#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
ZBTB48	3104	hgsc.bcm.edu	37	1	6642352	6642352	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:6642352C>T	ENST00000377674.4	+	3	1083	c.925C>T	c.(925-927)Cac>Tac	p.H309Y		NM_001278647.1|NM_001278648.1|NM_005341.2	NP_001265576.1|NP_001265577.1|NP_005332.1	P10074	ZBT48_HUMAN	zinc finger and BTB domain containing 48	309					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)			central_nervous_system(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	11	Ovarian(185;0.0212)|all_lung(157;0.154)	all_cancers(23;7.39e-28)|all_epithelial(116;1.76e-17)|all_lung(118;2.27e-05)|Lung NSC(185;9.97e-05)|Renal(390;0.00188)|Breast(487;0.00289)|Colorectal(325;0.00342)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.156)		Colorectal(212;1.35e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00109)|STAD - Stomach adenocarcinoma(132;0.017)|READ - Rectum adenocarcinoma(331;0.0642)		TCTAAAAGTCCACAACAGGTA	0.493																																					p.H309Y	Esophageal Squamous(125;1449 1657 4031 29866 49542)	Atlas-SNP	.											.	ZBTB48	33	.	0			c.C925T						.						80.0	87.0	84.0					1																	6642352		2203	4300	6503	SO:0001583	missense	3104	exon3			AAAGTCCACAACA	BC013573	CCDS84.1	1p36.3	2013-01-08	2006-09-20	2006-09-20	ENSG00000204859	ENSG00000204859		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	4930	protein-coding gene	gene with protein product		165270	"""GLI-Kruppel family member HKR3"""	HKR3		2850480, 8661141	Standard	NM_001278647		Approved	ZNF855	uc001anx.3	P10074	OTTHUMG00000001438	ENST00000377674.4:c.925C>T	chr1.hg19:g.6642352C>T	ENSP00000366902:p.His309Tyr	84.0	0.0		63.0	27.0	NM_005341	Q5SY19	Missense_Mutation	SNP	ENST00000377674.4	hg19	CCDS84.1	.	.	.	.	.	.	.	.	.	.	C	23.1	4.368859	0.82463	.	.	ENSG00000204859	ENST00000319084;ENST00000377674	T;D	0.86769	0.44;-2.17	5.52	5.52	0.82312	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.90270	0.6957	M	0.83384	2.64	0.80722	D	1	B	0.32968	0.392	B	0.38842	0.283	D	0.90571	0.4522	10	0.87932	D	0	-27.4086	18.4319	0.90628	0.0:1.0:0.0:0.0	.	309	P10074	ZBT48_HUMAN	Y	309	ENSP00000313416:H309Y;ENSP00000366902:H309Y	ENSP00000313416:H309Y	H	+	1	0	ZBTB48	6564939	1.000000	0.71417	0.997000	0.53966	0.988000	0.76386	5.336000	0.65935	2.600000	0.87896	0.561000	0.74099	CAC	.	.		0.493	ZBTB48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004193.1	NM_005341	
KIF1B	23095	hgsc.bcm.edu	37	1	10408742	10408742	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:10408742T>A	ENST00000377086.1	+	37	4102	c.3900T>A	c.(3898-3900)caT>caA	p.H1300Q	KIF1B_ENST00000263934.6_Missense_Mutation_p.H1254Q|KIF1B_ENST00000465635.1_3'UTR|KIF1B_ENST00000377081.1_Missense_Mutation_p.H1300Q			O60333	KIF1B_HUMAN	kinesin family member 1B	1300					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		CCATTATCCATGAGAAGGGGA	0.453																																					p.H1254Q		Atlas-SNP	.											.	KIF1B	242	.	0			c.T3762A						.						138.0	106.0	116.0					1																	10408742		2203	4300	6503	SO:0001583	missense	23095	exon35			TATCCATGAGAAG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.3900T>A	chr1.hg19:g.10408742T>A	ENSP00000366290:p.His1300Gln	78.0	0.0		79.0	25.0	NM_015074	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	T	22.7	4.319781	0.81469	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377086;ENST00000377081	T;T;T	0.75367	-0.85;-0.93;-0.93	5.52	-3.19	0.05171	.	0.000000	0.85682	D	0.000000	D	0.84911	0.5577	M	0.88640	2.97	0.58432	D	0.999994	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0;0.96	D;D;D;D;D;D	0.97110	1.0;0.999;0.999;0.999;0.999;0.962	D	0.84182	0.0440	10	0.44086	T	0.13	.	13.1574	0.59524	0.0:0.4586:0.0:0.5414	.	1286;1260;1300;1274;1300;1254	Q4R9M9;Q4R9M7;Q4VXC4;Q4R9M8;O60333;O60333-2	.;.;.;.;KIF1B_HUMAN;.	Q	1300;1254;1300;1300	ENSP00000263934:H1254Q;ENSP00000366290:H1300Q;ENSP00000366284:H1300Q	ENSP00000263934:H1254Q	H	+	3	2	KIF1B	10331329	0.014000	0.17966	0.989000	0.46669	0.996000	0.88848	-0.903000	0.04084	-0.526000	0.06383	-0.256000	0.11100	CAT	.	.		0.453	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
CELA2A	63036	hgsc.bcm.edu	37	1	15788106	15788106	+	Silent	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:15788106G>T	ENST00000359621.4	+	3	205	c.180G>T	c.(178-180)ggG>ggT	p.G60G		NM_033440.2	NP_254275.1	P08217	CEL2A_HUMAN	chymotrypsin-like elastase family, member 2A	60	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|keratohyalin granule (GO:0036457)	serine hydrolase activity (GO:0017171)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(7)|ovary(2)|prostate(1)	16						CCTGCGGAGGGTCCCTGATAG	0.592																																					p.G60G		Atlas-SNP	.											.	CELA2A	32	.	0			c.G180T						.						121.0	106.0	111.0					1																	15788106		2203	4300	6503	SO:0001819	synonymous_variant	63036	exon3			CGGAGGGTCCCTG		CCDS157.1	1p36.21	2009-07-09			ENSG00000142615	ENSG00000142615	3.4.21.71		24609	protein-coding gene	gene with protein product	"""elastase 2A"""	609443				3646943, 2834346	Standard	NM_033440		Approved	ELA2A	uc001awk.3	P08217	OTTHUMG00000002258	ENST00000359621.4:c.180G>T	chr1.hg19:g.15788106G>T		142.0	0.0		122.0	39.0	NM_033440	B2R5I4|Q14243	Silent	SNP	ENST00000359621.4	hg19	CCDS157.1																																																																																			.	.		0.592	CELA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006445.1	NM_033440	
AGO4	192670	hgsc.bcm.edu	37	1	36292423	36292423	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:36292423G>T	ENST00000373210.3	+	7	1080	c.835G>T	c.(835-837)Gcc>Tcc	p.A279S		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	279	PAZ. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										TAGACGGCCAGCCAGTCATCA	0.358																																					p.A279S		Atlas-SNP	.											.	.	.	.	0			c.G835T						.						81.0	69.0	73.0					1																	36292423		2203	4300	6503	SO:0001583	missense	192670	exon7			CGGCCAGCCAGTC	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"""Argonaute/PIWI family"""	18424	protein-coding gene	gene with protein product	"""argonaute 4"""	607356	"""eukaryotic translation initiation factor 2C, 4"""	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.835G>T	chr1.hg19:g.36292423G>T	ENSP00000362306:p.Ala279Ser	59.0	0.0		47.0	25.0	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	hg19	CCDS397.1	.	.	.	.	.	.	.	.	.	.	G	33	5.259789	0.95368	.	.	ENSG00000134698	ENST00000373210	T	0.08720	3.06	5.66	5.66	0.87406	Argonaute/Dicer protein, PAZ (4);	0.217896	0.47093	N	0.000245	T	0.34687	0.0906	M	0.82193	2.58	0.80722	D	1	B	0.20671	0.047	P	0.50617	0.646	T	0.17684	-1.0361	10	0.56958	D	0.05	-1.4061	18.4995	0.90876	0.0:0.0:1.0:0.0	.	279	Q9HCK5	AGO4_HUMAN	S	279	ENSP00000362306:A279S	ENSP00000362306:A279S	A	+	1	0	EIF2C4	36065010	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.679000	0.98649	2.673000	0.90976	0.585000	0.79938	GCC	.	.		0.358	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
HPDL	84842	hgsc.bcm.edu	37	1	45793225	45793225	+	Silent	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:45793225C>T	ENST00000334815.3	+	1	681	c.405C>T	c.(403-405)cgC>cgT	p.R135R		NM_032756.2	NP_116145.1	Q96IR7	HPDL_HUMAN	4-hydroxyphenylpyruvate dioxygenase-like	135					aromatic amino acid family metabolic process (GO:0009072)		4-hydroxyphenylpyruvate dioxygenase activity (GO:0003868)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)	4	Acute lymphoblastic leukemia(166;0.155)					TGCTGGAGCGCGCTGGCTACC	0.716																																					p.R135R		Atlas-SNP	.											.	HPDL	14	.	0			c.C405T						.						15.0	14.0	14.0					1																	45793225		2182	4260	6442	SO:0001819	synonymous_variant	84842	exon1			GGAGCGCGCTGGC	BC007293	CCDS519.1	1p34.1	2008-02-05	2007-03-14	2007-03-14	ENSG00000186603	ENSG00000186603			28242	protein-coding gene	gene with protein product			"""glyoxalase domain containing 1"""	GLOXD1		12477932	Standard	NM_032756		Approved	MGC15668, 4-HPPD-L	uc001cne.3	Q96IR7	OTTHUMG00000007681	ENST00000334815.3:c.405C>T	chr1.hg19:g.45793225C>T		80.0	0.0		104.0	40.0	NM_032756	B2R9B0	Silent	SNP	ENST00000334815.3	hg19	CCDS519.1																																																																																			.	.		0.716	HPDL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020527.1	NM_032756	
NPR1	4881	hgsc.bcm.edu	37	1	153653014	153653014	+	Silent	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:153653014C>T	ENST00000368680.3	+	2	1231	c.759C>T	c.(757-759)acC>acT	p.T253T		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	253					body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CCTTCAGAACCCTCATGCTCC	0.552																																					p.T253T	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.C759T						.						121.0	108.0	112.0					1																	153653014		2203	4300	6503	SO:0001819	synonymous_variant	4881	exon2			CAGAACCCTCATG	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.759C>T	chr1.hg19:g.153653014C>T		88.0	0.0		97.0	82.0	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Silent	SNP	ENST00000368680.3	hg19	CCDS1051.1																																																																																			.	.		0.552	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
OR6K2	81448	hgsc.bcm.edu	37	1	158669510	158669510	+	Silent	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:158669510T>A	ENST00000359610.2	-	1	976	c.933A>T	c.(931-933)atA>atT	p.I311I		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					CGGAAAAAAATATCTTAGCTT	0.378																																					p.I311I		Atlas-SNP	.											.	OR6K2	104	.	0			c.A933T						.						72.0	71.0	71.0					1																	158669510		2203	4300	6503	SO:0001819	synonymous_variant	81448	exon1			AAAAAATATCTTA	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.933A>T	chr1.hg19:g.158669510T>A		130.0	0.0		117.0	43.0	NM_001005279	B9EH33|Q6IFR6	Silent	SNP	ENST00000359610.2	hg19	CCDS30902.1																																																																																			.	.		0.378	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279	
OR6K2	81448	hgsc.bcm.edu	37	1	158669512	158669512	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:158669512T>A	ENST00000359610.2	-	1	974	c.931A>T	c.(931-933)Ata>Tta	p.I311L		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	311						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					GAAAAAAATATCTTAGCTTGA	0.388																																					p.I311L		Atlas-SNP	.											.	OR6K2	104	.	0			c.A931T						.						72.0	71.0	71.0					1																	158669512		2203	4300	6503	SO:0001583	missense	81448	exon1			AAAATATCTTAGC	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.931A>T	chr1.hg19:g.158669512T>A	ENSP00000352626:p.Ile311Leu	130.0	0.0		115.0	41.0	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	hg19	CCDS30902.1	.	.	.	.	.	.	.	.	.	.	T	0.316	-0.964707	0.02249	.	.	ENSG00000196171	ENST00000359610	T	0.36340	1.26	0.235	-0.47	0.12131	.	0.634765	0.12827	N	0.435973	T	0.03915	0.0110	N	0.04880	-0.145	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38628	-0.9652	10	0.34782	T	0.22	-0.1467	2.1533	0.03806	0.2522:0.2471:0.0:0.5007	.	311	Q8NGY2	OR6K2_HUMAN	L	311	ENSP00000352626:I311L	ENSP00000352626:I311L	I	-	1	0	OR6K2	156936136	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.498000	0.22530	-1.858000	0.01158	-1.843000	0.00578	ATA	.	.		0.388	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279	
MNDA	4332	hgsc.bcm.edu	37	1	158817562	158817562	+	Silent	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:158817562T>C	ENST00000368141.4	+	6	1293	c.1032T>C	c.(1030-1032)aaT>aaC	p.N344N		NM_002432.1	NP_002423.1	P41218	MNDA_HUMAN	myeloid cell nuclear differentiation antigen	344	HIN-200. {ECO:0000255|PROSITE- ProRule:PRU00106}.				B cell receptor signaling pathway (GO:0050853)|cellular defense response (GO:0006968)|cellular response to DNA damage stimulus (GO:0006974)|negative regulation of B cell proliferation (GO:0030889)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(2)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(1)|lung(26)|ovary(2)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	all_hematologic(112;0.0378)					TACAGGATAATACAGGATCCA	0.378																																					p.N344N		Atlas-SNP	.											.	MNDA	147	.	0			c.T1032C						.						130.0	126.0	128.0					1																	158817562		2203	4300	6503	SO:0001819	synonymous_variant	4332	exon6			GGATAATACAGGA	BC032319	CCDS1177.1	1q22	2008-02-05			ENSG00000163563	ENSG00000163563			7183	protein-coding gene	gene with protein product		159553				1644857, 7512843	Standard	NM_002432		Approved	PYHIN3	uc001fsz.1	P41218	OTTHUMG00000022776	ENST00000368141.4:c.1032T>C	chr1.hg19:g.158817562T>C		58.0	0.0		42.0	36.0	NM_002432		Silent	SNP	ENST00000368141.4	hg19	CCDS1177.1	.	.	.	.	.	.	.	.	.	.	T	4.680	0.126526	0.08931	.	.	ENSG00000163563	ENST00000438394	.	.	.	3.81	-3.59	0.04583	.	.	.	.	.	T	0.07007	0.0178	.	.	.	0.23577	N	0.997378	.	.	.	.	.	.	T	0.34229	-0.9837	4	.	.	.	-4.0499	2.8998	0.05701	0.3359:0.316:0.0:0.3481	.	.	.	.	H	50	.	.	Y	+	1	0	MNDA	157084186	0.000000	0.05858	0.044000	0.18714	0.114000	0.19823	-2.487000	0.00977	-0.895000	0.03920	0.460000	0.39030	TAC	.	.		0.378	MNDA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059069.1	NM_002432	
DUSP27	92235	hgsc.bcm.edu	37	1	167096118	167096118	+	Missense_Mutation	SNP	G	G	A	rs369939829		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:167096118G>A	ENST00000361200.2	+	6	1916	c.1750G>A	c.(1750-1752)Gtc>Atc	p.V584I	DUSP27_ENST00000271385.5_Missense_Mutation_p.V584I|DUSP27_ENST00000443333.1_Missense_Mutation_p.V584I|DUSP27_ENST00000485151.1_Intron			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	584					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.V584I(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						CCCCTCCGACGTCAGCCTGAC	0.582																																					p.V584I		Atlas-SNP	.											DUSP27,NS,carcinoma,0,2	DUSP27	235	.	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1750A						.						46.0	47.0	46.0					1																	167096118		2203	4300	6503	SO:0001583	missense	92235	exon5			TCCGACGTCAGCC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1750G>A	chr1.hg19:g.167096118G>A	ENSP00000354483:p.Val584Ile	37.0	0.0		46.0	31.0	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	hg19	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	g	2.890	-0.229957	0.06022	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.05081	3.5;3.5;3.5	5.32	2.43	0.29744	.	0.324845	0.23454	N	0.048008	T	0.03220	0.0094	M	0.66939	2.045	0.09310	N	1	B	0.11235	0.004	B	0.04013	0.001	T	0.35574	-0.9783	10	0.46703	T	0.11	-10.7021	13.2231	0.59899	0.2361:0.0:0.7639:0.0	.	584	Q5VZP5	DUS27_HUMAN	I	584	ENSP00000354483:V584I;ENSP00000271385:V584I;ENSP00000404874:V584I	ENSP00000271385:V584I	V	+	1	0	DUSP27	165362742	0.998000	0.40836	0.000000	0.03702	0.000000	0.00434	2.635000	0.46537	0.008000	0.14787	-1.985000	0.00452	GTC	.	.		0.582	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
RCSD1	92241	hgsc.bcm.edu	37	1	167666934	167666934	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:167666934G>T	ENST00000367854.3	+	6	1404	c.1073G>T	c.(1072-1074)gGc>gTc	p.G358V	RCSD1_ENST00000537350.1_Missense_Mutation_p.G328V	NM_052862.3	NP_443094.3	Q6JBY9	CPZIP_HUMAN	RCSD domain containing 1	358					cellular hyperosmotic response (GO:0071474)|skeletal muscle contraction (GO:0003009)	actin filament (GO:0005884)	actin filament binding (GO:0051015)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(2)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	24	all_hematologic(923;0.215)					GGAGTGAAGGGCGGAGATGTC	0.612																																					p.G358V		Atlas-SNP	.											.	RCSD1	64	.	0			c.G1073T						.						33.0	32.0	32.0					1																	167666934		2200	4296	6496	SO:0001583	missense	92241	exon6			TGAAGGGCGGAGA	BC072399	CCDS1263.1	1q24.2	2008-02-05			ENSG00000198771	ENSG00000198771			28310	protein-coding gene	gene with protein product		610579				12477932	Standard	NM_052862		Approved	MK2S4, MGC21854	uc001gem.3	Q6JBY9	OTTHUMG00000035318	ENST00000367854.3:c.1073G>T	chr1.hg19:g.167666934G>T	ENSP00000356828:p.Gly358Val	37.0	0.0		29.0	27.0	NM_052862	B1AK48|Q4G0E7|Q6IN93|Q8IZM2|Q96DX0|Q9NST4	Missense_Mutation	SNP	ENST00000367854.3	hg19	CCDS1263.1	.	.	.	.	.	.	.	.	.	.	G	14.49	2.550229	0.45383	.	.	ENSG00000198771	ENST00000367854;ENST00000537350	T;T	0.71461	-0.33;-0.57	4.64	2.65	0.31530	.	0.848487	0.10531	N	0.663853	T	0.58018	0.2093	L	0.34521	1.04	0.30576	N	0.762964	P;D	0.67145	0.906;0.996	P;P	0.61940	0.521;0.896	T	0.48115	-0.9063	9	0.36615	T	0.2	-5.3467	6.5071	0.22202	0.3321:0.0:0.6679:0.0	.	328;358	B7ZKW8;Q6JBY9	.;CPZIP_HUMAN	V	358;328	ENSP00000356828:G358V;ENSP00000439409:G328V	ENSP00000356828:G358V	G	+	2	0	RCSD1	165933558	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.018000	0.12568	0.403000	0.25479	0.585000	0.79938	GGC	.	.		0.612	RCSD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085451.1	NM_052862	
ASTN1	460	hgsc.bcm.edu	37	1	177030375	177030375	+	Missense_Mutation	SNP	G	G	T	rs138326291		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:177030375G>T	ENST00000367654.3	-	2	521	c.310C>A	c.(310-312)Cct>Act	p.P104T	ASTN1_ENST00000281881.3_5'UTR|ASTN1_ENST00000424564.2_Missense_Mutation_p.P104T|ASTN1_ENST00000361833.2_Missense_Mutation_p.P104T|ASTN1_ENST00000367657.3_Missense_Mutation_p.P104T	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	104					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)				NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						CGCACCAAAGGGATATCCTCT	0.502																																					p.P104T		Atlas-SNP	.											.	ASTN1	314	.	0			c.C310A						.						147.0	141.0	143.0					1																	177030375		2203	4300	6503	SO:0001583	missense	460	exon2			CCAAAGGGATATC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.310C>A	chr1.hg19:g.177030375G>T	ENSP00000356626:p.Pro104Thr	79.0	0.0		63.0	50.0	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	hg19		.	.	.	.	.	.	.	.	.	.	G	27.0	4.793774	0.90453	.	.	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.14266	2.52;2.94;2.94;2.52	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	T	0.32164	0.0820	L	0.47716	1.5	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	T	0.00498	-1.1704	10	0.19147	T	0.46	-20.2983	20.2159	0.98296	0.0:0.0:1.0:0.0	.	104;104;104	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	T	104	ENSP00000356629:P104T;ENSP00000354536:P104T;ENSP00000356626:P104T;ENSP00000395041:P104T	ENSP00000354536:P104T	P	-	1	0	ASTN1	175296998	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.689000	0.98673	2.882000	0.98803	0.655000	0.94253	CCT	.	G|1.000;C|0.000		0.502	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
SLC45A3	85414	hgsc.bcm.edu	37	1	205628667	205628667	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:205628667G>T	ENST00000367145.3	-	5	1652	c.1357C>A	c.(1357-1359)Ctg>Atg	p.L453M	SLC45A3_ENST00000460934.1_5'UTR	NM_033102.2	NP_149093.1	Q96JT2	S45A3_HUMAN	solute carrier family 45, member 3	453					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)			SLC45A3/BRAF(2)|SLC45A3/ELK4(18)|SLC45A3/ETV1(3)|SLC45A3/ETV5_ENST00000306376(2)|SLC45A3/ERG(50)	cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|ovary(3)|prostate(5)	21	Breast(84;0.07)		BRCA - Breast invasive adenocarcinoma(75;0.0194)			GGTGGGAGCAGGCCACTGCCT	0.667			T	"""ETV1, ETV5, ELK4, ERG"""	prostate						OREG0014161	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L453M		Atlas-SNP	.		Dom	yes		1	1q32	85414	"""solute carrier family 45, member 3"""		E	.	SLC45A3	54	.	0			c.C1357A						.						45.0	43.0	44.0					1																	205628667		2202	4300	6502	SO:0001583	missense	85414	exon5			GGAGCAGGCCACT	AF109301	CCDS1458.1	1q32.1	2013-05-22	2005-10-04	2005-10-04	ENSG00000158715	ENSG00000158715		"""Solute carriers"""	8642	protein-coding gene	gene with protein product		605097	"""prostate cancer associated protein 6"", ""prostate cancer associated protein 2"", ""prostate cancer associated protein 8"""	PCANAP6, PCANAP2, PCANAP8		10613842, 11245466	Standard	XM_005245556		Approved	IPCA-6, prostein, IPCA-2, IPCA-8	uc001hda.1	Q96JT2	OTTHUMG00000037223	ENST00000367145.3:c.1357C>A	chr1.hg19:g.205628667G>T	ENSP00000356113:p.Leu453Met	73.0	0.0	2153	76.0	60.0	NM_033102	A8K2U9	Missense_Mutation	SNP	ENST00000367145.3	hg19	CCDS1458.1	.	.	.	.	.	.	.	.	.	.	G	10.27	1.303763	0.23736	.	.	ENSG00000158715	ENST00000367145	T	0.45276	0.9	5.38	4.44	0.53790	.	0.803881	0.10968	N	0.614223	T	0.30696	0.0773	N	0.22421	0.69	0.24516	N	0.994189	B	0.29805	0.257	B	0.26310	0.068	T	0.14671	-1.0464	10	0.30854	T	0.27	-4.4745	13.0093	0.58722	0.0:0.0:0.8327:0.1673	.	453	Q96JT2	S45A3_HUMAN	M	453	ENSP00000356113:L453M	ENSP00000356113:L453M	L	-	1	2	SLC45A3	203895290	0.994000	0.37717	0.812000	0.32479	0.234000	0.25298	2.062000	0.41413	1.201000	0.43203	0.491000	0.48974	CTG	.	.		0.667	SLC45A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090619.1	NM_033102	
KIF26B	55083	hgsc.bcm.edu	37	1	245530263	245530263	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:245530263C>A	ENST00000407071.2	+	3	1033	c.593C>A	c.(592-594)gCc>gAc	p.A198D	KIF26B_ENST00000479506.1_3'UTR	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	198					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			AAGCAGGAGGCCATCCAGATG	0.627																																					p.A198D		Atlas-SNP	.											.	KIF26B	343	.	0			c.C593A						.						42.0	46.0	45.0					1																	245530263		2183	4267	6450	SO:0001583	missense	55083	exon3			AGGAGGCCATCCA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.593C>A	chr1.hg19:g.245530263C>A	ENSP00000385545:p.Ala198Asp	69.0	0.0		67.0	29.0	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.303731	0.81136	.	.	ENSG00000162849	ENST00000407071	D	0.87966	-2.32	5.44	5.44	0.79542	.	.	.	.	.	D	0.93559	0.7944	M	0.74881	2.28	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93799	0.7099	9	0.87932	D	0	.	19.6436	0.95767	0.0:1.0:0.0:0.0	.	198	Q2KJY2	KI26B_HUMAN	D	198	ENSP00000385545:A198D	ENSP00000385545:A198D	A	+	2	0	KIF26B	243596886	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.712000	0.92718	0.650000	0.86243	GCC	.	.		0.627	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
NLRP3	114548	hgsc.bcm.edu	37	1	247588229	247588229	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:247588229A>G	ENST00000336119.3	+	3	2230	c.1484A>G	c.(1483-1485)cAg>cGg	p.Q495R	NLRP3_ENST00000391828.3_Missense_Mutation_p.Q495R|NLRP3_ENST00000366496.2_Missense_Mutation_p.Q495R|NLRP3_ENST00000366497.2_Missense_Mutation_p.Q495R|NLRP3_ENST00000348069.2_Missense_Mutation_p.Q495R|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391827.2_Missense_Mutation_p.Q495R	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	495	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			CATGGACTGCAGAAGGCGGAT	0.522																																					p.Q495R		Atlas-SNP	.											.	NLRP3	286	.	0			c.A1484G						.						52.0	51.0	52.0					1																	247588229		2203	4300	6503	SO:0001583	missense	114548	exon3			GACTGCAGAAGGC	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1484A>G	chr1.hg19:g.247588229A>G	ENSP00000337383:p.Gln495Arg	21.0	0.0		40.0	28.0	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Missense_Mutation	SNP	ENST00000336119.3	hg19	CCDS1632.1	.	.	.	.	.	.	.	.	.	.	A	4.169	0.029902	0.08101	.	.	ENSG00000162711	ENST00000391828;ENST00000366497;ENST00000336119;ENST00000348069;ENST00000366496;ENST00000391827	D;D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79;-1.79	4.17	1.86	0.25419	NACHT nucleoside triphosphatase (1);	0.133374	0.35013	N	0.003504	T	0.68842	0.3045	N	0.17723	0.515	0.26785	N	0.969515	B;B;B;B;B	0.25048	0.086;0.117;0.094;0.02;0.016	B;B;B;B;B	0.31442	0.061;0.13;0.07;0.07;0.032	T	0.58741	-0.7583	10	0.42905	T	0.14	.	5.6856	0.17801	0.7826:0.0:0.2174:0.0	.	495;495;495;495;495	B7ZKS9;Q96P20-4;Q96P20-2;Q96P20-5;Q96P20	.;.;.;.;NALP3_HUMAN	R	495	ENSP00000375704:Q495R;ENSP00000355453:Q495R;ENSP00000337383:Q495R;ENSP00000294752:Q495R;ENSP00000355452:Q495R;ENSP00000375703:Q495R	ENSP00000337383:Q495R	Q	+	2	0	NLRP3	245654852	0.901000	0.30685	0.939000	0.37840	0.020000	0.10135	1.959000	0.40412	0.404000	0.25506	-0.250000	0.11733	CAG	.	.		0.522	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
OR14A16	284532	hgsc.bcm.edu	37	1	247978654	247978654	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:247978654G>T	ENST00000357627.1	-	1	377	c.378C>A	c.(376-378)caC>caA	p.H126Q		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	126						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						AGTGCAGAGGGTGACATATAG	0.507																																					p.H126Q	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.C378A						.						121.0	113.0	116.0					1																	247978654		2203	4300	6503	SO:0001583	missense	284532	exon1			CAGAGGGTGACAT	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"""GPCR / Class A : Olfactory receptors"""	15022	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AT, member 1"""	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.378C>A	chr1.hg19:g.247978654G>T	ENSP00000350248:p.His126Gln	88.0	0.0		60.0	46.0	NM_001001966	Q6IF96	Missense_Mutation	SNP	ENST00000357627.1	hg19	CCDS31097.1	.	.	.	.	.	.	.	.	.	.	G	0.049	-1.256553	0.01457	.	.	ENSG00000196772	ENST00000357627	T	0.01068	5.38	3.65	-2.42	0.06542	GPCR, rhodopsin-like superfamily (1);	1.138130	0.06749	U	0.779703	T	0.01222	0.0040	L	0.37466	1.105	0.21802	N	0.999534	B	0.26081	0.141	B	0.23419	0.046	T	0.46247	-0.9205	10	0.35671	T	0.21	.	7.2542	0.26166	0.3799:0.1364:0.4836:0.0	.	126	Q8NHC5	O14AG_HUMAN	Q	126	ENSP00000350248:H126Q	ENSP00000350248:H126Q	H	-	3	2	OR14A16	246045277	0.000000	0.05858	0.697000	0.30258	0.157000	0.22087	-6.769000	0.00054	-0.517000	0.06461	-0.225000	0.12378	CAC	.	.		0.507	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966	
OR2T8	343172	hgsc.bcm.edu	37	1	248085221	248085221	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr1:248085221G>T	ENST00000319968.4	+	1	902	c.902G>T	c.(901-903)aGg>aTg	p.R301M		NM_001005522.1	NP_001005522.1	A6NH00	OR2T8_HUMAN	olfactory receptor, family 2, subfamily T, member 8	301						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R301K(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(20)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	34	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0211)	OV - Ovarian serous cystadenocarcinoma(106;0.0319)			GCCCTGACAAGGTGTATGGGT	0.443																																					p.R301M		Atlas-SNP	.											OR2T8,NS,carcinoma,0,1	OR2T8	67	.	1	Substitution - Missense(1)	lung(1)	c.G902T						.						156.0	152.0	154.0					1																	248085221		2203	4300	6503	SO:0001583	missense	343172	exon1			TGACAAGGTGTAT		CCDS31100.1	1q44	2012-08-09		2004-03-10	ENSG00000177462	ENSG00000177462		"""GPCR / Class A : Olfactory receptors"""	15020	protein-coding gene	gene with protein product				OR2T8P			Standard	XM_005273117		Approved		uc010pzc.2	A6NH00	OTTHUMG00000040205	ENST00000319968.4:c.902G>T	chr1.hg19:g.248085221G>T	ENSP00000326225:p.Arg301Met	86.0	0.0		70.0	52.0	NM_001005522		Missense_Mutation	SNP	ENST00000319968.4	hg19	CCDS31100.1	.	.	.	.	.	.	.	.	.	.	G	9.211	1.030912	0.19590	.	.	ENSG00000177462	ENST00000319968	T	0.41065	1.01	3.54	0.688	0.18027	.	0.928799	0.08661	N	0.912382	T	0.39172	0.1068	L	0.58969	1.84	0.09310	N	1	B	0.18968	0.032	B	0.22601	0.04	T	0.43278	-0.9401	10	0.72032	D	0.01	.	7.4323	0.27134	0.763:0.0:0.237:0.0	.	301	A6NH00	OR2T8_HUMAN	M	301	ENSP00000326225:R301M	ENSP00000326225:R301M	R	+	2	0	OR2T8	246151844	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-0.126000	0.10563	0.266000	0.21894	-0.310000	0.09108	AGG	.	.		0.443	OR2T8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096862.1	NM_001005522	
MATN3	4148	hgsc.bcm.edu	37	2	20202976	20202976	+	Missense_Mutation	SNP	G	G	A	rs376404727		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:20202976G>A	ENST00000407540.3	-	3	924	c.862C>T	c.(862-864)Cac>Tac	p.H288Y	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Intron	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	288	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CACTCACAGTGGTGCTTGCCT	0.532																																					p.H288Y		Atlas-SNP	.											.	MATN3	28	.	0			c.C862T						.	G	TYR/HIS	0,4076		0,0,2038	118.0	113.0	115.0		862	5.5	1.0	2		115	1,8381		0,1,4190	no	missense	MATN3	NM_002381.4	83	0,1,6228	AA,AG,GG		0.0119,0.0,0.0080	benign	288/487	20202976	1,12457	2038	4191	6229	SO:0001583	missense	4148	exon3			CACAGTGGTGCTT	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.862C>T	chr2.hg19:g.20202976G>A	ENSP00000383894:p.His288Tyr	68.0	0.0		89.0	39.0	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	hg19	CCDS46226.1	.	.	.	.	.	.	.	.	.	.	G	3.172	-0.169756	0.06461	0.0	1.19E-4	ENSG00000132031	ENST00000407540	D	0.87029	-2.2	5.5	5.5	0.81552	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.252898	0.40302	N	0.001125	T	0.74989	0.3789	N	0.11106	0.095	0.80722	D	1	B	0.17852	0.024	B	0.11329	0.006	T	0.70099	-0.4965	10	0.11182	T	0.66	-33.7623	16.1448	0.81559	0.0:0.0:1.0:0.0	.	288	O15232	MATN3_HUMAN	Y	288	ENSP00000383894:H288Y	ENSP00000383894:H288Y	H	-	1	0	MATN3	20066457	0.950000	0.32346	1.000000	0.80357	0.783000	0.44284	0.555000	0.23422	2.596000	0.87737	0.650000	0.86243	CAC	.	.		0.532	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
C2orf71	388939	hgsc.bcm.edu	37	2	29297116	29297116	+	Silent	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:29297116T>C	ENST00000331664.5	-	1	11	c.12A>G	c.(10-12)acA>acG	p.T4T		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	4					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						TGTGTGAAGGTGTACACCCCA	0.433																																					p.T4T		Atlas-SNP	.											.	C2orf71	146	.	0			c.A12G						.						80.0	73.0	75.0					2																	29297116		1965	4156	6121	SO:0001819	synonymous_variant	388939	exon1			TGAAGGTGTACAC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.12A>G	chr2.hg19:g.29297116T>C		52.0	0.0		47.0	17.0	NM_001029883		Silent	SNP	ENST00000331664.5	hg19	CCDS42669.1																																																																																			.	.		0.433	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
LRPPRC	10128	hgsc.bcm.edu	37	2	44162019	44162019	+	Splice_Site	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:44162019T>A	ENST00000260665.7	-	24	2562		c.e24-2			NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing						mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				AGGTCGCCCCTTAGAAACAAA	0.333																																					.		Atlas-SNP	.											.	LRPPRC	105	.	0			c.2505-2A>T						.						49.0	50.0	50.0					2																	44162019		2202	4299	6501	SO:0001630	splice_region_variant	10128	exon25			CGCCCCTTAGAAA	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2505-2A>T	chr2.hg19:g.44162019T>A		144.0	0.0		108.0	44.0	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Splice_Site	SNP	ENST00000260665.7	hg19	CCDS33189.1	.	.	.	.	.	.	.	.	.	.	T	12.63	1.995152	0.35226	.	.	ENSG00000138095	ENST00000465633;ENST00000260665	.	.	.	5.84	5.84	0.93424	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.9036	0.79403	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRPPRC	44015523	1.000000	0.71417	0.989000	0.46669	0.058000	0.15608	7.246000	0.78247	2.228000	0.72767	0.533000	0.62120	.	.	.		0.333	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	Intron
PRKCE	5581	hgsc.bcm.edu	37	2	45879477	45879477	+	Nonsense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:45879477G>T	ENST00000306156.3	+	1	565	c.238G>T	c.(238-240)Gag>Tag	p.E80*		NM_005400.2	NP_005391.1	Q02156	KPCE_HUMAN	protein kinase C, epsilon	80	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				activation of phospholipase C activity (GO:0007202)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|cellular response to ethanol (GO:0071361)|cellular response to hypoxia (GO:0071456)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|locomotory exploration behavior (GO:0035641)|macrophage activation involved in immune response (GO:0002281)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cellular glucuronidation (GO:2001031)|positive regulation of cytokinesis (GO:0032467)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of insulin secretion (GO:0032024)|positive regulation of lipid catabolic process (GO:0050996)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mucus secretion (GO:0070257)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|release of sequestered calcium ion into cytosol (GO:0051209)|response to morphine (GO:0043278)|signal transduction (GO:0007165)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|calcium-independent protein kinase C activity (GO:0004699)|enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|ethanol binding (GO:0035276)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|receptor activator activity (GO:0030546)|signal transducer activity (GO:0004871)		MBOAT2/PRKCE(2)	breast(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(13)|ovary(3)|upper_aerodigestive_tract(2)	34		all_hematologic(82;0.155)|Acute lymphoblastic leukemia(82;0.209)	LUSC - Lung squamous cell carcinoma(58;0.171)		Tamoxifen(DB00675)	ACGCAAGATCGAGCTGGCTGT	0.612																																					p.E80X		Atlas-SNP	.											.	PRKCE	58	.	0			c.G238T						.						81.0	68.0	73.0					2																	45879477		2203	4300	6503	SO:0001587	stop_gained	5581	exon1			AAGATCGAGCTGG		CCDS1824.1	2p21	2009-07-10			ENSG00000171132	ENSG00000171132	2.7.11.1		9401	protein-coding gene	gene with protein product		176975				1382605, 7877991	Standard	NM_005400		Approved		uc002rut.3	Q02156	OTTHUMG00000128817	ENST00000306156.3:c.238G>T	chr2.hg19:g.45879477G>T	ENSP00000306124:p.Glu80*	27.0	0.0		30.0	15.0	NM_005400	B0LPH7|Q32MQ3|Q53SL4|Q53SM5|Q9UE81	Nonsense_Mutation	SNP	ENST00000306156.3	hg19	CCDS1824.1	.	.	.	.	.	.	.	.	.	.	G	43	10.189166	0.99355	.	.	ENSG00000171132	ENST00000421201;ENST00000306156	.	.	.	4.71	4.71	0.59529	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	.	17.673	0.88224	0.0:0.0:1.0:0.0	.	.	.	.	X	80	.	ENSP00000306124:E80X	E	+	1	0	PRKCE	45732981	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.802000	0.99131	2.152000	0.67230	0.561000	0.74099	GAG	.	.		0.612	PRKCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250751.2		
ERCC3	2071	hgsc.bcm.edu	37	2	128038082	128038082	+	Nonsense_Mutation	SNP	C	C	A	rs367552856		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:128038082C>A	ENST00000285398.2	-	9	1562	c.1468G>T	c.(1468-1470)Gaa>Taa	p.E490*	ERCC3_ENST00000493187.2_Nonsense_Mutation_p.E426*	NM_000122.1	NP_000113.1	P19447	ERCC3_HUMAN	excision repair cross-complementation group 3	490					7-methylguanosine mRNA capping (GO:0006370)|apoptotic process (GO:0006915)|DNA repair (GO:0006281)|DNA topological change (GO:0006265)|gene expression (GO:0010467)|hair cell differentiation (GO:0035315)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA duplex unwinding (GO:0000717)|nucleotide-excision repair, DNA incision (GO:0033683)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein localization (GO:0008104)|regulation of mitotic cell cycle phase transition (GO:1901990)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)|response to UV (GO:0009411)|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 initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)|viral process (GO:0016032)	holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' DNA helicase activity (GO:0043138)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|damaged DNA binding (GO:0003684)|dATP binding (GO:0032564)|DNA binding (GO:0003677)|GTP binding (GO:0005525)|peptide binding (GO:0042277)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	31	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CAGTTGGCTTCGTAGAGCTTA	0.547			"""Mis, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum																												p.E490X		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (B)	2	2q21	2071	"""excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing)"""		E	.	ERCC3	73	.	0			c.G1468T						.						58.0	52.0	54.0					2																	128038082		2203	4300	6503	SO:0001587	stop_gained	2071	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGGCTTCGTAGAG	M31899	CCDS2144.1	2q21	2014-09-17	2014-03-07		ENSG00000163161	ENSG00000163161		"""General transcription factors"", ""General transcription factor IIH complex subunits"""	3435	protein-coding gene	gene with protein product	"""xeroderma pigmentosum group B complementing"""	133510	"""excision repair cross-complementing rodent repair deficiency, complementation group 3"""			8202161	Standard	NM_000122		Approved	XPB, BTF2, RAD25, TFIIH, GTF2H	uc002toh.1	P19447	OTTHUMG00000131530	ENST00000285398.2:c.1468G>T	chr2.hg19:g.128038082C>A	ENSP00000285398:p.Glu490*	107.0	0.0		114.0	40.0	NM_000122	Q53QM0	Nonsense_Mutation	SNP	ENST00000285398.2	hg19	CCDS2144.1	.	.	.	.	.	.	.	.	.	.	c	43	10.103434	0.99337	.	.	ENSG00000163161	ENST00000285398;ENST00000493187	.	.	.	5.6	5.6	0.85130	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-25.294	19.6423	0.95763	0.0:1.0:0.0:0.0	.	.	.	.	X	490;426	.	ENSP00000285398:E490X	E	-	1	0	ERCC3	127754552	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	7.808000	0.86044	2.636000	0.89361	0.645000	0.84053	GAA	.	.		0.547	ERCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331028.1	NM_000122	
ACVR2A	92	hgsc.bcm.edu	37	2	148674983	148674983	+	Silent	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:148674983A>G	ENST00000241416.7	+	6	1440	c.804A>G	c.(802-804)gcA>gcG	p.A268A	ACVR2A_ENST00000404590.1_Silent_p.A268A|ACVR2A_ENST00000535787.1_Silent_p.A160A	NM_001278579.1|NM_001278580.1|NM_001616.3	NP_001265508.1|NP_001265509.1|NP_001607.1	P27037	AVR2A_HUMAN	activin A receptor, type IIA	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|gastrulation with mouth forming second (GO:0001702)|mesoderm development (GO:0007498)|penile erection (GO:0043084)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein phosphorylation (GO:0001934)|regulation of BMP signaling pathway (GO:0030510)|regulation of nitric-oxide synthase activity (GO:0050999)|Sertoli cell proliferation (GO:0060011)|sperm ejaculation (GO:0042713)|spermatogenesis (GO:0007283)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|inhibin-betaglycan-ActRII complex (GO:0034673)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|coreceptor activity (GO:0015026)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(5)|large_intestine(14)|liver(1)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(8)	45				BRCA - Breast invasive adenocarcinoma(221;0.0969)		TGATCACAGCATTTCATGAAA	0.398																																					p.A268A		Atlas-SNP	.											.	ACVR2A	125	.	0			c.A804G						.						101.0	86.0	91.0					2																	148674983		2203	4299	6502	SO:0001819	synonymous_variant	92	exon6			CACAGCATTTCAT		CCDS33301.1, CCDS63030.1	2q22.2-q23.3	2008-02-05	2005-05-10	2005-05-10	ENSG00000121989	ENSG00000121989			173	protein-coding gene	gene with protein product		102581	"""activin A receptor, type II"""	ACVR2		1314589, 10702675	Standard	NM_001278579		Approved	ACTRII	uc002twh.3	P27037	OTTHUMG00000150603	ENST00000241416.7:c.804A>G	chr2.hg19:g.148674983A>G		127.0	0.0		110.0	29.0	NM_001616	B2RAB8|B4DWQ2|D3DP85|Q53TH4|Q6NWV2|Q92474	Silent	SNP	ENST00000241416.7	hg19	CCDS33301.1																																																																																			.	.		0.398	ACVR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319051.1	NM_001616	
TTN	7273	hgsc.bcm.edu	37	2	179472259	179472259	+	Missense_Mutation	SNP	A	A	T	rs564121832		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:179472259A>T	ENST00000591111.1	-	227	48457	c.48233T>A	c.(48232-48234)gTa>gAa	p.V16078E	TTN_ENST00000589042.1_Missense_Mutation_p.V17719E|TTN_ENST00000342175.6_Missense_Mutation_p.V8846E|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V8779E|TTN_ENST00000460472.2_Missense_Mutation_p.V8654E|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V15151E|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000419746.1_RNA			Q8WZ42	TITIN_HUMAN	titin	16078	Ig-like 99.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GTTGTCTATTACAACACGGTC	0.448																																					p.V17719E		Atlas-SNP	.											.	TTN	18412	.	0			c.T53156A						.						434.0	410.0	418.0					2																	179472259		1899	4124	6023	SO:0001583	missense	7273	exon277			TCTATTACAACAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.48233T>A	chr2.hg19:g.179472259A>T	ENSP00000465570:p.Val16078Glu	152.0	0.0		165.0	57.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	A	10.42	1.344158	0.24339	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65732	-0.17;-0.17;-0.17;-0.17	5.99	4.81	0.61882	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.43077	0.1231	N	0.05534	-0.03	0.40995	D	0.984883	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.08055	0.003;0.003;0.003;0.001	T	0.35301	-0.9794	9	0.87932	D	0	.	12.5224	0.56067	0.8689:0.0:0.0:0.1311	.	8654;8779;8846;16078	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	E	15151;8654;8846;8779;8654	ENSP00000343764:V15151E;ENSP00000434586:V8654E;ENSP00000340554:V8846E;ENSP00000352154:V8779E	ENSP00000340554:V8846E	V	-	2	0	TTN	179180504	0.931000	0.31567	0.997000	0.53966	0.922000	0.55478	1.555000	0.36277	1.041000	0.40125	0.533000	0.62120	GTA	.	.		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TTN	7273	hgsc.bcm.edu	37	2	179501228	179501228	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:179501228C>A	ENST00000591111.1	-	175	36527	c.36303G>T	c.(36301-36303)aaG>aaT	p.K12101N	TTN_ENST00000589042.1_Missense_Mutation_p.K13742N|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K4869N|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000418062.1_RNA|TTN-AS1_ENST00000589487.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K4802N|TTN_ENST00000460472.2_Missense_Mutation_p.K4677N|TTN-AS1_ENST00000589830.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K11174N|TTN-AS1_ENST00000585451.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12101	Ig-like 80.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGATGTGCAGCTTTCTGTCTT	0.443																																					p.K13742N		Atlas-SNP	.											.	TTN	18412	.	0			c.G41226T						.						110.0	103.0	106.0					2																	179501228		1863	4114	5977	SO:0001583	missense	7273	exon225			GTGCAGCTTTCTG	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.36303G>T	chr2.hg19:g.179501228C>A	ENSP00000465570:p.Lys12101Asn	146.0	0.0		148.0	54.0	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	hg19		.	.	.	.	.	.	.	.	.	.	C	9.284	1.048873	0.19827	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.68	4.8	0.61643	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.73202	0.3557	L	0.39245	1.2	0.46078	D	0.998852	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.998;0.998	T	0.75158	-0.3416	9	0.87932	D	0	.	10.1437	0.42751	0.0:0.791:0.0:0.209	.	4677;4802;4869;12101	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	N	11174;4677;4869;4802;4677	ENSP00000343764:K11174N;ENSP00000434586:K4677N;ENSP00000340554:K4869N;ENSP00000352154:K4802N	ENSP00000340554:K4869N	K	-	3	2	TTN	179209473	0.994000	0.37717	1.000000	0.80357	0.584000	0.36387	0.475000	0.22164	1.415000	0.47037	-0.162000	0.13425	AAG	.	.		0.443	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SPEG	10290	hgsc.bcm.edu	37	2	220348586	220348586	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:220348586G>T	ENST00000312358.7	+	30	6533	c.6401G>T	c.(6400-6402)gGt>gTt	p.G2134V	AC053503.11_ENST00000429882.1_RNA|SPEG_ENST00000485813.1_3'UTR	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2134					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		TTCTCCCAGGGTGAGGCGGAg	0.731																																					p.G2134V		Atlas-SNP	.											.	SPEG	272	.	0			c.G6401T						.						7.0	9.0	8.0					2																	220348586		1801	3972	5773	SO:0001583	missense	10290	exon30			CCCAGGGTGAGGC	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.6401G>T	chr2.hg19:g.220348586G>T	ENSP00000311684:p.Gly2134Val	13.0	0.0		11.0	5.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	hg19	CCDS42824.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.741843	0.30865	.	.	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.65916	-0.18	4.16	2.31	0.28768	.	0.000000	0.35870	U	0.002936	T	0.49474	0.1559	L	0.29908	0.895	0.80722	D	1	B	0.20052	0.041	B	0.18263	0.021	T	0.46925	-0.9156	10	0.66056	D	0.02	.	13.0329	0.58854	0.0:0.3093:0.6907:0.0	.	2134	Q15772	SPEG_HUMAN	V	2134	ENSP00000311684:G2134V	ENSP00000265327:G2134V	G	+	2	0	SPEG	220056830	1.000000	0.71417	0.159000	0.22649	0.951000	0.60555	4.955000	0.63638	0.387000	0.25024	0.455000	0.32223	GGT	.	.		0.731	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
SLC4A3	6508	hgsc.bcm.edu	37	2	220500505	220500505	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:220500505C>T	ENST00000358055.3	+	14	2595	c.2083C>T	c.(2083-2085)Cac>Tac	p.H695Y	SLC4A3_ENST00000317151.3_Missense_Mutation_p.H695Y|SLC4A3_ENST00000373762.3_Missense_Mutation_p.H722Y|SLC4A3_ENST00000373760.2_Missense_Mutation_p.H695Y|SLC4A3_ENST00000273063.6_Missense_Mutation_p.H722Y			P48751	B3A3_HUMAN	solute carrier family 4 (anion exchanger), member 3	695					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	51		Renal(207;0.0183)		Epithelial(149;2.53e-07)|all cancers(144;5.57e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGGTACCCGCACTACCCCAG	0.647																																					p.H722Y		Atlas-SNP	.											SLC4A3,NS,carcinoma,0,1	SLC4A3	144	.	0			c.C2164T						.						35.0	35.0	35.0					2																	220500505		2203	4300	6503	SO:0001583	missense	6508	exon14			TACCCGCACTACC		CCDS2445.1, CCDS2446.1	2q35	2013-07-19	2013-07-19		ENSG00000114923	ENSG00000114923		"""Solute carriers"""	11029	protein-coding gene	gene with protein product	"""Anion exchanger 3, neuronal"""	106195	"""solute carrier family 4, anion exchanger, member 3"""			8001971	Standard	NM_005070		Approved	AE3, SLC2C	uc002vmo.4	P48751	OTTHUMG00000059238	ENST00000358055.3:c.2083C>T	chr2.hg19:g.220500505C>T	ENSP00000350756:p.His695Tyr	63.0	0.0		66.0	31.0	NM_201574	A6H8L2|A8K1Q9|B7ZVX6|B9EGD1|Q6YIQ9	Missense_Mutation	SNP	ENST00000358055.3	hg19	CCDS2445.1	.	.	.	.	.	.	.	.	.	.	C	12.72	2.022579	0.35701	.	.	ENSG00000114923	ENST00000358055;ENST00000373760;ENST00000273063;ENST00000373762;ENST00000317151	T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2	4.09	3.21	0.36854	Bicarbonate transporter, C-terminal (1);	0.889253	0.09963	N	0.733115	T	0.63307	0.2500	L	0.33624	1.015	0.24725	N	0.993126	B;B;B	0.13145	0.001;0.007;0.005	B;B;B	0.19391	0.002;0.019;0.025	T	0.49283	-0.8956	10	0.09843	T	0.71	.	5.7029	0.17893	0.3353:0.5635:0.0:0.1012	.	399;695;722	P48751-2;P48751;P48751-3	.;B3A3_HUMAN;.	Y	695;695;722;722;695	ENSP00000350756:H695Y;ENSP00000362865:H695Y;ENSP00000273063:H722Y;ENSP00000362867:H722Y;ENSP00000314006:H695Y	ENSP00000273063:H722Y	H	+	1	0	SLC4A3	220208749	0.806000	0.28996	0.861000	0.33841	0.991000	0.79684	1.638000	0.37165	1.059000	0.40554	0.643000	0.83706	CAC	.	.		0.647	SLC4A3-009	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316472.1	NM_005070	
AGAP1	116987	hgsc.bcm.edu	37	2	237032735	237032735	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:237032735A>G	ENST00000304032.8	+	18	3123	c.2543A>G	c.(2542-2544)aAc>aGc	p.N848S	AGAP1_ENST00000428334.2_Missense_Mutation_p.N687S|AGAP1_ENST00000409538.1_Missense_Mutation_p.N1060S|AGAP1_ENST00000336665.5_Missense_Mutation_p.N795S	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	848					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						AACCGGAACAACAGCAGTGGG	0.637																																					p.N848S		Atlas-SNP	.											.	AGAP1	95	.	0			c.A2543G						.						58.0	63.0	61.0					2																	237032735		2203	4300	6503	SO:0001583	missense	116987	exon18			GGAACAACAGCAG	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.2543A>G	chr2.hg19:g.237032735A>G	ENSP00000307634:p.Asn848Ser	80.0	0.0		124.0	26.0	NM_001037131	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	hg19	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	A	14.34	2.507666	0.44558	.	.	ENSG00000157985	ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T	0.70516	-0.49;-0.44;-0.44;0.59	4.5	3.27	0.37495	.	0.476338	0.22398	N	0.060589	T	0.70971	0.3285	L	0.38175	1.15	0.45108	D	0.998124	B;P	0.52842	0.002;0.956	B;D	0.65010	0.002;0.931	T	0.63449	-0.6635	10	0.15066	T	0.55	.	8.9317	0.35675	0.9001:0.0:0.0999:0.0	.	795;848	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	S	848;795;1060;687	ENSP00000307634:N848S;ENSP00000338378:N795S;ENSP00000386897:N1060S;ENSP00000411824:N687S	ENSP00000307634:N848S	N	+	2	0	AGAP1	236697474	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.418000	0.52721	0.530000	0.28619	0.460000	0.39030	AAC	.	.		0.637	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	
HDAC4	9759	hgsc.bcm.edu	37	2	240056268	240056268	+	Silent	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:240056268G>A	ENST00000345617.3	-	10	1841	c.1050C>T	c.(1048-1050)tcC>tcT	p.S350S	HDAC4_ENST00000553145.1_5'UTR|HDAC4_ENST00000543185.1_5'UTR|HDAC4_ENST00000541256.1_Silent_p.S319S	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	350					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TGTTGGGCAAGGATGGCGATG	0.637																																					p.S350S		Atlas-SNP	.											.	HDAC4	127	.	0			c.C1050T						.						117.0	118.0	117.0					2																	240056268		2203	4300	6503	SO:0001819	synonymous_variant	9759	exon10			GGGCAAGGATGGC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1050C>T	chr2.hg19:g.240056268G>A		52.0	0.0		71.0	16.0	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	hg19	CCDS2529.1	.	.	.	.	.	.	.	.	.	.	G	1.601	-0.526577	0.04141	.	.	ENSG00000068024	ENST00000445704	.	.	.	4.32	3.44	0.39384	.	.	.	.	.	T	0.54431	0.1858	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50145	-0.8862	4	.	.	.	.	5.5916	0.17303	0.2438:0.1494:0.6068:0.0	.	.	.	.	L	94	.	.	P	-	2	0	HDAC4	239721205	0.429000	0.25530	0.584000	0.28653	0.117000	0.20001	0.304000	0.19228	1.126000	0.42016	0.561000	0.74099	CCT	.	.		0.637	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
PDCD1	5133	hgsc.bcm.edu	37	2	242793440	242793440	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:242793440G>A	ENST00000334409.5	-	5	706	c.637C>T	c.(637-639)Ccc>Tcc	p.P213S		NM_005018.2	NP_005009.2	Q15116	PDCD1_HUMAN	programmed cell death 1	213					apoptotic process (GO:0006915)|humoral immune response (GO:0006959)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			endometrium(1)|lung(2)|ovary(1)|prostate(3)|skin(1)	8		all_cancers(19;1.09e-40)|all_epithelial(40;2.03e-18)|Breast(86;1.53e-05)|all_lung(227;0.00338)|Renal(207;0.00502)|Ovarian(221;0.00716)|Lung NSC(271;0.012)|Esophageal squamous(248;0.129)|Melanoma(123;0.144)|all_hematologic(139;0.158)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;3.84e-33)|all cancers(36;8.08e-31)|OV - Ovarian serous cystadenocarcinoma(60;7.41e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.63e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0219)		ACGGCTGAGGGGTCCTCCTTC	0.662																																					p.P213S		Atlas-SNP	.											.	PDCD1	31	.	0			c.C637T						.						34.0	39.0	37.0					2																	242793440		2203	4300	6503	SO:0001583	missense	5133	exon5			CTGAGGGGTCCTC	AY206416	CCDS33428.1	2q37.3	2014-01-29			ENSG00000188389	ENSG00000188389		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	8760	protein-coding gene	gene with protein product		600244	"""systemic lupus erythematosus susceptibility 2"""	SLEB2		7851902, 12402038	Standard	NM_005018		Approved	CD279, PD1, hSLE1	uc002wcq.4	Q15116	OTTHUMG00000151342	ENST00000334409.5:c.637C>T	chr2.hg19:g.242793440G>A	ENSP00000335062:p.Pro213Ser	46.0	0.0		44.0	20.0	NM_005018	O00517|Q8IX89	Missense_Mutation	SNP	ENST00000334409.5	hg19	CCDS33428.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.63|13.63	2.294624|2.294624	0.40594|0.40594	.|.	.|.	ENSG00000188389|ENSG00000188389	ENST00000343705|ENST00000334409;ENST00000539073	.|T	.|0.68025	.|-0.3	3.79|3.79	1.78|1.78	0.24846|0.24846	.|.	0.503154|0.503154	0.16273|0.16273	N|N	0.221708|0.221708	T|T	0.51907|0.51907	0.1702|0.1702	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999999|0.999999	.|B;B	.|0.25235	.|0.121;0.121	.|B;B	.|0.20577	.|0.03;0.03	T|T	0.40739|0.40739	-0.9547|-0.9547	6|10	.|0.41790	.|T	.|0.15	-4.7864|-4.7864	5.037|5.037	0.14440|0.14440	0.133:0.214:0.653:0.0|0.133:0.214:0.653:0.0	.|.	.|213;213	.|Q8IX89;Q15116	.|.;PDCD1_HUMAN	L|S	104|213;161	.|ENSP00000335062:P213S	.|ENSP00000335062:P213S	P|P	-|-	2|1	0|0	PDCD1|PDCD1	242442113|242442113	0.001000|0.001000	0.12720|0.12720	0.003000|0.003000	0.11579|0.11579	0.741000|0.741000	0.42261|0.42261	0.304000|0.304000	0.19228|0.19228	0.283000|0.283000	0.22279|0.22279	0.555000|0.555000	0.69702|0.69702	CCC|CCC	.	.		0.662	PDCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322313.1	NM_005018	
XIRP1	165904	hgsc.bcm.edu	37	3	39228092	39228092	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:39228092G>A	ENST00000340369.3	-	2	3073	c.2845C>T	c.(2845-2847)Ccg>Tcg	p.P949S	XIRP1_ENST00000396251.1_Missense_Mutation_p.P949S|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	949					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		GGGTCAGCCGGGGGCTCCCAC	0.632																																					p.P949S		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2845T						.						32.0	35.0	34.0					3																	39228092		2203	4300	6503	SO:0001583	missense	165904	exon2			CAGCCGGGGGCTC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2845C>T	chr3.hg19:g.39228092G>A	ENSP00000343140:p.Pro949Ser	63.0	0.0		53.0	38.0	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	hg19	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	G	7.739	0.700886	0.15172	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05580	3.42;3.72	5.03	4.16	0.48862	.	0.999489	0.08095	N	0.998728	T	0.15435	0.0372	L	0.57536	1.79	0.80722	D	1	P;P	0.43094	0.799;0.748	P;P	0.50537	0.643;0.541	T	0.00880	-1.1529	10	0.56958	D	0.05	.	10.0178	0.42024	0.0943:0.0:0.9057:0.0	.	949;949	Q702N8;Q702N8-2	XIRP1_HUMAN;.	S	949	ENSP00000379550:P949S;ENSP00000343140:P949S	ENSP00000343140:P949S	P	-	1	0	XIRP1	39203096	0.900000	0.30661	0.231000	0.23993	0.119000	0.20118	2.049000	0.41288	1.289000	0.44618	-0.126000	0.14955	CCG	.	.		0.632	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
STAB1	23166	hgsc.bcm.edu	37	3	52553354	52553354	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:52553354C>A	ENST00000321725.6	+	49	5185	c.5109C>A	c.(5107-5109)ttC>ttA	p.F1703L		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1703	FAS1 5. {ECO:0000255|PROSITE- ProRule:PRU00082, ECO:0000305}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		TCCTGCACTTCATTGACCGTG	0.642																																					p.F1703L		Atlas-SNP	.											.	STAB1	178	.	0			c.C5109A						.						122.0	122.0	122.0					3																	52553354		2203	4299	6502	SO:0001583	missense	23166	exon49			GCACTTCATTGAC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.5109C>A	chr3.hg19:g.52553354C>A	ENSP00000312946:p.Phe1703Leu	99.0	0.0		74.0	50.0	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Missense_Mutation	SNP	ENST00000321725.6	hg19	CCDS33768.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.886623	0.51908	.	.	ENSG00000010327	ENST00000321725	D	0.90004	-2.6	5.5	5.5	0.81552	FAS1 domain (5);	0.121338	0.64402	D	0.000018	D	0.88969	0.6582	N	0.16790	0.44	0.44531	D	0.997487	D	0.67145	0.996	D	0.64776	0.929	D	0.88017	0.2766	10	0.30078	T	0.28	.	17.5833	0.87973	0.0:1.0:0.0:0.0	.	1703	Q9NY15	STAB1_HUMAN	L	1703	ENSP00000312946:F1703L	ENSP00000312946:F1703L	F	+	3	2	STAB1	52528394	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	1.229000	0.32600	2.574000	0.86865	0.655000	0.94253	TTC	.	.		0.642	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
GPR15	2838	hgsc.bcm.edu	37	3	98251158	98251158	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:98251158C>A	ENST00000284311.3	+	1	416	c.281C>A	c.(280-282)gCa>gAa	p.A94E		NM_005290.1	NP_005281.1	P49685	GPR15_HUMAN	G protein-coupled receptor 15	94					G-protein coupled receptor signaling pathway (GO:0007186)|T cell migration (GO:0072678)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|kidney(3)|large_intestine(1)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Lung NSC(201;7.93e-06)|all_neural(597;0.00172)|Hepatocellular(537;0.00825)|Myeloproliferative disorder(1037;0.0255)		Lung(72;0.246)		GATAAAGAAGCATCTCTAGGA	0.502																																					p.A94E		Atlas-SNP	.											GPR15,NS,carcinoma,+1,1	GPR15	55	.	0			c.C281A						.						79.0	80.0	79.0					3																	98251158		2203	4300	6503	SO:0001583	missense	2838	exon1			AAGAAGCATCTCT		CCDS2931.1	3q11.2-q13.1	2014-01-30			ENSG00000154165	ENSG00000154165		"""GPCR / Class A : Orphans"""	4469	protein-coding gene	gene with protein product		601166				8838812	Standard	NM_005290		Approved		uc011bgy.3	P49685	OTTHUMG00000160017	ENST00000284311.3:c.281C>A	chr3.hg19:g.98251158C>A	ENSP00000284311:p.Ala94Glu	115.0	0.0		85.0	32.0	NM_005290	Q3MIL4|Q6ISN6	Missense_Mutation	SNP	ENST00000284311.3	hg19	CCDS2931.1	.	.	.	.	.	.	.	.	.	.	C	15.90	2.968982	0.53614	.	.	ENSG00000154165	ENST00000284311	T	0.38401	1.14	4.8	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000101	T	0.49712	0.1573	M	0.80422	2.495	0.22500	N	0.999046	P	0.47841	0.901	P	0.47299	0.543	T	0.53690	-0.8403	10	0.72032	D	0.01	-2.4607	15.7547	0.78015	0.0:1.0:0.0:0.0	.	94	P49685	GPR15_HUMAN	E	94	ENSP00000284311:A94E	ENSP00000284311:A94E	A	+	2	0	GPR15	99733848	0.000000	0.05858	0.986000	0.45419	0.970000	0.65996	-0.160000	0.10041	2.656000	0.90262	0.591000	0.81541	GCA	.	.		0.502	GPR15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358907.1		
PODXL2	50512	hgsc.bcm.edu	37	3	127379537	127379537	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:127379537T>A	ENST00000342480.6	+	3	705	c.666T>A	c.(664-666)caT>caA	p.H222Q		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	222					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						AAAGCAGGCATGAAGACTCCG	0.602																																					p.H222Q		Atlas-SNP	.											.	PODXL2	53	.	0			c.T666A						.						80.0	90.0	87.0					3																	127379537		2203	4300	6503	SO:0001583	missense	50512	exon3			CAGGCATGAAGAC	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.666T>A	chr3.hg19:g.127379537T>A	ENSP00000345359:p.His222Gln	67.0	0.0		85.0	26.0	NM_015720	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	hg19	CCDS3044.1	.	.	.	.	.	.	.	.	.	.	T	0.015	-1.564193	0.00903	.	.	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.21031	2.03	4.67	-9.34	0.00636	.	1.210160	0.06044	N	0.655417	T	0.06462	0.0166	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.21109	-1.0255	10	0.12766	T	0.61	0.7936	1.9438	0.03352	0.2678:0.2701:0.3304:0.1318	.	222	Q9NZ53	PDXL2_HUMAN	Q	222	ENSP00000345359:H222Q	ENSP00000304498:H222Q	H	+	3	2	PODXL2	128862227	0.001000	0.12720	0.000000	0.03702	0.004000	0.04260	-2.370000	0.01075	-3.428000	0.00165	-0.415000	0.06103	CAT	.	.		0.602	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
MFSD1	64747	hgsc.bcm.edu	37	3	158519925	158519925	+	5'UTR	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:158519925C>G	ENST00000264266.8	+	0	46				MFSD1_ENST00000392813.4_Missense_Mutation_p.P44R|MFSD1_ENST00000415822.2_Missense_Mutation_p.P44R|RP11-379F4.9_ENST00000607044.1_RNA			Q9H3U5	MFSD1_HUMAN	major facilitator superfamily domain containing 1						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	26			Lung(72;0.00372)|LUSC - Lung squamous cell carcinoma(72;0.00523)			TTCCCCTCTCCGTCTCCTGCG	0.677																																					p.P44R	Pancreas(62;1186 1654 36636 37908)	Atlas-SNP	.											.	MFSD1	88	.	0			c.C131G						.						18.0	21.0	20.0					3																	158519925		2198	4287	6485	SO:0001623	5_prime_UTR_variant	64747	exon1			CCTCTCCGTCTCC	BC017661	CCDS3185.1, CCDS3185.2, CCDS54666.1	3q25.32	2005-11-17			ENSG00000118855	ENSG00000118855			25874	protein-coding gene	gene with protein product							Standard	NM_022736		Approved	FLJ14153, UG0581B09	uc003fcl.2	Q9H3U5	OTTHUMG00000158835	ENST00000264266.8:c.-17C>G	chr3.hg19:g.158519925C>G		59.0	0.0		74.0	25.0	NM_022736	B4DGJ8|B4DMR8|B4DU49|B4DWU1|C9JS94|J3KQL7|Q05C07|Q5XKJ1|Q8IVS1|Q8IXG4|Q9H7X1	Missense_Mutation	SNP	ENST00000264266.8	hg19		.	.	.	.	.	.	.	.	.	.	C	0.004	-2.300542	0.00243	.	.	ENSG00000118855	ENST00000415822;ENST00000392813	T;T	0.21734	1.99;1.99	2.8	-5.61	0.02489	.	.	.	.	.	T	0.05547	0.0146	N	0.03608	-0.345	0.20196	N	0.999926	.	.	.	.	.	.	T	0.19844	-1.0293	7	0.12766	T	0.61	.	0.6164	0.00770	0.2113:0.2615:0.1845:0.3427	.	.	.	.	R	44	ENSP00000403117:P44R;ENSP00000376560:P44R	ENSP00000376560:P44R	P	+	2	0	MFSD1	160002619	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.031000	0.00637	-3.388000	0.00173	-2.100000	0.00362	CCG	.	.		0.677	MFSD1-018	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470730.1	NM_022736	
SLITRK3	22865	hgsc.bcm.edu	37	3	164908256	164908256	+	Silent	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:164908256G>A	ENST00000475390.1	-	2	806	c.363C>T	c.(361-363)ttC>ttT	p.F121F	SLITRK3_ENST00000241274.3_Silent_p.F121F			O94933	SLIK3_HUMAN	SLIT and NTRK-like family, member 3	121					axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(66)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(5)	119						TAAGACCATTGAAAGCTCCAG	0.348										HNSCC(40;0.11)																											p.F121F		Atlas-SNP	.											.	SLITRK3	263	.	0			c.C363T						.						45.0	45.0	45.0					3																	164908256		2202	4299	6501	SO:0001819	synonymous_variant	22865	exon2			ACCATTGAAAGCT	AB020655	CCDS3197.1	3q26.1	2004-07-28			ENSG00000121871	ENSG00000121871			23501	protein-coding gene	gene with protein product		609679				10048485, 14557068	Standard	NM_014926		Approved	KIAA0848	uc003fek.3	O94933	OTTHUMG00000158072	ENST00000475390.1:c.363C>T	chr3.hg19:g.164908256G>A		80.0	0.0		80.0	34.0	NM_014926	Q1RMY6	Silent	SNP	ENST00000475390.1	hg19	CCDS3197.1																																																																																			.	.		0.348	SLITRK3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350126.1	NM_014926	
TNK2	10188	hgsc.bcm.edu	37	3	195610026	195610026	+	Splice_Site	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:195610026A>T	ENST00000333602.6	-	5	1227		c.e5+1		TNK2_ENST00000381916.2_Splice_Site|TNK2_ENST00000468819.1_Splice_Site|TNK2_ENST00000392400.1_Splice_Site|TNK2_ENST00000316664.3_Splice_Site|TNK2_ENST00000428187.1_Splice_Site	NM_005781.4	NP_005772.3	Q07912	ACK1_HUMAN	tyrosine kinase, non-receptor, 2						cell surface receptor signaling pathway (GO:0007166)|endocytosis (GO:0006897)|negative regulation of catalytic activity (GO:0043086)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of clathrin-mediated endocytosis (GO:2000369)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endosome (GO:0005768)|Grb2-EGFR complex (GO:0070436)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|WW domain binding (GO:0050699)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(11)|ovary(3)|prostate(4)|skin(2)|stomach(1)|urinary_tract(1)	29	all_cancers(143;6.48e-09)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;1.46e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.3e-19)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;0.000757)	Adenosine triphosphate(DB00171)	CGCAGTACTCACCATCTTCAT	0.627																																					.		Atlas-SNP	.											.	TNK2	246	.	0			c.609+2T>A						.						55.0	48.0	51.0					3																	195610026		2203	4300	6503	SO:0001630	splice_region_variant	10188	exon6			GTACTCACCATCT	L13738	CCDS33927.1, CCDS33928.1	3q29	2013-09-02			ENSG00000061938	ENSG00000061938			19297	protein-coding gene	gene with protein product	"""activated Cdc42-associated kinase 1"""	606994				8497321, 14506255	Standard	XM_006713460		Approved	p21cdc42Hs, ACK, ACK1	uc003fvt.1	Q07912	OTTHUMG00000155737	ENST00000333602.6:c.609+1T>A	chr3.hg19:g.195610026A>T		23.0	0.0		12.0	6.0	NM_005781	Q6ZMQ0|Q8N6U7|Q96H59	Splice_Site	SNP	ENST00000333602.6	hg19	CCDS33928.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.271323	0.80469	.	.	ENSG00000061938	ENST00000333602;ENST00000381916;ENST00000428187;ENST00000392400;ENST00000316664;ENST00000438207	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.3226	0.66496	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TNK2	197094423	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.192000	0.77771	2.068000	0.61886	0.533000	0.62120	.	.	.		0.627	TNK2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341437.3	NM_005781	Intron
APBB2	323	hgsc.bcm.edu	37	4	40892391	40892391	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:40892391C>T	ENST00000295974.8	-	12	2145	c.1516G>A	c.(1516-1518)Gac>Aac	p.D506N	APBB2_ENST00000506352.1_Missense_Mutation_p.D485N|APBB2_ENST00000508593.1_Missense_Mutation_p.D507N|APBB2_ENST00000513140.1_Missense_Mutation_p.D485N	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	506	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						CGGCCATTGTCGCGGCCCACG	0.642																																					p.D507N	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.G1519A						.						40.0	44.0	43.0					4																	40892391		2140	4262	6402	SO:0001583	missense	323	exon12			CATTGTCGCGGCC	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.1516G>A	chr4.hg19:g.40892391C>T	ENSP00000295974:p.Asp506Asn	64.0	0.0		57.0	24.0	NM_004307	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	hg19	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	27.4|27.4	4.828290|4.828290	0.90955|0.90955	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352;ENST00000512510|ENST00000513611	T;T;T;T;T|T	0.26373|0.14391	2.39;2.39;2.39;2.39;1.74|2.51	5.98|5.98	5.98|5.98	0.97165|0.97165	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.23451|0.23451	0.0567|0.0567	L|L	0.43757|0.43757	1.38|1.38	0.80722|0.80722	D|D	1|1	D;D;D;D|.	0.69078|.	0.997;0.988;0.985;0.988|.	P;P;P;P|.	0.57324|.	0.818;0.647;0.515;0.647|.	T|T	0.00067|0.00067	-1.2142|-1.2142	10|7	0.49607|0.87932	T|D	0.09|0	-30.3771|-30.3771	13.6272|13.6272	0.62173|0.62173	0.0:0.9295:0.0:0.0705|0.0:0.9295:0.0:0.0705	.|.	468;507;485;506|.	B4DJ88;E9PG87;Q92870-2;Q92870|.	.;.;.;APBB2_HUMAN|.	N|Q	506;505;485;507;485;18|475	ENSP00000295974:D506N;ENSP00000426018:D485N;ENSP00000427211:D507N;ENSP00000421539:D485N;ENSP00000426429:D18N|ENSP00000427307:R475Q	ENSP00000295974:D506N|ENSP00000427307:R475Q	D|R	-|-	1|2	0|0	APBB2|APBB2	40587148|40587148	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.968000|0.968000	0.65278|0.65278	7.406000|7.406000	0.80017|0.80017	2.838000|2.838000	0.97847|0.97847	0.591000|0.591000	0.81541|0.81541	GAC|CGA	.	.		0.642	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
SHISA3	152573	hgsc.bcm.edu	37	4	42400220	42400220	+	Silent	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:42400220C>T	ENST00000319234.4	+	1	365	c.147C>T	c.(145-147)gaC>gaT	p.D49D		NM_001080505.1	NP_001073974.1	A0PJX4	SHSA3_HUMAN	shisa family member 3	49					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	12						AGGACTTCGACACGCTGGACG	0.716																																					p.D49D		Atlas-SNP	.											.	SHISA3	27	.	0			c.C147T						.						23.0	22.0	22.0					4																	42400220		2199	4298	6497	SO:0001819	synonymous_variant	152573	exon1			CTTCGACACGCTG	BC012029	CCDS33979.1	4p13	2013-07-31	2013-07-31		ENSG00000178343	ENSG00000178343		"""Shisa homologs"""	25159	protein-coding gene	gene with protein product			"""shisa homolog 3 (Xenopus laevis)"""				Standard	NM_001080505		Approved	hShisa3	uc003gwp.3	A0PJX4	OTTHUMG00000161043	ENST00000319234.4:c.147C>T	chr4.hg19:g.42400220C>T		53.0	0.0		75.0	21.0	NM_001080505	A0PJX3|Q96EQ5	Silent	SNP	ENST00000319234.4	hg19	CCDS33979.1																																																																																			.	.		0.716	SHISA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363539.1	NM_001080505	
ADAD1	132612	hgsc.bcm.edu	37	4	123302161	123302161	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:123302161C>A	ENST00000296513.2	+	4	372	c.187C>A	c.(187-189)Ccg>Acg	p.P63T	ADAD1_ENST00000388725.2_Missense_Mutation_p.P45T|ADAD1_ENST00000388724.2_Missense_Mutation_p.P63T|ADAD1_ENST00000492454.1_3'UTR	NM_139243.3	NP_640336.1	Q96M93	ADAD1_HUMAN	adenosine deaminase domain containing 1 (testis-specific)	63					multicellular organismal development (GO:0007275)|RNA processing (GO:0006396)|spermatid development (GO:0007286)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|RNA binding (GO:0003723)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	35						TTTTCCAGAGCCGTTGCTTTC	0.313																																					p.P63T		Atlas-SNP	.											.	ADAD1	94	.	0			c.C187A						.						64.0	66.0	66.0					4																	123302161		2203	4300	6503	SO:0001583	missense	132612	exon4			CCAGAGCCGTTGC	AK057303	CCDS34058.1, CCDS54800.1, CCDS54801.1	4q27	2007-05-31			ENSG00000164113	ENSG00000164113			30713	protein-coding gene	gene with protein product		614130				7543294, 9541871	Standard	NM_139243		Approved	Tenr	uc003iep.3	Q96M93	OTTHUMG00000150128	ENST00000296513.2:c.187C>A	chr4.hg19:g.123302161C>A	ENSP00000296513:p.Pro63Thr	289.0	0.0		357.0	96.0	NM_139243	A6NKN4|B7WPB0|D3DNX2|Q8IWG6|Q8NA06	Missense_Mutation	SNP	ENST00000296513.2	hg19	CCDS34058.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.736709	0.30774	.	.	ENSG00000164113	ENST00000446706;ENST00000296513;ENST00000439307;ENST00000388724;ENST00000388725	T;T;T	0.34667	1.35;1.35;1.37	5.23	4.37	0.52481	.	0.000000	0.64402	D	0.000005	T	0.41994	0.1183	L	0.32530	0.975	0.41237	D	0.986619	D;D	0.63880	0.993;0.993	P;P	0.59221	0.854;0.827	T	0.12915	-1.0529	10	0.32370	T	0.25	-15.9499	13.1832	0.59666	0.0:0.9193:0.0:0.0807	.	63;63	Q96M93-2;Q96M93	.;ADAD1_HUMAN	T	63;63;63;63;45	ENSP00000296513:P63T;ENSP00000373376:P63T;ENSP00000373377:P45T	ENSP00000296513:P63T	P	+	1	0	ADAD1	123521611	0.000000	0.05858	0.993000	0.49108	0.018000	0.09664	0.346000	0.19997	2.423000	0.82170	0.563000	0.77884	CCG	.	.		0.313	ADAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316452.1	NM_139243	
FAT4	79633	hgsc.bcm.edu	37	4	126367528	126367528	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:126367528G>A	ENST00000394329.3	+	8	7287	c.7274G>A	c.(7273-7275)aGg>aAg	p.R2425K	FAT4_ENST00000335110.5_Missense_Mutation_p.R723K	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	2425	Cadherin 23. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TTGTTAGATAGGGAAACAAAA	0.448																																					p.R2425K		Atlas-SNP	.											.	FAT4	1752	.	0			c.G7274A						.						134.0	132.0	133.0					4																	126367528		2203	4300	6503	SO:0001583	missense	79633	exon8			TAGATAGGGAAAC	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.7274G>A	chr4.hg19:g.126367528G>A	ENSP00000377862:p.Arg2425Lys	92.0	0.0		69.0	30.0	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	hg19	CCDS3732.3	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722245	0.89298	.	.	ENSG00000196159	ENST00000394329;ENST00000335110	T;T	0.59224	0.28;0.28	5.69	5.69	0.88448	Cadherin (4);Cadherin-like (1);	0.000000	0.34906	U	0.003596	T	0.82047	0.4952	M	0.92026	3.265	0.58432	D	0.99999	D;D	0.69078	0.984;0.997	D;D	0.80764	0.946;0.994	D	0.84515	0.0624	10	0.54805	T	0.06	.	19.8199	0.96589	0.0:0.0:1.0:0.0	.	723;2425	Q6V0I7-2;Q6V0I7	.;FAT4_HUMAN	K	2425;723	ENSP00000377862:R2425K;ENSP00000335169:R723K	ENSP00000335169:R723K	R	+	2	0	FAT4	126586978	1.000000	0.71417	0.996000	0.52242	0.266000	0.26442	9.666000	0.98612	2.677000	0.91161	0.655000	0.94253	AGG	.	.		0.448	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
TKTL2	84076	hgsc.bcm.edu	37	4	164394657	164394657	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:164394657C>T	ENST00000280605.3	-	1	390	c.230G>A	c.(229-231)gGa>gAa	p.G77E		NM_032136.4	NP_115512.3	Q9H0I9	TKTL2_HUMAN	transketolase-like 2	77						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(42)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	70	all_hematologic(180;0.166)	Prostate(90;0.0959)|all_neural(102;0.223)				AGCAGCATGTCCCCTGGAGAG	0.532																																					p.G77E		Atlas-SNP	.											.	TKTL2	130	.	0			c.G230A						.						174.0	117.0	136.0					4																	164394657		2203	4300	6503	SO:0001583	missense	84076	exon1			GCATGTCCCCTGG	BC028707	CCDS3805.1	4q32.2	2009-10-06			ENSG00000151005	ENSG00000151005			25313	protein-coding gene	gene with protein product	"""similar to transketolase"""					11230166	Standard	NM_032136		Approved	FLJ32975, DKFZP434L1717	uc003iqp.4	Q9H0I9	OTTHUMG00000161527	ENST00000280605.3:c.230G>A	chr4.hg19:g.164394657C>T	ENSP00000280605:p.Gly77Glu	148.0	0.0		129.0	47.0	NM_032136	A4FVB4|Q8NCT0|Q96M82	Missense_Mutation	SNP	ENST00000280605.3	hg19	CCDS3805.1	.	.	.	.	.	.	.	.	.	.	C	12.92	2.082657	0.36758	.	.	ENSG00000151005	ENST00000280605	T	0.71579	-0.58	3.8	2.95	0.34219	Transketolase, N-terminal (1);	0.000000	0.64402	U	0.000001	D	0.89546	0.6746	H	0.99507	4.6	0.58432	D	0.999999	D	0.76494	0.999	D	0.76575	0.988	D	0.90589	0.4535	10	0.87932	D	0	-14.6618	9.4321	0.38617	0.0:0.8921:0.0:0.1079	.	77	Q9H0I9	TKTL2_HUMAN	E	77	ENSP00000280605:G77E	ENSP00000280605:G77E	G	-	2	0	TKTL2	164614107	1.000000	0.71417	0.998000	0.56505	0.012000	0.07955	2.369000	0.44231	1.171000	0.42768	0.491000	0.48974	GGA	.	.		0.532	TKTL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365207.1	NM_032136	
PALLD	23022	hgsc.bcm.edu	37	4	169825044	169825044	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:169825044C>A	ENST00000505667.1	+	15	2782	c.2609C>A	c.(2608-2610)gCt>gAt	p.A870D	CBR4_ENST00000509108.1_Intron|PALLD_ENST00000512127.1_Missense_Mutation_p.A471D|PALLD_ENST00000261509.6_Missense_Mutation_p.A853D|PALLD_ENST00000507735.1_Missense_Mutation_p.A366D|PALLD_ENST00000335742.7_Missense_Mutation_p.A695D			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	1077	Interaction with ACTN.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		ACAATTATGGCTGCAAACCCT	0.443									Pancreatic Cancer, Familial Clustering of																												p.A870D	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C2609A						.						104.0	107.0	106.0					4																	169825044		2203	4300	6503	SO:0001583	missense	23022	exon15	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	TTATGGCTGCAAA	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.2609C>A	chr4.hg19:g.169825044C>A	ENSP00000425556:p.Ala870Asp	88.0	0.0		81.0	38.0	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Missense_Mutation	SNP	ENST00000505667.1	hg19	CCDS54818.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.604519	0.87157	.	.	ENSG00000129116	ENST00000261509;ENST00000335742;ENST00000505667;ENST00000512127;ENST00000393726;ENST00000507735	T;T;T;T;T;T	0.76968	-1.06;-1.06;-1.06;-1.06;-1.06;-1.06	5.36	5.36	0.76844	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.31897	U	0.006890	D	0.93061	0.7791	H	0.97874	4.095	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;0.999;0.999;1.0	D	0.95170	0.8289	10	0.87932	D	0	.	19.277	0.94036	0.0:1.0:0.0:0.0	.	870;1077;471;853	B7ZMM5;Q8WX93;B3KTG2;B2RTX2	.;PALLD_HUMAN;.;.	D	853;695;870;471;146;366	ENSP00000261509:A853D;ENSP00000336735:A695D;ENSP00000425556:A870D;ENSP00000426947:A471D;ENSP00000377327:A146D;ENSP00000424016:A366D	ENSP00000261509:A853D	A	+	2	0	PALLD	170061619	1.000000	0.71417	1.000000	0.80357	0.636000	0.38137	7.644000	0.83416	2.782000	0.95742	0.655000	0.94253	GCT	.	.		0.443	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
AADAT	51166	hgsc.bcm.edu	37	4	170991792	170991792	+	Silent	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:170991792T>C	ENST00000337664.4	-	6	942	c.666A>G	c.(664-666)aaA>aaG	p.K222K	AADAT_ENST00000353187.2_Silent_p.K222K|AADAT_ENST00000515480.1_Silent_p.K222K|AADAT_ENST00000509167.1_Silent_p.K226K	NM_016228.3	NP_057312.1	Q8N5Z0	AADAT_HUMAN	aminoadipate aminotransferase	222					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)|tryptophan catabolic process to kynurenine (GO:0019441)	mitochondrial matrix (GO:0005759)	2-aminoadipate transaminase activity (GO:0047536)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|pancreas(1)|stomach(1)	11		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0355)|LUSC - Lung squamous cell carcinoma(193;0.118)		GGAAATCATATTTTCTTGCAA	0.239																																					p.K222K		Atlas-SNP	.											.	AADAT	28	.	0			c.A666G						.						62.0	66.0	65.0					4																	170991792		2197	4289	6486	SO:0001819	synonymous_variant	51166	exon7			ATCATATTTTCTT	AF097994	CCDS3814.1, CCDS75209.1	4q33	2010-12-09			ENSG00000109576	ENSG00000109576	2.6.1.39		17929	protein-coding gene	gene with protein product	"""kynurenine aminotransferase II"", ""L kynurenine/alpha aminoadipate aminotransferase"""	611754				12126930, 10441733	Standard	NM_182662		Approved	KATII, KAT2	uc003isr.3	Q8N5Z0	OTTHUMG00000160912	ENST00000337664.4:c.666A>G	chr4.hg19:g.170991792T>C		173.0	0.0		157.0	69.0	NM_182662	B3KP84|Q9UL02	Silent	SNP	ENST00000337664.4	hg19	CCDS3814.1																																																																																			.	.		0.239	AADAT-004	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362952.1	NM_016228	
SLC6A3	6531	hgsc.bcm.edu	37	5	1422086	1422086	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:1422086G>T	ENST00000270349.9	-	5	824	c.697C>A	c.(697-699)Ctg>Atg	p.L233M	SLC6A3_ENST00000453492.2_Missense_Mutation_p.L233M	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	233					adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GGAGGCCCCAGGTCGTCGATG	0.647																																					p.L233M		Atlas-SNP	.											SLC6A3,right_upper_lobe,carcinoma,0,1	SLC6A3	102	.	0			c.C697A						.						73.0	70.0	71.0					5																	1422086		2203	4300	6503	SO:0001583	missense	6531	exon5			GCCCCAGGTCGTC		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.697C>A	chr5.hg19:g.1422086G>T	ENSP00000270349:p.Leu233Met	38.0	0.0		40.0	15.0	NM_001044	A2RUN4|Q14996	Missense_Mutation	SNP	ENST00000270349.9	hg19	CCDS3863.1	.	.	.	.	.	.	.	.	.	.	G	15.90	2.969409	0.53614	.	.	ENSG00000142319	ENST00000270349;ENST00000453492;ENST00000513308	T;T;T	0.75367	-0.93;-0.93;-0.93	4.4	0.848	0.18966	.	0.176408	0.38217	N	0.001772	T	0.67915	0.2944	L	0.42632	1.34	0.46478	D	0.99906	P	0.44429	0.835	P	0.49477	0.612	T	0.60939	-0.7163	10	0.34782	T	0.22	.	5.7503	0.18142	0.5699:0.0:0.4301:0.0	.	233	Q01959	SC6A3_HUMAN	M	233;233;159	ENSP00000270349:L233M;ENSP00000399806:L233M;ENSP00000429101:L159M	ENSP00000270349:L233M	L	-	1	2	SLC6A3	1475086	0.999000	0.42202	0.997000	0.53966	0.965000	0.64279	0.474000	0.22148	0.360000	0.24265	0.462000	0.41574	CTG	.	.		0.647	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
CAST	831	hgsc.bcm.edu	37	5	96083056	96083056	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:96083056A>G	ENST00000341926.3	+	16	1205	c.1043A>G	c.(1042-1044)gAt>gGt	p.D348G	CAST_ENST00000511782.1_Missense_Mutation_p.D334G|CAST_ENST00000508830.1_Missense_Mutation_p.D431G|CAST_ENST00000359176.4_Missense_Mutation_p.D412G|CAST_ENST00000509903.1_Missense_Mutation_p.D313G|CAST_ENST00000508579.1_Missense_Mutation_p.D63G|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000338252.3_Missense_Mutation_p.D335G|CAST_ENST00000508608.1_Missense_Mutation_p.D394G|CAST_ENST00000515663.1_Missense_Mutation_p.D71G|CAST_ENST00000325674.7_Missense_Mutation_p.D396G|CAST_ENST00000395812.2_Missense_Mutation_p.D390G|CAST_ENST00000395813.1_Missense_Mutation_p.D431G|CAST_ENST00000511049.1_Missense_Mutation_p.D334G|CAST_ENST00000309190.5_Missense_Mutation_p.D326G|CAST_ENST00000504465.1_Missense_Mutation_p.D276G|CAST_ENST00000510756.1_Missense_Mutation_p.D409G			P20810	ICAL_HUMAN	calpastatin	348					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		CAGGATAAAGATGGAAAACCA	0.303																																					p.D390G		Atlas-SNP	.											.	CAST	58	.	0			c.A1169G						.						41.0	44.0	43.0					5																	96083056		2201	4300	6501	SO:0001583	missense	831	exon16			ATAAAGATGGAAA	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.1043A>G	chr5.hg19:g.96083056A>G	ENSP00000339914:p.Asp348Gly	319.0	0.0		279.0	77.0	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	17.02|17.02	3.281934|3.281934	0.59867|0.59867	.|.	.|.	ENSG00000153113|ENSG00000153113	ENST00000338252;ENST00000508830;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000509259;ENST00000503828;ENST00000515663|ENST00000437034	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.55930|.	2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;2.04;0.49;2.04;2.04|.	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	0.412813|.	0.27549|.	N|.	0.018863|.	T|T	0.79953|0.79953	0.4535|0.4535	M|M	0.88775|0.88775	2.98|2.98	0.51233|0.51233	D|D	0.999917|0.999917	P;P;P;B;D;P;D;P;B;P;P;P;P;B;B;P;P|.	0.89917|.	0.614;0.942;0.725;0.1;1.0;0.472;0.968;0.942;0.41;0.56;0.942;0.822;0.658;0.281;0.368;0.783;0.716|.	P;P;B;B;D;B;P;P;P;P;P;P;P;B;B;P;P|.	0.97110|.	0.671;0.813;0.335;0.101;1.0;0.438;0.908;0.813;0.542;0.542;0.813;0.542;0.565;0.424;0.226;0.565;0.61|.	T|T	0.83322|0.83322	-0.0017|-0.0017	10|5	0.66056|.	D|.	0.02|.	-19.7012|-19.7012	13.5561|13.5561	0.61759|0.61759	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	276;196;394;71;99;71;334;313;326;307;348;396;390;412;409;431;335|.	E9PDE4;B7Z8S8;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2|.	.;.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.|.	G|V	335;431;431;412;396;390;409;394;348;334;326;348;276;313;334;63;35;63;71|100	ENSP00000343421:D335G;ENSP00000425721:D431G;ENSP00000379158:D431G;ENSP00000352098:D412G;ENSP00000320319:D396G;ENSP00000379157:D390G;ENSP00000422176:D409G;ENSP00000422677:D394G;ENSP00000339914:D348G;ENSP00000421130:D334G;ENSP00000312523:D326G;ENSP00000422325:D348G;ENSP00000425670:D276G;ENSP00000426946:D313G;ENSP00000423638:D334G;ENSP00000425787:D63G;ENSP00000423846:D35G;ENSP00000422807:D63G;ENSP00000422929:D71G|.	ENSP00000312523:D326G|.	D|M	+|+	2|1	0|0	CAST|CAST	96108812|96108812	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.978000|0.978000	0.69477|0.69477	5.319000|5.319000	0.65835|0.65835	2.197000|2.197000	0.70478|0.70478	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.303	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	
FTMT	94033	hgsc.bcm.edu	37	5	121188325	121188325	+	Missense_Mutation	SNP	G	G	A	rs149286328	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:121188325G>A	ENST00000321339.1	+	1	676	c.667G>A	c.(667-669)Gct>Act	p.A223T		NM_177478.1	NP_803431.1	Q8N4E7	FTMT_HUMAN	ferritin mitochondrial	223					cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)|positive regulation of cell proliferation (GO:0008284)|positive regulation of lyase activity (GO:0051349)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of transferase activity (GO:0051347)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ferric iron binding (GO:0008199)|ferroxidase activity (GO:0004322)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	33		all_cancers(142;0.0124)|Prostate(80;0.0322)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	Epithelial(69;0.000171)|OV - Ovarian serous cystadenocarcinoma(64;0.000188)|all cancers(49;0.0027)		GGCCCCGGATGCTGGCCTGGC	0.507																																					p.A223T		Atlas-SNP	.											.	FTMT	71	.	0			c.G667A						.						104.0	117.0	112.0					5																	121188325		2203	4300	6503	SO:0001583	missense	94033	exon1			CCGGATGCTGGCC	BC034419	CCDS4128.1	5q23.1	2008-02-05			ENSG00000181867	ENSG00000181867			17345	protein-coding gene	gene with protein product		608847				11323407	Standard	NM_177478		Approved	MtF	uc003kss.3	Q8N4E7	OTTHUMG00000128912	ENST00000321339.1:c.667G>A	chr5.hg19:g.121188325G>A	ENSP00000313691:p.Ala223Thr	57.0	0.0		76.0	24.0	NM_177478		Missense_Mutation	SNP	ENST00000321339.1	hg19	CCDS4128.1	.	.	.	.	.	.	.	.	.	.	G	2.379	-0.342536	0.05243	.	.	ENSG00000181867	ENST00000321339	T	0.69040	-0.37	3.68	-1.23	0.09465	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);	0.297217	0.29594	N	0.011703	T	0.48205	0.1487	L	0.34521	1.04	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34601	-0.9822	10	0.48119	T	0.1	.	7.1617	0.25667	0.1098:0.0:0.2013:0.6889	.	223	Q8N4E7	FTMT_HUMAN	T	223	ENSP00000313691:A223T	ENSP00000313691:A223T	A	+	1	0	FTMT	121216224	0.974000	0.33945	0.000000	0.03702	0.040000	0.13550	1.944000	0.40263	-0.244000	0.09639	-1.296000	0.01341	GCT	.	G|0.999;T|0.001		0.507	FTMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250884.1	NM_177478	
FNIP1	96459	hgsc.bcm.edu	37	5	131007517	131007517	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:131007517A>T	ENST00000510461.1	-	14	2715	c.2620T>A	c.(2620-2622)Tgt>Agt	p.C874S	FNIP1_ENST00000307954.8_Missense_Mutation_p.C829S|CTC-432M15.3_ENST00000514667.1_Intron|FNIP1_ENST00000307968.7_Missense_Mutation_p.C846S	NM_133372.2	NP_588613	Q8TF40	FNIP1_HUMAN	folliculin interacting protein 1	874					cellular response to starvation (GO:0009267)|immature B cell differentiation (GO:0002327)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell apoptotic process (GO:0002904)|positive regulation of GTPase activity (GO:0043547)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein phosphorylation (GO:0001934)|regulation of pro-B cell differentiation (GO:2000973)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(11)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		all_cancers(142;0.00347)|Lung NSC(810;0.106)|all_lung(232;0.123)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0665)		TTTTTTGTACACAATATTTTT	0.328																																					p.C874S		Atlas-SNP	.											.	FNIP1	104	.	0			c.T2620A						.						61.0	63.0	63.0					5																	131007517		2203	4300	6503	SO:0001583	missense	96459	exon14			TTGTACACAATAT	DQ145719	CCDS34226.1, CCDS34227.1	5q23.3	2014-01-28				ENSG00000217128			29418	protein-coding gene	gene with protein product		610594				11853319, 17028174	Standard	NM_001008738		Approved	KIAA1961		Q8TF40		ENST00000510461.1:c.2620T>A	chr5.hg19:g.131007517A>T	ENSP00000421985:p.Cys874Ser	110.0	0.0		135.0	58.0	NM_133372	D6RJH5|Q86T47|Q9BUT0	Missense_Mutation	SNP	ENST00000510461.1	hg19	CCDS34227.1	.	.	.	.	.	.	.	.	.	.	A	7.006	0.555848	0.13436	.	.	ENSG00000217128	ENST00000307968;ENST00000307954;ENST00000544351;ENST00000510461	T;T;T	0.12255	2.72;2.7;2.71	5.16	5.16	0.70880	.	.	.	.	.	T	0.15565	0.0375	L	0.54323	1.7	0.80722	D	1	B;B;B	0.16603	0.005;0.018;0.002	B;B;B	0.17722	0.007;0.019;0.001	T	0.04360	-1.0957	9	0.21540	T	0.41	0.0848	14.9998	0.71462	1.0:0.0:0.0:0.0	.	874;846;874	A8K8V8;Q8TF40-3;Q8TF40	.;.;FNIP1_HUMAN	S	846;829;626;874	ENSP00000309266:C846S;ENSP00000310453:C829S;ENSP00000421985:C874S	ENSP00000310453:C829S	C	-	1	0	FNIP1	131035416	0.996000	0.38824	0.986000	0.45419	0.495000	0.33615	4.050000	0.57404	1.950000	0.56595	0.260000	0.18958	TGT	.	.		0.328	FNIP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370077.1	NM_133372	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222105	140222105	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:140222105C>T	ENST00000531613.1	+	1	1199	c.1199C>T	c.(1198-1200)aCc>aTc	p.T400I	PCDHA8_ENST00000378123.3_Missense_Mutation_p.T400I|PCDHA5_ENST00000529859.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	400	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGTGTCCACCTTCAAGAAT	0.602																																					p.T400I		Atlas-SNP	.											.	PCDHA8	366	.	0			c.C1199T						.						150.0	136.0	140.0					5																	140222105		2203	4300	6503	SO:0001583	missense	56140	exon1			TGTCCACCTTCAA	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1199C>T	chr5.hg19:g.140222105C>T	ENSP00000434655:p.Thr400Ile	192.0	0.0		184.0	68.0	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	hg19	CCDS54919.1	.	.	.	.	.	.	.	.	.	.	C	17.75	3.466874	0.63625	.	.	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.29142	1.58;1.58	3.57	3.57	0.40892	Cadherin (4);Cadherin-like (1);	0.000000	0.37761	U	0.001960	T	0.46249	0.1383	L	0.39633	1.23	0.30253	N	0.793912	D;D	0.76494	0.999;0.998	D;D	0.77004	0.989;0.989	T	0.50955	-0.8766	10	0.87932	D	0	.	15.5787	0.76414	0.0:1.0:0.0:0.0	.	400;400	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	I	400	ENSP00000434655:T400I;ENSP00000367363:T400I	ENSP00000367363:T400I	T	+	2	0	PCDHA8	140202289	0.011000	0.17503	1.000000	0.80357	0.781000	0.44180	2.166000	0.42406	1.709000	0.51313	0.306000	0.20318	ACC	.	.		0.602	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558291	140558291	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:140558291A>T	ENST00000239444.2	+	1	921	c.676A>T	c.(676-678)Act>Tct	p.T226S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	226	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGATCTGGCACTGCTCAGGT	0.522																																					p.T226S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.A676T						.						133.0	169.0	157.0					5																	140558291		2203	4296	6499	SO:0001583	missense	56128	exon1			TCTGGCACTGCTC	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.676A>T	chr5.hg19:g.140558291A>T	ENSP00000239444:p.Thr226Ser	340.0	0.0		301.0	77.0	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	hg19	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	a	12.14	1.847870	0.32606	.	.	ENSG00000120322	ENST00000239444	T	0.55760	0.5	4.25	1.69	0.24217	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.49915	0.1585	M	0.65975	2.015	0.19775	N	0.999955	B	0.27656	0.184	B	0.33196	0.159	T	0.51012	-0.8759	9	0.66056	D	0.02	.	5.814	0.18481	0.7677:0.0:0.0855:0.1468	.	226	Q9UN66	PCDB8_HUMAN	S	226	ENSP00000239444:T226S	ENSP00000239444:T226S	T	+	1	0	PCDHB8	140538475	0.000000	0.05858	0.104000	0.21259	0.263000	0.26337	1.528000	0.35985	0.470000	0.27294	0.477000	0.44152	ACT	.	.		0.522	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
DOCK2	1794	hgsc.bcm.edu	37	5	169111319	169111319	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:169111319G>C	ENST00000256935.8	+	8	806	c.726G>C	c.(724-726)atG>atC	p.M242I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	242					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)			AGCTCTTCATGTCTCTCTACG	0.488																																					p.M242I		Atlas-SNP	.											.	DOCK2	389	.	0			c.G726C						.						188.0	168.0	175.0					5																	169111319		2203	4300	6503	SO:0001583	missense	1794	exon8			CTTCATGTCTCTC	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.726G>C	chr5.hg19:g.169111319G>C	ENSP00000256935:p.Met242Ile	96.0	0.0		147.0	44.0	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	hg19	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	G	19.33	3.807494	0.70797	.	.	ENSG00000134516	ENST00000256935	T	0.49720	0.77	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.62356	0.2421	L	0.53249	1.67	0.80722	D	1	D	0.54964	0.969	D	0.63381	0.914	T	0.54450	-0.8292	10	0.21540	T	0.41	.	19.2567	0.93948	0.0:0.0:1.0:0.0	.	242	Q92608	DOCK2_HUMAN	I	242	ENSP00000256935:M242I	ENSP00000256935:M242I	M	+	3	0	DOCK2	169043897	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.544000	0.85801	0.655000	0.94253	ATG	.	.		0.488	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
EIF4E1B	253314	hgsc.bcm.edu	37	5	176070686	176070686	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:176070686G>T	ENST00000318682.6	+	5	831	c.247G>T	c.(247-249)Gac>Tac	p.D83Y	EIF4E1B_ENST00000504597.1_Missense_Mutation_p.D83Y	NM_001099408.1	NP_001092878.1	A6NMX2	I4E1B_HUMAN	eukaryotic translation initiation factor 4E family member 1B	83					regulation of translation (GO:0006417)	cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)	translation initiation factor activity (GO:0003743)			breast(1)|large_intestine(1)|lung(2)|pancreas(1)	5	all_cancers(89;0.00185)|Renal(175;0.000269)|Lung NSC(126;0.00902)|all_lung(126;0.0142)	Medulloblastoma(196;0.00498)|all_neural(177;0.0212)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCCTGGCAGGACAACCTGCA	0.637																																					p.D83Y		Atlas-SNP	.											.	EIF4E1B	24	.	0			c.G247T						.						30.0	33.0	32.0					5																	176070686		2051	4179	6230	SO:0001583	missense	253314	exon5			TGGCAGGACAACC		CCDS47345.1	5q35.2	2008-06-12			ENSG00000175766	ENSG00000175766			33179	protein-coding gene	gene with protein product						16191198	Standard	NM_001099408		Approved	FLJ36951	uc010jkf.1	A6NMX2	OTTHUMG00000163227	ENST00000318682.6:c.247G>T	chr5.hg19:g.176070686G>T	ENSP00000323714:p.Asp83Tyr	75.0	0.0		90.0	25.0	NM_001099408		Missense_Mutation	SNP	ENST00000318682.6	hg19	CCDS47345.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	19.58|19.58	3.855048|3.855048	0.71719|0.71719	.|.	.|.	ENSG00000175766|ENSG00000175766	ENST00000318682;ENST00000510660;ENST00000504597|ENST00000505497	T;T;T|.	0.46819|.	0.86;0.86;0.86|.	5.33|5.33	4.46|4.46	0.54185|0.54185	Translation Initiation factor eIF- 4e-like  domain (2);|.	0.350201|.	0.28853|.	N|.	0.013925|.	T|T	0.79417|0.79417	0.4442|0.4442	M|M	0.93062|0.93062	3.375|3.375	0.50313|0.50313	D|D	0.999863|0.999863	D|.	0.59357|.	0.985|.	D|.	0.65323|.	0.934|.	T|T	0.82143|0.82143	-0.0603|-0.0603	10|5	0.87932|.	D|.	0|.	.|.	8.7057|8.7057	0.34354|0.34354	0.0772:0.0:0.7731:0.1497|0.0772:0.0:0.7731:0.1497	.|.	83|.	A6NMX2|.	I4E1B_HUMAN|.	Y|S	83|23	ENSP00000323714:D83Y;ENSP00000421009:D83Y;ENSP00000427633:D83Y|.	ENSP00000323714:D83Y|.	D|R	+|+	1|3	0|2	EIF4E1B|EIF4E1B	176003292|176003292	1.000000|1.000000	0.71417|0.71417	0.800000|0.800000	0.32199|0.32199	0.905000|0.905000	0.53344|0.53344	6.445000|6.445000	0.73456|0.73456	1.263000|1.263000	0.44181|0.44181	0.491000|0.491000	0.48974|0.48974	GAC|AGG	.	.		0.637	EIF4E1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372187.1	NM_001099408	
DBN1	1627	hgsc.bcm.edu	37	5	176893949	176893949	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:176893949G>A	ENST00000309007.5	-	7	889	c.670C>T	c.(670-672)Cgc>Tgc	p.R224C	DBN1_ENST00000393565.1_Missense_Mutation_p.R224C|DBN1_ENST00000292385.5_Missense_Mutation_p.R226C	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	224					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TCCCGGTAGCGCCGCTCGCGC	0.716																																					p.R226C		Atlas-SNP	.											.	DBN1	122	.	0			c.C676T						.						51.0	52.0	52.0					5																	176893949		2203	4300	6503	SO:0001583	missense	1627	exon8			GGTAGCGCCGCTC		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.670C>T	chr5.hg19:g.176893949G>A	ENSP00000308532:p.Arg224Cys	39.0	0.0		31.0	14.0	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	hg19	CCDS4420.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.805042	0.90623	.	.	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000477391	T;T;T	0.45668	0.89;0.89;1.5	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.66228	0.2768	M	0.75777	2.31	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.995;0.996;0.998	T	0.70182	-0.4942	10	0.87932	D	0	-17.5793	18.0729	0.89417	0.0:0.0:1.0:0.0	.	174;224;224;226	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	C	224;226;224;223	ENSP00000308532:R224C;ENSP00000292385:R226C;ENSP00000377195:R224C	ENSP00000292385:R226C	R	-	1	0	DBN1	176826555	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.286000	0.51724	2.586000	0.87340	0.655000	0.94253	CGC	.	.		0.716	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
OR5V1	81696	hgsc.bcm.edu	37	6	29323327	29323327	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:29323327G>C	ENST00000377154.1	-	4	945	c.646C>G	c.(646-648)Ctt>Gtt	p.L216V	OR5V1_ENST00000543825.1_Missense_Mutation_p.L216V			Q9UGF6	OR5V1_HUMAN	olfactory receptor, family 5, subfamily V, member 1	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(3)|large_intestine(3)|liver(1)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						ATGTAGGAAAGTACGATACAA	0.473																																					p.L216V	Ovarian(32;43 883 21137 32120 42650)	Atlas-SNP	.											OR5V1,NS,carcinoma,0,1	OR5V1	63	.	0			c.C646G						.						100.0	90.0	93.0					6																	29323327		2203	4300	6503	SO:0001583	missense	81696	exon1			AGGAAAGTACGAT		CCDS4657.1	6p22.1	2013-09-23				ENSG00000243729		"""GPCR / Class A : Olfactory receptors"""	13972	protein-coding gene	gene with protein product							Standard	NM_030876		Approved	hs6M1-21	uc011dlo.2	Q9UGF6		ENST00000377154.1:c.646C>G	chr6.hg19:g.29323327G>C	ENSP00000366359:p.Leu216Val	38.0	0.0		34.0	10.0	NM_030876	A2BDZ0|B0S860|Q5SQI9|Q6NTB5|Q8IVL3	Missense_Mutation	SNP	ENST00000377154.1	hg19	CCDS4657.1	.	.	.	.	.	.	.	.	.	.	G	0.001	-3.139742	0.00030	.	.	ENSG00000243729	ENST00000377154;ENST00000377151;ENST00000543825	T;T	0.35421	1.31;1.31	4.43	0.346	0.16017	GPCR, rhodopsin-like superfamily (1);	0.000000	0.30068	N	0.010488	T	0.01870	0.0059	N	0.00811	-1.165	0.09310	N	1	B	0.11235	0.004	B	0.12156	0.007	T	0.41893	-0.9483	10	0.02654	T	1	-13.8363	4.4796	0.11760	0.1502:0.4738:0.2548:0.1211	.	216	Q9UGF6	OR5V1_HUMAN	V	216	ENSP00000366359:L216V;ENSP00000443309:L216V	ENSP00000366356:L216V	L	-	1	0	OR5V1	29431306	0.000000	0.05858	0.036000	0.18154	0.019000	0.09904	-1.970000	0.01504	-0.055000	0.13244	0.543000	0.68304	CTT	.	.		0.473	OR5V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076398.3		
UBD	10537	hgsc.bcm.edu	37	6	29524084	29524084	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:29524084G>C	ENST00000377050.4	-	2	294	c.71C>G	c.(70-72)gCc>gGc	p.A24G	GABBR1_ENST00000355973.3_3'UTR	NM_006398.3	NP_006389.2	O15205	UBD_HUMAN	ubiquitin D	24	Ubiquitin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00214}.				aggresome assembly (GO:0070842)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|protein modification by small protein conjugation (GO:0032446)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|response to interferon-gamma (GO:0034341)|response to organonitrogen compound (GO:0010243)|response to tumor necrosis factor (GO:0034612)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	proteasome binding (GO:0070628)			kidney(1)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	6						ATATGGGTTGGCATCAAAGGT	0.473																																					p.A24G		Atlas-SNP	.											.	UBD	13	.	0			c.C71G						.						97.0	77.0	84.0					6																	29524084		1511	2709	4220	SO:0001583	missense	10537	exon2			GGGTTGGCATCAA	Y12653	CCDS4662.1	6p21.3	2008-04-11			ENSG00000213886	ENSG00000213886			18795	protein-coding gene	gene with protein product		606050				9368598, 8662070	Standard	NM_006398		Approved	FAT10	uc003nmo.3	O15205	OTTHUMG00000031289	ENST00000377050.4:c.71C>G	chr6.hg19:g.29524084G>C	ENSP00000366249:p.Ala24Gly	86.0	0.0		69.0	23.0	NM_006398	B0UZT6|Q5STL2|Q5SUK2|Q96EC7	Missense_Mutation	SNP	ENST00000377050.4	hg19	CCDS4662.1	.	.	.	.	.	.	.	.	.	.	G	16.96	3.265470	0.59431	.	.	ENSG00000213886	ENST00000377050	T	0.12361	2.69	5.38	3.58	0.41010	Ubiquitin supergroup (1);Ubiquitin (2);	0.232106	0.21375	U	0.075571	T	0.08358	0.0208	M	0.64567	1.98	0.21020	N	0.999801	B	0.33266	0.404	B	0.39590	0.304	T	0.11348	-1.0591	10	0.87932	D	0	-22.1327	8.7048	0.34347	0.1819:0.0:0.8181:0.0	.	24	O15205	UBD_HUMAN	G	24	ENSP00000366249:A24G	ENSP00000366249:A24G	A	-	2	0	UBD	29632063	0.015000	0.18098	0.038000	0.18304	0.169000	0.22640	1.133000	0.31430	1.260000	0.44134	-0.192000	0.12808	GCC	.	.		0.473	UBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076628.3		
HLA-DMA	3108	hgsc.bcm.edu	37	6	32918508	32918508	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:32918508C>T	ENST00000374843.4	-	2	246	c.161G>A	c.(160-162)aGt>aAt	p.S54N	HLA-DMA_ENST00000395303.3_Missense_Mutation_p.S54N|HLA-DMA_ENST00000395305.3_Intron|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000464392.1_Intron	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	54	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						CACACTGGGACTCCCATCCTG	0.557																																					p.S54N		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G161A						.						116.0	119.0	118.0					6																	32918508		1508	2708	4216	SO:0001583	missense	3108	exon2			CTGGGACTCCCAT		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.161G>A	chr6.hg19:g.32918508C>T	ENSP00000363976:p.Ser54Asn	45.0	0.0		46.0	13.0	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	hg19	CCDS4761.1	.	.	.	.	.	.	.	.	.	.	C	8.301	0.819933	0.16678	.	.	ENSG00000204257	ENST00000395303;ENST00000374843;ENST00000456800;ENST00000422832;ENST00000341486	T;T;T;T	0.00669	5.9;5.9;5.9;5.9	5.53	-2.42	0.06542	MHC class II, alpha/beta chain, N-terminal (1);MHC classes I/II-like antigen recognition protein (1);MHC class II, alpha chain, N-terminal (2);	0.498364	0.24559	N	0.037487	T	0.00178	0.0005	N	0.22421	0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46803	-0.9165	10	0.39692	T	0.17	.	1.1982	0.01879	0.128:0.2924:0.2629:0.3167	.	54;54	P28067;Q31604	DMA_HUMAN;.	N	54;54;84;21;46	ENSP00000378714:S54N;ENSP00000363976:S54N;ENSP00000409668:S84N;ENSP00000403122:S21N	ENSP00000345804:S46N	S	-	2	0	HLA-DMA	33026486	0.000000	0.05858	0.002000	0.10522	0.432000	0.31715	-5.566000	0.00113	-0.104000	0.12154	0.643000	0.83706	AGT	.	.		0.557	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120	
DEF6	50619	hgsc.bcm.edu	37	6	35285774	35285774	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:35285774C>T	ENST00000316637.5	+	6	919	c.914C>T	c.(913-915)gCt>gTt	p.A305V	DEF6_ENST00000468102.1_3'UTR|DEF6_ENST00000542066.1_Missense_Mutation_p.A50V	NM_022047.3	NP_071330.3	Q9H4E7	DEFI6_HUMAN	differentially expressed in FDCP 6 homolog (mouse)	305	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	15						GAGTGGACAGCTGGTGAGTGC	0.592																																					p.A305V		Atlas-SNP	.											.	DEF6	36	.	0			c.C914T						.						37.0	34.0	35.0					6																	35285774		2203	4300	6503	SO:0001583	missense	50619	exon6			GGACAGCTGGTGA	AJ276095	CCDS4802.1	6p21.33-p21.1	2013-01-10	2001-11-28		ENSG00000023892	ENSG00000023892		"""Pleckstrin homology (PH) domain containing"""	2760	protein-coding gene	gene with protein product	"""SWAP-70-like adaptor protein of T cells"""	610094	"""differentially expressed in FDCP (mouse homolog) 6"""			19251698	Standard	NM_022047		Approved	IBP, SLAT, SWAP70L	uc003okk.3	Q9H4E7	OTTHUMG00000014563	ENST00000316637.5:c.914C>T	chr6.hg19:g.35285774C>T	ENSP00000319831:p.Ala305Val	72.0	0.0		56.0	20.0	NM_022047	Q86VF4	Missense_Mutation	SNP	ENST00000316637.5	hg19	CCDS4802.1	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465389	0.43839	.	.	ENSG00000023892	ENST00000542066;ENST00000316637	T;T	0.32023	1.47;2.64	5.35	5.35	0.76521	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.384871	0.29034	N	0.013356	T	0.11196	0.0273	L	0.52823	1.66	0.18873	N	0.999981	B;P;B	0.35656	0.144;0.514;0.292	B;B;B	0.34931	0.107;0.192;0.138	T	0.14783	-1.0460	10	0.12430	T	0.62	-7.3359	8.2534	0.31739	0.0:0.8643:0.0:0.1357	.	50;305;305	F5H853;B2RBP7;Q9H4E7	.;.;DEFI6_HUMAN	V	50;305	ENSP00000442166:A50V;ENSP00000319831:A305V	ENSP00000319831:A305V	A	+	2	0	DEF6	35393752	0.846000	0.29590	0.793000	0.32043	0.950000	0.60333	4.687000	0.61708	2.516000	0.84829	0.460000	0.39030	GCT	.	.		0.592	DEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040276.1	NM_022047	
LRFN2	57497	hgsc.bcm.edu	37	6	40360374	40360374	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:40360374A>T	ENST00000338305.6	-	3	2220	c.1678T>A	c.(1678-1680)Tgc>Agc	p.C560S		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	560						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					TCGTGGTTGCAGACCTTGTAG	0.642																																					p.C560S		Atlas-SNP	.											.	LRFN2	133	.	0			c.T1678A						.						62.0	51.0	54.0					6																	40360374		2203	4300	6503	SO:0001583	missense	57497	exon3			GGTTGCAGACCTT	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1678T>A	chr6.hg19:g.40360374A>T	ENSP00000345985:p.Cys560Ser	52.0	0.0		51.0	21.0	NM_020737	A5PKU3|Q5SYP9	Missense_Mutation	SNP	ENST00000338305.6	hg19	CCDS34443.1	.	.	.	.	.	.	.	.	.	.	a	11.20	1.567480	0.28003	.	.	ENSG00000156564	ENST00000338305	T	0.56611	0.45	5.41	4.25	0.50352	.	0.244211	0.48767	D	0.000169	T	0.31451	0.0797	M	0.64404	1.975	0.36600	D	0.874602	B	0.22541	0.071	B	0.25987	0.065	T	0.12243	-1.0555	10	0.30078	T	0.28	.	9.9406	0.41578	0.919:0.0:0.081:0.0	.	560	Q9ULH4	LRFN2_HUMAN	S	560	ENSP00000345985:C560S	ENSP00000345985:C560S	C	-	1	0	LRFN2	40468352	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	4.779000	0.62375	0.891000	0.36235	0.529000	0.55759	TGC	.	.		0.642	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
TFEB	7942	hgsc.bcm.edu	37	6	41658400	41658400	+	Splice_Site	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:41658400C>T	ENST00000230323.4	-	4	770		c.e4+1		TFEB_ENST00000394283.1_Splice_Site|TFEB_ENST00000403298.4_Splice_Site|TFEB_ENST00000373033.1_Splice_Site|TFEB_ENST00000358871.2_Splice_Site|TFEB_ENST00000420312.1_Intron	NM_001271945.1|NM_007162.2	NP_001258874.1|NP_009093.1	P19484	TFEB_HUMAN	transcription factor EB						autophagy (GO:0006914)|embryonic placenta development (GO:0001892)|humoral immune response (GO:0006959)|lysosome organization (GO:0007040)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	11	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;7.61e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			TCCTCACTCACCTCCCTCTCA	0.622			T	ALPHA	renal (childhood epithelioid)																																.		Atlas-SNP	.		Dom	yes		6	6p21	7942	transcription factor EB		"""E,M"""	.	TFEB	37	.	0			c.468+1G>A						.						23.0	23.0	23.0					6																	41658400		2203	4300	6503	SO:0001630	splice_region_variant	7942	exon5			CACTCACCTCCCT	M33782	CCDS4858.1, CCDS64424.1, CCDS64425.1	6p21	2013-05-21			ENSG00000112561	ENSG00000112561		"""Basic helix-loop-helix proteins"""	11753	protein-coding gene	gene with protein product		600744				2115126	Standard	NM_007162		Approved	TCFEB, bHLHe35	uc003oqu.2	P19484	OTTHUMG00000014684	ENST00000230323.4:c.468+1G>A	chr6.hg19:g.41658400C>T		27.0	0.0		19.0	8.0	NM_007162	Q709B3|Q7Z6P9|Q9BRJ5|Q9UJD8	Splice_Site	SNP	ENST00000230323.4	hg19	CCDS4858.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.842283	0.32513	.	.	ENSG00000112561	ENST00000343317;ENST00000230323;ENST00000358871;ENST00000403298;ENST00000373033;ENST00000394283;ENST00000419396;ENST00000416140;ENST00000419574	.	.	.	5.06	5.06	0.68205	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0186	0.89249	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	TFEB	41766378	1.000000	0.71417	0.999000	0.59377	0.311000	0.27955	5.978000	0.70501	2.351000	0.79841	0.462000	0.41574	.	.	.		0.622	TFEB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040522.3		Intron
TCTE1	202500	hgsc.bcm.edu	37	6	44254246	44254246	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:44254246G>C	ENST00000371505.4	-	3	423	c.301C>G	c.(301-303)Ctc>Gtc	p.L101V	TMEM151B_ENST00000438774.2_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TCTE1_ENST00000371504.1_5'Flank|TCTE1_ENST00000371503.3_5'UTR	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	101										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGTTCCGGGAGCATCTGCTTC	0.582																																					p.L101V		Atlas-SNP	.											.	TCTE1	77	.	0			c.C301G						.						122.0	112.0	116.0					6																	44254246		2203	4300	6503	SO:0001583	missense	202500	exon3			CCGGGAGCATCTG	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.301C>G	chr6.hg19:g.44254246G>C	ENSP00000360560:p.Leu101Val	87.0	0.0		73.0	17.0	NM_182539	B4DX59|Q8IYS6	Missense_Mutation	SNP	ENST00000371505.4	hg19	CCDS4910.1	.	.	.	.	.	.	.	.	.	.	G	13.34	2.209162	0.39003	.	.	ENSG00000146221	ENST00000371505	T	0.22743	1.94	4.95	3.03	0.35002	.	0.607447	0.17402	N	0.175484	T	0.10294	0.0252	M	0.71581	2.175	0.80722	D	1	B	0.29378	0.243	B	0.21360	0.034	T	0.05599	-1.0875	10	0.17369	T	0.5	-7.2632	13.5372	0.61653	0.0:0.0:0.7172:0.2828	.	101	Q5JU00	TCTE1_HUMAN	V	101	ENSP00000360560:L101V	ENSP00000360560:L101V	L	-	1	0	TCTE1	44362224	0.997000	0.39634	0.985000	0.45067	0.983000	0.72400	2.473000	0.45145	1.027000	0.39758	0.563000	0.77884	CTC	.	.		0.582	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
DEFB114	245928	hgsc.bcm.edu	37	6	49928115	49928115	+	Missense_Mutation	SNP	C	C	G	rs533824519		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:49928115C>G	ENST00000322066.3	-	2	99	c.100G>C	c.(100-102)Ggt>Cgt	p.G34R		NM_001037499.1	NP_001032588.1	Q30KQ6	DB114_HUMAN	defensin, beta 114	34					defense response to bacterium (GO:0042742)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)	extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	Lung NSC(77;0.042)					TTACAACGACCGTAACGTTTG	0.353																																					p.G34R		Atlas-SNP	.											.	DEFB114	12	.	0			c.G100C						.						110.0	99.0	103.0					6																	49928115		2203	4299	6502	SO:0001583	missense	245928	exon2			AACGACCGTAACG	DQ012018	CCDS34474.1	6p12.3	2010-03-30			ENSG00000177684	ENSG00000177684		"""Defensins, beta"""	18095	protein-coding gene	gene with protein product		615243				11854508, 16033865	Standard	NM_001037499		Approved	DEFB-14	uc011dwp.2	Q30KQ6	OTTHUMG00000160209	ENST00000322066.3:c.100G>C	chr6.hg19:g.49928115C>G	ENSP00000312702:p.Gly34Arg	126.0	0.0		121.0	54.0	NM_001037499	Q8NES9	Missense_Mutation	SNP	ENST00000322066.3	hg19	CCDS34474.1	.	.	.	.	.	.	.	.	.	.	C	11.73	1.727238	0.30593	.	.	ENSG00000177684	ENST00000322066	T	0.62639	0.01	3.55	3.55	0.40652	.	0.000000	0.39407	N	0.001367	T	0.66268	0.2772	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.54997	-0.8209	8	.	.	.	-20.8631	10.939	0.47262	0.0:1.0:0.0:0.0	.	34	Q30KQ6	DB114_HUMAN	R	34	ENSP00000312702:G34R	.	G	-	1	0	DEFB114	50036074	0.121000	0.22262	0.140000	0.22221	0.008000	0.06430	3.207000	0.51106	2.288000	0.76882	0.650000	0.86243	GGT	.	.		0.353	DEFB114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359665.1	NM_001037499	
CCZ1	51622	hgsc.bcm.edu	37	7	5944735	5944735	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:5944735C>T	ENST00000325974.6	+	7	599	c.533C>T	c.(532-534)aCg>aTg	p.T178M	CCZ1_ENST00000537980.1_Missense_Mutation_p.T35M	NM_015622.5	NP_056437.4	P86791	CCZ1_HUMAN	CCZ1 vacuolar protein trafficking and biogenesis associated homolog (S. cerevisiae)	178						lysosome (GO:0005764)|membrane (GO:0016020)				large_intestine(3)|lung(1)|stomach(1)|upper_aerodigestive_tract(1)	6						TATTTGCAAACGCTACATTTG	0.323																																					p.T178M		Atlas-SNP	.											.	CCZ1	21	.	0			c.C533T						.						79.0	80.0	79.0					7																	5944735		2179	4298	6477	SO:0001583	missense	51622	exon7			TGCAAACGCTACA	AF151801	CCDS34597.1	7p22.1	2014-02-13	2010-06-29	2010-06-29	ENSG00000122674	ENSG00000122674			21691	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 28A"""	C7orf28A		10810093, 20305638	Standard	NM_015622		Approved	CGI-43, CCZ1A	uc003spf.3	P86791	OTTHUMG00000155502	ENST00000325974.6:c.533C>T	chr7.hg19:g.5944735C>T	ENSP00000325681:p.Thr178Met	737.0	0.0		638.0	208.0	NM_015622	A2RU45|O95766|Q9UG65|Q9Y359	Missense_Mutation	SNP	ENST00000325974.6	hg19	CCDS34597.1	.	.	.	.	.	.	.	.	.	.	C	22.2	4.262753	0.80358	.	.	ENSG00000122674	ENST00000325974;ENST00000537980	.	.	.	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.59905	0.2228	L	0.46157	1.445	0.80722	D	1	P	0.52061	0.95	P	0.47206	0.541	T	0.57130	-0.7864	9	0.37606	T	0.19	-18.35	19.1488	0.93479	0.0:1.0:0.0:0.0	.	178	P86790	CCZ1L_HUMAN	M	178;35	.	ENSP00000325681:T178M	T	+	2	0	CCZ1	5911261	1.000000	0.71417	0.956000	0.39512	0.907000	0.53573	7.722000	0.84778	2.772000	0.95346	0.650000	0.86243	ACG	.	.		0.323	CCZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340391.1	NM_015622	
DAGLB	221955	hgsc.bcm.edu	37	7	6474591	6474591	+	Silent	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:6474591C>T	ENST00000297056.6	-	4	649	c.480G>A	c.(478-480)ggG>ggA	p.G160G	DAGLB_ENST00000479922.2_5'Flank|DAGLB_ENST00000421761.2_Intron|DAGLB_ENST00000425398.2_Intron|DAGLB_ENST00000436575.1_Silent_p.G119G|DAGLB_ENST00000428902.2_Silent_p.G33G	NM_139179.3	NP_631918.3	Q8NCG7	DGLB_HUMAN	diacylglycerol lipase, beta	160					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|lipid catabolic process (GO:0016042)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|urinary_tract(2)	26		Ovarian(82;0.232)		UCEC - Uterine corpus endometrioid carcinoma (126;0.102)		GAGCCATTTTCCCCCCAAGAG	0.527																																					p.G160G		Atlas-SNP	.											.	DAGLB	74	.	0			c.G480A						.						86.0	87.0	87.0					7																	6474591		2203	4300	6503	SO:0001819	synonymous_variant	221955	exon4			CATTTTCCCCCCA	AF450090	CCDS5350.1, CCDS47536.1	7p22.1	2008-03-18			ENSG00000164535	ENSG00000164535	3.1.1.-		28923	protein-coding gene	gene with protein product		614016					Standard	NM_139179		Approved	KCCR13L, DAGLBETA	uc003sqa.3	Q8NCG7	OTTHUMG00000125513	ENST00000297056.6:c.480G>A	chr7.hg19:g.6474591C>T		61.0	0.0		72.0	28.0	NM_139179	A4D2P3|B3KV90|B4DQU0|Q6PIX3|Q8N2N2|Q8N9S1|Q8TED3|Q8WXE6	Silent	SNP	ENST00000297056.6	hg19	CCDS5350.1																																																																																			.	.		0.527	DAGLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000246840.2	NM_139179	
ZNF107	51427	hgsc.bcm.edu	37	7	64166839	64166839	+	Nonsense_Mutation	SNP	G	G	T	rs201422104		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:64166839G>T	ENST00000395391.1	+	4	1532	c.157G>T	c.(157-159)Gag>Tag	p.E53*	ZNF107_ENST00000344930.3_Nonsense_Mutation_p.E53*|ZNF107_ENST00000423627.1_Nonsense_Mutation_p.E53*			Q9UII5	ZN107_HUMAN	zinc finger protein 107	53					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				ACATGTGGATGAGTGTACGGG	0.363																																					p.E53X		Atlas-SNP	.											.	ZNF107	107	.	0			c.G157T						.						80.0	72.0	74.0					7																	64166839		2203	4300	6503	SO:0001587	stop_gained	51427	exon7			GTGGATGAGTGTA	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.157G>T	chr7.hg19:g.64166839G>T	ENSP00000378789:p.Glu53*	176.0	0.0		208.0	67.0	NM_016220		Nonsense_Mutation	SNP	ENST00000395391.1	hg19	CCDS5527.1	.	.	.	.	.	.	.	.	.	.	.	17.87	3.495890	0.64186	.	.	ENSG00000196247	ENST00000541526;ENST00000360117;ENST00000344930;ENST00000423627;ENST00000395391	.	.	.	0.828	-0.215	0.13157	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	.	3.0584	0.06191	0.3639:0.0:0.6361:0.0	.	.	.	.	X	53	.	ENSP00000343443:E53X	E	+	1	0	ZNF107	63804274	0.129000	0.22400	0.002000	0.10522	0.048000	0.14542	0.703000	0.25646	-0.092000	0.12417	0.305000	0.20034	GAG	.	.		0.363	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
CCDC146	57639	hgsc.bcm.edu	37	7	76889445	76889445	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:76889445A>T	ENST00000285871.4	+	8	1005	c.878A>T	c.(877-879)gAa>gTa	p.E293V	CCDC146_ENST00000415740.2_3'UTR|AC073635.5_ENST00000476561.2_RNA|CCDC146_ENST00000431197.1_Missense_Mutation_p.E39V	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	293										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				GTAATAAAGGAAGTTGAAGGC	0.363																																					p.E293V		Atlas-SNP	.											.	CCDC146	87	.	0			c.A878T						.						111.0	109.0	110.0					7																	76889445		2203	4300	6503	SO:0001583	missense	57639	exon8			TAAAGGAAGTTGA	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.878A>T	chr7.hg19:g.76889445A>T	ENSP00000285871:p.Glu293Val	146.0	0.0		178.0	31.0	NM_020879	A8K8X6|Q9P223	Missense_Mutation	SNP	ENST00000285871.4	hg19	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.577866	0.86645	.	.	ENSG00000135205	ENST00000285871;ENST00000431197	T;T	0.28255	1.62;1.95	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.41328	0.1154	L	0.34521	1.04	0.80722	D	1	D;D	0.62365	0.976;0.991	P;P	0.59643	0.629;0.861	T	0.18681	-1.0329	10	0.51188	T	0.08	-23.4368	15.3627	0.74492	1.0:0.0:0.0:0.0	.	39;293	Q8IYE0-2;Q8IYE0	.;CC146_HUMAN	V	293;39	ENSP00000285871:E293V;ENSP00000413885:E39V	ENSP00000285871:E293V	E	+	2	0	AC007000.1	76727381	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.286000	0.72665	2.330000	0.79161	0.528000	0.53228	GAA	.	.		0.363	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
SEMA3E	9723	hgsc.bcm.edu	37	7	83014738	83014738	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:83014738C>A	ENST00000307792.3	-	16	2214	c.1747G>T	c.(1747-1749)Gat>Tat	p.D583Y	SEMA3E_ENST00000427262.1_Missense_Mutation_p.D523Y	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	583	Ig-like C2-type.				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				TCAGTCTTATCCAAAGCATCC	0.363																																					p.D583Y		Atlas-SNP	.											.	SEMA3E	125	.	0			c.G1747T						.						178.0	157.0	164.0					7																	83014738		2203	4300	6503	SO:0001583	missense	9723	exon16			TCTTATCCAAAGC	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.1747G>T	chr7.hg19:g.83014738C>A	ENSP00000303212:p.Asp583Tyr	213.0	0.0		255.0	63.0	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	hg19	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.432817	0.62844	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.32023	1.52;1.47	5.54	5.54	0.83059	.	1.159070	0.06007	N	0.648826	T	0.32255	0.0823	N	0.19112	0.55	0.38789	D	0.954931	P	0.36909	0.573	B	0.38500	0.275	T	0.36744	-0.9735	10	0.62326	D	0.03	.	19.4854	0.95027	0.0:1.0:0.0:0.0	.	583	O15041	SEM3E_HUMAN	Y	583;523;583	ENSP00000303212:D583Y;ENSP00000405052:D523Y	ENSP00000303212:D583Y	D	-	1	0	SEMA3E	82852674	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.615000	0.67702	2.597000	0.87782	0.650000	0.86243	GAT	.	.		0.363	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
ANKIB1	54467	hgsc.bcm.edu	37	7	92015870	92015870	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:92015870T>G	ENST00000265742.3	+	12	2041	c.1665T>G	c.(1663-1665)caT>caG	p.H555Q		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	555							zinc ion binding (GO:0008270)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GGAAAAAACATAGTTCGTCCA	0.388																																					p.H555Q		Atlas-SNP	.											.	ANKIB1	92	.	0			c.T1665G						.						130.0	115.0	120.0					7																	92015870		1877	4122	5999	SO:0001583	missense	54467	exon12			AAAACATAGTTCG	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.1665T>G	chr7.hg19:g.92015870T>G	ENSP00000265742:p.His555Gln	196.0	0.0		278.0	51.0	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	hg19	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	T	12.70	2.015192	0.35511	.	.	ENSG00000001629	ENST00000265742	T	0.80304	-1.36	5.37	4.33	0.51752	Zinc finger, C6HC-type (2);Zinc finger, RING-type (1);	0.095503	0.64402	D	0.000001	D	0.90109	0.6910	M	0.93763	3.455	0.47621	D	0.99947	D	0.89917	1.0	D	0.97110	1.0	D	0.88865	0.3329	10	0.87932	D	0	.	4.5802	0.12255	0.0:0.4313:0.0:0.5687	.	555	Q9P2G1	AKIB1_HUMAN	Q	555	ENSP00000265742:H555Q	ENSP00000265742:H555Q	H	+	3	2	ANKIB1	91853806	0.996000	0.38824	1.000000	0.80357	0.995000	0.86356	0.499000	0.22546	1.028000	0.39785	0.533000	0.62120	CAT	.	.		0.388	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
CYP3A43	64816	hgsc.bcm.edu	37	7	99434099	99434099	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:99434099T>G	ENST00000354829.2	+	2	198	c.95T>G	c.(94-96)cTt>cGt	p.L32R	CYP3A43_ENST00000312017.5_Missense_Mutation_p.L32R|CYP3A43_ENST00000342499.4_Intron|CYP3A43_ENST00000222382.5_Missense_Mutation_p.L32R|CYP3A43_ENST00000415413.1_Missense_Mutation_p.L32R|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000421837.2_Missense_Mutation_p.L32R|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000417625.1_Missense_Mutation_p.L32R	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	32			YGTHSHKLFKKLGIPGPTPLPFLGTILFYLRGLWNFDRECN EKYGEMWGLYEGQQPMLVIMDPD -> LGPIHINFLRSWEF LGQPLCLFWELFCSTLGVFGILTENVMKNTEKCGGCMRGNS PCWSSWIPT (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TCACATAAACTTTTTAAGAAG	0.403																																					p.L32R		Atlas-SNP	.											.	CYP3A43	52	.	0			c.T95G						.						87.0	86.0	86.0					7																	99434099		2203	4300	6503	SO:0001583	missense	64816	exon2			ATAAACTTTTTAA	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"""Cytochrome P450s"""	17450	protein-coding gene	gene with protein product		606534	"""cytochrome P450, subfamily IIIA, polypeptide 43"""			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.95T>G	chr7.hg19:g.99434099T>G	ENSP00000346887:p.Leu32Arg	150.0	0.0		262.0	124.0	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	hg19	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	T	14.83	2.653775	0.47362	.	.	ENSG00000021461	ENST00000354829;ENST00000421837;ENST00000417625;ENST00000415413;ENST00000312017;ENST00000222382;ENST00000379654	T;T;T;T;T;T	0.11277	2.79;2.79;2.79;2.79;2.79;2.79	2.44	-0.424	0.12321	.	0.747128	0.11878	N	0.520777	T	0.17280	0.0415	L	0.54323	1.7	0.09310	N	1	D;P;P;P	0.57257	0.979;0.697;0.886;0.69	P;P;B;B	0.56612	0.802;0.52;0.407;0.105	T	0.12167	-1.0558	10	0.66056	D	0.02	.	4.8642	0.13600	0.5131:0.0:0.0:0.4869	.	32;32;32;32	Q495Y1;Q9HB55-3;Q75MK2;Q9HB55	.;.;.;CP343_HUMAN	R	32	ENSP00000346887:L32R;ENSP00000397332:L32R;ENSP00000416581:L32R;ENSP00000401521:L32R;ENSP00000312110:L32R;ENSP00000222382:L32R	ENSP00000222382:L32R	L	+	2	0	CYP3A43	99272035	0.000000	0.05858	0.004000	0.12327	0.687000	0.40016	-0.630000	0.05502	-0.088000	0.12506	0.172000	0.16884	CTT	.	.		0.403	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
CYP3A43	64816	hgsc.bcm.edu	37	7	99447235	99447235	+	Silent	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:99447235C>T	ENST00000354829.2	+	7	691	c.588C>T	c.(586-588)ctC>ctT	p.L196L	CYP3A43_ENST00000312017.5_Silent_p.L196L|CYP3A43_ENST00000342499.4_Nonsense_Mutation_p.Q59*|CYP3A43_ENST00000222382.5_Silent_p.L196L|CYP3A43_ENST00000415413.1_Intron|CYP3A43_ENST00000444905.1_Intron|CYP3A43_ENST00000477658.1_Intron|CYP3A43_ENST00000417625.1_Intron	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	196			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	TGGATTCTCTCAACAATCCAC	0.343																																					p.L196L		Atlas-SNP	.											.	CYP3A43	52	.	0			c.C588T						.						150.0	139.0	143.0					7																	99447235		2203	4300	6503	SO:0001819	synonymous_variant	64816	exon7			TTCTCTCAACAAT	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"""Cytochrome P450s"""	17450	protein-coding gene	gene with protein product		606534	"""cytochrome P450, subfamily IIIA, polypeptide 43"""			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.588C>T	chr7.hg19:g.99447235C>T		173.0	0.0		246.0	145.0	NM_057096	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Silent	SNP	ENST00000354829.2	hg19	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	C	17.50	3.405889	0.62288	.	.	ENSG00000021461	ENST00000342499;ENST00000379654	.	.	.	3.14	-0.235	0.13071	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	3.2478	0.06803	0.0:0.3795:0.2144:0.4061	.	.	.	.	X	59;90	.	ENSP00000345351:Q59X	Q	+	1	0	CYP3A43	99285171	0.999000	0.42202	0.757000	0.31301	0.224000	0.24922	0.467000	0.22035	0.142000	0.18901	0.195000	0.17529	CAA	.	.		0.343	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
ZCWPW1	55063	hgsc.bcm.edu	37	7	99999574	99999574	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:99999574G>C	ENST00000398027.2	-	17	1809	c.1562C>G	c.(1561-1563)gCt>gGt	p.A521G	ZCWPW1_ENST00000324725.6_Intron|ZCWPW1_ENST00000360951.4_Intron|ZCWPW1_ENST00000490721.1_Intron	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	521							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGCAGGAGGAGCTGTGGATTT	0.542																																					p.A521G		Atlas-SNP	.											.	ZCWPW1	41	.	0			c.C1562G						.						151.0	147.0	149.0					7																	99999574		1966	4159	6125	SO:0001583	missense	55063	exon17			GGAGGAGCTGTGG	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1562C>G	chr7.hg19:g.99999574G>C	ENSP00000381109:p.Ala521Gly	142.0	0.0		268.0	17.0	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Missense_Mutation	SNP	ENST00000398027.2	hg19	CCDS43623.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.51|14.51	2.556654|2.556654	0.45487|0.45487	.|.	.|.	ENSG00000078487|ENSG00000233389	ENST00000398027|ENST00000449355	T|.	0.54866|.	0.55|.	5.0|5.0	3.0|3.0	0.34707|0.34707	.|.	.|.	.|.	.|.	.|.	T|T	0.22551|0.22551	0.0544|0.0544	N|N	0.24115|0.24115	0.695|0.695	0.20975|0.20975	N|N	0.999812|0.999812	P;P|.	0.45044|.	0.849;0.849|.	B;B|.	0.42798|.	0.398;0.398|.	T|T	0.19844|0.19844	-1.0293|-1.0293	8|5	.|.	.|.	.|.	-0.0893|-0.0893	3.9574|3.9574	0.09396|0.09396	0.1367:0.0:0.6343:0.2291|0.1367:0.0:0.6343:0.2291	.|.	482;521|.	B4DXS7;Q9H0M4|.	.;ZCPW1_HUMAN|.	G|P	521|98	ENSP00000381109:A521G|.	.|.	A|A	-|+	2|1	0|0	ZCWPW1|AC005071.3	99837510|99837510	0.216000|0.216000	0.23585|0.23585	0.050000|0.050000	0.19076|0.19076	0.276000|0.276000	0.26787|0.26787	0.285000|0.285000	0.18883|0.18883	0.626000|0.626000	0.30322|0.30322	0.655000|0.655000	0.94253|0.94253	GCT|GCT	.	.		0.542	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984	
MUC17	140453	hgsc.bcm.edu	37	7	100682876	100682876	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:100682876G>A	ENST00000306151.4	+	3	8243	c.8179G>A	c.(8179-8181)Gct>Act	p.A2727T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2727	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)					CACCACTTCTGCTGAAGCCAG	0.463																																					p.A2727T		Atlas-SNP	.											.	MUC17	804	.	0			c.G8179A						.						250.0	253.0	252.0					7																	100682876		2203	4300	6503	SO:0001583	missense	140453	exon3			ACTTCTGCTGAAG	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.8179G>A	chr7.hg19:g.100682876G>A	ENSP00000302716:p.Ala2727Thr	55.0	0.0		78.0	9.0	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	4.278	0.050786	0.08243	.	.	ENSG00000169876	ENST00000306151	T	0.01998	4.51	1.21	-2.42	0.06542	.	.	.	.	.	T	0.00845	0.0028	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44267	-0.9339	9	0.02654	T	1	.	2.5247	0.04689	0.2649:0.0:0.329:0.4061	.	2727	Q685J3	MUC17_HUMAN	T	2727	ENSP00000302716:A2727T	ENSP00000302716:A2727T	A	+	1	0	MUC17	100469596	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.971000	0.03806	-1.404000	0.02050	-1.616000	0.00795	GCT	.	.		0.463	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MUC17	140453	hgsc.bcm.edu	37	7	100682890	100682890	+	Silent	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:100682890T>C	ENST00000306151.4	+	3	8257	c.8193T>C	c.(8191-8193)tcT>tcC	p.S2731S		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2731	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)					AAGCCAGTTCTTCTCCTACAA	0.502																																					p.S2731S		Atlas-SNP	.											.	MUC17	804	.	0			c.T8193C						.						255.0	256.0	256.0					7																	100682890		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CAGTTCTTCTCCT	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.8193T>C	chr7.hg19:g.100682890T>C		58.0	0.0		75.0	5.0	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	hg19	CCDS34711.1																																																																																			.	.		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
RAB19	401409	hgsc.bcm.edu	37	7	140111745	140111745	+	Missense_Mutation	SNP	C	C	G	rs375880877		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:140111745C>G	ENST00000356407.3	+	2	341	c.273C>G	c.(271-273)caC>caG	p.H91Q	RAB19_ENST00000537763.1_Missense_Mutation_p.H91Q|RAB19_ENST00000275874.5_Missense_Mutation_p.H138Q			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	91					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					GCAGTGCCCACGCAGCCATCA	0.562																																					p.H91Q		Atlas-SNP	.											.	RAB19	21	.	0			c.C273G						.						145.0	118.0	127.0					7																	140111745		2203	4300	6503	SO:0001583	missense	401409	exon3			TGCCCACGCAGCC		CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"""RAB, member RAS oncogene"""	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.273C>G	chr7.hg19:g.140111745C>G	ENSP00000348778:p.His91Gln	39.0	0.0		46.0	21.0	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Missense_Mutation	SNP	ENST00000356407.3	hg19	CCDS34762.2	.	.	.	.	.	.	.	.	.	.	C	13.77	2.336151	0.41398	.	.	ENSG00000146955	ENST00000495590;ENST00000275874;ENST00000537763;ENST00000356407	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	5.59	0.691	0.18045	Small GTP-binding protein domain (1);	0.087311	0.85682	N	0.000000	T	0.79353	0.4431	L	0.38838	1.175	0.80722	D	1	D	0.53312	0.959	P	0.61533	0.89	T	0.75741	-0.3211	10	0.87932	D	0	.	5.8763	0.18830	0.1208:0.5255:0.0:0.3536	.	91	A4D1S5	RAB19_HUMAN	Q	91;138;91;91	ENSP00000420782:H91Q;ENSP00000275874:H138Q;ENSP00000440167:H91Q;ENSP00000348778:H91Q	ENSP00000275874:H138Q	H	+	3	2	RAB19	139758214	0.055000	0.20627	0.969000	0.41365	0.304000	0.27724	-0.541000	0.06099	0.066000	0.16515	-1.177000	0.01723	CAC	.	.		0.562	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1		
GIMAP4	55303	hgsc.bcm.edu	37	7	150269571	150269571	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:150269571T>A	ENST00000255945.2	+	3	588	c.413T>A	c.(412-414)cTg>cAg	p.L138Q	GIMAP4_ENST00000494750.1_3'UTR|GIMAP4_ENST00000461940.1_Missense_Mutation_p.L152Q	NM_018326.2	NP_060796.1	Q9NUV9	GIMA4_HUMAN	GTPase, IMAP family member 4	138	AIG1-type G.					cytosol (GO:0005829)	GTP binding (GO:0005525)			breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(82;0.0179)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		GAGAAGATCCTGAAAATGTTT	0.488																																					p.L138Q		Atlas-SNP	.											.	GIMAP4	61	.	0			c.T413A						.						79.0	76.0	77.0					7																	150269571		2203	4300	6503	SO:0001583	missense	55303	exon3			AGATCCTGAAAAT	AK001972	CCDS5904.1	7q36.1	2014-04-04			ENSG00000133574	ENSG00000133574		"""GTPases, IMAP"""	21872	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 1"""	608087				15474311, 18701445	Standard	NM_018326		Approved	HIMAP4, FLJ11110, IMAP4, IAN1	uc003whl.3	Q9NUV9	OTTHUMG00000157475	ENST00000255945.2:c.413T>A	chr7.hg19:g.150269571T>A	ENSP00000255945:p.Leu138Gln	91.0	0.0		66.0	18.0	NM_018326		Missense_Mutation	SNP	ENST00000255945.2	hg19	CCDS5904.1	.	.	.	.	.	.	.	.	.	.	T	10.74	1.436104	0.25813	.	.	ENSG00000133574	ENST00000255945;ENST00000461940;ENST00000466938	T;T	0.04454	3.62;3.62	4.72	3.55	0.40652	AIG1 (1);	0.340109	0.28338	N	0.015706	T	0.07683	0.0193	N	0.25647	0.755	0.20873	N	0.999833	D;P	0.89917	1.0;0.898	D;P	0.91635	0.999;0.84	T	0.10543	-1.0625	10	0.05525	T	0.97	.	7.5774	0.27944	0.1894:0.0:0.0:0.8106	.	152;138	G5E9W9;Q9NUV9	.;GIMA4_HUMAN	Q	138;152;70	ENSP00000255945:L138Q;ENSP00000419545:L152Q	ENSP00000255945:L138Q	L	+	2	0	GIMAP4	149900504	0.000000	0.05858	0.026000	0.17262	0.001000	0.01503	0.622000	0.24433	0.831000	0.34780	-0.327000	0.08410	CTG	.	.		0.488	GIMAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348927.1	NM_018326	
BHLHE22	27319	hgsc.bcm.edu	37	8	65494023	65494023	+	Missense_Mutation	SNP	A	A	G	rs62519837		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:65494023A>G	ENST00000321870.1	+	1	1210	c.676A>G	c.(676-678)Agc>Ggc	p.S226G	RP11-21C4.1_ENST00000517909.1_RNA	NM_152414.4	NP_689627.1	Q8NFJ8	BHE22_HUMAN	basic helix-loop-helix family, member e22	226	Ser-rich.				anterior commissure morphogenesis (GO:0021960)|cerebral cortex regionalization (GO:0021796)|corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|retinal bipolar neuron differentiation (GO:0060040)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.S234delS(1)|p.S226G(1)		NS(1)|central_nervous_system(1)|lung(1)|prostate(1)|skin(1)	5						cagcggcggcagcagcagcag	0.706																																					p.S226G	Colon(113;104 1586 2865 9855 18065)	Atlas-SNP	.											BHLHE22,extremity,malignant_melanoma,0,1	BHLHE22	21	.	2	Substitution - Missense(1)|Deletion - In frame(1)	central_nervous_system(1)|skin(1)	c.A676G						.						3.0	4.0	4.0					8																	65494023		1652	3428	5080	SO:0001583	missense	27319	exon1			GGCGGCAGCAGCA	U80755	CCDS6179.1	8q12.1	2009-01-12	2009-01-12	2009-01-12		ENSG00000180828		"""Basic helix-loop-helix proteins"""	11963	protein-coding gene	gene with protein product		613483	"""trinucleotide repeat containing 20"", ""basic helix-loop-helix domain containing, class B, 5"""	TNRC20, BHLHB5		9225980, 12213201, 18557763	Standard	NM_152414		Approved	CAGL85, Beta3, bHLHe22	uc003xvi.3	Q8NFJ8		ENST00000321870.1:c.676A>G	chr8.hg19:g.65494023A>G	ENSP00000318799:p.Ser226Gly	2.0	1.0		9.0	3.0	NM_152414		Missense_Mutation	SNP	ENST00000321870.1	hg19	CCDS6179.1	.	.	.	.	.	.	.	.	.	.	A	0.001	-3.714868	0.00005	.	.	ENSG00000180828	ENST00000321870	T	0.80033	-1.33	0.79	-1.26	0.09376	.	.	.	.	.	T	0.48642	0.1511	N	0.00926	-1.1	0.09310	N	1	B	0.26041	0.14	B	0.32805	0.153	T	0.47368	-0.9123	9	0.15499	T	0.54	.	3.5404	0.07809	0.3747:0.0:0.6253:0.0	rs62519837	226	Q8NFJ8	BHE22_HUMAN	G	226	ENSP00000318799:S226G	ENSP00000318799:S226G	S	+	1	0	BHLHE22	65656577	0.273000	0.24181	0.215000	0.23724	0.107000	0.19398	-0.535000	0.06142	-0.333000	0.08476	0.136000	0.15936	AGC	.	G|1.000;|0.000		0.706	BHLHE22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378549.1	NM_152414	
EXT1	2131	hgsc.bcm.edu	37	8	118817113	118817113	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:118817113A>C	ENST00000378204.2	-	10	2709	c.1903T>G	c.(1903-1905)Tcc>Gcc	p.S635A		NM_000127.2	NP_000118.2	Q16394	EXT1_HUMAN	exostosin glycosyltransferase 1	635					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular polysaccharide biosynthetic process (GO:0033692)|embryonic skeletal joint development (GO:0072498)|endoderm development (GO:0007492)|gastrulation (GO:0007369)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm development (GO:0007498)|olfactory bulb development (GO:0021772)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(7)|kidney(1)|large_intestine(12)|lung(10)|ovary(3)|prostate(1)|stomach(1)|urinary_tract(2)	38	all_cancers(13;2.36e-26)|Lung NSC(37;5.02e-07)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.012)			AGGTAATGGGAGTATAGGTAG	0.443			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Langer-Giedion syndrome;Hereditary Multiple Exostoses																												p.S635A		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 1	8	8q24.11-q24.13	2131	multiple exostoses type 1 gene		M	.	EXT1	98	.	0			c.T1903G						.						138.0	131.0	133.0					8																	118817113		2203	4300	6503	SO:0001583	missense	2131	exon10	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II;HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	AATGGGAGTATAG	S79639	CCDS6324.1	8q24.11	2014-09-17	2013-03-01		ENSG00000182197	ENSG00000182197	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3512	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608177	"""Langer-Giedion syndrome chromosome region"", ""exostoses (multiple) 1"", ""exostosin 1"""	LGCR, LGS			Standard	NM_000127		Approved	ttv	uc003yok.1	Q16394	OTTHUMG00000059718	ENST00000378204.2:c.1903T>G	chr8.hg19:g.118817113A>C	ENSP00000367446:p.Ser635Ala	101.0	0.0		177.0	74.0	NM_000127	B2R7V2|Q9BVI9	Missense_Mutation	SNP	ENST00000378204.2	hg19	CCDS6324.1	.	.	.	.	.	.	.	.	.	.	a	15.26	2.779734	0.49891	.	.	ENSG00000182197	ENST00000378204	T	0.78126	-1.15	5.68	1.79	0.24919	EXTL2, alpha-1,4-N-acetylhexosaminyltransferase (1);	0.142966	0.64402	D	0.000007	T	0.74275	0.3695	M	0.67517	2.055	0.30894	N	0.730014	B	0.12013	0.005	B	0.19946	0.027	T	0.71052	-0.4704	10	0.66056	D	0.02	-5.5207	11.7874	0.52049	0.2458:0.0:0.0:0.7542	.	635	Q16394	EXT1_HUMAN	A	635	ENSP00000367446:S635A	ENSP00000367446:S635A	S	-	1	0	EXT1	118886294	1.000000	0.71417	0.993000	0.49108	0.995000	0.86356	2.388000	0.44398	0.062000	0.16340	0.477000	0.44152	TCC	.	.		0.443	EXT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132768.3	NM_000127	
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119936632	119936632	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:119936632A>C	ENST00000297350.4	-	5	1565	c.1187T>G	c.(1186-1188)gTa>gGa	p.V396G		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	396					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			GCTTATTTTTACTGATTGGAC	0.398																																					p.V396G		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.T1187G						.						154.0	153.0	153.0					8																	119936632		2203	4300	6503	SO:0001583	missense	4982	exon5			ATTTTTACTGATT	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.1187T>G	chr8.hg19:g.119936632A>C	ENSP00000297350:p.Val396Gly	111.0	0.0		151.0	55.0	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	hg19	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	A	7.844	0.722642	0.15439	.	.	ENSG00000164761	ENST00000297350	T	0.74737	-0.87	5.69	3.12	0.35913	.	0.774326	0.11707	N	0.537358	T	0.53658	0.1810	N	0.12182	0.205	0.23751	N	0.996945	B	0.02656	0.0	B	0.04013	0.001	T	0.36359	-0.9751	9	.	.	.	-4.0333	8.4443	0.32833	0.6648:0.2656:0.0696:0.0	.	396	O00300	TR11B_HUMAN	G	396	ENSP00000297350:V396G	.	V	-	2	0	TNFRSF11B	120005813	0.099000	0.21834	0.997000	0.53966	0.997000	0.91878	1.762000	0.38451	0.970000	0.38263	0.533000	0.62120	GTA	.	.		0.398	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
TG	7038	hgsc.bcm.edu	37	8	133935646	133935646	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:133935646C>G	ENST00000220616.4	+	22	4632	c.4592C>G	c.(4591-4593)gCc>gGc	p.A1531G	TG_ENST00000542445.1_5'UTR|TG_ENST00000377869.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1531	Thyroglobulin type-1 11. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CAGTATCGAGCCAGCCAGAAG	0.572																																					p.A1531G		Atlas-SNP	.											.	TG	416	.	0			c.C4592G						.						90.0	83.0	86.0					8																	133935646		2203	4300	6503	SO:0001583	missense	7038	exon22			ATCGAGCCAGCCA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.4592C>G	chr8.hg19:g.133935646C>G	ENSP00000220616:p.Ala1531Gly	65.0	0.0		101.0	51.0	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	hg19	CCDS34944.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.433|9.433	1.086002|1.086002	0.20390|0.20390	.|.	.|.	ENSG00000042832|ENSG00000042832	ENST00000543313;ENST00000220616|ENST00000519178	D|.	0.82984|.	-1.67|.	4.84|4.84	3.95|3.95	0.45737|0.45737	Thyroglobulin type-1 (5);|.	0.116516|.	0.38164|.	N|.	0.001788|.	T|T	0.64472|0.64472	0.2601|0.2601	M|M	0.68317|0.68317	2.08|2.08	0.58432|0.58432	D|D	0.999999|0.999999	B|.	0.30741|.	0.293|.	B|.	0.24269|.	0.052|.	T|T	0.62690|0.62690	-0.6801|-0.6801	10|5	0.52906|.	T|.	0.07|.	.|.	10.4246|10.4246	0.44369|0.44369	0.1954:0.8046:0.0:0.0|0.1954:0.8046:0.0:0.0	.|.	1531|.	P01266|.	THYG_HUMAN|.	G|R	337;1531|50	ENSP00000220616:A1531G|.	ENSP00000220616:A1531G|.	A|S	+|+	2|3	0|2	TG|TG	134004828|134004828	0.932000|0.932000	0.31603|0.31603	0.999000|0.999000	0.59377|0.59377	0.023000|0.023000	0.10783|0.10783	2.916000|2.916000	0.48813|0.48813	1.020000|1.020000	0.39573|0.39573	-0.324000|-0.324000	0.08512|0.08512	GCC|AGC	.	.		0.572	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
COL22A1	169044	hgsc.bcm.edu	37	8	139620230	139620230	+	Silent	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:139620230G>T	ENST00000303045.6	-	57	4427	c.3981C>A	c.(3979-3981)ggC>ggA	p.G1327G	COL22A1_ENST00000435777.1_Silent_p.G1307G|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1327	Collagen-like 13.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			ATCCATTCTTGCCCTGGTGGA	0.517										HNSCC(7;0.00092)																											p.G1327G		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	.	0			c.C3981A						.						85.0	86.0	85.0					8																	139620230		2203	4300	6503	SO:0001819	synonymous_variant	169044	exon57			ATTCTTGCCCTGG	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.3981C>A	chr8.hg19:g.139620230G>T		54.0	1.0		68.0	29.0	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Silent	SNP	ENST00000303045.6	hg19	CCDS6376.1																																																																																			.	.		0.517	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
LINGO2	158038	hgsc.bcm.edu	37	9	27949554	27949554	+	Silent	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:27949554G>T	ENST00000379992.2	-	6	1565	c.1116C>A	c.(1114-1116)acC>acA	p.T372T	LINGO2_ENST00000308675.3_Silent_p.T372T	NM_152570.2	NP_689783.1	Q7L985	LIGO2_HUMAN	leucine rich repeat and Ig domain containing 2	372	LRRCT.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	44	Melanoma(11;0.242)	all_neural(11;2.78e-09)		UCEC - Uterine corpus endometrioid carcinoma (5;0.0818)|GBM - Glioblastoma multiforme(2;1.31e-34)|all cancers(2;2.37e-25)|Lung(2;7.48e-08)|LUSC - Lung squamous cell carcinoma(38;5.09e-07)|KIRC - Kidney renal clear cell carcinoma(2;0.0465)|Kidney(2;0.0604)		CAAACTGCAGGGTGGGCTGTC	0.532																																					p.T372T		Atlas-SNP	.											.	LINGO2	244	.	0			c.C1116A						.						41.0	39.0	40.0					9																	27949554		2203	4300	6503	SO:0001819	synonymous_variant	158038	exon7			CTGCAGGGTGGGC	AL353746	CCDS6524.1	9p21.2	2013-01-11	2007-02-01	2007-02-01	ENSG00000174482	ENSG00000174482		"""Immunoglobulin superfamily / I-set domain containing"""	21207	protein-coding gene	gene with protein product		609793	"""leucine rich repeat neuronal 6C"""	LRRN6C		14686891	Standard	NM_152570		Approved	LERN3	uc003zqu.2	Q7L985	OTTHUMG00000019721	ENST00000379992.2:c.1116C>A	chr9.hg19:g.27949554G>T		51.0	0.0		33.0	22.0	NM_001258282	A8K4K7|B2RPM5|Q6ZMD0	Silent	SNP	ENST00000379992.2	hg19	CCDS6524.1																																																																																			.	.		0.532	LINGO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051978.2	NM_152570	
PIGO	84720	hgsc.bcm.edu	37	9	35094331	35094331	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:35094331A>C	ENST00000378617.3	-	3	931	c.537T>G	c.(535-537)gaT>gaG	p.D179E	PIGO_ENST00000341666.3_Missense_Mutation_p.D179E|PIGO_ENST00000361778.2_Missense_Mutation_p.D179E|PIGO_ENST00000492770.1_5'Flank|PIGO_ENST00000298004.5_Missense_Mutation_p.D179E|RP11-182N22.8_ENST00000431804.1_RNA	NM_032634.3	NP_116023.2	Q8TEQ8	PIGO_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class O	179				DDT -> ARG (in Ref. 7; AAH13987). {ECO:0000305}.	C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity (GO:0016740)			endometrium(3)|kidney(2)|large_intestine(8)|lung(13)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)	38			LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)			TCCAGGTATCATCTCCCATGA	0.488																																					p.D179E		Atlas-SNP	.											.	PIGO	86	.	0			c.T537G						.						110.0	95.0	100.0					9																	35094331		2203	4300	6503	SO:0001583	missense	84720	exon4			GGTATCATCTCCC	AB083625	CCDS6575.1, CCDS6576.1	9p13.2	2013-02-26	2006-06-28		ENSG00000165282	ENSG00000165282		"""Phosphatidylinositol glycan anchor biosynthesis"""	23215	protein-coding gene	gene with protein product		614730	"""phosphatidylinositol glycan, class O"""			10781593	Standard	NM_032634		Approved	DKFZp434M222, FLJ00135	uc003zwd.3	Q8TEQ8	OTTHUMG00000019854	ENST00000378617.3:c.537T>G	chr9.hg19:g.35094331A>C	ENSP00000367880:p.Asp179Glu	42.0	0.0		43.0	23.0	NM_001201484	B1AML3|Q6P154|Q6UX80|Q8TDS8|Q96CS9|Q9BVN9|Q9Y4B0	Missense_Mutation	SNP	ENST00000378617.3	hg19	CCDS6575.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.112297	0.77210	.	.	ENSG00000165282	ENST00000298004;ENST00000378617;ENST00000341666;ENST00000361778	T;T;T;T	0.32753	1.44;1.44;1.44;1.44	5.84	1.09	0.20402	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.000000	0.85682	D	0.000000	T	0.59569	0.2203	M	0.93016	3.37	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.996;0.999	T	0.65685	-0.6108	10	0.87932	D	0	-19.2345	9.9491	0.41628	0.6816:0.0:0.3184:0.0	.	179;179	Q8TEQ8-2;Q8TEQ8	.;PIGO_HUMAN	E	179	ENSP00000298004:D179E;ENSP00000367880:D179E;ENSP00000339382:D179E;ENSP00000354678:D179E	ENSP00000298004:D179E	D	-	3	2	PIGO	35084331	0.980000	0.34600	1.000000	0.80357	0.996000	0.88848	0.373000	0.20484	0.496000	0.27904	-0.250000	0.11733	GAT	.	.		0.488	PIGO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052284.1	NM_032634	
ANKS6	203286	hgsc.bcm.edu	37	9	101498813	101498813	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:101498813G>C	ENST00000353234.4	-	15	2651	c.2604C>G	c.(2602-2604)agC>agG	p.S868R	ANKS6_ENST00000375019.2_Missense_Mutation_p.S567R|ANKS6_ENST00000540940.1_Missense_Mutation_p.S673R|ANKS6_ENST00000375018.1_Missense_Mutation_p.S869R			Q68DC2	ANKS6_HUMAN	ankyrin repeat and sterile alpha motif domain containing 6	868						cilium (GO:0005929)|cytoplasm (GO:0005737)				endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	21		Acute lymphoblastic leukemia(62;0.0527)				ACGCACAGGGGCTGTTGCCAG	0.602																																					p.S868R		Atlas-SNP	.											.	ANKS6	59	.	0			c.C2604G						.						52.0	58.0	56.0					9																	101498813		1994	4163	6157	SO:0001583	missense	203286	exon15			ACAGGGGCTGTTG	AK094247	CCDS43856.1	9q31.1	2013-09-10	2006-02-17	2006-02-17	ENSG00000165138	ENSG00000165138		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	26724	protein-coding gene	gene with protein product		615370	"""sterile alpha motif domain containing 6"", ""ankyrin repeat domain 14"""	SAMD6, ANKRD14		23793029	Standard	XM_005251793		Approved	FLJ36928, NPHP16	uc004ayu.3	Q68DC2	OTTHUMG00000020347	ENST00000353234.4:c.2604C>G	chr9.hg19:g.101498813G>C	ENSP00000297837:p.Ser868Arg	38.0	0.0		38.0	13.0	NM_173551	A0SE62|Q5VSL0|Q5VSL2|Q5VSL3|Q5VSL4|Q68DB8|Q6P2R2|Q8N9L6|Q96D62	Missense_Mutation	SNP	ENST00000353234.4	hg19	CCDS43856.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.18|12.18	1.860643|1.860643	0.32884|0.32884	.|.	.|.	ENSG00000165138|ENSG00000165138	ENST00000444472|ENST00000375019;ENST00000375018;ENST00000353234;ENST00000540940	.|T;T;T;T	.|0.69040	.|1.84;-0.37;-0.37;2.07	5.31|5.31	-1.61|-1.61	0.08399|0.08399	.|.	.|0.975523	.|0.08507	.|N	.|0.935498	T|T	0.42359|0.42359	0.1199|0.1199	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999998|0.999998	.|B;B	.|0.20459	.|0.045;0.026	.|B;B	.|0.21151	.|0.033;0.018	T|T	0.29181|0.29181	-1.0020|-1.0020	5|10	.|0.59425	.|D	.|0.04	0.0805|0.0805	5.4632|5.4632	0.16627|0.16627	0.5934:0.1399:0.2668:0.0|0.5934:0.1399:0.2668:0.0	.|.	.|869;868	.|Q68DC2-4;Q68DC2	.|.;ANKS6_HUMAN	A|R	338|567;869;868;673	.|ENSP00000364159:S567R;ENSP00000364158:S869R;ENSP00000297837:S868R;ENSP00000442189:S673R	.|ENSP00000297837:S868R	P|S	-|-	1|3	0|2	ANKS6|ANKS6	100538634|100538634	0.009000|0.009000	0.17119|0.17119	0.136000|0.136000	0.22124|0.22124	0.905000|0.905000	0.53344|0.53344	-0.389000|-0.389000	0.07342|0.07342	-0.470000|-0.470000	0.06901|0.06901	0.655000|0.655000	0.94253|0.94253	CCC|AGC	.	.		0.602	ANKS6-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277053.1	NM_173551	
SPTAN1	6709	hgsc.bcm.edu	37	9	131369944	131369944	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:131369944G>T	ENST00000372731.4	+	32	4218	c.4108G>T	c.(4108-4110)Gat>Tat	p.D1370Y	SPTAN1_ENST00000358161.5_Missense_Mutation_p.D1370Y|SPTAN1_ENST00000372739.3_Missense_Mutation_p.D1370Y	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1370					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						GCTAGCCAAGGATGTCACCGG	0.552																																					p.D1370Y	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.G4108T						.						166.0	161.0	163.0					9																	131369944		2203	4300	6503	SO:0001583	missense	6709	exon32			GCCAAGGATGTCA	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4108G>T	chr9.hg19:g.131369944G>T	ENSP00000361816:p.Asp1370Tyr	98.0	0.0		56.0	15.0	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	hg19	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	G	29.2	4.984460	0.93044	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.50277	0.75;0.75;0.75	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	T	0.79191	0.4404	H	0.94847	3.59	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.997;0.998	D	0.84317	0.0514	10	0.87932	D	0	.	20.0442	0.97604	0.0:0.0:1.0:0.0	.	1350;1370;1370	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	Y	1370;1370;1370;1350	ENSP00000350882:D1370Y;ENSP00000361816:D1370Y;ENSP00000361824:D1370Y	ENSP00000350882:D1370Y	D	+	1	0	SPTAN1	130409765	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.420000	0.97426	2.814000	0.96858	0.655000	0.94253	GAT	.	.		0.552	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
ITIH2	3698	hgsc.bcm.edu	37	10	7786905	7786905	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:7786905C>T	ENST00000358415.4	+	19	2726	c.2560C>T	c.(2560-2562)Cct>Tct	p.P854S	ITIH2_ENST00000379587.4_Missense_Mutation_p.P843S	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	854					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						CAAGTTCTCACCTAAAGCCCA	0.438																																					p.P854S		Atlas-SNP	.											.	ITIH2	144	.	0			c.C2560T						.						136.0	123.0	128.0					10																	7786905		2203	4300	6503	SO:0001583	missense	3698	exon19			TTCTCACCTAAAG	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.2560C>T	chr10.hg19:g.7786905C>T	ENSP00000351190:p.Pro854Ser	98.0	0.0		146.0	13.0	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	hg19	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	C	8.329	0.826124	0.16749	.	.	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.09817	2.94;2.94	5.88	4.98	0.66077	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.309508	0.35555	N	0.003131	T	0.07683	0.0193	L	0.39514	1.22	0.09310	N	1	B	0.26577	0.153	B	0.27262	0.078	T	0.39921	-0.9590	10	0.06625	T	0.88	-7.1882	7.4463	0.27213	0.0:0.7191:0.1447:0.1363	.	854	P19823	ITIH2_HUMAN	S	854;843	ENSP00000351190:P854S;ENSP00000368906:P843S	ENSP00000351190:P854S	P	+	1	0	ITIH2	7826911	0.060000	0.20803	0.207000	0.23584	0.005000	0.04900	1.714000	0.37961	2.785000	0.95823	0.655000	0.94253	CCT	.	.		0.438	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
ITGA8	8516	hgsc.bcm.edu	37	10	15688879	15688879	+	Silent	SNP	T	T	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:15688879T>G	ENST00000378076.3	-	12	1526	c.1173A>C	c.(1171-1173)gcA>gcC	p.A391A		NM_003638.1	NP_003629	P53708	ITA8_HUMAN	integrin, alpha 8	391					brain development (GO:0007420)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|metanephros development (GO:0001656)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|substrate adhesion-dependent cell spreading (GO:0034446)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|dendritic spine membrane (GO:0032591)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integrin alpha8-beta1 complex (GO:0034678)|integrin complex (GO:0008305)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	metal ion binding (GO:0046872)			NS(2)|breast(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(57)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	96						CTCCTAAGTGTGCCATAGCAC	0.478																																					p.A391A		Atlas-SNP	.											.	ITGA8	230	.	0			c.A1173C						.						114.0	103.0	107.0					10																	15688879		2203	4300	6503	SO:0001819	synonymous_variant	8516	exon12			TAAGTGTGCCATA	L36531	CCDS31155.1	10p13	2010-03-23			ENSG00000077943	ENSG00000077943		"""Integrins"""	6144	protein-coding gene	gene with protein product		604063				7768999	Standard	XM_005252633		Approved		uc001ioc.1	P53708	OTTHUMG00000017733	ENST00000378076.3:c.1173A>C	chr10.hg19:g.15688879T>G		80.0	0.0		79.0	26.0	NM_003638	B0YJ31|Q5VX94	Silent	SNP	ENST00000378076.3	hg19	CCDS31155.1																																																																																			.	.		0.478	ITGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046987.1	NM_003638	
CFAP43	80217	hgsc.bcm.edu	37	10	105944803	105944803	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:105944803A>T	ENST00000278064.2	-	16	2230	c.1905T>A	c.(1903-1905)gaT>gaA	p.D635E	WDR96_ENST00000357060.3_Missense_Mutation_p.D704E|WDR96_ENST00000428666.1_Missense_Mutation_p.D705E																NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GGGTGCCATCATCTCTCCCAT	0.378																																					p.D704E		Atlas-SNP	.											.	WDR96	183	.	0			c.T2112A						.						208.0	181.0	190.0					10																	105944803		2203	4300	6503	SO:0001583	missense	80217	exon16			GCCATCATCTCTC																												ENST00000278064.2:c.1905T>A	chr10.hg19:g.105944803A>T	ENSP00000278064:p.Asp635Glu	83.0	0.0		65.0	12.0	NM_025145		Missense_Mutation	SNP	ENST00000278064.2	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	5.124|5.124	0.208527|0.208527	0.09757|0.09757	.|.	.|.	ENSG00000197748|ENSG00000197748	ENST00000357060;ENST00000428666;ENST00000278064|ENST00000434629	T;T;T|.	0.12879|.	2.66;2.65;2.64|.	5.18|5.18	-3.37|-3.37	0.04898|0.04898	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);|.	0.434585|.	0.22991|.	N|.	0.053199|.	T|T	0.25644|0.25644	0.0624|0.0624	L|L	0.42245|0.42245	1.32|1.32	0.20821|0.20821	N|N	0.999842|0.999842	B;B;B|.	0.16603|.	0.016;0.018;0.012|.	B;B;B|.	0.17722|.	0.01;0.019;0.01|.	T|T	0.33266|0.33266	-0.9875|-0.9875	10|5	0.18276|.	T|.	0.48|.	.|.	2.0703|2.0703	0.03612|0.03612	0.5127:0.218:0.1503:0.1189|0.5127:0.218:0.1503:0.1189	.|.	705;705;704|.	G5E9L1;B4DHB6;Q8NDM7|.	.;.;WDR96_HUMAN|.	E|K	704;705;635|65	ENSP00000349568:D704E;ENSP00000400289:D705E;ENSP00000278064:D635E|.	ENSP00000278064:D635E|.	D|M	-|-	3|2	2|0	WDR96|WDR96	105934793|105934793	0.118000|0.118000	0.22208|0.22208	0.906000|0.906000	0.35671|0.35671	0.997000|0.997000	0.91878|0.91878	-0.034000|-0.034000	0.12225|0.12225	-0.313000|-0.313000	0.08728|0.08728	0.533000|0.533000	0.62120|0.62120	GAT|ATG	.	.		0.378	WDR96-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000050200.1		
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118360697	118360697	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:118360697G>T	ENST00000528052.1	+	10	1118	c.1047G>T	c.(1045-1047)gaG>gaT	p.E349D	PNLIPRP1_ENST00000358834.4_Missense_Mutation_p.E349D|PNLIPRP1_ENST00000534537.1_Missense_Mutation_p.E349D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	349					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		ACACAGGAGAGGCTAGCAATT	0.438																																					p.E349D		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.G1047T						.						132.0	108.0	116.0					10																	118360697		2203	4300	6503	SO:0001583	missense	5407	exon10			AGGAGAGGCTAGC	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.1047G>T	chr10.hg19:g.118360697G>T	ENSP00000433933:p.Glu349Asp	55.0	0.0		57.0	22.0	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Missense_Mutation	SNP	ENST00000528052.1	hg19	CCDS7595.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.689179	0.00100	.	.	ENSG00000187021	ENST00000358834;ENST00000528052;ENST00000534537	D;D;D	0.90069	-2.61;-2.61;-2.61	5.25	-10.5	0.00291	Lipase, N-terminal (1);	0.537821	0.19744	N	0.107057	T	0.49064	0.1535	N	0.00633	-1.31	0.34251	D	0.678819	B	0.02656	0.0	B	0.01281	0.0	T	0.66787	-0.5835	10	0.02654	T	1	-4.0281	1.1013	0.01684	0.2985:0.1768:0.3364:0.1883	.	349	P54315	LIPR1_HUMAN	D	349	ENSP00000351695:E349D;ENSP00000433933:E349D;ENSP00000434159:E349D	ENSP00000351695:E349D	E	+	3	2	PNLIPRP1	118350687	0.000000	0.05858	0.088000	0.20740	0.436000	0.31835	-3.641000	0.00406	-3.289000	0.00195	-1.564000	0.00881	GAG	.	.		0.438	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
FGFR2	2263	hgsc.bcm.edu	37	10	123274695	123274695	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr10:123274695T>C	ENST00000358487.5	-	9	1495	c.1223A>G	c.(1222-1224)gAc>gGc	p.D408G	FGFR2_ENST00000360144.3_Missense_Mutation_p.D320G|FGFR2_ENST00000369059.1_Missense_Mutation_p.D294G|FGFR2_ENST00000356226.4_Missense_Mutation_p.D293G|FGFR2_ENST00000357555.5_Missense_Mutation_p.D319G|FGFR2_ENST00000369056.1_Missense_Mutation_p.D409G|FGFR2_ENST00000346997.2_Missense_Mutation_p.D408G|FGFR2_ENST00000369061.4_Missense_Mutation_p.D296G|FGFR2_ENST00000351936.6_Missense_Mutation_p.D408G|FGFR2_ENST00000369060.4_Intron|FGFR2_ENST00000478859.1_Missense_Mutation_p.D180G|FGFR2_ENST00000457416.2_Missense_Mutation_p.D409G|FGFR2_ENST00000490349.1_5'Flank	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	408					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	GCTGCTGAAGTCTGGCTTCTT	0.478		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome																												p.D409G		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.A1226G						.						109.0	115.0	113.0					10																	123274695		2203	4300	6503	SO:0001583	missense	2263	exon9	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CTGAAGTCTGGCT	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.1223A>G	chr10.hg19:g.123274695T>C	ENSP00000351276:p.Asp408Gly	172.0	0.0		158.0	31.0	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	hg19	CCDS31298.1	.	.	.	.	.	.	.	.	.	.	T	19.28	3.797616	0.70567	.	.	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553	T;T;T;T;T;T;T;T;T;T;T;T	0.79454	-1.21;-1.27;-1.21;-1.19;-1.17;-1.22;-1.2;-1.21;-1.19;-1.19;-1.19;-1.2	6.03	6.03	0.97812	.	0.086489	0.85682	D	0.000000	D	0.83876	0.5349	M	0.79926	2.475	0.58432	D	0.999999	B;P;P;D;B;B;B;P	0.55385	0.004;0.734;0.717;0.971;0.086;0.05;0.225;0.917	B;P;B;P;B;B;B;P	0.50109	0.002;0.562;0.373;0.631;0.066;0.022;0.233;0.524	D	0.84937	0.0863	10	0.45353	T	0.12	.	16.5655	0.84588	0.0:0.0:0.0:1.0	.	427;409;319;293;408;320;409;313	D3DRD5;P21802-18;P21802-21;P21802-20;P21802;P21802-22;P21802-17;D3DRD3	.;.;.;.;FGFR2_HUMAN;.;.;.	G	319;411;296;408;293;294;408;409;408;320;409;409;319	ENSP00000350166:D319G;ENSP00000358057:D296G;ENSP00000351276:D408G;ENSP00000348559:D293G;ENSP00000358055:D294G;ENSP00000263451:D408G;ENSP00000410294:D409G;ENSP00000309878:D408G;ENSP00000353262:D320G;ENSP00000358052:D409G;ENSP00000358054:D409G;ENSP00000337665:D319G	ENSP00000337665:D319G	D	-	2	0	FGFR2	123264685	1.000000	0.71417	0.999000	0.59377	0.949000	0.60115	6.113000	0.71553	2.302000	0.77476	0.533000	0.62120	GAC	.	.		0.478	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
OR51M1	390059	hgsc.bcm.edu	37	11	5410935	5410935	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:5410935A>T	ENST00000328611.3	+	1	329	c.307A>T	c.(307-309)Agt>Tgt	p.S103C	HBG2_ENST00000380259.2_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380252.1_Intron	NM_001004756.2	NP_001004756.2	Q9H341	O51M1_HUMAN	olfactory receptor, family 51, subfamily M, member 1	103					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(16)|upper_aerodigestive_tract(1)	30		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.98e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TAACTCCCATAGTATCTACTT	0.498																																					p.S103C		Atlas-SNP	.											.	OR51M1	60	.	0			c.A307T						.						187.0	176.0	179.0					11																	5410935		1996	4185	6181	SO:0001583	missense	390059	exon1			TCCCATAGTATCT	BK004382	CCDS53596.1	11p15.4	2012-08-09			ENSG00000184698	ENSG00000184698		"""GPCR / Class A : Olfactory receptors"""	14847	protein-coding gene	gene with protein product							Standard	NM_001004756		Approved		uc010qzc.2	Q9H341	OTTHUMG00000066680	ENST00000328611.3:c.307A>T	chr11.hg19:g.5410935A>T	ENSP00000333196:p.Ser103Cys	104.0	0.0		66.0	30.0	NM_001004756	Q6IF80	Missense_Mutation	SNP	ENST00000328611.3	hg19	CCDS53596.1	.	.	.	.	.	.	.	.	.	.	A	6.444	0.450050	0.12223	.	.	ENSG00000184698	ENST00000328611	T	0.00605	6.27	5.15	-1.98	0.07480	GPCR, rhodopsin-like superfamily (1);	1.434210	0.04961	U	0.462006	T	0.01189	0.0039	M	0.74546	2.27	0.09310	N	1	P	0.40250	0.709	P	0.44359	0.447	T	0.33675	-0.9859	10	0.87932	D	0	.	5.8339	0.18597	0.3836:0.2404:0.376:0.0	.	92	Q9H341	O51M1_HUMAN	C	103	ENSP00000333196:S103C	ENSP00000333196:S103C	S	+	1	0	OR51M1	5367511	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.581000	0.05820	-0.973000	0.03555	-1.334000	0.01262	AGT	.	.		0.498	OR51M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142981.1	NM_001004756	
CNGA4	1262	hgsc.bcm.edu	37	11	6261787	6261787	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:6261787G>A	ENST00000379936.2	+	4	878	c.763G>A	c.(763-765)Gtc>Atc	p.V255I	CNGA4_ENST00000533426.1_Intron	NM_001037329.3	NP_001032406.1	Q8IV77	CNGA4_HUMAN	cyclic nucleotide gated channel alpha 4	255					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			endometrium(2)|kidney(1)|large_intestine(9)|lung(24)|prostate(3)|skin(1)	40		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;2.04e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CCTGCTGGCCGTCATGGGTTT	0.532																																					p.V255I		Atlas-SNP	.											.	CNGA4	96	.	0			c.G763A						.						85.0	78.0	81.0					11																	6261787		2201	4296	6497	SO:0001583	missense	1262	exon4			CTGGCCGTCATGG	AK122736	CCDS31408.1	11p15.4	2011-07-05		2002-01-18		ENSG00000132259		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2152	protein-coding gene	gene with protein product		609472	"""cyclic nucleotide gated channel beta 2"""	CNCA2, CNGB2		11764791, 16382102	Standard	NM_001037329		Approved	OCNC2, OCNCb, CNG5	uc001mco.3	Q8IV77		ENST00000379936.2:c.763G>A	chr11.hg19:g.6261787G>A	ENSP00000369268:p.Val255Ile	60.0	0.0		76.0	24.0	NM_001037329		Missense_Mutation	SNP	ENST00000379936.2	hg19	CCDS31408.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.861084	0.91433	.	.	ENSG00000132259	ENST00000379936	D	0.98400	-4.91	5.3	5.3	0.74995	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98074	0.9365	M	0.84846	2.72	0.58432	D	0.999999	P;P	0.51147	0.942;0.893	P;B	0.45167	0.472;0.436	D	0.98939	1.0790	10	0.56958	D	0.05	.	17.8807	0.88840	0.0:0.0:1.0:0.0	.	255;215	Q8IV77;Q8IV77-2	CNGA4_HUMAN;.	I	255	ENSP00000369268:V255I	ENSP00000369268:V255I	V	+	1	0	CNGA4	6218363	1.000000	0.71417	0.970000	0.41538	0.980000	0.70556	9.420000	0.97426	2.640000	0.89533	0.561000	0.74099	GTC	.	.		0.532	CNGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383765.2	NM_001037329	
USH1C	10083	hgsc.bcm.edu	37	11	17544442	17544442	+	Missense_Mutation	SNP	C	C	A	rs397517884		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:17544442C>A	ENST00000318024.4	-	12	1016	c.908G>T	c.(907-909)cGg>cTg	p.R303L	USH1C_ENST00000005226.7_Missense_Mutation_p.R303L|USH1C_ENST00000527720.1_Missense_Mutation_p.R272L|USH1C_ENST00000527020.1_Missense_Mutation_p.R284L	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)	303					auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						CTCTGCCAGCCGCTCCCGGTC	0.662																																					p.R303L		Atlas-SNP	.											.	USH1C	157	.	0			c.G908T						.						10.0	13.0	12.0					11																	17544442		2044	4076	6120	SO:0001583	missense	10083	exon12			GCCAGCCGCTCCC	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.908G>T	chr11.hg19:g.17544442C>A	ENSP00000317018:p.Arg303Leu	61.0	0.0		69.0	28.0	NM_005709	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	hg19	CCDS31438.1	.	.	.	.	.	.	.	.	.	.	C	25.9	4.690131	0.88735	.	.	ENSG00000006611	ENST00000318024;ENST00000527720;ENST00000527020;ENST00000005226;ENST00000526181	T;T;T;T;T	0.65364	1.72;1.7;1.94;-0.15;2.01	5.33	5.33	0.75918	PDZ/DHR/GLGF (1);	0.193191	0.44902	D	0.000404	T	0.65678	0.2714	L	0.29908	0.895	0.54753	D	0.999982	D;P;D	0.60575	0.969;0.91;0.988	P;P;P	0.57468	0.753;0.47;0.821	T	0.69007	-0.5259	10	0.66056	D	0.02	.	15.9446	0.79784	0.0:1.0:0.0:0.0	.	284;303;303	Q9Y6N9-4;Q9Y6N9;Q7RTU8	.;USH1C_HUMAN;.	L	303;272;284;303;314	ENSP00000317018:R303L;ENSP00000432944:R272L;ENSP00000436934:R284L;ENSP00000005226:R303L;ENSP00000437128:R314L	ENSP00000005226:R303L	R	-	2	0	USH1C	17501018	1.000000	0.71417	1.000000	0.80357	0.621000	0.37620	3.077000	0.50089	2.509000	0.84616	0.455000	0.32223	CGG	.	.		0.662	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
WT1	7490	hgsc.bcm.edu	37	11	32414292	32414292	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:32414292G>C	ENST00000379079.2	-	8	896	c.623C>G	c.(622-624)cCa>cGa	p.P208R	WT1_ENST00000448076.3_Missense_Mutation_p.P420R|WT1_ENST00000530998.1_Missense_Mutation_p.P191R|WT1_ENST00000332351.3_Missense_Mutation_p.P420R	NM_001198551.1	NP_001185480.1	P19544	WT1_HUMAN	Wilms tumor 1	352					adrenal cortex formation (GO:0035802)|adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye development (GO:0043010)|cardiac muscle cell fate commitment (GO:0060923)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|diaphragm development (GO:0060539)|epithelial cell differentiation (GO:0030855)|germ cell development (GO:0007281)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|gonad development (GO:0008406)|heart development (GO:0007507)|kidney development (GO:0001822)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|mesenchymal to epithelial transition (GO:0060231)|metanephric epithelium development (GO:0072207)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of female gonad development (GO:2000195)|negative regulation of metanephric glomerular mesangial cell proliferation (GO:0072302)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of heart growth (GO:0060421)|positive regulation of male gonad development (GO:2000020)|positive regulation of metanephric ureteric bud development (GO:2001076)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior mesonephric tubule development (GO:0072166)|regulation of organ formation (GO:0003156)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|sex determination (GO:0007530)|thorax and anterior abdomen determination (GO:0007356)|tissue development (GO:0009888)|ureteric bud development (GO:0001657)|vasculogenesis (GO:0001570)|visceral serous pericardium development (GO:0061032)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|RNA binding (GO:0003723)|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)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.?(1)	EWSR1/WT1(234)	NS(1)|haematopoietic_and_lymphoid_tissue(348)|kidney(149)|large_intestine(9)|lung(20)|peritoneum(1)|pleura(2)|skin(2)|upper_aerodigestive_tract(1)	533	Breast(20;0.247)		OV - Ovarian serous cystadenocarcinoma(30;0.128)			ACACTGGTATGGTTTCTCACC	0.433			"""D, Mis, N, F, S"""	EWSR1	"""Wilms, desmoplastic small round cell tumor"""	Wilms			Wilms' tumor-Aniridia-ambiguous Genitals-mental Retardation;Frasier syndrome;Familial Wilms' tumor;Denys-Drash syndrome																												p.P420R		Atlas-SNP	.	yes	Rec	yes	"""Denys-Drash syndrome, Frasier syndrome, Familial Wilms tumor"""	11	11p13	7490	Wilms tumour 1 gene		O	.	WT1	744	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1259G						.						143.0	125.0	131.0					11																	32414292		2202	4299	6501	SO:0001583	missense	7490	exon8	Familial Cancer Database	WAGR syndrome; ; ;incl.: Early Onset Nephrotic Syndrome-WT1 associated	TGGTATGGTTTCT		CCDS7878.2, CCDS44561.1, CCDS44562.1, CCDS55750.1, CCDS55751.1	11p13	2014-09-17			ENSG00000184937	ENSG00000184937		"""Zinc fingers, C2H2-type"""	12796	protein-coding gene	gene with protein product		607102		GUD		14681303	Standard	NM_024424		Approved	WAGR, WIT-2, AWT1	uc001mtn.2	P19544	OTTHUMG00000039556	ENST00000379079.2:c.623C>G	chr11.hg19:g.32414292G>C	ENSP00000368370:p.Pro208Arg	90.0	0.0		81.0	28.0	NM_024424	A8K6S1|B3KSA5|Q15881|Q16256|Q16575|Q4VXV4|Q4VXV5|Q4VXV6|Q8IYZ5	Missense_Mutation	SNP	ENST00000379079.2	hg19	CCDS55751.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.939603	0.92526	.	.	ENSG00000184937	ENST00000379079;ENST00000332351;ENST00000530998;ENST00000452863;ENST00000448076	T;T;T;T;T	0.27890	1.64;1.64;1.64;1.64;1.64	5.73	5.73	0.89815	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	U	0.000002	T	0.62527	0.2435	M	0.84082	2.675	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0	T	0.65302	-0.6201	10	0.87932	D	0	.	20.263	0.98456	0.0:0.0:1.0:0.0	.	408;352;425;191;208	P19544-8;P19544;P19544-7;B3KSA5;P19544-6	.;WT1_HUMAN;.;.;.	R	208;420;191;403;420	ENSP00000368370:P208R;ENSP00000331327:P420R;ENSP00000435307:P191R;ENSP00000415516:P403R;ENSP00000413452:P420R	ENSP00000331327:P420R	P	-	2	0	WT1	32370868	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.782000	0.99034	2.868000	0.98415	0.555000	0.69702	CCA	.	.		0.433	WT1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000095434.1	NM_000378	
OR5T2	219464	hgsc.bcm.edu	37	11	56000068	56000068	+	Silent	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:56000068A>G	ENST00000313264.4	-	1	669	c.594T>C	c.(592-594)caT>caC	p.H198H		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	198						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					TAGCCACTGTATGTATAGTAG	0.433																																					p.H198H		Atlas-SNP	.											.	OR5T2	107	.	0			c.T594C						.						186.0	164.0	172.0					11																	56000068		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			CACTGTATGTATA	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.594T>C	chr11.hg19:g.56000068A>G		139.0	0.0		133.0	58.0	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	hg19	CCDS31523.1																																																																																			.	.		0.433	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
MS4A2	2206	hgsc.bcm.edu	37	11	59861471	59861472	+	Missense_Mutation	DNP	TG	TG	AT			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T|G	T|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:59861471_59861472TG>AT	ENST00000278888.3	+	6	674_675	c.572_573TG>AT	c.(571-573)cTG>cAT	p.L191H		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	191					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	CTCACCATTCTGGGACTTGGTA	0.406																																					p.L191Q|p.L191L		Atlas-SNP	.											.	MS4A2	41	.	0			c.T572A|c.G573T						.																																			SO:0001583	missense	2206	exon6			CCATTCTGGGACT|CATTCTGGGACTT	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"""Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"""	147138	"""IgE responsiveness (atopic)"", ""membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"""	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	Exception_encountered	chr11.hg19:g.59861471_59861472delinsAT	ENSP00000278888:p.Leu191His	112.0|113.0	0.0		91.0|90.0	39.0	NM_000139	Q54A81	Missense_Mutation|Silent	SNP	ENST00000278888.3	hg19	CCDS7980.1																																																																																			.	.		0.406	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1		
MS4A2	2206	hgsc.bcm.edu	37	11	59861474	59861474	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:59861474G>T	ENST00000278888.3	+	6	677	c.575G>T	c.(574-576)gGa>gTa	p.G192V		NM_000139.4	NP_000130.1	Q01362	FCERB_HUMAN	membrane-spanning 4-domains, subfamily A, member 2	192					activation of phospholipase C activity (GO:0007202)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of mast cell degranulation (GO:0043306)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|Fc-epsilon receptor I complex (GO:0032998)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(4)|lung(9)|ovary(1)|upper_aerodigestive_tract(2)	17		all_epithelial(135;0.245)			Omalizumab(DB00043)	ACCATTCTGGGACTTGGTAGT	0.403																																					p.G192V		Atlas-SNP	.											.	MS4A2	41	.	0			c.G575T						.						123.0	110.0	115.0					11																	59861474		2201	4295	6496	SO:0001583	missense	2206	exon6			TTCTGGGACTTGG	M89796	CCDS7980.1, CCDS73292.1	11q12-q13	2012-02-28	2012-02-28		ENSG00000149534	ENSG00000149534			7316	protein-coding gene	gene with protein product	"""Fc fragment of IgE, high affinity I, receptor for; beta polypeptide"""	147138	"""IgE responsiveness (atopic)"", ""membrane-spanning 4-domains, subfamily A, member 2 (Fc fragment of IgE, high affinity I, receptor for; beta polypeptide)"""	FCER1B, IGER, APY		1386024	Standard	NM_000139		Approved	MS4A1	uc001nop.3	Q01362	OTTHUMG00000167239	ENST00000278888.3:c.575G>T	chr11.hg19:g.59861474G>T	ENSP00000278888:p.Gly192Val	113.0	0.0		89.0	38.0	NM_000139	Q54A81	Missense_Mutation	SNP	ENST00000278888.3	hg19	CCDS7980.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109866	0.37242	.	.	ENSG00000149534	ENST00000278888	T	0.02301	4.35	4.23	1.26	0.21427	.	0.581365	0.17388	N	0.176033	T	0.06917	0.0176	M	0.63428	1.95	0.45415	D	0.998393	D	0.76494	0.999	D	0.68353	0.957	T	0.32929	-0.9888	10	0.56958	D	0.05	-6.5188	4.0346	0.09724	0.222:0.2093:0.5686:0.0	.	192	Q01362	FCERB_HUMAN	V	192	ENSP00000278888:G192V	ENSP00000278888:G192V	G	+	2	0	MS4A2	59618050	0.994000	0.37717	0.925000	0.36789	0.446000	0.32137	0.265000	0.18515	0.295000	0.22570	0.573000	0.79308	GGA	.	.		0.403	MS4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393844.1		
MYO7A	4647	hgsc.bcm.edu	37	11	76925722	76925722	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:76925722G>T	ENST00000409709.3	+	49	6901	c.6629G>T	c.(6628-6630)gGc>gTc	p.G2210V	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.G2161V|MYO7A_ENST00000458637.2_Missense_Mutation_p.G2170V	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2210					actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AAACAGCGGGGCTCCAGGAGC	0.592																																					p.G2210V		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6629T						.						28.0	31.0	30.0					11																	76925722		2031	4167	6198	SO:0001583	missense	4647	exon49			AGCGGGGCTCCAG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6629G>T	chr11.hg19:g.76925722G>T	ENSP00000386331:p.Gly2210Val	66.0	0.0		60.0	26.0	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	hg19	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	14.62	2.589804	0.46214	.	.	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	D;D;D;D	0.87412	-2.24;-2.23;-2.25;-2.04	5.47	4.54	0.55810	.	0.422930	0.28921	N	0.013718	D	0.82430	0.5035	N	0.22421	0.69	0.58432	D	0.999992	B;B	0.29136	0.234;0.164	B;B	0.37650	0.255;0.075	T	0.81219	-0.1032	10	0.62326	D	0.03	.	13.3396	0.60537	0.0769:0.0:0.9231:0.0	.	2170;2210	F8VUN5;Q13402	.;MYO7A_HUMAN	V	2210;2170;2161;1383;2209;2179;2086;1352	ENSP00000386331:G2210V;ENSP00000392185:G2170V;ENSP00000386635:G2161V;ENSP00000417017:G1352V	ENSP00000345075:G2086V	G	+	2	0	MYO7A	76603370	0.995000	0.38212	1.000000	0.80357	0.558000	0.35554	2.761000	0.47589	1.272000	0.44329	0.467000	0.42956	GGC	.	.		0.592	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
PCF11	51585	hgsc.bcm.edu	37	11	82895887	82895887	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:82895887C>T	ENST00000298281.4	+	16	5071	c.4619C>T	c.(4618-4620)gCa>gTa	p.A1540V	RP11-727A23.11_ENST00000602322.1_lincRNA|RP11-727A23.4_ENST00000528133.1_RNA	NM_015885.3	NP_056969.2	O94913	PCF11_HUMAN	PCF11 cleavage and polyadenylation factor subunit	1540					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage factor complex (GO:0005849)|nucleoplasm (GO:0005654)				cervix(1)|endometrium(3)|kidney(4)|large_intestine(1)|lung(22)|ovary(1)|urinary_tract(1)	33						GAAAGCATAGCAACACCCTCT	0.368																																					p.A1540V		Atlas-SNP	.											.	PCF11	220	.	0			c.C4619T						.						83.0	77.0	79.0					11																	82895887		1860	4101	5961	SO:0001583	missense	51585	exon16			GCATAGCAACACC	AB020631	CCDS44689.1	11q13	2013-07-02	2013-07-02		ENSG00000165494	ENSG00000165494			30097	protein-coding gene	gene with protein product		608876	"""PCF11, cleavage and polyadenylation factor II subunit, homolog (S. cerevisiae)"", ""PCF11, cleavage and polyadenylation factor subunit, homolog (S. cerevisiae)"""			11060040	Standard	NM_015885		Approved	KIAA0824	uc001ozx.4	O94913	OTTHUMG00000167031	ENST00000298281.4:c.4619C>T	chr11.hg19:g.82895887C>T	ENSP00000298281:p.Ala1540Val	65.0	0.0		70.0	24.0	NM_015885	A6H8W7|O43671|Q6P0X8	Missense_Mutation	SNP	ENST00000298281.4	hg19	CCDS44689.1	.	.	.	.	.	.	.	.	.	.	C	12.62	1.993321	0.35131	.	.	ENSG00000165494	ENST00000298281	T	0.22743	1.94	5.4	3.51	0.40186	.	0.369985	0.23060	N	0.052388	T	0.10895	0.0266	N	0.12182	0.205	0.24550	N	0.994026	B	0.02656	0.0	B	0.06405	0.002	T	0.26292	-1.0107	9	.	.	.	-4.0911	10.5959	0.45338	0.0:0.7941:0.1342:0.0718	.	1540	O94913	PCF11_HUMAN	V	1540	ENSP00000298281:A1540V	.	A	+	2	0	PCF11	82573535	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	1.091000	0.30915	1.278000	0.44430	0.585000	0.79938	GCA	.	.		0.368	PCF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392548.2	NM_015885	
B3GAT1	27087	hgsc.bcm.edu	37	11	134252717	134252717	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:134252717T>G	ENST00000524765.1	-	4	5349	c.805A>C	c.(805-807)Agc>Cgc	p.S269R	B3GAT1_ENST00000312527.4_Missense_Mutation_p.S269R|B3GAT1_ENST00000392580.1_Missense_Mutation_p.S269R|B3GAT1_ENST00000531510.1_5'Flank|B3GAT1_ENST00000537389.1_Missense_Mutation_p.S282R			Q9P2W7	B3GA1_HUMAN	beta-1,3-glucuronyltransferase 1	269					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase activity (GO:0015018)|metal ion binding (GO:0046872)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.127)	all_cancers(12;1.39e-23)|all_epithelial(12;7.17e-17)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|Medulloblastoma(222;0.0125)|all_neural(223;0.0137)|Esophageal squamous(93;0.0559)		Epithelial(10;2.58e-11)|all cancers(11;5.75e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.000879)|Lung(977;0.0864)		TAGGCCTGGCTTCGCTGCAGA	0.587																																					p.S269R		Atlas-SNP	.											.	B3GAT1	49	.	0			c.A805C						.						123.0	95.0	104.0					11																	134252717		2201	4297	6498	SO:0001583	missense	27087	exon4			CCTGGCTTCGCTG	AB029396	CCDS8500.1	11q25	2014-07-08	2014-07-08		ENSG00000109956	ENSG00000109956	2.4.1.135	"""CD molecules"", ""Beta-1,3-glucuronyltransferases"""	921	protein-coding gene	gene with protein product	"""galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1"", ""glucuronosyltransferase P"""	151290	"""CD57 antigen"""	CD57, LEU7			Standard	XM_005271506		Approved	GlcAT-P, HNK-1, NK-1	uc001qhq.3	Q9P2W7	OTTHUMG00000167180	ENST00000524765.1:c.805A>C	chr11.hg19:g.134252717T>G	ENSP00000433847:p.Ser269Arg	76.0	0.0		76.0	34.0	NM_054025	Q96FS7	Missense_Mutation	SNP	ENST00000524765.1	hg19	CCDS8500.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.620610	0.66787	.	.	ENSG00000109956	ENST00000392580;ENST00000312527;ENST00000524765;ENST00000537389	T;T;T;T	0.64803	-0.12;-0.12;-0.12;-0.12	5.22	5.22	0.72569	.	0.230399	0.52532	D	0.000078	T	0.45875	0.1364	N	0.21373	0.66	0.42993	D	0.994499	B;B	0.19935	0.032;0.04	B;B	0.24394	0.053;0.019	T	0.48536	-0.9027	10	0.72032	D	0.01	-49.614	6.2368	0.20768	0.1528:0.0:0.2643:0.5829	.	282;269	F5H0S0;Q9P2W7	.;B3GA1_HUMAN	R	269;269;269;282	ENSP00000376359:S269R;ENSP00000307875:S269R;ENSP00000433847:S269R;ENSP00000445983:S282R	ENSP00000307875:S269R	S	-	1	0	B3GAT1	133757927	0.979000	0.34478	0.954000	0.39281	0.990000	0.78478	1.915000	0.39976	2.197000	0.70478	0.402000	0.26972	AGC	.	.		0.587	B3GAT1-002	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393639.1	NM_018644	
SLC6A13	6540	hgsc.bcm.edu	37	12	335639	335639	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:335639A>C	ENST00000343164.4	-	9	1029	c.977T>G	c.(976-978)tTt>tGt	p.F326C	SLC6A13_ENST00000445055.2_Missense_Mutation_p.F234C|SLC6A13_ENST00000539668.1_5'Flank	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	326					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GCCGGCCACAAAGCTGGTGCC	0.617																																					p.F326C		Atlas-SNP	.											.	SLC6A13	62	.	0			c.T977G						.						64.0	56.0	59.0					12																	335639		2203	4300	6503	SO:0001583	missense	6540	exon9			GCCACAAAGCTGG	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.977T>G	chr12.hg19:g.335639A>C	ENSP00000339260:p.Phe326Cys	47.0	0.0		31.0	11.0	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	hg19	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	A	24.4	4.531110	0.85706	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.76316	-1.01;-1.01	5.34	5.34	0.76211	.	0.046786	0.85682	D	0.000000	D	0.92701	0.7680	H	0.98314	4.2	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.79108	0.992;0.99;0.984	D	0.95445	0.8529	10	0.87932	D	0	.	15.3028	0.73966	1.0:0.0:0.0:0.0	.	234;305;326	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	C	234;305;326	ENSP00000407104:F234C;ENSP00000339260:F326C	ENSP00000318097:F305C	F	-	2	0	SLC6A13	205900	1.000000	0.71417	0.993000	0.49108	0.984000	0.73092	9.260000	0.95568	2.010000	0.58986	0.402000	0.26972	TTT	.	.		0.617	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
EMP1	2012	hgsc.bcm.edu	37	12	13366481	13366481	+	Nonsense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:13366481C>A	ENST00000256951.5	+	3	346	c.147C>A	c.(145-147)tgC>tgA	p.C49*	EMP1_ENST00000431267.2_Intron|EMP1_ENST00000544053.1_5'UTR|EMP1_ENST00000396301.3_Nonsense_Mutation_p.C49*|EMP1_ENST00000537612.1_Nonsense_Mutation_p.C49*|EMP1_ENST00000542289.1_Intron	NM_001423.2	NP_001414.1	P54849	EMP1_HUMAN	epithelial membrane protein 1	49					cell growth (GO:0016049)|cell proliferation (GO:0008283)|epidermis development (GO:0008544)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)							Prostate(47;0.194)		BRCA - Breast invasive adenocarcinoma(232;0.153)		ACATTAGCTGCAGTGACAGCC	0.433																																					p.C49X		Atlas-SNP	.											.	EMP1	14	.	0			c.C147A						.						169.0	156.0	160.0					12																	13366481		2203	4300	6503	SO:0001587	stop_gained	2012	exon3			TAGCTGCAGTGAC	U43916	CCDS8660.1	12p12.3	2008-08-04				ENSG00000134531			3333	protein-coding gene	gene with protein product		602333				8996089, 9126480	Standard	NM_001423		Approved	TMP, CL-20	uc001rbr.3	P54849		ENST00000256951.5:c.147C>A	chr12.hg19:g.13366481C>A	ENSP00000256951:p.Cys49*	294.0	0.0		254.0	69.0	NM_001423	B2R5N1|B4DRR1|O00681|Q13481|Q13834	Nonsense_Mutation	SNP	ENST00000256951.5	hg19	CCDS8660.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.271341	0.59649	.	.	ENSG00000134531	ENST00000256951;ENST00000538364;ENST00000396301;ENST00000537612	.	.	.	5.78	-3.22	0.05125	.	0.341114	0.39759	N	0.001275	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-17.357	13.8116	0.63266	0.0:0.4345:0.0:0.5655	.	.	.	.	X	49	.	ENSP00000256951:C49X	C	+	3	2	EMP1	13257748	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.457000	0.02374	-0.577000	0.05967	-0.150000	0.13652	TGC	.	.		0.433	EMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401019.1	NM_001423	
IRAK4	51135	hgsc.bcm.edu	37	12	44165082	44165083	+	Missense_Mutation	DNP	GG	GG	TT			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:44165082_44165083GG>TT	ENST00000448290.2	+	3	292_293	c.221_222GG>TT	c.(220-222)tGG>tTT	p.W74F	IRAK4_ENST00000551736.1_Missense_Mutation_p.W74F|IRAK4_ENST00000431837.1_Intron|IRAK4_ENST00000440781.2_Intron	NM_016123.3	NP_057207.2	Q9NWZ3	IRAK4_HUMAN	interleukin-1 receptor-associated kinase 4	74	Death.				cytokine production (GO:0001816)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)					all_cancers(12;0.00149)	Lung NSC(34;0.0804)|all_lung(34;0.181)		GBM - Glioblastoma multiforme(48;0.04)		CTGTTTGACTGGGGCACCACAA	0.371																																					p.W74L|p.W74C		Atlas-SNP	.											.	IRAK4	77	.	0			c.G221T|c.G222T						.																																			SO:0001583	missense	51135	exon3			TTGACTGGGGCAC|TGACTGGGGCACC	AF155118	CCDS8744.1, CCDS44862.1	12q12	2014-09-17				ENSG00000198001			17967	protein-coding gene	gene with protein product		606883				3772297, 10508479	Standard	NM_001114182		Approved	NY-REN-64	uc001rnt.3	Q9NWZ3		Exception_encountered	chr12.hg19:g.44165082_44165083delinsTT	ENSP00000390651:p.Trp74Phe	143.0|142.0	0.0		114.0|115.0	47.0	NM_016123	Q69FE1|Q8TDF7|Q9Y589	Missense_Mutation	SNP	ENST00000448290.2	hg19	CCDS8744.1																																																																																			.	.		0.371	IRAK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403947.1		
RAPGEF3	10411	hgsc.bcm.edu	37	12	48134734	48134734	+	Silent	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:48134734C>A	ENST00000449771.2	-	20	2101	c.2013G>T	c.(2011-2013)acG>acT	p.T671T	RAPGEF3_ENST00000171000.4_Silent_p.T629T|RAPGEF3_ENST00000389212.3_Silent_p.T671T|RAPGEF3_ENST00000548919.1_Silent_p.T580T|RAPGEF3_ENST00000549151.1_Silent_p.T629T|RAPGEF3_ENST00000405493.2_Silent_p.T629T|RP1-197B17.3_ENST00000547799.1_lincRNA			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	671	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		AGTCGTGGTCCGTCAGCTGGC	0.687																																					p.T671T		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.G2013T						.						35.0	32.0	33.0					12																	48134734		2203	4300	6503	SO:0001819	synonymous_variant	10411	exon20			GTGGTCCGTCAGC	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.2013G>T	chr12.hg19:g.48134734C>A		79.0	0.0		84.0	4.0	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Silent	SNP	ENST00000449771.2	hg19	CCDS41775.1																																																																																			.	.		0.687	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
STAC3	246329	hgsc.bcm.edu	37	12	57640644	57640644	+	Silent	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:57640644G>A	ENST00000332782.2	-	6	747	c.546C>T	c.(544-546)cgC>cgT	p.R182R	STAC3_ENST00000546246.2_5'UTR|STAC3_ENST00000554578.1_Silent_p.R143R	NM_145064.1	NP_659501.1	Q96MF2	STAC3_HUMAN	SH3 and cysteine rich domain 3	182					intracellular signal transduction (GO:0035556)|neuromuscular synaptic transmission (GO:0007274)|skeletal muscle contraction (GO:0003009)|skeletal muscle fiber development (GO:0048741)		identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(2)|skin(1)	18						TCACCCCAGTGCGCAGGGTTT	0.507																																					p.R182R		Atlas-SNP	.											.	STAC3	32	.	0			c.C546T						.						263.0	211.0	228.0					12																	57640644		2203	4300	6503	SO:0001819	synonymous_variant	246329	exon6			CCCAGTGCGCAGG	AK057013	CCDS8936.1, CCDS66405.1, CCDS66406.1	12q13.3	2014-08-12			ENSG00000185482	ENSG00000185482			28423	protein-coding gene	gene with protein product		615521				12477932	Standard	NM_001286257		Approved	MGC2793	uc009zpl.2	Q96MF2	OTTHUMG00000171271	ENST00000332782.2:c.546C>T	chr12.hg19:g.57640644G>A		122.0	0.0		125.0	40.0	NM_145064	B4DUK9|Q96HU5	Silent	SNP	ENST00000332782.2	hg19	CCDS8936.1																																																																																			.	.		0.507	STAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412724.2	NM_145064	
METTL21B	25895	hgsc.bcm.edu	37	12	58166537	58166537	+	Silent	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:58166537T>A	ENST00000300209.8	+	1	155	c.30T>A	c.(28-30)tcT>tcA	p.S10S	RP11-571M6.15_ENST00000471530.1_5'Flank|METTL1_ENST00000324871.7_5'UTR|METTL21B_ENST00000333012.5_Silent_p.S10S|METTL1_ENST00000548681.1_5'Flank|METTL21B_ENST00000548256.1_Intron|AC025165.1_ENST00000582738.1_RNA|METTL21B_ENST00000551420.1_Intron|METTL1_ENST00000257848.7_5'Flank|METTL21B_ENST00000552307.1_3'UTR	NM_015433.2	NP_056248.2	Q96AZ1	MT21B_HUMAN	methyltransferase like 21B	10						cytoplasm (GO:0005737)|intracellular (GO:0005622)	methyltransferase activity (GO:0008168)			endometrium(1)|lung(1)	2						ATCCCGAATCTGAGTCGGAAT	0.662																																					p.S10S		Atlas-SNP	.											.	METTL21B	16	.	0			c.T30A						.						26.0	26.0	26.0					12																	58166537		2201	4299	6500	SO:0001819	synonymous_variant	25895	exon1			CGAATCTGAGTCG	AL050100, AF455816	CCDS8957.1, CCDS31848.1	12q14.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000123427	ENSG00000123427			24936	protein-coding gene	gene with protein product		615258	"""family with sequence similarity 119, member B"""	FAM119B		12477932	Standard	NM_015433		Approved	DKFZP586D0919	uc001sqg.3	Q96AZ1	OTTHUMG00000170459	ENST00000300209.8:c.30T>A	chr12.hg19:g.58166537T>A		52.0	0.0		73.0	26.0	NM_015433	Q9H749|Q9Y3W2	Silent	SNP	ENST00000300209.8	hg19	CCDS8957.1																																																																																			.	.		0.662	METTL21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409268.1	NM_015433	
PTPRR	5801	hgsc.bcm.edu	37	12	71054875	71054875	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:71054875T>G	ENST00000283228.2	-	12	2063	c.1611A>C	c.(1609-1611)caA>caC	p.Q537H	PTPRR_ENST00000440835.2_Missense_Mutation_p.Q292H|PTPRR_ENST00000342084.4_Missense_Mutation_p.Q425H|PTPRR_ENST00000549308.1_Missense_Mutation_p.Q292H|PTPRR_ENST00000537619.2_5'UTR|PTPRR_ENST00000378778.1_Missense_Mutation_p.Q331H	NM_002849.3	NP_002840.2	Q15256	PTPRR_HUMAN	protein tyrosine phosphatase, receptor type, R	537	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				ERBB2 signaling pathway (GO:0038128)|in utero embryonic development (GO:0001701)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	41			GBM - Glioblastoma multiforme(2;5.67e-07)|Lung(24;0.00283)|OV - Ovarian serous cystadenocarcinoma(12;0.00578)|LUSC - Lung squamous cell carcinoma(43;0.132)	COAD - Colon adenocarcinoma(1;0.136)		TGTGGCTTCCTTGCTGAAAAT	0.478																																					p.Q537H		Atlas-SNP	.											.	PTPRR	109	.	0			c.A1611C						.						120.0	79.0	93.0					12																	71054875		2203	4300	6503	SO:0001583	missense	5801	exon12			GCTTCCTTGCTGA	D64053	CCDS8998.1, CCDS44945.1, CCDS55847.1, CCDS55848.1	12q15	2011-10-07			ENSG00000153233	ENSG00000153233		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9680	protein-coding gene	gene with protein product		602853		PTPRQ		7557444, 10393441	Standard	NM_002849		Approved	PTPBR7, PTP-SL, EC-PTP, PCPTP1	uc001swi.2	Q15256	OTTHUMG00000169502	ENST00000283228.2:c.1611A>C	chr12.hg19:g.71054875T>G	ENSP00000283228:p.Gln537His	84.0	0.0		62.0	20.0	NM_002849	B2R5Z7|B7Z3J1|F5GXR7|O00342|Q92682|Q9UE65	Missense_Mutation	SNP	ENST00000283228.2	hg19	CCDS8998.1	.	.	.	.	.	.	.	.	.	.	T	13.17	2.158540	0.38119	.	.	ENSG00000153233	ENST00000440835;ENST00000283228;ENST00000378778;ENST00000342084;ENST00000549308	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	5.02	3.83	0.44106	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.257379	0.27473	N	0.019209	T	0.72070	0.3415	N	0.11818	0.18	0.47094	D	0.999312	P;P;P	0.38395	0.576;0.576;0.629	B;B;B	0.43990	0.311;0.106;0.438	T	0.66217	-0.5979	10	0.23302	T	0.38	-3.3389	11.1591	0.48505	0.1382:0.0:0.0:0.8618	.	425;331;537	F5GXR7;Q15256-4;Q15256	.;.;PTPRR_HUMAN	H	292;537;331;425;292	ENSP00000391750:Q292H;ENSP00000283228:Q537H;ENSP00000368054:Q331H;ENSP00000339605:Q425H;ENSP00000446943:Q292H	ENSP00000283228:Q537H	Q	-	3	2	PTPRR	69341142	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.014000	0.40951	0.814000	0.34374	0.528000	0.53228	CAA	.	.		0.478	PTPRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404485.1	NM_002849	
ANKS1B	56899	hgsc.bcm.edu	37	12	99640465	99640465	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:99640465G>C	ENST00000547776.2	-	13	1933	c.1934C>G	c.(1933-1935)cCt>cGt	p.P645R	ANKS1B_ENST00000547010.1_Missense_Mutation_p.P225R|ANKS1B_ENST00000550833.1_5'UTR|ANKS1B_ENST00000329257.7_Missense_Mutation_p.P645R	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	645						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		GAAAGGCAAAGGACTGTTTGC	0.383																																					p.P645R		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1934G						.						93.0	85.0	87.0					12																	99640465		1838	4088	5926	SO:0001583	missense	56899	exon13			GGCAAAGGACTGT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1934C>G	chr12.hg19:g.99640465G>C	ENSP00000449629:p.Pro645Arg	206.0	0.0		180.0	73.0	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.032079	0.35893	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702	T;T;T	0.61040	0.95;0.14;0.95	5.25	5.25	0.73442	.	0.140861	0.48286	D	0.000197	T	0.36608	0.0973	N	0.12182	0.205	0.80722	D	1	B;B	0.23650	0.012;0.089	B;B	0.21151	0.022;0.033	T	0.21449	-1.0245	9	.	.	.	-8.2951	11.8254	0.52265	0.0814:0.0:0.9186:0.0	.	225;645	Q7Z6G8-6;Q7Z6G8	.;ANS1B_HUMAN	R	645;225;645;224	ENSP00000449629:P645R;ENSP00000448512:P225R;ENSP00000331381:P645R	.	P	-	2	0	ANKS1B	98164596	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.777000	0.62361	2.619000	0.88677	0.462000	0.41574	CCT	.	.		0.383	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
NUAK1	9891	hgsc.bcm.edu	37	12	106532400	106532400	+	Missense_Mutation	SNP	T	T	G	rs201298691		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:106532400T>G	ENST00000261402.2	-	1	1411	c.32A>C	c.(31-33)gAc>gCc	p.D11A		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	11					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GTCGGGGCGGTCCCCCGCCAC	0.771																																					p.D11A		Atlas-SNP	.											.	NUAK1	196	.	0			c.A32C						.						4.0	5.0	5.0					12																	106532400		2004	3866	5870	SO:0001583	missense	9891	exon1			GGGCGGTCCCCCG	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.32A>C	chr12.hg19:g.106532400T>G	ENSP00000261402:p.Asp11Ala	26.0	0.0		24.0	15.0	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	hg19	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	T	1.939	-0.444155	0.04604	.	.	ENSG00000074590	ENST00000261402;ENST00000359413	T	0.72394	-0.65	2.76	1.52	0.23074	.	0.497641	0.16531	U	0.210347	T	0.43366	0.1244	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.06405	0.002	T	0.18808	-1.0325	10	0.30854	T	0.27	.	4.6048	0.12372	0.0:0.1699:0.0:0.8301	.	11	O60285	NUAK1_HUMAN	A	11	ENSP00000261402:D11A	ENSP00000261402:D11A	D	-	2	0	NUAK1	105056530	0.000000	0.05858	0.774000	0.31636	0.236000	0.25371	-0.289000	0.08365	1.154000	0.42482	0.260000	0.18958	GAC	.	.		0.771	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840	
NUAK1	9891	hgsc.bcm.edu	37	12	106532406	106532406	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:106532406G>T	ENST00000261402.2	-	1	1405	c.26C>A	c.(25-27)gCg>gAg	p.A9E		NM_014840.2	NP_055655.1	O60285	NUAK1_HUMAN	NUAK family, SNF1-like kinase, 1	9					cell adhesion (GO:0007155)|cellular response to DNA damage stimulus (GO:0006974)|regulation of cell adhesion (GO:0030155)|regulation of cell proliferation (GO:0042127)|regulation of cellular senescence (GO:2000772)|regulation of myosin-light-chain-phosphatase activity (GO:0035507)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37						GCGGTCCCCCGCCACAGGCGC	0.771																																					p.A9E		Atlas-SNP	.											NUAK1_ENST00000261402,NS,carcinoma,0,2	NUAK1	196	.	0			c.C26A						.						3.0	5.0	4.0					12																	106532406		1637	3215	4852	SO:0001583	missense	9891	exon1			TCCCCCGCCACAG	AB011109	CCDS31892.1	12q23.3	2005-08-09				ENSG00000074590			14311	protein-coding gene	gene with protein product	"""AMP-activated protein kinase family member 5"""	608130				12409306, 13679856	Standard	NM_014840		Approved	ARK5, KIAA0537, NuaK1	uc001tlj.1	O60285	OTTHUMG00000169763	ENST00000261402.2:c.26C>A	chr12.hg19:g.106532406G>T	ENSP00000261402:p.Ala9Glu	23.0	0.0		25.0	17.0	NM_014840	A7MD39|Q96KA8	Missense_Mutation	SNP	ENST00000261402.2	hg19	CCDS31892.1	.	.	.	.	.	.	.	.	.	.	G	12.76	2.035473	0.35893	.	.	ENSG00000074590	ENST00000261402;ENST00000359413	T	0.72725	-0.68	3.75	2.76	0.32466	.	0.298784	0.23608	N	0.046363	T	0.49813	0.1579	N	0.08118	0	0.34977	D	0.753727	P	0.43431	0.807	B	0.42163	0.378	T	0.62186	-0.6907	10	0.40728	T	0.16	.	10.2065	0.43116	0.0:0.2049:0.7951:0.0	.	9	O60285	NUAK1_HUMAN	E	9	ENSP00000261402:A9E	ENSP00000261402:A9E	A	-	2	0	NUAK1	105056536	0.063000	0.20901	0.719000	0.30619	0.503000	0.33858	1.713000	0.37951	1.663000	0.50791	0.313000	0.20887	GCG	.	.		0.771	NUAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405767.2	NM_014840	
NCOR2	9612	hgsc.bcm.edu	37	12	124887093	124887093	+	Silent	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:124887093C>T	ENST00000405201.1	-	14	1497	c.1497G>A	c.(1495-1497)caG>caA	p.Q499Q	NCOR2_ENST00000429285.2_Silent_p.Q498Q|NCOR2_ENST00000404621.1_Silent_p.Q498Q|NCOR2_ENST00000356219.3_Silent_p.Q499Q|NCOR2_ENST00000404121.2_Silent_p.Q69Q|NCOR2_ENST00000397355.1_Silent_p.Q499Q			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	499	Poly-Gln.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)	p.Q499Q(9)		breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		gctgctgctgctgttgttgct	0.617																																					p.Q499Q		Atlas-SNP	.											NCOR2_ENST00000405201,NS,carcinoma,0,11	NCOR2	475	.	9	Substitution - coding silent(9)	endometrium(4)|large_intestine(3)|kidney(2)	c.G1497A						.						9.0	10.0	10.0					12																	124887093		2051	4183	6234	SO:0001819	synonymous_variant	9612	exon16			CTGCTGCTGTTGT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.1497G>A	chr12.hg19:g.124887093C>T		52.0	2.0		43.0	4.0	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	hg19	CCDS41858.2																																																																																			.	.		0.617	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
RIMBP2	23504	hgsc.bcm.edu	37	12	130929724	130929724	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:130929724A>T	ENST00000261655.4	-	7	784	c.621T>A	c.(619-621)gaT>gaA	p.D207E	RIMBP2_ENST00000536002.1_Missense_Mutation_p.D115E|RIMBP2_ENST00000535703.1_Missense_Mutation_p.D115E	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	207	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		ACCCATCCTCATCCATGTCTC	0.572																																					p.D207E		Atlas-SNP	.											.	RIMBP2	220	.	0			c.T621A						.						165.0	147.0	153.0					12																	130929724		2203	4300	6503	SO:0001583	missense	23504	exon7			ATCCTCATCCATG	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.621T>A	chr12.hg19:g.130929724A>T	ENSP00000261655:p.Asp207Glu	63.0	0.0		33.0	25.0	NM_015347	Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	hg19	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	A	19.80	3.893886	0.72639	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.34667	1.35;1.35;1.35	3.38	-5.1	0.02911	Src homology-3 domain (3);Variant SH3 (1);	0.000000	0.85682	D	0.000000	T	0.48484	0.1502	L	0.60067	1.865	0.42729	D	0.993702	D;D	0.89917	1.0;0.998	D;D	0.85130	0.997;0.997	T	0.51092	-0.8749	10	0.52906	T	0.07	-26.3678	13.1646	0.59562	0.7814:0.0:0.2186:0.0	.	115;207	O15034-2;O15034	.;RIMB2_HUMAN	E	207;115;115;115	ENSP00000261655:D207E;ENSP00000440347:D115E;ENSP00000439159:D115E	ENSP00000261655:D207E	D	-	3	2	RIMBP2	129495677	0.986000	0.35501	0.931000	0.37212	0.918000	0.54935	0.411000	0.21115	-1.128000	0.02922	-0.366000	0.07423	GAT	.	.		0.572	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
ZMYM2	7750	hgsc.bcm.edu	37	13	20657109	20657109	+	Missense_Mutation	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:20657109A>G	ENST00000382874.2	+	24	3947	c.3757A>G	c.(3757-3759)Acg>Gcg	p.T1253A	ZMYM2_ENST00000382869.3_Missense_Mutation_p.T1253A|ZMYM2_ENST00000382871.2_Missense_Mutation_p.T1253A|ZMYM2_ENST00000494061.2_3'UTR	NM_001190964.1	NP_001177893.1	Q9UBW7	ZMYM2_HUMAN	zinc finger, MYM-type 2	1253					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|PML body (GO:0016605)	ubiquitin conjugating enzyme binding (GO:0031624)|zinc ion binding (GO:0008270)			large_intestine(3)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	10		all_cancers(29;8.65e-21)|all_epithelial(30;1.04e-18)|all_lung(29;6.75e-18)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;0.000148)|Epithelial(112;0.000249)|OV - Ovarian serous cystadenocarcinoma(117;0.00816)|Lung(94;0.0173)|LUSC - Lung squamous cell carcinoma(192;0.0856)		AAATCCTTTAACGATGGAAAA	0.338																																					p.T1253A		Atlas-SNP	.											.	ZMYM2	191	.	0			c.A3757G						.						85.0	80.0	81.0					13																	20657109		1860	4097	5957	SO:0001583	missense	7750	exon24			CCTTTAACGATGG	AF012126	CCDS45016.1	13q11-q12	2013-01-08	2006-07-13	2006-07-13	ENSG00000121741	ENSG00000121741		"""Zinc fingers, MYM type"""	12989	protein-coding gene	gene with protein product		602221	"""zinc finger protein 198"""	ZNF198		9499416, 9425908	Standard	XM_005266517		Approved	RAMP, FIM, MYM	uc001ums.3	Q9UBW7	OTTHUMG00000016507	ENST00000382874.2:c.3757A>G	chr13.hg19:g.20657109A>G	ENSP00000372327:p.Thr1253Ala	249.0	0.0		229.0	100.0	NM_001190964	A6NDG0|A6NI02|O43212|O43434|O60898|Q5W0Q4|Q5W0T3|Q63HP0|Q8NE39|Q9H0V5|Q9H538|Q9UEU2	Missense_Mutation	SNP	ENST00000382874.2	hg19	CCDS45016.1	.	.	.	.	.	.	.	.	.	.	A	15.04	2.714502	0.48622	.	.	ENSG00000121741	ENST00000382869;ENST00000456228;ENST00000382874;ENST00000382871;ENST00000382870	T	0.17691	2.26	5.0	5.0	0.66597	.	0.143070	0.64402	D	0.000007	T	0.12646	0.0307	L	0.29908	0.895	0.80722	D	1	P	0.36909	0.573	B	0.36666	0.23	T	0.05289	-1.0894	10	0.07990	T	0.79	-14.803	14.9966	0.71436	1.0:0.0:0.0:0.0	.	1253	Q9UBW7	ZMYM2_HUMAN	A	1253;1253;1251;1251;631	ENSP00000372322:T1253A	ENSP00000372322:T1253A	T	+	1	0	ZMYM2	19555109	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.150000	0.64869	2.001000	0.58596	0.397000	0.26171	ACG	.	.		0.338	ZMYM2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044051.2	NM_003453	
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679220	37679220	+	Silent	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:37679220C>G	ENST00000379800.3	-	1	583	c.174G>C	c.(172-174)ctG>ctC	p.L58L		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	58	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		TGCTCTCATACAGCAACTGGG	0.522																																					p.L58L		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.G174C						.						160.0	135.0	143.0					13																	37679220		2203	4300	6503	SO:0001819	synonymous_variant	122011	exon1			CTCATACAGCAAC	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.174G>C	chr13.hg19:g.37679220C>G		54.0	0.0		48.0	18.0	NM_145203	Q5T2N2	Silent	SNP	ENST00000379800.3	hg19	CCDS9363.1																																																																																			.	.		0.522	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
EDNRB	1910	hgsc.bcm.edu	37	13	78477336	78477336	+	Silent	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:78477336C>G	ENST00000334286.5	-	3	992	c.756G>C	c.(754-756)ctG>ctC	p.L252L	EDNRB_ENST00000446573.1_Silent_p.L252L|EDNRB_ENST00000377211.4_Silent_p.L342L	NM_000115.3|NM_001122659.2	NP_000106.1|NP_001116131.1	P24530	EDNRB_HUMAN	endothelin receptor type B	252					aging (GO:0007568)|cell surface receptor signaling pathway (GO:0007166)|cellular response to lipopolysaccharide (GO:0071222)|cGMP-mediated signaling (GO:0019934)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|enteric smooth muscle cell differentiation (GO:0035645)|epithelial fluid transport (GO:0042045)|macrophage chemotaxis (GO:0048246)|melanocyte differentiation (GO:0030318)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of neuron maturation (GO:0014043)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|peripheral nervous system development (GO:0007422)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of penile erection (GO:0060406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|posterior midgut development (GO:0007497)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|regulation of fever generation (GO:0031620)|regulation of pH (GO:0006885)|regulation of sensory perception of pain (GO:0051930)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|sensory perception of pain (GO:0019233)|vasoconstriction (GO:0042310)|vasodilation (GO:0042311)|vein smooth muscle contraction (GO:0014826)	integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)	endothelin receptor activity (GO:0004962)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(2)|kidney(1)|large_intestine(18)|lung(16)|skin(3)	42		Acute lymphoblastic leukemia(28;0.0279)|Breast(118;0.037)		GBM - Glioblastoma multiforme(99;0.0933)	Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	AGCAGATTCGCAGATAACTTC	0.383																																					p.L342L		Atlas-SNP	.											.	EDNRB	172	.	0			c.G1026C						.						150.0	151.0	151.0					13																	78477336		2203	4300	6503	SO:0001819	synonymous_variant	1910	exon4			GATTCGCAGATAA	L06623	CCDS9461.1, CCDS55902.1	13q22	2012-08-08			ENSG00000136160	ENSG00000136160		"""GPCR / Class A : Endothelin receptors"""	3180	protein-coding gene	gene with protein product		131244		HSCR2, HSCR		1659806, 9556633	Standard	NM_000115		Approved	ETB	uc001vkp.1	P24530	OTTHUMG00000017111	ENST00000334286.5:c.756G>C	chr13.hg19:g.78477336C>G		130.0	0.0		87.0	26.0	NM_001201397	A2A2Z8|A8K3T4|O15343|Q59GB1|Q5W0G9|Q8NHM6|Q8NHM7|Q8NHM8|Q8NHM9|Q9UD23|Q9UQK3	Silent	SNP	ENST00000334286.5	hg19	CCDS9461.1																																																																																			.	.		0.383	EDNRB-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276505.1		
OR4Q3	441669	hgsc.bcm.edu	37	14	20215690	20215690	+	Missense_Mutation	SNP	A	A	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:20215690A>C	ENST00000331723.1	+	1	104	c.104A>C	c.(103-105)tAc>tCc	p.Y35S		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		TTGTTTTTTTACATTGCTATT	0.378																																					p.Y35S		Atlas-SNP	.											OR4Q3,NS,carcinoma,0,1	OR4Q3	117	.	0			c.A104C						.						169.0	173.0	172.0					14																	20215690		2203	4300	6503	SO:0001583	missense	441669	exon1			TTTTTTACATTGC	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.104A>C	chr14.hg19:g.20215690A>C	ENSP00000330049:p.Tyr35Ser	348.0	0.0		311.0	63.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	15.54	2.862966	0.51482	.	.	ENSG00000182652	ENST00000331723	T	0.04654	3.58	4.32	3.09	0.35607	.	0.000000	0.36591	U	0.002508	T	0.29355	0.0731	H	0.97265	3.97	0.32490	N	0.540313	D	0.89917	1.0	D	0.74674	0.984	T	0.53294	-0.8459	10	0.87932	D	0	.	8.4189	0.32687	0.8259:0.0:0.0:0.1741	.	35	Q8NH05	OR4Q3_HUMAN	S	35	ENSP00000330049:Y35S	ENSP00000330049:Y35S	Y	+	2	0	OR4Q3	19285530	0.740000	0.28207	0.136000	0.22124	0.867000	0.49689	1.606000	0.36826	1.814000	0.52955	0.416000	0.27883	TAC	.	.		0.378	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
OR4Q3	441669	hgsc.bcm.edu	37	14	20216358	20216358	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:20216358A>T	ENST00000331723.1	+	1	772	c.772A>T	c.(772-774)Atc>Ttc	p.I258F		NM_172194.1	NP_751944.1	Q8NH05	OR4Q3_HUMAN	olfactory receptor, family 4, subfamily Q, member 3	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(4)|endometrium(3)|kidney(2)|large_intestine(1)|lung(28)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	47	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		ATGCGTATTCATCTATTTGAG	0.478																																					p.I258F		Atlas-SNP	.											.	OR4Q3	117	.	0			c.A772T						.						174.0	175.0	174.0					14																	20216358		2203	4300	6503	SO:0001583	missense	441669	exon1			GTATTCATCTATT	AF179768	CCDS32020.1	14p13	2012-08-09				ENSG00000182652		"""GPCR / Class A : Olfactory receptors"""	15426	protein-coding gene	gene with protein product				OR4Q4			Standard	NM_172194		Approved	C14orf13	uc010tkt.2	Q8NH05		ENST00000331723.1:c.772A>T	chr14.hg19:g.20216358A>T	ENSP00000330049:p.Ile258Phe	189.0	0.0		164.0	19.0	NM_172194	Q6IEX4	Missense_Mutation	SNP	ENST00000331723.1	hg19	CCDS32020.1	.	.	.	.	.	.	.	.	.	.	.	13.40	2.225277	0.39300	.	.	ENSG00000182652	ENST00000331723	T	0.00158	8.65	4.37	1.83	0.25207	GPCR, rhodopsin-like superfamily (1);	0.368833	0.19196	U	0.120319	T	0.00328	0.0010	M	0.84683	2.71	0.31834	N	0.624428	P	0.41420	0.749	P	0.51550	0.673	T	0.18053	-1.0349	10	0.66056	D	0.02	.	5.6496	0.17608	0.7335:0.1704:0.0961:0.0	.	258	Q8NH05	OR4Q3_HUMAN	F	258	ENSP00000330049:I258F	ENSP00000330049:I258F	I	+	1	0	OR4Q3	19286198	0.000000	0.05858	1.000000	0.80357	0.476000	0.33039	0.382000	0.20635	0.718000	0.32166	0.416000	0.27883	ATC	.	.		0.478	OR4Q3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409818.2		
APEX1	328	hgsc.bcm.edu	37	14	20925548	20925548	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:20925548T>A	ENST00000216714.3	+	5	1106	c.838T>A	c.(838-840)Tgg>Agg	p.W280R	OSGEP_ENST00000556252.1_5'Flank|APEX1_ENST00000557054.1_3'UTR|OSGEP_ENST00000206542.4_5'Flank|APEX1_ENST00000398030.4_Missense_Mutation_p.W280R|APEX1_ENST00000555414.1_Missense_Mutation_p.W280R	NM_001244249.1|NM_001641.3	NP_001231178.1|NP_001632.2	P27695	APEX1_HUMAN	APEX nuclease (multifunctional DNA repair enzyme) 1	280					aging (GO:0007568)|base-excision repair (GO:0006284)|cell redox homeostasis (GO:0045454)|cellular response to cAMP (GO:0071320)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to peptide hormone stimulus (GO:0071375)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA demethylation (GO:0080111)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|negative regulation of smooth muscle cell migration (GO:0014912)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|oxidation-reduction process (GO:0055114)|positive regulation of DNA repair (GO:0045739)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribosome (GO:0005840)|transcription factor complex (GO:0005667)	3'-5' exonuclease activity (GO:0008408)|chromatin DNA binding (GO:0031490)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA 3'-5' exodeoxyribonuclease activity (GO:0008311)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|phosphodiesterase I activity (GO:0004528)|phosphoric diester hydrolase activity (GO:0008081)|poly(A) RNA binding (GO:0044822)|RNA-DNA hybrid ribonuclease activity (GO:0004523)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|uracil DNA N-glycosylase activity (GO:0004844)			breast(2)|endometrium(1)|large_intestine(4)|ovary(2)	9	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;1.09e-07)|all cancers(55;1.19e-06)	GBM - Glioblastoma multiforme(265;0.0224)|READ - Rectum adenocarcinoma(17;0.193)	Lucanthone(DB04967)	GAATGTTGGTTGGCGCCTTGA	0.493								Other BER factors																													p.W280R		Atlas-SNP	.											.	APEX1	23	.	0			c.T838A						.						251.0	216.0	228.0					14																	20925548		2203	4300	6503	SO:0001583	missense	328	exon5			GTTGGTTGGCGCC	X59764	CCDS9550.1	14q11.2	2008-02-05	2002-09-11	2002-09-13	ENSG00000100823	ENSG00000100823	4.2.99.18		587	protein-coding gene	gene with protein product		107748	"""APEX nuclease (multifunctional DNA repair enzyme)"""	APEX			Standard	NM_001641		Approved	APE, REF1, HAP1, APX, APEN, REF-1, APE-1	uc021rnr.1	P27695	OTTHUMG00000029544	ENST00000216714.3:c.838T>A	chr14.hg19:g.20925548T>A	ENSP00000216714:p.Trp280Arg	175.0	0.0		156.0	52.0	NM_080648	Q969L5|Q99775	Missense_Mutation	SNP	ENST00000216714.3	hg19	CCDS9550.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.036268	0.75617	.	.	ENSG00000100823	ENST00000555414;ENST00000216714;ENST00000398030;ENST00000557054	T;T;T	0.64438	-0.1;-0.1;-0.1	6.06	6.06	0.98353	Endonuclease/exonuclease/phosphatase (2);AP endonuclease, family 1, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.82495	0.5049	M	0.88640	2.97	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.85810	0.1379	10	0.87932	D	0	.	15.5919	0.76537	0.0:0.0:0.0:1.0	.	280	P27695	APEX1_HUMAN	R	280;280;280;11	ENSP00000451979:W280R;ENSP00000216714:W280R;ENSP00000381111:W280R	ENSP00000216714:W280R	W	+	1	0	APEX1	19995388	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.610000	0.82949	2.324000	0.78689	0.533000	0.62120	TGG	.	.		0.493	APEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073641.3	NM_001641	
RIPK3	11035	hgsc.bcm.edu	37	14	24807239	24807239	+	Silent	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:24807239G>T	ENST00000216274.5	-	6	890	c.672C>A	c.(670-672)acC>acA	p.T224T	RIPK3_ENST00000554338.1_5'Flank|RP11-934B9.3_ENST00000555591.1_5'Flank|ADCY4_ENST00000558563.1_5'Flank|ADCY4_ENST00000310677.4_5'Flank|ADCY4_ENST00000554068.2_5'Flank	NM_006871.3	NP_006862.2	Q9Y572	RIPK3_HUMAN	receptor-interacting serine-threonine kinase 3	224	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|amyloid fibril formation (GO:1990000)|apoptotic signaling pathway (GO:0097190)|cellular protein modification process (GO:0006464)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic process (GO:0070266)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of ligase activity (GO:0051351)|positive regulation of necroptotic process (GO:0060545)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of phosphatase activity (GO:0010922)|positive regulation of protein deacetylation (GO:0090312)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of type I interferon production (GO:0032481)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of activated T cell proliferation (GO:0046006)|regulation of activation-induced cell death of T cells (GO:0070235)|regulation of adaptive immune response (GO:0002819)|regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000452)|regulation of interferon-gamma production (GO:0032649)|regulation of T cell mediated cytotoxicity (GO:0001914)|signal transduction (GO:0007165)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|ripoptosome (GO:0097342)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|NF-kappaB-inducing kinase activity (GO:0004704)|protein complex binding (GO:0032403)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transcription coactivator activity (GO:0003713)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23				GBM - Glioblastoma multiforme(265;0.0181)		GTGATGGTTCGGTTGGCACTG	0.552																																					p.T224T	Pancreas(58;918 1191 4668 13304 15331)	Atlas-SNP	.											.	RIPK3	43	.	0			c.C672A						.						75.0	70.0	72.0					14																	24807239		2203	4300	6503	SO:0001819	synonymous_variant	11035	exon6			TGGTTCGGTTGGC	AF156884	CCDS9628.1	14q12	2006-05-15			ENSG00000129465	ENSG00000129465			10021	protein-coding gene	gene with protein product		605817				10339433, 10358032	Standard	NM_006871		Approved	RIP3	uc001wpb.3	Q9Y572	OTTHUMG00000029349	ENST00000216274.5:c.672C>A	chr14.hg19:g.24807239G>T		77.0	0.0		80.0	36.0	NM_006871	B4DJL9|C4AM87|Q5J795|Q5J796|Q6P5Y1	Silent	SNP	ENST00000216274.5	hg19	CCDS9628.1																																																																																			.	.		0.552	RIPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073203.4	NM_006871	
JKAMP	51528	hgsc.bcm.edu	37	14	59961929	59961929	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:59961929G>T	ENST00000261247.9	+	4	592	c.445G>T	c.(445-447)Gcc>Tcc	p.A149S	JKAMP_ENST00000556985.1_Missense_Mutation_p.A149S|JKAMP_ENST00000554271.1_Missense_Mutation_p.A163S|JKAMP_ENST00000356057.5_Missense_Mutation_p.A157S|RP11-701B16.2_ENST00000554253.1_RNA|JKAMP_ENST00000425728.2_Missense_Mutation_p.A143S	NM_001098625.1|NM_001284203.1|NM_016475.3	NP_001092095.1|NP_001271132.1|NP_057559.2	Q9P055	JKAMP_HUMAN	JNK1/MAPK8-associated membrane protein	164				N -> S (in Ref. 2; AAF36133). {ECO:0000305}.	ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(1)|kidney(1)|lung(3)	6						TACTCATGAAGCCGTCTACCC	0.363																																					p.A149S		Atlas-SNP	.											.	JKAMP	49	.	0			c.G445T						.						158.0	139.0	145.0					14																	59961929		1891	4118	6009	SO:0001583	missense	51528	exon4			CATGAAGCCGTCT	AF212245	CCDS45116.1, CCDS45117.1, CCDS61462.1, CCDS61463.1	14q22.3	2014-02-14	2009-08-13	2009-08-13	ENSG00000050130	ENSG00000050130			20184	protein-coding gene	gene with protein product	"""Jun N-terminal kinase 1-associated membrane protein"""	611176	"""chromosome 14 open reading frame 100"""	C14orf100		16166642, 19269966	Standard	NM_001284202		Approved	HSPC213, JAMP, HSPC327, CDA06	uc001xef.4	Q9P055	OTTHUMG00000171054	ENST00000261247.9:c.445G>T	chr14.hg19:g.59961929G>T	ENSP00000261247:p.Ala149Ser	211.0	0.0		190.0	69.0	NM_016475	B4DP67|Q6FIB6|Q6IAJ2|Q7Z5D4|Q86SY6|Q9H0Q6|Q9H2W0|Q9HAH5|Q9P0R3	Missense_Mutation	SNP	ENST00000261247.9	hg19	CCDS45116.1	.	.	.	.	.	.	.	.	.	.	G	32	5.106693	0.94292	.	.	ENSG00000050130	ENST00000261247;ENST00000425728;ENST00000556985;ENST00000554271;ENST00000554795;ENST00000356057	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.83658	0.5302	M	0.81112	2.525	0.80722	D	1	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999	D;D;D;D;D	0.85130	0.997;0.994;0.994;0.994;0.994	D	0.85237	0.1036	9	0.87932	D	0	-45.1741	19.6948	0.96021	0.0:0.0:1.0:0.0	.	164;163;143;157;149	Q9P055;G3V2M4;Q9P055-3;Q9P055-5;Q9P055-4	JKAMP_HUMAN;.;.;.;.	S	149;143;149;163;157;157	.	ENSP00000261247:A149S	A	+	1	0	JKAMP	59031682	1.000000	0.71417	1.000000	0.80357	0.832000	0.47134	9.710000	0.98732	2.723000	0.93209	0.655000	0.94253	GCC	.	.		0.363	JKAMP-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411430.1	NM_001098625	
BCL11B	64919	hgsc.bcm.edu	37	14	99640967	99640967	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr14:99640967G>T	ENST00000357195.3	-	4	2215	c.2206C>A	c.(2206-2208)Ccc>Acc	p.P736T	BCL11B_ENST00000345514.2_Missense_Mutation_p.P665T|BCL11B_ENST00000443726.2_Missense_Mutation_p.P542T	NM_001282237.1|NM_138576.2	NP_001269166.1|NP_612808.1	Q9C0K0	BC11B_HUMAN	B-cell CLL/lymphoma 11B (zinc finger protein)	736					alpha-beta T cell differentiation (GO:0046632)|epithelial cell morphogenesis (GO:0003382)|keratinocyte development (GO:0003334)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|odontogenesis of dentin-containing tooth (GO:0042475)|olfactory bulb axon guidance (GO:0071678)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive T cell selection (GO:0043368)|post-embryonic camera-type eye development (GO:0031077)|regulation of keratinocyte proliferation (GO:0010837)|regulation of lipid metabolic process (GO:0019216)|regulation of neuron differentiation (GO:0045664)|striatal medium spiny neuron differentiation (GO:0021773)|T cell differentiation in thymus (GO:0033077)|T cell receptor V(D)J recombination (GO:0033153)|thymus development (GO:0048538)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(3)|breast(1)|central_nervous_system(9)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(9)|prostate(2)|skin(2)	34		Melanoma(154;0.0866)|all_epithelial(191;0.241)		COAD - Colon adenocarcinoma(157;0.103)		GTGGCGAAGGGCGACTGTCGT	0.706			T	TLX3	T-ALL																																p.P736T		Atlas-SNP	.		Dom	yes		14	14q32.1	64919	B-cell CLL/lymphoma 11B  (CTIP2)		L	.	BCL11B	108	.	0			c.C2206A						.						17.0	15.0	16.0					14																	99640967		2189	4287	6476	SO:0001583	missense	64919	exon4			CGAAGGGCGACTG	AJ404614	CCDS9949.1, CCDS9950.1	14q32	2013-01-08			ENSG00000127152	ENSG00000127152		"""Zinc fingers, C2H2-type"""	13222	protein-coding gene	gene with protein product		606558		ZNF856B		11719382, 16950772	Standard	NM_138576		Approved	CTIP-2, CTIP2, hRIT1-alpha	uc001yga.3	Q9C0K0	OTTHUMG00000028967	ENST00000357195.3:c.2206C>A	chr14.hg19:g.99640967G>T	ENSP00000349723:p.Pro736Thr	14.0	0.0		33.0	14.0	NM_138576	Q9H162	Missense_Mutation	SNP	ENST00000357195.3	hg19	CCDS9950.1	.	.	.	.	.	.	.	.	.	.	G	20.0	3.930812	0.73327	.	.	ENSG00000127152	ENST00000357195;ENST00000345514;ENST00000443726	T;T;T	0.14766	2.48;2.56;2.5	4.07	4.07	0.47477	.	0.000000	0.56097	D	0.000024	T	0.35998	0.0951	M	0.68952	2.095	0.80722	D	1	D;B	0.89917	1.0;0.022	D;B	0.97110	1.0;0.002	T	0.18524	-1.0334	10	0.51188	T	0.08	-11.0253	16.6199	0.84927	0.0:0.0:1.0:0.0	.	665;736	Q9C0K0-2;Q9C0K0	.;BC11B_HUMAN	T	736;665;542	ENSP00000349723:P736T;ENSP00000280435:P665T;ENSP00000387419:P542T	ENSP00000280435:P665T	P	-	1	0	BCL11B	98710720	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.498000	0.90492	1.975000	0.57531	0.561000	0.74099	CCC	.	.		0.706	BCL11B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000072332.2	NM_138576	
CYFIP1	23191	hgsc.bcm.edu	37	15	22947043	22947043	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr15:22947043C>T	ENST00000313077.7	+	13	1441	c.1316C>T	c.(1315-1317)aCg>aTg	p.T439M	CYFIP1_ENST00000560848.1_Missense_Mutation_p.T439M	NM_014608.2	NP_055423.1			cytoplasmic FMR1 interacting protein 1											endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(1)|lung(14)|ovary(4)|pancreas(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	40		all_cancers(20;2.26e-25)|all_epithelial(15;2.1e-22)|Lung NSC(15;3.36e-17)|all_lung(15;1.04e-16)|Breast(32;0.000776)|Colorectal(260;0.0488)		all cancers(64;2.22e-06)|Epithelial(43;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00101)		GAGCGTGCCACGCGCTACAAC	0.577																																					p.T439M		Atlas-SNP	.											CYFIP1,NS,carcinoma,0,1	CYFIP1	159	.	0			c.C1316T						.						147.0	123.0	131.0					15																	22947043		2203	4300	6503	SO:0001583	missense	23191	exon13			GTGCCACGCGCTA	D38549	CCDS73695.1, CCDS73696.1	15q11	2008-07-18			ENSG00000068793	ENSG00000273749			13759	protein-coding gene	gene with protein product	"""selective hybridizing clone"", ""cytoplasmic FMRP interacting protein 1"""	606322				11438699	Standard	XM_005272543		Approved	KIAA0068, P140SRA-1, SHYC	uc001yus.3	Q7L576	OTTHUMG00000129100	ENST00000313077.7:c.1316C>T	chr15.hg19:g.22947043C>T	ENSP00000324549:p.Thr439Met	63.0	0.0		58.0	3.0	NM_014608		Missense_Mutation	SNP	ENST00000313077.7	hg19	CCDS10009.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.522217	0.85600	.	.	ENSG00000068793	ENST00000313077;ENST00000412127	T	0.22743	1.94	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	T	0.53318	0.1789	M	0.85710	2.77	0.80722	D	1	D;D	0.89917	1.0;0.97	D;P	0.87578	0.998;0.768	T	0.59337	-0.7473	10	0.72032	D	0.01	-28.2339	18.3595	0.90370	0.0:1.0:0.0:0.0	.	467;439	E7EQ04;Q7L576	.;CYFP1_HUMAN	M	439;467	ENSP00000324549:T439M	ENSP00000324549:T439M	T	+	2	0	CYFIP1	20498484	1.000000	0.71417	0.960000	0.40013	0.484000	0.33280	7.610000	0.82949	2.575000	0.86900	0.655000	0.94253	ACG	.	.		0.577	CYFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251136.2	NM_014608	
CCDC33	80125	hgsc.bcm.edu	37	15	74560789	74560789	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr15:74560789T>C	ENST00000398814.3	+	5	967	c.536T>C	c.(535-537)aTg>aCg	p.M179T	CCDC33_ENST00000321288.5_Missense_Mutation_p.M382T	NM_025055.3	NP_079331.3	Q8N5R6	CCD33_HUMAN	coiled-coil domain containing 33	382										breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(4)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						TGCAACCACATGGCTCTGGAG	0.622																																					p.M179T		Atlas-SNP	.											.	CCDC33	160	.	0			c.T536C						.						38.0	44.0	42.0					15																	74560789		1920	4139	6059	SO:0001583	missense	80125	exon5			ACCACATGGCTCT	BC025689	CCDS42058.1, CCDS42059.1, CCDS73753.1	15q24.1	2009-08-06				ENSG00000140481			26552	protein-coding gene	gene with protein product	"""cancer/testis antigen 61"""					12477932	Standard	NM_025055		Approved	FLJ32855, CT61	uc002axo.4	Q8N5R6		ENST00000398814.3:c.536T>C	chr15.hg19:g.74560789T>C	ENSP00000381795:p.Met179Thr	32.0	0.0		25.0	6.0	NM_025055	A8K3U4|A8MPQ6|A8MV61|A8MVU9|B3KQ49|Q8TAX6|Q9H5Q6	Missense_Mutation	SNP	ENST00000398814.3	hg19	CCDS42058.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.192316	0.00302	.	.	ENSG00000140481	ENST00000321288;ENST00000398814	T;T	0.20332	2.08;2.43	4.69	2.75	0.32379	.	0.596788	0.14684	N	0.304556	T	0.04048	0.0113	N	0.00138	-2.015	0.20196	N	0.999923	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39418	-0.9615	10	0.21014	T	0.42	.	6.4392	0.21841	0.0:0.7136:0.1844:0.1021	.	382;179	C9JFX2;Q8N5R6-6	.;.	T	382;179	ENSP00000325012:M382T;ENSP00000381795:M179T	ENSP00000325012:M382T	M	+	2	0	CCDC33	72347842	0.908000	0.30866	0.790000	0.31976	0.116000	0.19942	1.639000	0.37176	0.396000	0.25283	-0.300000	0.09419	ATG	.	.		0.622	CCDC33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000419491.2	NM_182791	
SIN3A	25942	hgsc.bcm.edu	37	15	75705361	75705361	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr15:75705361G>A	ENST00000394947.3	-	5	813	c.499C>T	c.(499-501)Cgt>Tgt	p.R167C	SIN3A_ENST00000394949.4_Missense_Mutation_p.R167C|SIN3A_ENST00000360439.4_Missense_Mutation_p.R167C	NM_001145358.1	NP_001138830.1			SIN3 transcription regulator family member A											breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	63						TGGGACACACGACTAATCACT	0.408																																					p.R167C		Atlas-SNP	.											.	SIN3A	152	.	0			c.C499T						.						97.0	92.0	94.0					15																	75705361		2197	4294	6491	SO:0001583	missense	25942	exon5			ACACACGACTAAT	AK027559	CCDS10279.1	15q22.33	2013-08-21	2013-08-21		ENSG00000169375	ENSG00000169375			19353	protein-coding gene	gene with protein product		607776	"""SIN3 homolog A, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog A (yeast)"""			10773092, 7601471	Standard	NM_001145357		Approved	KIAA0700, DKFZP434K2235	uc002bai.3	Q96ST3	OTTHUMG00000142834	ENST00000394947.3:c.499C>T	chr15.hg19:g.75705361G>A	ENSP00000378402:p.Arg167Cys	108.0	0.0		123.0	41.0	NM_001145358		Missense_Mutation	SNP	ENST00000394947.3	hg19	CCDS10279.1	.	.	.	.	.	.	.	.	.	.	G	27.2	4.813041	0.90707	.	.	ENSG00000169375	ENST00000394947;ENST00000394949;ENST00000360439	T;T;T	0.62941	-0.01;-0.01;-0.01	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	D	0.87569	0.6210	H	0.97491	4.015	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90993	0.4836	10	0.87932	D	0	-15.5025	19.5674	0.95401	0.0:0.0:1.0:0.0	.	167	Q96ST3	SIN3A_HUMAN	C	167	ENSP00000378402:R167C;ENSP00000378403:R167C;ENSP00000353622:R167C	ENSP00000353622:R167C	R	-	1	0	SIN3A	73492414	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.809000	0.62591	2.873000	0.98535	0.561000	0.74099	CGT	.	.		0.408	SIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286469.1	NM_015477	
PIGQ	9091	hgsc.bcm.edu	37	16	625870	625870	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:625870G>A	ENST00000026218.5	+	3	809	c.721G>A	c.(721-723)Ggg>Agg	p.G241R	PIGQ_ENST00000470411.2_Missense_Mutation_p.G241R|PIGQ_ENST00000409527.2_Missense_Mutation_p.G241R|PIGQ_ENST00000321878.5_Missense_Mutation_p.G241R	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q	241	Leu-rich.				C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GTCCTTCCTCGGGAGCAAACT	0.617																																					p.G241R		Atlas-SNP	.											.	PIGQ	43	.	0			c.G721A						.						85.0	73.0	77.0					16																	625870		2186	4290	6476	SO:0001583	missense	9091	exon3			TTCCTCGGGAGCA	AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.721G>A	chr16.hg19:g.625870G>A	ENSP00000026218:p.Gly241Arg	33.0	0.0		18.0	14.0	NM_148920	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	hg19	CCDS10411.1	.	.	.	.	.	.	.	.	.	.	G	4.288	0.052620	0.08291	.	.	ENSG00000007541	ENST00000409527;ENST00000409439;ENST00000422307;ENST00000321878;ENST00000026218;ENST00000470411	T;T;T;T;T;T	0.41065	1.01;1.03;1.03;1.01;2.28;1.02	4.88	0.087	0.14448	.	0.637390	0.17677	N	0.165753	T	0.13030	0.0316	N	0.01352	-0.895	0.09310	N	1	B;B;B;B	0.21309	0.018;0.03;0.004;0.054	B;B;B;B	0.14578	0.004;0.005;0.004;0.011	T	0.19943	-1.0290	10	0.34782	T	0.22	0.2096	5.6045	0.17371	0.2336:0.0:0.3524:0.414	.	255;241;241;241	E7ERP4;Q9BRB3;Q9BRB3-2;Q9BRB3-3	.;PIGQ_HUMAN;.;.	R	241	ENSP00000386760:G241R;ENSP00000386554:G241R;ENSP00000413753:G241R;ENSP00000326674:G241R;ENSP00000026218:G241R;ENSP00000439650:G241R	ENSP00000026218:G241R	G	+	1	0	PIGQ	565871	0.997000	0.39634	0.000000	0.03702	0.434000	0.31775	2.798000	0.47884	-0.165000	0.10908	0.591000	0.81541	GGG	.	.		0.617	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2	NM_004204	
PTX4	390667	hgsc.bcm.edu	37	16	1537527	1537527	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:1537527G>T	ENST00000447419.2	-	2	611	c.586C>A	c.(586-588)Cct>Act	p.P196T	PTX4_ENST00000293922.1_Missense_Mutation_p.P191T|PTX4_ENST00000440447.2_Intron			Q96A99	PTX4_HUMAN	pentraxin 4, long	196						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						AGCTCCTCAGGCTGGGTTGGG	0.736																																					p.P191T		Atlas-SNP	.											.	PTX4	46	.	0			c.C571A						.						10.0	12.0	11.0					16																	1537527		2177	4253	6430	SO:0001583	missense	390667	exon2			CCTCAGGCTGGGT		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.586C>A	chr16.hg19:g.1537527G>T	ENSP00000445277:p.Pro196Thr	71.0	0.0		55.0	34.0	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	hg19		.	.	.	.	.	.	.	.	.	.	G	11.15	1.552971	0.27739	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.05319	3.62;3.46	4.92	1.9	0.25705	.	1.497440	0.04395	N	0.363053	T	0.14743	0.0356	L	0.48642	1.525	0.09310	N	1	D	0.63880	0.993	P	0.59424	0.857	T	0.27571	-1.0070	10	0.23891	T	0.37	.	7.2869	0.26344	0.2795:0.0:0.7205:0.0	.	191	Q96A99-2	.	T	196;191	ENSP00000445277:P196T;ENSP00000293922:P191T	ENSP00000293922:P191T	P	-	1	0	PTX4	1477528	0.003000	0.15002	0.001000	0.08648	0.001000	0.01503	0.450000	0.21762	0.237000	0.21200	-0.768000	0.03414	CCT	.	.		0.736	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
CLEC16A	23274	hgsc.bcm.edu	37	16	11056338	11056338	+	Missense_Mutation	SNP	T	T	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:11056338T>G	ENST00000409790.1	+	3	466	c.236T>G	c.(235-237)gTt>gGt	p.V79G	CLEC16A_ENST00000409552.3_Missense_Mutation_p.V79G	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AATATGTTTGTTTTCTTCTTG	0.453																																					p.V79G		Atlas-SNP	.											.	CLEC16A	101	.	0			c.T236G						.						195.0	183.0	187.0					16																	11056338		1970	4162	6132	SO:0001583	missense	23274	exon3			TGTTTGTTTTCTT	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.236T>G	chr16.hg19:g.11056338T>G	ENSP00000387122:p.Val79Gly	99.0	0.0		94.0	38.0	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	hg19	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.018863	0.35606	.	.	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000409552	T	0.41065	1.01	4.78	4.78	0.61160	.	0.054657	0.64402	D	0.000001	T	0.17109	0.0411	N	0.00413	-1.525	0.80722	D	1	P;B	0.35684	0.515;0.4	B;B	0.41412	0.356;0.173	T	0.35276	-0.9795	10	0.21540	T	0.41	-14.0854	13.8146	0.63283	0.0:0.0:0.0:1.0	.	79;79	Q2KHT3;Q2KHT3-2	CL16A_HUMAN;.	G	79	ENSP00000387122:V79G	ENSP00000386495:V79G	V	+	2	0	CLEC16A	10963839	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.923000	0.56469	1.926000	0.55796	0.460000	0.39030	GTT	.	.		0.453	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
SYT17	51760	hgsc.bcm.edu	37	16	19234475	19234475	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:19234475A>T	ENST00000355377.2	+	6	1458	c.1060A>T	c.(1060-1062)Agc>Tgc	p.S354C	SYT17_ENST00000568115.1_Missense_Mutation_p.S293C|SYT17_ENST00000568433.1_Missense_Mutation_p.S48C|SYT17_ENST00000562034.1_Missense_Mutation_p.S293C|SYT17_ENST00000562711.2_Missense_Mutation_p.S350C	NM_016524.2	NP_057608.2	Q9BSW7	SYT17_HUMAN	synaptotagmin XVII	354	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				exocytosis (GO:0006887)	membrane (GO:0016020)|synaptic vesicle (GO:0008021)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			NS(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)	17						GACAGATGTGAGCCAAGGTTC	0.483																																					p.S354C		Atlas-SNP	.											.	SYT17	51	.	0			c.A1060T						.						110.0	87.0	95.0					16																	19234475		2197	4300	6497	SO:0001583	missense	51760	exon6			GATGTGAGCCAAG		CCDS10575.1	16p12.3	2013-01-21			ENSG00000103528	ENSG00000103528		"""Synaptotagmins"""	24119	protein-coding gene	gene with protein product	"""B/K protein"""					10493829	Standard	NM_016524		Approved		uc002dfw.3	Q9BSW7	OTTHUMG00000131461	ENST00000355377.2:c.1060A>T	chr16.hg19:g.19234475A>T	ENSP00000347538:p.Ser354Cys	91.0	0.0		89.0	33.0	NM_016524	O43330|Q9NZ18	Missense_Mutation	SNP	ENST00000355377.2	hg19	CCDS10575.1	.	.	.	.	.	.	.	.	.	.	A	14.83	2.652025	0.47362	.	.	ENSG00000103528	ENST00000355377	T	0.70869	-0.52	4.83	4.83	0.62350	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.315023	0.29178	N	0.012906	T	0.60843	0.2300	L	0.31752	0.955	0.48632	D	0.999682	B;B	0.10296	0.002;0.003	B;B	0.20577	0.021;0.03	T	0.57429	-0.7813	10	0.38643	T	0.18	.	15.1215	0.72447	1.0:0.0:0.0:0.0	.	354;293	Q9BSW7;B4DJB2	SYT17_HUMAN;.	C	354	ENSP00000347538:S354C	ENSP00000347538:S354C	S	+	1	0	SYT17	19141976	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.210000	0.65214	2.099000	0.63709	0.533000	0.62120	AGC	.	.		0.483	SYT17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254286.2	NM_016524	
PLK1	5347	hgsc.bcm.edu	37	16	23703609	23703609	+	IGR	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:23703609T>C	ENST00000300093.4	+	0	2227				ERN2_ENST00000256797.4_Missense_Mutation_p.Y763C|ERN2_ENST00000457008.2_Missense_Mutation_p.Y663C	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1						activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		AGAAAGCACGTAGTAGAACAC	0.567																																					p.Y763C	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	ERN2	131	.	0			c.A2288G						.						75.0	74.0	74.0					16																	23703609		2197	4300	6497	SO:0001628	intergenic_variant	10595	exon18			AGCACGTAGTAGA		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"""polo-like kinase (Drosophila)"""	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984		chr16.hg19:g.23703609T>C		21.0	0.0		21.0	8.0	NM_033266	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	hg19	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	T	19.62	3.861209	0.71949	.	.	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.50277	0.75;0.75	5.65	5.65	0.86999	.	0.137817	0.50627	D	0.000113	T	0.63105	0.2483	L	0.52206	1.635	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.65882	-0.6060	10	0.87932	D	0	.	13.8429	0.63451	0.0:0.0:0.0:1.0	.	663;715	E7ETG2;A5YM65	.;.	C	763;663	ENSP00000256797:Y763C;ENSP00000413812:Y663C	ENSP00000256797:Y763C	Y	-	2	0	ERN2	23611110	1.000000	0.71417	0.982000	0.44146	0.974000	0.67602	5.877000	0.69675	2.146000	0.66826	0.533000	0.62120	TAC	.	.		0.567	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030	
GPR114	221188	hgsc.bcm.edu	37	16	57604440	57604440	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:57604440A>T	ENST00000340339.4	+	10	1724	c.1201A>T	c.(1201-1203)Atg>Ttg	p.M401L	GPR114_ENST00000349457.3_Missense_Mutation_p.M401L|GPR114_ENST00000394361.4_Intron	NM_153837.1	NP_722579.1	Q8IZF4	GP114_HUMAN	G protein-coupled receptor 114	401					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(5)|lung(5)|ovary(2)|stomach(1)|urinary_tract(1)	23						CTTCCAGAACATGTCCATGTG	0.592																																					p.M401L		Atlas-SNP	.											.	GPR114	52	.	0			c.A1201T						.						58.0	50.0	53.0					16																	57604440		2198	4300	6498	SO:0001583	missense	221188	exon10			CAGAACATGTCCA	AY140956	CCDS10785.1	16q13	2014-08-08			ENSG00000159618	ENSG00000159618		"""-"", ""GPCR / Class B : Orphans"""	19010	protein-coding gene	gene with protein product						12435584	Standard	NM_153837		Approved	PGR27	uc002ely.3	Q8IZF4	OTTHUMG00000133461	ENST00000340339.4:c.1201A>T	chr16.hg19:g.57604440A>T	ENSP00000342981:p.Met401Leu	18.0	0.0		20.0	8.0	NM_153837	B3KXZ5|Q6ZMH7|Q6ZML4|Q86SL8|Q8IZ14	Missense_Mutation	SNP	ENST00000340339.4	hg19	CCDS10785.1	.	.	.	.	.	.	.	.	.	.	A	10.80	1.452929	0.26161	.	.	ENSG00000159618	ENST00000340339;ENST00000349457	T;T	0.27557	1.66;1.66	4.58	-5.32	0.02722	GPCR, family 2-like (1);	2.158560	0.01693	N	0.026755	T	0.19366	0.0465	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.22661	-1.0210	10	0.29301	T	0.29	.	9.4502	0.38721	0.1622:0.0:0.6956:0.1423	.	401	Q8IZF4	GP114_HUMAN	L	401	ENSP00000342981:M401L;ENSP00000290823:M401L	ENSP00000342981:M401L	M	+	1	0	GPR114	56161941	0.000000	0.05858	0.001000	0.08648	0.056000	0.15407	-1.029000	0.03585	-0.507000	0.06549	-0.421000	0.06004	ATG	.	.		0.592	GPR114-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257336.3	NM_153837	
VAC14	55697	hgsc.bcm.edu	37	16	70778459	70778459	+	Silent	SNP	C	C	A	rs145571853		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:70778459C>A	ENST00000261776.5	-	13	1655	c.1395G>T	c.(1393-1395)gtG>gtT	p.V465V	RP11-394B2.6_ENST00000567186.1_RNA	NM_018052.3	NP_060522.3	Q08AM6	VAC14_HUMAN	Vac14 homolog (S. cerevisiae)	465					phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|regulation of lipid kinase activity (GO:0043550)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|PAS complex (GO:0070772)	receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(10)|large_intestine(1)|lung(10)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	33		Ovarian(137;0.0699)				TTTCTGCCAGCACCTCCAGGT	0.662																																					p.V465V		Atlas-SNP	.											.	VAC14	65	.	0			c.G1395T						.						38.0	41.0	40.0					16																	70778459		2198	4300	6498	SO:0001819	synonymous_variant	55697	exon13			TGCCAGCACCTCC	AK056433	CCDS10896.1	16q22.1	2010-03-23	2005-02-09		ENSG00000103043	ENSG00000103043			25507	protein-coding gene	gene with protein product		604632	"""Tax1 (human T-cell leukemia virus type I) binding protein 2"""	TAX1BP2		15542851, 12719380	Standard	NM_018052		Approved	FLJ10305, ArPIKfyve	uc002ezm.3	Q08AM6	OTTHUMG00000137583	ENST00000261776.5:c.1395G>T	chr16.hg19:g.70778459C>A		54.0	0.0		64.0	16.0	NM_018052	B3KPJ5|B3KSM8|Q13174|Q6IA12|Q7L4Y1|Q9BW96|Q9H6V6	Silent	SNP	ENST00000261776.5	hg19	CCDS10896.1																																																																																			.	C|1.000;T|0.000		0.662	VAC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268973.3	NM_018052	
TLDC1	57707	hgsc.bcm.edu	37	16	84514214	84514214	+	Missense_Mutation	SNP	G	G	A	rs149378530		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:84514214G>A	ENST00000343629.6	-	7	1360	c.1178C>T	c.(1177-1179)cCg>cTg	p.P393L	TLDC1_ENST00000535580.1_Missense_Mutation_p.P366L	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	393	TLD.					lysosomal membrane (GO:0005765)											CGACAGCTGCGGGCTGTTGTA	0.567																																					p.P393L		Atlas-SNP	.											.	KIAA1609	39	.	0			c.C1178T						.	G	LEU/PRO	0,4400		0,0,2200	113.0	91.0	98.0		1178	5.2	1.0	16	dbSNP_134	98	1,8599	1.2+/-3.3	0,1,4299	no	missense	KIAA1609	NM_020947.3	98	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	393/457	84514214	1,12999	2200	4300	6500	SO:0001583	missense	57707	exon7			AGCTGCGGGCTGT	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.1178C>T	chr16.hg19:g.84514214G>A	ENSP00000343635:p.Pro393Leu	88.0	0.0		91.0	43.0	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	hg19	CCDS32498.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.850028	0.91277	0.0	1.16E-4	ENSG00000140950	ENST00000343629;ENST00000545792;ENST00000535580	T;T	0.46819	0.86;0.86	5.18	5.18	0.71444	TLDc (2);	0.000000	0.85682	D	0.000000	T	0.72961	0.3526	M	0.85542	2.76	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.97110	1.0;0.88	T	0.78006	-0.2373	10	0.72032	D	0.01	-31.88	17.6786	0.88236	0.0:0.0:1.0:0.0	.	366;393	F5GWS3;Q6P9B6	.;K1609_HUMAN	L	393;61;366	ENSP00000343635:P393L;ENSP00000441997:P366L	ENSP00000343635:P393L	P	-	2	0	KIAA1609	83071715	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	9.267000	0.95665	2.415000	0.81967	0.563000	0.77884	CCG	.	G|1.000;T|0.000		0.567	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
GSE1	23199	hgsc.bcm.edu	37	16	85696964	85696964	+	Silent	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:85696964G>A	ENST00000253458.7	+	11	2564	c.2388G>A	c.(2386-2388)ttG>ttA	p.L796L	GSE1_ENST00000393243.1_Silent_p.L723L|GSE1_ENST00000405402.2_Silent_p.L692L	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	796																	TAGAGTTTTTGCAACTTTTTG	0.562																																					p.L796L		Atlas-SNP	.											.	.	.	.	0			c.G2388A						.						104.0	123.0	116.0					16																	85696964		2198	4300	6498	SO:0001819	synonymous_variant	23199	exon11			GTTTTTGCAACTT	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.2388G>A	chr16.hg19:g.85696964G>A		20.0	0.0		20.0	9.0	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	hg19	CCDS10952.1	.	.	.	.	.	.	.	.	.	.	G	8.887	0.953023	0.18431	.	.	ENSG00000131149	ENST00000412692	.	.	.	5.21	4.25	0.50352	.	.	.	.	.	T	0.54287	0.1849	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52177	-0.8610	4	.	.	.	-12.8675	5.6565	0.17644	0.1538:0.0:0.6779:0.1683	.	.	.	.	Y	603	.	.	C	+	2	0	KIAA0182	84254465	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.943000	0.49026	2.438000	0.82558	0.561000	0.74099	TGC	.	.		0.562	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
ACAP1	9744	hgsc.bcm.edu	37	17	7254302	7254302	+	Silent	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:7254302G>A	ENST00000158762.3	+	21	2312	c.2106G>A	c.(2104-2106)gcG>gcA	p.A702A	KCTD11_ENST00000333751.3_5'Flank|ACAP1_ENST00000574499.1_Silent_p.A27A|ACAP1_ENST00000570504.1_Silent_p.A6A|ACAP1_ENST00000571471.1_Silent_p.A6A|ACAP1_ENST00000575415.1_Silent_p.A6A|RP11-542C16.1_ENST00000572417.1_RNA	NM_014716.3	NP_055531.1	Q15027	ACAP1_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 1	702	Required for interaction with GULP1.				protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)	endosome (GO:0005768)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(3)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(6)|prostate(3)|skin(1)|urinary_tract(1)	33						AGGCTGAAGCGGCCCAGGGGC	0.597																																					p.A702A		Atlas-SNP	.											.	ACAP1	66	.	0			c.G2106A						.						81.0	80.0	80.0					17																	7254302		2203	4300	6503	SO:0001819	synonymous_variant	9744	exon21			TGAAGCGGCCCAG	D30758	CCDS11101.1	17p13.1	2013-01-11	2008-09-22	2008-09-22	ENSG00000072818	ENSG00000072818		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16467	protein-coding gene	gene with protein product		607763	"""centaurin, beta 1"""	CENTB1		11050434, 11062263	Standard	NM_014716		Approved	KIAA0050	uc002ggd.2	Q15027	OTTHUMG00000102199	ENST00000158762.3:c.2106G>A	chr17.hg19:g.7254302G>A		53.0	0.0		30.0	20.0	NM_014716	Q53XN9	Silent	SNP	ENST00000158762.3	hg19	CCDS11101.1																																																																																			.	.		0.597	ACAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220049.4	NM_014716	
TP53	7157	hgsc.bcm.edu	37	17	7577064	7577064	+	Nonsense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:7577064T>A	ENST00000269305.4	-	8	1063	c.874A>T	c.(874-876)Aaa>Taa	p.K292*	TP53_ENST00000420246.2_Nonsense_Mutation_p.K292*|TP53_ENST00000445888.2_Nonsense_Mutation_p.K292*|TP53_ENST00000455263.2_Nonsense_Mutation_p.K292*|TP53_ENST00000413465.2_Intron|TP53_ENST00000359597.4_Nonsense_Mutation_p.K292*|TP53_ENST00000574684.1_5'Flank	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	292	Interaction with AXIN1. {ECO:0000250}.|Interaction with E4F1.|Interaction with HIPK1. {ECO:0000250}.|Required for interaction with ZNF385A.		K -> E (in sporadic cancers; somatic mutation).|K -> G (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions).|K -> I (in LFS; germline mutation and in a sporadic cancer; somatic mutation). {ECO:0000269|PubMed:10484981}.|K -> N (in sporadic cancers; somatic mutation).|K -> Q (in a sporadic cancer; somatic mutation).|K -> R (in sporadic cancers; somatic mutation).|K -> T (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.K291fs*48(8)|p.0?(8)|p.?(2)|p.E294fs*51(2)|p.K292E(2)|p.K292*(2)|p.K292fs*13(1)|p.T284_G293del10(1)|p.L265_K305del41(1)|p.R290fs*12(1)|p.R290fs*50(1)|p.K291fs*12(1)|p.R290_P295>X(1)|p.E285fs*13(1)|p.V272_K292del21(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)	GGCTCCCCTTTCTTGCGGAGA	0.577		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.K292X	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_ENST00000269305,NS,carcinoma,0,1	TP53	33396	.	33	Deletion - Frameshift(15)|Whole gene deletion(8)|Deletion - In frame(3)|Substitution - Nonsense(2)|Unknown(2)|Substitution - Missense(2)|Complex - deletion inframe(1)	upper_aerodigestive_tract(12)|urinary_tract(4)|bone(4)|haematopoietic_and_lymphoid_tissue(3)|stomach(2)|central_nervous_system(2)|breast(2)|salivary_gland(1)|large_intestine(1)|endometrium(1)|oesophagus(1)	c.A874T						.						104.0	89.0	94.0					17																	7577064		2203	4300	6503	SO:0001587	stop_gained	7157	exon8	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;	CCCCTTTCTTGCG	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.874A>T	chr17.hg19:g.7577064T>A	ENSP00000269305:p.Lys292*	60.0	0.0		35.0	17.0	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	Nonsense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.521424	0.85600	.	.	ENSG00000141510	ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000509690	.	.	.	5.12	4.03	0.46877	.	0.183996	0.46145	D	0.000309	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-23.716	5.2408	0.15471	0.0:0.0898:0.182:0.7282	.	.	.	.	X	292;292;292;292;292;281;160	.	ENSP00000269305:K292X	K	-	1	0	TP53	7517789	0.998000	0.40836	0.909000	0.35828	0.257000	0.26127	1.203000	0.32284	0.944000	0.37579	0.459000	0.35465	AAA	.	.		0.577	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
GAS7	8522	hgsc.bcm.edu	37	17	9846500	9846500	+	Silent	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:9846500C>A	ENST00000432992.2	-	7	829	c.669G>T	c.(667-669)ctG>ctT	p.L223L	GAS7_ENST00000585266.1_Silent_p.L163L|GAS7_ENST00000580865.1_Silent_p.L83L|GAS7_ENST00000323816.4_Silent_p.L163L|GAS7_ENST00000396115.2_Intron|GAS7_ENST00000540214.1_Intron|GAS7_ENST00000583882.1_Intron|GAS7_ENST00000579158.1_Silent_p.L159L|GAS7_ENST00000578655.1_5'Flank|GAS7_ENST00000542249.1_Silent_p.L159L|GAS7_ENST00000437099.2_Silent_p.L159L	NM_201433.1	NP_958839.1	O60861	GAS7_HUMAN	growth arrest-specific 7	223	FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				actin filament bundle assembly (GO:0051017)|actin filament polymerization (GO:0030041)|cell cycle arrest (GO:0007050)|neuron projection morphogenesis (GO:0048812)|regulation of cell shape (GO:0008360)|regulation of transcription, DNA-templated (GO:0006355)	actin filament (GO:0005884)|cytoplasm (GO:0005737)|ruffle (GO:0001726)	sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(7)|lung(18)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	39						GTTTCTGGAGCAGTAGTTCAA	0.552			T	MLL	AML*																																p.L223L		Atlas-SNP	.		Dom	yes		17	17p	8522	growth arrest-specific 7		L	.	GAS7	113	.	0			c.G669T						.						181.0	163.0	169.0					17																	9846500		2203	4300	6503	SO:0001819	synonymous_variant	8522	exon7			CTGGAGCAGTAGT	AB007854	CCDS11152.1, CCDS42263.1, CCDS45611.1, CCDS58518.1	17p13.1	2004-02-18							4169	protein-coding gene	gene with protein product		603127				9736752	Standard	NM_001130831		Approved	KIAA0394, MGC1348	uc002gmg.1	O60861		ENST00000432992.2:c.669G>T	chr17.hg19:g.9846500C>A		84.0	0.0		36.0	24.0	NM_201433	A8KAC2|B2RCK9|O43144|Q53Y77|Q7Z571	Silent	SNP	ENST00000432992.2	hg19	CCDS11152.1																																																																																			.	.		0.552	GAS7-017	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439883.1	NM_003644, NM_201432, NM_201433	
MYH8	4626	hgsc.bcm.edu	37	17	10307807	10307807	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:10307807A>T	ENST00000403437.2	-	22	2622	c.2528T>A	c.(2527-2529)cTc>cAc	p.L843H	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	843					ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						TGCACTCTTGAGGAGGGGCTT	0.478									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling																												p.L843H		Atlas-SNP	.											.	MYH8	346	.	0			c.T2528A						.						129.0	123.0	125.0					17																	10307807		2203	4300	6503	SO:0001583	missense	4626	exon22	Familial Cancer Database	Carney Complex Variant	CTCTTGAGGAGGG		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.2528T>A	chr17.hg19:g.10307807A>T	ENSP00000384330:p.Leu843His	411.0	1.0		257.0	169.0	NM_002472	Q14910	Missense_Mutation	SNP	ENST00000403437.2	hg19	CCDS11153.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.582791	0.86748	.	.	ENSG00000133020	ENST00000252173;ENST00000403437	D	0.87491	-2.26	5.31	5.31	0.75309	.	0.000000	0.36444	U	0.002587	D	0.96358	0.8812	H	0.98965	4.385	0.54753	D	0.999988	D	0.89917	1.0	D	0.91635	0.999	D	0.98081	1.0404	10	0.87932	D	0	.	15.4343	0.75133	1.0:0.0:0.0:0.0	.	843	P13535	MYH8_HUMAN	H	843	ENSP00000384330:L843H	ENSP00000252173:L843H	L	-	2	0	MYH8	10248532	1.000000	0.71417	0.997000	0.53966	0.904000	0.53231	9.058000	0.93896	2.231000	0.72958	0.533000	0.62120	CTC	.	.		0.478	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
MYH1	4619	hgsc.bcm.edu	37	17	10411951	10411951	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:10411951C>T	ENST00000226207.5	-	16	1720	c.1626G>A	c.(1624-1626)atG>atA	p.M542I	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	542	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CCTTGGGGAACATGCACTCCT	0.433																																					p.M542I		Atlas-SNP	.											.	MYH1	403	.	0			c.G1626A						.						111.0	116.0	114.0					17																	10411951		2203	4300	6503	SO:0001583	missense	4619	exon16			GGGGAACATGCAC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.1626G>A	chr17.hg19:g.10411951C>T	ENSP00000226207:p.Met542Ile	81.0	0.0		46.0	33.0	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	hg19	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	C	31	5.087659	0.94100	.	.	ENSG00000109061	ENST00000226207	T	0.71341	-0.56	4.8	4.8	0.61643	Myosin head, motor domain (2);	0.000000	0.52532	U	0.000072	T	0.71239	0.3316	L	0.49571	1.57	0.58432	D	0.999999	B	0.17038	0.02	B	0.33295	0.161	T	0.69026	-0.5254	10	0.51188	T	0.08	.	18.405	0.90532	0.0:1.0:0.0:0.0	.	542	P12882	MYH1_HUMAN	I	542	ENSP00000226207:M542I	ENSP00000226207:M542I	M	-	3	0	MYH1	10352676	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.414000	0.80117	2.665000	0.90641	0.650000	0.86243	ATG	.	.		0.433	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
LHX1	3975	hgsc.bcm.edu	37	17	35298050	35298050	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:35298050C>T	ENST00000254457.5	+	3	1952	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	RP11-445F12.2_ENST00000607336.1_RNA	NM_005568.3	NP_005559.2	P48742	LHX1_HUMAN	LIM homeobox 1	181					anatomical structure formation involved in morphogenesis (GO:0048646)|anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|anterior/posterior pattern specification (GO:0009952)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell signaling (GO:0007267)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation (GO:0021937)|cerebellum development (GO:0021549)|cervix development (GO:0060067)|comma-shaped body morphogenesis (GO:0072049)|dorsal/ventral pattern formation (GO:0009953)|ectoderm formation (GO:0001705)|embryonic pattern specification (GO:0009880)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|embryonic viscerocranium morphogenesis (GO:0048703)|endoderm formation (GO:0001706)|epithelium development (GO:0060429)|forebrain regionalization (GO:0021871)|gastrulation with mouth forming second (GO:0001702)|head development (GO:0060322)|horizontal cell localization (GO:0035852)|kidney development (GO:0001822)|lateral motor column neuron migration (GO:0097477)|mesonephric duct development (GO:0072177)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerulus development (GO:0072224)|metanephric part of ureteric bud development (GO:0035502)|metanephric renal vesicle morphogenesis (GO:0072283)|metanephric S-shaped body morphogenesis (GO:0072284)|motor neuron axon guidance (GO:0008045)|negative regulation of transcription, DNA-templated (GO:0045892)|nephric duct elongation (GO:0035849)|nephric duct morphogenesis (GO:0072178)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|oviduct development (GO:0060066)|oviduct epithelium development (GO:0035846)|paramesonephric duct development (GO:0061205)|pattern specification process (GO:0007389)|positive regulation of anterior head development (GO:2000744)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of nephron tubule epithelial cell differentiation (GO:2000768)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|primitive streak formation (GO:0090009)|pronephros development (GO:0048793)|regulation of gene expression (GO:0010468)|renal vesicle morphogenesis (GO:0072077)|retina layer formation (GO:0010842)|S-shaped body morphogenesis (GO:0072050)|somite rostral/caudal axis specification (GO:0032525)|spinal cord association neuron differentiation (GO:0021527)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|ureteric bud development (GO:0001657)|urogenital system development (GO:0001655)|uterine epithelium development (GO:0035847)|uterus development (GO:0060065)|vagina development (GO:0060068)|ventral spinal cord development (GO:0021517)	nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Breast(25;0.00607)				CGCCAAGCGGCGGGGACCGCG	0.667																																					p.R181W		Atlas-SNP	.											.	LHX1	48	.	0			c.C541T						.						41.0	47.0	45.0					17																	35298050		2203	4300	6503	SO:0001583	missense	3975	exon3			AAGCGGCGGGGAC	U14755	CCDS11316.1	17q12	2014-04-11			ENSG00000132130	ENSG00000273706		"""Homeoboxes / LIM class"""	6593	protein-coding gene	gene with protein product		601999				9212161	Standard	NM_005568		Approved	LIM-1, LIM1	uc002hnh.2	P48742	OTTHUMG00000188456	ENST00000254457.5:c.541C>T	chr17.hg19:g.35298050C>T	ENSP00000254457:p.Arg181Trp	28.0	0.0		39.0	14.0	NM_005568	Q3MIW0	Missense_Mutation	SNP	ENST00000254457.5	hg19	CCDS11316.1	.	.	.	.	.	.	.	.	.	.	C	19.75	3.884970	0.72410	.	.	ENSG00000132130	ENST00000254457	D	0.97352	-4.35	4.26	-0.887	0.10587	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.64402	D	0.000001	D	0.98394	0.9466	M	0.88377	2.95	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98556	1.0639	10	0.87932	D	0	.	16.8083	0.85711	0.75:0.25:0.0:0.0	.	167;181	B4DPA6;P48742	.;LHX1_HUMAN	W	181	ENSP00000254457:R181W	ENSP00000254457:R181W	R	+	1	2	LHX1	32372163	0.049000	0.20398	0.812000	0.32479	0.986000	0.74619	0.110000	0.15437	-0.086000	0.12550	-0.268000	0.10319	CGG	.	.		0.667	LHX1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256704.3	NM_005568	
KRT9	3857	hgsc.bcm.edu	37	17	39723992	39723992	+	Nonsense_Mutation	SNP	C	C	A	rs201817471		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:39723992C>A	ENST00000246662.4	-	7	1470	c.1405G>T	c.(1405-1407)Gga>Tga	p.G469*	KRT9_ENST00000588431.1_Nonsense_Mutation_p.G236*	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	469	Tail.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				TTTCCAGCTCCGGAGGATTCA	0.502																																					p.G469X		Atlas-SNP	.											.	KRT9	78	.	0			c.G1405T						.						72.0	70.0	71.0					17																	39723992		2203	4300	6503	SO:0001587	stop_gained	3857	exon7			CAGCTCCGGAGGA		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1405G>T	chr17.hg19:g.39723992C>A	ENSP00000246662:p.Gly469*	32.0	0.0		29.0	17.0	NM_000226	O00109|Q0IJ47|Q14665	Nonsense_Mutation	SNP	ENST00000246662.4	hg19	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	C	37	6.064804	0.97251	.	.	ENSG00000171403	ENST00000246662	.	.	.	3.64	3.64	0.41730	.	0.873431	0.09295	N	0.821854	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	10.7325	0.46104	0.0:1.0:0.0:0.0	.	.	.	.	X	469	.	ENSP00000246662:G469X	G	-	1	0	KRT9	36977518	0.236000	0.23804	0.781000	0.31783	0.600000	0.36913	1.783000	0.38664	1.886000	0.54624	0.465000	0.42564	GGA	.	C|1.000;G|0.000		0.502	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
TMC6	11322	hgsc.bcm.edu	37	17	76120809	76120809	+	Silent	SNP	C	C	T	rs369185930		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:76120809C>T	ENST00000590602.1	-	8	846	c.687G>A	c.(685-687)ccG>ccA	p.P229P	TMC6_ENST00000589553.1_Silent_p.P2P|TMC6_ENST00000322933.4_De_novo_Start_OutOfFrame|TMC6_ENST00000306591.7_Silent_p.P229P|TMC6_ENST00000591436.1_5'Flank|TMC6_ENST00000392467.3_Silent_p.P229P|TMC6_ENST00000592076.1_5'Flank|TMC6_ENST00000322914.3_Silent_p.P229P			Q7Z403	TMC6_HUMAN	transmembrane channel-like 6	229					ion transport (GO:0006811)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	14			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)			CGTAGCGCCACGGCATCAGGG	0.677																																					p.P229P		Atlas-SNP	.											.	TMC6	42	.	0			c.G687A						.	C	,	0,4322		0,0,2161	12.0	11.0	11.0		687,687	-6.3	0.0	17		11	4,8442		0,4,4219	no	coding-synonymous,coding-synonymous	TMC6	NM_001127198.1,NM_007267.6	,	0,4,6380	TT,TC,CC		0.0474,0.0,0.0313	,	229/806,229/806	76120809	4,12764	2161	4223	6384	SO:0001819	synonymous_variant	11322	exon8			GCGCCACGGCATC	AY057379	CCDS32748.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000141524	ENSG00000141524			18021	protein-coding gene	gene with protein product		605828	"""epidermodysplasia verruciformis 1"""	EVER1		12426567	Standard	NM_007267		Approved	LAK-4P, EVIN1	uc002juk.2	Q7Z403	OTTHUMG00000177466	ENST00000590602.1:c.687G>A	chr17.hg19:g.76120809C>T		50.0	0.0		89.0	26.0	NM_001127198	O43284|Q45VJ2|Q8IU98|Q8IUI7|Q8IWU8|Q8TEQ7|Q9HAG5	Silent	SNP	ENST00000590602.1	hg19	CCDS32748.1																																																																																			.	.		0.677	TMC6-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437146.1		
DNAH17	8632	hgsc.bcm.edu	37	17	76490821	76490821	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:76490821C>G	ENST00000585328.1	-	40	6233	c.6109G>C	c.(6109-6111)Gca>Cca	p.A2037P	DNAH17_ENST00000389840.5_Missense_Mutation_p.A2028P|RP11-559N14.5_ENST00000591373.1_RNA|RP11-559N14.5_ENST00000585969.1_RNA	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	2028					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(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			TGGTCCTCTGCCCGGCTGGGG	0.622																																					p.A2042P		Atlas-SNP	.											.	DNAH17	347	.	0			c.G6124C						.						31.0	37.0	35.0					17																	76490821		2130	4252	6382	SO:0001583	missense	8632	exon40			CCTCTGCCCGGCT	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.6109G>C	chr17.hg19:g.76490821C>G	ENSP00000465516:p.Ala2037Pro	32.0	0.0		33.0	15.0	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Missense_Mutation	SNP	ENST00000585328.1	hg19		.	.	.	.	.	.	.	.	.	.	C	1.406	-0.576862	0.03854	.	.	ENSG00000187775	ENST00000300671;ENST00000389840	T	0.24151	1.87	4.12	4.12	0.48240	.	.	.	.	.	T	0.05318	0.0141	N	0.00186	-1.895	0.35981	D	0.835992	.	.	.	.	.	.	T	0.28332	-1.0047	7	0.02654	T	1	.	12.4486	0.55666	0.0:0.8309:0.1691:0.0	.	.	.	.	P	2037;2028	ENSP00000374490:A2028P	ENSP00000300671:A2037P	A	-	1	0	DNAH17	74002416	0.888000	0.30383	0.920000	0.36463	0.611000	0.37282	1.414000	0.34736	2.105000	0.64084	0.511000	0.50034	GCA	.	.		0.622	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
DLGAP1	9229	hgsc.bcm.edu	37	18	3879551	3879551	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:3879551G>A	ENST00000315677.3	-	4	1113	c.518C>T	c.(517-519)gCg>gTg	p.A173V	DLGAP1_ENST00000515196.2_Missense_Mutation_p.A173V|DLGAP1_ENST00000584874.1_Missense_Mutation_p.A173V|DLGAP1_ENST00000581527.1_Missense_Mutation_p.A173V|DLGAP1-AS3_ENST00000577649.1_RNA	NM_004746.3	NP_004737.2	O14490	DLGP1_HUMAN	discs, large (Drosophila) homolog-associated protein 1	173					synaptic transmission (GO:0007268)	cell junction (GO:0030054)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)				breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	56		Colorectal(8;0.0257)				CGCCGCCTGCGCCTCGTCAGG	0.706																																					p.A173V		Atlas-SNP	.											.	DLGAP1	201	.	0			c.C518T						.						51.0	60.0	57.0					18																	3879551		2201	4299	6500	SO:0001583	missense	9229	exon4			GCCTGCGCCTCGT	AB000277	CCDS11836.1, CCDS42406.1, CCDS56049.1, CCDS56050.1, CCDS56051.1, CCDS56052.1, CCDS56053.1, CCDS74191.1	18p11.3	2008-07-28	2001-11-28		ENSG00000170579	ENSG00000170579			2905	protein-coding gene	gene with protein product		605445	"""discs, large (Drosophila) homolog-associated protein 1"""			9024696, 9286858	Standard	NM_004746		Approved	GKAP, SAPAP1, DAP-1	uc002kmf.3	O14490	OTTHUMG00000131537	ENST00000315677.3:c.518C>T	chr18.hg19:g.3879551G>A	ENSP00000316377:p.Ala173Val	26.0	0.0		31.0	11.0	NM_001242761	A8MWN8|B2RMU8|B7WPA1|B7Z2H2|B7Z2I2|B7Z9Y4|O14489|P78335	Missense_Mutation	SNP	ENST00000315677.3	hg19	CCDS11836.1	.	.	.	.	.	.	.	.	.	.	G	13.41	2.228993	0.39399	.	.	ENSG00000170579	ENST00000315677;ENST00000515196	T;T	0.17054	2.3;2.3	5.75	4.88	0.63580	.	0.864654	0.10464	N	0.671579	T	0.12050	0.0293	N	0.14661	0.345	0.21719	N	0.999575	B;B;B	0.12013	0.0;0.003;0.005	B;B;B	0.04013	0.0;0.001;0.001	T	0.21484	-1.0244	10	0.52906	T	0.07	-1.1329	10.8725	0.46891	0.1435:0.0:0.8565:0.0	.	173;173;173	B7Z9Y4;Q6IS01;O14490	.;.;DLGP1_HUMAN	V	173	ENSP00000316377:A173V;ENSP00000445973:A173V	ENSP00000316377:A173V	A	-	2	0	DLGAP1	3869551	0.999000	0.42202	0.960000	0.40013	0.863000	0.49368	5.382000	0.66213	1.442000	0.47568	0.655000	0.94253	GCG	.	.		0.706	DLGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254394.4		
SPIRE1	56907	hgsc.bcm.edu	37	18	12454401	12454401	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:12454401C>T	ENST00000409402.4	-	13	1987	c.1720G>A	c.(1720-1722)Gag>Aag	p.E574K	SPIRE1_ENST00000309836.5_Missense_Mutation_p.E363K|SPIRE1_ENST00000383356.2_Missense_Mutation_p.E401K|SPIRE1_ENST00000410092.3_Missense_Mutation_p.E560K|SPIRE1_ENST00000453447.2_Missense_Mutation_p.E440K|SPIRE1_ENST00000464481.1_5'UTR	NM_001128626.1	NP_001122098.1			spire-type actin nucleation factor 1											breast(3)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)	28						TTTTCCAGCTCTGCCTTCACC	0.433																																					p.E574K		Atlas-SNP	.											.	SPIRE1	120	.	0			c.G1720A						.						223.0	201.0	208.0					18																	12454401		2203	4300	6503	SO:0001583	missense	56907	exon13			CCAGCTCTGCCTT	AL833817	CCDS32790.2, CCDS45829.1, CCDS45830.1	18p11.21	2013-08-27	2013-08-27		ENSG00000134278	ENSG00000134278			30622	protein-coding gene	gene with protein product		609216	"""spire homolog 1 (Drosophila)"", ""spire family actin nucleation factor 1"""			10574461, 11747823	Standard	NM_001128626		Approved	spir-1, KIAA1135	uc002kre.3	Q08AE8	OTTHUMG00000153940	ENST00000409402.4:c.1720G>A	chr18.hg19:g.12454401C>T	ENSP00000387266:p.Glu574Lys	183.0	0.0		174.0	63.0	NM_001128626		Missense_Mutation	SNP	ENST00000409402.4	hg19	CCDS45829.1	.	.	.	.	.	.	.	.	.	.	C	36	5.867872	0.97043	.	.	ENSG00000134278	ENST00000453447;ENST00000409402;ENST00000410092;ENST00000309836;ENST00000383356	T;T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1;-1.1	5.96	5.96	0.96718	Zinc finger, FYVE/PHD-type (1);	0.000000	0.85682	D	0.000000	D	0.89784	0.6815	M	0.84082	2.675	0.80722	D	1	D;D;D	0.89917	0.998;1.0;0.999	D;D;D	0.91635	0.991;0.999;0.997	D	0.90074	0.4165	10	0.87932	D	0	-13.7881	20.3928	0.98949	0.0:1.0:0.0:0.0	.	560;363;574	Q08AE8-2;B4DWX0;Q08AE8	.;.;SPIR1_HUMAN	K	440;574;560;363;401	ENSP00000407050:E440K;ENSP00000387266:E574K;ENSP00000387226:E560K;ENSP00000309661:E363K;ENSP00000372847:E401K	ENSP00000309661:E363K	E	-	1	0	SPIRE1	12444401	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.294000	0.78760	2.813000	0.96785	0.655000	0.94253	GAG	.	.		0.433	SPIRE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333109.2	XM_290818	
LAMA3	3909	hgsc.bcm.edu	37	18	21523852	21523852	+	Missense_Mutation	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:21523852C>A	ENST00000313654.9	+	69	9368	c.9127C>A	c.(9127-9129)Cgt>Agt	p.R3043S	LAMA3_ENST00000587184.1_Missense_Mutation_p.R1378S|LAMA3_ENST00000399516.3_Missense_Mutation_p.R2987S|LAMA3_ENST00000269217.6_Missense_Mutation_p.R1434S|LAMA3_ENST00000588770.1_3'UTR	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	3043	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TTCAAAAGGACGTCTGGTCTT	0.473																																					p.R3043S		Atlas-SNP	.											.	LAMA3	397	.	0			c.C9127A						.						125.0	113.0	117.0					18																	21523852		2203	4300	6503	SO:0001583	missense	3909	exon69			AAAGGACGTCTGG	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.9127C>A	chr18.hg19:g.21523852C>A	ENSP00000324532:p.Arg3043Ser	85.0	0.0		74.0	31.0	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Missense_Mutation	SNP	ENST00000313654.9	hg19	CCDS42419.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.432036	0.62844	.	.	ENSG00000053747	ENST00000313654;ENST00000399516;ENST00000269217	T;T;T	0.78481	-1.18;-1.18;-1.18	5.23	4.36	0.52297	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	.	.	.	.	D	0.83110	0.5183	M	0.69185	2.1	0.19945	N	0.999942	B;B;D;D	0.56968	0.251;0.299;0.978;0.962	B;B;P;P	0.54924	0.142;0.187;0.764;0.684	T	0.75031	-0.3461	9	0.52906	T	0.07	.	13.7668	0.62999	0.0:0.9266:0.0:0.0734	.	1378;1434;2987;3043	Q6VU69;B0YJ33;Q6VU67;Q16787	.;.;.;LAMA3_HUMAN	S	3043;2987;1434	ENSP00000324532:R3043S;ENSP00000382432:R2987S;ENSP00000269217:R1434S	ENSP00000269217:R1434S	R	+	1	0	LAMA3	19777850	0.290000	0.24343	0.006000	0.13384	0.927000	0.56198	1.326000	0.33735	1.442000	0.47568	0.655000	0.94253	CGT	.	.		0.473	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
RTTN	25914	hgsc.bcm.edu	37	18	67802444	67802444	+	Missense_Mutation	SNP	T	T	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr18:67802444T>C	ENST00000255674.6	-	22	3147	c.2861A>G	c.(2860-2862)gAt>gGt	p.D954G	RTTN_ENST00000437017.1_Missense_Mutation_p.D954G|RTTN_ENST00000454359.1_3'UTR	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	954					determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				CGATACTTCATCAAATAATAG	0.303																																					p.D954G		Atlas-SNP	.											.	RTTN	184	.	0			c.A2861G						.						85.0	75.0	78.0					18																	67802444		1799	4069	5868	SO:0001583	missense	25914	exon22			ACTTCATCAAATA	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.2861A>G	chr18.hg19:g.67802444T>C	ENSP00000255674:p.Asp954Gly	171.0	0.0		193.0	42.0	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	hg19	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.295111	0.81025	.	.	ENSG00000176225	ENST00000255674;ENST00000437017	T;T	0.69435	0.31;-0.4	5.22	5.22	0.72569	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.80783	0.4689	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.83150	-0.0104	10	0.72032	D	0.01	.	15.0872	0.72165	0.0:0.0:0.0:1.0	.	954	Q86VV8	RTTN_HUMAN	G	954	ENSP00000255674:D954G;ENSP00000399520:D954G	ENSP00000255674:D954G	D	-	2	0	RTTN	65953424	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.134000	0.71689	1.969000	0.57287	0.454000	0.30748	GAT	.	.		0.303	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
ABCA7	10347	hgsc.bcm.edu	37	19	1051046	1051046	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:1051046T>A	ENST00000263094.6	+	19	2910	c.2679T>A	c.(2677-2679)ttT>ttA	p.F893L	ABCA7_ENST00000433129.1_Missense_Mutation_p.F893L|ABCA7_ENST00000435683.2_Missense_Mutation_p.F755L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	893	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGTGCTGTTTGACATGTGCG	0.652																																					p.F893L		Atlas-SNP	.											.	ABCA7	174	.	0			c.T2679A						.						60.0	61.0	61.0					19																	1051046		2196	4292	6488	SO:0001583	missense	10347	exon19			GCTGTTTGACATG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.2679T>A	chr19.hg19:g.1051046T>A	ENSP00000263094:p.Phe893Leu	47.0	0.0		24.0	14.0	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	hg19	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.327090	0.81690	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.80480	-1.38;-1.38	4.07	0.231	0.15377	ATPase, AAA+ type, core (1);ABC transporter-like (2);	.	.	.	.	D	0.83138	0.5189	L	0.43701	1.375	0.30328	N	0.786934	D;D	0.89917	0.998;1.0	D;D	0.85130	0.984;0.997	T	0.76567	-0.2912	9	0.87932	D	0	.	7.5503	0.27793	0.0:0.3303:0.0:0.6697	.	755;893	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	L	893	ENSP00000263094:F893L;ENSP00000414062:F893L	ENSP00000263094:F893L	F	+	3	2	ABCA7	1002046	0.324000	0.24652	0.598000	0.28837	0.949000	0.60115	-0.399000	0.07250	-0.205000	0.10219	0.374000	0.22700	TTT	.	.		0.652	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
MATK	4145	hgsc.bcm.edu	37	19	3783884	3783884	+	Silent	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:3783884G>A	ENST00000310132.6	-	6	908	c.510C>T	c.(508-510)cgC>cgT	p.R170R	MATK_ENST00000585778.1_Silent_p.R170R|MATK_ENST00000395040.2_Silent_p.R129R|MATK_ENST00000395045.2_Silent_p.R171R	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase	170	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		GGTGCAGCACGCGGTAGTGGA	0.667																																					p.R171R		Atlas-SNP	.											.	MATK	108	.	0			c.C513T						.						57.0	48.0	51.0					19																	3783884		2203	4300	6503	SO:0001819	synonymous_variant	4145	exon6			CAGCACGCGGTAG	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679		ENST00000310132.6:c.510C>T	chr19.hg19:g.3783884G>A		80.0	0.0		59.0	39.0	NM_002378	B3KNZ9|Q9NST8	Silent	SNP	ENST00000310132.6	hg19	CCDS12114.1																																																																																			.	.		0.667	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
KEAP1	9817	hgsc.bcm.edu	37	19	10610444	10610444	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:10610444G>A	ENST00000171111.5	-	2	813	c.266C>T	c.(265-267)cCg>cTg	p.P89L	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Missense_Mutation_p.P89L	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	89	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)				breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CTGGGCGGCCGGTGCATCCTG	0.612																																					p.P89L		Atlas-SNP	.											.	KEAP1	182	.	0			c.C266T						.						95.0	72.0	80.0					19																	10610444		2203	4300	6503	SO:0001583	missense	9817	exon2			GCGGCCGGTGCAT	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.266C>T	chr19.hg19:g.10610444G>A	ENSP00000171111:p.Pro89Leu	54.0	0.0		38.0	30.0	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Missense_Mutation	SNP	ENST00000171111.5	hg19	CCDS12239.1	.	.	.	.	.	.	.	.	.	.	G	12.58	1.981897	0.34942	.	.	ENSG00000079999	ENST00000171111;ENST00000393623	T;T	0.72282	-0.64;-0.64	4.68	4.68	0.58851	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.234176	0.44097	D	0.000491	T	0.53818	0.1820	L	0.33293	1	0.41368	D	0.987472	P	0.36378	0.55	B	0.28784	0.094	T	0.56238	-0.8012	10	0.33940	T	0.23	.	10.3791	0.44101	0.0:0.0:0.8042:0.1958	.	89	Q14145	KEAP1_HUMAN	L	89	ENSP00000171111:P89L;ENSP00000377245:P89L	ENSP00000171111:P89L	P	-	2	0	KEAP1	10471444	1.000000	0.71417	0.048000	0.18961	0.137000	0.21094	4.407000	0.59754	2.162000	0.67917	0.462000	0.41574	CCG	.	.		0.612	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
F2RL3	9002	hgsc.bcm.edu	37	19	17001135	17001135	+	Silent	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:17001135G>T	ENST00000248076.3	+	2	1191	c.861G>T	c.(859-861)gtG>gtT	p.V287V		NM_003950.2	NP_003941.2	Q96RI0	PAR4_HUMAN	coagulation factor II (thrombin) receptor-like 3	287					blood coagulation (GO:0007596)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|platelet activation (GO:0030168)|platelet dense granule organization (GO:0060155)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	thrombin receptor activity (GO:0015057)			cervix(1)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						TGACCGCAGTGGTGCTGGCCT	0.706																																					p.V287V		Atlas-SNP	.											.	F2RL3	20	.	0			c.G861T						.						10.0	11.0	11.0					19																	17001135		2179	4277	6456	SO:0001819	synonymous_variant	9002	exon2			CGCAGTGGTGCTG	AF055917	CCDS12350.1	19p12	2012-08-08						"""GPCR / Class A : Protease activated receptors"""	3540	protein-coding gene	gene with protein product	"""proteinase-activated receptor-4"""	602779				9618465	Standard	XM_005260139		Approved	PAR4	uc002nfa.3	Q96RI0		ENST00000248076.3:c.861G>T	chr19.hg19:g.17001135G>T		18.0	0.0		36.0	19.0	NM_003950	O76067|Q6DK42	Silent	SNP	ENST00000248076.3	hg19	CCDS12350.1																																																																																			.	.		0.706	F2RL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462875.1		
ZNF729	100287226	hgsc.bcm.edu	37	19	22497002	22497002	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:22497002G>C	ENST00000601693.1	+	4	901	c.783G>C	c.(781-783)gaG>gaC	p.E261D	ZNF729_ENST00000357491.6_Missense_Mutation_p.E261D			A6NN14	ZN729_HUMAN	zinc finger protein 729	261					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(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						ATACTGGAGAGACACCTTTCA	0.343																																					p.E261D		Atlas-SNP	.											.	ZNF729	78	.	0			c.G783C						.																																			SO:0001583	missense	100287226	exon4			TGGAGAGACACCT		CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.783G>C	chr19.hg19:g.22497002G>C	ENSP00000469582:p.Glu261Asp	16.0	0.0		20.0	6.0	NM_001242680	M0QY45	Missense_Mutation	SNP	ENST00000601693.1	hg19	CCDS59368.1	.	.	.	.	.	.	.	.	.	.	.	9.013	0.982997	0.18889	.	.	ENSG00000196350	ENST00000357491	T	0.26810	1.71	1.2	1.2	0.21068	.	.	.	.	.	T	0.32376	0.0827	L	0.58669	1.825	.	.	.	.	.	.	.	.	.	T	0.45614	-0.9249	6	0.45353	T	0.12	.	9.25	0.37549	0.0:0.0:1.0:0.0	.	.	.	.	D	261	ENSP00000350085:E261D	ENSP00000350085:E261D	E	+	3	2	ZNF729	22288842	0.987000	0.35691	0.028000	0.17463	0.067000	0.16453	0.873000	0.28052	0.602000	0.29896	0.430000	0.28490	GAG	.	.		0.343	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
ZNF98	148198	hgsc.bcm.edu	37	19	22574550	22574550	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:22574550C>G	ENST00000357774.5	-	4	1608	c.1487G>C	c.(1486-1488)gGc>gCc	p.G496A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	496					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AAAAGCTTTGCCACATTCTTC	0.393																																					p.G496A		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,+1,2	ZNF98	230	.	0			c.G1487C						.						77.0	69.0	71.0					19																	22574550		2186	4284	6470	SO:0001583	missense	148198	exon4			GCTTTGCCACATT		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.1487G>C	chr19.hg19:g.22574550C>G	ENSP00000350418:p.Gly496Ala	257.0	0.0		330.0	85.0	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	hg19	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	12.60	1.987010	0.35036	.	.	ENSG00000197360	ENST00000357774	T	0.57595	0.39	1.26	1.26	0.21427	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.69504	0.3118	M	0.79805	2.47	0.25332	N	0.989022	D	0.69078	0.997	D	0.69824	0.966	T	0.57533	-0.7795	9	0.87932	D	0	.	9.3872	0.38349	0.0:1.0:0.0:0.0	.	496	A6NK75	ZNF98_HUMAN	A	496	ENSP00000350418:G496A	ENSP00000350418:G496A	G	-	2	0	ZNF98	22366390	0.865000	0.29922	0.024000	0.17045	0.026000	0.11368	1.422000	0.34826	0.665000	0.31066	0.289000	0.19496	GGC	.	.		0.393	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
CEACAM3	1084	hgsc.bcm.edu	37	19	42301829	42301829	+	Missense_Mutation	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:42301829A>T	ENST00000357396.3	+	2	614	c.373A>T	c.(373-375)Ata>Tta	p.I125L	CEACAM3_ENST00000344550.4_Missense_Mutation_p.I125L|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Missense_Mutation_p.I125L	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	125	Ig-like V-type.					integral component of membrane (GO:0016021)				endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						CCTACAAGTCATAAAGTCAGA	0.473																																					p.I125L		Atlas-SNP	.											.	CEACAM3	37	.	0			c.A373T						.						241.0	248.0	245.0					19																	42301829		2203	4300	6503	SO:0001583	missense	1084	exon2			CAAGTCATAAAGT	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.373A>T	chr19.hg19:g.42301829A>T	ENSP00000349971:p.Ile125Leu	99.0	0.0		63.0	38.0	NM_001815	G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	hg19	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	A	13.89	2.371809	0.42003	.	.	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.66099	-0.19;-0.19;-0.19	2.91	-2.78	0.05859	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.65048	0.2654	L	0.56199	1.76	0.09310	N	1	P;P	0.50369	0.934;0.599	P;P	0.62560	0.904;0.728	T	0.57033	-0.7880	9	0.87932	D	0	.	2.4276	0.04463	0.408:0.0:0.252:0.34	.	125;125	G5E978;P40198	.;CEAM3_HUMAN	L	125	ENSP00000349971:I125L;ENSP00000221999:I125L;ENSP00000341725:I125L	ENSP00000221999:I125L	I	+	1	0	CEACAM3	46993669	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.368000	0.02580	-0.974000	0.03550	-0.476000	0.04901	ATA	.	.		0.473	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815	
LRRC4B	94030	hgsc.bcm.edu	37	19	51021453	51021453	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:51021453G>A	ENST00000599957.1	-	3	1714	c.1517C>T	c.(1516-1518)cCg>cTg	p.P506L	LRRC4B_ENST00000389201.3_Missense_Mutation_p.P506L			Q9NT99	LRC4B_HUMAN	leucine rich repeat containing 4B	506	Gly-rich.				positive regulation of synapse assembly (GO:0051965)	cell junction (GO:0030054)|cerebellar mossy fiber (GO:0044300)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(1)|lung(11)|prostate(4)|skin(1)|urinary_tract(1)	30		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00284)|GBM - Glioblastoma multiforme(134;0.0188)		CGTCCCCCGCGGCTGCAGGGC	0.716																																					p.P506L		Atlas-SNP	.											.	LRRC4B	89	.	0			c.C1517T						.						8.0	10.0	9.0					19																	51021453		1824	3931	5755	SO:0001583	missense	94030	exon3			CCCCGCGGCTGCA	BC032460	CCDS42595.1	19q13.33	2014-01-30	2004-06-14	2004-06-16	ENSG00000131409	ENSG00000131409		"""Immunoglobulin superfamily / I-set domain containing"", ""Endogenous ligands"""	25042	protein-coding gene	gene with protein product	"""netrin-G3 ligand"""		"""leucine-rich repeats and immunoglobulin-like domains 4"""	LRIG4		11441184	Standard	NM_001080457		Approved	DKFZp761A179, HSM	uc002pss.3	Q9NT99		ENST00000599957.1:c.1517C>T	chr19.hg19:g.51021453G>A	ENSP00000471502:p.Pro506Leu	15.0	0.0		15.0	14.0	NM_001080457	Q3ZCQ4|Q58F20	Missense_Mutation	SNP	ENST00000599957.1	hg19	CCDS42595.1	.	.	.	.	.	.	.	.	.	.	G	6.564	0.472324	0.12461	.	.	ENSG00000131409	ENST00000389201	T	0.58940	0.3	3.15	3.15	0.36227	.	1.571100	0.04028	U	0.300945	T	0.31263	0.0791	N	0.01048	-1.04	0.09310	N	0.999993	B	0.25206	0.12	B	0.16289	0.015	T	0.14420	-1.0473	10	0.30854	T	0.27	.	12.1443	0.54014	0.0:0.0:1.0:0.0	.	506	Q9NT99	LRC4B_HUMAN	L	506	ENSP00000373853:P506L	ENSP00000373853:P506L	P	-	2	0	LRRC4B	55713265	0.962000	0.33011	0.988000	0.46212	0.473000	0.32948	3.486000	0.53215	1.764000	0.52075	0.462000	0.41574	CCG	.	.		0.716	LRRC4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464907.1	NM_001080457	
ZNF577	84765	hgsc.bcm.edu	37	19	52376841	52376841	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:52376841T>A	ENST00000301399.5	-	7	767	c.402A>T	c.(400-402)agA>agT	p.R134S	ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	134					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		GTTTAACACATCTATGGTATT	0.433																																					p.R134S		Atlas-SNP	.											.	ZNF577	63	.	0			c.A402T						.						118.0	115.0	116.0					19																	52376841		2203	4300	6503	SO:0001583	missense	84765	exon7			AACACATCTATGG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.402A>T	chr19.hg19:g.52376841T>A	ENSP00000301399:p.Arg134Ser	135.0	0.0		60.0	37.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	7.067	0.567571	0.13560	.	.	ENSG00000161551	ENST00000301399;ENST00000458390	T;T	0.06294	3.33;3.32	2.4	0.197	0.15164	.	.	.	.	.	T	0.03608	0.0103	N	0.22421	0.69	0.80722	D	1	B	0.16603	0.018	B	0.08055	0.003	T	0.43940	-0.9360	9	0.72032	D	0.01	.	0.8947	0.01261	0.1838:0.1249:0.2087:0.4826	.	134	Q9BSK1	ZN577_HUMAN	S	134	ENSP00000301399:R134S;ENSP00000404509:R134S	ENSP00000301399:R134S	R	-	3	2	ZNF577	57068653	0.000000	0.05858	0.129000	0.21949	0.522000	0.34438	-2.710000	0.00818	-0.029000	0.13827	0.383000	0.25322	AGA	.	.		0.433	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
ZNF577	84765	hgsc.bcm.edu	37	19	52376925	52376925	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:52376925T>A	ENST00000301399.5	-	7	683	c.318A>T	c.(316-318)aaA>aaT	p.K106N	ZNF577_ENST00000451628.2_Intron|ZNF577_ENST00000420592.1_Intron|ZNF577_ENST00000485702.1_Intron|ZNF577_ENST00000412216.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	106					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		CATCAGAATCTTTTCCTGCAT	0.363																																					p.K106N		Atlas-SNP	.											.	ZNF577	63	.	0			c.A318T						.						60.0	54.0	56.0					19																	52376925		2203	4300	6503	SO:0001583	missense	84765	exon7			AGAATCTTTTCCT	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.318A>T	chr19.hg19:g.52376925T>A	ENSP00000301399:p.Lys106Asn	93.0	0.0		49.0	33.0	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Missense_Mutation	SNP	ENST00000301399.5	hg19	CCDS12842.2	.	.	.	.	.	.	.	.	.	.	.	9.540	1.113190	0.20795	.	.	ENSG00000161551	ENST00000301399;ENST00000458390	T;T	0.07444	3.2;3.19	2.68	-0.81	0.10860	.	.	.	.	.	T	0.08492	0.0211	M	0.66439	2.03	0.18873	N	0.999982	B	0.25312	0.123	B	0.17979	0.02	T	0.32188	-0.9916	9	0.44086	T	0.13	.	3.522	0.07745	0.1756:0.4689:0.0:0.3555	.	106	Q9BSK1	ZN577_HUMAN	N	106	ENSP00000301399:K106N;ENSP00000404509:K106N	ENSP00000301399:K106N	K	-	3	2	ZNF577	57068737	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-1.363000	0.02592	-0.102000	0.12197	-0.456000	0.05471	AAA	.	.		0.363	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
PRPF31	26121	hgsc.bcm.edu	37	19	54626868	54626868	+	Missense_Mutation	SNP	T	T	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:54626868T>A	ENST00000321030.4	+	6	805	c.456T>A	c.(454-456)aaT>aaA	p.N152K	PRPF31_ENST00000498612.1_3'UTR|PRPF31_ENST00000419967.1_Missense_Mutation_p.N152K|AC012314.8_ENST00000452097.1_RNA|PRPF31_ENST00000391755.1_Missense_Mutation_p.N152K	NM_015629.3	NP_056444.3	Q8WWY3	PRP31_HUMAN	pre-mRNA processing factor 31	152					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal tri-snRNP complex assembly (GO:0000244)	Cajal body (GO:0015030)|MLL1 complex (GO:0071339)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|U2-type spliceosomal complex (GO:0005684)|U4 snRNP (GO:0005687)|U4/U6 x U5 tri-snRNP complex (GO:0046540)|U4atac snRNP (GO:0005690)	poly(A) RNA binding (GO:0044822)|ribonucleoprotein complex binding (GO:0043021)|snRNP binding (GO:0070990)			breast(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(2)|urinary_tract(3)	12	all_cancers(19;0.00681)|all_epithelial(19;0.00362)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					GCAAGAACAATGAGAACCTGC	0.617																																					p.N152K		Atlas-SNP	.											.	PRPF31	48	.	0			c.T456A						.						171.0	149.0	157.0					19																	54626868		2203	4300	6503	SO:0001583	missense	26121	exon6			GAACAATGAGAAC	AL050369	CCDS12879.1	19q13.4	2013-07-16	2013-06-10		ENSG00000105618	ENSG00000105618			15446	protein-coding gene	gene with protein product		606419	"""PRP31 pre-mRNA processing factor 31 homolog (yeast)"", ""PRP31 pre-mRNA processing factor 31 homolog (S. cerevisiae)"""	RP11		11545739	Standard	NM_015629		Approved	NY-BR-99, PRP31, hPrp31, SNRNP61	uc002qdh.2	Q8WWY3	OTTHUMG00000066040	ENST00000321030.4:c.456T>A	chr19.hg19:g.54626868T>A	ENSP00000324122:p.Asn152Lys	74.0	0.0		81.0	44.0	NM_015629	Q17RB4|Q8N7F9|Q9H271|Q9Y439	Missense_Mutation	SNP	ENST00000321030.4	hg19	CCDS12879.1	.	.	.	.	.	.	.	.	.	.	T	14.43	2.532455	0.45073	.	.	ENSG00000105618	ENST00000321030;ENST00000445811;ENST00000263436;ENST00000419967;ENST00000445124;ENST00000447810;ENST00000391755	T;T;T;T;T;T	0.75821	-0.97;-0.97;-0.97;-0.97;-0.97;-0.97	4.82	-9.38	0.00623	.	0.000000	0.85682	D	0.000000	T	0.51941	0.1704	L	0.52011	1.625	0.48975	D	0.999733	P;P	0.45283	0.855;0.577	B;B	0.32724	0.151;0.065	T	0.64114	-0.6483	10	0.22109	T	0.4	-35.0544	11.5211	0.50551	0.0:0.209:0.0932:0.6978	.	152;152	E7ESA8;Q8WWY3	.;PRP31_HUMAN	K	152	ENSP00000324122:N152K;ENSP00000395894:N152K;ENSP00000405166:N152K;ENSP00000408980:N152K;ENSP00000395089:N152K;ENSP00000375635:N152K	ENSP00000263436:N152K	N	+	3	2	PRPF31	59318680	0.003000	0.15002	0.666000	0.29783	0.995000	0.86356	-1.374000	0.02566	-1.692000	0.01428	-0.290000	0.09829	AAT	.	.		0.617	PRPF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141417.2		
NFATC2	4773	hgsc.bcm.edu	37	20	50071174	50071174	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr20:50071174C>T	ENST00000396009.3	-	6	1979	c.1760G>A	c.(1759-1761)aGc>aAc	p.S587N	NFATC2_ENST00000609507.1_Missense_Mutation_p.S368N|NFATC2_ENST00000414705.1_Missense_Mutation_p.S567N|MIR3194_ENST00000582236.1_RNA|NFATC2_ENST00000610033.1_Missense_Mutation_p.S368N|NFATC2_ENST00000609943.1_Missense_Mutation_p.S567N|NFATC2_ENST00000371564.3_Missense_Mutation_p.S587N	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	587					B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|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 negative regulation of transcription (GO:0001078)|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 transcription factor activity (GO:0003700)		EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					GACCAGGCAGCTGTCTGTGTC	0.512																																					p.S587N		Atlas-SNP	.											.	NFATC2	112	.	0			c.G1760A						.						168.0	166.0	167.0					20																	50071174		2203	4300	6503	SO:0001583	missense	4773	exon6			AGGCAGCTGTCTG	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1760G>A	chr20.hg19:g.50071174C>T	ENSP00000379330:p.Ser587Asn	74.0	0.0		120.0	71.0	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	hg19	CCDS13437.1	.	.	.	.	.	.	.	.	.	.	C	25.3	4.622635	0.87460	.	.	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000414705	D;D;D	0.84070	-1.8;-1.8;-1.8	5.9	5.9	0.94986	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.081544	0.85682	D	0.000000	D	0.89729	0.6799	L	0.54323	1.7	0.45464	D	0.998436	P;D;P;P	0.52996	0.818;0.957;0.85;0.91	P;D;P;P	0.68483	0.565;0.958;0.565;0.565	D	0.89099	0.3488	10	0.59425	D	0.04	-27.6046	20.2789	0.98501	0.0:1.0:0.0:0.0	.	567;567;587;587	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	N	587;587;567	ENSP00000360619:S587N;ENSP00000379330:S587N;ENSP00000396471:S567N	ENSP00000360619:S587N	S	-	2	0	NFATC2	49504581	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	2.901000	0.48695	2.788000	0.95919	0.650000	0.86243	AGC	.	.		0.512	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
ATP9A	10079	hgsc.bcm.edu	37	20	50292712	50292712	+	Missense_Mutation	SNP	C	C	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr20:50292712C>G	ENST00000338821.5	-	10	1099	c.835G>C	c.(835-837)Gaa>Caa	p.E279Q	ATP9A_ENST00000311637.5_Missense_Mutation_p.E143Q|ATP9A_ENST00000402822.1_Missense_Mutation_p.E158Q	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	279					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CTCCGGAGTTCTCTGCCAGTG	0.438																																					p.E279Q		Atlas-SNP	.											.	ATP9A	135	.	0			c.G835C						.						95.0	84.0	88.0					20																	50292712		2203	4300	6503	SO:0001583	missense	10079	exon10			GGAGTTCTCTGCC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.835G>C	chr20.hg19:g.50292712C>G	ENSP00000342481:p.Glu279Gln	105.0	0.0		132.0	7.0	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Missense_Mutation	SNP	ENST00000338821.5	hg19	CCDS33489.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.477373	0.84640	.	.	ENSG00000054793	ENST00000311637;ENST00000338821;ENST00000402822	T;D;T	0.88818	-1.32;-2.43;-1.32	5.61	5.61	0.85477	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.103305	0.64402	D	0.000004	D	0.93572	0.7948	M	0.61703	1.905	0.80722	D	1	B;D	0.89917	0.174;1.0	B;D	0.97110	0.071;1.0	D	0.91715	0.5384	10	0.31617	T	0.26	-23.1249	19.6283	0.95689	0.0:1.0:0.0:0.0	.	158;279	O75110-2;O75110	.;ATP9A_HUMAN	Q	143;279;158	ENSP00000309086:E143Q;ENSP00000342481:E279Q;ENSP00000385875:E158Q	ENSP00000309086:E143Q	E	-	1	0	ATP9A	49726119	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	7.429000	0.80309	2.627000	0.88993	0.655000	0.94253	GAA	.	.		0.438	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
PDXK	8566	hgsc.bcm.edu	37	21	45175644	45175644	+	Splice_Site	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr21:45175644A>T	ENST00000291565.4	+	10	1008	c.825A>T	c.(823-825)aaA>aaT	p.K275N	PDXK_ENST00000467908.1_Splice_Site_p.K235N|PDXK_ENST00000468090.1_Splice_Site_p.K247N	NM_003681.4	NP_003672.1	O00764	PDXK_HUMAN	pyridoxal (pyridoxine, vitamin B6) kinase	275					cell proliferation (GO:0008283)|pyridoxal 5'-phosphate salvage (GO:0009443)|pyridoxal phosphate biosynthetic process (GO:0042823)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|lithium ion binding (GO:0031403)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|protein homodimerization activity (GO:0042803)|pyridoxal kinase activity (GO:0008478)|pyridoxal phosphate binding (GO:0030170)|sodium ion binding (GO:0031402)|zinc ion binding (GO:0008270)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5				Colorectal(79;0.109)|READ - Rectum adenocarcinoma(84;0.161)|STAD - Stomach adenocarcinoma(101;0.18)	Pyridoxal(DB00147)|Pyridoxine(DB00165)	AGTGTGCAAAAGGTACGGCGG	0.627																																					p.K275N		Atlas-SNP	.											.	PDXK	17	.	0			c.A825T						.						114.0	87.0	96.0					21																	45175644		2203	4300	6503	SO:0001630	splice_region_variant	8566	exon10			TGCAAAAGGTACG	U89606	CCDS13699.1	21q22.3	2007-05-10			ENSG00000160209	ENSG00000160209	2.7.1.35		8819	protein-coding gene	gene with protein product		179020	"""chromosome 21 open reading frame 97"", ""chromosome 21 open reading frame 124"""	C21orf97, C21orf124		9099727	Standard	NM_003681		Approved	PNK, PKH, FLJ21324, PRED79, FLJ31940, MGC15873	uc002zdm.4	O00764	OTTHUMG00000086870	ENST00000291565.4:c.826+1A>T	chr21.hg19:g.45175644A>T		24.0	0.0		14.0	8.0	NM_003681	Q7Z2Y0|Q9BS02	Missense_Mutation	SNP	ENST00000291565.4	hg19	CCDS13699.1	.	.	.	.	.	.	.	.	.	.	A	8.357	0.832196	0.16820	.	.	ENSG00000160209	ENST00000468090;ENST00000291565;ENST00000467908	T;T;T	0.75821	-0.97;-0.97;-0.97	5.14	2.66	0.31614	Carbohydrate/purine kinase (1);	0.334600	0.33792	N	0.004547	T	0.51381	0.1671	N	0.16098	0.37	0.58432	D	0.999999	B;B	0.09022	0.002;0.002	B;B	0.12156	0.005;0.007	T	0.36504	-0.9745	10	0.33940	T	0.23	-6.6336	4.3141	0.10984	0.6952:0.0:0.1583:0.1465	.	247;275	O00764-2;O00764	.;PDXK_HUMAN	N	247;275;235	ENSP00000418359:K247N;ENSP00000291565:K275N;ENSP00000420708:K235N	ENSP00000291565:K275N	K	+	3	2	PDXK	44000072	1.000000	0.71417	0.869000	0.34112	0.166000	0.22503	1.657000	0.37366	0.814000	0.34374	0.533000	0.62120	AAA	.	.		0.627	PDXK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195636.1	NM_003681	Missense_Mutation
PCNT	5116	hgsc.bcm.edu	37	21	47856895	47856895	+	Silent	SNP	A	A	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr21:47856895A>T	ENST00000359568.5	+	40	9107	c.9000A>T	c.(8998-9000)acA>acT	p.T3000T	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	3000	Interaction with NEK2.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TTTACAGGACAGTTAATGATT	0.478																																					p.T3000T		Atlas-SNP	.											.	PCNT	283	.	0			c.A9000T						.						108.0	92.0	98.0					21																	47856895		2203	4300	6503	SO:0001819	synonymous_variant	5116	exon40			CAGGACAGTTAAT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.9000A>T	chr21.hg19:g.47856895A>T		39.0	0.0		25.0	11.0	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	hg19	CCDS33592.1																																																																																			.	.		0.478	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
RIMBP3	85376	hgsc.bcm.edu	37	22	20458090	20458090	+	Missense_Mutation	SNP	G	G	T	rs563786718	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:20458090G>T	ENST00000426804.1	-	1	3696	c.3212C>A	c.(3211-3213)aCt>aAt	p.T1071N	SCARNA17_ENST00000516762.1_RNA|SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1071	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.									breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			GGAGGACATAGTTCCCCAATA	0.657													g|||	2	0.000399361	0.0015	0.0	5008	,	,		30441	0.0		0.0	False		,,,				2504	0.0				p.T1071N		Atlas-SNP	.											.	RIMBP3	42	.	0			c.C3212A						.						65.0	85.0	78.0					22																	20458090		2115	4238	6353	SO:0001583	missense	85376	exon1			GACATAGTTCCCC	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3212C>A	chr22.hg19:g.20458090G>T	ENSP00000391564:p.Thr1071Asn	466.0	1.0		408.0	94.0	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	hg19	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	G	10.09	1.255813	0.22965	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.53640	0.61	3.56	-1.62	0.08372	Fibronectin, type III (1);	0.628193	0.15951	N	0.236738	T	0.29976	0.0750	L	0.50919	1.6	0.09310	N	1	B	0.31769	0.339	B	0.27500	0.08	T	0.13980	-1.0489	10	0.18710	T	0.47	-5.0717	3.8307	0.08873	0.213:0.0:0.464:0.323	.	977	Q9UFD9	RIM3A_HUMAN	N	977;1071	ENSP00000391564:T1071N	ENSP00000347318:T977N	T	-	2	0	RIMBP3	18838090	0.000000	0.05858	0.038000	0.18304	0.506000	0.33950	-0.020000	0.12525	0.002000	0.14630	0.398000	0.26397	ACT	.	.		0.657	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
VPREB3	29802	hgsc.bcm.edu	37	22	24096504	24096504	+	Missense_Mutation	SNP	G	G	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:24096504G>A	ENST00000248948.3	-	1	151	c.47C>T	c.(46-48)tCa>tTa	p.S16L	VPREB3_ENST00000398465.3_Missense_Mutation_p.S16L	NM_013378.2	NP_037510.1	Q9UKI3	VPRE3_HUMAN	pre-B lymphocyte 3	16						endoplasmic reticulum (GO:0005783)				large_intestine(1)|lung(1)|skin(1)	3		Medulloblastoma(6;7.87e-06)|all_neural(6;0.00334)				AGATTCACCTGACAGGAAGGT	0.597																																					p.S16L		Atlas-SNP	.											.	VPREB3	11	.	0			c.C47T						.						50.0	38.0	42.0					22																	24096504		2198	4299	6497	SO:0001583	missense	29802	exon1			TCACCTGACAGGA		CCDS13813.1	22q11.23	2013-01-11	2008-09-12		ENSG00000128218	ENSG00000128218		"""Immunoglobulin superfamily / V-set domain containing"""	12710	protein-coding gene	gene with protein product		605017				10702669, 14670953	Standard	NM_013378		Approved	8HS20	uc002zxt.3	Q9UKI3	OTTHUMG00000150738	ENST00000248948.3:c.47C>T	chr22.hg19:g.24096504G>A	ENSP00000248948:p.Ser16Leu	100.0	0.0		74.0	24.0	NM_013378	B2R587	Missense_Mutation	SNP	ENST00000248948.3	hg19	CCDS13813.1	.	.	.	.	.	.	.	.	.	.	G	8.457	0.854444	0.17106	.	.	ENSG00000128218	ENST00000398465;ENST00000248948	T;T	0.64803	-0.12;1.39	3.95	2.92	0.33932	.	1.312800	0.05641	N	0.583349	T	0.63908	0.2551	M	0.70842	2.15	0.26173	N	0.979831	B	0.19331	0.035	B	0.17433	0.018	T	0.56232	-0.8013	10	0.87932	D	0	.	9.7867	0.40681	0.0:0.2092:0.7908:0.0	.	16	Q9UKI3	VPRE3_HUMAN	L	16	ENSP00000381483:S16L;ENSP00000248948:S16L	ENSP00000248948:S16L	S	-	2	0	VPREB3	22426504	0.996000	0.38824	0.812000	0.32479	0.054000	0.15201	2.998000	0.49465	1.246000	0.43901	0.650000	0.86243	TCA	.	.		0.597	VPREB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319879.2	NM_013378	
PRR14L	253143	hgsc.bcm.edu	37	22	32112941	32112941	+	Missense_Mutation	SNP	C	C	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:32112941C>T	ENST00000327423.6	-	4	1073	c.884G>A	c.(883-885)gGg>gAg	p.G295E	PRR14L_ENST00000434485.1_Missense_Mutation_p.G295E|PRR14L_ENST00000397493.2_Missense_Mutation_p.G295E|PRR14L_ENST00000461722.1_5'UTR	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	295										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						CTCTTCCTTCCCATTGTCCAC	0.398																																					p.G295E		Atlas-SNP	.											.	PRR14L	198	.	0			c.G884A						.						324.0	254.0	275.0					22																	32112941		692	1591	2283	SO:0001583	missense	253143	exon4			TCCTTCCCATTGT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.884G>A	chr22.hg19:g.32112941C>T	ENSP00000331845:p.Gly295Glu	201.0	0.0		181.0	39.0	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	hg19	CCDS13900.2	.	.	.	.	.	.	.	.	.	.	C	11.65	1.702135	0.30232	.	.	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.10288	2.89;2.91;2.89	4.56	3.54	0.40534	.	0.522514	0.17769	N	0.162655	T	0.12220	0.0297	L	0.53249	1.67	0.25093	N	0.990844	B;B;B	0.31680	0.221;0.221;0.335	B;B;B	0.34931	0.126;0.126;0.192	T	0.13495	-1.0507	10	0.52906	T	0.07	-3.8075	8.1195	0.30963	0.0:0.7544:0.1582:0.0875	.	295;295;295	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	E	295	ENSP00000380630:G295E;ENSP00000331845:G295E;ENSP00000388314:G295E	ENSP00000331845:G295E	G	-	2	0	PRR14L	30442941	0.000000	0.05858	0.749000	0.31150	0.774000	0.43823	-0.054000	0.11826	1.284000	0.44531	0.650000	0.86243	GGG	.	.		0.398	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
CSF2RB	1439	hgsc.bcm.edu	37	22	37334154	37334154	+	Missense_Mutation	SNP	G	G	T	rs373820480		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:37334154G>T	ENST00000403662.3	+	14	2526	c.2304G>T	c.(2302-2304)gaG>gaT	p.E768D	CSF2RB_ENST00000406230.1_Missense_Mutation_p.E774D|CSF2RB_ENST00000262825.5_Missense_Mutation_p.E774D|CSF2RB_ENST00000536485.1_Missense_Mutation_p.E715D			P32927	IL3RB_HUMAN	colony stimulating factor 2 receptor, beta, low-affinity (granulocyte-macrophage)	768					cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)|interleukin-5-mediated signaling pathway (GO:0038043)|respiratory gaseous exchange (GO:0007585)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	granulocyte macrophage colony-stimulating factor receptor complex (GO:0030526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(18)|ovary(3)|pancreas(1)|skin(5)|upper_aerodigestive_tract(2)	42					Sargramostim(DB00020)	GCTATGTGGAGCTCCCTCCAA	0.652																																					p.E768D		Atlas-SNP	.											.	CSF2RB	104	.	0			c.G2304T						.						44.0	42.0	43.0					22																	37334154		2203	4300	6503	SO:0001583	missense	1439	exon14			TGTGGAGCTCCCT	M59941	CCDS13936.1	22q12.3	2014-09-09			ENSG00000100368	ENSG00000100368		"""CD molecules"", ""Fibronectin type III domain containing"""	2436	protein-coding gene	gene with protein product		138981		IL3RB		1833064, 1424804	Standard	NM_000395		Approved	IL5RB, CD131	uc003aqa.4	P32927	OTTHUMG00000150546	ENST00000403662.3:c.2304G>T	chr22.hg19:g.37334154G>T	ENSP00000384053:p.Glu768Asp	33.0	0.0		36.0	16.0	NM_000395	Q5JZI1|Q6ICE0	Missense_Mutation	SNP	ENST00000403662.3	hg19	CCDS13936.1	.	.	.	.	.	.	.	.	.	.	G	10.79	1.449283	0.26074	.	.	ENSG00000100368	ENST00000403662;ENST00000539104;ENST00000262825;ENST00000406230;ENST00000536485	D;D;D;D	0.93426	-2.7;-3.21;-3.21;-3.22	5.5	-0.294	0.12831	.	0.639614	0.13672	N	0.370808	D	0.83175	0.5197	N	0.21142	0.635	0.24286	N	0.995187	B;B	0.21606	0.058;0.034	B;B	0.16722	0.016;0.007	T	0.68762	-0.5323	10	0.25106	T	0.35	-7.4029	1.9057	0.03276	0.1563:0.1337:0.4347:0.2753	.	774;768	P32927-2;P32927	.;IL3RB_HUMAN	D	768;768;774;774;715	ENSP00000384053:E768D;ENSP00000262825:E774D;ENSP00000385271:E774D;ENSP00000440003:E715D	ENSP00000262825:E774D	E	+	3	2	CSF2RB	35664100	0.792000	0.28813	0.987000	0.45799	0.472000	0.32918	0.021000	0.13489	0.037000	0.15575	0.555000	0.69702	GAG	.	.		0.652	CSF2RB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318854.1	NM_000395	
GTPBP1	9567	hgsc.bcm.edu	37	22	39125539	39125539	+	Missense_Mutation	SNP	G	G	T			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:39125539G>T	ENST00000216044.5	+	11	2022	c.1789G>T	c.(1789-1791)Ggc>Tgc	p.G597C		NM_004286.4	NP_004277.2	O00178	GTPB1_HUMAN	GTP binding protein 1	597					GTP catabolic process (GO:0006184)|immune response (GO:0006955)|positive regulation of mRNA catabolic process (GO:0061014)|signal transduction (GO:0007165)	cytoplasmic exosome (RNase complex) (GO:0000177)|cytosol (GO:0005829)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	18	Melanoma(58;0.04)					GACGAAAAAGGGCCCCCTGAC	0.612																																					p.G597C		Atlas-SNP	.											.	GTPBP1	51	.	0			c.G1789T						.						37.0	33.0	34.0					22																	39125539		2203	4300	6503	SO:0001583	missense	9567	exon11			AAAAAGGGCCCCC	U87964	CCDS13977.2	22q13.1	2008-07-01			ENSG00000100226	ENSG00000100226			4669	protein-coding gene	gene with protein product		602245				9070279	Standard	XM_005261857		Approved	GP-1, HSPC018	uc003awg.3	O00178	OTTHUMG00000151002	ENST00000216044.5:c.1789G>T	chr22.hg19:g.39125539G>T	ENSP00000216044:p.Gly597Cys	76.0	0.0		70.0	18.0	NM_004286	Q6IC67	Missense_Mutation	SNP	ENST00000216044.5	hg19	CCDS13977.2	.	.	.	.	.	.	.	.	.	.	G	20.5	3.997452	0.74818	.	.	ENSG00000100226	ENST00000216044;ENST00000458073	T	0.31769	1.48	5.26	5.26	0.73747	.	0.149182	0.46145	D	0.000315	T	0.28001	0.0690	L	0.44542	1.39	0.49299	D	0.999771	P	0.46020	0.871	B	0.40702	0.338	T	0.03898	-1.0994	10	0.66056	D	0.02	.	12.3971	0.55391	0.0761:0.0:0.9239:0.0	.	597	O00178	GTPB1_HUMAN	C	597;175	ENSP00000216044:G597C	ENSP00000216044:G597C	G	+	1	0	GTPBP1	37455485	1.000000	0.71417	0.998000	0.56505	0.931000	0.56810	5.428000	0.66489	2.731000	0.93534	0.650000	0.86243	GGC	.	.		0.612	GTPBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075532.1	NM_004286	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24383090	24383090	+	IGR	SNP	C	C	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:24383090C>A								AC004552.1 (16067 upstream) : PDK3 (100247 downstream)																							CAAGGGCAGGCCTTCCCTGCT	0.617																																					p.A738D		Atlas-SNP	.											.	.	.	.	0			c.C2213A						.						32.0	33.0	33.0					X																	24383090		1568	3582	5150	SO:0001628	intergenic_variant	100130302	exon1			GGCAGGCCTTCCC																													chrX.hg19:g.24383090C>A		113.0	0.0		124.0	96.0	NM_001136234		Missense_Mutation	SNP		hg19																																																																																				.	.	0	0.617								
FAM47A	158724	hgsc.bcm.edu	37	X	34149528	34149528	+	Missense_Mutation	SNP	G	G	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:34149528G>C	ENST00000346193.3	-	1	919	c.868C>G	c.(868-870)Ccc>Gcc	p.P290A		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	290										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						GGCTCTGTGGGTTCGTCAGTT	0.572																																					p.P290A		Atlas-SNP	.											.	FAM47A	249	.	0			c.C868G						.						25.0	26.0	26.0					X																	34149528		2202	4300	6502	SO:0001583	missense	158724	exon1			CTGTGGGTTCGTC	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.868C>G	chrX.hg19:g.34149528G>C	ENSP00000345029:p.Pro290Ala	70.0	0.0		71.0	56.0	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	hg19	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	g	2.132	-0.398926	0.04865	.	.	ENSG00000185448	ENST00000346193	T	0.21734	1.99	0.13	0.13	0.14746	.	.	.	.	.	T	0.17066	0.0410	L	0.55990	1.75	0.09310	N	1	B	0.26445	0.149	B	0.14578	0.011	T	0.19910	-1.0291	8	0.46703	T	0.11	.	.	.	.	.	290	Q5JRC9	FA47A_HUMAN	A	290	ENSP00000345029:P290A	ENSP00000345029:P290A	P	-	1	0	FAM47A	34059449	0.250000	0.23951	0.019000	0.16419	0.019000	0.09904	0.136000	0.15974	0.171000	0.19730	0.173000	0.16961	CCC	.	.		0.572	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
POF1B	79983	hgsc.bcm.edu	37	X	84561303	84561303	+	Silent	SNP	A	A	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:84561303A>G	ENST00000262753.4	-	12	1346	c.1201T>C	c.(1201-1203)Ttg>Ctg	p.L401L	POF1B_ENST00000373145.3_Silent_p.L401L	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	401						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						TTTTCTTCCAATGCCTGGCAT	0.358																																					p.L401L		Atlas-SNP	.											.	POF1B	77	.	0			c.T1201C						.						175.0	137.0	150.0					X																	84561303		2203	4300	6503	SO:0001819	synonymous_variant	79983	exon12			CTTCCAATGCCTG	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.1201T>C	chrX.hg19:g.84561303A>G		113.0	0.0		87.0	67.0	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Silent	SNP	ENST00000262753.4	hg19	CCDS14452.1																																																																																			.	.		0.358	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
TENM1	10178	hgsc.bcm.edu	37	X	123540198	123540198	+	Silent	SNP	C	C	T	rs148101479		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chrX:123540198C>T	ENST00000371130.3	-	25	5166	c.5103G>A	c.(5101-5103)acG>acA	p.T1701T	TENM1_ENST00000422452.2_Silent_p.T1708T|STAG2_ENST00000469481.1_Intron	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	1701					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TACTAGTTGCCGTCAAGTTGG	0.438																																					p.T1708T		Atlas-SNP	.											.	.	.	.	0			c.G5124A						.	C	,,	2,3833		0,2,1630,571	201.0	181.0	188.0		5124,5121,5103	-1.6	1.0	X	dbSNP_134	188	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	0,2,4058,2443	TT,TC,CC,C		0.0,0.0522,0.0189	,,	1708/2733,1707/2732,1701/2726	123540198	2,10561	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon26			AGTTGCCGTCAAG	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.5103G>A	chrX.hg19:g.123540198C>T		83.0	0.0		76.0	59.0	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	hg19	CCDS14609.1																																																																																			.	C|1.000;T|0.000		0.438	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
RGMB	285704	hgsc.bcm.edu	37	5	98109681	98109682	+	5'UTR	INS	-	-	C			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:98109681_98109682insC	ENST00000513185.1	+	0	343_344				RGMB-AS1_ENST00000501938.2_RNA|RGMB_ENST00000308234.7_Frame_Shift_Ins_p.P11fs|RGMB-AS1_ENST00000505677.1_RNA|RGMB_ENST00000504776.1_3'UTR|RGMB-AS1_ENST00000498871.2_RNA|RGMB-AS1_ENST00000515003.1_RNA|RGMB-AS1_ENST00000505362.1_RNA			Q6NW40	RGMB_HUMAN	repulsive guidance molecule family member b						axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell adhesion (GO:0007155)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)	identical protein binding (GO:0042802)			haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	10		all_cancers(142;2.76e-08)|all_epithelial(76;2.98e-11)|all_lung(232;0.000485)|Lung NSC(167;0.000693)|Prostate(80;0.000986)|Ovarian(225;0.024)|Colorectal(57;0.117)		COAD - Colon adenocarcinoma(37;0.0587)		AGCGAAGCGCGCCCCCCGGCCC	0.752																																					p.A10fs		Atlas-Indel,Pindel	.											.	RGMB	29	.	0			c.30_31insC						.																																			SO:0001623	5_prime_UTR_variant	285704	exon3			.	AK074887	CCDS47251.1	5q21.1	2013-11-06	2013-11-06		ENSG00000174136	ENSG00000174136			26896	protein-coding gene	gene with protein product		612687	"""RGM domain family, member B"""			19324014	Standard	NM_001012761		Approved	FLJ90406, DRAGON	uc003knc.3	Q6NW40	OTTHUMG00000162745	ENST00000513185.1:c.-93->C	chr5.hg19:g.98109687_98109687dupC		9.0	0.0		29.0	15.0	NM_001012761	D6R9A0|Q8NC92	Frame_Shift_Ins	INS	ENST00000513185.1	hg19																																																																																				.	.		0.752	RGMB-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000370308.1	NM_173670	
SLC9A4	389015	hgsc.bcm.edu	37	2	103121886	103121912	+	In_Frame_Del	DEL	TCATCTGCTTCACCCTGGCCTTCTGCC	TCATCTGCTTCACCCTGGCCTTCTGCC	-	rs377204289		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TCATCTGCTTCACCCTGGCCTTCTGCC	TCATCTGCTTCACCCTGGCCTTCTGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:103121886_103121912delTCATCTGCTTCACCCTGGCCTTCTGCC	ENST00000295269.4	+	4	1611_1637	c.1154_1180delTCATCTGCTTCACCCTGGCCTTCTGCC	c.(1153-1182)ttcatctgcttcaccctggccttctgccaa>taa	p.385_394FICFTLAFCQ>*		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	385					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						AACTGGGCCTTCATCTGCTTCACCCTGGCCTTCTGCCAAATCTGGAG	0.511																																					p.385_393del		Atlas-INDEL	.											.	SLC9A4	115	.	0			c.1153_1179del						.																																			SO:0001651	inframe_deletion	389015	exon4			.		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1154_1180delTCATCTGCTTCACCCTGGCCTTCTGCC	chr2.hg19:g.103121886_103121912delTCATCTGCTTCACCCTGGCCTTCTGCC	ENSP00000295269:p.Phe385_Gln394delins*	47.0	0.0		38.0	10.0	NM_001011552	Q69YK0	In_Frame_Del	DEL	ENST00000295269.4	hg19	CCDS33264.1																																																																																			.	.		0.511	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
PPIL2	23759	hgsc.bcm.edu	37	22	22025285	22025298	+	Splice_Site	DEL	GTCTCTCTCTGCAG	GTCTCTCTCTGCAG	-	rs370871572|rs202229100		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	GTCTCTCTCTGCAG	GTCTCTCTCTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:22025285_22025298delGTCTCTCTCTGCAG	ENST00000335025.8	+	4	219_232	c.128_141delGTCTCTCTCTGCAG	c.(127-141)agtctctctctgcag>a	p.SLSLQ43fs	PPIL2_ENST00000406385.1_Splice_Site_p.SLSLQ43fs|PPIL2_ENST00000398831.3_Splice_Site_p.SLSLQ43fs|PPIL2_ENST00000412327.1_Splice_Site_p.SLSLQ43fs|PPIL2_ENST00000456792.2_Intron|PPIL2_ENST00000492445.2_Splice_Site_p.SLSLQ43fs					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					TCCTTTTTCAGTCTCTCTCTGCAGCCCTTTGTCT	0.505																																					p.43_47del		Atlas-INDEL	.											.	PPIL2	38	.	0			c.129_140del						.																																			SO:0001630	splice_region_variant	23759	exon4			.		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.129-1GTCTCTCTCTGCAG>-	chr22.hg19:g.22025285_22025298delGTCTCTCTCTGCAG		206.0	0.0		139.0	10.0	NM_014337		In_Frame_Del	DEL	ENST00000335025.8	hg19	CCDS13793.1																																																																																			.	.		0.505	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		Frame_Shift_Del
RABL6	55684	hgsc.bcm.edu	37	9	139722950	139722951	+	Frame_Shift_Ins	INS	-	-	AG			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr9:139722950_139722951insAG	ENST00000311502.7	+	4	554_555	c.318_319insAG	c.(319-321)tgcfs	p.C107fs	RABL6_ENST00000371663.4_Frame_Shift_Ins_p.C107fs|RP11-216L13.18_ENST00000471502.1_RNA|RABL6_ENST00000371675.3_5'UTR|RABL6_ENST00000466096.1_3'UTR|RABL6_ENST00000371671.4_Frame_Shift_Ins_p.C107fs|RABL6_ENST00000357466.2_Frame_Shift_Ins_p.C107fs|RABL6_ENST00000432842.2_Frame_Shift_Ins_p.C69fs|MIR4292_ENST00000585012.1_RNA			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	107	Small GTPase-like.				small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										AATAAGGAAAATGCAAAAAGCG	0.574																																					p.K106fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.318_319insAG						.																																			SO:0001589	frameshift_variant	55684	exon4			.	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	Exception_encountered	chr9.hg19:g.139722950_139722951insAG	ENSP00000311134:p.Cys107fs	27.0	0.0		69.0	46.0	NM_001173989	A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Frame_Shift_Ins	INS	ENST00000311502.7	hg19	CCDS48058.1																																																																																			.	.		0.574	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718	
TRIM39	56658	hgsc.bcm.edu	37	6	30298592	30298593	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:30298592_30298593delAG	ENST00000396547.1	+	3	648_649	c.488_489delAG	c.(487-489)cagfs	p.Q163fs	TRIM39_ENST00000376659.5_Frame_Shift_Del_p.Q163fs|TRIM39-RPP21_ENST00000513556.1_Frame_Shift_Del_p.Q75fs|TRIM39_ENST00000376656.4_Frame_Shift_Del_p.Q163fs|TRIM39_ENST00000396551.3_Frame_Shift_Del_p.Q163fs|TRIM39_ENST00000396548.1_Frame_Shift_Del_p.Q163fs|TRIM39_ENST00000540416.1_Frame_Shift_Del_p.Q163fs			Q9HCM9	TRI39_HUMAN	tripartite motif containing 39	163					apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of apoptotic signaling pathway (GO:2001235)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			ovary(3)	3						CCCCTGGAACAGAAGCTGCAGG	0.535																																					p.163_163del		Atlas-Indel,Pindel	.											.	TRIM39	56	.	0			c.487_488del						.																																			SO:0001589	frameshift_variant	56658	exon4			.	BC034985	CCDS34377.1, CCDS34378.1	6p22.1	2013-01-09	2011-01-25	2002-06-07	ENSG00000204599	ENSG00000204599		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10065	protein-coding gene	gene with protein product		605700	"""ring finger protein 23"", ""tripartite motif-containing 39"""	RNF23		11006080	Standard	NM_021253		Approved			Q9HCM9	OTTHUMG00000031066	ENST00000396547.1:c.488_489delAG	chr6.hg19:g.30298592_30298593delAG	ENSP00000379796:p.Gln163fs	72.0	0.0		68.0	21.0	NM_172016	Q5STG3|Q5STG4|Q76BL3|Q8IYT9|Q96IB6	Frame_Shift_Del	DEL	ENST00000396547.1	hg19	CCDS34377.1																																																																																			.	.		0.535	TRIM39-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076086.2	NM_172016	
HPR	3250	hgsc.bcm.edu	37	16	72108240	72108240	+	Frame_Shift_Del	DEL	G	G	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr16:72108240delG	ENST00000540303.2	+	3	181	c.149delG	c.(148-150)cgcfs	p.R50fs	HPR_ENST00000228226.8_Frame_Shift_Del_p.R87fs|HPR_ENST00000561690.1_Frame_Shift_Del_p.R50fs|HPR_ENST00000356967.5_Frame_Shift_Del_p.R50fs	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	50	Sushi.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CACTTGTTTCGCTACCAGTGT	0.483																																					p.R50fs		Atlas-Indel,Pindel	.											HPR,NS,carcinoma,0,1	HPR	43	.	0			c.148delC						.						216.0	133.0	160.0					16																	72108240		1966	4141	6107	SO:0001589	frameshift_variant	3250	exon3			.	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.149delG	chr16.hg19:g.72108240delG	ENSP00000441828:p.Arg50fs	346.0	0.0		345.0	106.0	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Frame_Shift_Del	DEL	ENST00000540303.2	hg19	CCDS42193.1																																																																																			.	.		0.483	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995	
CYTIP	9595	hgsc.bcm.edu	37	2	158283867	158283867	+	Frame_Shift_Del	DEL	A	A	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:158283867delA	ENST00000264192.3	-	6	663	c.542delT	c.(541-543)ttafs	p.L181fs	CYTIP_ENST00000540637.1_Frame_Shift_Del_p.L75fs	NM_004288.4	NP_004279.3	O60759	CYTIP_HUMAN	cytohesin 1 interacting protein	181	Interaction with CYTH1.				regulation of cell adhesion (GO:0030155)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	15						AATTACCTTTAAAACCTGCAG	0.353																																					p.L181fs		Atlas-Indel,Pindel	.											.	CYTIP	45	.	0			c.543delA						.						59.0	58.0	58.0					2																	158283867		2201	4297	6498	SO:0001589	frameshift_variant	9595	exon6			.	L06633	CCDS2204.1	2q11.2	2011-09-08	2008-08-14	2008-08-19	ENSG00000115165	ENSG00000115165			9506	protein-coding gene	gene with protein product	"""cytohesin binding protein HE"", ""cytohesin binder and regulator"""	604448	"""pleckstrin homology, Sec7 and coiled-coil domains, binding protein"""	PSCDBP		18926288, 10343115, 11867758, 20530790, 21562043	Standard	NM_004288		Approved	B3-1, HE, CYBR, CASP, CYTHIP	uc002tzj.1	O60759	OTTHUMG00000154551	ENST00000264192.3:c.542delT	chr2.hg19:g.158283867delA	ENSP00000264192:p.Leu181fs	91.0	0.0		96.0	38.0	NM_004288	B4DWH9|Q15630|Q8NE32	Frame_Shift_Del	DEL	ENST00000264192.3	hg19	CCDS2204.1																																																																																			.	.		0.353	CYTIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254926.1	NM_004288	
XIRP2	129446	hgsc.bcm.edu	37	2	168105997	168105997	+	Frame_Shift_Del	DEL	C	C	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:168105997delC	ENST00000409195.1	+	9	8184	c.8095delC	c.(8095-8097)cccfs	p.P2699fs	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.P2477fs|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.P2699fs|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2524					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GTTGCACTTGCCCCAAAGCAA	0.368																																					p.L2698fs		Atlas-Indel,Pindel	.											.	XIRP2	914	.	0			c.8094delG						.						93.0	91.0	92.0					2																	168105997		1853	4088	5941	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8095delC	chr2.hg19:g.168105997delC	ENSP00000386840:p.Pro2699fs	135.0	0.0		127.0	43.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.368	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
C3	718	hgsc.bcm.edu	37	19	6678293	6678293	+	Frame_Shift_Del	DEL	C	C	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:6678293delC	ENST00000245907.6	-	40	4812	c.4720delG	c.(4720-4722)gatfs	p.D1574fs	C3_ENST00000599668.1_5'UTR	NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	1574	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	TGCACCTCATCCGAGCCTGGA	0.597																																					p.D1574fs		Atlas-Indel,Pindel	.											.	C3	192	.	0			c.4721delA						.						83.0	65.0	71.0					19																	6678293		2203	4300	6503	SO:0001589	frameshift_variant	718	exon40			.	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.4720delG	chr19.hg19:g.6678293delC	ENSP00000245907:p.Asp1574fs	93.0	0.0		51.0	29.0	NM_000064	A7E236	Frame_Shift_Del	DEL	ENST00000245907.6	hg19	CCDS32883.1																																																																																			.	.		0.597	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50656529	50656539	+	Frame_Shift_Del	DEL	TTCTCCGTGAG	TTCTCCGTGAG	-	rs35231253	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TTCTCCGTGAG	TTCTCCGTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:50656529_50656539delTTCTCCGTGAG	ENST00000248846.5	-	24	5280_5290	c.5176_5186delCTCACGGAGAA	c.(5176-5187)ctcacggagaagfs	p.LTEK1726fs	TUBGCP6_ENST00000491449.1_5'UTR|TUBGCP6_ENST00000439308.2_3'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1726					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GGGCGCCGCCTTCTCCGTGAGCAGGCCCCTG	0.687																																					p.1726_1729del		Atlas-INDEL	.											.	TUBGCP6	132	.	0			c.5177_5187del						.																																			SO:0001589	frameshift_variant	85378	exon24			.	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.5176_5186delCTCACGGAGAA	chr22.hg19:g.50656529_50656539delTTCTCCGTGAG	ENSP00000248846:p.Leu1726fs	37.0	0.0		34.0	12.0	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Frame_Shift_Del	DEL	ENST00000248846.5	hg19	CCDS14087.1																																																																																			.	.		0.687	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
EFR3B	22979	hgsc.bcm.edu	37	2	25351059	25351060	+	Frame_Shift_Ins	INS	-	-	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:25351059_25351060insG	ENST00000403714.3	+	6	676_677	c.493_494insG	c.(493-495)atgfs	p.M165fs	EFR3B_ENST00000401432.3_Frame_Shift_Ins_p.M165fs|EFR3B_ENST00000402191.1_Frame_Shift_Ins_p.M130fs|EFR3B_ENST00000405108.1_Frame_Shift_Ins_p.M17fs	NM_014971.1	NP_055786.1	Q9Y2G0	EFR3B_HUMAN	EFR3 homolog B (S. cerevisiae)	165										endometrium(1)	1						CAGAATTCGAATGTCAGGCATC	0.515																																					p.M165fs		Atlas-Indel,Pindel	.											.	EFR3B	29	.	0			c.493_494insG						.																																			SO:0001589	frameshift_variant	22979	exon6			.	AB023170	CCDS46231.1	2p24.1	2008-02-05	2007-11-14	2007-11-14	ENSG00000084710	ENSG00000084710			29155	protein-coding gene	gene with protein product			"""KIAA0953"""	KIAA0953		10231032	Standard	NM_014971		Approved	FLJ37871	uc010eyh.3	Q9Y2G0	OTTHUMG00000151988	Exception_encountered	chr2.hg19:g.25351059_25351060insG	ENSP00000384081:p.Met165fs	64.0	0.0		63.0	20.0	NM_014971	B7WPL8|Q86XU6	Frame_Shift_Ins	INS	ENST00000403714.3	hg19	CCDS46231.1																																																																																			.	.		0.515	EFR3B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324808.1	NM_014971	
DNAH7	56171	hgsc.bcm.edu	37	2	196771386	196771387	+	Frame_Shift_Ins	INS	-	-	A			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:196771386_196771387insA	ENST00000312428.6	-	27	4431_4432	c.4331_4332insT	c.(4330-4332)ctgfs	p.L1444fs		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1444	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TCCATACCTTCAGGTTATCTGG	0.391																																					p.L1444fs		Atlas-Indel,Pindel	.											.	DNAH7	512	.	0			c.4332_4333insT						.																																			SO:0001589	frameshift_variant	56171	exon27			.	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.4332dupT	chr2.hg19:g.196771387_196771387dupA	ENSP00000311273:p.Leu1444fs	326.0	0.0		303.0	107.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Frame_Shift_Ins	INS	ENST00000312428.6	hg19	CCDS42794.1																																																																																			.	.		0.391	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
ANK1	286	hgsc.bcm.edu	37	8	41574509	41574514	+	In_Frame_Del	DEL	AATATT	AATATT	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	AATATT	AATATT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:41574509_41574514delAATATT	ENST00000347528.4	-	13	1444_1449	c.1361_1366delAATATT	c.(1360-1368)aaatattta>ata	p.454_456KYL>I	ANK1_ENST00000396942.1_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000352337.4_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000396945.1_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000289734.7_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000379758.2_In_Frame_Del_p.454_456KYL>I|ANK1_ENST00000265709.8_In_Frame_Del_p.487_489KYL>I	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	454	89 kDa domain.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			TTCTGGAGTAAATATTTGGCCACTTC	0.481																																					p.487_489del		Atlas-Indel,Pindel	.											.	ANK1	497	.	0			c.1461_1466del						.																																			SO:0001651	inframe_deletion	286	exon13			.	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.1361_1366delAATATT	chr8.hg19:g.41574509_41574514delAATATT	ENSP00000339620:p.Lys454_Leu456delinsIle	237.0	0.0		217.0	49.0	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	In_Frame_Del	DEL	ENST00000347528.4	hg19	CCDS6119.1																																																																																			.	.		0.481	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
XIRP2	129446	hgsc.bcm.edu	37	2	168102891	168102891	+	Frame_Shift_Del	DEL	A	A	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:168102891delA	ENST00000409195.1	+	9	5078	c.4989delA	c.(4987-4989)atafs	p.I1663fs	XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409273.1_Frame_Shift_Del_p.I1441fs|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Frame_Shift_Del_p.I1663fs|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	1488					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						AACAAGCAATAAAAAACCTGT	0.313																																					p.I1663fs		Atlas-Indel,Pindel	.											.	XIRP2	914	.	0			c.4988delT						.						67.0	63.0	64.0					2																	168102891		1856	4084	5940	SO:0001589	frameshift_variant	129446	exon9			.	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.4989delA	chr2.hg19:g.168102891delA	ENSP00000386840:p.Ile1663fs	207.0	0.0		211.0	95.0	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Frame_Shift_Del	DEL	ENST00000409195.1	hg19	CCDS42769.1																																																																																			.	.		0.313	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
IRX1	79192	hgsc.bcm.edu	37	5	3596419	3596419	+	Frame_Shift_Del	DEL	C	C	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr5:3596419delC	ENST00000302006.3	+	1	252	c.200delC	c.(199-201)gcgfs	p.A67fs	CTD-2012M11.3_ENST00000559410.1_RNA	NM_024337.3	NP_077313.3	P78414	IRX1_HUMAN	iroquois homeobox 1	67					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			biliary_tract(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(18)|ovary(2)|pancreas(1)|prostate(5)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	43						TACGCGGCGGCGGGGCCGTAC	0.776																																					p.A67fs		Atlas-INDEL	.											.	IRX1	106	.	0			c.199delG						.						6.0	7.0	7.0					5																	3596419		1838	3768	5606	SO:0001589	frameshift_variant	79192	exon1			.	U90307	CCDS34132.1	5p15.33	2011-12-16	2007-07-13		ENSG00000170549	ENSG00000170549		"""Homeoboxes / TALE class"""	14358	protein-coding gene	gene with protein product		606197					Standard	NM_024337		Approved	IRX-5	uc003jde.3	P78414	OTTHUMG00000161632	ENST00000302006.3:c.200delC	chr5.hg19:g.3596419delC	ENSP00000305244:p.Ala67fs	28.0	0.0		37.0	13.0	NM_024337	Q7Z2F8|Q8N312	Frame_Shift_Del	DEL	ENST00000302006.3	hg19	CCDS34132.1																																																																																			.	.		0.776	IRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365546.1	NM_024337	
KMT2C	58508	hgsc.bcm.edu	37	7	151927092	151927092	+	Frame_Shift_Del	DEL	G	G	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:151927092delG	ENST00000262189.6	-	18	3110	c.2892delC	c.(2890-2892)ggcfs	p.G964fs	KMT2C_ENST00000355193.2_Frame_Shift_Del_p.G964fs	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	964					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GGCCAAAACTGCCACAAACTA	0.348																																					p.S965fs		Atlas-INDEL	.											.	MLL3	1564	.	0			c.2893delA						.						62.0	51.0	55.0					7																	151927092		2200	4278	6478	SO:0001589	frameshift_variant	58508	exon18			.	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.2892delC	chr7.hg19:g.151927092delG	ENSP00000262189:p.Gly964fs	730.0	0.0		565.0	44.0	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Frame_Shift_Del	DEL	ENST00000262189.6	hg19	CCDS5931.1																																																																																			.	.		0.348	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
APC2	10297	hgsc.bcm.edu	37	19	1468353	1468354	+	In_Frame_Ins	INS	-	-	AGT			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr19:1468353_1468354insAGT	ENST00000535453.1	+	14	6766_6767	c.5053_5054insAGT	c.(5053-5055)gag>gAGTag	p.1685_1686ins*	APC2_ENST00000238483.4_In_Frame_Ins_p.1411_1412ins*|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000233607.2_In_Frame_Ins_p.1685_1686ins*			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGATAGCGTGGAGTGGCGCGCC	0.718																																					p.E1685delinsEX		Atlas-Indel,Pindel	.											.	APC2	50	.	0			c.5053_5054insAGT						.																																			SO:0001652	inframe_insertion	10297	exon15			.		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5054_5056dupAGT	chr19.hg19:g.1468354_1468356dupAGT	ENSP00000442954:p.Trp1686*	50.0	0.0		36.0	24.0	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	In_Frame_Ins	INS	ENST00000535453.1	hg19	CCDS12068.1																																																																																			.	.		0.718	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	
LMBR1	64327	hgsc.bcm.edu	37	7	156619307	156619308	+	Frame_Shift_Ins	INS	-	-	G			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr7:156619307_156619308insG	ENST00000353442.5	-	4	546_547	c.310_311insC	c.(310-312)ctgfs	p.L104fs	LMBR1_ENST00000540390.1_Frame_Shift_Ins_p.L83fs|LMBR1_ENST00000354505.4_Frame_Shift_Ins_p.L104fs	NM_022458.3	NP_071903.2	Q8WVP7	LMBR1_HUMAN	limb development membrane protein 1	104					embryonic digit morphogenesis (GO:0042733)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	18	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00231)	UCEC - Uterine corpus endometrioid carcinoma (81;0.208)		ACCATGAATCAGGGAGCCATTT	0.322																																					p.L104fs		Atlas-Indel,Pindel	.											.	LMBR1	35	.	0			c.311_312insC						.																																			SO:0001589	frameshift_variant	64327	exon4			.	AF107454	CCDS5945.1	7q36.3	2013-08-05	2013-08-05	2005-07-25	ENSG00000105983	ENSG00000105983			13243	protein-coding gene	gene with protein product		605522	"""chromosome 7 open reading frame 2"", ""limb region 1 homolog (mouse)"""	C7orf2		10329000, 11090342	Standard	NM_022458		Approved	ACHP, FLJ11665, ZRS	uc003wmw.4	Q8WVP7	OTTHUMG00000151510	ENST00000353442.5:c.311dupC	chr7.hg19:g.156619310_156619310dupG	ENSP00000326604:p.Leu104fs	60.0	0.0		42.0	30.0	NM_022458	A4D242|Q8N3E3|Q96QZ5|Q9H5N0|Q9HAG9|Q9UDN5|Q9Y6U2	Frame_Shift_Ins	INS	ENST00000353442.5	hg19	CCDS5945.1																																																																																			.	.		0.322	LMBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347939.3	NM_022458	
CTC-497E21.3	0	hgsc.bcm.edu	37	11	13031752	13031752	+	lincRNA	DEL	G	G	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr11:13031752delG	ENST00000533002.1	-	0	0																											GCCTCGTCCTGCTCTTCGTCG	0.647																																					p.C210fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.628delT						.						11.0	11.0	11.0					11																	13031752		2152	4230	6382			644943	exon1			.																													chr11.hg19:g.13031752delG		68.0	0.0		90.0	28.0	NM_001080521		Frame_Shift_Del	DEL	ENST00000533002.1	hg19																																																																																				.	.		0.647	CTC-497E21.3-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000387000.1		
SPEG	10290	hgsc.bcm.edu	37	2	220326629	220326631	+	In_Frame_Del	DEL	CCC	CCC	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	CCC	CCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:220326629_220326631delCCC	ENST00000312358.7	+	7	2598_2600	c.2466_2468delCCC	c.(2464-2469)agcccc>agc	p.P823del	SPEG_ENST00000396686.1_5'UTR|SPEG_ENST00000396698.1_In_Frame_Del_p.P719del|SPEG_ENST00000485813.1_3'UTR|SPEG_ENST00000396689.2_5'UTR|SPEG_ENST00000396688.1_5'UTR|SPEG_ENST00000396695.2_In_Frame_Del_p.P31del	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	823					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		CTTTCAGCAGCCCCATCACCTCC	0.635																																					p.822_823del		Atlas-Indel,Pindel	.											.	SPEG	272	.	0			c.2465_2467del						.																																			SO:0001651	inframe_deletion	10290	exon7			.	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.2466_2468delCCC	chr2.hg19:g.220326629_220326631delCCC	ENSP00000311684:p.Pro823del	60.0	0.0		65.0	24.0	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	In_Frame_Del	DEL	ENST00000312358.7	hg19	CCDS42824.1																																																																																			.	.		0.635	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
KIAA1211L	343990	hgsc.bcm.edu	37	2	99439712	99439712	+	Frame_Shift_Del	DEL	C	C	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr2:99439712delC	ENST00000397899.2	-	7	1355	c.1024delG	c.(1024-1026)gccfs	p.A342fs		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	342	Pro-rich.																TCGGGCTCGGCGAGCTCCGGG	0.786																																					p.A342fs		Atlas-INDEL	.											.	.	.	.	0			c.1025delC						.																																			SO:0001589	frameshift_variant	343990	exon7			.	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 55"""	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.1024delG	chr2.hg19:g.99439712delC	ENSP00000380996:p.Ala342fs	11.0	0.0		19.0	11.0	NM_207362		Frame_Shift_Del	DEL	ENST00000397899.2	hg19	CCDS42720.1																																																																																			.	.		0.786	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362	
XKR4	114786	hgsc.bcm.edu	37	8	56436755	56436757	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr8:56436755_56436757delAGG	ENST00000327381.6	+	3	2022_2024	c.1922_1924delAGG	c.(1921-1926)caggag>cag	p.E642del		NM_052898.1	NP_443130.1	Q5GH76	XKR4_HUMAN	XK, Kell blood group complex subunit-related family, member 4	642						integral component of membrane (GO:0016021)				NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(3)|large_intestine(4)|liver(2)|lung(12)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	34			Epithelial(17;0.000117)|all cancers(17;0.000836)			GCCCTTATTCAGGAGCGGTTGGA	0.483																																					p.641_641del		Atlas-Indel,Pindel	.											.	XKR4	104	.	0			c.1921_1923del						.																																			SO:0001651	inframe_deletion	114786	exon3			.	AY534241	CCDS34893.1	8q12.1	2006-01-12	2006-01-12		ENSG00000206579	ENSG00000206579			29394	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 4"""				Standard	NM_052898		Approved	KIAA1889	uc003xsf.3	Q5GH76	OTTHUMG00000164288	ENST00000327381.6:c.1922_1924delAGG	chr8.hg19:g.56436755_56436757delAGG	ENSP00000328326:p.Glu642del	33.0	0.0		41.0	11.0	NM_052898	Q96PZ8	In_Frame_Del	DEL	ENST00000327381.6	hg19	CCDS34893.1																																																																																			.	.		0.483	XKR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378129.2	NM_052898	
TRIM13	10206	hgsc.bcm.edu	37	13	50588496	50588497	+	3'UTR	INS	-	-	AC	rs199807501|rs35381218|rs377384125		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr13:50588496_50588497insAC	ENST00000378182.3	+	0	3158_3159				KCNRG_ENST00000312942.1_5'Flank|KCNRG_ENST00000360473.4_5'Flank|TRIM13_ENST00000478111.1_Intron	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13						anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		tatatatatatacacacacaca	0.292																																					.		Atlas-INDEL	.											.	TRIM13	30	.	0			.						.																																			SO:0001624	3_prime_UTR_variant	10206	.			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.*1197->AC	chr13.hg19:g.50588505_50588506dupAC		52.0	0.0		37.0	16.0	.	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	RNA	INS	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.		0.292	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
BSN	8927	hgsc.bcm.edu	37	3	49690047	49690048	+	In_Frame_Ins	INS	-	-	AGCAGC			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:49690047_49690048insAGCAGC	ENST00000296452.4	+	5	3172_3173	c.3058_3059insAGCAGC	c.(3058-3060)aag>aAGCAGCag	p.1022_1023insQQ		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	1022					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		AGAAGAAGCAAAGCAGCAGCGC	0.653																																					p.K1020delinsKQQ		Atlas-Indel,Pindel	.											.	BSN	272	.	0			c.3058_3059insAGCAGC						.																																			SO:0001652	inframe_insertion	8927	exon5			.	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.3059_3064dupAGCAGC	chr3.hg19:g.49690048_49690053dupAGCAGC	ENSP00000296452:p.Gln1021_Gln1022dup	44.0	0.0		49.0	17.0	NM_003458	O43161|Q7LGH3	In_Frame_Ins	INS	ENST00000296452.4	hg19	CCDS2800.1																																																																																			.	.		0.653	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
SENP2	59343	hgsc.bcm.edu	37	3	185318578	185318578	+	Frame_Shift_Del	DEL	T	T	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr3:185318578delT	ENST00000296257.5	+	5	624	c.384delT	c.(382-384)agtfs	p.S128fs	SENP2_ENST00000545472.1_Frame_Shift_Del_p.S118fs|SENP2_ENST00000465201.1_3'UTR|SENP2_ENST00000427465.2_5'UTR	NM_021627.2	NP_067640.2	Q9HC62	SENP2_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 2	128					cellular protein metabolic process (GO:0044267)|dorsal/ventral axis specification (GO:0009950)|heart development (GO:0007507)|labyrinthine layer development (GO:0060711)|mRNA transport (GO:0051028)|negative regulation of chromatin binding (GO:0035562)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of protein binding (GO:0032091)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-translational protein modification (GO:0043687)|protein desumoylation (GO:0016926)|protein sumoylation (GO:0016925)|protein transport (GO:0015031)|regulation of DNA endoreduplication (GO:0032875)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of Wnt signaling pathway (GO:0030111)|spongiotrophoblast layer development (GO:0060712)|trophoblast giant cell differentiation (GO:0060707)|Wnt signaling pathway (GO:0016055)	cytoplasmic vesicle (GO:0031410)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|PML body (GO:0016605)	SUMO-specific protease activity (GO:0016929)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|skin(3)	12	all_cancers(143;1.28e-10)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;1.31e-21)			ATGGAATAAGTGACTATCCAA	0.338																																					p.S128fs		Atlas-Indel,Pindel	.											.	SENP2	88	.	0			c.383delG						.						150.0	160.0	156.0					3																	185318578		2203	4300	6503	SO:0001589	frameshift_variant	59343	exon5			.	AF151697	CCDS33902.1	3q28	2005-08-17	2005-08-17		ENSG00000163904	ENSG00000163904			23116	protein-coding gene	gene with protein product		608261	"""SUMO1/sentrin/SMT3 specific protease 2"""			11896061, 11489887	Standard	XM_005247690		Approved	SMT3IP2, KIAA1331, DKFZp762A2316, AXAM2	uc003fpn.3	Q9HC62	OTTHUMG00000156658	ENST00000296257.5:c.384delT	chr3.hg19:g.185318578delT	ENSP00000296257:p.Ser128fs	136.0	0.0		153.0	56.0	NM_021627	B4DQ42|Q8IW97|Q96SR2|Q9P2L5	Frame_Shift_Del	DEL	ENST00000296257.5	hg19	CCDS33902.1																																																																																			.	.		0.338	SENP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345159.1	NM_021627	
EVPL	2125	hgsc.bcm.edu	37	17	74014610	74014611	+	Frame_Shift_Ins	INS	-	-	CCCT			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr17:74014610_74014611insCCCT	ENST00000301607.3	-	12	1608_1609	c.1355_1356insAGGG	c.(1354-1356)ggcfs	p.G452fs	EVPL_ENST00000586740.1_Frame_Shift_Ins_p.G452fs	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	452	Globular 1.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CCCCGCCAGGGCCCTGCACGAC	0.653																																					p.G452fs		Atlas-Indel,Pindel	.											.	EVPL	155	.	0			c.1356_1357insAGGG						.																																			SO:0001589	frameshift_variant	2125	exon12			.	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.1352_1355dupAGGG	chr17.hg19:g.74014611_74014614dupCCCT	ENSP00000301607:p.Gly452fs	77.0	0.0		125.0	26.0	NM_001988	A0AUV5	Frame_Shift_Ins	INS	ENST00000301607.3	hg19	CCDS11737.1																																																																																			.	.		0.653	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
ABCE1	6059	hgsc.bcm.edu	37	4	146032129	146032129	+	Frame_Shift_Del	DEL	A	A	-			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr4:146032129delA	ENST00000296577.4	+	8	1138	c.623delA	c.(622-624)cacfs	p.H208fs	ABCE1_ENST00000502803.1_Intron|OTUD4_ENST00000455611.2_5'UTR	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	208	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					GATTTAACCCACCTAAAAGAA	0.373																																					p.H208fs		Atlas-Indel,Pindel	.											.	ABCE1	47	.	0			c.622delC						.						113.0	105.0	108.0					4																	146032129		2203	4300	6503	SO:0001589	frameshift_variant	6059	exon8			.	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"""ATP binding cassette transporters / subfamily E"""	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.623delA	chr4.hg19:g.146032129delA	ENSP00000296577:p.His208fs	114.0	0.0		122.0	47.0	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Frame_Shift_Del	DEL	ENST00000296577.4	hg19	CCDS34071.1																																																																																			.	.		0.373	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	
PPIL2	23759	hgsc.bcm.edu	37	22	22025284	22025309	+	Splice_Site	DEL	TGTCCTTTTTCAGTCTCTCTCTGCAG	TGTCCTTTTTCAGTCTCTCTCTGCAG	-	rs370871572|rs202229100		TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TGTCCTTTTTCAGTCTCTCTCTGCAG	TGTCCTTTTTCAGTCTCTCTCTGCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr22:22025284_22025309delTGTCCTTTTTCAGTCTCTCTCTGCAG	ENST00000335025.8	+	4	219_243	c.128_152delTGTCCTTTTTCAGTCTCTCTCTGCAG	c.(127-153)atgtcctttttcagtctctctctgcag>ag	p.MSFFSLSLQ43fs	PPIL2_ENST00000406385.1_Splice_Site_p.MSFFSLSLQ43fs|PPIL2_ENST00000398831.3_Splice_Site_p.MSFFSLSLQ43fs|PPIL2_ENST00000412327.1_Splice_Site_p.MSFFSLSLQ43fs|PPIL2_ENST00000456792.2_Intron|PPIL2_ENST00000492445.2_Splice_Site_p.MSFFSLSLQ43fs					peptidylprolyl isomerase (cyclophilin)-like 2											endometrium(4)|kidney(2)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	17	Colorectal(54;0.105)					GTCCTTTTTCAGTCTCTCTCTGCAGCCCTTTGTCTACCCAGTCTGC	0.496																																					p.43_47del		Pindel	.											.	PPIL2	38	.	0			c.129_140del						.																																			SO:0001630	splice_region_variant	23759	exon4			.		CCDS13793.1	22q11.21	2013-01-29			ENSG00000100023	ENSG00000100023		"""U-box domain containing"""	9261	protein-coding gene	gene with protein product	"""U-box domain containing 7"""	607588				10591208	Standard	NM_014337		Approved	UBOX7, CYC4, Cyp-60	uc002zvh.4	Q13356	OTTHUMG00000030174	ENST00000335025.8:c.129-1TGTCCTTTTTCAGTCTCTCTCTGCAG>-	chr22.hg19:g.22025284_22025309delTGTCCTTTTTCAGTCTCTCTCTGCAG		213.0	0.0		160.0	21.0	NM_014337		In_Frame_Del	DEL	ENST00000335025.8	hg19	CCDS13793.1																																																																																			.	.		0.496	PPIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075028.4		Frame_Shift_Del
LATS1	9113	hgsc.bcm.edu	37	6	150004716	150004717	+	De_novo_Start_OutOfFrame	INS	-	-	ACACGCATACTTTTCACAGGCTGTTGAATAGG			TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr6:150004716_150004717insACACGCATACTTTTCACAGGCTGTTGAATAGG	ENST00000542747.1	-	0	1344_1345				LATS1_ENST00000543571.1_Frame_Shift_Ins_p.V503fs|LATS1_ENST00000253339.5_Frame_Shift_Ins_p.V503fs|LATS1_ENST00000392273.3_Frame_Shift_Ins_p.V503fs					large tumor suppressor kinase 1											central_nervous_system(1)|lung(5)	6		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;6.93e-13)|GBM - Glioblastoma multiforme(68;0.116)		CTGGTTTTAATACACGCATACT	0.455																																					p.V503_L504delinsVLFNSLX		Pindel	.											.	LATS1	241	.	0			c.1509_1510insCCTATTCAACAGCCTGTGAAAAGTATGCGTGT						.																																					9113	exon4			.	AF104413	CCDS34551.1, CCDS59040.1	6q25.1	2013-04-25	2013-04-25		ENSG00000131023	ENSG00000131023			6514	protein-coding gene	gene with protein product		603473	"""LATS (large tumor suppressor, Drosophila) homolog 1"", ""LATS, large tumor suppressor, homolog 1 (Drosophila)"""			9988268, 15122335	Standard	NM_004690		Approved	WARTS	uc003qmu.2	O95835	OTTHUMG00000016437	ENST00000542747.1:c.-1940->CCTATTCAACAGCCTGTGAAAAGTATGCGTGT	chr6.hg19:g.150004716_150004717insACACGCATACTTTTCACAGGCTGTTGAATAGG		127.0	0.0		64.0	14.0	NM_004690		Frame_Shift_Ins	INS	ENST00000542747.1	hg19																																																																																				.	.		0.455	LATS1-006	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000396940.1	NM_004690	
PRB2	653247	hgsc.bcm.edu	37	12	11545952	11546074	+	In_Frame_Del	DEL	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	-	rs372626172|rs77906063|rs375050877|rs370021759|rs201391404|rs568468055|rs377197500|rs374100662|rs202244094|rs75059624|rs368880039|rs560061246|rs200026492|rs540027572|rs200510401|rs201001689|rs547882513|rs185711312|rs376831456|rs527497030|rs201848322|rs545655808|rs538733280	byFrequency	TCGA-RC-A6M6-01A-11D-A32G-10	TCGA-RC-A6M6-10A-01D-A32G-10	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	TGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	01e01f50-bbe6-4594-a0ce-609338dc94ef	607d33ab-246a-4caa-94da-4af6591ea60e	g.chr12:11545952_11546074delTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	ENST00000389362.4	-	3	973_1095	c.938_1060delACCAGCCTCAAGGTCCCCCACCTCCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCA	c.(937-1062)aaccagcctcaaggtcccccacctcctccaggaaagccacaaggaccacccccacaaggaggcaacaaacctcaaggtcccccacctccaggaaagccacaaggaccacccccacaaggaggcagc>agc	p.NQPQGPPPPPGKPQGPPPQGGNKPQGPPPPGKPQGPPPQGG313del	PRB1_ENST00000546254.1_Intron|PRB2_ENST00000545829.1_5'Flank	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	313	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)		p.P315P(3)|p.P294P(3)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			CGGGACTTGCTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGTTGCCTCCTTG	0.604																																					p.313_354del		Pindel	.											.	PRB2	168	.	6	Substitution - coding silent(6)	large_intestine(4)|prostate(2)	c.939_1061del						.																																			SO:0001651	inframe_deletion	653247	exon3			.	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.938_1060delACCAGCCTCAAGGTCCCCCACCTCCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCAACAAACCTCAAGGTCCCCCACCTCCAGGAAAGCCACAAGGACCACCCCCACAAGGAGGCA	chr12.hg19:g.11545952_11546074delTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGTGGGGGACCTTGAGGTTTGTTGCCTCCTTGTGGGGGTGGTCCTTGTGGCTTTCCTGGAGGAGGTGGGGGACCTTGAGGCTGGT	ENSP00000374013:p.Asn313_Gly353del	322.0	0.0		321.0	13.0	NM_006248	O00599|P02811|P04281	In_Frame_Del	DEL	ENST00000389362.4	hg19	CCDS41757.2																																																																																			.	.		0.604	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
