|ventricular septum morphogenesis (GO:0060412)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)			endometrium(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	13			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			CCCAGGGAAGGAGAGCCTGGG	0.697																																					p.E125X		Atlas-SNP	.											.	FGFRL1	77	.	0			c.G373T						.						11.0	13.0	12.0					4																	1017449		2191	4291	6482	SO:0001587	stop_gained	53834	exon4			GGGAAGGAGAGCC		CCDS3344.1	4p16	2013-01-11			ENSG00000127418	ENSG00000127418		"""Immunoglobulin superfamily / I-set domain containing"""	3693	protein-coding gene	gene with protein product		605830					Standard	NM_021923		Approved		uc003gcg.3	Q8N441	OTTHUMG00000118998	ENST00000398484.2:c.373G>T	chr4.hg19:g.1017449G>T	ENSP00000381498:p.Glu125*	182.0	0.0		114.0	68.0	NM_001004356	B2RAU9|Q6PJN1|Q9BXN7|Q9H4D7	Nonsense_Mutation	SNP	ENST00000398484.2	hg19	CCDS3344.1	.	.	.	.	.	.	.	.	.	.	g	15.25	2.776659	0.49786	.	.	ENSG00000127418	ENST00000398484;ENST00000542622;ENST00000510644;ENST00000504138;ENST00000507339;ENST00000264748	.	.	.	4.24	2.44	0.29823	.	1.293420	0.05166	N	0.498823	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-17.007	4.7739	0.13169	0.2713:0.1616:0.5672:0.0	.	.	.	.	X	125;95;125;125;125;125	.	ENSP00000264748:E125X	E	+	1	0	FGFRL1	1007449	0.476000	0.25901	0.136000	0.22124	0.580000	0.36256	2.004000	0.40854	0.229000	0.21039	0.436000	0.28706	GAG	.	.		0.697	FGFRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239195.2	NM_021923	
PRDM8	56978	hgsc.bcm.edu	37	4	81123578	81123578	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:81123578C>T	ENST00000504452.1	+	8	1801	c.962C>T	c.(961-963)gCg>gTg	p.A321V	PRDM8_ENST00000339711.4_Missense_Mutation_p.A321V|PRDM8_ENST00000415738.2_Missense_Mutation_p.A321V			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	321	Gly-rich.				corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GAGGAGGCGGCGGAGGGCGGC	0.741																																					p.A321V		Atlas-SNP	.											.	PRDM8	44	.	0			c.C962T						.						2.0	3.0	3.0					4																	81123578		1143	2876	4019	SO:0001583	missense	56978	exon4			AGGCGGCGGAGGG	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.962C>T	chr4.hg19:g.81123578C>T	ENSP00000423985:p.Ala321Val	119.0	0.0		82.0	47.0	NM_001099403	A8K7X2|Q6IQ36	Missense_Mutation	SNP	ENST00000504452.1	hg19	CCDS43243.1	.	.	.	.	.	.	.	.	.	.	C	8.401	0.842005	0.16963	.	.	ENSG00000152784	ENST00000504452;ENST00000515013;ENST00000339711;ENST00000415738	T;T;T;T	0.65549	-0.16;0.37;-0.16;-0.16	4.11	-1.67	0.08238	.	0.809757	0.10439	N	0.674507	T	0.37210	0.0995	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.14980	-1.0453	10	0.27785	T	0.31	.	1.8168	0.03102	0.1481:0.4421:0.132:0.2777	.	321	Q9NQV8	PRDM8_HUMAN	V	321	ENSP00000423985:A321V;ENSP00000425149:A321V;ENSP00000339764:A321V;ENSP00000406998:A321V	ENSP00000339764:A321V	A	+	2	0	PRDM8	81342602	0.028000	0.19301	0.006000	0.13384	0.327000	0.28475	0.389000	0.20751	-0.184000	0.10567	0.313000	0.20887	GCG	.	.		0.741	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
SPARCL1	8404	hgsc.bcm.edu	37	4	88411474	88411474	+	Silent	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:88411474C>A	ENST00000282470.6	-	7	1952	c.1482G>T	c.(1480-1482)ggG>ggT	p.G494G	SPARCL1_ENST00000418378.1_Silent_p.G494G|SPARCL1_ENST00000503414.1_Silent_p.G369G	NM_004684.4	NP_004675.3	Q14515	SPRL1_HUMAN	SPARC-like 1 (hevin)	494	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				signal transduction (GO:0007165)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(2)	21				OV - Ovarian serous cystadenocarcinoma(123;0.00118)		CCTTTTTGGTCCCCTCCAGTC	0.458																																					p.G494G		Atlas-SNP	.											.	SPARCL1	59	.	0			c.G1482T						.						257.0	265.0	262.0					4																	88411474		2203	4300	6503	SO:0001819	synonymous_variant	8404	exon7			TTTGGTCCCCTCC	X86693	CCDS3622.1	4q22-q25	2013-01-10	2008-08-29		ENSG00000152583	ENSG00000152583		"""EF-hand domain containing"""	11220	protein-coding gene	gene with protein product		606041	"""SPARC-like 1 (mast9, hevin)"""			8488563, 7600298, 16844696	Standard	NM_001128310		Approved	MAST9	uc003hqs.4	Q14515	OTTHUMG00000130605	ENST00000282470.6:c.1482G>T	chr4.hg19:g.88411474C>A		80.0	0.0		57.0	28.0	NM_004684	B4E2Z0|E7ESU2|Q14800	Silent	SNP	ENST00000282470.6	hg19	CCDS3622.1																																																																																			.	.		0.458	SPARCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253059.2		
PLRG1	5356	hgsc.bcm.edu	37	4	155460255	155460255	+	Splice_Site	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:155460255A>G	ENST00000499023.2	-	12	1278		c.e12+1		PLRG1_ENST00000393905.2_Splice_Site|PLRG1_ENST00000302078.5_Splice_Site	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1						mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				AAATACACTTACTGTCTTGGA	0.368																																					.		Atlas-SNP	.											.	PLRG1	43	.	0			c.1151+2T>C						.						192.0	178.0	183.0					4																	155460255		2202	4300	6502	SO:0001630	splice_region_variant	5356	exon13			ACACTTACTGTCT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1151+1T>C	chr4.hg19:g.155460255A>G		80.0	0.0		90.0	53.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Splice_Site	SNP	ENST00000499023.2	hg19	CCDS34083.1	.	.	.	.	.	.	.	.	.	.	A	20.0	3.931131	0.73327	.	.	ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000503251;ENST00000302078	.	.	.	5.83	5.83	0.93111	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2127	0.82178	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	PLRG1	155679705	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	8.730000	0.91510	2.236000	0.73375	0.533000	0.62120	.	.	.		0.368	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	Intron
MARCH1	55016	hgsc.bcm.edu	37	4	165118847	165118847	+	Intron	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr4:165118847C>T	ENST00000503008.1	-	2	864				MARCH1_ENST00000508725.1_Intron|MARCH1_ENST00000514618.1_Intron	NM_001166373.1	NP_001159845.1	Q8TCQ1	MARH1_HUMAN	membrane-associated ring finger (C3HC4) 1, E3 ubiquitin protein ligase						antigen processing and presentation of peptide antigen via MHC class II (GO:0002495)|immune response (GO:0006955)|protein polyubiquitination (GO:0000209)	cytoplasmic vesicle (GO:0031410)|early endosome membrane (GO:0031901)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	ligase activity (GO:0016874)|MHC protein binding (GO:0042287)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(3)|large_intestine(3)|lung(20)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	36	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				TGAATGAATCCGTCTGCCCAT	0.547																																					p.R6Q		Atlas-SNP	.											.	ANP32C	59	.	0			c.G17A						.						99.0	102.0	101.0					4																	165118847		2203	4300	6503	SO:0001627	intron_variant	23520	exon1			TGAATCCGTCTGC	AK000675	CCDS3806.1, CCDS54814.1	4q32.2	2013-01-09	2012-02-23			ENSG00000145416		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	26077	protein-coding gene	gene with protein product		613331	"""membrane-associated ring finger (C3HC4) 1"""			14722266	Standard	NM_017923		Approved	FLJ20668, MARCH-I, RNF171	uc003iqs.2	Q8TCQ1		ENST00000503008.1:c.113-86033G>A	chr4.hg19:g.165118847C>T		86.0	0.0		67.0	17.0	NM_012403	D3DP29|Q9NWR0	Missense_Mutation	SNP	ENST00000503008.1	hg19	CCDS54814.1																																																																																			.	.		0.547	MARCH1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364493.2	NM_017923	
FBN2	2201	hgsc.bcm.edu	37	5	127595357	127595357	+	Silent	SNP	G	G	A	rs140437100		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:127595357G>A	ENST00000508053.1	-	71	9503	c.8529C>T	c.(8527-8529)agC>agT	p.S2843S	FBN2_ENST00000262464.4_Silent_p.S2843S			P35556	FBN2_HUMAN	fibrillin 2	2843					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.S2843S(2)		NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TGCGGAAGACGCTGTCATCGT	0.552																																					p.S2843S		Atlas-SNP	.											FBN2_ENST00000508053,NS,carcinoma,0,1	FBN2	858	.	2	Substitution - coding silent(2)	endometrium(2)	c.C8529T						.	G		1,4405	2.1+/-5.4	0,1,2202	209.0	181.0	190.0		8529	-0.6	0.0	5	dbSNP_134	190	0,8600		0,0,4300	no	coding-synonymous	FBN2	NM_001999.3		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2843/2913	127595357	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon65			GAAGACGCTGTCA	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.8529C>T	chr5.hg19:g.127595357G>A		134.0	0.0		143.0	69.0	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	hg19	CCDS34222.1																																																																																			.	G|1.000;A|0.000		0.552	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736155	140736155	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:140736155A>C	ENST00000571252.1	+	1	1388	c.1388A>C	c.(1387-1389)gAa>gCa	p.E463A	PCDHGA2_ENST00000394576.2_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	463	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACATTCCTGAAAACAACCCC	0.488																																					p.E463A		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.A1388C						.						106.0	110.0	109.0					5																	140736155		2063	4247	6310	SO:0001583	missense	56111	exon1			TTCCTGAAAACAA	AF152511	CCDS58979.1, CCDS58979.2, CCDS75331.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8702	other	protocadherin		606291				10380929	Standard	NM_018917		Approved	PCDH-GAMMA-A4		Q9Y5G9		ENST00000571252.1:c.1388A>C	chr5.hg19:g.140736155A>C	ENSP00000458570:p.Glu463Ala	107.0	0.0		126.0	58.0	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	hg19	CCDS58979.1																																																																																			.	.		0.488	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
DIAPH1	1729	hgsc.bcm.edu	37	5	140908429	140908429	+	Missense_Mutation	SNP	A	A	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:140908429A>C	ENST00000398557.4	-	22	2998	c.2858T>G	c.(2857-2859)aTc>aGc	p.I953S	DIAPH1_ENST00000389057.5_Missense_Mutation_p.I944S|DIAPH1_ENST00000494967.1_5'UTR|DIAPH1_ENST00000520569.1_Missense_Mutation_p.I896S|DIAPH1_ENST00000389054.3_Missense_Mutation_p.I950S|DIAPH1_ENST00000398562.2_Missense_Mutation_p.I929S|DIAPH1_ENST00000518047.1_Missense_Mutation_p.I941S|DIAPH1_ENST00000253811.6_Missense_Mutation_p.I954S|DIAPH1_ENST00000398566.3_Missense_Mutation_p.I945S	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	953	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCTGGCTTGATATTCTCCAC	0.473																																					p.I953S		Atlas-SNP	.											.	DIAPH1	64	.	0			c.T2858G						.						80.0	75.0	77.0					5																	140908429		2046	4201	6247	SO:0001583	missense	1729	exon22			GGCTTGATATTCT	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"""diaphanous (Drosophila, homolog) 1"", ""diaphanous homolog 1 (Drosophila)"""	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.2858T>G	chr5.hg19:g.140908429A>C	ENSP00000381565:p.Ile953Ser	98.0	0.0		85.0	37.0	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Missense_Mutation	SNP	ENST00000398557.4	hg19	CCDS43374.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.702334	0.68501	.	.	ENSG00000131504	ENST00000389054;ENST00000520569;ENST00000398562;ENST00000389057;ENST00000398566;ENST00000398557;ENST00000253811;ENST00000518047	T;T;T;T;T;T;T;T	0.19669	2.13;2.13;2.13;2.13;2.13;2.13;2.13;2.13	5.27	5.27	0.74061	Actin-binding FH2/DRF autoregulatory (1);Actin-binding FH2 (3);	0.202993	0.40469	N	0.001098	T	0.47985	0.1475	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.986;0.986	T	0.52675	-0.8544	10	0.87932	D	0	.	14.1712	0.65510	1.0:0.0:0.0:0.0	.	896;944;953	E7ERW8;E9PEZ2;O60610	.;.;DIAP1_HUMAN	S	950;896;929;944;945;953;954;941	ENSP00000373706:I950S;ENSP00000429282:I896S;ENSP00000381570:I929S;ENSP00000373709:I944S;ENSP00000381572:I945S;ENSP00000381565:I953S;ENSP00000253811:I954S;ENSP00000428268:I941S	ENSP00000253811:I954S	I	-	2	0	DIAPH1	140888613	1.000000	0.71417	0.996000	0.52242	0.951000	0.60555	9.339000	0.96797	1.975000	0.57531	0.455000	0.32223	ATC	.	.		0.473	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219	
ATOX1	475	hgsc.bcm.edu	37	5	151138108	151138108	+	Splice_Site	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:151138108G>A	ENST00000524142.1	-	2	362	c.5C>T	c.(4-6)cCg>cTg	p.P2L	ATOX1_ENST00000313115.6_Splice_Site_p.P2L|ATOX1_ENST00000522710.1_Splice_Site_p.P2L|CTB-113P19.3_ENST00000518182.1_RNA			O00244	ATOX1_HUMAN	antioxidant 1 copper chaperone	2	HMA. {ECO:0000255|PROSITE- ProRule:PRU00280}.				cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	copper chaperone activity (GO:0016531)|copper ion binding (GO:0005507)|copper-dependent protein binding (GO:0032767)|metallochaperone activity (GO:0016530)						Medulloblastoma(196;0.091)|all_hematologic(541;0.103)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)			ACCACTCACCGGCATGACTGA	0.682																																					p.P2L		Atlas-SNP	.											.	ATOX1	4	.	0			c.C5T						.						10.0	15.0	13.0					5																	151138108		2010	4146	6156	SO:0001630	splice_region_variant	475	exon1			CTCACCGGCATGA	U70660	CCDS47317.1	5q32	2013-05-01	2013-05-01			ENSG00000177556			798	protein-coding gene	gene with protein product		602270	"""ATX1 (antioxidant protein 1, yeast) homolog 1"", ""ATX1 antioxidant protein 1 homolog (yeast)"""			9083055	Standard	NM_004045		Approved	HAH1	uc003luk.3	O00244		ENST00000524142.1:c.6+1C>T	chr5.hg19:g.151138108G>A		404.0	0.0		426.0	59.0	NM_004045	A8KAJ8|D3DQI2|Q2M1R6|Q56AP3	Missense_Mutation	SNP	ENST00000524142.1	hg19	CCDS47317.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.185572	0.38609	.	.	ENSG00000177556	ENST00000524142;ENST00000313115;ENST00000522710	.	.	.	3.81	3.81	0.43845	Heavy metal-associated domain, HMA (1);	0.424673	0.23738	N	0.045058	T	0.44138	0.1279	.	.	.	0.44736	D	0.997738	B	0.02656	0.0	B	0.01281	0.0	T	0.33854	-0.9852	8	0.31617	T	0.26	-2.2352	11.5135	0.50507	0.0:0.0:1.0:0.0	.	2	O00244	ATOX1_HUMAN	L	2	.	ENSP00000316854:P2L	P	-	2	0	ATOX1	151118301	1.000000	0.71417	1.000000	0.80357	0.079000	0.17450	3.513000	0.53414	2.425000	0.82216	0.491000	0.48974	CCG	.	.		0.682	ATOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373823.2	NM_004045	Missense_Mutation
DOCK2	1794	hgsc.bcm.edu	37	5	169111291	169111291	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:169111291G>T	ENST00000256935.8	+	8	778	c.698G>T	c.(697-699)aGa>aTa	p.R233I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	233					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TTTGTGTGCAGAATTGGGGAA	0.483																																					p.R233I		Atlas-SNP	.											.	DOCK2	389	.	0			c.G698T						.						193.0	175.0	181.0					5																	169111291		2203	4300	6503	SO:0001583	missense	1794	exon8			TGTGCAGAATTGG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.698G>T	chr5.hg19:g.169111291G>T	ENSP00000256935:p.Arg233Ile	119.0	0.0		86.0	36.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.761599	0.89932	.	.	ENSG00000134516	ENST00000256935	T	0.51071	0.72	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.70037	0.3178	M	0.74258	2.255	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	T	0.70464	-0.4864	10	0.48119	T	0.1	.	19.2567	0.93948	0.0:0.0:1.0:0.0	.	233	Q92608	DOCK2_HUMAN	I	233	ENSP00000256935:R233I	ENSP00000256935:R233I	R	+	2	0	DOCK2	169043869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.372000	0.73123	2.544000	0.85801	0.655000	0.94253	AGA	.	.		0.483	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
DOCK2	1794	hgsc.bcm.edu	37	5	169494540	169494540	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr5:169494540C>T	ENST00000256935.8	+	45	4574	c.4494C>T	c.(4492-4494)gcC>gcT	p.A1498A	DOCK2_ENST00000540750.1_Silent_p.A559A|DOCK2_ENST00000520908.1_Silent_p.A990A|DOCK2_ENST00000523351.1_3'UTR	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1498	DHR-2.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			TGGAGAATGCCATAGAAACCA	0.428																																					p.A1498A		Atlas-SNP	.											.	DOCK2	389	.	0			c.C4494T						.						149.0	136.0	141.0					5																	169494540		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon45			GAATGCCATAGAA	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.4494C>T	chr5.hg19:g.169494540C>T		149.0	0.0		119.0	48.0	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	hg19	CCDS4371.1																																																																																			.	.		0.428	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
BTN1A1	696	hgsc.bcm.edu	37	6	26508294	26508294	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:26508294A>G	ENST00000244513.6	+	6	952	c.886A>G	c.(886-888)Aaa>Gaa	p.K296E		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	296	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						TGCAGAATGGAAAAAGGCTAC	0.403																																					p.K296E		Atlas-SNP	.											.	BTN1A1	68	.	0			c.A886G						.						170.0	169.0	169.0					6																	26508294		2203	4300	6503	SO:0001583	missense	696	exon6			GAATGGAAAAAGG	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.886A>G	chr6.hg19:g.26508294A>G	ENSP00000244513:p.Lys296Glu	102.0	0.0		111.0	45.0	NM_001732	Q4VAN3|Q4VAN4|Q9H458	Missense_Mutation	SNP	ENST00000244513.6	hg19	CCDS4614.1	.	.	.	.	.	.	.	.	.	.	A	16.80	3.223381	0.58668	.	.	ENSG00000124557	ENST00000244513;ENST00000377586	T	0.59502	0.26	5.68	5.68	0.88126	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	0.106321	0.42420	D	0.000720	T	0.31979	0.0814	L	0.31065	0.9	0.37965	D	0.933099	B	0.17038	0.02	B	0.12837	0.008	T	0.33675	-0.9859	10	0.72032	D	0.01	.	12.5848	0.56410	1.0:0.0:0.0:0.0	.	296	Q13410	BT1A1_HUMAN	E	296	ENSP00000244513:K296E	ENSP00000244513:K296E	K	+	1	0	BTN1A1	26616273	1.000000	0.71417	0.998000	0.56505	0.846000	0.48090	5.352000	0.66028	2.284000	0.76573	0.533000	0.62120	AAA	.	.		0.403	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	
MDC1	9656	hgsc.bcm.edu	37	6	30668320	30668320	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:30668320G>A	ENST00000376406.3	-	15	6839	c.6192C>T	c.(6190-6192)ttC>ttT	p.F2064F	MDC1_ENST00000376405.2_Silent_p.F1800F|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	2064	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						CAGTCAGCAGGAACTCAGGCG	0.567								Other conserved DNA damage response genes																													p.F2064F		Atlas-SNP	.											.	MDC1	218	.	0			c.C6192T						.						133.0	125.0	128.0					6																	30668320		1511	2709	4220	SO:0001819	synonymous_variant	9656	exon15			CAGCAGGAACTCA	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.6192C>T	chr6.hg19:g.30668320G>A		197.0	0.0		235.0	63.0	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.		0.567	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
DNAH8	1769	hgsc.bcm.edu	37	6	38941510	38941510	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:38941510C>T	ENST00000359357.3	+	82	12202	c.11948C>T	c.(11947-11949)aCc>aTc	p.T3983I	DNAH8_ENST00000441566.1_Missense_Mutation_p.T3947I			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3983	AAA 6. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						ACGCTAATTACCACTGAAGCC	0.388																																					p.T4200I		Atlas-SNP	.											.	DNAH8	1239	.	0			c.C12599T						.						96.0	96.0	96.0					6																	38941510		2203	4300	6503	SO:0001583	missense	1769	exon84			TAATTACCACTGA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.11948C>T	chr6.hg19:g.38941510C>T	ENSP00000352312:p.Thr3983Ile	97.0	0.0		144.0	40.0	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Missense_Mutation	SNP	ENST00000359357.3	hg19		.	.	.	.	.	.	.	.	.	.	C	7.928	0.740127	0.15642	.	.	ENSG00000124721	ENST00000327475;ENST00000359357;ENST00000441566	T;T;T	0.08634	3.07;3.07;3.07	5.99	-0.037	0.13886	Dynein heavy chain (1);	0.488542	0.22998	N	0.053120	T	0.04272	0.0118	M	0.86028	2.79	0.09310	N	1	B;B	0.16166	0.013;0.016	B;B	0.26969	0.045;0.075	T	0.31308	-0.9948	10	0.51188	T	0.08	.	4.1261	0.10128	0.3571:0.3827:0.0:0.2602	.	3947;3983	Q96JB1-2;Q96JB1	.;DYH8_HUMAN	I	4188;3983;3947	ENSP00000333363:T4188I;ENSP00000352312:T3983I;ENSP00000402294:T3947I	ENSP00000333363:T4188I	T	+	2	0	DNAH8	39049488	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	-0.242000	0.08928	-0.318000	0.08665	0.655000	0.94253	ACC	.	.		0.388	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
DST	667	hgsc.bcm.edu	37	6	56504967	56504967	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:56504967G>T	ENST00000361203.3	-	14	1838	c.1831C>A	c.(1831-1833)Ctt>Att	p.L611I	DST_ENST00000518935.1_Missense_Mutation_p.L285I|DST_ENST00000446842.2_Missense_Mutation_p.L285I|DST_ENST00000370769.4_Missense_Mutation_p.L611I|DST_ENST00000370765.6_Missense_Mutation_p.L285I|DST_ENST00000312431.6_Missense_Mutation_p.L611I|DST_ENST00000370754.5_Missense_Mutation_p.L789I|DST_ENST00000370788.2_Missense_Mutation_p.L611I|DST_ENST00000244364.6_Missense_Mutation_p.L285I|DST_ENST00000421834.2_Missense_Mutation_p.L611I			Q03001	DYST_HUMAN	dystonin	611					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			CAATTCAAAAGATCCTGAACA	0.299																																					p.L285I		Atlas-SNP	.											.	DST	1427	.	0			c.C853A						.						36.0	39.0	38.0					6																	56504967		2202	4298	6500	SO:0001583	missense	667	exon4			TCAAAAGATCCTG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1831C>A	chr6.hg19:g.56504967G>T	ENSP00000354508:p.Leu611Ile	83.0	0.0		138.0	52.0	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	hg19		.	.	.	.	.	.	.	.	.	.	G	24.0	4.480621	0.84747	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000312431;ENST00000370788;ENST00000361203;ENST00000439203;ENST00000520645;ENST00000370765;ENST00000518935	D;D;D;D;D;D;D;D;D;D;D;D	0.94417	-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42;-3.42	4.99	4.99	0.66335	.	0.000000	0.41194	D	0.000933	D	0.96691	0.8920	M	0.78456	2.415	0.29535	N	0.852531	D;D;D;D;D;P;D;D;D;P	0.65815	0.967;0.967;0.967;0.967;0.981;0.71;0.982;0.995;0.967;0.937	D;D;D;D;D;P;D;D;D;D	0.91635	0.979;0.992;0.979;0.992;0.991;0.769;0.991;0.999;0.992;0.96	D	0.95214	0.8328	9	0.32370	T	0.25	.	18.4618	0.90741	0.0:0.0:1.0:0.0	.	640;611;611;789;727;285;285;285;611;285	B4DGY0;Q5TBT1;E7ERU2;E9PEB9;Q03001-13;Q6P0N6;Q03001-3;Q03001-9;Q03001;Q03001-8	.;.;.;.;.;.;.;.;DYST_HUMAN;.	I	285;789;611;611;285;611;611;611;285;651;285;285	ENSP00000244364:L285I;ENSP00000359790:L789I;ENSP00000359805:L611I;ENSP00000400883:L611I;ENSP00000393645:L285I;ENSP00000307959:L611I;ENSP00000359824:L611I;ENSP00000354508:L611I;ENSP00000404924:L285I;ENSP00000431030:L651I;ENSP00000359801:L285I;ENSP00000431003:L285I	ENSP00000244364:L285I	L	-	1	0	DST	56612926	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	6.155000	0.71833	2.603000	0.88011	0.655000	0.94253	CTT	.	.		0.299	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
MMS22L	253714	hgsc.bcm.edu	37	6	97610000	97610000	+	Missense_Mutation	SNP	C	C	A	rs149054595	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:97610000C>A	ENST00000275053.4	-	22	3528	c.3263G>T	c.(3262-3264)cGc>cTc	p.R1088L	MMS22L_ENST00000369251.2_Missense_Mutation_p.R1048L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1088					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)		p.R1088H(2)		breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						GGATGCTAAGCGAGGAGGAGG	0.408																																					p.R1088L		Atlas-SNP	.											MMS22L,colon,carcinoma,0,2	MMS22L	102	.	2	Substitution - Missense(2)	large_intestine(1)|lung(1)	c.G3263T						.						120.0	115.0	117.0					6																	97610000		2203	4300	6503	SO:0001583	missense	253714	exon22			GCTAAGCGAGGAG		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3263G>T	chr6.hg19:g.97610000C>A	ENSP00000275053:p.Arg1088Leu	77.0	0.0		48.0	40.0	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	hg19	CCDS5039.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238564	0.79800	.	.	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.33654	1.4;1.4	5.68	4.81	0.61882	.	0.052393	0.85682	D	0.000000	T	0.44138	0.1279	M	0.69823	2.125	0.51233	D	0.999916	D;D	0.71674	0.998;0.979	D;P	0.63033	0.91;0.736	T	0.47824	-0.9087	10	0.52906	T	0.07	-19.3496	11.5924	0.50953	0.0:0.8568:0.0:0.1432	.	1048;1088	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1088;1048	ENSP00000275053:R1088L;ENSP00000358254:R1048L	ENSP00000275053:R1088L	R	-	2	0	MMS22L	97716721	1.000000	0.71417	0.971000	0.41717	0.952000	0.60782	2.641000	0.46587	1.395000	0.46643	0.650000	0.86243	CGC	.	C|1.000;T|0.000		0.408	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
ABCA13	154664	hgsc.bcm.edu	37	7	48315020	48315020	+	Silent	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:48315020A>G	ENST00000435803.1	+	17	5781	c.5757A>G	c.(5755-5757)aaA>aaG	p.K1919K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	1919					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						CTGTGCAGAAATTTTGGCATA	0.383																																					p.K1919K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.A5757G						.						121.0	123.0	123.0					7																	48315020		1827	4083	5910	SO:0001819	synonymous_variant	154664	exon17			GCAGAAATTTTGG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.5757A>G	chr7.hg19:g.48315020A>G		180.0	0.0		193.0	97.0	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	hg19	CCDS47584.1																																																																																			.	.		0.383	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
ZPBP	11055	hgsc.bcm.edu	37	7	50121482	50121482	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:50121482G>A	ENST00000046087.2	-	3	291	c.222C>T	c.(220-222)gtC>gtT	p.V74V	ZPBP_ENST00000419417.1_Silent_p.V74V	NM_001159878.1|NM_007009.2	NP_001153350.1|NP_008940.2	Q9BS86	ZPBP1_HUMAN	zona pellucida binding protein	74					acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(3)	29	Glioma(55;0.08)|all_neural(89;0.245)					GATGGAGCATGACATACGCTT	0.353																																					p.V74V		Atlas-SNP	.											.	ZPBP	65	.	0			c.C222T						.						126.0	115.0	119.0					7																	50121482		2202	4300	6502	SO:0001819	synonymous_variant	11055	exon3			GAGCATGACATAC	D17570	CCDS5509.1, CCDS55110.1	7p14.3	2013-01-11			ENSG00000042813	ENSG00000042813		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15662	protein-coding gene	gene with protein product		608498				9378618	Standard	NM_007009		Approved	SP38, ZPBP1	uc003tou.3	Q9BS86	OTTHUMG00000023528	ENST00000046087.2:c.222C>T	chr7.hg19:g.50121482G>A		32.0	0.0		81.0	37.0	NM_007009	A4D253|C9JPU1|Q15941|Q75KX9|Q75MI3	Silent	SNP	ENST00000046087.2	hg19	CCDS5509.1																																																																																			.	.		0.353	ZPBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251374.1	NM_007009	
SEMA3C	10512	hgsc.bcm.edu	37	7	80374265	80374265	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:80374265G>A	ENST00000265361.3	-	18	2762	c.2201C>T	c.(2200-2202)gCc>gTc	p.A734V	SEMA3C_ENST00000419255.2_Missense_Mutation_p.A734V|SEMA3C_ENST00000544525.1_Missense_Mutation_p.A752V	NM_006379.3	NP_006370.1	Q99985	SEM3C_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3C	734	Arg/Lys-rich (basic).				axon guidance (GO:0007411)|blood vessel remodeling (GO:0001974)|cardiac right ventricle morphogenesis (GO:0003215)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|immune response (GO:0006955)|limb bud formation (GO:0060174)|neural crest cell migration (GO:0001755)|neural tube development (GO:0021915)|outflow tract morphogenesis (GO:0003151)|post-embryonic development (GO:0009791)|pulmonary myocardium development (GO:0003350)|response to drug (GO:0042493)|somitogenesis (GO:0001756)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						ATTGATGAGGGCCTTTAACTT	0.408																																					p.A734V		Atlas-SNP	.											.	SEMA3C	106	.	0			c.C2201T						.						149.0	141.0	144.0					7																	80374265		2203	4300	6503	SO:0001583	missense	10512	exon18			ATGAGGGCCTTTA	AB000220	CCDS5596.1	7q21-q31	2013-01-11			ENSG00000075223	ENSG00000075223		"""Semaphorins"", ""Immunoglobulin superfamily / I-set domain containing"""	10725	protein-coding gene	gene with protein product		602645		SEMAE		7748561, 9168980	Standard	NM_006379		Approved	SemE	uc003uhj.3	Q99985	OTTHUMG00000023447	ENST00000265361.3:c.2201C>T	chr7.hg19:g.80374265G>A	ENSP00000265361:p.Ala734Val	98.0	0.0		113.0	49.0	NM_006379	B4DRL8	Missense_Mutation	SNP	ENST00000265361.3	hg19	CCDS5596.1	.	.	.	.	.	.	.	.	.	.	G	13.09	2.132115	0.37630	.	.	ENSG00000075223	ENST00000265361;ENST00000419255;ENST00000544525	T;T;T	0.26067	1.77;1.77;1.76	5.56	5.56	0.83823	.	0.105207	0.64402	D	0.000004	T	0.13756	0.0333	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.003	T	0.14727	-1.0462	10	0.22706	T	0.39	.	12.8104	0.57637	0.075:0.0:0.9249:0.0	.	752;734	F5H1Z7;Q99985	.;SEM3C_HUMAN	V	734;734;752	ENSP00000265361:A734V;ENSP00000411193:A734V;ENSP00000445649:A752V	ENSP00000265361:A734V	A	-	2	0	SEMA3C	80212201	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	7.610000	0.82949	2.606000	0.88127	0.557000	0.71058	GCC	.	.		0.408	SEMA3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253279.1	NM_006379	
MCM7	4176	hgsc.bcm.edu	37	7	99697718	99697718	+	Splice_Site	SNP	T	T	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:99697718T>C	ENST00000303887.5	-	2	677		c.e2-2		AP4M1_ENST00000359593.4_5'Flank|MCM7_ENST00000343023.6_Splice_Site|AP4M1_ENST00000421755.1_5'Flank|AP4M1_ENST00000429084.1_5'Flank|MCM7_ENST00000354230.3_Splice_Site|AP4M1_ENST00000422582.1_5'Flank	NM_005916.3	NP_005907.3	P33993	MCM7_HUMAN	minichromosome maintenance complex component 7						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)					TAACCTTTTCTGTAACATGAA	0.353																																					.		Atlas-SNP	.											.	MCM7	136	.	0			c.32-2A>G						.						71.0	66.0	68.0					7																	99697718		2203	4300	6503	SO:0001630	splice_region_variant	4176	exon3			CTTTTCTGTAACA		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.32-2A>G	chr7.hg19:g.99697718T>C		121.0	0.0		158.0	67.0	NM_005916	A4D2A1|A4D2A2|E9PGN9|Q15076|Q96D34|Q96GL1	Splice_Site	SNP	ENST00000303887.5	hg19	CCDS5683.1	.	.	.	.	.	.	.	.	.	.	T	9.841	1.190978	0.21954	.	.	ENSG00000166508	ENST00000343023;ENST00000303887	.	.	.	4.0	2.79	0.32731	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.5406	0.22378	0.0:0.1101:0.0:0.8899	.	.	.	.	.	-1	.	.	.	-	.	.	MCM7	99535654	1.000000	0.71417	0.730000	0.30809	0.418000	0.31294	6.639000	0.74314	0.830000	0.34757	0.533000	0.62120	.	.	.		0.353	MCM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336534.3		Intron
MUC17	140453	hgsc.bcm.edu	37	7	100682982	100682982	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:100682982C>A	ENST00000306151.4	+	3	8349	c.8285C>A	c.(8284-8286)cCa>cAa	p.P2762Q		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2762	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCACCCTGCCAGTGGCCAGT	0.493																																					p.P2762Q		Atlas-SNP	.											.	MUC17	804	.	0			c.C8285A						.						252.0	247.0	248.0					7																	100682982		2203	4300	6503	SO:0001583	missense	140453	exon3			CCCTGCCAGTGGC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8285C>A	chr7.hg19:g.100682982C>A	ENSP00000302716:p.Pro2762Gln	100.0	0.0		112.0	22.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	5.606	0.296472	0.10622	.	.	ENSG00000169876	ENST00000306151	T	0.01548	4.78	0.778	-0.297	0.12820	.	.	.	.	.	T	0.03136	0.0092	L	0.32530	0.975	0.09310	N	1	D	0.64830	0.994	D	0.65684	0.937	T	0.44065	-0.9352	9	0.12766	T	0.61	.	5.2309	0.15422	0.0:0.7573:0.0:0.2427	.	2762	Q685J3	MUC17_HUMAN	Q	2762	ENSP00000302716:P2762Q	ENSP00000302716:P2762Q	P	+	2	0	MUC17	100469702	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.135000	0.15952	-0.104000	0.12154	0.134000	0.15878	CCA	.	.		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
GRM8	2918	hgsc.bcm.edu	37	7	126746765	126746765	+	Splice_Site	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:126746765A>G	ENST00000339582.2	-	3	1320	c.512T>C	c.(511-513)aTa>aCa	p.I171T	GRM8_ENST00000444921.2_Splice_Site_p.I171T|GRM8_ENST00000405249.1_Splice_Site_p.I171T|GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000358373.3_Splice_Site_p.I171T			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	171					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				GATTTGAGGTATCTGCAAAAC	0.448										HNSCC(24;0.065)																											p.I171T		Atlas-SNP	.											.	GRM8	377	.	0			c.T512C						.						101.0	103.0	102.0					7																	126746765		2203	4300	6503	SO:0001630	splice_region_variant	2918	exon2			TGAGGTATCTGCA		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.511-1T>C	chr7.hg19:g.126746765A>G		119.0	0.0		115.0	58.0	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	hg19	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	A	19.69	3.875587	0.72180	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249;ENST00000457830	D;D;D;D;D	0.86694	-2.16;-2.16;-2.16;-2.16;-2.16	4.91	4.91	0.64330	GPCR, family 3, conserved site (1);Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.93946	0.8062	M	0.92317	3.295	0.80722	D	1	D;D	0.61697	0.99;0.972	P;P	0.60682	0.878;0.877	D	0.95218	0.8331	10	0.87932	D	0	.	13.764	0.62983	1.0:0.0:0.0:0.0	.	171;171	O00222-2;O00222	.;GRM8_HUMAN	T	171	ENSP00000344173:I171T;ENSP00000409790:I171T;ENSP00000351142:I171T;ENSP00000385731:I171T;ENSP00000415522:I171T	ENSP00000344173:I171T	I	-	2	0	GRM8	126534001	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.339000	0.96797	1.850000	0.53721	0.460000	0.39030	ATA	.	.		0.448	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		Missense_Mutation
FLNC	2318	hgsc.bcm.edu	37	7	128485212	128485212	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:128485212C>T	ENST00000325888.8	+	21	3954	c.3693C>T	c.(3691-3693)ggC>ggT	p.G1231G	FLNC_ENST00000346177.6_Silent_p.G1231G	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	1231					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TCAAGTATGGCGGGCATCCCG	0.602																																					p.G1231G		Atlas-SNP	.											FLNC,NS,carcinoma,0,1	FLNC	339	.	0			c.C3693T						.						60.0	70.0	67.0					7																	128485212		2180	4261	6441	SO:0001819	synonymous_variant	2318	exon21			GTATGGCGGGCAT	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.3693C>T	chr7.hg19:g.128485212C>T		173.0	0.0		112.0	47.0	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Silent	SNP	ENST00000325888.8	hg19	CCDS43644.1																																																																																			.	.		0.602	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
PPP2R2A	5520	hgsc.bcm.edu	37	8	26220351	26220351	+	Silent	SNP	T	T	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr8:26220351T>C	ENST00000380737.3	+	7	1118	c.789T>C	c.(787-789)gaT>gaC	p.D263D	PPP2R2A_ENST00000315985.7_Silent_p.D273D	NM_002717.3	NP_002708.1	P63151	2ABA_HUMAN	protein phosphatase 2, regulatory subunit B, alpha	263					G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein dephosphorylation (GO:0006470)|regulation of catalytic activity (GO:0050790)|response to morphine (GO:0043278)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			kidney(1)|large_intestine(2)|ovary(1)	4		all_cancers(63;0.086)|Ovarian(32;2.61e-05)|all_epithelial(46;0.0514)|Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.000754)|Epithelial(17;3.02e-15)|all cancers(2;1.52e-13)|OV - Ovarian serous cystadenocarcinoma(2;1.89e-10)|Colorectal(74;0.155)		CCCTCTGTGATAGACATTCTA	0.368																																					p.D273D		Atlas-SNP	.											.	PPP2R2A	44	.	0			c.T819C						.						70.0	64.0	66.0					8																	26220351		2203	4300	6503	SO:0001819	synonymous_variant	5520	exon7			CTGTGATAGACAT	M64929	CCDS34867.1, CCDS55213.1	8p21.2	2013-01-10	2010-04-14		ENSG00000221914	ENSG00000221914	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"", ""WD repeat domain containing"""	9304	protein-coding gene	gene with protein product	"""PP2A subunit B isoform alpha"""	604941	"""protein phosphatase 2 (formerly 2A), regulatory subunit B (PR 52), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B, alpha isoform"""			1849734	Standard	NM_001177591		Approved	PR52A, PR55A, B55A		P63151	OTTHUMG00000163850	ENST00000380737.3:c.789T>C	chr8.hg19:g.26220351T>C		82.0	0.0		82.0	27.0	NM_001177591	B2RBU8|B4E1T7|P50409|Q00007	Silent	SNP	ENST00000380737.3	hg19	CCDS34867.1																																																																																			.	.		0.368	PPP2R2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375954.2	NM_002717	
DMRT3	58524	hgsc.bcm.edu	37	9	990709	990709	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:990709A>G	ENST00000190165.2	+	2	1161	c.1123A>G	c.(1123-1125)Act>Gct	p.T375A		NM_021240.2	NP_067063.1	Q9NQL9	DMRT3_HUMAN	doublesex and mab-3 related transcription factor 3	375					adult walking behavior (GO:0007628)|male sex differentiation (GO:0046661)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sex differentiation (GO:0007548)|transcription, DNA-templated (GO:0006351)|transmission of nerve impulse (GO:0019226)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(10;1.39e-08)|Lung NSC(10;1.42e-08)		Lung(218;0.0196)		GCTGAGGAATACTTTGGCGAG	0.587																																					p.T375A		Atlas-SNP	.											.	DMRT3	83	.	0			c.A1123G						.						44.0	43.0	44.0					9																	990709		2203	4300	6503	SO:0001583	missense	58524	exon2			AGGAATACTTTGG	AJ301581	CCDS6443.1	9p24.3	2008-07-21	2001-12-17	2001-12-07	ENSG00000064218	ENSG00000064218			13909	protein-coding gene	gene with protein product	"""testis-specific protein"""	614754	"""DMRT-like family A3"""	DMRTA3		11543627, 10729223	Standard	NM_021240		Approved		uc003zgw.2	Q9NQL9	OTTHUMG00000019436	ENST00000190165.2:c.1123A>G	chr9.hg19:g.990709A>G	ENSP00000190165:p.Thr375Ala	74.0	0.0		76.0	27.0	NM_021240	Q7LA03|Q7LCH8|Q96SC7|Q9NRQ9	Missense_Mutation	SNP	ENST00000190165.2	hg19	CCDS6443.1	.	.	.	.	.	.	.	.	.	.	A	17.23	3.336566	0.60963	.	.	ENSG00000064218	ENST00000190165	T	0.23552	1.9	5.15	5.15	0.70609	.	0.204155	0.40908	D	0.000995	T	0.20333	0.0489	L	0.27053	0.805	0.38314	D	0.943341	P	0.48089	0.905	B	0.40825	0.341	T	0.06698	-1.0812	10	0.45353	T	0.12	-20.5388	15.0003	0.71466	1.0:0.0:0.0:0.0	.	375	Q9NQL9	DMRT3_HUMAN	A	375	ENSP00000190165:T375A	ENSP00000190165:T375A	T	+	1	0	DMRT3	980709	1.000000	0.71417	0.976000	0.42696	0.998000	0.95712	6.447000	0.73465	1.939000	0.56221	0.533000	0.62120	ACT	.	.		0.587	DMRT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051490.1	NM_021240	
C9orf24	84688	hgsc.bcm.edu	37	9	34380993	34380993	+	Silent	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:34380993G>T	ENST00000297623.2	-	5	807	c.609C>A	c.(607-609)ggC>ggA	p.G203G	C9orf24_ENST00000481295.1_5'Flank|C9orf24_ENST00000379127.1_Silent_p.G68G|C9orf24_ENST00000379124.1_Silent_p.G68G|C9orf24_ENST00000379126.3_Intron|C9orf24_ENST00000379133.3_Silent_p.G68G	NM_032596.3	NP_115985.2	Q8NCR6	SMRP1_HUMAN	chromosome 9 open reading frame 24	203					cell differentiation (GO:0030154)|cellular protein complex assembly (GO:0043623)|spermatogenesis (GO:0007283)	manchette (GO:0002177)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5			LUSC - Lung squamous cell carcinoma(29;0.0107)	GBM - Glioblastoma multiforme(74;0.123)		AGTAGTGGCGGCCCGAGCAAG	0.706																																					p.G203G		Atlas-SNP	.											.	C9orf24	15	.	0			c.C609A						.						14.0	18.0	17.0					9																	34380993		2116	4168	6284	SO:0001819	synonymous_variant	84688	exon5			GTGGCGGCCCGAG	BC029484	CCDS6553.1, CCDS6554.1, CCDS6555.1, CCDS59121.1	9p11.2	2013-01-11			ENSG00000164972	ENSG00000164972			19919	protein-coding gene	gene with protein product	"""ciliated bronchial epithelium 1"", ""spermatid-specific manchette-related protein 1"""					12029067	Standard	NM_147168		Approved	bA573M23.4, NYD-SP22, MGC32921, MGC33614, CBE1, SMRP1	uc003zuh.1	Q8NCR6	OTTHUMG00000000437	ENST00000297623.2:c.609C>A	chr9.hg19:g.34380993G>T		63.0	0.0		57.0	34.0	NM_032596	Q5T598|Q5T599|Q5T5A0|Q8N9G4|Q96KD1|Q96LN1	Silent	SNP	ENST00000297623.2	hg19	CCDS6554.1																																																																																			.	.		0.706	C9orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001098.3	NM_147169	
FBXO10	26267	hgsc.bcm.edu	37	9	37525102	37525102	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:37525102T>A	ENST00000432825.2	-	6	1822	c.1774A>T	c.(1774-1776)Aca>Tca	p.T592S	FBXO10_ENST00000543968.1_5'UTR|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Missense_Mutation_p.T117S	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	592					apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		TCCGTACCTGTGATGAGGCCT	0.577																																					p.T592S		Atlas-SNP	.											.	FBXO10	75	.	0			c.A1774T						.						34.0	34.0	34.0					9																	37525102		2022	4153	6175	SO:0001583	missense	26267	exon6			TACCTGTGATGAG	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.1774A>T	chr9.hg19:g.37525102T>A	ENSP00000403802:p.Thr592Ser	76.0	0.0		82.0	37.0	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	hg19	CCDS47966.1	.	.	.	.	.	.	.	.	.	.	T	18.03	3.532211	0.64972	.	.	ENSG00000147912	ENST00000432825;ENST00000541829	T;T	0.79749	-1.15;-1.3	4.96	3.75	0.43078	Pectin lyase fold/virulence factor (1);Carbohydrate-binding/sugar hydrolysis domain (1);	0.000000	0.85682	D	0.000000	T	0.78521	0.4296	N	0.20401	0.57	0.48762	D	0.999709	P;B;D	0.69078	0.816;0.267;0.997	B;B;D	0.65773	0.265;0.089;0.938	T	0.75246	-0.3385	10	0.27082	T	0.32	.	10.5322	0.44983	0.0:0.0:0.1621:0.8378	.	471;117;592	Q59F51;Q08AL4;Q9UK96	.;.;FBX10_HUMAN	S	592;117	ENSP00000403802:T592S;ENSP00000441307:T117S	ENSP00000403802:T592S	T	-	1	0	FBXO10	37515102	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.746000	0.62133	1.858000	0.53909	0.533000	0.62120	ACA	.	.		0.577	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
PGM5	5239	hgsc.bcm.edu	37	9	71006638	71006638	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:71006638G>T	ENST00000396396.1	+	5	1115	c.886G>T	c.(886-888)Ggg>Tgg	p.G296W	PGM5_ENST00000604870.2_3'UTR|PGM5_ENST00000396392.1_Missense_Mutation_p.G296W	NM_021965.3	NP_068800.2	Q15124	PGM5_HUMAN	phosphoglucomutase 5	296					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)	cell-cell adherens junction (GO:0005913)|costamere (GO:0043034)|cytoplasmic side of plasma membrane (GO:0009898)|dystrophin-associated glycoprotein complex (GO:0016010)|focal adhesion (GO:0005925)|intercalated disc (GO:0014704)|sarcolemma (GO:0042383)|spot adherens junction (GO:0005914)|stress fiber (GO:0001725)|Z disc (GO:0030018)	intramolecular transferase activity, phosphotransferases (GO:0016868)|magnesium ion binding (GO:0000287)|structural molecule activity (GO:0005198)			endometrium(5)|kidney(1)|large_intestine(5)|liver(2)|lung(15)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	34						TGATGCTGATGGGGTAAGTAG	0.458																																					p.G296W		Atlas-SNP	.											.	PGM5	80	.	0			c.G886T						.						84.0	79.0	81.0					9																	71006638		2201	4298	6499	SO:0001583	missense	5239	exon5			GCTGATGGGGTAA	L40933	CCDS6622.2	9q13	2008-02-05			ENSG00000154330	ENSG00000154330			8908	protein-coding gene	gene with protein product	"""phosphoglucomutase-related protein"""	600981				8586438, 8631316	Standard	NM_021965		Approved	PGMRP	uc004agr.3	Q15124	OTTHUMG00000019966	ENST00000396396.1:c.886G>T	chr9.hg19:g.71006638G>T	ENSP00000379678:p.Gly296Trp	130.0	0.0		145.0	63.0	NM_021965	B1AM46|B4DLQ6|Q5VYV3|Q8N527|Q9UDH4	Missense_Mutation	SNP	ENST00000396396.1	hg19	CCDS6622.2	.	.	.	.	.	.	.	.	.	.	.	23.7	4.449125	0.84101	.	.	ENSG00000154330	ENST00000396396;ENST00000396392	T;T	0.67523	-0.25;-0.27	5.13	5.13	0.70059	Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III (2);Alpha-D-phosphohexomutase, alpha/beta/alpha domain II (1);	0.000000	0.85682	D	0.000000	D	0.88526	0.6460	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92693	0.6168	10	0.87932	D	0	.	17.3325	0.87269	0.0:0.0:1.0:0.0	.	296	Q15124	PGM5_HUMAN	W	296	ENSP00000379678:G296W;ENSP00000379674:G296W	ENSP00000379674:G296W	G	+	1	0	PGM5	70196458	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	9.736000	0.98828	2.386000	0.81285	0.555000	0.69702	GGG	.	.		0.458	PGM5-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052548.2	NM_021965	
PCSK5	5125	hgsc.bcm.edu	37	9	78722181	78722181	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:78722181G>A	ENST00000545128.1	+	9	1660	c.1122G>A	c.(1120-1122)ctG>ctA	p.L374L	PCSK5_ENST00000376767.3_Silent_p.L374L|PCSK5_ENST00000376752.4_Silent_p.L374L	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	374	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						CTACAGATCTGAGGCAGCGTT	0.473																																					p.L374L		Atlas-SNP	.											.	PCSK5	329	.	0			c.G1122A						.						61.0	54.0	57.0					9																	78722181		2203	4300	6503	SO:0001819	synonymous_variant	5125	exon9			AGATCTGAGGCAG		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.1122G>A	chr9.hg19:g.78722181G>A		52.0	0.0		65.0	25.0	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	hg19	CCDS55320.1																																																																																			.	.		0.473	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PIP5KL1	138429	hgsc.bcm.edu	37	9	130688228	130688228	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:130688228G>A	ENST00000388747.4	-	8	725	c.681C>T	c.(679-681)cgC>cgT	p.R227R	PIP5KL1_ENST00000300432.3_Silent_p.R24R|PIP5KL1_ENST00000490773.1_Intron	NM_001135219.1	NP_001128691.1	Q5T9C9	PI5L1_HUMAN	phosphatidylinositol-4-phosphate 5-kinase-like 1	227	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cell projection (GO:0042995)|cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|skin(1)	8						GATCCACCCAGCGGCTCACCT	0.572																																					p.R227R		Atlas-SNP	.											.	PIP5KL1	38	.	0			c.C681T						.						43.0	45.0	44.0					9																	130688228		2203	4300	6503	SO:0001819	synonymous_variant	138429	exon8			CACCCAGCGGCTC	BC042184	CCDS6885.1, CCDS48030.1	9q34.13	2008-02-05			ENSG00000167103	ENSG00000167103			28711	protein-coding gene	gene with protein product		612865				12477932	Standard	NM_001135219		Approved	bA203J24.5, MGC46424	uc011mao.2	Q5T9C9	OTTHUMG00000020719	ENST00000388747.4:c.681C>T	chr9.hg19:g.130688228G>A		75.0	0.0		56.0	28.0	NM_001135219	Q8IVS3	Silent	SNP	ENST00000388747.4	hg19	CCDS48030.1																																																																																			.	.		0.572	PIP5KL1-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054289.2	NM_173492	
USP20	10868	hgsc.bcm.edu	37	9	132614914	132614914	+	Splice_Site	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:132614914A>G	ENST00000315480.4	+	3	238	c.80A>G	c.(79-81)aAg>aGg	p.K27R	USP20_ENST00000358355.1_Splice_Site_p.K27R|USP20_ENST00000372429.3_Splice_Site_p.K27R			Q9Y2K6	UBP20_HUMAN	ubiquitin specific peptidase 20	27					endocytosis (GO:0006897)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|ubiquitin-dependent protein catabolic process (GO:0006511)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	cysteine-type endopeptidase activity (GO:0004197)|G-protein coupled receptor binding (GO:0001664)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|urinary_tract(1)	11		Ovarian(14;0.00556)				CTCAAATCTAAGGTAAAGGGT	0.567																																					p.K27R		Atlas-SNP	.											.	USP20	186	.	0			c.A80G						.						26.0	27.0	27.0					9																	132614914		1895	4111	6006	SO:0001630	splice_region_variant	10868	exon3			AATCTAAGGTAAA	AB023220	CCDS43892.1	9q34.2	2014-07-15	2005-08-08		ENSG00000136878	ENSG00000136878		"""Ubiquitin-specific peptidases"""	12619	protein-coding gene	gene with protein product		615143	"""ubiquitin specific protease 20"""			12838346	Standard	NM_006676		Approved	KIAA1003	uc004byr.3	Q9Y2K6	OTTHUMG00000020793	ENST00000315480.4:c.81+1A>G	chr9.hg19:g.132614914A>G		121.0	0.0		125.0	55.0	NM_001008563	Q541F1|Q8IXQ1|Q96LG5|Q9UQN8|Q9UQP0	Missense_Mutation	SNP	ENST00000315480.4	hg19	CCDS43892.1	.	.	.	.	.	.	.	.	.	.	A	18.46	3.629852	0.67015	.	.	ENSG00000136878	ENST00000372429;ENST00000315480;ENST00000358355	T;T;T	0.18810	2.19;2.19;2.19	5.69	5.69	0.88448	Zinc finger, RING/FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	T	0.38081	0.1027	L	0.50333	1.59	0.80722	D	1	D	0.71674	0.998	D	0.76071	0.987	T	0.06320	-1.0833	10	0.20519	T	0.43	.	13.9059	0.63836	1.0:0.0:0.0:0.0	.	27	Q9Y2K6	UBP20_HUMAN	R	27	ENSP00000361506:K27R;ENSP00000313811:K27R;ENSP00000351122:K27R	ENSP00000313811:K27R	K	+	2	0	USP20	131654735	1.000000	0.71417	1.000000	0.80357	0.476000	0.33039	8.165000	0.89663	2.163000	0.67991	0.533000	0.62120	AAG	.	.		0.567	USP20-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054604.2		Missense_Mutation
PRRC2B	84726	hgsc.bcm.edu	37	9	134323169	134323169	+	Silent	SNP	C	C	G	rs569503281		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:134323169C>G	ENST00000357304.4	+	8	1153	c.1098C>G	c.(1096-1098)gcC>gcG	p.A366A	PRRC2B_ENST00000372249.1_5'UTR|PRRC2B_ENST00000458550.1_Silent_p.A366A|PRRC2B_ENST00000405995.1_Silent_p.A366A	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	366							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						ATCTGGACGCCGATGCCGATG	0.602																																					p.A366A		Atlas-SNP	.											.	PRRC2B	266	.	0			c.C1098G						.						41.0	43.0	42.0					9																	134323169		2013	4173	6186	SO:0001819	synonymous_variant	84726	exon8			GGACGCCGATGCC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1098C>G	chr9.hg19:g.134323169C>G		85.0	0.0		62.0	27.0	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Silent	SNP	ENST00000357304.4	hg19	CCDS48044.1																																																																																			.	.		0.602	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
EGFL7	51162	hgsc.bcm.edu	37	9	139564771	139564772	+	Missense_Mutation	DNP	CC	CC	AA			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr9:139564771_139564772CC>AA	ENST00000371699.1	+	7	1471_1472	c.560_561CC>AA	c.(559-561)cCC>cAA	p.P187Q	EGFL7_ENST00000308874.7_Missense_Mutation_p.P187Q|EGFL7_ENST00000492002.1_3'UTR|EGFL7_ENST00000406555.3_Missense_Mutation_p.P187Q|EGFL7_ENST00000371698.3_Missense_Mutation_p.P187Q|MIR126_ENST00000362291.1_RNA			Q9UHF1	EGFL7_HUMAN	EGF-like-domain, multiple 7	187					angiogenesis (GO:0001525)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|negative regulation of cell migration (GO:0030336)|negative regulation of Notch signaling pathway (GO:0045746)|positive regulation of endothelial cell proliferation (GO:0001938)|vasculogenesis (GO:0001570)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	calcium ion binding (GO:0005509)			kidney(2)|ovary(1)|prostate(2)|urinary_tract(1)	6	all_cancers(76;0.109)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		AGGGTGGCCCCCAACCCGACAG	0.663																																					p.P187H|p.P187P		Atlas-SNP	.											.	EGFL7	11	.	0			c.C560A|c.C561A						.																																			SO:0001583	missense	51162	exon8			TGGCCCCCAACCC|GGCCCCCAACCCG	AF186111	CCDS7002.1	9q34.3	2008-02-05			ENSG00000172889	ENSG00000172889			20594	protein-coding gene	gene with protein product		608582					Standard	NM_016215		Approved	ZNEU1	uc004cih.3	Q9UHF1	OTTHUMG00000020938	Exception_encountered	chr9.hg19:g.139564771_139564772delinsAA	ENSP00000360764:p.Pro187Gln	138.0|135.0	0.0		136.0|134.0	61.0|60.0	NM_016215	B3KRP0|M9VTX9|Q5M7Y5|Q5VUD5|Q96EG0	Missense_Mutation|Silent	SNP	ENST00000371699.1	hg19	CCDS7002.1																																																																																			.	.		0.663	EGFL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055094.1	NM_016215	
PCDH15	65217	hgsc.bcm.edu	37	10	55955639	55955639	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr10:55955639T>A	ENST00000320301.6	-	11	1503	c.1109A>T	c.(1108-1110)gAc>gTc	p.D370V	PCDH15_ENST00000373957.3_Missense_Mutation_p.D348V|PCDH15_ENST00000373965.2_Missense_Mutation_p.D370V|PCDH15_ENST00000395433.1_Missense_Mutation_p.D348V|PCDH15_ENST00000395445.1_Missense_Mutation_p.D370V|PCDH15_ENST00000361849.3_Missense_Mutation_p.D370V|PCDH15_ENST00000395440.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395438.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395446.1_Missense_Mutation_p.D370V|PCDH15_ENST00000373955.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395430.1_Missense_Mutation_p.D370V|PCDH15_ENST00000395432.2_Missense_Mutation_p.D333V|PCDH15_ENST00000409834.1_5'UTR|PCDH15_ENST00000437009.1_Missense_Mutation_p.D370V|PCDH15_ENST00000414778.1_Missense_Mutation_p.D375V	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	370	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)			NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATGACCATTGTCTTGTTCAGC	0.348										HNSCC(58;0.16)																											p.D375V		Atlas-SNP	.											.	PCDH15	1715	.	0			c.A1124T						.						97.0	95.0	96.0					10																	55955639		2203	4300	6503	SO:0001583	missense	65217	exon12			CCATTGTCTTGTT	AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.1109A>T	chr10.hg19:g.55955639T>A	ENSP00000322604:p.Asp370Val	116.0	0.0		106.0	34.0	NM_001142763	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	hg19	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	T	19.70	3.876232	0.72180	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000395445;ENST00000395446;ENST00000395440;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000373957;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.37584	1.19;1.19;1.19;1.19;1.19;1.19;2.48;1.19;1.19;1.19;1.19;1.19;1.19;1.19	5.17	5.17	0.71159	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.52092	0.1713	M	0.64567	1.98	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.999;0.999;1.0;1.0;1.0;1.0;1.0;0.999;0.974;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;P;D;D;D;D	0.97110	0.998;0.991;0.986;0.96;0.999;0.991;0.998;0.987;0.991;0.986;0.841;0.993;1.0;0.999;0.993	T	0.51309	-0.8722	9	0.06365	T	0.9	.	14.6657	0.68907	0.0:0.0:0.0:1.0	.	348;370;370;375;370;333;370;370;370;370;370;375;370;348;370	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;A2A3D8;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	V	370;375;370;370;370;370;370;333;370;348;348;370;370;375;370;370	ENSP00000363076:D370V;ENSP00000410304:D375V;ENSP00000378826:D370V;ENSP00000378832:D370V;ENSP00000378833:D370V;ENSP00000378827:D370V;ENSP00000378820:D333V;ENSP00000354950:D370V;ENSP00000378821:D348V;ENSP00000363068:D348V;ENSP00000322604:D370V;ENSP00000378818:D370V;ENSP00000412628:D370V;ENSP00000363066:D370V	ENSP00000322604:D370V	D	-	2	0	PCDH15	55625645	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	8.008000	0.88588	1.963000	0.57068	0.482000	0.46254	GAC	.	.		0.348	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2	NM_033056	
CDKN1C	1028	hgsc.bcm.edu	37	11	2906108	2906108	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:2906108C>T	ENST00000414822.3	-	1	1003	c.612G>A	c.(610-612)ccG>ccA	p.P204P	CDKN1C_ENST00000313407.6_Silent_p.P193P|CDKN1C_ENST00000380725.1_Intron|CDKN1C_ENST00000440480.2_Silent_p.P193P|CDKN1C_ENST00000430149.2_Silent_p.P204P	NM_000076.2	NP_000067.1	P49918	CDN1C_HUMAN	cyclin-dependent kinase inhibitor 1C (p57, Kip2)	204	9 X 4 AA repeats of P-A-P-A.				adrenal gland development (GO:0030325)|aging (GO:0007568)|camera-type eye development (GO:0043010)|cell cycle arrest (GO:0007050)|digestive system development (GO:0055123)|embryonic placenta morphogenesis (GO:0060669)|genetic imprinting (GO:0071514)|kidney development (GO:0001822)|multicellular organism growth (GO:0035264)|myeloid cell differentiation (GO:0030099)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of kinase activity (GO:0033673)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron maturation (GO:0042551)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|skeletal system development (GO:0001501)|uterus development (GO:0060065)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)			central_nervous_system(1)|lung(1)	2		all_epithelial(84;0.000187)|Medulloblastoma(188;0.00106)|Ovarian(85;0.0014)|Breast(177;0.00328)|all_neural(188;0.00681)|all_lung(207;0.157)|Lung NSC(207;0.216)		BRCA - Breast invasive adenocarcinoma(625;0.0025)|LUSC - Lung squamous cell carcinoma(625;0.19)		gggccggggccggggccgggg	0.866																																					p.P204P	GBM(111;59 1151 2497 5746 16112 18241 29216)	Atlas-SNP	.											.	CDKN1C	4	.	0			c.G612A						.						1.0	1.0	1.0					11																	2906108		7	20	27	SO:0001819	synonymous_variant	1028	exon1			CGGGGCCGGGGCC	D64137	CCDS7738.1, CCDS44519.1	11p15.5	2014-09-17	2004-02-13		ENSG00000129757	ENSG00000129757			1786	protein-coding gene	gene with protein product		600856	"""Beckwith-Wiedemann syndrome"""	BWCR, BWS		7729684	Standard	NM_000076		Approved	P57, KIP2	uc001lws.4	P49918	OTTHUMG00000010040	ENST00000414822.3:c.612G>A	chr11.hg19:g.2906108C>T		13.0	0.0		22.0	9.0	NM_000076		Silent	SNP	ENST00000414822.3	hg19	CCDS7738.1																																																																																			.	.		0.866	CDKN1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027774.2	NM_000076	
CPSF7	79869	hgsc.bcm.edu	37	11	61196760	61196760	+	5'UTR	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:61196760C>T	ENST00000394888.4	-	0	120				CPSF7_ENST00000439958.3_5'UTR|SDHAF2_ENST00000301761.2_5'Flank|CPSF7_ENST00000340437.4_Missense_Mutation_p.G26D|SDHAF2_ENST00000534878.1_5'Flank|RP11-286N22.8_ENST00000543044.1_5'Flank|SDHAF2_ENST00000543265.1_5'Flank|CPSF7_ENST00000448745.1_5'UTR|SDHAF2_ENST00000542074.1_5'Flank|CPSF7_ENST00000541963.1_5'UTR|SDHAF2_ENST00000537782.1_5'Flank	NM_001136040.2	NP_001129512.1	Q8N684	CPSF7_HUMAN	cleavage and polyadenylation specific factor 7, 59kDa						gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|protein tetramerization (GO:0051262)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(5)|skin(2)|upper_aerodigestive_tract(1)	22						AAGGAAGATGCCACTGCGGGA	0.512																																					p.G26D		Atlas-SNP	.											.	CPSF7	46	.	0			c.G77A						.						75.0	66.0	69.0					11																	61196760		692	1591	2283	SO:0001623	5_prime_UTR_variant	79869	exon2			AAGATGCCACTGC		CCDS8006.2, CCDS44619.1, CCDS44620.1	11q12.2	2013-06-18			ENSG00000149532	ENSG00000149532		"""RNA binding motif (RRM) containing"""	30098	protein-coding gene	gene with protein product	"""pre mRNA cleavage factor I, 59 kDa subunit"", ""cleavage factor Im complex 59 kDa subunit"""					12477932	Standard	NM_024811		Approved	FLJ12529	uc001nrp.3	Q8N684	OTTHUMG00000168198	ENST00000394888.4:c.-53G>A	chr11.hg19:g.61196760C>T		59.0	0.0		65.0	4.0	NM_024811	B3KU04|C9K0Q4|Q7Z3H9|Q9H025|Q9H9V1	Missense_Mutation	SNP	ENST00000394888.4	hg19	CCDS44619.1	.	.	.	.	.	.	.	.	.	.	C	14.43	2.532142	0.45073	.	.	ENSG00000149532	ENST00000340437	.	.	.	4.82	3.89	0.44902	.	.	.	.	.	T	0.60183	0.2249	.	.	.	0.80722	D	1	D	0.61080	0.989	P	0.49252	0.604	T	0.65022	-0.6269	7	0.87932	D	0	.	10.4887	0.44737	0.1941:0.8059:0.0:0.0	.	26	Q8N684-3	.	D	26	.	ENSP00000345412:G26D	G	-	2	0	CPSF7	60953336	1.000000	0.71417	1.000000	0.80357	0.452000	0.32318	1.572000	0.36461	1.367000	0.46095	0.563000	0.77884	GGC	.	.		0.512	CPSF7-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347835.2	NM_024811	
MAML2	84441	hgsc.bcm.edu	37	11	95712358	95712358	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:95712358G>A	ENST00000524717.1	-	5	4509	c.3225C>T	c.(3223-3225)ggC>ggT	p.G1075G		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	1075					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				GCTGGTTGATGCCCGTCCTCG	0.502			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.G1075G		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.C3225T						.						140.0	139.0	139.0					11																	95712358		1977	4160	6137	SO:0001819	synonymous_variant	84441	exon5			GTTGATGCCCGTC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.3225C>T	chr11.hg19:g.95712358G>A		67.0	0.0		77.0	29.0	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	hg19	CCDS44714.1																																																																																			.	.		0.502	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
PRDM10	56980	hgsc.bcm.edu	37	11	129814881	129814881	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:129814881C>A	ENST00000360871.3	-	6	778	c.547G>T	c.(547-549)Gct>Tct	p.A183S	PRDM10_ENST00000423662.2_Missense_Mutation_p.A97S|PRDM10_ENST00000358825.5_Missense_Mutation_p.A183S|PRDM10_ENST00000304538.6_Missense_Mutation_p.A97S|PRDM10_ENST00000526082.1_Missense_Mutation_p.A97S|PRDM10_ENST00000528746.1_Missense_Mutation_p.A157S	NM_199437.1	NP_955469.1	Q9NQV6	PRD10_HUMAN	PR domain containing 10	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(2)|endometrium(6)|kidney(3)|large_intestine(14)|lung(15)|pancreas(2)|skin(1)|stomach(3)|urinary_tract(2)	48	all_hematologic(175;0.0537)	Breast(109;0.000496)|Lung NSC(97;0.000693)|all_lung(97;0.00151)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0174)|Lung(977;0.176)|LUSC - Lung squamous cell carcinoma(976;0.185)		CACACTGAAGCATGCGCGTTA	0.557																																					p.A183S		Atlas-SNP	.											.	PRDM10	120	.	0			c.G547T						.						47.0	46.0	47.0					11																	129814881		2201	4297	6498	SO:0001583	missense	56980	exon6			CTGAAGCATGCGC	AF275817	CCDS8484.1, CCDS8485.1, CCDS44771.1, CCDS44772.1	11q24.3	2013-01-08			ENSG00000170325	ENSG00000170325		"""Zinc fingers, C2H2-type"""	13995	protein-coding gene	gene with protein product	"""PRDM zinc finger transcription factor"", ""PR-domain family member 7"", ""tristanin"""					12175877	Standard	NM_020228		Approved	KIAA1231, PFM7, MGC131802	uc001qfm.3	Q9NQV6	OTTHUMG00000165762	ENST00000360871.3:c.547G>T	chr11.hg19:g.129814881C>A	ENSP00000354118:p.Ala183Ser	289.0	0.0		282.0	134.0	NM_020228	B7ZL71|G3XAE5|J3KP23|Q17R90|Q2KHR4|Q863Z2|Q9NXI4|Q9ULI9	Missense_Mutation	SNP	ENST00000360871.3	hg19	CCDS8484.1	.	.	.	.	.	.	.	.	.	.	A	9.276	1.046957	0.19748	.	.	ENSG00000170325	ENST00000358825;ENST00000304538;ENST00000360871;ENST00000423662;ENST00000528746;ENST00000526082	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	5.5	4.37	0.52481	.	0.067621	0.64402	N	0.000014	T	0.19248	0.0462	N	0.14661	0.345	0.22412	N	0.999128	B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0;0.0;0.0	T	0.18555	-1.0333	10	0.11794	T	0.64	-14.9963	2.9904	0.05981	0.5479:0.2324:0.2197:0.0	.	97;183;183;183;97;97;97	B7ZL72;Q9NQV6-4;G3XAE5;Q9NQV6;Q9NQV6-5;Q9NQV6-2;Q9NQV6-1	.;.;.;PRD10_HUMAN;.;.;.	S	183;97;183;97;157;97	ENSP00000351686:A183S;ENSP00000302669:A97S;ENSP00000354118:A183S;ENSP00000398431:A97S;ENSP00000431262:A157S;ENSP00000432237:A97S	ENSP00000302669:A97S	A	-	1	0	PRDM10	129320091	1.000000	0.71417	0.969000	0.41365	0.987000	0.75469	4.106000	0.57804	1.026000	0.39733	-0.264000	0.10439	GCT	.	.		0.557	PRDM10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386076.1	NM_199437	
JAM3	83700	hgsc.bcm.edu	37	11	134018672	134018672	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr11:134018672G>A	ENST00000299106.4	+	8	1015	c.856G>A	c.(856-858)Ggg>Agg	p.G286R	NCAPD3_ENST00000526787.2_5'Flank|JAM3_ENST00000441717.3_Missense_Mutation_p.G235R|JAM3_ENST00000529443.2_Missense_Mutation_p.G331R			Q9BX67	JAM3_HUMAN	junctional adhesion molecule 3	286					adaptive immune response (GO:0002250)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|establishment of cell polarity (GO:0030010)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|myelination (GO:0042552)|myeloid progenitor cell differentiation (GO:0002318)|neutrophil homeostasis (GO:0001780)|regulation of actin cytoskeleton organization by cell-cell adhesion (GO:0090138)|regulation of neutrophil chemotaxis (GO:0090022)|spermatid development (GO:0007286)|transmission of nerve impulse (GO:0019226)	cell-cell contact zone (GO:0044291)|desmosome (GO:0030057)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|plasma membrane (GO:0005886)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	integrin binding (GO:0005178)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)	10	all_hematologic(175;0.127)	all_cancers(12;1.06e-21)|all_epithelial(12;3.37e-16)|all_lung(97;7.03e-06)|Lung NSC(97;1.67e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0506)|Esophageal squamous(93;0.0566)		Epithelial(10;1.55e-09)|BRCA - Breast invasive adenocarcinoma(10;1.35e-08)|all cancers(11;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00402)|Lung(977;0.245)		CAAGAACCCAGGGAAACCAGA	0.448																																					p.G286R		Atlas-SNP	.											.	JAM3	41	.	0			c.G856A						.						79.0	76.0	77.0					11																	134018672		2201	4297	6498	SO:0001583	missense	83700	exon8			AACCCAGGGAAAC	AF356518	CCDS8494.1, CCDS55799.1, CCDS8494.2	11q25	2013-01-29			ENSG00000166086	ENSG00000166086		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15532	protein-coding gene	gene with protein product		606871					Standard	NM_032801		Approved	JAM-C, JAMC	uc001qhb.3	Q9BX67	OTTHUMG00000167130	ENST00000299106.4:c.856G>A	chr11.hg19:g.134018672G>A	ENSP00000299106:p.Gly286Arg	256.0	0.0		262.0	150.0	NM_032801	B3KWG9|Q8WWL8|Q96FL1	Missense_Mutation	SNP	ENST00000299106.4	hg19	CCDS8494.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.9|20.9	4.068672|4.068672	0.76301|0.76301	.|.	.|.	ENSG00000166086|ENSG00000166086	ENST00000299106;ENST00000441717|ENST00000529443	T|.	0.77877|.	-1.13|.	6.04|6.04	6.04|6.04	0.98038|0.98038	.|.	0.059506|.	0.64402|.	D|.	0.000003|.	T|T	0.51736|0.51736	0.1692|0.1692	L|L	0.36672|0.36672	1.1|1.1	0.35080|0.35080	D|D	0.763311|0.763311	P;P|.	0.47302|.	0.893;0.893|.	B;B|.	0.42319|.	0.383;0.383|.	T|T	0.58358|0.58358	-0.7650|-0.7650	10|5	0.13108|.	T|.	0.6|.	.|.	13.0035|13.0035	0.58690|0.58690	0.0735:0.0:0.9265:0.0|0.0735:0.0:0.9265:0.0	.|.	235;286|.	B3KWG9;Q9BX67|.	.;JAM3_HUMAN|.	R|K	331;235|239	ENSP00000395742:G235R|.	ENSP00000299106:G331R|.	G|R	+|+	1|2	0|0	JAM3|JAM3	133523882|133523882	1.000000|1.000000	0.71417|0.71417	0.974000|0.974000	0.42286|0.42286	0.952000|0.952000	0.60782|0.60782	5.576000|5.576000	0.67437|0.67437	2.873000|2.873000	0.98535|0.98535	0.563000|0.563000	0.77884|0.77884	GGG|AGG	.	.		0.448	JAM3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000393303.4	NM_032801	
ARID2	196528	hgsc.bcm.edu	37	12	46243941	46243941	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr12:46243941C>T	ENST00000334344.6	+	15	2207	c.2035C>T	c.(2035-2037)Caa>Taa	p.Q679*	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Nonsense_Mutation_p.Q289*|ARID2_ENST00000422737.1_Nonsense_Mutation_p.Q530*|ARID2_ENST00000457135.1_5'Flank	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	679					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TACTGTGGCACAAACTGTTTC	0.413			"""N, S, F"""		hepatocellular carcinoma																																p.Q679X		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.C2035T						.						146.0	139.0	142.0					12																	46243941		2203	4300	6503	SO:0001587	stop_gained	196528	exon15			GTGGCACAAACTG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.2035C>T	chr12.hg19:g.46243941C>T	ENSP00000335044:p.Gln679*	178.0	0.0		175.0	68.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Nonsense_Mutation	SNP	ENST00000334344.6	hg19	CCDS31783.1	.	.	.	.	.	.	.	.	.	.	C	40	7.956362	0.98580	.	.	ENSG00000189079	ENST00000334344;ENST00000422737;ENST00000444670	.	.	.	5.95	5.95	0.96441	.	0.325040	0.32002	N	0.006735	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.08599	T	0.76	-3.6635	18.5659	0.91116	0.0:1.0:0.0:0.0	.	.	.	.	X	679;530;289	.	ENSP00000335044:Q679X	Q	+	1	0	ARID2	44530208	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.036000	0.70948	2.825000	0.97269	0.655000	0.94253	CAA	.	.		0.413	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	
CEP290	80184	hgsc.bcm.edu	37	12	88447463	88447463	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr12:88447463G>T	ENST00000552810.1	-	52	7438	c.7095C>A	c.(7093-7095)aaC>aaA	p.N2365K	CEP290_ENST00000309041.7_Missense_Mutation_p.N2367K|CEP290_ENST00000397838.3_Missense_Mutation_p.N1425K|RNA5SP364_ENST00000516938.1_RNA|CEP290_ENST00000547691.2_Missense_Mutation_p.N1425K	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	2365					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						TTTGGTCCTTGTTAGCTTCTA	0.333																																					p.N2365K		Atlas-SNP	.											.	CEP290	195	.	0			c.C7095A						.						104.0	93.0	97.0					12																	88447463		1815	4068	5883	SO:0001583	missense	80184	exon52			GTCCTTGTTAGCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.7095C>A	chr12.hg19:g.88447463G>T	ENSP00000448012:p.Asn2365Lys	39.0	0.0		73.0	26.0	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Missense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	G	4.353	0.064952	0.08388	.	.	ENSG00000198707	ENST00000547691;ENST00000552810;ENST00000309041;ENST00000397838	T;T;T;T	0.62639	0.59;0.01;0.01;0.59	4.95	2.09	0.27110	.	0.977834	0.08439	N	0.945765	T	0.47173	0.1431	L	0.40543	1.245	0.09310	N	1	B	0.18166	0.026	B	0.20767	0.031	T	0.34775	-0.9815	10	0.06099	T	0.92	.	7.1342	0.25519	0.4593:0.0:0.5407:0.0	.	2365	O15078	CE290_HUMAN	K	1425;2365;2367;1425	ENSP00000446905:N1425K;ENSP00000448012:N2365K;ENSP00000308021:N2367K;ENSP00000380938:N1425K	ENSP00000308021:N2367K	N	-	3	2	CEP290	86971594	0.005000	0.15991	0.731000	0.30826	0.138000	0.21146	0.712000	0.25779	0.634000	0.30469	-0.136000	0.14681	AAC	.	.		0.333	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
PARP4	143	hgsc.bcm.edu	37	13	25068806	25068806	+	Missense_Mutation	SNP	C	C	T	rs145170390		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr13:25068806C>T	ENST00000381989.3	-	7	751	c.646G>A	c.(646-648)Gaa>Aaa	p.E216K		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	216					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		ATGTAATTTTCAAAGTATTCA	0.338																																					p.E216K		Atlas-SNP	.											.	PARP4	142	.	0			c.G646A						.						142.0	139.0	140.0					13																	25068806		2203	4300	6503	SO:0001583	missense	143	exon7			AATTTTCAAAGTA	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.646G>A	chr13.hg19:g.25068806C>T	ENSP00000371419:p.Glu216Lys	87.0	0.0		54.0	17.0	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	C	14.06	2.421784	0.43020	.	.	ENSG00000102699	ENST00000381989	T	0.46819	0.86	4.52	4.52	0.55395	.	0.214121	0.36972	N	0.002302	T	0.63908	0.2551	M	0.73598	2.24	0.31828	N	0.625074	D	0.67145	0.996	D	0.65443	0.935	T	0.65751	-0.6092	10	0.18276	T	0.48	-20.4413	14.772	0.69688	0.0:1.0:0.0:0.0	.	216	Q9UKK3	PARP4_HUMAN	K	216	ENSP00000371419:E216K	ENSP00000371419:E216K	E	-	1	0	PARP4	23966806	0.997000	0.39634	0.621000	0.29145	0.045000	0.14185	2.644000	0.46613	2.361000	0.80049	0.549000	0.68633	GAA	.	C|1.000;G|0.000		0.338	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
TM9SF2	9375	hgsc.bcm.edu	37	13	100193842	100193842	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr13:100193842T>A	ENST00000376387.4	+	9	1128	c.938T>A	c.(937-939)tTc>tAc	p.F313Y		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	313					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					ATTGTTCTCTTCTTATCTGGA	0.353																																					p.F313Y		Atlas-SNP	.											.	TM9SF2	52	.	0			c.T938A						.						245.0	218.0	227.0					13																	100193842		2203	4300	6503	SO:0001583	missense	9375	exon9			TTCTCTTCTTATC	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.938T>A	chr13.hg19:g.100193842T>A	ENSP00000365567:p.Phe313Tyr	145.0	0.0		95.0	49.0	NM_004800	A8K399|Q2TAY5	Missense_Mutation	SNP	ENST00000376387.4	hg19	CCDS9493.1	.	.	.	.	.	.	.	.	.	.	T	32	5.158203	0.94686	.	.	ENSG00000125304	ENST00000376387	T	0.59906	0.23	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.84352	0.5453	H	0.98218	4.175	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.71656	0.968;0.974	D	0.90402	0.4403	10	0.87932	D	0	-24.4181	15.1335	0.72545	0.0:0.0:0.0:1.0	.	279;313	E9PHW5;Q99805	.;TM9S2_HUMAN	Y	313	ENSP00000365567:F313Y	ENSP00000365567:F313Y	F	+	2	0	TM9SF2	98991843	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.015000	0.88690	1.965000	0.57142	0.477000	0.44152	TTC	.	.		0.353	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		
KTN1	3895	hgsc.bcm.edu	37	14	56139682	56139682	+	Silent	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr14:56139682A>G	ENST00000395314.3	+	39	3707	c.3639A>G	c.(3637-3639)ctA>ctG	p.L1213L	KTN1_ENST00000413890.2_Silent_p.L1190L|KTN1_ENST00000438792.2_Silent_p.L1184L|KTN1_ENST00000395308.1_Silent_p.L1190L|KTN1_ENST00000395311.1_Silent_p.L1190L|KTN1_ENST00000416613.1_Silent_p.L1213L|KTN1_ENST00000554507.1_Silent_p.L479L|KTN1_ENST00000555573.1_Silent_p.L218L|KTN1_ENST00000395309.3_Silent_p.L1213L	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	1213					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						AAATGGAACTAGAAAAGGCAG	0.353			T	RET	papillary thryoid																																p.L1213L		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.A3639G						.						104.0	99.0	101.0					14																	56139682		2203	4300	6503	SO:0001819	synonymous_variant	3895	exon39			GGAACTAGAAAAG		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.3639A>G	chr14.hg19:g.56139682A>G		171.0	0.0		234.0	98.0	NM_001079521	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	hg19	CCDS41957.1	.	.	.	.	.	.	.	.	.	.	A	8.283	0.815967	0.16607	.	.	ENSG00000126777	ENST00000554294	.	.	.	6.17	3.57	0.40892	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-5.4107	4.9122	0.13827	0.6628:0.0:0.2113:0.1259	.	.	.	.	W	12	.	.	X	+	2	0	KTN1	55209435	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.611000	0.46334	0.444000	0.26612	0.533000	0.62120	TAG	.	.		0.353	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
PLEKHH1	57475	hgsc.bcm.edu	37	14	68028676	68028676	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr14:68028676G>A	ENST00000329153.5	+	6	561	c.429G>A	c.(427-429)gaG>gaA	p.E143E		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	143						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		CTCAGCTTGAGATGGAGAATC	0.438																																					p.E143E		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G429A						.						67.0	68.0	67.0					14																	68028676		1949	4145	6094	SO:0001819	synonymous_variant	57475	exon6			GCTTGAGATGGAG	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.429G>A	chr14.hg19:g.68028676G>A		182.0	0.0		169.0	92.0	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Silent	SNP	ENST00000329153.5	hg19	CCDS45128.1																																																																																			.	.		0.438	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
TBL3	10607	hgsc.bcm.edu	37	16	2026919	2026919	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr16:2026919C>T	ENST00000568546.1	+	14	1525	c.1397C>T	c.(1396-1398)cCt>cTt	p.P466L		NM_006453.2	NP_006444.2	Q12788	TBL3_HUMAN	transducin (beta)-like 3	466					G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|intracellular signal transduction (GO:0035556)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|endometrium(2)|kidney(4)|lung(7)|ovary(1)|prostate(2)|skin(1)	18						GACAACGGCCCTATCCTCCTG	0.607																																					p.P466L	Melanoma(118;616 1651 35077 38081 48633)	Atlas-SNP	.											.	TBL3	54	.	0			c.C1397T						.						110.0	89.0	96.0					16																	2026919		2198	4300	6498	SO:0001583	missense	10607	exon14			ACGGCCCTATCCT	U02609	CCDS10453.1	16p13.3	2013-01-10			ENSG00000183751	ENSG00000183751		"""WD repeat domain containing"""	11587	protein-coding gene	gene with protein product		605915				8307582	Standard	NM_006453		Approved	SAZD, UTP13	uc002cnu.1	Q12788	OTTHUMG00000128710	ENST00000568546.1:c.1397C>T	chr16.hg19:g.2026919C>T	ENSP00000454836:p.Pro466Leu	129.0	0.0		101.0	56.0	NM_006453	Q59GD6|Q8IVB7|Q96A78	Missense_Mutation	SNP	ENST00000568546.1	hg19	CCDS10453.1	.	.	.	.	.	.	.	.	.	.	C	3.105	-0.183853	0.06340	.	.	ENSG00000183751	ENST00000332704	.	.	.	5.27	3.28	0.37604	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.283721	0.29239	N	0.012723	T	0.42675	0.1213	M	0.71036	2.16	0.18873	N	0.999981	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.001	T	0.29212	-1.0019	9	0.27082	T	0.32	-13.1892	8.2339	0.31614	0.0:0.7559:0.0:0.2441	.	228;466	A0JLS5;Q12788	.;TBL3_HUMAN	L	466	.	ENSP00000331815:P466L	P	+	2	0	TBL3	1966920	0.137000	0.22531	0.007000	0.13788	0.015000	0.08874	1.400000	0.34577	1.182000	0.42928	0.561000	0.74099	CCT	.	.		0.607	TBL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250615.3	NM_006453	
VPS9D1	9605	hgsc.bcm.edu	37	16	89777150	89777150	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr16:89777150C>A	ENST00000389386.3	-	10	1226	c.1102G>T	c.(1102-1104)Gac>Tac	p.D368Y	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Missense_Mutation_p.D298Y	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	368					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										GATGCGGTGTCCCCCAGGGGT	0.731																																					p.D368Y		Atlas-SNP	.											.	.	.	.	0			c.G1102T						.						7.0	8.0	7.0					16																	89777150		1864	4077	5941	SO:0001583	missense	9605	exon10			CGGTGTCCCCCAG	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1102G>T	chr16.hg19:g.89777150C>A	ENSP00000374037:p.Asp368Tyr	148.0	0.0		122.0	13.0	NM_004913		Missense_Mutation	SNP	ENST00000389386.3	hg19	CCDS42220.1	.	.	.	.	.	.	.	.	.	.	C	5.460	0.269970	0.10349	.	.	ENSG00000075399	ENST00000389386	.	.	.	4.02	1.96	0.26148	.	0.443923	0.25086	N	0.033260	T	0.31420	0.0796	L	0.36672	1.1	0.09310	N	1	B	0.29136	0.234	B	0.22753	0.041	T	0.21930	-1.0231	9	0.72032	D	0.01	-1.6351	12.2821	0.54769	0.0:0.4574:0.5426:0.0	.	368	Q9Y2B5	CP007_HUMAN	Y	368	.	ENSP00000374037:D368Y	D	-	1	0	C16orf7	88304651	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.408000	0.21065	0.258000	0.21686	0.561000	0.74099	GAC	.	.		0.731	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
TP53	7157	hgsc.bcm.edu	37	17	7578177	7578177	+	Splice_Site	SNP	C	C	T	rs267605076		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:7578177C>T	ENST00000269305.4	-	6	861	c.672G>A	c.(670-672)gaG>gaA	p.E224E	TP53_ENST00000359597.4_Splice_Site_p.E224E|TP53_ENST00000413465.2_Splice_Site_p.E224E|TP53_ENST00000455263.2_Splice_Site_p.E224E|TP53_ENST00000574684.1_Intron|TP53_ENST00000420246.2_Splice_Site_p.E224E|TP53_ENST00000445888.2_Splice_Site_p.E224E	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	224	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with FBXO42.|Required for interaction with ZNF385A.		E -> D (in sporadic cancers; somatic mutation).|E -> G (in sporadic cancers; somatic mutation).|E -> K (in sporadic cancers; somatic mutation).|E -> V (in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.E224D(20)|p.?(13)|p.E224E(12)|p.0?(8)|p.E131D(3)|p.E131E(2)|p.V218_E224delVPYEPPE(1)|p.V225fs*24(1)|p.E224_V225insXX(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	CAAACCAGACCTCAGGCGGCT	0.532		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.E224E	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,colon,carcinoma,0,1	TP53	33396	.	61	Substitution - Missense(23)|Substitution - coding silent(14)|Unknown(13)|Whole gene deletion(8)|Deletion - In frame(1)|Insertion - Frameshift(1)|Insertion - In frame(1)	lung(23)|large_intestine(7)|bone(6)|biliary_tract(5)|endometrium(5)|oesophagus(3)|breast(3)|stomach(2)|central_nervous_system(2)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)|ovary(1)|liver(1)	c.G672A						.						81.0	76.0	78.0					17																	7578177		2203	4300	6503	SO:0001630	splice_region_variant	7157	exon6	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	CCAGACCTCAGGC	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.672+1G>A	chr17.hg19:g.7578177C>T		134.0	0.0		56.0	41.0	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Silent	SNP	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.532	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	Silent
DNAH2	146754	hgsc.bcm.edu	37	17	7695575	7695575	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:7695575G>A	ENST00000572933.1	+	46	8519	c.7059G>A	c.(7057-7059)acG>acA	p.T2353T	DNAH2_ENST00000389173.2_Silent_p.T2353T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2353					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CTTAGGACACGGTATATGAGT	0.532																																					p.T2353T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G7059A						.						84.0	79.0	81.0					17																	7695575		2203	4300	6503	SO:0001819	synonymous_variant	146754	exon45			GGACACGGTATAT	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.7059G>A	chr17.hg19:g.7695575G>A		122.0	0.0		45.0	32.0	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	hg19	CCDS32551.1																																																																																			.	.		0.532	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
RCVRN	5957	hgsc.bcm.edu	37	17	9808459	9808459	+	Silent	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:9808459G>T	ENST00000226193.5	-	1	479	c.39C>A	c.(37-39)atC>atA	p.I13I		NM_002903.2	NP_002894.1	P35243	RECO_HUMAN	recoverin	13					phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of calcium ion transport (GO:0051924)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	dendrite (GO:0030425)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	12						GCTCCTCCAGGATCTCCTTGG	0.637																																					p.I13I		Atlas-SNP	.											.	RCVRN	34	.	0			c.C39A						.						26.0	25.0	26.0					17																	9808459		2203	4300	6503	SO:0001819	synonymous_variant	5957	exon1			CTCCAGGATCTCC	BC001720	CCDS11151.1	17p13.1	2013-01-10		2006-09-26	ENSG00000109047	ENSG00000109047		"""EF-hand domain containing"""	9937	protein-coding gene	gene with protein product		179618		RCV1		1387789, 12507501, 1467959, 12789533	Standard	NM_002903		Approved		uc002gme.1	P35243	OTTHUMG00000130268	ENST00000226193.5:c.39C>A	chr17.hg19:g.9808459G>T		71.0	0.0		42.0	38.0	NM_002903	Q53XL0	Silent	SNP	ENST00000226193.5	hg19	CCDS11151.1																																																																																			.	.		0.637	RCVRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252600.2	NM_002903	
SYNRG	11276	hgsc.bcm.edu	37	17	35913872	35913872	+	Silent	SNP	A	A	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:35913872A>T	ENST00000339208.6	-	14	2093	c.1953T>A	c.(1951-1953)tcT>tcA	p.S651S	SYNRG_ENST00000345615.4_Silent_p.S573S|SYNRG_ENST00000585472.1_Silent_p.S572S|SYNRG_ENST00000588194.1_5'UTR|SYNRG_ENST00000591288.1_Silent_p.S490S|SYNRG_ENST00000502449.2_Silent_p.S573S|SYNRG_ENST00000346661.4_Silent_p.S651S|SYNRG_ENST00000394378.2_Silent_p.S573S	NM_001163544.1|NM_001163545.1|NM_007247.4	NP_001157016.1|NP_001157017.1|NP_009178.3	Q9UMZ2	SYNRG_HUMAN	synergin, gamma	651	Interaction with A1P1G1 and A1P1G2.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)	AP-1 adaptor complex (GO:0030121)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(14)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						TAGTAGCAGCAGAACCTGTTG	0.408																																					p.S651S		Atlas-SNP	.											.	SYNRG	101	.	0			c.T1953A						.						94.0	86.0	89.0					17																	35913872		2203	4300	6503	SO:0001819	synonymous_variant	11276	exon14			AGCAGCAGAACCT	AF169548	CCDS11321.1, CCDS11322.1, CCDS11322.2, CCDS54113.1, CCDS54114.1, CCDS59284.1, CCDS59285.1	17q12	2014-04-16	2009-07-20	2009-07-20	ENSG00000006114	ENSG00000275066			557	protein-coding gene	gene with protein product	"""gamma-synergin"", ""adaptor-related protein complex 1 gamma subunit-binding protein 1"""	607291	"""AP1 gamma subunit binding protein 1"""	AP1GBP1		10477754	Standard	XM_005256980		Approved	SYNG, MGC104959	uc010wdf.2	Q9UMZ2	OTTHUMG00000188473	ENST00000339208.6:c.1953T>A	chr17.hg19:g.35913872A>T		122.0	0.0		91.0	39.0	NM_007247	A8MWU4|B7ZKZ2|B7ZKZ3|Q17RI2|Q5BKU5|Q6ZT17	Silent	SNP	ENST00000339208.6	hg19	CCDS11321.1																																																																																			.	.		0.408	SYNRG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256811.2	NM_007247	
FASN	2194	hgsc.bcm.edu	37	17	80038356	80038356	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:80038356C>T	ENST00000306749.2	-	40	7155	c.6937G>A	c.(6937-6939)Gtg>Atg	p.V2313M	FASN_ENST00000579758.1_Intron	NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	2313	Thioesterase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	TCAAAGGCCACGCAGGCCCCG	0.657																																					p.V2313M	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G6937A						.						18.0	17.0	17.0					17																	80038356		2171	4278	6449	SO:0001583	missense	2194	exon40			AGGCCACGCAGGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.6937G>A	chr17.hg19:g.80038356C>T	ENSP00000304592:p.Val2313Met	86.0	0.0		63.0	31.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.397298	0.83120	.	.	ENSG00000169710	ENST00000306749	T	0.32988	1.43	4.63	3.63	0.41609	Thioesterase (1);	0.073354	0.53938	D	0.000048	T	0.57475	0.2056	M	0.83384	2.64	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.65496	-0.6154	10	0.87932	D	0	-25.8076	13.9652	0.64205	0.1529:0.8471:0.0:0.0	.	2313	P49327	FAS_HUMAN	M	2313	ENSP00000304592:V2313M	ENSP00000304592:V2313M	V	-	1	0	FASN	77631645	1.000000	0.71417	0.995000	0.50966	0.945000	0.59286	7.469000	0.80959	1.128000	0.42052	0.591000	0.81541	GTG	.	.		0.657	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
FOXK2	3607	hgsc.bcm.edu	37	17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						.						1.0	1.0	1.0					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	4.0	0.0		5.0	2.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
POTEC	388468	hgsc.bcm.edu	37	18	14542926	14542926	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr18:14542926C>A	ENST00000358970.5	-	1	219	c.220G>T	c.(220-222)Ggg>Tgg	p.G74W	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	74										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						GTGCCGCTCCCCCTGCAGCAG	0.567																																					p.G74W		Atlas-SNP	.											.	POTEC	129	.	0			c.G220T						.						46.0	56.0	53.0					18																	14542926		692	1591	2283	SO:0001583	missense	388468	exon1			CGCTCCCCCTGCA	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.220G>T	chr18.hg19:g.14542926C>A	ENSP00000351856:p.Gly74Trp	565.0	0.0		390.0	83.0	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	hg19	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	C	9.225	1.034438	0.19590	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.48522	0.81	0.429	-0.773	0.10995	.	.	.	.	.	T	0.53642	0.1809	L	0.43152	1.355	0.09310	N	1	D	0.89917	1.0	D	0.78314	0.991	T	0.43956	-0.9359	8	0.66056	D	0.02	.	.	.	.	.	74	B2RU33	POTEC_HUMAN	W	74	ENSP00000351856:G74W	ENSP00000351856:G74W	G	-	1	0	POTEC	14532926	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	-0.144000	0.10280	-0.401000	0.07644	0.175000	0.17021	GGG	.	.		0.567	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
ANKRD24	170961	hgsc.bcm.edu	37	19	4202880	4202880	+	Silent	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:4202880G>A	ENST00000600132.1	+	7	699	c.423G>A	c.(421-423)gtG>gtA	p.V141V	ANKRD24_ENST00000262970.5_Silent_p.V231V|ANKRD24_ENST00000318934.4_Silent_p.V141V	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	141										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CCTGCGTGGTGGACGTCGTGG	0.647																																					p.V141V		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G423A						.						18.0	22.0	21.0					19																	4202880		2030	4184	6214	SO:0001819	synonymous_variant	170961	exon7			CGTGGTGGACGTC	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.423G>A	chr19.hg19:g.4202880G>A		271.0	0.0		248.0	105.0	NM_133475	O75268|O95781	Silent	SNP	ENST00000600132.1	hg19	CCDS45925.1																																																																																			.	.		0.647	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
MUC16	94025	hgsc.bcm.edu	37	19	9066696	9066696	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:9066696A>T	ENST00000397910.4	-	3	20953	c.20750T>A	c.(20749-20751)aTg>aAg	p.M6917K		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	6919	Thr-rich.				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						GGTGGTATCCATTGGAGCTGT	0.458																																					p.M6917K		Atlas-SNP	.											.	MUC16	4315	.	0			c.T20750A						.						306.0	288.0	294.0					19																	9066696		2079	4206	6285	SO:0001583	missense	94025	exon3			GTATCCATTGGAG	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.20750T>A	chr19.hg19:g.9066696A>T	ENSP00000381008:p.Met6917Lys	89.0	0.0		82.0	39.0	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	hg19	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	a	4.484	0.089666	0.08632	.	.	ENSG00000181143	ENST00000397910	T	0.23754	1.89	2.77	0.355	0.16069	.	.	.	.	.	T	0.21022	0.0506	L	0.50333	1.59	.	.	.	B	0.24426	0.103	B	0.28385	0.089	T	0.31586	-0.9938	8	0.87932	D	0	.	2.757	0.05295	0.4099:0.2102:0.0:0.3799	.	6917	B5ME49	.	K	6917	ENSP00000381008:M6917K	ENSP00000381008:M6917K	M	-	2	0	MUC16	8927696	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.748000	0.01826	-0.049000	0.13379	0.334000	0.21626	ATG	.	.		0.458	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
ZNF302	55900	hgsc.bcm.edu	37	19	35175888	35175888	+	Missense_Mutation	SNP	C	C	T	rs528898854	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:35175888C>T	ENST00000446502.2	+	6	1286	c.1078C>T	c.(1078-1080)Cgt>Tgt	p.R360C	ZNF302_ENST00000505365.2_3'UTR|ZNF302_ENST00000505242.1_Missense_Mutation_p.R316C|ZNF302_ENST00000423823.2_Missense_Mutation_p.R316C|ZNF302_ENST00000457781.2_Missense_Mutation_p.R316C			Q9NR11	ZN302_HUMAN	zinc finger protein 302	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|skin(1)	6	all_lung(56;6.16e-07)|Lung NSC(56;9.71e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0849)			CTATGAGTGTCGTATATGTGG	0.408													C|||	2	0.000399361	0.0	0.0014	5008	,	,		22638	0.001		0.0	False		,,,				2504	0.0				p.R316C		Atlas-SNP	.											.	ZNF302	27	.	0			c.C946T						.						62.0	63.0	63.0					19																	35175888		2203	4300	6503	SO:0001583	missense	55900	exon5			GAGTGTCGTATAT	AF155656	CCDS46042.1, CCDS74330.1, CCDS74331.1, CCDS74332.1, CCDS74333.1	19q13.2	2013-01-08			ENSG00000089335	ENSG00000089335		"""Zinc fingers, C2H2-type"", ""-"""	13848	protein-coding gene	gene with protein product							Standard	NM_018675		Approved	ZNF327, ZNF135L, ZNF140L	uc002nvq.1	Q9NR11	OTTHUMG00000163329	ENST00000446502.2:c.1078C>T	chr19.hg19:g.35175888C>T	ENSP00000396379:p.Arg360Cys	138.0	0.0		164.0	53.0	NM_018443	Q658J3|Q9BZD8|Q9P0J4	Missense_Mutation	SNP	ENST00000446502.2	hg19		.	.	.	.	.	.	.	.	.	.	C	12.77	2.037061	0.35893	.	.	ENSG00000089335	ENST00000457781;ENST00000505242;ENST00000423823;ENST00000446502	T;T;T;T	0.15139	3.13;3.13;3.13;2.45	0.967	0.967	0.19674	.	.	.	.	.	T	0.22975	0.0555	L	0.41824	1.3	0.33248	D	0.558185	D;D	0.76494	0.999;0.999	P;P	0.61800	0.894;0.784	T	0.37361	-0.9709	9	0.87932	D	0	.	4.1867	0.10402	0.3993:0.6006:0.0:0.0	.	360;316	E7EVR1;Q9NR11-2	.;.	C	316;316;316;360	ENSP00000391067:R316C;ENSP00000421028:R316C;ENSP00000405219:R316C;ENSP00000396379:R360C	ENSP00000405219:R316C	R	+	1	0	ZNF302	39867728	0.000000	0.05858	0.999000	0.59377	0.876000	0.50452	-0.811000	0.04500	0.822000	0.34565	0.467000	0.42956	CGT	.	.		0.408	ZNF302-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000372731.1		
ZNF383	163087	hgsc.bcm.edu	37	19	37734077	37734077	+	Missense_Mutation	SNP	G	G	C			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:37734077G>C	ENST00000589413.1	+	8	1522	c.939G>C	c.(937-939)aaG>aaC	p.K313N	ZNF383_ENST00000590503.1_Missense_Mutation_p.K313N|ZNF383_ENST00000352998.3_Missense_Mutation_p.K313N			Q8NA42	ZN383_HUMAN	zinc finger protein 383	313					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|skin(1)	15			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATGAATGTAAGGAATGTGGCA	0.413																																					p.K313N		Atlas-SNP	.											.	ZNF383	42	.	0			c.G939C						.						71.0	75.0	74.0					19																	37734077		2203	4300	6503	SO:0001583	missense	163087	exon5			ATGTAAGGAATGT	AY438646	CCDS12501.1	19q13.13	2013-01-08				ENSG00000188283		"""Zinc fingers, C2H2-type"", ""-"""	18609	protein-coding gene	gene with protein product							Standard	NM_152604		Approved	FLJ35863	uc002ofu.1	Q8NA42		ENST00000589413.1:c.939G>C	chr19.hg19:g.37734077G>C	ENSP00000464871:p.Lys313Asn	86.0	0.0		94.0	38.0	NM_152604	Q6X2C7	Missense_Mutation	SNP	ENST00000589413.1	hg19	CCDS12501.1	.	.	.	.	.	.	.	.	.	.	G	9.761	1.170025	0.21621	.	.	ENSG00000188283	ENST00000352998	T	0.07908	3.15	3.84	1.65	0.23941	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.33364	N	0.004984	T	0.05593	0.0147	N	0.03238	-0.38	0.09310	N	1	P	0.49358	0.923	P	0.59761	0.863	T	0.31447	-0.9943	10	0.08179	T	0.78	.	4.693	0.12790	0.1062:0.0:0.5101:0.3837	.	313	Q8NA42	ZN383_HUMAN	N	313	ENSP00000340132:K313N	ENSP00000340132:K313N	K	+	3	2	ZNF383	42425917	0.000000	0.05858	0.998000	0.56505	0.992000	0.81027	-1.608000	0.02068	0.394000	0.25230	0.563000	0.77884	AAG	.	.		0.413	ZNF383-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458141.1	NM_152604	
CCDC155	147872	hgsc.bcm.edu	37	19	49899026	49899026	+	Splice_Site	SNP	G	G	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:49899026G>A	ENST00000447857.3	+	5	541	c.336G>A	c.(334-336)ggG>ggA	p.G112G		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	112						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						TTTGATACAGGGGATTAGAGC	0.602																																					p.G112G		Atlas-SNP	.											.	CCDC155	46	.	0			c.G336A						.						21.0	23.0	22.0					19																	49899026		1948	4129	6077	SO:0001630	splice_region_variant	147872	exon5			ATACAGGGGATTA		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.336-1G>A	chr19.hg19:g.49899026G>A		42.0	0.0		33.0	16.0	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	hg19	CCDS46140.1																																																																																			.	.		0.602	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	Silent
SHANK1	50944	hgsc.bcm.edu	37	19	51170472	51170472	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:51170472G>T	ENST00000293441.1	-	22	4763	c.4745C>A	c.(4744-4746)tCg>tAg	p.S1582*	SHANK1_ENST00000391814.1_Nonsense_Mutation_p.S1590*|SHANK1_ENST00000359082.3_Nonsense_Mutation_p.S1573*|SHANK1_ENST00000391813.1_Nonsense_Mutation_p.S969*|SYT3_ENST00000544769.1_Intron	NM_016148.2	NP_057232.2	Q9Y566	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains 1	1582					adult behavior (GO:0030534)|associative learning (GO:0008306)|cytoskeletal anchoring at plasma membrane (GO:0007016)|dendritic spine morphogenesis (GO:0060997)|determination of affect (GO:0050894)|habituation (GO:0046959)|long-term memory (GO:0007616)|negative regulation of actin filament bundle assembly (GO:0032232)|neuromuscular process controlling balance (GO:0050885)|olfactory behavior (GO:0042048)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|protein complex assembly (GO:0006461)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|righting reflex (GO:0060013)|social behavior (GO:0035176)|synapse maturation (GO:0060074)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|excitatory synapse (GO:0060076)|intracellular (GO:0005622)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	ankyrin repeat binding (GO:0071532)|GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|somatostatin receptor binding (GO:0031877)			breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)	64		all_neural(266;0.057)		OV - Ovarian serous cystadenocarcinoma(262;0.00493)|GBM - Glioblastoma multiforme(134;0.0199)		CGTGAGGGGCGACTCTGGCTT	0.682																																					p.S1582X		Atlas-SNP	.											.	SHANK1	210	.	0			c.C4745A						.						23.0	21.0	21.0					19																	51170472		2191	4290	6481	SO:0001587	stop_gained	50944	exon22			AGGGGCGACTCTG	AF163302	CCDS12799.1	19q13.3	2013-01-10			ENSG00000161681	ENSG00000161681		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	15474	protein-coding gene	gene with protein product	"""somatostatin receptor-interacting protein"""	604999				10551867	Standard	NM_016148		Approved	SSTRIP, SPANK-1, synamon	uc002psx.1	Q9Y566	OTTHUMG00000137380	ENST00000293441.1:c.4745C>A	chr19.hg19:g.51170472G>T	ENSP00000293441:p.Ser1582*	98.0	0.0		63.0	12.0	NM_016148	A8MXP5|B7WNY6|Q9NYW9	Nonsense_Mutation	SNP	ENST00000293441.1	hg19	CCDS12799.1	.	.	.	.	.	.	.	.	.	.	G	41	9.073028	0.99057	.	.	ENSG00000161681	ENST00000293441;ENST00000391813;ENST00000359082;ENST00000391814	.	.	.	2.01	2.01	0.26516	.	1.276450	0.06678	U	0.767426	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	.	11.0388	0.47818	0.0:0.0:1.0:0.0	.	.	.	.	X	1582;969;1573;1590	.	ENSP00000293441:S1582X	S	-	2	0	SHANK1	55862284	0.163000	0.22920	1.000000	0.80357	0.269000	0.26545	1.626000	0.37039	1.141000	0.42275	0.205000	0.17691	TCG	.	.		0.682	SHANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268071.1	NM_016148	
HAS1	3036	hgsc.bcm.edu	37	19	52222893	52222893	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:52222893C>A	ENST00000222115.1	-	2	302	c.268G>T	c.(268-270)Gat>Tat	p.D90Y	HAS1_ENST00000601714.1_Missense_Mutation_p.D97Y|HAS1_ENST00000540069.2_Missense_Mutation_p.D89Y|HAS1_ENST00000594621.1_5'Flank	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	90					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		GTGGCTGCATCCAgcggcccc	0.741																																					p.D90Y	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G268T						.						2.0	3.0	3.0					19																	52222893		1753	3453	5206	SO:0001583	missense	3036	exon2			CTGCATCCAGCGG	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.268G>T	chr19.hg19:g.52222893C>A	ENSP00000222115:p.Asp90Tyr	104.0	0.0		89.0	45.0	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	hg19	CCDS12838.1	.	.	.	.	.	.	.	.	.	.	.	11.01	1.511895	0.27036	.	.	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.32988	1.43;1.43	3.8	2.47	0.30058	.	22.652400	0.00649	U	0.000543	T	0.20088	0.0483	N	0.24115	0.695	0.09310	N	0.999999	B;B;P	0.34699	0.092;0.056;0.464	B;B;B	0.27796	0.077;0.035;0.083	T	0.28996	-1.0026	10	0.66056	D	0.02	-4.7942	3.3268	0.07070	0.0:0.5427:0.265:0.1923	.	89;90;89	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	Y	89;90	ENSP00000445021:D89Y;ENSP00000222115:D90Y	ENSP00000222115:D90Y	D	-	1	0	HAS1	56914705	0.000000	0.05858	0.018000	0.16275	0.012000	0.07955	0.212000	0.17497	1.815000	0.52974	0.397000	0.26171	GAT	.	.		0.741	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
ZNF628	89887	hgsc.bcm.edu	37	19	55995321	55995321	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:55995321G>T	ENST00000598519.1	+	3	3314	c.2761G>T	c.(2761-2763)Gat>Tat	p.D921Y	ZNF628_ENST00000391718.2_Missense_Mutation_p.D917Y|NAT14_ENST00000591590.1_5'Flank|NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000587400.1_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	921					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TGTGGTCCAGGATGTCCTCTT	0.657																																					p.D921Y		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2761T						.						43.0	32.0	36.0					19																	55995321		2201	4299	6500	SO:0001583	missense	89887	exon3			GTCCAGGATGTCC	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2761G>T	chr19.hg19:g.55995321G>T	ENSP00000469591:p.Asp921Tyr	96.0	0.0		108.0	47.0	NM_033113	Q86X34	Missense_Mutation	SNP	ENST00000598519.1	hg19	CCDS33116.3	.	.	.	.	.	.	.	.	.	.	.	13.80	2.344801	0.41498	.	.	ENSG00000197483	ENST00000391718	T	0.13307	2.6	3.81	3.81	0.43845	.	0.000000	0.48286	U	0.000191	T	0.16300	0.0392	N	0.19112	0.55	0.25303	N	0.989265	D	0.61080	0.989	P	0.53912	0.737	T	0.04078	-1.0979	10	0.87932	D	0	.	13.5636	0.61804	0.0:0.0:1.0:0.0	.	917	Q5EBL2	ZN628_HUMAN	Y	917	ENSP00000375598:D917Y	ENSP00000375598:D917Y	D	+	1	0	ZNF628	60687133	0.998000	0.40836	0.990000	0.47175	0.834000	0.47266	3.860000	0.55995	1.850000	0.53721	0.289000	0.19496	GAT	.	.		0.657	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
ZNF304	57343	hgsc.bcm.edu	37	19	57867488	57867488	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:57867488T>A	ENST00000282286.5	+	3	424	c.251T>A	c.(250-252)cTt>cAt	p.L84H	ZNF304_ENST00000391705.3_Missense_Mutation_p.L84H|ZNF304_ENST00000598744.1_Missense_Mutation_p.L42H|ZNF304_ENST00000443917.2_Missense_Mutation_p.L131H			Q9HCX3	ZN304_HUMAN	zinc finger protein 304	84	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)	26		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0265)		GAGTCAGGTCTTTTCCAGAAA	0.488																																					p.L84H		Atlas-SNP	.											.	ZNF304	74	.	0			c.T251A						.						119.0	101.0	107.0					19																	57867488		2203	4300	6503	SO:0001583	missense	57343	exon3			CAGGTCTTTTCCA	AJ276316	CCDS12950.1, CCDS74462.1	19q13.4	2013-01-08				ENSG00000131845		"""Zinc fingers, C2H2-type"", ""-"""	13505	protein-coding gene	gene with protein product		613840					Standard	XM_005259090		Approved		uc010ygw.2	Q9HCX3		ENST00000282286.5:c.251T>A	chr19.hg19:g.57867488T>A	ENSP00000282286:p.Leu84His	187.0	0.0		156.0	66.0	NM_020657		Missense_Mutation	SNP	ENST00000282286.5	hg19	CCDS12950.1	.	.	.	.	.	.	.	.	.	.	T	2.328	-0.354132	0.05173	.	.	ENSG00000131845	ENST00000282286;ENST00000391705;ENST00000443917	T;T;T	0.08807	3.05;3.05;3.05	3.37	-2.58	0.06228	Krueppel-associated box (1);	.	.	.	.	T	0.03263	0.0095	N	0.19112	0.55	0.09310	N	1	B;B	0.33379	0.41;0.41	B;B	0.28849	0.044;0.095	T	0.41858	-0.9485	9	0.15499	T	0.54	.	0.3201	0.00302	0.1943:0.2914:0.1923:0.322	.	84;131	Q9HCX3;E7EQD3	ZN304_HUMAN;.	H	84;84;131	ENSP00000282286:L84H;ENSP00000375586:L84H;ENSP00000401642:L131H	ENSP00000282286:L84H	L	+	2	0	ZNF304	62559300	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.184000	0.03076	-0.329000	0.08527	-1.247000	0.01520	CTT	.	.		0.488	ZNF304-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465785.1		
TPX2	22974	hgsc.bcm.edu	37	20	30381706	30381706	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr20:30381706C>T	ENST00000300403.6	+	14	2093	c.1565C>T	c.(1564-1566)cCt>cTt	p.P522L	TPX2_ENST00000340513.4_Missense_Mutation_p.P558L	NM_012112.4	NP_036244.2	Q9ULW0	TPX2_HUMAN	TPX2, microtubule-associated	522					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|mitotic nuclear division (GO:0007067)|regulation of mitotic spindle organization (GO:0060236)	axon hillock (GO:0043203)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	28			Epithelial(4;0.000771)|Colorectal(19;0.00306)|all cancers(5;0.004)|COAD - Colon adenocarcinoma(19;0.0347)|OV - Ovarian serous cystadenocarcinoma(3;0.0656)			TATGGGGTGCCTTTTAAGCCC	0.433																																					p.P522L		Atlas-SNP	.											.	TPX2	61	.	0			c.C1565T						.						167.0	172.0	170.0					20																	30381706		2203	4300	6503	SO:0001583	missense	22974	exon14			GGGTGCCTTTTAA	AF098158	CCDS13190.1	20q11.2	2013-07-23	2013-07-23	2003-10-08	ENSG00000088325	ENSG00000088325			1249	protein-coding gene	gene with protein product		605917	"""chromosome 20 open reading frame 1"", ""TPX2, microtubule-associated, homolog (Xenopus laevis)"""	C20orf2, C20orf1		9207457, 10393424	Standard	NM_012112		Approved	p100, DIL-2	uc002wwp.1	Q9ULW0	OTTHUMG00000032190	ENST00000300403.6:c.1565C>T	chr20.hg19:g.30381706C>T	ENSP00000300403:p.Pro522Leu	230.0	0.0		226.0	91.0	NM_012112	Q9H1R4|Q9NRA3|Q9UFN9|Q9UL00|Q9Y2M1	Missense_Mutation	SNP	ENST00000300403.6	hg19	CCDS13190.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.981270	0.93044	.	.	ENSG00000088325	ENST00000300403;ENST00000340513	T	0.56103	0.48	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	T	0.78188	0.4244	M	0.86343	2.81	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.80476	-0.1366	10	0.87932	D	0	-12.8529	19.545	0.95291	0.0:1.0:0.0:0.0	.	558;522	Q96RR5;Q9ULW0	.;TPX2_HUMAN	L	522;558	ENSP00000341145:P558L	ENSP00000300403:P522L	P	+	2	0	TPX2	29845367	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.824000	0.75288	2.861000	0.98227	0.655000	0.94253	CCT	.	.		0.433	TPX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078569.2		
PRDM15	63977	hgsc.bcm.edu	37	21	43221607	43221607	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr21:43221607C>T	ENST00000269844.3	-	31	4427	c.4317G>A	c.(4315-4317)caG>caA	p.Q1439Q	PRDM15_ENST00000422911.1_Silent_p.Q1130Q|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000398548.1_Silent_p.Q1110Q|PRDM15_ENST00000447207.2_Silent_p.Q1073Q|PRDM15_ENST00000538201.1_Silent_p.Q1093Q	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1439					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						GGGCCACAGACTGTGGGTTCG	0.612																																					p.Q1439Q		Atlas-SNP	.											.	PRDM15	110	.	0			c.G4317A						.						111.0	92.0	98.0					21																	43221607		2203	4300	6503	SO:0001819	synonymous_variant	63977	exon31			CACAGACTGTGGG	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.4317G>A	chr21.hg19:g.43221607C>T		226.0	0.0		131.0	74.0	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	hg19	CCDS13676.1																																																																																			.	.		0.612	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
CDC42EP1	11135	hgsc.bcm.edu	37	22	37964811	37964811	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr22:37964811A>G	ENST00000249014.4	+	3	1580	c.1160A>G	c.(1159-1161)gAt>gGt	p.D387G		NM_152243.2	NP_689449.1	Q00587	BORG5_HUMAN	CDC42 effector protein (Rho GTPase binding) 1	387					positive regulation of pseudopodium assembly (GO:0031274)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)				endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(4)|prostate(5)	15	Melanoma(58;0.0574)					GAGGAGGATGATGAGGTCAAG	0.637																																					p.D387G		Atlas-SNP	.											.	CDC42EP1	53	.	0			c.A1160G						.						28.0	32.0	31.0					22																	37964811		2203	4300	6503	SO:0001583	missense	11135	exon3			AGGATGATGAGGT	M88338	CCDS13949.1	22q13.1	2008-06-11			ENSG00000128283	ENSG00000128283			17014	protein-coding gene	gene with protein product	"""55 kDa bone marrow stromal/endothelial cell protein"", ""serum constituent protein"""	606084				1629197, 10430899	Standard	NM_152243		Approved	MSE55, CEP1, Borg5	uc003asz.4	Q00587	OTTHUMG00000150591	ENST00000249014.4:c.1160A>G	chr22.hg19:g.37964811A>G	ENSP00000249014:p.Asp387Gly	214.0	0.0		191.0	77.0	NM_152243	A8K825|Q96GN1	Missense_Mutation	SNP	ENST00000249014.4	hg19	CCDS13949.1	.	.	.	.	.	.	.	.	.	.	A	19.57	3.851629	0.71719	.	.	ENSG00000128283	ENST00000249014	T	0.51325	0.71	4.67	4.67	0.58626	.	0.385400	0.22547	N	0.058645	T	0.46229	0.1382	L	0.32530	0.975	0.41557	D	0.988603	D	0.58268	0.982	P	0.50314	0.637	T	0.50980	-0.8763	10	0.87932	D	0	-9.1493	12.161	0.54103	1.0:0.0:0.0:0.0	.	387	Q00587	BORG5_HUMAN	G	387	ENSP00000249014:D387G	ENSP00000249014:D387G	D	+	2	0	CDC42EP1	36294757	0.999000	0.42202	0.881000	0.34555	0.610000	0.37248	6.580000	0.74040	1.856000	0.53863	0.459000	0.35465	GAT	.	.		0.637	CDC42EP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318993.1	NM_152243	
TCF20	6942	hgsc.bcm.edu	37	22	42608026	42608026	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr22:42608026C>A	ENST00000359486.3	-	1	3422	c.3286G>T	c.(3286-3288)Gag>Tag	p.E1096*	TCF20_ENST00000404876.1_5'Flank|TCF20_ENST00000335626.4_Nonsense_Mutation_p.E1096*	NM_005650.1	NP_005641.1	Q9UGU0	TCF20_HUMAN	transcription factor 20 (AR1)	1096					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(13)|lung(22)|ovary(5)|prostate(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(5)	66						TCTTTATACTCCTCTGGTTGC	0.507																																					p.E1096X		Atlas-SNP	.											.	TCF20	164	.	0			c.G3286T						.						66.0	65.0	65.0					22																	42608026		2203	4300	6503	SO:0001587	stop_gained	6942	exon1			TATACTCCTCTGG	U19345	CCDS14032.1, CCDS14033.1	22q13.3	2011-02-08			ENSG00000100207	ENSG00000100207			11631	protein-coding gene	gene with protein product	"""stromelysin-1 platelet-derived growth factor-responsive element binding protein"""	603107				9730594, 10995766	Standard	NM_005650		Approved	AR1, SPBP	uc003bcj.1	Q9UGU0	OTTHUMG00000150920	ENST00000359486.3:c.3286G>T	chr22.hg19:g.42608026C>A	ENSP00000352463:p.Glu1096*	107.0	0.0		103.0	44.0	NM_181492	A9JX12|O14528|Q13078|Q4V353|Q9H4M0	Nonsense_Mutation	SNP	ENST00000359486.3	hg19	CCDS14033.1	.	.	.	.	.	.	.	.	.	.	C	43	10.404770	0.99399	.	.	ENSG00000100207	ENST00000359486;ENST00000335626	.	.	.	5.81	5.81	0.92471	.	0.077866	0.52532	D	0.000066	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-23.5711	20.0628	0.97684	0.0:1.0:0.0:0.0	.	.	.	.	X	1096	.	ENSP00000335561:E1096X	E	-	1	0	TCF20	40937970	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.311000	0.65786	2.745000	0.94114	0.655000	0.94253	GAG	.	.		0.507	TCF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320531.1	NM_181492	
A4GALT	53947	hgsc.bcm.edu	37	22	43089164	43089164	+	Missense_Mutation	SNP	C	C	T	rs549273376		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr22:43089164C>T	ENST00000401850.1	-	2	1283	c.794G>A	c.(793-795)cGc>cAc	p.R265H	A4GALT_ENST00000381278.3_Missense_Mutation_p.R265H|A4GALT_ENST00000249005.2_Missense_Mutation_p.R265H|A4GALT_ENST00000465765.2_5'Flank			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	265					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						GGCCAGGCTGCGGATGGAACA	0.652																																					p.R265H		Atlas-SNP	.											.	A4GALT	35	.	0			c.G794A						.						21.0	19.0	20.0					22																	43089164		2194	4293	6487	SO:0001583	missense	53947	exon3			AGGCTGCGGATGG		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.794G>A	chr22.hg19:g.43089164C>T	ENSP00000384794:p.Arg265His	65.0	0.0		56.0	27.0	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	hg19	CCDS14041.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.927372	0.34002	.	.	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.72725	-0.68;-0.68;-0.68	5.29	0.791	0.18619	Alpha 1,4-glycosyltransferase domain (1);	0.242179	0.27143	N	0.020738	T	0.57301	0.2044	L	0.39397	1.21	0.25679	N	0.985815	B	0.16802	0.019	B	0.15484	0.013	T	0.49908	-0.8889	10	0.42905	T	0.14	-2.2733	9.5259	0.39165	0.0:0.7006:0.0:0.2994	.	265	Q9NPC4	A4GAT_HUMAN	H	265	ENSP00000384794:R265H;ENSP00000249005:R265H;ENSP00000370678:R265H	ENSP00000249005:R265H	R	-	2	0	A4GALT	41419108	0.001000	0.12720	1.000000	0.80357	0.562000	0.35680	-0.071000	0.11505	0.234000	0.21139	-0.258000	0.10820	CGC	.	.		0.652	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
ASB11	140456	hgsc.bcm.edu	37	X	15306022	15306022	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:15306022C>T	ENST00000480796.1	-	6	878	c.828G>A	c.(826-828)caG>caA	p.Q276Q	ASB11_ENST00000380470.3_Silent_p.Q259Q|ASB11_ENST00000537676.1_Silent_p.Q255Q|ASB11_ENST00000344384.4_Silent_p.Q255Q			Q8WXH4	ASB11_HUMAN	ankyrin repeat and SOCS box containing 11, E3 ubiquitin protein ligase	276	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|skin(1)	16	Hepatocellular(33;0.183)					GCAAGAGTGCCTGCTCCACGC	0.507																																					p.Q276Q		Atlas-SNP	.											.	ASB11	79	.	0			c.G828A						.						97.0	74.0	82.0					X																	15306022		2203	4300	6503	SO:0001819	synonymous_variant	140456	exon6			GAGTGCCTGCTCC	AF425642	CCDS14164.1, CCDS35209.1, CCDS56596.1	Xp22.31	2014-02-10	2014-02-10		ENSG00000165192	ENSG00000165192		"""Ankyrin repeat domain containing"""	17186	protein-coding gene	gene with protein product		300626	"""ankyrin repeat and SOCS box-containing 11"", ""ankyrin repeat and SOCS box containing 11"""			24337577	Standard	NM_080873		Approved	DKFZp779E2460	uc004cwp.2	Q8WXH4	OTTHUMG00000021173	ENST00000480796.1:c.828G>A	chrX.hg19:g.15306022C>T		189.0	0.0		143.0	35.0	NM_080873	E9PEN1|Q3SYC4|Q7Z667	Silent	SNP	ENST00000480796.1	hg19	CCDS14164.1																																																																																			.	.		0.507	ASB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055852.2		
MAGEB10	139422	hgsc.bcm.edu	37	X	27839801	27839801	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:27839801C>T	ENST00000356790.2	+	3	623	c.378C>T	c.(376-378)taC>taT	p.Y126Y		NM_182506.3	NP_872312.2	Q96LZ2	MAGBA_HUMAN	melanoma antigen family B, 10	126	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									NS(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	26						TGTACAAGTACCAAATGAAAG	0.443																																					p.Y126Y		Atlas-SNP	.											.	MAGEB10	107	.	0			c.C378T						.						59.0	54.0	56.0					X																	27839801		2202	4300	6502	SO:0001819	synonymous_variant	139422	exon3			CAAGTACCAAATG		CCDS35221.1	Xp21.3	2008-02-05			ENSG00000177689	ENSG00000177689			25377	protein-coding gene	gene with protein product		300761				11454705	Standard	NM_182506		Approved	FLJ32965	uc004dbw.3	Q96LZ2	OTTHUMG00000046084	ENST00000356790.2:c.378C>T	chrX.hg19:g.27839801C>T		391.0	0.0		264.0	146.0	NM_182506	Q494Y6|Q494Y7|Q9BZ78	Silent	SNP	ENST00000356790.2	hg19	CCDS35221.1																																																																																			.	.		0.443	MAGEB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106216.1	NM_182506	
TAF1	6872	hgsc.bcm.edu	37	X	70595090	70595090	+	Silent	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:70595090C>T	ENST00000373790.4	+	4	537	c.486C>T	c.(484-486)ccC>ccT	p.P162P	TAF1_ENST00000449580.1_Silent_p.P162P|TAF1_ENST00000276072.3_Silent_p.P162P|TAF1_ENST00000423759.1_Silent_p.P162P	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	162	Pro-rich.|Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CACCTCCACCCCCGGGACCAA	0.423																																					p.P162P		Atlas-SNP	.											.	TAF1	439	.	0			c.C486T						.						133.0	112.0	119.0					X																	70595090		2203	4300	6503	SO:0001819	synonymous_variant	6872	exon4			TCCACCCCCGGGA		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.486C>T	chrX.hg19:g.70595090C>T		158.0	0.0		117.0	36.0	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	hg19	CCDS35325.1																																																																																			.	.		0.423	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
BCAP31	10134	hgsc.bcm.edu	37	X	152966418	152966418	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chrX:152966418C>T	ENST00000345046.6	-	8	1122	c.715G>A	c.(715-717)Ggt>Agt	p.G239S	BCAP31_ENST00000441714.1_Missense_Mutation_p.G239S|BCAP31_ENST00000458587.2_Missense_Mutation_p.G306S	NM_001256447.1	NP_001243376.1	P51572	BAP31_HUMAN	B-cell receptor-associated protein 31	239		Cleavage; by caspase-8. {ECO:0000255}.			antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein localization to endoplasmic reticulum exit site (GO:0070973)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|integral component of plasma membrane (GO:0005887)|lipid particle (GO:0005811)|membrane (GO:0016020)				endometrium(2)|large_intestine(2)|lung(2)|prostate(1)	7	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCCATGGGACCATCTACTGCA	0.637																																					p.G306S		Atlas-SNP	.											.	BCAP31	33	.	0			c.G916A						.						121.0	82.0	95.0					X																	152966418		2203	4300	6503	SO:0001583	missense	10134	exon8			TGGGACCATCTAC	X81109	CCDS14727.1, CCDS48191.1	Xq28	2005-10-11			ENSG00000185825	ENSG00000185825			16695	protein-coding gene	gene with protein product		300398					Standard	NM_001139441		Approved	DXS1357E, BAP31, 6C6-Ag, CDM	uc011mza.1	P51572	OTTHUMG00000024218	ENST00000345046.6:c.715G>A	chrX.hg19:g.152966418C>T	ENSP00000343458:p.Gly239Ser	318.0	0.0		202.0	70.0	NM_001139457	B3KQ79|D3DWV5|Q13836|Q96CF0	Missense_Mutation	SNP	ENST00000345046.6	hg19	CCDS14727.1	.	.	.	.	.	.	.	.	.	.	c	12.19	1.864450	0.32977	.	.	ENSG00000185825	ENST00000441714;ENST00000345046;ENST00000426131;ENST00000458587	.	.	.	4.44	4.44	0.53790	.	0.141544	0.44483	D	0.000445	T	0.34164	0.0888	L	0.42686	1.345	0.39241	D	0.963856	B;P	0.43788	0.22;0.817	B;B	0.33454	0.024;0.164	T	0.42068	-0.9473	9	0.02654	T	1	-5.4705	12.0095	0.53278	0.0:1.0:0.0:0.0	.	239;306	P51572;B3KQ79	BAP31_HUMAN;.	S	239;239;306;306	.	ENSP00000343458:G239S	G	-	1	0	BCAP31	152619612	0.069000	0.21087	0.481000	0.27354	0.278000	0.26855	2.025000	0.41059	1.965000	0.57142	0.525000	0.51046	GGT	.	.		0.637	BCAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061071.1	NM_005745	
IFIT2	3433	hgsc.bcm.edu	37	10	91066639	91066653	+	In_Frame_Del	DEL	AAAGAAAGTTACTGG	AAAGAAAGTTACTGG	-			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	AAAGAAAGTTACTGG	AAAGAAAGTTACTGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr10:91066639_91066653delAAAGAAAGTTACTGG	ENST00000371826.3	+	2	1095_1109	c.926_940delAAAGAAAGTTACTGG	c.(925-942)aaaagaaagttactggaa>aaa	p.RKLLE310del	LIPA_ENST00000487618.1_Intron|LIPA_ENST00000371837.1_Intron	NM_001547.4	NP_001538.4	P09913	IFIT2_HUMAN	interferon-induced protein with tetratricopeptide repeats 2	310					apoptotic mitochondrial changes (GO:0008637)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|negative regulation of protein binding (GO:0032091)|positive regulation of apoptotic process (GO:0043065)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	poly(A) RNA binding (GO:0044822)	p.R310I(1)		endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|skin(1)	12		Colorectal(252;0.0161)				ATGTATGGGAAAAGAAAGTTACTGGAACTAATAGG	0.437																																					p.309_313del		Atlas-Indel,Pindel	.											.	IFIT2	39	.	1	Substitution - Missense(1)	large_intestine(1)	c.925_939del						.																																			SO:0001651	inframe_deletion	3433	exon2			.	M14660	CCDS41548.1	10q23.31	2013-01-11			ENSG00000119922	ENSG00000119922		"""Tetratricopeptide (TTC) repeat domain containing"""	5409	protein-coding gene	gene with protein product		147040		IFI54, G10P2		3175763, 3360121	Standard	NM_001547		Approved	IFI-54, ISG-54K, cig42, GARG-39	uc009xts.3	P09913	OTTHUMG00000018707	ENST00000371826.3:c.926_940delAAAGAAAGTTACTGG	chr10.hg19:g.91066639_91066653delAAAGAAAGTTACTGG	ENSP00000360891:p.Arg310_Glu314del	117.0	0.0		86.0	14.0	NM_001547	Q5T767	In_Frame_Del	DEL	ENST00000371826.3	hg19	CCDS41548.1																																																																																			.	.		0.437	IFIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049293.1	NM_001547	
BTN1A1	696	hgsc.bcm.edu	37	6	26508287	26508307	+	Splice_Site	DEL	ATCTTTCTCTTTTGTTGCAGA	ATCTTTCTCTTTTGTTGCAGA	-	rs41267931	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	ATCTTTCTCTTTTGTTGCAGA	ATCTTTCTCTTTTGTTGCAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:26508287_26508307delATCTTTCTCTTTTGTTGCAGA	ENST00000244513.6	+	6	946_965	c.880_899delATCTTTCTCTTTTGTTGCAGA	c.(880-900)atctttctcttttgttgcaga>a	p.IFLFCCR294del		NM_001732.2	NP_001723.2	Q13410	BT1A1_HUMAN	butyrophilin, subfamily 1, member A1	294	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(1)	26						CTTTTGTTGCAGAATGGAAAAAGGCTACCTTGCATGCAGGT	0.398																																					.		Atlas-Indel,Pindel	.											.	BTN1A1	68	.	0			.						.																																			SO:0001630	splice_region_variant	696	.			.	U39576	CCDS4614.1	6p22.1	2014-01-14			ENSG00000124557	ENSG00000124557		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1135	protein-coding gene	gene with protein product		601610		BTN		8114113, 9382921	Standard	NM_001732		Approved	BT, BTN1	uc003nif.4	Q13410	OTTHUMG00000016358	ENST00000244513.6:c.881-1ATCTTTCTCTTTTGTTGCAGA>-	chr6.hg19:g.26508287_26508307delATCTTTCTCTTTTGTTGCAGA		111.0	0.0		103.0	30.0	.	Q4VAN3|Q4VAN4|Q9H458	Splice_Site	DEL	ENST00000244513.6	hg19	CCDS4614.1																																																																																			.	.		0.398	BTN1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043776.1	NM_001732	In_Frame_Del
GPR4	2828	hgsc.bcm.edu	37	19	46094909	46094932	+	In_Frame_Del	DEL	CAGCGGCAGCGTGCAGATGTACAG	CAGCGGCAGCGTGCAGATGTACAG	-	rs188005857		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	CAGCGGCAGCGTGCAGATGTACAG	CAGCGGCAGCGTGCAGATGTACAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr19:46094909_46094932delCAGCGGCAGCGTGCAGATGTACAG	ENST00000323040.4	-	2	1137_1160	c.193_216delCTGTACATCTGCACGCTGCCGCTG	c.(193-216)ctgtacatctgcacgctgccgctgdel	p.LYICTLPL65del	OPA3_ENST00000544371.1_Intron|GPR4_ENST00000591614.1_5'Flank	NM_005282.2	NP_005273.1	P46093	GPR4_HUMAN	G protein-coupled receptor 4	65					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;0.0071)|GBM - Glioblastoma multiforme(486;0.128)|Epithelial(262;0.223)		AGTCCACCCACAGCGGCAGCGTGCAGATGTACAGCAGGTCGGCG	0.603																																					p.65_73del	Esophageal Squamous(117;181 1612 1673 14956 42937)	Atlas-Indel,Pindel	.											.	GPR4	54	.	0			c.194_217del						.																																			SO:0001651	inframe_deletion	2828	exon2			.	BC067536	CCDS12669.1	19q13.3	2012-08-21				ENSG00000177464		"""GPCR / Class A : Orphans"""	4497	protein-coding gene	gene with protein product		600551				8595909	Standard	NM_005282		Approved		uc002pcm.3	P46093		ENST00000323040.4:c.193_216delCTGTACATCTGCACGCTGCCGCTG	chr19.hg19:g.46094909_46094932delCAGCGGCAGCGTGCAGATGTACAG	ENSP00000319744:p.Leu65_Leu72del	147.0	0.0		92.0	23.0	NM_005282	A8K3T3|B0M0K1|Q6NWM4	In_Frame_Del	DEL	ENST00000323040.4	hg19	CCDS12669.1																																																																																			.	.		0.603	GPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459603.1	NM_005282	
TBP	6908	hgsc.bcm.edu	37	6	170871073	170871074	+	In_Frame_Ins	INS	-	-	CAA	rs551889211	byFrequency	TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr6:170871073_170871074insCAA	ENST00000392092.2	+	3	528_529	c.249_250insCAA	c.(250-252)cag>CAAcag	p.84_84Q>QQ	TBP_ENST00000230354.6_In_Frame_Ins_p.84_84Q>QQ|TBP_ENST00000540980.1_In_Frame_Ins_p.64_64Q>QQ	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	84	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q83Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcagcagcagca	0.594																																					p.Q83delinsQQ		Atlas-INDEL	.											TBP,NS,carcinoma,0,1	TBP	58	.	1	Substitution - coding silent(1)	lung(1)	c.249_250insCAA						.																																			SO:0001652	inframe_insertion	6908	exon3			.	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	Exception_encountered	chr6.hg19:g.170871073_170871074insCAA	ENSP00000375942:p.Gln95dup	74.0	0.0		27.0	17.0	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Ins	INS	ENST00000392092.2	hg19	CCDS5315.1																																																																																			.	-|0.138;CAG|0.862		0.594	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
ARID2	196528	hgsc.bcm.edu	37	12	46230522	46230549	+	Splice_Site	DEL	TTGTAGAAGGTACATCAGGAGAATGGAT	TTGTAGAAGGTACATCAGGAGAATGGAT	-	rs200449496|rs143391973|rs201031100|rs372591699		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	TTGTAGAAGGTACATCAGGAGAATGGAT	TTGTAGAAGGTACATCAGGAGAATGGAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr12:46230522_46230549delTTGTAGAAGGTACATCAGGAGAATGGAT	ENST00000334344.6	+	8	944_970	c.772_798delTTGTAGAAGGTACATCAGGAGAATGGAT	c.(772-798)ttgtagaaggtacatcaggagaatggadel	p.L*KVHQENG258fs	ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_5'Flank|ARID2_ENST00000422737.1_Splice_Site_p.L*KVHQENG109fs	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	258					chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		TTTCTATTGTAGAAGGTACATCAGGAGAATGGATTTGGGAGTCTTTAT	0.342			"""N, S, F"""		hepatocellular carcinoma																																p.258_265del		Atlas-Indel,Pindel	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.773_793del						.																																			SO:0001630	splice_region_variant	196528	exon8			.		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.773-1TTGTAGAAGGTACATCAGGAGAATGGAT>-	chr12.hg19:g.46230522_46230549delTTGTAGAAGGTACATCAGGAGAATGGAT		184.0	0.0		145.0	30.0	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	In_Frame_Del	DEL	ENST00000334344.6	hg19	CCDS31783.1																																																																																			.	.		0.342	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	Frame_Shift_Del
ABHD11	83451	hgsc.bcm.edu	37	7	73152683	73152692	+	Frame_Shift_Del	DEL	ATCTTGGCGA	ATCTTGGCGA	-			TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	ATCTTGGCGA	ATCTTGGCGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr7:73152683_73152692delATCTTGGCGA	ENST00000222800.3	-	2	323_332	c.254_263delTCGCCAAGAT	c.(253-264)atcgccaagatcfs	p.IAKI85fs	LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000395147.4_Frame_Shift_Del_p.IAKI85fs|ABHD11_ENST00000437775.2_Frame_Shift_Del_p.IAKI78fs|ABHD11_ENST00000468998.1_5'UTR|ABHD11_ENST00000458339.1_Frame_Shift_Del_p.IAKI85fs	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	85						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				CTGGGCCAAGATCTTGGCGATGGAGTTGAA	0.657																																					p.85_88del		Atlas-Indel,Pindel	.											.	ABHD11	11	.	0			c.255_264del						.																																			SO:0001589	frameshift_variant	83451	exon2			.	AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"""Abhydrolase domain containing"""	16407	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 21"""	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.254_263delTCGCCAAGAT	chr7.hg19:g.73152683_73152692delATCTTGGCGA	ENSP00000222800:p.Ile85fs	222.0	0.0		123.0	42.0	NM_001145364	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Frame_Shift_Del	DEL	ENST00000222800.3	hg19	CCDS5558.1																																																																																			.	.		0.657	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1		
SMPD4	55627	hgsc.bcm.edu	37	2	130914822	130914851	+	Splice_Site	DEL	CCGCAAGGGCCACCCACCGTTTGAACTCCT	CCGCAAGGGCCACCCACCGTTTGAACTCCT	-	rs541644496		TCGA-G3-AAV4-01A-11D-A382-10	TCGA-G3-AAV4-10A-01D-A385-10	CCGCAAGGGCCACCCACCGTTTGAACTCCT	CCGCAAGGGCCACCCACCGTTTGAACTCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	06bccdcf-87ad-48ed-aa9c-22d424205377	1b9df221-8334-487b-8fa2-09fb7b75273d	g.chr2:130914822_130914851delCCGCAAGGGCCACCCACCGTTTGAACTCCT	ENST00000409031.1	-	12	2335_2363	c.1187_1215delAGGAGTTCAAACGGTGGGTGGCCCTTGCGG	c.(1186-1215)gaggagttcaaacggtgggtggcccttgcg>g	p.EEFKRWVALA396del	SMPD4_ENST00000452225.2_Splice_Site_p.EEFKRWVALA137del|SMPD4_ENST00000351288.6_Splice_Site_p.EEFKRWVALA367del|SMPD4_ENST00000339679.7_Splice_Site_p.EEFKRWVALA254del|SMPD4_ENST00000426662.2_Intron|SMPD4_ENST00000443958.2_Splice_Site_p.EEFKRWVALA60del|SMPD4_ENST00000473720.1_Intron|SMPD4_ENST00000431183.2_Splice_Site_p.EEFKRWVALA294del|SMPD4_ENST00000453750.1_Splice_Site_p.EEFKRWVALA145del	NM_017951.4	NP_060421.2	Q9NXE4	NSMA3_HUMAN	sphingomyelin phosphodiesterase 4, neutral membrane (neutral sphingomyelinase-3)	357					cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glycerophospholipid catabolic process (GO:0046475)|glycosphingolipid metabolic process (GO:0006687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|trans-Golgi network (GO:0005802)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)|sphingomyelin phosphodiesterase D activity (GO:0050290)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(17)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29	Colorectal(110;0.1)				Phosphatidylserine(DB00144)	AGGGCCACCCACCGTTTGAACTCCTCCAGGGGGCTGGTGGCGTGGGAGTG	0.665																																					p.401_405del		Pindel	.											.	SMPD4	67	.	0			c.1203_1214del						.																																			SO:0001630	splice_region_variant	55627	exon12			.	AF052134	CCDS2156.2, CCDS42751.1, CCDS54398.1	2q21.1	2009-11-06			ENSG00000136699	ENSG00000136699			32949	protein-coding gene	gene with protein product		610457				16517606	Standard	NM_001171083		Approved	FLJ20297, FLJ20756, nSMase-3, KIAA1418, NSMASE3, NET13	uc002tqr.2	Q9NXE4	OTTHUMG00000131624	ENST00000409031.1:c.1214+1AGGAGTTCAAACGGTGGGTGGCCCTTGCGG>-	chr2.hg19:g.130914822_130914851delCCGCAAGGGCCACCCACCGTTTGAACTCCT		236.0	0.0		148.0	11.0	NM_017951	B4DM23|B4DQ31|B4DRB8|B4DWK7|B4E0L6|E7ESA2|E9PCE6|Q6FI76|Q6P1P7|Q6ZT43|Q9H0M2|Q9NW20|Q9NWL2|Q9P2C9	In_Frame_Del	DEL	ENST00000409031.1	hg19	CCDS42751.1																																																																																			.	.		0.665	SMPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254516.3	NM_017751	In_Frame_Del
