#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_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_Trna_alt1	i_Trna_alt2	i_Trna_ref	i_Trna_tot	i_Trna_var	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
AGMAT	79814	hgsc.bcm.edu	37	1	15911349	15911349	+	Silent	SNP	G	G	A	rs3737705	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:15911349G>A	ENST00000375826.3	-	1	256	c.114C>T	c.(112-114)gaC>gaT	p.D38D	DNAJC16_ENST00000483270.1_Intron|RP4-680D5.2_ENST00000428945.1_RNA	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	38					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		TCCGGGGCGCGTCGGAAGCCT	0.791													G|||	1691	0.33766	0.2685	0.3084	5008	,	,		9254	0.5794		0.2952	False		,,,				2504	0.2464				p.D38D	NSCLC(126;1678 1780 25805 43508 49531)	.											.	AGMAT-91	0			c.C114T						.	G		446,1872		44,358,757	2.0	3.0	3.0		114	-4.1	0.0	1	dbSNP_107	3	1412,4272		187,1038,1617	no	coding-synonymous	AGMAT	NM_024758.4		231,1396,2374	AA,AG,GG		24.8417,19.2407,23.2192		38/353	15911349	1858,6144	1159	2842	4001	SO:0001819	synonymous_variant	79814	exon1			GGGCGCGTCGGAA	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.114C>T	1.37:g.15911349G>A		0	0		8	4	NM_024758	0	0	0	0	0	Q5TDH1|Q9H5J3	Silent	SNP	ENST00000375826.3	37	CCDS160.1																																																																																			G|0.647;A|0.353		0.791	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
RPS6KA1	6195	hgsc.bcm.edu	37	1	26856462	26856462	+	Silent	SNP	T	T	G	rs11800553	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:26856462T>G	ENST00000374168.2	+	1	205	c.51T>G	c.(49-51)ccT>ccG	p.P17P	RPS6KA1_ENST00000374162.2_5'Flank|RPS6KA1_ENST00000526792.1_5'Flank|RPS6KA1_ENST00000374166.4_Silent_p.P17P	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	17					axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		AGCTAGTGCCTCTGGACCCGG	0.786													G|||	4691	0.936701	0.9259	0.9179	5008	,	,		6031	0.9583		0.9553	False		,,,				2504	0.9233				p.P17P		.											.	RPS6KA1-510	0			c.T51G						.						2.0	2.0	2.0					1																	26856462		1084	2070	3154	SO:0001819	synonymous_variant	6195	exon1			AGTGCCTCTGGAC	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.51T>G	1.37:g.26856462T>G		0	0		4	4	NM_002953	0	0	0	0	0	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Silent	SNP	ENST00000374168.2	37	CCDS284.1																																																																																			T|0.065;G|0.935		0.786	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953	
L1TD1	54596	hgsc.bcm.edu	37	1	62675664	62675664	+	Silent	SNP	G	G	A	rs200931139|rs532563709		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:62675664G>A	ENST00000498273.1	+	4	1513	c.1218G>A	c.(1216-1218)gaG>gaA	p.E406E	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	406	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						Tggaggaggaggaggaagagc	0.547																																					p.E406E		.											.	L1TD1-92	0			c.G1218A						.						36.0	40.0	39.0					1																	62675664		2200	4298	6498	SO:0001819	synonymous_variant	54596	exon5			GGAGGAGGAGGAA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1218G>A	1.37:g.62675664G>A		192	0		166	22	NM_001164835	0	0	0	0	0	Q8NDA1|Q9NUV8|Q9NV78	Silent	SNP	ENST00000498273.1	37	CCDS619.1																																																																																			.		0.547	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
L1TD1	54596	ucsc.edu	37	1	62675673	62675673	+	Missense_Mutation	SNP	G	G	T	rs532563709|rs386631745|rs200789118	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:62675673G>T	ENST00000498273.1	+	4	1522	c.1227G>T	c.(1225-1227)gaG>gaT	p.E409D	Y_RNA_ENST00000363304.1_RNA	NM_001164835.1|NM_019079.4	NP_001158307.1|NP_061952.3	Q5T7N2	LITD1_HUMAN	LINE-1 type transposase domain containing 1	409	Glu-rich.									breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	35						aggaggaagagccctcagggc	0.557													G|||	160	0.0319489	0.0658	0.0231	5008	,	,		15817	0.001		0.0417	False		,,,				2504	0.0143				p.E409D		.											.	L1TD1-92	0			c.G1227T						.						34.0	38.0	36.0					1																	62675673		2200	4298	6498	SO:0001583	missense	54596	exon5			GGAAGAGCCCTCA	BC060808	CCDS619.1	1p31.3	2009-01-12			ENSG00000240563	ENSG00000240563			25595	protein-coding gene	gene with protein product						12477932	Standard	NM_001164835		Approved	FLJ10884, ECAT11	uc001dae.4	Q5T7N2	OTTHUMG00000008914	ENST00000498273.1:c.1227G>T	1.37:g.62675673G>T	ENSP00000419901:p.Glu409Asp	202	1		156	36	NM_001164835	0	0	0	0	0	Q8NDA1|Q9NUV8|Q9NV78	Missense_Mutation	SNP	ENST00000498273.1	37	CCDS619.1	.	.	.	.	.	.	.	.	.	.	G	11.63	1.695799	0.30052	.	.	ENSG00000240563	ENST00000498273	T	0.18810	2.19	3.26	-1.27	0.09347	.	.	.	.	.	T	0.08088	0.0202	N	0.12182	0.205	0.09310	N	1	B	0.17852	0.024	B	0.15870	0.014	T	0.39099	-0.9630	9	0.13108	T	0.6	.	2.2943	0.04146	0.1154:0.3623:0.3374:0.1849	.	409	Q5T7N2	LITD1_HUMAN	D	409	ENSP00000419901:E409D	ENSP00000419901:E409D	E	+	3	2	L1TD1	62448261	0.001000	0.12720	0.000000	0.03702	0.109000	0.19521	-0.211000	0.09332	-0.223000	0.09943	0.448000	0.29417	GAG	.		0.557	L1TD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024688.1	NM_019079	
ATP1A2	477	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	1	160105320	160105320	+	Missense_Mutation	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:160105320G>A	ENST00000361216.3	+	16	2301	c.2212G>A	c.(2212-2214)Gtc>Atc	p.V738I	ATP1A2_ENST00000392233.3_Missense_Mutation_p.V738I	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	738					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			TGGCTCTGACGTCTCTAAGCA	0.597																																					p.V738I		.											.	ATP1A2-518	0			c.G2212A						.						152.0	113.0	126.0					1																	160105320		2203	4298	6501	SO:0001583	missense	477	exon16			TCTGACGTCTCTA	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.2212G>A	1.37:g.160105320G>A	ENSP00000354490:p.Val738Ile	315	0		418	60	NM_000702	0	0	0	0	0	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Missense_Mutation	SNP	ENST00000361216.3	37	CCDS1196.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.560337	0.86335	.	.	ENSG00000018625	ENST00000361216;ENST00000392233;ENST00000435866	D;D	0.99105	-5.43;-5.43	4.31	4.31	0.51392	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.98988	0.9655	M	0.85373	2.75	0.80722	D	1	P;P	0.43938	0.822;0.727	P;B	0.53518	0.728;0.415	D	0.99899	1.1156	10	0.87932	D	0	.	16.0832	0.81020	0.0:0.0:1.0:0.0	.	638;738	F5GXJ7;P50993	.;AT1A2_HUMAN	I	738;738;441	ENSP00000354490:V738I;ENSP00000376066:V738I	ENSP00000354490:V738I	V	+	1	0	ATP1A2	158371944	1.000000	0.71417	0.939000	0.37840	0.626000	0.37791	9.501000	0.97979	2.383000	0.81215	0.561000	0.74099	GTC	.		0.597	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
TOR3A	64222	hgsc.bcm.edu	37	1	179051300	179051300	+	Missense_Mutation	SNP	T	T	C	rs2296377	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:179051300T>C	ENST00000367627.3	+	1	789	c.37T>C	c.(37-39)Ttc>Ctc	p.F13L	TOR3A_ENST00000352445.6_Missense_Mutation_p.F13L	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	13			F -> L (in dbSNP:rs2296377). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						TTGGCTCTTTTTCCTGCTGCT	0.751													C|||	3842	0.767173	0.9879	0.6441	5008	,	,		12722	0.6677		0.7117	False		,,,				2504	0.7157				p.F13L		.											.	TOR3A-90	0			c.T37C						.	C	LEU/PHE	3262,174		1547,168,3	2.0	3.0	3.0		37	-0.8	0.0	1	dbSNP_100	3	5365,1739		2051,1263,238	yes	missense	TOR3A	NM_022371.3	22	3598,1431,241	CC,CT,TT		24.4792,5.064,18.1499	benign	13/398	179051300	8627,1913	1718	3552	5270	SO:0001583	missense	64222	exon1			CTCTTTTTCCTGC	BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.37T>C	1.37:g.179051300T>C	ENSP00000356599:p.Phe13Leu	0	0		5	5	NM_022371	0	0	0	0	0	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	1679	0.7687728937728938	484	0.983739837398374	250	0.6906077348066298	393	0.6870629370629371	552	0.7282321899736148	C	0.033	-1.323382	0.01309	0.94936	0.755208	ENSG00000186283	ENST00000367627;ENST00000367625;ENST00000352445	T;T;T	0.35421	1.31;1.4;1.63	0.427	-0.794	0.10918	.	1.274350	0.05916	N	0.632520	T	0.00012	0.0000	N	0.00368	-1.59	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45906	-0.9229	8	0.02654	T	1	-1.1524	.	.	.	rs2296377;rs17844883;rs17856371;rs17857600;rs17857917;rs17858479;rs59034332;rs2296377	13	Q9H497	TOR3A_HUMAN	L	13	ENSP00000356599:F13L;ENSP00000356597:F13L;ENSP00000335351:F13L	ENSP00000335351:F13L	F	+	1	0	TOR3A	177317923	0.000000	0.05858	0.002000	0.10522	0.004000	0.04260	-1.490000	0.02304	-1.608000	0.01587	-1.610000	0.00802	TTC	T|0.229;C|0.771		0.751	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1	NM_022371	
C1orf106	55765	hgsc.bcm.edu	37	1	200880978	200880978	+	Missense_Mutation	SNP	C	C	T	rs296520	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:200880978C>T	ENST00000367342.4	+	9	1812	c.1612C>T	c.(1612-1614)Cgc>Tgc	p.R538C	C1orf106_ENST00000413687.2_Missense_Mutation_p.R453C	NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	538			R -> C (in dbSNP:rs296520). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.							endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GTGGGAGCTGCGCCGCGCAGC	0.736													T|||	3966	0.791933	0.6089	0.8213	5008	,	,		12017	0.997		0.7256	False		,,,				2504	0.8753				p.R552C		.											.	C1orf106-93	0			c.C1654T						.	T	CYS/ARG,CYS/ARG	2547,1503		890,767,368	5.0	7.0	6.0		1357,1612	0.8	0.0	1	dbSNP_79	6	5587,2355		2124,1339,508	no	missense,missense	C1orf106	NM_001142569.2,NM_018265.3	180,180	3014,2106,876	TT,TC,CC		29.6525,37.1111,32.1714	benign,benign	453/579,538/664	200880978	8134,3858	2025	3971	5996	SO:0001583	missense	55765	exon9			GAGCTGCGCCGCG	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.1612C>T	1.37:g.200880978C>T	ENSP00000356311:p.Arg538Cys	0	0		26	26	NM_018265	0	0	0	0	0	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Missense_Mutation	SNP	ENST00000367342.4	37		1677	0.7678571428571429	261	0.5304878048780488	285	0.787292817679558	569	0.9947552447552448	562	0.741424802110818	T	0.366	-0.936884	0.02340	0.628889	0.703475	ENSG00000163362	ENST00000367342;ENST00000413687	T;T	0.28454	1.61;1.61	3.39	0.759	0.18438	.	0.912041	0.09365	N	0.812206	T	0.00012	0.0000	N	0.01576	-0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.16188	-1.0411	9	0.29301	T	0.29	-23.0614	3.796	0.08740	0.0:0.2241:0.1856:0.5903	rs296520;rs7519373;rs56757010	538	Q3KP66	CA106_HUMAN	C	538;453	ENSP00000356311:R538C;ENSP00000392105:R453C	ENSP00000356311:R538C	R	+	1	0	C1orf106	199147601	0.004000	0.15560	0.002000	0.10522	0.007000	0.05969	-0.731000	0.04909	-0.124000	0.11724	-0.381000	0.06696	CGC	C|0.242;T|0.758		0.736	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
C1orf198	84886	broad.mit.edu	37	1	231004230	231004230	+	Missense_Mutation	SNP	G	G	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:231004230G>T	ENST00000366663.5	-	1	169	c.29C>A	c.(28-30)gCt>gAt	p.A10D	C1orf198_ENST00000470540.1_Intron|C1orf198_ENST00000427697.2_Intron	NM_032800.2	NP_116189.1	Q9H425	CA198_HUMAN	chromosome 1 open reading frame 198	10						cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	17	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				CGAGCGCGAAGCCGCGATCGC	0.751																																					p.A10D		.											.	C1orf198-90	0			c.C29A						.						7.0	10.0	9.0					1																	231004230		2131	4199	6330	SO:0001583	missense	84886	exon1			CGCGAAGCCGCGA	BC066649	CCDS1587.1, CCDS44330.1, CCDS44331.1	1q42.2	2008-02-05			ENSG00000119280	ENSG00000119280			25900	protein-coding gene	gene with protein product							Standard	NM_032800		Approved	FLJ14525, MGC10710, FLJ16283, DKFZp667D152, FLJ38847	uc001hub.3	Q9H425	OTTHUMG00000037790	ENST00000366663.5:c.29C>A	1.37:g.231004230G>T	ENSP00000355623:p.Ala10Asp	16	0		91	6	NM_032800	0	0	0	0	0	A8K8R8|B3KTW1|G5EA08	Missense_Mutation	SNP	ENST00000366663.5	37	CCDS1587.1	.	.	.	.	.	.	.	.	.	.	g	17.66	3.445252	0.63178	.	.	ENSG00000119280	ENST00000366663	T	0.45276	0.9	3.38	3.38	0.38709	.	0.236842	0.27155	U	0.020668	T	0.48804	0.1520	N	0.24115	0.695	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	T	0.51772	-0.8663	10	0.46703	T	0.11	.	14.5276	0.67900	0.0:0.0:1.0:0.0	.	10	Q9H425	CA198_HUMAN	D	10	ENSP00000355623:A10D	ENSP00000355623:A10D	A	-	2	0	C1orf198	229070853	1.000000	0.71417	1.000000	0.80357	0.614000	0.37383	5.713000	0.68415	1.697000	0.51169	0.306000	0.20318	GCT	.		0.751	C1orf198-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092236.2	NM_032800	
SH3BP5L	80851	hgsc.bcm.edu	37	1	249106348	249106348	+	Silent	SNP	G	G	C	rs202116012	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:249106348G>C	ENST00000366472.5	-	7	2162	c.933C>G	c.(931-933)gcC>gcG	p.A311A	SH3BP5L_ENST00000411742.2_Silent_p.A279A|SH3BP5L_ENST00000475978.1_5'UTR	NM_030645.1	NP_085148.1	Q7L8J4	3BP5L_HUMAN	SH3-binding domain protein 5-like	311										endometrium(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23	all_cancers(71;3.33e-06)|all_epithelial(71;2.41e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.0458)|Lung NSC(105;0.0494)|Melanoma(84;0.199)	all_cancers(173;0.19)	OV - Ovarian serous cystadenocarcinoma(106;0.00805)			CCGCACCCTCGGCCCCCTCAA	0.746													G|||	23	0.00459265	0.0008	0.0144	5008	,	,		12601	0.0		0.0119	False		,,,				2504	0.0				p.A311A		.											.	SH3BP5L-90	0			c.C933G						.	G		17,4377		0,17,2180	13.0	16.0	15.0		933	-8.6	0.4	1		15	135,8433		2,131,4151	no	coding-synonymous	SH3BP5L	NM_030645.1		2,148,6331	CC,CG,GG		1.5756,0.3869,1.1727		311/394	249106348	152,12810	2197	4284	6481	SO:0001819	synonymous_variant	80851	exon7			ACCCTCGGCCCCC	AB051507	CCDS31126.1	1q44	2008-02-05			ENSG00000175137	ENSG00000175137			29360	protein-coding gene	gene with protein product							Standard	NM_030645		Approved	KIAA1720	uc001iew.1	Q7L8J4	OTTHUMG00000040389	ENST00000366472.5:c.933C>G	1.37:g.249106348G>C		1	0		45	13	NM_030645	0	0	0	0	0	B4DQ94|Q96FI5|Q9BQH8|Q9C0E3	Silent	SNP	ENST00000366472.5	37	CCDS31126.1																																																																																			G|0.991;C|0.008		0.746	SH3BP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097140.1	NM_030645	
PTCHD3	374308	hgsc.bcm.edu;broad.mit.edu	37	10	27702894	27702923	+	In_Frame_Del	DEL	GGGGTGCATCGTCCAGCTCCAGCGGCAGGC	GGGGTGCATCGTCCAGCTCCAGCGGCAGGC	-	rs34349277|rs371045387|rs201821343	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	GGGGTGCATCGTCCAGCTCCAGCGGCAGGC	GGGGTGCATCGTCCAGCTCCAGCGGCAGGC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr10:27702894_27702923delGGGGTGCATCGTCCAGCTCCAGCGGCAGGC	ENST00000438700.3	-	1	374_403	c.257_286delGCCTGCCGCTGGAGCTGGACGATGCACCCC	c.(256-288)cgcctgccgctggagctggacgatgcacccctg>ctg	p.RLPLELDDAP86del		NM_001034842.3	NP_001030014.2	Q3KNS1	PTHD3_HUMAN	patched domain containing 3	86					spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|sperm midpiece (GO:0097225)	hedgehog receptor activity (GO:0008158)	p.P88P(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(17)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	55						TCCTCCGGCAGGGGTGCATCGTCCAGCTCCAGCGGCAGGCGGGGTGCATC	0.704																																					p.86_96del		.											.	PTCHD3-94	1	Substitution - coding silent(1)	endometrium(1)	c.257_286del						.			7,4255		1,5,2125						-3.5	0.0			34	78,8172		8,62,4055	no	coding	PTCHD3	NM_001034842.3		9,67,6180	A1A1,A1R,RR		0.9455,0.1642,0.6793				85,12427				SO:0001651	inframe_deletion	374308	exon1			CCGGCAGGGGTGC	AK126025	CCDS31173.1	10p12.1	2006-05-26			ENSG00000182077	ENSG00000182077			24776	protein-coding gene	gene with protein product		611791					Standard	NM_001034842		Approved	FLJ44037, PTR	uc001itu.2	Q3KNS1	OTTHUMG00000017860	ENST00000438700.3:c.257_286delGCCTGCCGCTGGAGCTGGACGATGCACCCC	10.37:g.27702894_27702923delGGGGTGCATCGTCCAGCTCCAGCGGCAGGC	ENSP00000417658:p.Arg86_Pro95del	6	0		65	13	NM_001034842	0	0	0	0	0	I3L499|Q6ZU28	In_Frame_Del	DEL	ENST00000438700.3	37	CCDS31173.1																																																																																			.		0.704	PTCHD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047325.3	XM_370541	
NFKB2	4791	hgsc.bcm.edu	37	10	104159196	104159196	+	Silent	SNP	A	A	G	rs4919633	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr10:104159196A>G	ENST00000369966.3	+	13	1519	c.1269A>G	c.(1267-1269)ccA>ccG	p.P423P	NFKB2_ENST00000336486.5_3'UTR|NFKB2_ENST00000428099.1_Silent_p.P423P|NFKB2_ENST00000189444.6_Silent_p.P423P	NM_001077494.2	NP_001070962.1	Q00653	NFKB2_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)	423					extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|NIK/NF-kappaB signaling (GO:0038061)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription, DNA-templated (GO:0006355)|rhythmic process (GO:0048511)|spleen development (GO:0048536)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(10)|skin(2)	23		Colorectal(252;0.00957)		Epithelial(162;3.4e-08)|all cancers(201;6.41e-07)	Acetylsalicylic acid(DB00945)|Glucosamine(DB01296)	CCGCGGAGCCAAGCGCCCCCT	0.786			T	IGH@	B-NHL								G|||	4942	0.986821	0.9539	0.9942	5008	,	,		10589	1.0		0.999	False		,,,				2504	1.0				p.P423P		.		Dom	yes		10	10q24	4791	nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (p49/p100)		L	.	NFKB2-522	0			c.A1269G						.	G	,,	2876,76		1401,74,1	3.0	5.0	4.0		1269,1269,1269	-4.9	0.0	10	dbSNP_111	4	6622,2		3310,2,0	no	coding-synonymous,coding-synonymous,coding-synonymous	NFKB2	NM_001077493.1,NM_001077494.1,NM_002502.3	,,	4711,76,1	GG,GA,AA		0.0302,2.5745,0.8145	,,	423/900,423/901,423/900	104159196	9498,78	1476	3312	4788	SO:0001819	synonymous_variant	4791	exon13			GGAGCCAAGCGCC	X61498	CCDS41564.1, CCDS41565.1	10q24	2013-01-10			ENSG00000077150	ENSG00000077150		"""Ankyrin repeat domain containing"""	7795	protein-coding gene	gene with protein product		164012				1876189	Standard	XM_005269860		Approved	LYT-10, p52, p105, NF-kB2	uc001kvb.4	Q00653	OTTHUMG00000018962	ENST00000369966.3:c.1269A>G	10.37:g.104159196A>G		0	0		7	7	NM_001077494	0	0	0	0	0	A8K9D9|D3DR83|Q04860|Q9BU75|Q9H471|Q9H472	Silent	SNP	ENST00000369966.3	37	CCDS41564.1																																																																																			A|0.009;G|0.991		0.786	NFKB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050080.2		
GPR26	2849	hgsc.bcm.edu	37	10	125426253	125426253	+	Silent	SNP	C	C	T	rs62640898	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr10:125426253C>T	ENST00000284674.1	+	1	383	c.330C>T	c.(328-330)ttC>ttT	p.F110F		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	110					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				CCGTGGTCTTCCCGCTGAGCT	0.706													C|||	17	0.00339457	0.0	0.0	5008	,	,		13455	0.0		0.008	False		,,,				2504	0.0092				p.F110F		.											.	GPR26-91	0			c.C330T						.	C		6,4364		0,6,2179	10.0	11.0	10.0		330	-3.6	0.9	10	dbSNP_129	10	49,8509		0,49,4230	no	coding-synonymous	GPR26	NM_153442.3		0,55,6409	TT,TC,CC		0.5726,0.1373,0.4254		110/338	125426253	55,12873	2185	4279	6464	SO:0001819	synonymous_variant	2849	exon1			GGTCTTCCCGCTG		CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478		"""GPCR / Class A : Orphans"""	4481	protein-coding gene	gene with protein product		604847					Standard	NM_153442		Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.330C>T	10.37:g.125426253C>T		0	0		19	10	NM_153442	0	0	0	0	0	Q2M2E2	Silent	SNP	ENST00000284674.1	37	CCDS7636.1																																																																																			C|0.997;T|0.003		0.706	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1		
PTDSS2	81490	broad.mit.edu	37	11	489952	489952	+	Silent	SNP	C	C	T	rs150531471	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr11:489952C>T	ENST00000308020.5	+	11	1361	c.1185C>T	c.(1183-1185)atC>atT	p.I395I		NM_030783.1	NP_110410.1	Q9BVG9	PTSS2_HUMAN	phosphatidylserine synthase 2	395					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylserine biosynthetic process (GO:0006659)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	CDP-diacylglycerol-serine O-phosphatidyltransferase activity (GO:0003882)			autonomic_ganglia(1)|breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|skin(1)	9		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;2.76e-26)|Epithelial(43;2.56e-25)|OV - Ovarian serous cystadenocarcinoma(40;7.54e-20)|BRCA - Breast invasive adenocarcinoma(625;8.76e-05)|Lung(200;0.0407)|LUSC - Lung squamous cell carcinoma(625;0.0735)	Phosphatidylserine(DB00144)	AGCTGCTCATCGTGGTGAAGT	0.682																																					p.I395I		.											.	PTDSS2-90	0			c.C1185T						.	C		0,4398		0,0,2199	101.0	57.0	72.0		1185	1.2	1.0	11	dbSNP_134	72	8,8592	5.0+/-18.6	1,6,4293	no	coding-synonymous	PTDSS2	NM_030783.1		1,6,6492	TT,TC,CC		0.093,0.0,0.0615		395/488	489952	8,12990	2199	4300	6499	SO:0001819	synonymous_variant	81490	exon11			GCTCATCGTGGTG	BC001210	CCDS7696.1	11p15	2008-05-02			ENSG00000174915	ENSG00000174915			15463	protein-coding gene	gene with protein product		612793				14984733	Standard	NM_030783		Approved	PSS2	uc001lpj.3	Q9BVG9	OTTHUMG00000119087	ENST00000308020.5:c.1185C>T	11.37:g.489952C>T		42	0		82	4	NM_030783	0	0	0	0	0		Silent	SNP	ENST00000308020.5	37	CCDS7696.1																																																																																			C|0.999;T|0.001		0.682	PTDSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239301.2		
NAP1L4	4676	broad.mit.edu	37	11	2979678	2979678	+	Silent	SNP	C	C	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr11:2979678C>T	ENST00000380542.4	-	10	983	c.843G>A	c.(841-843)acG>acA	p.T281T	NAP1L4_ENST00000526115.1_Silent_p.T281T	NM_005969.3	NP_005960.1	Q99733	NP1L4_HUMAN	nucleosome assembly protein 1-like 4	281					nucleosome assembly (GO:0006334)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(2)|kidney(3)|large_intestine(1)|lung(6)|ovary(1)	13		all_epithelial(84;0.000236)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)		BRCA - Breast invasive adenocarcinoma(625;0.00301)|LUSC - Lung squamous cell carcinoma(625;0.211)		GTACTTGTTTCGTAATTGTTC	0.338																																					p.T281T		.											.	NAP1L4-91	0			c.G843A						.						202.0	189.0	193.0					11																	2979678		1897	4107	6004	SO:0001819	synonymous_variant	4676	exon10			TTGTTTCGTAATT	AA573896, BC022090, U77456	CCDS41599.1	11p15.5	2007-12-06			ENSG00000205531	ENSG00000205531			7640	protein-coding gene	gene with protein product		601651				8923002	Standard	NM_005969		Approved	NAP2	uc001lxc.3	Q99733	OTTHUMG00000011009	ENST00000380542.4:c.843G>A	11.37:g.2979678C>T		226	2		244	7	NM_005969	0	0	0	0	0	B2R6J4|F5HFY4	Silent	SNP	ENST00000380542.4	37	CCDS41599.1																																																																																			.		0.338	NAP1L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030273.3	NM_005969	
TMEM86A	144110	broad.mit.edu	37	11	18728650	18728650	+	IGR	SNP	T	T	C	rs2289965	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr11:18728650T>C	ENST00000280734.2	+	0	3595				IGSF22_ENST00000513874.1_Missense_Mutation_p.I1131V|RP11-1081L13.4_ENST00000527285.1_RNA|IGSF22_ENST00000510673.1_5'Flank	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A							integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						TTCATGATGATGTAGTGAGCC	0.582													C|||	947	0.189097	0.0166	0.3429	5008	,	,		20413	0.1339		0.3976	False		,,,				2504	0.1554				p.I1131V		.											.	IGSF22-140	0			c.A3391G						.	C	VAL/ILE	104,1280		8,88,596	176.0	140.0	151.0		3391	2.5	0.3	11	dbSNP_100	151	1267,1915		245,777,569	yes	missense	IGSF22	NM_173588.3	29	253,865,1165	CC,CT,TT		39.8177,7.5145,30.0263	benign	1131/1327	18728650	1371,3195	692	1591	2283	SO:0001628	intergenic_variant	283284	exon21			TGATGATGTAGTG	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4			11.37:g.18728650T>C		70	1		93	4	NM_173588	0	0	0	0	0	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	511	0.23397435897435898	13	0.026422764227642278	133	0.3674033149171271	68	0.11888111888111888	297	0.391820580474934	C	8.429	0.848099	0.17034	0.075145	0.398177	ENSG00000179057	ENST00000513874	T	0.56444	0.46	3.57	2.53	0.30540	.	.	.	.	.	T	0.00012	0.0000	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42732	-0.9434	8	0.08179	T	0.78	.	4.9575	0.14050	0.0:0.612:0.1654:0.2226	rs2289965;rs17400035;rs52807214;rs60072054;rs2289965	1131	D6RGV7	.	V	1131	ENSP00000421191:I1131V	ENSP00000421191:I1131V	I	-	1	0	IGSF22	18685226	0.000000	0.05858	0.252000	0.24328	0.490000	0.33462	-0.206000	0.09398	0.218000	0.20820	-0.213000	0.12676	ATC	T|0.800;C|0.200		0.582	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
KRTAP5-10	387273	hgsc.bcm.edu	37	11	71276876	71276876	+	Silent	SNP	A	A	G	rs12788123		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr11:71276876A>G	ENST00000398531.1	+	1	268	c.243A>G	c.(241-243)aaA>aaG	p.K81K	KRTAP5-10_ENST00000376536.4_Intron	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	81	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)		p.K81K(1)		endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						GGGGCTCCAAAGGGGGCTGTG	0.682																																					p.K81K		.											.	KRTAP5-10-91	1	Substitution - coding silent(1)	endometrium(1)	c.A243G						.						51.0	72.0	65.0					11																	71276876		2140	4257	6397	SO:0001819	synonymous_variant	387273	exon1			CTCCAAAGGGGGC	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.243A>G	11.37:g.71276876A>G		25	0		40	7	NM_001012710	0	0	0	0	0	B9EHA4	Silent	SNP	ENST00000398531.1	37	CCDS41684.1																																																																																			A|0.998;G|0.002		0.682	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000127968.2		
IQSEC3	440073	bcgsc.ca	37	12	274647	274647	+	Silent	SNP	T	T	C	rs4980859	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:274647T>C	ENST00000538872.1	+	10	2875	c.2757T>C	c.(2755-2757)ttT>ttC	p.F919F	RP11-598F7.6_ENST00000537295.1_lincRNA|IQSEC3_ENST00000326261.4_Silent_p.F919F|IQSEC3_ENST00000382841.2_Silent_p.F616F|RP11-598F7.5_ENST00000540136.1_RNA			Q9UPP2	IQEC3_HUMAN	IQ motif and Sec7 domain 3	919	PH.				actin cytoskeleton organization (GO:0030036)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|inhibitory synapse (GO:0060077)|postsynaptic membrane (GO:0045211)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(18)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_cancers(10;0.016)|all_lung(10;0.0222)|all_epithelial(11;0.0262)|Lung NSC(10;0.031)		OV - Ovarian serous cystadenocarcinoma(31;0.00456)	LUAD - Lung adenocarcinoma(1;0.172)|Lung(1;0.179)		CGTACACCTTTTGCAAGTCAG	0.488													C|||	1306	0.260783	0.087	0.3199	5008	,	,		23066	0.3393		0.326	False		,,,				2504	0.3057				p.F919F		.											.	IQSEC3-560	0			c.T2757C						.	C	,	593,3813	771.3+/-413.8	37,519,1647	189.0	176.0	180.0		2757,1848	4.9	1.0	12	dbSNP_111	180	2729,5871	680.5+/-403.6	434,1861,2005	yes	coding-synonymous,coding-synonymous	IQSEC3	NM_001170738.1,NM_015232.1	,	471,2380,3652	CC,CT,TT		31.7326,13.4589,25.5421	,	919/1183,616/760	274647	3322,9684	2203	4300	6503	SO:0001819	synonymous_variant	440073	exon10			CACCTTTTGCAAG	AB029033	CCDS31725.1, CCDS53728.1	12p13.33	2014-03-18			ENSG00000120645	ENSG00000120645			29193	protein-coding gene	gene with protein product		612118				10470851	Standard	NM_001170738		Approved	KIAA1110, MGC30156	uc001qhw.2	Q9UPP2	OTTHUMG00000167975	ENST00000538872.1:c.2757T>C	12.37:g.274647T>C		219	2		178	7	NM_001170738	0	0	0	0	0	A6NIF2|A6NKV9|Q8TB43	Silent	SNP	ENST00000538872.1	37	CCDS53728.1																																																																																			T|0.740;C|0.260		0.488	IQSEC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397382.3	XM_495902	
ZNF705A	440077	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	12	8329841	8329841	+	Missense_Mutation	SNP	C	C	T	rs145286690		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:8329841C>T	ENST00000359286.4	+	5	654	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	FAM66C_ENST00000544214.1_RNA|FAM66C_ENST00000456135.2_RNA|FAM66C_ENST00000454799.2_RNA	NM_001004328.2|NM_001278713.1	NP_001004328.1|NP_001265642.1	Q6ZN79	Z705A_HUMAN	zinc finger protein 705A	189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(3)|stomach(4)	18				Kidney(36;0.0877)		TCGCCTTAGACGGCACAAGAT	0.388													c|||	1	0.000199681	0.0008	0.0	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.R189W		.											.	ZNF705A-90	0			c.C565T						.						78.0	79.0	79.0					12																	8329841		2194	4291	6485	SO:0001583	missense	440077	exon5			CTTAGACGGCACA	AK131339	CCDS31737.1	12p13.31	2014-02-12	2005-09-22		ENSG00000196946	ENSG00000196946		"""Zinc fingers, C2H2-type"", ""-"""	32281	protein-coding gene	gene with protein product							Standard	NM_001004328		Approved	FLJ16353	uc001qud.1	Q6ZN79	OTTHUMG00000168635	ENST00000359286.4:c.565C>T	12.37:g.8329841C>T	ENSP00000352233:p.Arg189Trp	157	0		221	81	NM_001004328	0	0	0	0	0		Missense_Mutation	SNP	ENST00000359286.4	37	CCDS31737.1	.	.	.	.	.	.	.	.	.	.	.	2.904	-0.226805	0.06022	.	.	ENSG00000196946	ENST00000396570;ENST00000359286	T;T	0.07800	3.16;3.16	1.35	-2.7	0.06004	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08403	0.0209	M	0.73753	2.245	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.40608	-0.9554	8	.	.	.	.	1.2099	0.01902	0.2433:0.4125:0.1869:0.1574	.	189	Q6ZN79	Z705A_HUMAN	W	189	ENSP00000379816:R189W;ENSP00000352233:R189W	.	R	+	1	2	ZNF705A	8221108	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-6.202000	0.00076	-1.270000	0.02433	-0.526000	0.04340	CGG	C|1.000;T|0.000		0.388	ZNF705A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400449.1	NM_001004328	
KLRC2	3822	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	10584764	10584764	+	Silent	SNP	C	C	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:10584764C>T	ENST00000381902.2	-	5	531	c.525G>A	c.(523-525)gtG>gtA	p.V175V	KLRC2_ENST00000381901.1_Silent_p.V175V|NKG2-E_ENST00000539033.1_Intron|KLRC2_ENST00000536833.2_Silent_p.V116V	NM_002260.3	NP_002251.2	P26717	NKG2C_HUMAN	killer cell lectin-like receptor subfamily C, member 2	175	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			kidney(2)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11						TGTTACGAAACACACCAATCC	0.289																																					p.V175V		.											.	KLRC2-514	0			c.G525A						.						43.0	43.0	43.0					12																	10584764		2055	4147	6202	SO:0001819	synonymous_variant	3822	exon5			ACGAAACACACCA	X54869	CCDS31745.1	12p13	2009-12-03				ENSG00000205809		"""Killer cell lectin-like receptors"", ""CD molecules"""	6375	protein-coding gene	gene with protein product		602891				9598306	Standard	NM_002260		Approved	NKG2-C, CD159c		P26717		ENST00000381902.2:c.525G>A	12.37:g.10584764C>T		169	0		138	15	NM_002260	0	0	0	0	0	O43802|Q52M74|Q9NR42	Silent	SNP	ENST00000381902.2	37	CCDS31745.1	.	.	.	.	.	.	.	.	.	.	c	1.361	-0.588778	0.03799	.	.	ENSG00000205809	ENST00000537017	.	.	.	2.53	0.171	0.15026	.	.	.	.	.	T	0.32164	0.0820	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	7.7523	0.28904	0.0:0.5591:0.4409:0.0	.	.	.	.	Y	53	.	.	C	-	2	0	KLRC2	10476031	0.000000	0.05858	0.004000	0.12327	0.032000	0.12392	-0.393000	0.07305	0.344000	0.23847	-0.494000	0.04653	TGT	.		0.289	KLRC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400111.1	NM_002260	
PIP4K2C	79837	bcgsc.ca	37	12	57985204	57985204	+	Silent	SNP	C	C	T	rs11537654	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:57985204C>T	ENST00000354947.5	+	1	148	c.132C>T	c.(130-132)gcC>gcT	p.A44A	PIP4K2C_ENST00000550465.1_Silent_p.A44A|PIP4K2C_ENST00000540759.2_Silent_p.A44A|PIP4K2C_ENST00000422156.3_Silent_p.A44A			Q8TBX8	PI42C_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, gamma	44	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(13)|pancreas(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Melanoma(17;0.122)					TCCGGGCGGCCGACCCGCTGG	0.662													C|||	1561	0.311701	0.0204	0.4078	5008	,	,		14182	0.5337		0.2535	False		,,,				2504	0.4683				p.A44A		.											.	PIP4K2C-689	0			c.C132T						.	C	,,,	282,4124	158.9+/-191.5	6,270,1927	100.0	108.0	105.0		132,132,132,132	-1.2	1.0	12	dbSNP_120	105	2148,6452	368.8+/-335.2	279,1590,2431	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PIP4K2C	NM_001146258.1,NM_001146259.1,NM_001146260.1,NM_024779.4	,,,	285,1860,4358	TT,TC,CC		24.9767,6.4004,18.6837	,,,	44/422,44/404,44/374,44/422	57985204	2430,10576	2203	4300	6503	SO:0001819	synonymous_variant	79837	exon1			GGCGGCCGACCCG	AK125526	CCDS8946.1, CCDS53808.1, CCDS55839.1	12q13.3	2014-09-04	2007-08-14	2007-08-14	ENSG00000166908	ENSG00000166908			23786	protein-coding gene	gene with protein product			"""phosphatidylinositol-4-phosphate 5-kinase, type II, gamma"""	PIP5K2C		9367159	Standard	NM_024779		Approved	FLJ22055	uc001sot.3	Q8TBX8	OTTHUMG00000170144	ENST00000354947.5:c.132C>T	12.37:g.57985204C>T		233	1		338	11	NM_001146258	0	0	0	0	0	B2RDL3|B4DM11|B4DY44|Q9H6N2	Silent	SNP	ENST00000354947.5	37	CCDS8946.1																																																																																			C|0.763;T|0.237		0.662	PIP4K2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407644.1	NM_024779	
AMDHD1	144193	hgsc.bcm.edu	37	12	96337225	96337225	+	Silent	SNP	C	C	T	rs1436121	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:96337225C>T	ENST00000266736.2	+	1	155	c.49C>T	c.(49-51)Ctg>Ttg	p.L17L	CCDC38_ENST00000546386.1_5'Flank|CCDC38_ENST00000344280.3_5'Flank|CCDC38_ENST00000549752.1_5'Flank	NM_152435.2	NP_689648.2	Q96NU7	HUTI_HUMAN	amidohydrolase domain containing 1	17					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	imidazolonepropionase activity (GO:0050480)|metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|skin(1)	22						GCAAGTGGTGCTGGTGTGCGC	0.741													C|||	1276	0.254792	0.09	0.1297	5008	,	,		11076	0.4732		0.2445	False		,,,				2504	0.3517				p.L17L		.											.	AMDHD1-90	0			c.C49T						.	C		259,2703		9,241,1231	3.0	4.0	4.0		49	1.4	1.0	12	dbSNP_88	4	983,4553		75,833,1860	no	coding-synonymous	AMDHD1	NM_152435.2		84,1074,3091	TT,TC,CC		17.7565,8.7441,14.6152		17/427	96337225	1242,7256	1481	2768	4249	SO:0001819	synonymous_variant	144193	exon1			GTGGTGCTGGTGT	AB075878	CCDS9057.1	12q23.1	2006-02-02				ENSG00000139344			28577	protein-coding gene	gene with protein product							Standard	NM_152435		Approved	MGC35366	uc001tel.2	Q96NU7	OTTHUMG00000170353	ENST00000266736.2:c.49C>T	12.37:g.96337225C>T		0	0		9	8	NM_152435	0	0	0	0	0	A8K463|Q68CI8	Silent	SNP	ENST00000266736.2	37	CCDS9057.1																																																																																			C|0.752;T|0.248		0.741	AMDHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408640.1	NM_152435	
SETD1B	23067	broad.mit.edu	37	12	122243905	122243905	+	Silent	SNP	C	C	T	rs1168666	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:122243905C>T	ENST00000604567.1	+	4	506	c.438C>T	c.(436-438)atC>atT	p.I146I	SETD1B_ENST00000542440.1_Silent_p.I146I|SETD1B_ENST00000267197.5_Silent_p.I146I|RHOF_ENST00000545544.1_5'Flank			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	146	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						ACCTGGGCATCGCCAAGGTGG	0.552													C|||	3747	0.748203	0.4054	0.8372	5008	,	,		14717	0.9425		0.8101	False		,,,				2504	0.8845				p.I146I		.											.	SETD1B-86	0			c.C438T						.	C		647,737		149,349,194	123.0	116.0	118.0		438	-8.1	0.8	12	dbSNP_87	118	2581,601		1048,485,58	no	coding-synonymous	SETD1B	NM_015048.1		1197,834,252	TT,TC,CC		18.8875,46.7486,29.3035		146/1924	122243905	3228,1338	692	1591	2283	SO:0001819	synonymous_variant	23067	exon3			GGGCATCGCCAAG	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.438C>T	12.37:g.122243905C>T		263	1		315	7	NM_015048	0	0	0	0	0	F6MFW1	Silent	SNP	ENST00000604567.1	37																																																																																				C|0.273;T|0.727		0.552	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
SETD1B	23067	broad.mit.edu	37	12	122248078	122248078	+	Silent	SNP	A	A	C			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:122248078A>C	ENST00000604567.1	+	6	1295	c.1227A>C	c.(1225-1227)ccA>ccC	p.P409P	SETD1B_ENST00000542440.1_Silent_p.P409P|SETD1B_ENST00000267197.5_Silent_p.P409P			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	409	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						ACTTCCCTCCACCCCCGGAAG	0.672																																					p.P409P		.											.	SETD1B-86	0			c.A1227C						.																																			SO:0001819	synonymous_variant	23067	exon5			CCCTCCACCCCCG	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1227A>C	12.37:g.122248078A>C		54	6		86	17	NM_015048	0	0	0	0	0	F6MFW1	Silent	SNP	ENST00000604567.1	37																																																																																				.		0.672	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
FBRSL1	57666	hgsc.bcm.edu	37	12	133159733	133159733	+	Missense_Mutation	SNP	C	C	T	rs11550079	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr12:133159733C>T	ENST00000434748.2	+	17	3527	c.2507C>T	c.(2506-2508)gCc>gTc	p.A836V	FBRSL1_ENST00000261673.6_Missense_Mutation_p.A763V	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	836				A -> V (in Ref. 3; BAB13371). {ECO:0000305}.			poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						AAGGAGGAGGCCGCCAAGATG	0.761													C|||	2725	0.544129	0.4939	0.6225	5008	,	,		5355	0.7113		0.4026	False		,,,				2504	0.5297				p.A836V		.											.	FBRSL1-70	0			c.C2507T						.						2.0	6.0	5.0					12																	133159733		475	1282	1757	SO:0001583	missense	57666	exon17			AGGAGGCCGCCAA		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.2507C>T	12.37:g.133159733C>T	ENSP00000396160:p.Ala836Val	0	0		11	11	NM_001142641	0	0	0	0	0	Q86XQ1	Missense_Mutation	SNP	ENST00000434748.2	37	CCDS45010.1	1159	0.5306776556776557	248	0.5040650406504065	211	0.5828729281767956	393	0.6870629370629371	307	0.4050131926121372	c	9.709	1.156573	0.21454	.	.	ENSG00000112787	ENST00000434748;ENST00000261673	T;T	0.31769	1.48;1.49	3.17	-0.242	0.13039	.	0.664906	0.15256	U	0.272063	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	P	0.44627	0.839	B	0.40134	0.32	T	0.26677	-1.0096	9	0.45353	T	0.12	-3.3224	5.7681	0.18237	0.1838:0.5714:0.2447:0.0	rs11550079	836	Q9HCM7	FBSL_HUMAN	V	836;763	ENSP00000396160:A836V;ENSP00000261673:A763V	ENSP00000261673:A763V	A	+	2	0	FBRSL1	131669806	0.317000	0.24589	0.004000	0.12327	0.011000	0.07611	0.750000	0.26334	0.431000	0.26258	-0.720000	0.03607	GCC	C|0.470;T|0.530		0.761	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
SPERT	220082	hgsc.bcm.edu	37	13	46288017	46288017	+	Nonsense_Mutation	SNP	C	C	A	rs79707842	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr13:46288017C>A	ENST00000310521.1	+	3	937	c.857C>A	c.(856-858)tCa>tAa	p.S286*	SPERT_ENST00000378966.3_Nonsense_Mutation_p.S250*	NM_152719.1	NP_689932.1	Q8NA61	SPERT_HUMAN	spermatid associated	286						cytoplasmic membrane-bounded vesicle (GO:0016023)				NS(1)|central_nervous_system(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	15		Breast(56;0.000819)|Lung NSC(96;0.00227)|Prostate(109;0.00703)|Lung SC(185;0.0367)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;7.26e-05)		CCCGCCCCCTCACCCCACGAG	0.721													c|||	310	0.061901	0.0068	0.0865	5008	,	,		14469	0.0982		0.0875	False		,,,				2504	0.0552				p.S286X		.											.	SPERT-91	0			c.C857A						.		stop/SER	36,3866		0,36,1915	5.0	8.0	7.0		857	3.2	0.0	13	dbSNP_131	7	419,7219		3,413,3403	no	stop-gained	SPERT	NM_152719.1		3,449,5318	AA,AC,CC		5.4857,0.9226,3.9428		286/449	46288017	455,11085	1951	3819	5770	SO:0001587	stop_gained	220082	exon3			CCCCCTCACCCCA	AK093129	CCDS9399.1, CCDS66540.1	13q14.13	2010-03-23			ENSG00000174015	ENSG00000174015			30720	protein-coding gene	gene with protein product	"""spermatid flower-like structure protein"", ""testis specific leucine zipper protein nurit"", ""chibby homolog 2 (Drosophila)"""					12204287, 20096028	Standard	NM_001286341		Approved	NURIT, CBY2	uc001van.1	Q8NA61	OTTHUMG00000016861	ENST00000310521.1:c.857C>A	13.37:g.46288017C>A	ENSP00000309189:p.Ser286*	0	0		18	6	NM_152719	0	0	0	0	0	A8K8I5|Q8NHV2	Nonsense_Mutation	SNP	ENST00000310521.1	37	CCDS9399.1	161	0.07371794871794872	6	0.012195121951219513	23	0.06353591160220995	68	0.11888111888111888	64	0.08443271767810026	C	21.5	4.165935	0.78339	0.009226	0.054857	ENSG00000174015	ENST00000310521;ENST00000378966	.	.	.	5.05	3.24	0.37175	.	0.731762	0.12237	N	0.486921	.	.	.	.	.	.	0.09310	P	0.9999999999958166	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.5116	0.27577	0.1627:0.751:0.0:0.0863	.	.	.	.	X	286;250	.	ENSP00000309189:S286X	S	+	2	0	SPERT	45186018	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	0.355000	0.20163	1.350000	0.45770	0.655000	0.94253	TCA	C|0.925;A|0.075		0.721	SPERT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044786.2	NM_152719	
ING1	3621	hgsc.bcm.edu	37	13	111368316	111368316	+	Silent	SNP	C	C	T	rs9555726	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr13:111368316C>T	ENST00000375774.3	+	1	988	c.526C>T	c.(526-528)Ctg>Ttg	p.L176L	ING1_ENST00000464141.1_Intron|ING1_ENST00000375775.3_Intron|ING1_ENST00000333219.7_Intron|ING1_ENST00000338450.7_Intron|CARS2_ENST00000535398.1_5'Flank	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	176					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			GGCCGCATCTCTGCTGACCCG	0.706													C|||	2912	0.58147	0.23	0.6816	5008	,	,		11066	0.7252		0.6909	False		,,,				2504	0.7249				p.L176L		.											.	ING1-515	0			c.C526T						.	C	,,,	1347,2085		295,757,664	14.0	24.0	21.0		526,,,	-5.6	0.0	13	dbSNP_119	21	5238,1736		2020,1198,269	no	coding-synonymous,intron,intron,intron	ING1	NM_005537.3,NM_198217.1,NM_198218.1,NM_198219.1	,,,	2315,1955,933	TT,TC,CC		24.8925,39.2483,36.7192	,,,	176/423,,,	111368316	6585,3821	1716	3487	5203	SO:0001819	synonymous_variant	3621	exon1			GCATCTCTGCTGA		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"""Zinc fingers, PHD-type"""	6062	protein-coding gene	gene with protein product	"""inhibitor of growth 1"", ""tumor suppressor ING1"", ""growth inhibitor ING1"", ""growth inhibitory protein ING1"""	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.526C>T	13.37:g.111368316C>T		0	0		7	7	NM_005537	0	0	0	0	0	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Silent	SNP	ENST00000375774.3	37	CCDS9517.1																																																																																			C|0.372;T|0.628		0.706	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537	
FRMD6	122786	bcgsc.ca	37	14	52186966	52186966	+	Silent	SNP	G	G	A	rs2277495	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr14:52186966G>A	ENST00000344768.5	+	11	1414	c.1218G>A	c.(1216-1218)acG>acA	p.T406T	FRMD6_ENST00000356218.4_Silent_p.T398T|FRMD6_ENST00000554167.1_Silent_p.T329T|FRMD6_ENST00000395718.2_Silent_p.T398T|FRMD6_ENST00000553556.1_Silent_p.T48T			Q96NE9	FRMD6_HUMAN	FERM domain containing 6	406					apical constriction (GO:0003383)|cellular protein localization (GO:0034613)|regulation of actin filament-based process (GO:0032970)	apical junction complex (GO:0043296)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(7)|large_intestine(7)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_epithelial(31;0.0163)|Breast(41;0.089)					CCCGGGACACGGGGCCAGAAG	0.617													G|||	1149	0.229433	0.1021	0.2795	5008	,	,		17792	0.2649		0.3211	False		,,,				2504	0.2352				p.T406T		.											.	FRMD6-524	0			c.G1218A						.	G	,	550,3856	248.1+/-256.1	45,460,1698	64.0	61.0	62.0		1194,1194	-12.0	0.0	14	dbSNP_100	62	2673,5927	428.0+/-355.8	395,1883,2022	no	coding-synonymous,coding-synonymous	FRMD6	NM_001042481.1,NM_152330.3	,	440,2343,3720	AA,AG,GG		31.0814,12.483,24.7809	,	398/615,398/615	52186966	3223,9783	2203	4300	6503	SO:0001819	synonymous_variant	122786	exon11			GGACACGGGGCCA	BI465118	CCDS9704.1, CCDS58318.1, CCDS58319.1	14q22.1	2011-06-22	2005-07-20	2005-07-20	ENSG00000139926	ENSG00000139926			19839	protein-coding gene	gene with protein product	"""expanded homolog"""	614555	"""chromosome 14 open reading frame 31"""	C14orf31			Standard	NM_152330		Approved	MGC17921, willin, EX1	uc001wzd.3	Q96NE9	OTTHUMG00000140294	ENST00000344768.5:c.1218G>A	14.37:g.52186966G>A		132	1		198	8	NM_001267046	0	0	0	0	0	D3DSB9|Q5HYF2|Q8N2X1|Q8WUH7	Silent	SNP	ENST00000344768.5	37	CCDS58318.1																																																																																			T|0.062;G|0.558;C|0.194;A|0.186		0.617	FRMD6-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276881.1	NM_152330	
EXOC3L4	91828	hgsc.bcm.edu	37	14	103568729	103568729	+	Silent	SNP	A	A	G	rs10142200	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr14:103568729A>G	ENST00000380069.3	+	2	745	c.669A>G	c.(667-669)gaA>gaG	p.E223E		NM_001077594.1	NP_001071062.1	Q17RC7	EX3L4_HUMAN	exocyst complex component 3-like 4	223					exocytosis (GO:0006887)	exocyst (GO:0000145)				cervix(2)|endometrium(2)|lung(4)|ovary(1)|skin(1)	10						CGGAGGAGGAAGCCCACCCTT	0.756													G|||	2646	0.528355	0.5666	0.5303	5008	,	,		12079	0.6042		0.3917	False		,,,				2504	0.5378				p.E223E		.											.	EXOC3L4-23	0			c.A669G						.	G		2098,2000		603,892,554	5.0	5.0	5.0		669	2.5	0.8	14	dbSNP_119	5	2949,5055		663,1623,1716	no	coding-synonymous	EXOC3L4	NM_001077594.1		1266,2515,2270	GG,GA,AA		36.8441,48.8043,41.7039		223/723	103568729	5047,7055	2049	4002	6051	SO:0001819	synonymous_variant	91828	exon2			GGAGGAAGCCCAC	AK000671	CCDS32163.1	14q32.32	2011-01-31	2011-01-31	2011-01-31	ENSG00000205436	ENSG00000205436			20120	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 73"""	C14orf73			Standard	NM_001077594		Approved		uc001ymk.3	Q17RC7		ENST00000380069.3:c.669A>G	14.37:g.103568729A>G		0	0		6	6	NM_001077594	0	0	0	0	0	Q14CR2	Silent	SNP	ENST00000380069.3	37	CCDS32163.1																																																																																			A|0.486;G|0.514		0.756	EXOC3L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415663.1	XM_941093	
ARHGAP11A	9824	broad.mit.edu;bcgsc.ca	37	15	32921898	32921898	+	Missense_Mutation	SNP	A	A	G			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:32921898A>G	ENST00000361627.3	+	8	1762	c.1040A>G	c.(1039-1041)aAg>aGg	p.K347R	ARHGAP11A_ENST00000543522.1_Missense_Mutation_p.K158R|ARHGAP11A_ENST00000567348.1_Missense_Mutation_p.K347R|ARHGAP11A_ENST00000565905.1_Missense_Mutation_p.K158R|ARHGAP11A_ENST00000563864.1_Missense_Mutation_p.K347R	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	347					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AAGTCCATCAAGCACAATTTT	0.368																																					p.K347R	Colon(45;757 1134 30003 36652)	.											.	ARHGAP11A-292	0			c.A1040G						.						84.0	86.0	85.0					15																	32921898		2201	4297	6498	SO:0001583	missense	9824	exon8			CCATCAAGCACAA	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.1040A>G	15.37:g.32921898A>G	ENSP00000355090:p.Lys347Arg	160	1		170	27	NM_199357	0	0	0	0	0	B4DZN9|Q6PI96|Q9Y3S6	Missense_Mutation	SNP	ENST00000361627.3	37	CCDS10028.1	.	.	.	.	.	.	.	.	.	.	.	13.58	2.280577	0.40294	.	.	ENSG00000198826	ENST00000361627;ENST00000543522	D;D	0.92911	-3.13;-3.13	5.39	2.98	0.34508	.	0.229315	0.29995	N	0.010679	D	0.88665	0.6498	L	0.52266	1.64	0.45342	D	0.998333	P;P	0.45715	0.836;0.865	B;P	0.46585	0.245;0.521	D	0.85316	0.1081	10	0.33940	T	0.23	.	5.3455	0.16006	0.7271:0.0:0.1364:0.1365	.	347;158	Q6P4F7;B4DZN9	RHGBA_HUMAN;.	R	347;158	ENSP00000355090:K347R;ENSP00000440073:K158R	ENSP00000355090:K347R	K	+	2	0	ARHGAP11A	30709190	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	1.366000	0.34193	2.046000	0.60703	0.460000	0.39030	AAG	.		0.368	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
LTK	4058	hgsc.bcm.edu	37	15	41803754	41803754	+	Missense_Mutation	SNP	G	G	A	rs55739813	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:41803754G>A	ENST00000263800.6	-	6	776	c.680C>T	c.(679-681)cCg>cTg	p.P227L	LTK_ENST00000453182.2_Missense_Mutation_p.P227L|LTK_ENST00000355166.5_Missense_Mutation_p.P227L|LTK_ENST00000561619.1_Intron	NM_002344.5	NP_002335.2	P29376	LTK_HUMAN	leukocyte receptor tyrosine kinase	227					cell proliferation (GO:0008283)|cellular response to retinoic acid (GO:0071300)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of neuron projection development (GO:0010976)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(16)|skin(3)|urinary_tract(1)	26		all_cancers(109;1.89e-19)|all_epithelial(112;2.28e-16)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.172)		OV - Ovarian serous cystadenocarcinoma(18;2.1e-17)|GBM - Glioblastoma multiforme(113;1.34e-06)|Colorectal(105;0.0148)|BRCA - Breast invasive adenocarcinoma(123;0.113)		CACCAGCAACGGTTCCAGCTC	0.736										TSP Lung(18;0.14)			G|||	160	0.0319489	0.0038	0.0692	5008	,	,		8690	0.0119		0.0517	False		,,,				2504	0.044				p.P227L		.											.	LTK-1377	0			c.C680T						.	G	LEU/PRO,LEU/PRO,LEU/PRO	29,3047		0,29,1509	5.0	6.0	6.0		680,680,680	2.9	1.0	15	dbSNP_129	6	336,6434		4,328,3053	yes	missense,missense,missense	LTK	NM_001135685.1,NM_002344.5,NM_206961.3	98,98,98	4,357,4562	AA,AG,GG		4.9631,0.9428,3.7071	probably-damaging,probably-damaging,probably-damaging	227/735,227/865,227/804	41803754	365,9481	1538	3385	4923	SO:0001583	missense	4058	exon6			AGCAACGGTTCCA	D16105	CCDS10077.1, CCDS10078.1, CCDS45237.1	15q15.1-q21.1	2009-07-10	2008-01-23		ENSG00000062524	ENSG00000062524	2.7.10.1		6721	protein-coding gene	gene with protein product		151520	"""leukocyte tyrosine kinase"""			2320375	Standard	NM_206961		Approved	TYK1	uc001zoa.3	P29376	OTTHUMG00000130339	ENST00000263800.6:c.680C>T	15.37:g.41803754G>A	ENSP00000263800:p.Pro227Leu	0	0		14	7	NM_001135685	0	0	0	0	0	A6NNJ8|B4DL89|E9PFX4	Missense_Mutation	SNP	ENST00000263800.6	37	CCDS10077.1	80	0.03663003663003663	8	0.016260162601626018	26	0.0718232044198895	7	0.012237762237762238	39	0.051451187335092345	G	17.32	3.359770	0.61403	0.009428	0.049631	ENSG00000062524	ENST00000360087;ENST00000355166;ENST00000263800;ENST00000453182	T;T;T	0.40476	1.03;1.03;1.03	3.86	2.94	0.34122	.	.	.	.	.	T	0.09512	0.0234	M	0.62016	1.91	0.39097	D	0.961214	P;P;D	0.89917	0.658;0.606;1.0	B;B;D	0.97110	0.164;0.102;1.0	T	0.26052	-1.0114	9	0.87932	D	0	.	10.0097	0.41979	0.1032:0.0:0.8968:0.0	rs55739813	227;227;227	E9PFX4;P29376-4;P29376	.;.;LTK_HUMAN	L	227	ENSP00000347293:P227L;ENSP00000263800:P227L;ENSP00000392196:P227L	ENSP00000263800:P227L	P	-	2	0	LTK	39591046	1.000000	0.71417	0.999000	0.59377	0.333000	0.28666	5.205000	0.65186	0.603000	0.29913	0.455000	0.32223	CCG	G|0.962;A|0.038		0.736	LTK-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252690.2		
LACTB	114294	hgsc.bcm.edu	37	15	63414083	63414083	+	Missense_Mutation	SNP	A	A	C	rs34317102	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:63414083A>C	ENST00000261893.4	+	1	85	c.13A>C	c.(13-15)Atg>Ctg	p.M5L	LACTB_ENST00000413507.2_Missense_Mutation_p.M5L	NM_032857.3	NP_116246.2	P83111	LACTB_HUMAN	lactamase, beta	5				M -> L (in Ref. 1 and 2). {ECO:0000305}.		cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|stomach(1)	12						GTACCGGCTCATGTCAGCAGT	0.751													C|||	3981	0.794928	0.6725	0.8256	5008	,	,		8367	0.997		0.7316	False		,,,				2504	0.7955				p.M5L	Melanoma(85;443 1381 6215 27308 35583)	.											.	LACTB-90	0			c.A13C						.	C	LEU/MET,LEU/MET	1936,668		733,470,99	4.0	4.0	4.0		13,13	3.1	1.0	15	dbSNP_126	4	4375,1183		1737,901,141	yes	missense,missense	LACTB	NM_032857.3,NM_171846.2	15,15	2470,1371,240	CC,CA,AA		21.2846,25.6528,22.6783	benign,benign	5/548,5/374	63414083	6311,1851	1302	2779	4081	SO:0001583	missense	114294	exon1			CGGCTCATGTCAG	AK027808	CCDS10182.1, CCDS45275.1	15q22.1	2012-11-14	2001-12-12	2001-12-14	ENSG00000103642	ENSG00000103642		"""Mitochondrial ribosomal proteins / large subunits"""	16468	protein-coding gene	gene with protein product		608440	"""mitochondrial ribosomal protein L56"""	MRPL56		11707067	Standard	NM_032857		Approved	FLJ14902	uc002alw.3	P83111	OTTHUMG00000132807	ENST00000261893.4:c.13A>C	15.37:g.63414083A>C	ENSP00000261893:p.Met5Leu	0	0		7	6	NM_171846	0	0	0	0	0	P83096	Missense_Mutation	SNP	ENST00000261893.4	37	CCDS10182.1	1713	0.7843406593406593	304	0.6178861788617886	287	0.7928176795580111	568	0.993006993006993	554	0.7308707124010554	C	0.674	-0.800779	0.02841	0.743472	0.787154	ENSG00000103642	ENST00000261893;ENST00000413507	T	0.33216	1.42	3.1	3.1	0.35709	.	0.592824	0.14749	N	0.300689	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.37842	-0.9688	9	0.02654	T	1	0.0321	7.626	0.28212	0.2541:0.7459:0.0:0.0	rs34317102	5	P83111	LACTB_HUMAN	L	5	ENSP00000261893:M5L	ENSP00000261893:M5L	M	+	1	0	LACTB	61201136	0.994000	0.37717	0.956000	0.39512	0.117000	0.20001	0.346000	0.19997	0.640000	0.30582	-0.677000	0.03784	ATG	A|0.226;C|0.774		0.751	LACTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256224.1	NM_032857	
SMAD6	4091	hgsc.bcm.edu	37	15	66995915	66995915	+	Missense_Mutation	SNP	G	G	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:66995915G>T	ENST00000288840.5	+	1	1350	c.319G>T	c.(319-321)Gtg>Ttg	p.V107L	SMAD6_ENST00000457357.2_Missense_Mutation_p.V107L	NM_005585.4	NP_005576.3	O43541	SMAD6_HUMAN	SMAD family member 6	107					BMP signaling pathway (GO:0030509)|cell-substrate adhesion (GO:0031589)|fat cell differentiation (GO:0045444)|immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell proliferation (GO:0008285)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of SMAD protein complex assembly (GO:0010991)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|response to estrogen (GO:0043627)|response to laminar fluid shear stress (GO:0034616)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ureteric bud development (GO:0001657)|zygotic specification of dorsal/ventral axis (GO:0007352)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|protein complex (GO:0043234)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|I-SMAD binding (GO:0070411)|metal ion binding (GO:0046872)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|transforming growth factor beta receptor, inhibitory cytoplasmic mediator activity (GO:0030617)|type I activin receptor binding (GO:0070698)|type I transforming growth factor beta receptor binding (GO:0034713)|ubiquitin protein ligase binding (GO:0031625)			lung(1)|skin(1)	2						CCTGCTGGACGTGGCGGAGCC	0.786																																					p.V107L	Esophageal Squamous(179;72 2004 22333 39628 47290)	.											.	SMAD6-415	0			c.G319T						.						2.0	3.0	3.0					15																	66995915		1609	3272	4881	SO:0001583	missense	4091	exon1			CTGGACGTGGCGG	BC012986	CCDS10221.1	15q22.31	2014-09-11	2006-11-06	2004-05-26	ENSG00000137834	ENSG00000137834		"""SMADs"""	6772	protein-coding gene	gene with protein product		602931	"""MAD, mothers against decapentaplegic homolog 6 (Drosophila)"", ""SMAD, mothers against DPP homolog 6 (Drosophila)"""	MADH7, MADH6		9256479	Standard	NR_027654		Approved	HsT17432	uc002aqf.3	O43541	OTTHUMG00000133218	ENST00000288840.5:c.319G>T	15.37:g.66995915G>T	ENSP00000288840:p.Val107Leu	0	0		27	4	NM_005585	0	0	0	0	0	A9J6M5|O43654|Q15799|Q7Z7L4|Q96E31|Q9UKZ3	Missense_Mutation	SNP	ENST00000288840.5	37	CCDS10221.1	.	.	.	.	.	.	.	.	.	.	G	5.899	0.350022	0.11182	.	.	ENSG00000137834	ENST00000288840;ENST00000457357	T;T	0.75260	-0.92;-0.92	3.95	0.6	0.17524	.	0.708972	0.13270	N	0.400616	T	0.53578	0.1805	N	0.24115	0.695	0.58432	D	0.999997	B	0.02656	0.0	B	0.06405	0.002	T	0.29518	-1.0009	10	0.16896	T	0.51	.	5.8968	0.18943	0.0:0.1901:0.4202:0.3896	.	107	O43541	SMAD6_HUMAN	L	107	ENSP00000288840:V107L;ENSP00000396961:V107L	ENSP00000288840:V107L	V	+	1	0	SMAD6	64782969	0.000000	0.05858	0.895000	0.35142	0.070000	0.16714	0.097000	0.15168	0.150000	0.19136	-0.856000	0.03024	GTG	.		0.786	SMAD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256953.2	NM_005585	
SKOR1	390598	hgsc.bcm.edu	37	15	68120014	68120014	+	Silent	SNP	C	C	T	rs62015251	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:68120014C>T	ENST00000380035.2	+	2	1906	c.1848C>T	c.(1846-1848)taC>taT	p.Y616Y	SKOR1_ENST00000554054.1_Silent_p.Y588Y|SKOR1_ENST00000554240.1_Silent_p.Y577Y|SKOR1_ENST00000341418.5_Silent_p.Y556Y|SKOR1_ENST00000389002.1_Silent_p.Y572Y			P84550	SKOR1_HUMAN	SKI family transcriptional corepressor 1	616					negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	SMAD binding (GO:0046332)|transcription corepressor activity (GO:0003714)			endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(7)|urinary_tract(1)	23						GGGAGGCGTACGGCGCGGGGC	0.716													C|||	430	0.0858626	0.0106	0.121	5008	,	,		9530	0.1101		0.1193	False		,,,				2504	0.1033				p.Y556Y		.											.	SKOR1-90	0			c.C1668T						.	C		62,3022		0,62,1480	3.0	4.0	4.0		1716	-1.9	0.1	15	dbSNP_129	4	460,5730		9,442,2644	no	coding-synonymous	SKOR1	NM_001031807.1		9,504,4124	TT,TC,CC		7.4313,2.0104,5.6286		572/922	68120014	522,8752	1542	3095	4637	SO:0001819	synonymous_variant	390598	exon7			GGCGTACGGCGCG		CCDS58374.1	15q23	2011-08-04	2010-06-23	2010-06-23	ENSG00000188779	ENSG00000188779		"""SKI transcriptional corepressors"""	21326	protein-coding gene	gene with protein product	"""transcriptional corepressor CORL1"", ""functional smad suppressing element 15"", ""corepressor for LBX1"""	611273	"""Lbxcor1 homolog (mouse)"""	LBXCOR1		15528197	Standard	NM_001258024		Approved	CORL1, FUSSEL15	uc031qsn.1	P84550		ENST00000380035.2:c.1848C>T	15.37:g.68120014C>T		2	0		16	13	NM_001258024	0	0	0	0	0	A6NIP4|A6NJY0|Q2VWA5	Silent	SNP	ENST00000380035.2	37																																																																																				C|0.908;T|0.092		0.716	SKOR1-003	KNOWN	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000410832.1	NM_001031807	
MYO9A	4649	bcgsc.ca	37	15	72193564	72193564	+	Missense_Mutation	SNP	G	G	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:72193564G>T	ENST00000356056.5	-	23	3590	c.3118C>A	c.(3118-3120)Ctc>Atc	p.L1040I	MYO9A_ENST00000566885.1_Missense_Mutation_p.L660I|MYO9A_ENST00000564571.1_Missense_Mutation_p.L1040I|MYO9A_ENST00000563542.1_5'UTR|MYO9A_ENST00000424560.1_Missense_Mutation_p.L1040I|MYO9A_ENST00000444904.1_Missense_Mutation_p.L1021I	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1040	IQ 1. {ECO:0000255|PROSITE- ProRule:PRU00116}.|Neck or regulatory domain.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						CTCAGATGGAGGAAATGCTGC	0.448																																					p.L1040I		.											.	MYO9A-93	0			c.C3118A						.						125.0	104.0	111.0					15																	72193564		2199	4297	6496	SO:0001583	missense	4649	exon23			GATGGAGGAAATG	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.3118C>A	15.37:g.72193564G>T	ENSP00000348349:p.Leu1040Ile	113	0		119	5	NM_006901	0	0	0	0	0	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	.	.	.	.	.	.	.	.	.	.	G	25.3	4.625905	0.87560	.	.	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904;ENST00000261864	T;T;T	0.73047	-0.71;-0.71;-0.71	6.07	5.16	0.70880	.	.	.	.	.	T	0.69387	0.3105	L	0.48362	1.52	0.48975	D	0.999739	D;P;P	0.54207	0.965;0.638;0.745	P;B;B	0.47470	0.548;0.275;0.299	T	0.68496	-0.5393	9	0.33141	T	0.24	.	15.1361	0.72566	0.0673:0.0:0.9327:0.0	.	1021;1021;1040	B2RTY4-2;B7WP69;B2RTY4	.;.;MYO9A_HUMAN	I	1040;1040;1021;1021	ENSP00000348349:L1040I;ENSP00000399162:L1040I;ENSP00000398250:L1021I	ENSP00000261864:L1021I	L	-	1	0	MYO9A	69980618	1.000000	0.71417	0.974000	0.42286	0.985000	0.73830	2.491000	0.45303	1.571000	0.49722	0.655000	0.94253	CTC	.		0.448	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
ZNF710	374655	broad.mit.edu	37	15	90611149	90611149	+	Silent	SNP	T	T	G	rs201433675		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr15:90611149T>G	ENST00000268154.4	+	2	1031	c.780T>G	c.(778-780)ggT>ggG	p.G260G		NM_198526.2	NP_940928.2	Q8N1W2	ZN710_HUMAN	zinc finger protein 710	260					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(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(1)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	19	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.00769)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.129)			ACACGGCGGGTTCGACCGTGG	0.652																																					p.G260G		.											.	ZNF710-90	0			c.T780G						.						37.0	46.0	43.0					15																	90611149		2197	4292	6489	SO:0001819	synonymous_variant	374655	exon2			GGCGGGTTCGACC	AK094712	CCDS10358.1	15q26.1	2013-01-08			ENSG00000140548	ENSG00000140548		"""Zinc fingers, C2H2-type"""	25352	protein-coding gene	gene with protein product							Standard	XM_005254905		Approved	DKFZp547K1113, FLJ37393, FLJ00306	uc002bov.2	Q8N1W2	OTTHUMG00000149812	ENST00000268154.4:c.780T>G	15.37:g.90611149T>G		108	35		149	44	NM_198526	0	0	0	0	0	A0AVS3|Q6ZMK9|Q8NDU0	Silent	SNP	ENST00000268154.4	37	CCDS10358.1																																																																																			.		0.652	ZNF710-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313423.1	NM_198526	
FAM173A	65990	hgsc.bcm.edu	37	16	771286	771286	+	Silent	SNP	C	C	T	rs11540049	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:771286C>T	ENST00000569529.1	+	1	312	c.12C>T	c.(10-12)gaC>gaT	p.D4D	FAM173A_ENST00000219535.3_Silent_p.D4D|FAM173A_ENST00000564000.1_Silent_p.D4D	NM_023933.2	NP_076422.1	Q9BQD7	F173A_HUMAN	family with sequence similarity 173, member A	4						integral component of membrane (GO:0016021)				pancreas(1)	1						TGGAGCAGGACGACCCGGTCG	0.776													C|||	2702	0.539537	0.4576	0.5144	5008	,	,		9107	0.5337		0.4553	False		,,,				2504	0.7607				p.D4D		.											.	FAM173A-91	0			c.C12T						.						1.0	1.0	1.0					16																	771286		542	1076	1618	SO:0001819	synonymous_variant	65990	exon1			GCAGGACGACCCG	BC002624	CCDS10423.1, CCDS59254.1	16p13.3	2008-06-19	2008-06-19	2008-06-19	ENSG00000103254	ENSG00000103254			14152	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 24"""	C16orf24			Standard	NM_023933		Approved	MGC2494	uc002cje.4	Q9BQD7	OTTHUMG00000121177	ENST00000569529.1:c.12C>T	16.37:g.771286C>T		0	0		4	4	NM_001271285	0	0	0	0	0	A2IDD4	Silent	SNP	ENST00000569529.1	37	CCDS10423.1																																																																																			C|0.504;T|0.496		0.776	FAM173A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241667.2	NM_023933	
HAGHL	84264	hgsc.bcm.edu	37	16	779402	779402	+	3'UTR	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:779402G>A	ENST00000341413.4	+	0	1388				HAGHL_ENST00000389703.3_Silent_p.A265A|CCDC78_ENST00000293889.6_5'Flank|HAGHL_ENST00000564537.1_3'UTR|HAGHL_ENST00000549114.1_3'UTR|NARFL_ENST00000562862.1_5'Flank			Q6PII5	HAGHL_HUMAN	hydroxyacylglutathione hydrolase-like								hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			lung(3)	3		Hepatocellular(780;0.00335)				AGCCACAGGCGCGGGCCCTCC	0.721																																					p.A265A	Pancreas(46;538 1326 12403 32360)	.											.	HAGHL-90	0			c.G795A						.						2.0	3.0	3.0					16																	779402		1501	3083	4584	SO:0001624	3_prime_UTR_variant	84264	exon8			ACAGGCGCGGGCC	AK054841	CCDS32354.1	16p13.3	2008-02-05	2003-11-04						14177	protein-coding gene	gene with protein product			"""hydroxyacyl glutathione hydrolase-like"""			12477932	Standard	XM_005255629		Approved	MGC2605	uc002cjo.1	Q6PII5		ENST00000341413.4:c.*234G>A	16.37:g.779402G>A		0	0		28	5	NM_032304	0	0	0	0	0	A6NCC4|D3DU64|Q59FX8|Q96BZ3|Q96NR5|Q96S11|Q9BT45	Silent	SNP	ENST00000341413.4	37																																																																																				.		0.721	HAGHL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409607.1	NM_032304	
MRPS34	65993	hgsc.bcm.edu	37	16	1822947	1822947	+	Silent	SNP	C	C	G	rs1076695	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:1822947C>G	ENST00000397375.2	-	1	209	c.174G>C	c.(172-174)gtG>gtC	p.V58V	EME2_ENST00000307394.7_5'Flank|MRPS34_ENST00000177742.3_Silent_p.V58V|NME3_ENST00000219302.3_5'Flank|EME2_ENST00000568449.1_5'Flank|NME3_ENST00000563498.1_5'Flank	NM_023936.1	NP_076425.1	P82930	RT34_HUMAN	mitochondrial ribosomal protein S34	58						mitochondrion (GO:0005739)|ribosome (GO:0005840)				breast(1)|skin(2)	3						TCTCGCGGCGCACGTCGGCCC	0.726													C|||	251	0.0501198	0.0061	0.0965	5008	,	,		10499	0.002		0.1421	False		,,,				2504	0.0317				p.V58V		.											.	MRPS34-92	0			c.G174C						.	C		25,2311		0,25,1143	1.0	2.0	2.0		174	1.7	1.0	16	dbSNP_86	2	405,4871		9,387,2242	no	coding-synonymous	MRPS34	NM_023936.1		9,412,3385	GG,GC,CC		7.6763,1.0702,5.649		58/219	1822947	430,7182	1168	2638	3806	SO:0001819	synonymous_variant	65993	exon1			GCGGCGCACGTCG	BC001182	CCDS10444.1, CCDS73805.1	16p13.3	2012-09-13			ENSG00000074071	ENSG00000074071		"""Mitochondrial ribosomal proteins / small subunits"""	16618	protein-coding gene	gene with protein product		611994					Standard	NM_023936		Approved	MRP-S12, MGC2616	uc002cmo.3	P82930	OTTHUMG00000128636	ENST00000397375.2:c.174G>C	16.37:g.1822947C>G		0	0		5	4	NM_023936	0	0	0	0	0	Q9BVI7	Silent	SNP	ENST00000397375.2	37	CCDS10444.1																																																																																			C|0.923;G|0.077		0.726	MRPS34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250506.1	NM_023936	
ZNF598	90850	hgsc.bcm.edu	37	16	2059674	2059674	+	Missense_Mutation	SNP	T	T	C	rs71384660		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:2059674T>C	ENST00000431526.1	-	2	88	c.74A>G	c.(73-75)gAa>gGa	p.E25G	ZNF598_ENST00000562103.1_5'UTR|ZNF598_ENST00000563630.1_5'UTR	NM_178167.2	NP_835461.2	Q86UK7	ZN598_HUMAN	zinc finger protein 598	25							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GCTCCCGCCTTCCCGCTCAGG	0.766													C|||	5008	1.0	1.0	1.0	5008	,	,		5162	1.0		1.0	False		,,,				2504	1.0				p.E25G		.											.	ZNF598-432	0			c.A74G						.						1.0	2.0	2.0					16																	2059674		1089	2314	3403	SO:0001583	missense	90850	exon2			CCGCCTTCCCGCT	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000431526.1:c.74A>G	16.37:g.2059674T>C	ENSP00000411409:p.Glu25Gly	0	0		6	6	NM_178167	0	0	0	0	0	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Missense_Mutation	SNP	ENST00000431526.1	37		2168	0.9926739926739927	487	0.9898373983739838	361	0.9972375690607734	568	0.993006993006993	752	0.9920844327176781	N	1.560	-0.537056	0.04082	.	.	ENSG00000167962	ENST00000431526	T	0.77098	-1.07	3.3	3.3	0.37823	.	0.415485	0.23105	N	0.051871	T	0.00012	0.0000	.	.	.	0.48696	P	3.1000000000003247E-4	.	.	.	.	.	.	T	0.34650	-0.9820	6	0.22706	T	0.39	-7.8624	8.393	0.32540	0.0:0.8796:0.0:0.1204	.	.	.	.	G	25	ENSP00000411409:E25G	ENSP00000411409:E25G	E	-	2	0	ZNF598	1999675	1.000000	0.71417	1.000000	0.80357	0.107000	0.19398	0.911000	0.28584	0.691000	0.31592	-0.642000	0.03964	GAA	T|0.007;C|0.993		0.766	ZNF598-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178167	
SRRM2	23524	bcgsc.ca	37	16	2812939	2812939	+	Missense_Mutation	SNP	C	C	A	rs2240140	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:2812939C>A	ENST00000301740.8	+	11	2959	c.2410C>A	c.(2410-2412)Cct>Act	p.P804T		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	804	Arg-rich.|Ser-rich.		P -> T (in dbSNP:rs2240140). {ECO:0000269|PubMed:9205841}.		mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						ATCCTCCCAACCTAAAGCTAA	0.517													C|||	2075	0.414337	0.0242	0.6873	5008	,	,		19376	0.372		0.6262	False		,,,				2504	0.5736				p.P804T		.											.	SRRM2-93	0			c.C2410A						.	C	THR/PRO	583,3813	257.4+/-261.8	45,493,1660	215.0	213.0	213.0		2410	3.4	0.5	16	dbSNP_98	213	5246,3354	642.5+/-399.8	1607,2032,661	yes	missense	SRRM2	NM_016333.3	38	1652,2525,2321	AA,AC,CC		39.0,13.2621,44.8523	benign	804/2753	2812939	5829,7167	2198	4300	6498	SO:0001583	missense	23524	exon11			TCCCAACCTAAAG	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2410C>A	16.37:g.2812939C>A	ENSP00000301740:p.Pro804Thr	61	0		65	5	NM_016333	0	0	0	0	0	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	923	0.4226190476190476	10	0.02032520325203252	235	0.649171270718232	193	0.3374125874125874	485	0.6398416886543535	C	0.011	-1.693981	0.00731	0.132621	0.61	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.26373	1.74	5.36	3.39	0.38822	.	0.428538	0.22611	N	0.057840	T	0.00012	0.0000	L	0.27053	0.805	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.40270	-0.9572	9	0.10377	T	0.69	-3.8004	4.3612	0.11203	0.1608:0.5989:0.1556:0.0847	rs2240140;rs59555258;rs2240140	804	Q9UQ35	SRRM2_HUMAN	T	804;804;56;769	ENSP00000301740:P804T	ENSP00000301740:P804T	P	+	1	0	SRRM2	2752940	0.049000	0.20398	0.462000	0.27118	0.749000	0.42624	0.748000	0.26305	0.628000	0.30357	-0.181000	0.13052	CCT	C|0.569;A|0.431		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
USP31	57478	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	16	23079691	23079691	+	Silent	SNP	G	G	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:23079691G>T	ENST00000219689.7	-	16	3734	c.3735C>A	c.(3733-3735)ggC>ggA	p.G1245G	USP31_ENST00000567975.1_Silent_p.G538G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		AGGCTGTCTTGCCAAGATCCG	0.552																																					p.G1245G		.											.	USP31-663	0			c.C3735A						.						143.0	152.0	149.0					16																	23079691		2197	4300	6497	SO:0001819	synonymous_variant	57478	exon16			TGTCTTGCCAAGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.3735C>A	16.37:g.23079691G>T		53	0		75	6	NM_020718	0	0	0	0	0	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Silent	SNP	ENST00000219689.7	37	CCDS10607.1																																																																																			.		0.552	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
ZFPM1	161882	hgsc.bcm.edu	37	16	88599696	88599697	+	Frame_Shift_Del	DEL	GA	GA	-	rs368520732|rs67712719	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	GA	GA	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:88599696_88599697delGA	ENST00000319555.3	+	10	1652_1653	c.1330_1331delGA	c.(1330-1332)gagfs	p.E444fs	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	444				EPLA -> AP (in Ref. 1; AAN45858). {ECO:0000305}.	atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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 transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GGCCAGAGCGGAGCCTCTGGCC	0.743														4881	0.974641	0.9138	0.9914	5008	,	,		7261	0.996		1.0	False		,,,				2504	0.9969				p.444_444del	Pancreas(49;850 1106 29641 32847 38344)	.											.	ZFPM1-90	0			c.1330_1331del						.			2219,383		1063,93,145						-6.5	0.0		dbSNP_130	3	4709,133		2339,31,51	no	frameshift	ZFPM1	NM_153813.2		3402,124,196	A1A1,A1R,RR		2.7468,14.7194,6.9318				6928,516				SO:0001589	frameshift_variant	161882	exon10			AGAGCGGAGCCTC	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.1330_1331delGA	16.37:g.88599696_88599697delGA	ENSP00000326630:p.Glu444fs	0	0		14	10	NM_153813	0	0	0	0	0		Frame_Shift_Del	DEL	ENST00000319555.3	37	CCDS32502.1																																																																																			.		0.743	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
ZFPM1	161882	hgsc.bcm.edu	37	16	88599697	88599705	+	In_Frame_Del	DEL	AGCCTCTGG	AGCCTCTGG	-	rs67873604|rs149145771|rs368520732|rs67322929|rs201915453|rs67712719	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	AGCCTCTGG	AGCCTCTGG	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:88599697_88599705delAGCCTCTGG	ENST00000319555.3	+	10	1653_1661	c.1331_1339delAGCCTCTGG	c.(1330-1341)gagcctctggcc>gcc	p.EPL444del	RP11-21B21.4_ENST00000563243.1_RNA	NM_153813.2	NP_722520.2	Q8IX07	FOG1_HUMAN	zinc finger protein, FOG family member 1	444				EPLA -> AP (in Ref. 1; AAN45858). {ECO:0000305}.	atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|cardiac muscle tissue morphogenesis (GO:0055008)|definitive erythrocyte differentiation (GO:0060318)|embryonic hemopoiesis (GO:0035162)|erythrocyte differentiation (GO:0030218)|granulocyte differentiation (GO:0030851)|megakaryocyte development (GO:0035855)|megakaryocyte differentiation (GO:0030219)|mitral valve formation (GO:0003192)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of interleukin-4 biosynthetic process (GO:0045403)|negative regulation of mast cell differentiation (GO:0060377)|negative regulation of protein binding (GO:0032091)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|outflow tract morphogenesis (GO:0003151)|platelet formation (GO:0030220)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|primitive erythrocyte differentiation (GO:0060319)|regulation of chemokine production (GO:0032642)|regulation of definitive erythrocyte differentiation (GO:0010724)|T-helper cell lineage commitment (GO:0002295)|transcriptional activation by promoter-enhancer looping (GO:0071733)|tricuspid valve formation (GO:0003195)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|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 transcription factor binding (GO:0001085)|transcription factor binding (GO:0008134)			central_nervous_system(1)|ovary(2)|urinary_tract(1)	4				BRCA - Breast invasive adenocarcinoma(80;0.0478)		GCCAGAGCGGAGCCTCTGGCCCAGAATGG	0.746																																					p.444_447del	Pancreas(49;850 1106 29641 32847 38344)	.											.	ZFPM1-90	0			c.1331_1339del						.																																			SO:0001651	inframe_deletion	161882	exon10			GAGCGGAGCCTCT	AF488691	CCDS32502.1	16q24.2	2013-01-10	2012-11-27		ENSG00000179588	ENSG00000179588		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	19762	protein-coding gene	gene with protein product		601950	"""zinc finger protein, multitype 1"""				Standard	NM_153813		Approved	FOG1, FOG, ZNF89A, ZC2HC11A	uc002fkv.3	Q8IX07	OTTHUMG00000173152	ENST00000319555.3:c.1331_1339delAGCCTCTGG	16.37:g.88599697_88599705delAGCCTCTGG	ENSP00000326630:p.Glu444_Leu446del	0	0		12	0	NM_153813	0	0	0	0	0		In_Frame_Del	DEL	ENST00000319555.3	37	CCDS32502.1																																																																																			.		0.746	ZFPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422270.2		
RPL13	6137	hgsc.bcm.edu	37	16	89627671	89627671	+	Silent	SNP	C	C	T	rs174035	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:89627671C>T	ENST00000393099.3	+	2	390	c.141C>T	c.(139-141)gcC>gcT	p.A47A	RPL13_ENST00000452368.3_Silent_p.A47A|RPL13_ENST00000311528.5_Silent_p.A47A|SNORD68_ENST00000363214.1_RNA|RPL13_ENST00000567815.1_Silent_p.A47A	NM_033251.2	NP_150254.1	P26373	RL13_HUMAN	ribosomal protein L13	47					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|cytosolic ribosome (GO:0022626)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			lung(3)|skin(1)|upper_aerodigestive_tract(2)	6		all_hematologic(23;0.0748)		all cancers(4;1.15e-07)|OV - Ovarian serous cystadenocarcinoma(4;7.8e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0139)		GCCGCATCGCCCCGCGCCCCG	0.741													C|||	720	0.14377	0.1256	0.1282	5008	,	,		12083	0.13		0.1839	False		,,,				2504	0.1524				p.A47A		.											.	RPL13-90	0			c.C141T						.	C	,	382,2954		24,334,1310	3.0	4.0	3.0		141,141	0.9	1.0	16	dbSNP_79	3	1125,5851		71,983,2434	no	coding-synonymous,coding-synonymous	RPL13	NM_000977.3,NM_033251.2	,	95,1317,3744	TT,TC,CC		16.1267,11.4508,14.614	,	47/212,47/212	89627671	1507,8805	1668	3488	5156	SO:0001819	synonymous_variant	6137	exon3			CATCGCCCCGCGC	AB007172	CCDS10979.1, CCDS58492.1	16q24.3	2011-04-06			ENSG00000167526	ENSG00000167526		"""L ribosomal proteins"""	10303	protein-coding gene	gene with protein product		113703				9582194	Standard	NM_000977		Approved	D16S444E, BBC1, L13	uc002fnm.2	P26373	OTTHUMG00000133770	ENST00000393099.3:c.141C>T	16.37:g.89627671C>T		0	0		17	17	NM_001243131	0	0	0	0	0	B4DLX3|F5H1S2|Q3KQT8|Q567Q8|Q9BPX0	Silent	SNP	ENST00000393099.3	37	CCDS10979.1																																																																																			C|0.846;T|0.154		0.741	RPL13-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258294.2	NM_000977	
GLTPD2	388323	hgsc.bcm.edu	37	17	4693342	4693342	+	Missense_Mutation	SNP	C	C	A	rs35910358	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr17:4693342C>A	ENST00000331264.7	+	4	680	c.627C>A	c.(625-627)gaC>gaA	p.D209E		NM_001014985.2	NP_001014985	A6NH11	GLTD2_HUMAN	glycolipid transfer protein domain containing 2	209				D -> E (in Ref. 2; AAI50537). {ECO:0000305}.		cytoplasm (GO:0005737)	glycolipid binding (GO:0051861)|glycolipid transporter activity (GO:0017089)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)	4						GAGGCCCGGACGCGGGCGTGC	0.761													C|||	4904	0.979233	0.9228	1.0	5008	,	,		11019	1.0		0.998	False		,,,				2504	1.0				p.D209E		.											.	GLTPD2-68	0			c.C627A						.	C	GLU/ASP	2706,78		1314,78,0	2.0	2.0	2.0		627	0.2	0.1	17	dbSNP_126	2	6028,0		3014,0,0	no	missense	GLTPD2	NM_001014985.2	45	4328,78,0	AA,AC,CC		0.0,2.8017,0.8852	benign	209/292	4693342	8734,78	1392	3014	4406	SO:0001583	missense	388323	exon4			CCCGGACGCGGGC	BC029290	CCDS32534.1	17p13.2	2007-12-19				ENSG00000182327			33756	protein-coding gene	gene with protein product							Standard	NM_001014985		Approved		uc002fza.2	A6NH11		ENST00000331264.7:c.627C>A	17.37:g.4693342C>A	ENSP00000328070:p.Asp209Glu	0	0		8	8	NM_001014985	0	0	0	0	0	A7E2T2	Missense_Mutation	SNP	ENST00000331264.7	37	CCDS32534.1	2151	0.9848901098901099	466	0.9471544715447154	362	1.0	572	1.0	751	0.9907651715039578	C	9.155	1.017148	0.19355	0.971983	1.0	ENSG00000182327	ENST00000331264	.	.	.	4.58	0.162	0.14981	Glycolipid transfer protein domain (3);	.	.	.	.	T	0.00012	0.0000	L	0.41027	1.25	0.80722	P	0.0	B	0.22080	0.064	B	0.31614	0.133	T	0.34650	-0.9820	7	0.12103	T	0.63	-20.1635	5.889	0.18897	0.0:0.5269:0.298:0.1751	rs35910358	209	A6NH11	GLTD2_HUMAN	E	209	.	ENSP00000328070:D209E	D	+	3	2	GLTPD2	4640082	0.004000	0.15560	0.082000	0.20525	0.081000	0.17604	0.011000	0.13264	-0.068000	0.12953	0.555000	0.69702	GAC	C|0.015;A|0.985		0.761	GLTPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439781.1	NM_001014985	
NLGN2	57555	hgsc.bcm.edu	37	17	7320874	7320874	+	Missense_Mutation	SNP	C	C	T	rs62061174	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr17:7320874C>T	ENST00000302926.2	+	7	2337	c.2264C>T	c.(2263-2265)gCg>gTg	p.A755V	SPEM1_ENST00000323675.3_5'Flank|NLGN2_ENST00000575301.1_Missense_Mutation_p.A755V|RP11-104H15.7_ENST00000575310.1_RNA	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	755					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				GGCGTCGGGGCGGACCCTGCC	0.761													C|||	53	0.0105831	0.0008	0.0187	5008	,	,		6326	0.0		0.0338	False		,,,				2504	0.0051				p.A755V		.											.	NLGN2-90	0			c.C2264T						.	C	VAL/ALA	15,3913		0,15,1949	5.0	5.0	5.0		2264	2.3	1.0	17	dbSNP_129	5	206,7598		3,200,3699	yes	missense	NLGN2	NM_020795.2	64	3,215,5648	TT,TC,CC		2.6397,0.3819,1.8837	benign	755/836	7320874	221,11511	1964	3902	5866	SO:0001583	missense	57555	exon7			TCGGGGCGGACCC	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.2264C>T	17.37:g.7320874C>T	ENSP00000305288:p.Ala755Val	0	0		10	8	NM_020795	0	0	0	0	0	Q9P2I1	Missense_Mutation	SNP	ENST00000302926.2	37	CCDS11103.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	2	0.0034965034965034965	22	0.029023746701846966	C	9.067	0.995877	0.19043	0.003819	0.026397	ENSG00000169992	ENST00000302926	T	0.64803	-0.12	3.42	2.33	0.28932	.	0.633271	0.13495	N	0.383697	T	0.15739	0.0379	N	0.08118	0	0.28833	N	0.897033	B	0.09022	0.002	B	0.01281	0.0	T	0.07028	-1.0794	10	0.14656	T	0.56	.	10.3885	0.44154	0.0:0.798:0.202:0.0	rs62061174	755	Q8NFZ4	NLGN2_HUMAN	V	755	ENSP00000305288:A755V	ENSP00000305288:A755V	A	+	2	0	NLGN2	7261598	0.090000	0.21635	0.981000	0.43875	0.746000	0.42486	2.934000	0.48956	1.904000	0.55121	0.448000	0.29417	GCG	C|0.986;T|0.014		0.761	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
VTN	7448	hgsc.bcm.edu	37	17	26699121	26699121	+	5'Flank	SNP	G	G	C	rs7212814		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr17:26699121G>C	ENST00000226218.4	-	0	0				SARM1_ENST00000457710.3_5'UTR|TMEM199_ENST00000509083.1_Intron|VTN_ENST00000536498.1_5'Flank|SARM1_ENST00000379061.4_Intron|CTB-96E2.3_ENST00000591482.1_RNA	NM_000638.3	NP_000629.3	P04004	VTNC_HUMAN	vitronectin						cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|innate immune response (GO:0045087)|negative regulation of blood coagulation (GO:0030195)|negative regulation of endopeptidase activity (GO:0010951)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein binding (GO:0032092)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|positive regulation of wound healing (GO:0090303)|regulation of complement activation (GO:0030449)|smooth muscle cell-matrix adhesion (GO:0061302)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|blood microparticle (GO:0072562)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			kidney(2)|large_intestine(7)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	13	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Abciximab(DB00054)	GGCCCACGGCGGGGCGCCGAG	0.761													C|||	5008	1.0	1.0	1.0	5008	,	,		9002	1.0		1.0	False		,,,				2504	1.0				p.R23P		.											.	.	0			c.G68C						.						2.0	2.0	2.0					17																	26699121		1378	3066	4444	SO:0001631	upstream_gene_variant	23098	exon1			CACGGCGGGGCGC	BC005046	CCDS11229.1	17q11.2	2014-08-08	2006-02-10		ENSG00000109072	ENSG00000109072		"""Endogenous ligands"""	12724	protein-coding gene	gene with protein product	"""serum spreading factor"", ""somatomedin B"", ""complement S-protein"""	193190	"""vitronectin (serum spreading factor, somatomedin B, complement S-protein)"""			2447940	Standard	NM_000638		Approved	VN	uc002hbc.3	P04004	OTTHUMG00000132500		17.37:g.26699121G>C	Exception_encountered	0	0		8	8	NM_015077	0	0	0	0	0	B2R7G0|P01141|Q9BSH7	Missense_Mutation	SNP	ENST00000226218.4	37	CCDS11229.1	2181	0.9986263736263736	490	0.9959349593495935	362	1.0	571	0.9982517482517482	758	1.0	C	4.627	0.116613	0.08881	.	.	ENSG00000004139	ENST00000457710	.	.	.	4.93	3.94	0.45596	.	1.216040	0.06217	N	0.686070	T	0.00012	0.0000	.	.	.	0.45837	P	0.0012929999999999886	.	.	.	.	.	.	T	0.38757	-0.9646	5	0.02654	T	1	0.2642	5.2918	0.15731	0.1514:0.6261:0.1455:0.077	rs7212814	.	.	.	P	23	.	ENSP00000406738:R23P	R	+	2	0	SARM1	23723248	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	1.263000	0.33004	0.497000	0.27926	-1.514000	0.00941	CGG	G|0.001;C|0.999		0.761	VTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255680.2	NM_000638	
OMG	4974	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	17	29622398	29622398	+	Missense_Mutation	SNP	G	G	C			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr17:29622398G>C	ENST00000247271.4	-	2	1213	c.952C>G	c.(952-954)Cta>Gta	p.L318V	NF1_ENST00000358273.4_Intron|NF1_ENST00000356175.3_Intron	NM_002544.4	NP_002535.3	P23515	OMGP_HUMAN	oligodendrocyte myelin glycoprotein	318					cell adhesion (GO:0007155)|negative regulation of axonogenesis (GO:0050771)|neuron projection regeneration (GO:0031102)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of axonogenesis (GO:0050770)|regulation of collateral sprouting of intact axon in response to injury (GO:0048683)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)		p.0?(8)|p.?(3)		breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(1)|ovary(1)|prostate(1)|stomach(1)	13		all_cancers(10;6.97e-11)|all_epithelial(10;0.0051)|all_hematologic(16;0.0149)|Breast(31;0.0155)|Myeloproliferative disorder(56;0.0255)|Acute lymphoblastic leukemia(14;0.0257)|all_lung(9;0.0468)|Lung NSC(157;0.094)		UCEC - Uterine corpus endometrioid carcinoma (4;6.64e-05)|all cancers(4;1.81e-13)|Epithelial(4;4.04e-12)|OV - Ovarian serous cystadenocarcinoma(4;9.49e-12)|GBM - Glioblastoma multiforme(4;0.121)		TCTTTGCTTAGAGTGGCACCA	0.438																																					p.L318V		.											.	OMG-493	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.C952G						.						333.0	298.0	310.0					17																	29622398		2203	4300	6503	SO:0001583	missense	4974	exon2			TGCTTAGAGTGGC		CCDS11265.1	17q11-q12	2008-07-18			ENSG00000126861	ENSG00000126861			8135	protein-coding gene	gene with protein product		164345				1899288, 2277079	Standard	NM_002544		Approved	OMGP	uc002hgj.3	P23515	OTTHUMG00000132870	ENST00000247271.4:c.952C>G	17.37:g.29622398G>C	ENSP00000247271:p.Leu318Val	159	0		235	32	NM_002544	0	0	0	0	0	E1P659	Missense_Mutation	SNP	ENST00000247271.4	37	CCDS11265.1	.	.	.	.	.	.	.	.	.	.	G	12.66	2.004405	0.35320	.	.	ENSG00000126861	ENST00000247271	D	0.83992	-1.79	5.41	2.3	0.28687	.	0.162476	0.28062	N	0.016743	T	0.66287	0.2774	N	0.24115	0.695	0.34567	D	0.713031	B	0.02656	0.0	B	0.01281	0.0	T	0.59166	-0.7505	10	0.42905	T	0.14	-0.0107	2.3843	0.04362	0.2041:0.2334:0.4427:0.1199	.	318	P23515	OMGP_HUMAN	V	318	ENSP00000247271:L318V	ENSP00000247271:L318V	L	-	1	2	OMG	26646524	0.924000	0.31332	0.994000	0.49952	0.999000	0.98932	0.548000	0.23314	0.334000	0.23590	0.655000	0.94253	CTA	.		0.438	OMG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256350.2	NM_002544	
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346595	39346595	+	Missense_Mutation	SNP	T	T	A	rs377187211|rs148036927|rs11283848	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr17:39346595T>A	ENST00000398470.1	+	1	457	c.457T>A	c.(457-459)Tgc>Agc	p.C153S	KRTAP9-1_ENST00000377723.3_Intron|KRTAP9-1_ENST00000318329.5_Missense_Mutation_p.C70S	NM_001190460.1	NP_001177389.1	A8MXZ3	KRA91_HUMAN	keratin associated protein 9-1	153	30 X 5 AA repeats of C-C-[CGSVRQH]- [SQTNP]-[PTSI].					keratin filament (GO:0045095)		p.T152_C153>S(2)		breast(1)|lung(3)	4						CCAGCCCACCTGCTGTGGGTC	0.582																																					p.C153S		.											.	.	2	Complex - deletion inframe(2)	breast(2)	c.T457A						.																																			SO:0001583	missense	728318	exon1			CCCACCTGCTGTG	AC006070	CCDS56029.1	17q21.2	2010-06-03			ENSG00000240542	ENSG00000240542		"""Keratin associated proteins"""	18912	protein-coding gene	gene with protein product			"""keratin associated protein 9-like 3"""	KRTAP9L3			Standard	NM_001190460		Approved	KAP9.1	uc021txf.1	A8MXZ3	OTTHUMG00000133636	ENST00000398470.1:c.457T>A	17.37:g.39346595T>A	ENSP00000381488:p.Cys153Ser	111	0		176	3	NM_001190460	0	0	0	0	0		Missense_Mutation	SNP	ENST00000398470.1	37	CCDS56029.1	.	.	.	.	.	.	.	.	.	.	T	11.97	1.796850	0.31777	.	.	ENSG00000240542	ENST00000398470;ENST00000318329	T;T	0.02085	4.46;6.06	3.56	2.46	0.29980	.	.	.	.	.	T	0.06234	0.0161	M	0.73430	2.235	0.09310	N	0.999998	.	.	.	.	.	.	T	0.15636	-1.0430	7	0.51188	T	0.08	.	7.8228	0.29296	0.1856:0.0:0.0:0.8144	.	.	.	.	S	153;70	ENSP00000381488:C153S;ENSP00000325023:C70S	ENSP00000325023:C70S	C	+	1	0	KRTAP9-1	36600121	0.004000	0.15560	0.064000	0.19789	0.084000	0.17831	0.909000	0.28558	0.705000	0.31890	0.338000	0.21704	TGC	.		0.582	KRTAP9-1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257781.1		
RNF43	54894	ucsc.edu;bcgsc.ca	37	17	56492800	56492800	+	Missense_Mutation	SNP	T	T	C	rs3744093	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr17:56492800T>C	ENST00000584437.1	-	1	2094	c.139A>G	c.(139-141)Att>Gtt	p.I47V	BZRAP1-AS1_ENST00000583841.1_RNA|RNF43_ENST00000577716.1_Missense_Mutation_p.I47V|RNF43_ENST00000580014.1_5'Flank|RNF43_ENST00000581868.1_Intron|RNF43_ENST00000500597.2_Missense_Mutation_p.I47V|RNF43_ENST00000583753.1_Missense_Mutation_p.I47V|RNF43_ENST00000407977.2_Missense_Mutation_p.I47V			Q68DV7	RNF43_HUMAN	ring finger protein 43	47			I -> V (in dbSNP:rs3744093). {ECO:0000269|PubMed:14702039}.		negative regulation of Wnt signaling pathway (GO:0030178)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|stem cell proliferation (GO:0072089)|Wnt receptor catabolic process (GO:0038018)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	frizzled binding (GO:0005109)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(5)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(14)|lung(9)|ovary(2)|pancreas(10)|prostate(1)|skin(4)	60	Medulloblastoma(34;0.127)|all_neural(34;0.237)					ACTCTGATAATAGCTTTCTGT	0.517													T|||	1872	0.373802	0.1694	0.5317	5008	,	,		17973	0.5258		0.3718	False		,,,				2504	0.3834				p.I47V		.											.	RNF43-92	0			c.A139G						.	T	VAL/ILE	958,3448	362.1+/-316.0	116,726,1361	100.0	92.0	95.0		139	3.2	1.0	17	dbSNP_107	95	3312,5288	494.7+/-373.9	638,2036,1626	yes	missense	RNF43	NM_017763.4	29	754,2762,2987	CC,CT,TT		38.5116,21.7431,32.831	benign	47/784	56492800	4270,8736	2203	4300	6503	SO:0001583	missense	54894	exon2			TGATAATAGCTTT		CCDS11607.1	17q23.2	2013-01-09						"""RING-type (C3HC4) zinc fingers"""	18505	protein-coding gene	gene with protein product		612482					Standard	NM_017763		Approved	FLJ20315, DKFZp781H0392, URCC	uc002iwh.4	Q68DV7		ENST00000584437.1:c.139A>G	17.37:g.56492800T>C	ENSP00000463069:p.Ile47Val	48	0		53	6	NM_017763	0	0	0	0	0	A8K4R2|B7Z443|B7Z5D5|B7Z5J5|Q65ZA4|Q6AI04|Q9NXD0	Missense_Mutation	SNP	ENST00000584437.1	37	CCDS11607.1	855	0.3914835164835165	94	0.1910569105691057	184	0.5082872928176796	298	0.5209790209790209	279	0.36807387862796836	T	9.051	0.992132	0.18966	0.217431	0.385116	ENSG00000108375	ENST00000407977;ENST00000500597	T;T	0.09350	3.24;2.99	5.49	3.19	0.36642	.	0.436978	0.21813	N	0.068731	T	0.00012	0.0000	N	0.14661	0.345	0.42420	P	0.007365999999999984	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.40924	-0.9537	9	0.17832	T	0.49	-11.177	6.2359	0.20762	0.0:0.1484:0.1361:0.7155	rs3744093;rs52822933;rs58301389;rs3744093	47;47	Q68DV7-2;Q68DV7	.;RNF43_HUMAN	V	47	ENSP00000385328:I47V;ENSP00000441969:I47V	ENSP00000385328:I47V	I	-	1	0	RNF43	53847799	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	1.086000	0.30853	0.973000	0.38340	0.533000	0.62120	ATT	T|0.651;C|0.349		0.517	RNF43-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444713.1	NM_017763	
TMEM200C	645369	hgsc.bcm.edu	37	18	5890571	5890571	+	Missense_Mutation	SNP	T	T	C	rs7506026	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr18:5890571T>C	ENST00000581347.2	-	3	2137	c.1492A>G	c.(1492-1494)Agc>Ggc	p.S498G	RP11-945C19.4_ENST00000577694.1_RNA|RP11-945C19.4_ENST00000582939.1_RNA|RP11-945C19.4_ENST00000580845.1_RNA|TMEM200C_ENST00000383490.2_Missense_Mutation_p.S498G			A6NKL6	T200C_HUMAN	transmembrane protein 200C	498	Pro-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(4)|lung(5)|stomach(1)	12						GCCAGAGGGCTGGAGTCCGGG	0.791													T|||	237	0.0473243	0.0847	0.0375	5008	,	,		7356	0.001		0.0775	False		,,,				2504	0.0204				p.S498G		.											.	.	0			c.A1492G						.	T	GLY/SER	155,2477		3,149,1164	3.0	3.0	3.0		1492	-1.2	0.0	18	dbSNP_116	3	267,5869		4,259,2805	no	missense	TMEM200C	NM_001080209.1	56	7,408,3969	CC,CT,TT		4.3514,5.8891,4.813	benign	498/622	5890571	422,8346	1316	3068	4384	SO:0001583	missense	645369	exon1			GAGGGCTGGAGTC		CCDS45825.1	18p11.31	2009-09-08			ENSG00000206432	ENSG00000206432			37208	protein-coding gene	gene with protein product						15722956	Standard	NM_001080209		Approved	TTMA	uc002kmx.1	A6NKL6		ENST00000581347.2:c.1492A>G	18.37:g.5890571T>C	ENSP00000463375:p.Ser498Gly	2	0		19	10	NM_001080209	0	0	0	0	0		Missense_Mutation	SNP	ENST00000581347.2	37	CCDS45825.1	128	0.05860805860805861	46	0.09349593495934959	17	0.04696132596685083	3	0.005244755244755245	62	0.08179419525065963	T	13.97	2.397165	0.42512	0.058891	0.043514	ENSG00000206432	ENST00000383490	.	.	.	4.37	-1.18	0.09617	.	.	.	.	.	T	0.00496	0.0016	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22800	-1.0206	8	0.08599	T	0.76	.	4.9842	0.14182	0.1362:0.3204:0.0:0.5434	rs7506026	498	A6NKL6	T200C_HUMAN	G	498	.	ENSP00000372982:S498G	S	-	1	0	TMEM200C	5880571	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-0.166000	0.09954	-0.178000	0.10672	0.459000	0.35465	AGC	T|0.941;C|0.059		0.791	TMEM200C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441917.4	NM_001080209	
CBLN2	147381	hgsc.bcm.edu	37	18	70209321	70209321	+	Silent	SNP	C	C	A	rs7237888	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr18:70209321C>A	ENST00000269503.4	-	3	848	c.75G>T	c.(73-75)ccG>ccT	p.P25P	CBLN2_ENST00000584764.1_Intron|CBLN2_ENST00000583651.1_Intron|CBLN2_ENST00000581073.1_Intron|CBLN2_ENST00000585159.1_Silent_p.P25P	NM_182511.3	NP_872317.1	Q8IUK8	CBLN2_HUMAN	cerebellin 2 precursor	25					positive regulation of synapse assembly (GO:0051965)	extracellular space (GO:0005615)				endometrium(2)|lung(15)	17		Esophageal squamous(42;0.131)				CGCAgccgcccggctcgcgca	0.786													C|||	2820	0.563099	0.1868	0.8573	5008	,	,		7947	0.381		0.9304	False		,,,				2504	0.6728				p.P25P		.											.	CBLN2-90	0			c.G75T						.	C		1660,2420		328,1004,708	5.0	7.0	6.0		75	-0.8	1.0	18	dbSNP_116	6	7475,487		3530,415,36	no	coding-synonymous	CBLN2	NM_182511.3		3858,1419,744	AA,AC,CC		6.1166,40.6863,24.1405		25/225	70209321	9135,2907	2040	3981	6021	SO:0001819	synonymous_variant	147381	exon3			GCCGCCCGGCTCG	BC035789	CCDS11999.1	18q22.3	2007-11-19			ENSG00000141668	ENSG00000141668			1544	protein-coding gene	gene with protein product		600433				7877445	Standard	NM_182511		Approved		uc002lkv.2	Q8IUK8	OTTHUMG00000132825	ENST00000269503.4:c.75G>T	18.37:g.70209321C>A		0	0		6	6	NM_182511	0	0	0	0	0	Q53Z56	Silent	SNP	ENST00000269503.4	37	CCDS11999.1																																																																																			C|0.390;A|0.610		0.786	CBLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256288.1	NM_182511	
ZNF516	9658	hgsc.bcm.edu	37	18	74153712	74153712	+	Silent	SNP	G	G	A	rs113225589	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr18:74153712G>A	ENST00000443185.2	-	3	1616	c.1299C>T	c.(1297-1299)taC>taT	p.Y433Y	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	433					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(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		CGTACTTGAGGTACTCGGCCG	0.706													G|||	69	0.013778	0.0023	0.0159	5008	,	,		9389	0.0179		0.0328	False		,,,				2504	0.0041				p.Y433Y		.											.	ZNF516-69	0			c.C1299T						.	G		11,3887		0,11,1938	5.0	5.0	5.0		1299	3.8	1.0	18	dbSNP_132	5	181,7915		2,177,3869	no	coding-synonymous	ZNF516	NM_014643.3		2,188,5807	AA,AG,GG		2.2357,0.2822,1.6008		433/1164	74153712	192,11802	1949	4048	5997	SO:0001819	synonymous_variant	9658	exon3			CTTGAGGTACTCG	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.1299C>T	18.37:g.74153712G>A		0	0		22	15	NM_014643	0	0	0	0	0		Silent	SNP	ENST00000443185.2	37																																																																																				G|0.981;A|0.019		0.706	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
ARID3A	1820	hgsc.bcm.edu	37	19	929678	929678	+	Silent	SNP	G	G	A	rs3826948	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:929678G>A	ENST00000263620.3	+	2	477	c.150G>A	c.(148-150)gaG>gaA	p.E50E	AC005391.2_ENST00000585647.1_RNA	NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	50						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		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)		GAGAGCCCGAGAGTGCCCGGA	0.766													g|||	2308	0.460863	0.1112	0.487	5008	,	,		7932	0.6756		0.6223	False		,,,				2504	0.5276				p.E50E	Pancreas(29;54 1022 32760 50921)	.											.	ARID3A-90	0			c.G150A						.	G		470,2552		61,348,1102	3.0	4.0	3.0		150	1.1	0.4	19	dbSNP_107	3	3721,3153		1076,1569,792	no	coding-synonymous	ARID3A	NM_005224.2		1137,1917,1894	AA,AG,GG		45.8685,15.5526,42.3504		50/594	929678	4191,5705	1511	3437	4948	SO:0001819	synonymous_variant	1820	exon2			GCCCGAGAGTGCC	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.150G>A	19.37:g.929678G>A		0	0		4	4	NM_005224	0	0	0	0	0	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Silent	SNP	ENST00000263620.3	37	CCDS12050.1																																																																																			T|0.495;C|0.504		0.766	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
ARID3A	1820	hgsc.bcm.edu	37	19	929753	929753	+	Silent	SNP	A	A	G	rs1799595	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:929753A>G	ENST00000263620.3	+	2	552	c.225A>G	c.(223-225)ccA>ccG	p.P75P	AC005391.2_ENST00000585647.1_RNA	NM_005224.2	NP_005215.1	Q99856	ARI3A_HUMAN	AT rich interactive domain 3A (BRIGHT-like)	75						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|ovary(1)	10		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)		TGGGACACCCAGCCAGCCCCG	0.751													t|||	4428	0.884185	0.9062	0.804	5008	,	,		8534	0.998		0.836	False		,,,				2504	0.8436				p.P75P	Pancreas(29;54 1022 32760 50921)	.											.	ARID3A-90	0			c.A225G						.	G		3389,305		1555,279,13	4.0	5.0	5.0		225	-6.8	0.0	19	dbSNP_89	5	6619,1123		2834,951,86	no	coding-synonymous	ARID3A	NM_005224.2		4389,1230,99	GG,GA,AA		14.5053,8.2566,12.4869		75/594	929753	10008,1428	1847	3871	5718	SO:0001819	synonymous_variant	1820	exon2			ACACCCAGCCAGC	U88047	CCDS12050.1	19p13.3	2013-02-07	2006-11-08	2004-01-30		ENSG00000116017		"""-"""	3031	protein-coding gene	gene with protein product		603265	"""dead ringer-like 1 (Drosophila)"", ""AT rich interactive domain 3A (BRIGHT- like)"""	DRIL1		9722953	Standard	NM_005224		Approved	BRIGHT	uc002lql.3	Q99856		ENST00000263620.3:c.225A>G	19.37:g.929753A>G		0	0		9	9	NM_005224	0	0	0	0	0	Q5I858|Q6P9C6|Q8IZA7|Q8N4Z3	Silent	SNP	ENST00000263620.3	37	CCDS12050.1																																																																																			A|0.114;G|0.886		0.751	ARID3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458219.1	NM_005224	
NCLN	56926	hgsc.bcm.edu	37	19	3204732	3204732	+	Silent	SNP	C	C	T	rs61745459	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:3204732C>T	ENST00000246117.4	+	9	1622	c.1191C>T	c.(1189-1191)agC>agT	p.S397S	NCLN_ENST00000590671.1_Silent_p.S323S	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	397					regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		GCCAGCGCAGCAGCATCATGG	0.697													C|||	5	0.000998403	0.0	0.0014	5008	,	,		14030	0.0		0.003	False		,,,				2504	0.001				p.S397S		.											.	NCLN-90	0			c.C1191T						.	C		2,4386		0,2,2192	17.0	16.0	17.0		1191	3.9	1.0	19	dbSNP_129	17	21,8559		0,21,4269	no	coding-synonymous	NCLN	NM_020170.3		0,23,6461	TT,TC,CC		0.2448,0.0456,0.1774		397/564	3204732	23,12945	2194	4290	6484	SO:0001819	synonymous_variant	56926	exon9			GCGCAGCAGCATC	BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"""nicastrin-like protein"""	609156	"""nicalin homolog (zebrafish)"""			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.1191C>T	19.37:g.3204732C>T		1	0		121	66	NM_020170	0	0	0	0	0	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Silent	SNP	ENST00000246117.4	37	CCDS32869.1																																																																																			C|0.998;T|0.002		0.697	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
TNFSF9	8744	hgsc.bcm.edu	37	19	6531171	6531171	+	Missense_Mutation	SNP	G	G	A	rs2234174	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:6531171G>A	ENST00000245817.3	+	1	162	c.124G>A	c.(124-126)Gct>Act	p.A42T		NM_003811.3	NP_003802.1	P41273	TNFL9_HUMAN	tumor necrosis factor (ligand) superfamily, member 9	42					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|immune response (GO:0006955)|myeloid dendritic cell differentiation (GO:0043011)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cytotoxic T cell differentiation (GO:0045585)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	5						gctgctgctcgctgccgcCTG	0.786													g|||	50	0.00998403	0.0053	0.0115	5008	,	,		9598	0.0		0.0139	False		,,,				2504	0.0215				p.A42T		.											.	TNFSF9-227	0			c.G124A						.		THR/ALA	19,3135		0,19,1558	10.0	13.0	12.0		124	-0.1	0.0	19	dbSNP_98	12	78,6682		0,78,3302	no	missense	TNFSF9	NM_003811.3	58	0,97,4860	AA,AG,GG		1.1538,0.6024,0.9784	benign	42/255	6531171	97,9817	1577	3380	4957	SO:0001583	missense	8744	exon1			CTGCTCGCTGCCG	U03398	CCDS12169.1	19p13.3	2008-07-22				ENSG00000125657		"""Tumor necrosis factor (ligand) superfamily"""	11939	protein-coding gene	gene with protein product	"""receptor 4-1BB ligand"", ""homolog of mouse 4-1BB-L"""	606182				8405064, 8088337	Standard	NM_003811		Approved	4-1BB-L	uc002mfh.2	P41273		ENST00000245817.3:c.124G>A	19.37:g.6531171G>A	ENSP00000245817:p.Ala42Thr	0	0		5	4	NM_003811	0	0	0	0	0	Q2M3S2	Missense_Mutation	SNP	ENST00000245817.3	37	CCDS12169.1	20	0.009157509157509158	5	0.01016260162601626	4	0.011049723756906077	0	0.0	11	0.014511873350923483	g	15.71	2.913638	0.52439	0.006024	0.011538	ENSG00000125657	ENST00000245817	T	0.47177	0.85	2.09	-0.127	0.13510	.	2.277090	0.03093	U	0.160080	T	0.26376	0.0644	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.11329	0.006	T	0.09662	-1.0664	10	0.29301	T	0.29	.	4.112	0.10063	0.3866:0.0:0.6134:0.0	rs2234174	42	P41273	TNFL9_HUMAN	T	42	ENSP00000245817:A42T	ENSP00000245817:A42T	A	+	1	0	TNFSF9	6482171	0.000000	0.05858	0.010000	0.14722	0.006000	0.05464	-0.022000	0.12480	0.042000	0.15717	0.479000	0.44913	GCT	G|0.991;A|0.009		0.786	TNFSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457856.1	NM_003811	
MUC16	94025	bcgsc.ca	37	19	9065632	9065632	+	Missense_Mutation	SNP	T	T	C	rs1867691	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:9065632T>C	ENST00000397910.4	-	3	22017	c.21814A>G	c.(21814-21816)Att>Gtt	p.I7272V		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	7274	Ser-rich.|Thr-rich.				cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						GTAGCACCAATGGACACTTCA	0.488													t|||	1081	0.215855	0.0802	0.2061	5008	,	,		21790	0.249		0.3111	False		,,,				2504	0.274				p.I7272V		.											.	MUC16-566	0			c.A21814G						.	T	VAL/ILE	473,3545		28,417,1564	141.0	134.0	136.0		21814	-2.7	0.0	19	dbSNP_92	136	2385,5961		340,1705,2128	yes	missense	MUC16	NM_024690.2	29	368,2122,3692	CC,CT,TT		28.5766,11.772,23.1155	benign	7272/14508	9065632	2858,9506	2009	4173	6182	SO:0001583	missense	94025	exon3			CACCAATGGACAC	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.21814A>G	19.37:g.9065632T>C	ENSP00000381008:p.Ile7272Val	128	0		141	5	NM_024690	0	0	0	0	0	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	494	0.2261904761904762	53	0.10772357723577236	87	0.24033149171270718	122	0.21328671328671328	232	0.30606860158311344	t	2.759	-0.258393	0.05791	0.11772	0.285766	ENSG00000181143	ENST00000397910	T	0.02236	4.38	2.82	-2.74	0.05932	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	.	.	.	B	0.06786	0.001	B	0.09377	0.004	T	0.47724	-0.9095	8	0.87932	D	0	.	0.9168	0.01306	0.1569:0.2308:0.1592:0.4531	rs1867691;rs2547061;rs17515635;rs59475496;rs1867691	7272	B5ME49	.	V	7272	ENSP00000381008:I7272V	ENSP00000381008:I7272V	I	-	1	0	MUC16	8926632	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.502000	0.06390	-1.196000	0.02676	-1.120000	0.02017	ATT	T|0.778;C|0.222		0.488	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
PGLS	25796	hgsc.bcm.edu	37	19	17622614	17622614	+	Silent	SNP	C	C	T	rs11086075	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:17622614C>T	ENST00000252603.2	+	1	177	c.133C>T	c.(133-135)Ctg>Ttg	p.L45L	CTD-3131K8.2_ENST00000596643.1_lincRNA	NM_012088.2	NP_036220.1	O95336	6PGL_HUMAN	6-phosphogluconolactonase	45					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	6-phosphogluconolactonase activity (GO:0017057)|monosaccharide binding (GO:0048029)			endometrium(1)|lung(1)	2						CGCGCTCGGCCTGTCGGGCGG	0.736													C|||	1862	0.371805	0.2496	0.4207	5008	,	,		10575	0.377		0.4851	False		,,,				2504	0.3804				p.L45L		.											.	PGLS-90	0			c.C133T						.	C		662,2504		107,448,1028	2.0	2.0	2.0		133	2.6	1.0	19	dbSNP_120	2	2200,4094		507,1186,1454	no	coding-synonymous	PGLS	NM_012088.2		614,1634,2482	TT,TC,CC		34.9539,20.9097,30.2537		45/259	17622614	2862,6598	1583	3147	4730	SO:0001819	synonymous_variant	25796	exon1			CTCGGCCTGTCGG	AJ243972	CCDS12361.1	19p13.2	2008-02-05				ENSG00000130313	3.1.1.31		8903	protein-coding gene	gene with protein product		604951				10518023	Standard	NM_012088		Approved	6PGL	uc002ngw.3	O95336		ENST00000252603.2:c.133C>T	19.37:g.17622614C>T		1	0		4	4	NM_012088	0	0	0	0	0		Silent	SNP	ENST00000252603.2	37	CCDS12361.1																																																																																			C|0.617;T|0.383		0.736	PGLS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464154.1		
CRTC1	23373	broad.mit.edu	37	19	18794517	18794517	+	Missense_Mutation	SNP	C	C	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:18794517C>A	ENST00000321949.8	+	1	31	c.5C>A	c.(4-6)gCg>gAg	p.A2E	CRTC1_ENST00000338797.6_Missense_Mutation_p.A2E	NM_015321.2	NP_056136.2			CREB regulated transcription coactivator 1										CRTC1/MAML2(516)	NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	19						GAGAAGATGGCGACTTCGAAC	0.667																																					p.A2E		.											.	CRTC1-1361	0			c.C5A						.						55.0	36.0	43.0					19																	18794517		1971	3857	5828	SO:0001583	missense	23373	exon1			AGATGGCGACTTC	AY040323	CCDS32963.1, CCDS42525.1	19p13	2012-07-31	2005-11-24	2005-11-24					16062	protein-coding gene	gene with protein product	"""transducer of regulated cAMP response element-binding protein"""	607536	"""mucoepidermoid carcinoma translocated 1"""	MECT1		12539049, 14536081, 14506290	Standard	NM_015321		Approved	KIAA0616, FLJ14027, TORC1	uc010ebv.3	Q6UUV9		ENST00000321949.8:c.5C>A	19.37:g.18794517C>A	ENSP00000323332:p.Ala2Glu	108	2		235	11	NM_015321	0	0	0	0	0		Missense_Mutation	SNP	ENST00000321949.8	37	CCDS32963.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114431	0.94339	.	.	ENSG00000105662	ENST00000262813;ENST00000338797;ENST00000321949	T;T	0.20463	2.07;2.11	3.29	3.29	0.37713	.	0.000000	0.85682	U	0.000000	T	0.25531	0.0621	N	0.08118	0	0.50171	D	0.999851	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.34279	-0.9835	10	0.87932	D	0	.	13.6802	0.62479	0.0:1.0:0.0:0.0	.	2;2	Q6UUV9-2;Q6UUV9	.;CRTC1_HUMAN	E	2	ENSP00000345001:A2E;ENSP00000323332:A2E	ENSP00000262813:A2E	A	+	2	0	CRTC1	18655517	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.894000	0.69806	1.842000	0.53543	0.579000	0.79373	GCG	.		0.667	CRTC1-002	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465151.3	NM_025021	
CILP2	148113	hgsc.bcm.edu	37	19	19651140	19651140	+	Silent	SNP	A	A	G	rs4808970	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:19651140A>G	ENST00000291495.5	+	3	376	c.291A>G	c.(289-291)gaA>gaG	p.E97E	CILP2_ENST00000586018.1_Silent_p.E103E	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	97						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						TGGCGCTGGAAGCGCGCACCA	0.726													A|||	593	0.118411	0.1626	0.1167	5008	,	,		10102	0.0		0.168	False		,,,				2504	0.1309				p.E97E		.											.	CILP2-91	0			c.A291G						.	A		612,3678		42,528,1575	10.0	11.0	11.0		291	3.2	1.0	19	dbSNP_111	11	1223,7149		89,1045,3052	no	coding-synonymous	CILP2	NM_153221.2		131,1573,4627	GG,GA,AA		14.6082,14.2657,14.4922		97/1157	19651140	1835,10827	2145	4186	6331	SO:0001819	synonymous_variant	148113	exon3			GCTGGAAGCGCGC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.291A>G	19.37:g.19651140A>G		0	0		18	7	NM_153221	0	0	0	0	0	Q6NV88|Q8N4A6|Q8WV21	Silent	SNP	ENST00000291495.5	37	CCDS12405.1																																																																																			A|0.873;G|0.127		0.726	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
SIPA1L3	23094	hgsc.bcm.edu	37	19	38684261	38684261	+	Missense_Mutation	SNP	G	G	C	rs61735490	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:38684261G>C	ENST00000222345.6	+	18	5190	c.4681G>C	c.(4681-4683)Gct>Cct	p.A1561P		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	1561					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CGCCAGCCCCGCTGGCCTAGA	0.726													G|||	265	0.0529153	0.0431	0.0043	5008	,	,		9290	0.0804		0.0	False		,,,				2504	0.1268				p.A1561P		.											.	SIPA1L3-91	0			c.G4681C						.	G	PRO/ALA	88,4188		1,86,2051	8.0	8.0	8.0		4681	-0.9	0.0	19	dbSNP_129	8	2,8338		0,2,4168	no	missense	SIPA1L3	NM_015073.1	27	1,88,6219	CC,CG,GG		0.024,2.058,0.7134	benign	1561/1782	38684261	90,12526	2138	4170	6308	SO:0001583	missense	23094	exon18			AGCCCCGCTGGCC	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.4681G>C	19.37:g.38684261G>C	ENSP00000222345:p.Ala1561Pro	2	0		27	15	NM_015073	0	0	0	0	0	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	65	0.02976190476190476	20	0.04065040650406504	2	0.0055248618784530384	40	0.06993006993006994	3	0.00395778364116095	G	5.661	0.306582	0.10733	0.02058	2.4E-4	ENSG00000105738	ENST00000222345	T	0.31769	1.48	5.33	-0.925	0.10458	.	0.451517	0.21221	N	0.078159	T	0.01029	0.0034	L	0.29908	0.895	0.09310	N	1	B	0.09022	0.002	B	0.12837	0.008	T	0.10567	-1.0624	10	0.28530	T	0.3	-14.7677	1.5788	0.02630	0.1434:0.2313:0.2701:0.3551	rs61735490	1561	O60292	SI1L3_HUMAN	P	1561	ENSP00000222345:A1561P	ENSP00000222345:A1561P	A	+	1	0	SIPA1L3	43376101	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.128000	0.15810	0.027000	0.15297	-0.264000	0.10439	GCT	G|0.971;C|0.029		0.726	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
DYRK1B	9149	hgsc.bcm.edu	37	19	40317436	40317436	+	Silent	SNP	G	G	A	rs201098298		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:40317436G>A	ENST00000593685.1	-	9	1755	c.1287C>T	c.(1285-1287)ggC>ggT	p.G429G	DYRK1B_ENST00000348817.3_Silent_p.G401G|DYRK1B_ENST00000430012.2_Silent_p.G389G|DYRK1B_ENST00000323039.5_Silent_p.G429G|DYRK1B_ENST00000597639.1_Silent_p.G401G			Q9Y463	DYR1B_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1B	429	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adipose tissue development (GO:0060612)|myoblast fusion (GO:0007520)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(7)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	24	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)		Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)			GGCGGAAGAAGCCGTGCTGCA	0.721																																					p.G429G		.											.	DYRK1B-337	0			c.C1287T						.	G	,,	0,4088		0,0,2044	6.0	7.0	7.0		1287,1167,1203	2.2	1.0	19		7	6,7914		0,6,3954	no	coding-synonymous,coding-synonymous,coding-synonymous	DYRK1B	NM_004714.1,NM_006483.1,NM_006484.1	,,	0,6,5998	AA,AG,GG		0.0758,0.0,0.05	,,	429/630,389/590,401/602	40317436	6,12002	2044	3960	6004	SO:0001819	synonymous_variant	9149	exon9			GAAGAAGCCGTGC	Y17999	CCDS12543.1, CCDS12544.1, CCDS46075.1	19q13.2	2012-10-02			ENSG00000105204	ENSG00000105204	2.7.12.1		3092	protein-coding gene	gene with protein product	"""minibrain-related kinase"""	604556				9918863	Standard	XM_005259395		Approved	MIRK	uc002omj.3	Q9Y463		ENST00000593685.1:c.1287C>T	19.37:g.40317436G>A		0	0		29	14	NM_004714	0	0	0	0	0	O75258|O75788|O75789	Silent	SNP	ENST00000593685.1	37	CCDS12543.1																																																																																			G|0.999;A|0.000		0.721	DYRK1B-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462874.2	NM_004714	
VN1R4	317703	bcgsc.ca	37	19	53770764	53770764	+	Missense_Mutation	SNP	G	G	A	rs74429916	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:53770764G>A	ENST00000311170.4	-	1	208	c.155C>T	c.(154-156)gCc>gTc	p.A52V	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	52			A -> V (in allele VN1R4*3; dbSNP:rs112711591). {ECO:0000269|PubMed:12826614}.		response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		TAAGAAGTTGGCTACAATCAG	0.453										HNSCC(26;0.072)																											p.A52V		.											.	VN1R4-92	0			c.C155T						.	G	VAL/ALA	1197,3209		125,947,1131	43.0	44.0	44.0		155	0.1	0.1	19	dbSNP_132	44	1999,6597		219,1561,2518	no	missense	VN1R4	NM_173857.2	64	344,2508,3649	AA,AG,GG		23.255,27.1675,24.5808	probably-damaging	52/302	53770764	3196,9806	2203	4298	6501	SO:0001583	missense	317703	exon1			AAGTTGGCTACAA	AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.155C>T	19.37:g.53770764G>A	ENSP00000310856:p.Ala52Val	219	0		236	8	NM_173857	0	0	0	0	0	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	452	0.20695970695970695	155	0.3150406504065041	74	0.20441988950276244	48	0.08391608391608392	175	0.23087071240105542	G	14.88	2.666556	0.47677	0.271675	0.23255	ENSG00000228567	ENST00000311170	T	0.46451	0.87	2.49	0.0798	0.14418	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33346	U	0.005015	T	0.00012	0.0000	L	0.56199	1.76	0.49915	P	1.6899999999997473E-4	D	0.65815	0.995	D	0.63877	0.919	T	0.14420	-1.0473	9	0.72032	D	0.01	.	4.7929	0.13257	0.1357:0.4481:0.4162:0.0	.	52	Q7Z5H5	VN1R4_HUMAN	V	52	ENSP00000310856:A52V	ENSP00000310856:A52V	A	-	2	0	VN1R4	58462576	0.827000	0.29292	0.104000	0.21259	0.028000	0.11728	0.705000	0.25675	0.118000	0.18165	0.545000	0.68477	GCC	.		0.453	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
ZNF845	91664	broad.mit.edu	37	19	53854397	53854397	+	Missense_Mutation	SNP	G	G	C	rs10415799	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr19:53854397G>C	ENST00000595091.1	+	5	688	c.469G>C	c.(469-471)Gaa>Caa	p.E157Q	ZNF845_ENST00000458035.1_Missense_Mutation_p.E157Q			Q96IR2	ZN845_HUMAN	zinc finger protein 845	157					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.E157Q(3)		endometrium(2)|kidney(10)|lung(7)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	26						GTTTCAGACCGAAGGGAAAAT	0.408													.|||	1723	0.34405	0.2307	0.2882	5008	,	,		21024	0.4702		0.3738	False		,,,				2504	0.3763				p.E157Q		.											.	.	3	Substitution - Missense(3)	kidney(2)|stomach(1)	c.G469C						.	G	GLN/GLU	332,1052		44,244,404	69.0	48.0	54.0		469	-1.4	0.0	19	dbSNP_119	54	1198,1984		230,738,623	no	missense	ZNF845	NM_138374.1	29	274,982,1027	CC,CG,GG		37.6493,23.9884,33.5085	benign	157/971	53854397	1530,3036	692	1591	2283	SO:0001583	missense	91664	exon4			CAGACCGAAGGGA	BC007307	CCDS46170.1	19q13.42	2013-01-08			ENSG00000213799	ENSG00000213799		"""Zinc fingers, C2H2-type"", ""-"""	25112	protein-coding gene	gene with protein product							Standard	NM_138374		Approved		uc010ydv.1	Q96IR2		ENST00000595091.1:c.469G>C	19.37:g.53854397G>C	ENSP00000470005:p.Glu157Gln	219	1		205	4	NM_138374	0	0	0	0	0		Missense_Mutation	SNP	ENST00000595091.1	37	CCDS46170.1	792	0.3626373626373626	129	0.2621951219512195	114	0.3149171270718232	283	0.49475524475524474	266	0.35092348284960423	G	1.231	-0.624000	0.03636	0.239884	0.376493	ENSG00000213799	ENST00000458035;ENST00000427984	T	0.08282	3.11	1.2	-1.38	0.09027	.	.	.	.	.	T	0.00012	0.0000	L	0.48935	1.535	0.80722	P	0.0	B	0.28933	0.228	B	0.29663	0.105	T	0.42799	-0.9430	8	0.18276	T	0.48	.	3.6513	0.08205	0.1859:0.2581:0.556:0.0	rs10415799	157	Q96IR2	ZN845_HUMAN	Q	157	ENSP00000388311:E157Q	ENSP00000412086:E157Q	E	+	1	0	ZNF845	58546209	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.057000	0.14279	-0.374000	0.07967	0.411000	0.27672	GAA	G|0.643;C|0.357		0.408	ZNF845-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464359.1	XM_039908	
TMEM247	388946	bcgsc.ca	37	2	46707808	46707808	+	Missense_Mutation	SNP	C	C	G	rs70940616|rs74318890		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:46707808C>G	ENST00000434431.1	+	2	382	c.382C>G	c.(382-384)Cag>Gag	p.Q128E		NM_001145051.2	NP_001138523.1	A6NEH6	TM247_HUMAN	transmembrane protein 247	128						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											GAACCAGCGGCAGCGGCAGCA	0.662																																					p.Q128E		.											.	.	0			c.C382G						.						30.0	40.0	37.0					2																	46707808		692	1591	2283	SO:0001583	missense	388946	exon2			CAGCGGCAGCGGC		CCDS56117.1	2p21	2012-04-11			ENSG00000187600	ENSG00000187600			42967	protein-coding gene	gene with protein product							Standard	NM_001145051		Approved		uc010yod.3	A6NEH6	OTTHUMG00000153137	ENST00000434431.1:c.382C>G	2.37:g.46707808C>G	ENSP00000388684:p.Gln128Glu	107	1		311	30	NM_001145051	0	0	0	0	0		Missense_Mutation	SNP	ENST00000434431.1	37	CCDS56117.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447093	0.63178	.	.	ENSG00000187600	ENST00000434431	.	.	.	4.76	4.76	0.60689	.	0.000000	0.39475	N	0.001353	T	0.65606	0.2707	L	0.34521	1.04	.	.	.	D	0.56035	0.974	D	0.70487	0.969	T	0.71735	-0.4503	8	0.54805	T	0.06	-28.7409	14.7885	0.69821	0.0:1.0:0.0:0.0	.	128	A6NEH6	YB028_HUMAN	E	128	.	ENSP00000388684:Q128E	Q	+	1	0	AC018682.6	46561312	1.000000	0.71417	1.000000	0.80357	0.569000	0.35902	3.910000	0.56371	2.484000	0.83849	0.563000	0.77884	CAG	G|1.000;|0.000		0.662	TMEM247-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329726.1	NM_001145051	
C2orf81	388963	broad.mit.edu	37	2	74642280	74642280	+	Missense_Mutation	SNP	T	T	G			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:74642280T>G	ENST00000517883.1	-	1	1430	c.739A>C	c.(739-741)Acc>Ccc	p.T247P	C2orf81_ENST00000290390.5_Missense_Mutation_p.T315P			A6NN90	CB081_HUMAN	chromosome 2 open reading frame 81	308										endometrium(3)|kidney(1)	4						GAGGGGCGGGTGGCGCCGCCC	0.716																																					p.T315P		.											.	.	0			c.A943C						.						7.0	10.0	9.0					2																	74642280		682	1575	2257	SO:0001583	missense	388963	exon4			GGCGGGTGGCGCC	AC005041, CH471053		2p13.1	2012-08-07			ENSG00000159239	ENSG00000159239			34350	protein-coding gene	gene with protein product						15815621	Standard	NM_001145054		Approved	LOC388963, hCG40743	uc010yrq.1	A6NN90	OTTHUMG00000164184	ENST00000517883.1:c.739A>C	2.37:g.74642280T>G	ENSP00000431103:p.Thr247Pro	37	4		122	43	NM_001145054	0	0	0	0	0		Missense_Mutation	SNP	ENST00000517883.1	37		.	.	.	.	.	.	.	.	.	.	t	12.14	1.849844	0.32699	.	.	ENSG00000159239	ENST00000517883;ENST00000290390	.	.	.	3.91	-3.99	0.04069	.	1.321610	0.05237	N	0.511487	T	0.30135	0.0755	L	0.44542	1.39	0.09310	N	1	B	0.19073	0.033	B	0.22601	0.04	T	0.39396	-0.9616	9	0.72032	D	0.01	-3.9874	1.2321	0.01946	0.1409:0.2887:0.2874:0.283	.	315	G3XAA6	.	P	247;315	.	ENSP00000290390:T315P	T	-	1	0	C2orf81	74495788	0.007000	0.16637	0.000000	0.03702	0.008000	0.06430	0.309000	0.19332	-0.435000	0.07264	0.454000	0.30748	ACC	.		0.716	C2orf81-002	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000377683.1	NM_001145054	
RPIA	22934	hgsc.bcm.edu	37	2	88991242	88991242	+	Missense_Mutation	SNP	C	C	G			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:88991242C>G	ENST00000283646.4	+	1	81	c.26C>G	c.(25-27)aCc>aGc	p.T9S		NM_144563.2	NP_653164.2	P49247	RPIA_HUMAN	ribose 5-phosphate isomerase A	9					carbohydrate metabolic process (GO:0005975)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, non-oxidative branch (GO:0009052)|ribose phosphate metabolic process (GO:0019693)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	monosaccharide binding (GO:0048029)|ribose-5-phosphate isomerase activity (GO:0004751)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18		Acute lymphoblastic leukemia(2;0.000456)|all_hematologic(2;0.00287)				CCCTTCAGCACCCTCTACGGG	0.756																																					p.T9S		.											.	RPIA-91	0			c.C26G						.						10.0	13.0	12.0					2																	88991242		1562	3605	5167	SO:0001583	missense	22934	exon1			TCAGCACCCTCTA	L35035	CCDS2004.2	2p11.2	2008-07-31	2008-07-31		ENSG00000153574	ENSG00000153574	5.3.1.6		10297	protein-coding gene	gene with protein product	"""ribose 5-phosphate epimerase"""	180430				7758956	Standard	NM_144563		Approved		uc002ste.3	P49247	OTTHUMG00000130333	ENST00000283646.4:c.26C>G	2.37:g.88991242C>G	ENSP00000283646:p.Thr9Ser	0	0		22	13	NM_144563	0	0	0	0	0	Q541P9|Q96BJ6	Missense_Mutation	SNP	ENST00000283646.4	37	CCDS2004.2	.	.	.	.	.	.	.	.	.	.	C	17.04	3.286192	0.59867	.	.	ENSG00000153574	ENST00000283646	T	0.78126	-1.15	4.87	4.87	0.63330	.	0.526148	0.12236	U	0.486947	T	0.76371	0.3978	N	0.08118	0	0.31309	N	0.687335	D	0.63880	0.993	D	0.65443	0.935	T	0.76479	-0.2944	10	0.87932	D	0	-16.0708	13.6852	0.62511	0.0:1.0:0.0:0.0	.	9	P49247	RPIA_HUMAN	S	9	ENSP00000283646:T9S	ENSP00000283646:T9S	T	+	2	0	RPIA	88772357	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.080000	0.50112	2.694000	0.91930	0.484000	0.47621	ACC	.		0.756	RPIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252683.2		
SOWAHC	65124	hgsc.bcm.edu	37	2	110372192	110372192	+	Silent	SNP	A	A	G	rs6594048		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:110372192A>G	ENST00000356454.3	+	1	282	c.126A>G	c.(124-126)ctA>ctG	p.L42L	SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000415095.1_5'Flank|SEPT10_ENST00000437928.1_5'Flank|SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000397712.2_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	42																	GGGGCGCCCTAGGCGGCGAAC	0.771													G|||	5008	1.0	1.0	1.0	5008	,	,		6158	1.0		1.0	False		,,,				2504	1.0				p.L42L		.											.	.	0			c.A126G						.						1.0	2.0	2.0					2																	110372192		1239	2477	3716	SO:0001819	synonymous_variant	65124	exon1			CGCCCTAGGCGGC	AK023346	CCDS33270.1	2q13	2013-01-10	2012-01-12	2012-01-12	ENSG00000198142	ENSG00000198142		"""Ankyrin repeat domain containing"""	26149	protein-coding gene	gene with protein product			"""ankyrin repeat domain 57"""	C2orf26, ANKRD57		22234889	Standard	NM_023016		Approved	FLJ21870	uc002tfb.3	Q53LP3	OTTHUMG00000153219	ENST00000356454.3:c.126A>G	2.37:g.110372192A>G		0	0		4	4	NM_023016	0	0	0	0	0	Q8NE15|Q9H6U1	Silent	SNP	ENST00000356454.3	37	CCDS33270.1																																																																																			A|0.029;G|0.971		0.771	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016	
TNS1	7145	bcgsc.ca	37	2	218669225	218669225	+	Missense_Mutation	SNP	T	T	C	rs61741262	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:218669225T>C	ENST00000171887.4	-	33	5617	c.5165A>G	c.(5164-5166)aAc>aGc	p.N1722S	TNS1_ENST00000419504.1_Missense_Mutation_p.N1708S|TNS1_ENST00000430930.1_Missense_Mutation_p.N1701S	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1722					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GGAGACGAAGTTGACGATGGC	0.637													.|||	192	0.0383387	0.0045	0.0548	5008	,	,		17943	0.001		0.1252	False		,,,				2504	0.0215				p.N1722S		.											.	TNS1-156	0			c.A5165G						.		SER/ASN	99,4307	79.9+/-118.3	3,93,2107	110.0	105.0	107.0		5165	3.6	1.0	2	dbSNP_129	107	1017,7583	218.5+/-256.9	60,897,3343	yes	missense	TNS1	NM_022648.4	46	63,990,5450	CC,CT,TT		11.8256,2.2469,8.5807	benign	1722/1736	218669225	1116,11890	2203	4300	6503	SO:0001583	missense	7145	exon33			ACGAAGTTGACGA	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.5165A>G	2.37:g.218669225T>C	ENSP00000171887:p.Asn1722Ser	250	0		361	8	NM_022648	0	0	0	0	0	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	129	0.059065934065934064	5	0.01016260162601626	26	0.0718232044198895	1	0.0017482517482517483	97	0.1279683377308707	t	12.49	1.953929	0.34471	0.022469	0.118256	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	T;T;T;T	0.28069	1.63;1.63;1.63;1.63	4.79	3.63	0.41609	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.049009	0.85682	N	0.000000	T	0.00210	0.0006	L	0.31526	0.94	0.09310	P	1.0	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.07908	-1.0748	9	0.36615	T	0.2	.	10.3973	0.44209	0.0:0.0774:0.0:0.9226	.	1722;1701;1708	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	S	1722;860;1708;1701	ENSP00000171887:N1722S;ENSP00000394171:N860S;ENSP00000408724:N1708S;ENSP00000406016:N1701S	ENSP00000171887:N1722S	N	-	2	0	TNS1	218377470	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.131000	0.42074	0.857000	0.35407	0.370000	0.22315	AAC	T|0.921;C|0.079		0.637	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
SPEG	10290	hgsc.bcm.edu	37	2	220348518	220348518	+	Silent	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:220348518G>A	ENST00000312358.7	+	30	6465	c.6333G>A	c.(6331-6333)gaG>gaA	p.E2111E	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	2111					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)		CCTCCAGCGAGGCAGCGCCCC	0.741																																					p.E2111E		.											.	SPEG-383	0			c.G6333A						.						4.0	5.0	5.0					2																	220348518		1666	3727	5393	SO:0001819	synonymous_variant	10290	exon30			CAGCGAGGCAGCG	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.6333G>A	2.37:g.220348518G>A		0	0		9	6	NM_005876	0	0	0	0	0	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Silent	SNP	ENST00000312358.7	37	CCDS42824.1																																																																																			.		0.741	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
ECEL1	9427	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	233347170	233347170	+	Missense_Mutation	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr2:233347170G>A	ENST00000304546.1	-	12	1964	c.1754C>T	c.(1753-1755)gCg>gTg	p.A585V	ECEL1_ENST00000409941.1_Missense_Mutation_p.A583V	NM_004826.2	NP_004817.2	O95672	ECEL1_HUMAN	endothelin converting enzyme-like 1	585					neuropeptide signaling pathway (GO:0007218)|respiratory system process (GO:0003016)	integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000771)|Lung(119;0.00213)|LUSC - Lung squamous cell carcinoma(224;0.00746)		CAGGATGCCCGCGGGGAACAC	0.612																																					p.A585V		.											.	ECEL1-90	0			c.C1754T						.						138.0	142.0	141.0					2																	233347170		2203	4300	6503	SO:0001583	missense	9427	exon12			ATGCCCGCGGGGA	Y16187	CCDS2493.1	2q37.1	2010-09-29			ENSG00000171551	ENSG00000171551			3147	protein-coding gene	gene with protein product	"""damage induced neuronal endopeptidase"""	605896				9931490, 11352565	Standard	NM_004826		Approved	XCE, DINE	uc002vsv.2	O95672	OTTHUMG00000133262	ENST00000304546.1:c.1754C>T	2.37:g.233347170G>A	ENSP00000302051:p.Ala585Val	129	0		164	20	NM_004826	0	0	0	0	0	Q45UD9|Q53RF9|Q6UW86|Q86TH4|Q9NY95	Missense_Mutation	SNP	ENST00000304546.1	37	CCDS2493.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.481054	0.84747	.	.	ENSG00000171551	ENST00000304546;ENST00000409941	D;D	0.84873	-1.91;-1.91	4.9	4.01	0.46588	Peptidase M13, neprilysin, C-terminal (2);Metallopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.90738	0.7093	M	0.80422	2.495	0.80722	D	1	D;D	0.76494	0.999;0.99	P;P	0.60886	0.88;0.808	D	0.91061	0.4885	9	.	.	.	-18.1964	13.6758	0.62454	0.0:0.1546:0.8454:0.0	.	583;585	O95672-2;O95672	.;ECEL1_HUMAN	V	585;583	ENSP00000302051:A585V;ENSP00000386333:A583V	.	A	-	2	0	ECEL1	233055414	1.000000	0.71417	0.034000	0.17996	0.190000	0.23558	9.244000	0.95423	1.277000	0.44412	0.650000	0.86243	GCG	.		0.612	ECEL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257039.2	NM_004826	
SLC23A2	9962	broad.mit.edu;bcgsc.ca	37	20	4893560	4893560	+	Missense_Mutation	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr20:4893560G>A	ENST00000379333.1	-	4	565	c.173C>T	c.(172-174)gCg>gTg	p.A58V	SLC23A2_ENST00000424750.2_Missense_Mutation_p.A58V|SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000338244.1_Missense_Mutation_p.A58V	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	58					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						AGTGTAGATCGCCATGAGCTC	0.582																																					p.A58V		.											.	SLC23A2-92	0			c.C173T						.						247.0	197.0	214.0					20																	4893560		2203	4300	6503	SO:0001583	missense	9962	exon4			TAGATCGCCATGA	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.173C>T	20.37:g.4893560G>A	ENSP00000368637:p.Ala58Val	106	0		147	7	NM_203327	0	0	0	0	0	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Missense_Mutation	SNP	ENST00000379333.1	37	CCDS13085.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.027004	0.75390	.	.	ENSG00000089057	ENST00000379333;ENST00000338244;ENST00000424750	T;T;T	0.62364	0.03;0.03;0.03	5.56	5.56	0.83823	.	0.057533	0.64402	D	0.000001	T	0.66036	0.2749	N	0.24115	0.695	0.31981	N	0.605883	P;D;D	0.76494	0.624;0.999;0.999	B;D;D	0.65874	0.107;0.939;0.939	T	0.66516	-0.5904	10	0.26408	T	0.33	-17.5486	17.0142	0.86414	0.0:0.0:1.0:0.0	.	58;58;58	B4DJZ1;A0MSJ5;Q9UGH3	.;.;S23A2_HUMAN	V	58	ENSP00000368637:A58V;ENSP00000344322:A58V;ENSP00000406601:A58V	ENSP00000344322:A58V	A	-	2	0	SLC23A2	4841560	1.000000	0.71417	0.987000	0.45799	0.928000	0.56348	6.948000	0.75965	2.598000	0.87819	0.655000	0.94253	GCG	.		0.582	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
ACTR5	79913	hgsc.bcm.edu	37	20	37377139	37377139	+	Silent	SNP	C	C	T	rs2254105	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr20:37377139C>T	ENST00000243903.4	+	1	55	c.18C>T	c.(16-18)ttC>ttT	p.F6F		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	6					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				CGAACGTGTTCCCGTTCCGCG	0.756													C|||	1227	0.245008	0.205	0.2334	5008	,	,		10427	0.2679		0.2565	False		,,,				2504	0.272				p.F6F		.											.	ACTR5-90	0			c.C18T						.						3.0	4.0	4.0					20																	37377139		1470	2633	4103	SO:0001819	synonymous_variant	79913	exon1			CGTGTTCCCGTTC	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"""INO80 complex subunits"""	14671	protein-coding gene	gene with protein product	"""INO80 complex subunit M"""		"""ARP5 (actin-related protein 5, yeast) homolog"""			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.18C>T	20.37:g.37377139C>T		0	0		9	7	NM_024855	0	0	0	0	0	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	37	CCDS13308.1																																																																																			C|0.769;T|0.231		0.756	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855	
CLIC6	54102	hgsc.bcm.edu	37	21	36042579	36042579	+	Missense_Mutation	SNP	C	C	G	rs13049028	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr21:36042579C>G	ENST00000360731.3	+	1	892	c.892C>G	c.(892-894)Caa>Gaa	p.Q298E	CLIC6_ENST00000349499.2_Missense_Mutation_p.Q298E			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	298						chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						TGAGCCGCAGCAATCGGGGGA	0.756													G|||	1116	0.222843	0.2648	0.1657	5008	,	,		8796	0.1825		0.2137	False		,,,				2504	0.2577				p.Q298E		.											.	CLIC6-91	0			c.C892G						.	G	GLU/GLN	454,2348		41,372,988	2.0	2.0	2.0		892	-0.8	0.0	21	dbSNP_121	2	925,5025		74,777,2124	no	missense	CLIC6	NM_053277.1	29	115,1149,3112	GG,GC,CC		15.5462,16.2027,15.7564	benign	298/687	36042579	1379,7373	1401	2975	4376	SO:0001583	missense	54102	exon1			CCGCAGCAATCGG	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"""Ion channels / Chloride channels : Intracellular"""	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.892C>G	21.37:g.36042579C>G	ENSP00000353959:p.Gln298Glu	2	0		25	15	NM_053277	0	0	0	0	0	A8K0U8|Q8IX31	Missense_Mutation	SNP	ENST00000360731.3	37		434	0.1987179487179487	125	0.2540650406504065	63	0.17403314917127072	81	0.14160839160839161	165	0.21767810026385223	G	0.195	-1.050076	0.01981	0.162027	0.155462	ENSG00000159212	ENST00000360731;ENST00000349499	T;T	0.21361	2.02;2.01	3.75	-0.792	0.10925	.	.	.	.	.	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43861	-0.9365	8	0.02654	T	1	-10.3162	7.3436	0.26650	0.1642:0.3831:0.4527:0.0	rs13049028	298;298	Q96NY7;Q96NY7-2	CLIC6_HUMAN;.	E	298	ENSP00000353959:Q298E;ENSP00000290332:Q298E	ENSP00000290332:Q298E	Q	+	1	0	CLIC6	34964449	0.256000	0.24012	0.012000	0.15200	0.009000	0.06853	0.804000	0.27098	-0.082000	0.12640	-0.676000	0.03789	CAA	C|0.802;G|0.198		0.756	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1		
CLIC6	54102	hgsc.bcm.edu	37	21	36042584	36042584	+	Silent	SNP	G	G	A	rs13049239	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr21:36042584G>A	ENST00000360731.3	+	1	897	c.897G>A	c.(895-897)tcG>tcA	p.S299S	CLIC6_ENST00000349499.2_Silent_p.S299S			Q96NY7	CLIC6_HUMAN	chloride intracellular channel 6	299						chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19						CGCAGCAATCGGGGGACGGCA	0.751													A|||	1101	0.219848	0.2549	0.1628	5008	,	,		9144	0.1825		0.2137	False		,,,				2504	0.2577				p.S299S		.											.	CLIC6-91	0			c.G897A						.	A		412,2410		18,376,1017	2.0	2.0	2.0		897	-0.2	0.0	21	dbSNP_121	2	842,5136		42,758,2189	no	coding-synonymous	CLIC6	NM_053277.1		60,1134,3206	AA,AG,GG		14.085,14.5996,14.25		299/687	36042584	1254,7546	1411	2989	4400	SO:0001819	synonymous_variant	54102	exon1			GCAATCGGGGGAC	AF426169	CCDS13638.1	21q22.12	2012-09-26			ENSG00000159212	ENSG00000159212		"""Ion channels / Chloride channels : Intracellular"""	2065	protein-coding gene	gene with protein product		615321		CLIC1L		10830953	Standard	NM_053277		Approved	CLIC5	uc002yuf.1	Q96NY7	OTTHUMG00000086237	ENST00000360731.3:c.897G>A	21.37:g.36042584G>A		2	0		27	16	NM_053277	0	0	0	0	0	A8K0U8|Q8IX31	Silent	SNP	ENST00000360731.3	37																																																																																				G|0.803;A|0.197		0.751	CLIC6-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000194156.1		
CHEK2	11200	broad.mit.edu	37	22	29091841	29091841	+	Silent	SNP	G	G	A	rs146546850	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr22:29091841G>A	ENST00000405598.1	-	12	1307	c.1116C>T	c.(1114-1116)tcC>tcT	p.S372S	CHEK2_ENST00000382580.2_Silent_p.S415S|CHEK2_ENST00000382578.1_Silent_p.S281S|CHEK2_ENST00000382565.1_Intron|CHEK2_ENST00000464581.1_5'Flank|CHEK2_ENST00000348295.3_Silent_p.S343S|CHEK2_ENST00000328354.6_Silent_p.S372S|CHEK2_ENST00000402731.1_Silent_p.S343S|CHEK2_ENST00000544772.1_Silent_p.S151S|CHEK2_ENST00000403642.1_Silent_p.S281S|CHEK2_ENST00000382566.1_3'UTR|CHEK2_ENST00000404276.1_Silent_p.S372S			O96017	CHK2_HUMAN	checkpoint kinase 2	372	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|T-loop/activation segment.				cellular protein catabolic process (GO:0044257)|cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA damage induced protein phosphorylation (GO:0006975)|double-strand break repair (GO:0006302)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of transcription, DNA-templated (GO:0045893)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of protein catabolic process (GO:0042176)|regulation of transcription, DNA-templated (GO:0006355)|replicative senescence (GO:0090399)|response to gamma radiation (GO:0010332)|signal transduction in response to DNA damage (GO:0042770)|signal transduction involved in intra-S DNA damage checkpoint (GO:0072428)|spindle assembly involved in mitosis (GO:0090307)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|PML body (GO:0016605)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)	p.S372S(8)		central_nervous_system(17)|endometrium(2)|kidney(11)|large_intestine(2)|lung(11)|ovary(1)|prostate(4)|stomach(2)	50						CCAAAATCTTGGAGTGCCCAA	0.413			F			breast		Direct reversal of damage;Other conserved DNA damage response genes																													p.S415S		.	yes	Rec		familial breast cancer	22	22q12.1	11200	CHK2 checkpoint homolog (S. pombe)		E	.	CHEK2-1515	8	Substitution - coding silent(8)	kidney(4)|prostate(2)|endometrium(1)|central_nervous_system(1)	c.C1245T						.						43.0	44.0	44.0					22																	29091841		2203	4300	6503	SO:0001819	synonymous_variant	11200	exon12			AATCTTGGAGTGC	AF086904	CCDS13843.1, CCDS13844.1, CCDS33629.1	22q12.1	2014-09-17	2011-11-11	2001-09-27	ENSG00000183765	ENSG00000183765			16627	protein-coding gene	gene with protein product		604373	"""CHK2 (checkpoint, S.pombe) homolog"", ""CHK2 checkpoint homolog (S. pombe)"""	RAD53		9836640, 10097108	Standard	NM_001257387		Approved	CDS1, CHK2, HuCds1, PP1425, bA444G7	uc003adt.1	O96017	OTTHUMG00000151023	ENST00000405598.1:c.1116C>T	22.37:g.29091841G>A		174	2		136	13	NM_001005735	0	0	0	0	0	A8K3Y9|B7ZBF3|B7ZBF4|B7ZBF5|Q6QA03|Q6QA04|Q6QA05|Q6QA06|Q6QA07|Q6QA08|Q6QA10|Q6QA11|Q6QA12|Q6QA13|Q9HBS5|Q9HCQ8|Q9UGF0|Q9UGF1	Silent	SNP	ENST00000405598.1	37	CCDS13843.1	.	.	.	.	.	.	.	.	.	.	G	5.792	0.330417	0.10956	.	.	ENSG00000183765	ENST00000434810	.	.	.	5.89	-2.11	0.07187	.	.	.	.	.	T	0.42154	0.1190	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33854	-0.9852	4	.	.	.	-7.6356	3.2532	0.06822	0.327:0.1103:0.4613:0.1014	.	.	.	.	L	116	.	.	P	-	2	0	CHEK2	27421841	0.997000	0.39634	0.996000	0.52242	0.470000	0.32858	0.318000	0.19504	-0.075000	0.12798	-0.907000	0.02831	CCA	.		0.413	CHEK2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000321150.1	NM_001005735	
TRIOBP	11078	hgsc.bcm.edu	37	22	38122462	38122462	+	Missense_Mutation	SNP	A	A	G	rs739138	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr22:38122462A>G	ENST00000406386.3	+	7	4154	c.3899A>G	c.(3898-3900)cAc>cGc	p.H1300R		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1300			H -> R (in dbSNP:rs739138).		actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GGCCGCACCCACAGCCCTGGC	0.741													G|||	3010	0.601038	0.1944	0.5836	5008	,	,		13399	0.8859		0.7157	False		,,,				2504	0.7515				p.H1300R		.											.	TRIOBP-136	0			c.A3899G						.	G	ARG/HIS	1221,2235		265,691,772	4.0	6.0	5.0		3899	3.9	1.0	22	dbSNP_86	5	5694,1808		2238,1218,295	yes	missense	TRIOBP	NM_001039141.2	29	2503,1909,1067	GG,GA,AA		24.1002,35.3299,36.8954	benign	1300/2366	38122462	6915,4043	1728	3751	5479	SO:0001583	missense	11078	exon7			GCACCCACAGCCC	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3899A>G	22.37:g.38122462A>G	ENSP00000384312:p.His1300Arg	0	0		10	10	NM_001039141	0	0	0	0	0	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	1409	0.6451465201465202	110	0.22357723577235772	222	0.6132596685082873	531	0.9283216783216783	546	0.7203166226912929	G	12.86	2.065195	0.36470	0.353299	0.758998	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.11063	2.81	4.93	3.9	0.45041	.	.	.	.	.	T	0.00012	0.0000	N	0.01576	-0.805	0.09310	P	0.999999999370294	B	0.02656	0.0	B	0.01281	0.0	T	0.29671	-1.0004	8	0.02654	T	1	.	4.383	0.11304	0.2555:0.0:0.5874:0.1571	rs739138	1300	Q9H2D6	TARA_HUMAN	R	1300	ENSP00000384312:H1300R	ENSP00000384312:H1300R	H	+	2	0	TRIOBP	36452408	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	1.338000	0.33873	0.503000	0.28060	-0.366000	0.07423	CAC	A|0.354;G|0.646		0.741	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
TMEM42	131616	hgsc.bcm.edu	37	3	44903434	44903434	+	Silent	SNP	G	G	C	rs2292181	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr3:44903434G>C	ENST00000302392.4	+	1	74	c.18G>C	c.(16-18)ggG>ggC	p.G6G	MIR564_ENST00000385049.1_RNA	NM_144638.1	NP_653239.1	Q69YG0	TMM42_HUMAN	transmembrane protein 42	6						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00839)|KIRC - Kidney renal clear cell carcinoma(197;0.0461)|Kidney(197;0.0576)		AGAGGCCGGGGCCTCCGGGCG	0.746													G|||	273	0.0545128	0.056	0.0951	5008	,	,		7698	0.0437		0.0567	False		,,,				2504	0.0327				p.G6G		.											.	TMEM42-90	0			c.G18C						.	G		93,3451		1,91,1680	3.0	4.0	4.0		18	3.2	0.0	3	dbSNP_100	4	184,7076		1,182,3447	no	coding-synonymous	TMEM42	NM_144638.1		2,273,5127	CC,CG,GG		2.5344,2.6242,2.5639		6/160	44903434	277,10527	1772	3630	5402	SO:0001819	synonymous_variant	131616	exon1			GCCGGGGCCTCCG	AL834253	CCDS2722.1	3p21.31	2005-01-19			ENSG00000169964	ENSG00000169964			28444	protein-coding gene	gene with protein product						12477932	Standard	NM_144638		Approved	MGC29956	uc003cnz.3	Q69YG0	OTTHUMG00000133092	ENST00000302392.4:c.18G>C	3.37:g.44903434G>C		0	0		13	10	NM_144638	0	0	0	0	0	Q8WUQ6	Silent	SNP	ENST00000302392.4	37	CCDS2722.1																																																																																			G|0.938;C|0.062		0.746	TMEM42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256750.2	NM_144638	
SACM1L	22908	hgsc.bcm.edu;bcgsc.ca	37	3	45751105	45751105	+	Missense_Mutation	SNP	G	G	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr3:45751105G>T	ENST00000389061.5	+	5	653	c.449G>T	c.(448-450)aGt>aTt	p.S150I	SACM1L_ENST00000464524.1_3'UTR|SACM1L_ENST00000541314.1_Missense_Mutation_p.S89I|SACM1L_ENST00000418611.1_Missense_Mutation_p.S47I	NM_014016.3	NP_054735.3	Q9NTJ5	SAC1_HUMAN	SAC1 suppressor of actin mutations 1-like (yeast)	150	SAC. {ECO:0000255|PROSITE- ProRule:PRU00183}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of endoplasmic reticulum membrane (GO:0030176)	phosphatase activity (GO:0016791)|phosphatidylinositol bisphosphate phosphatase activity (GO:0034593)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphatidylinositol-4-phosphate phosphatase activity (GO:0043812)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.0102)|KIRC - Kidney renal clear cell carcinoma(197;0.0234)|Kidney(197;0.0277)		TCCAACACTAGTCCTGAATTC	0.368																																					p.S150I		.											.	SACM1L-91	0			c.G449T						.						95.0	90.0	92.0					3																	45751105		2203	4300	6503	SO:0001583	missense	22908	exon5			ACACTAGTCCTGA	AB020658	CCDS33745.1	3p21.3	2010-03-11			ENSG00000211456	ENSG00000211456			17059	protein-coding gene	gene with protein product		606569				10048485, 11352561	Standard	NM_014016		Approved	SAC1, KIAA0851	uc003cos.2	Q9NTJ5	OTTHUMG00000156653	ENST00000389061.5:c.449G>T	3.37:g.45751105G>T	ENSP00000373713:p.Ser150Ile	129	0		71	4	NM_014016	0	0	0	0	0	A8K527|B4DK71|O94935|Q7LA14|Q7LA22|Q96AX7|Q9NQ46|Q9NQ57	Missense_Mutation	SNP	ENST00000389061.5	37	CCDS33745.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233324	0.79688	.	.	ENSG00000211456	ENST00000418611;ENST00000389061;ENST00000438671;ENST00000541314	T;T;T;T	0.58797	0.31;0.31;0.31;0.31	6.17	6.17	0.99709	Synaptojanin, N-terminal (2);	0.000000	0.85682	D	0.000000	T	0.61825	0.2378	L	0.58925	1.835	0.80722	D	1	P;P	0.38788	0.647;0.467	B;B	0.41135	0.348;0.179	T	0.57694	-0.7767	10	0.38643	T	0.18	-22.7161	20.8794	0.99867	0.0:0.0:1.0:0.0	.	89;150	B4DK71;Q9NTJ5	.;SAC1_HUMAN	I	47;150;89;89	ENSP00000396387:S47I;ENSP00000373713:S150I;ENSP00000411966:S89I;ENSP00000443373:S89I	ENSP00000373713:S150I	S	+	2	0	SACM1L	45726109	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.459000	0.97638	2.941000	0.99782	0.655000	0.94253	AGT	.		0.368	SACM1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345065.2	NM_014016	
SEMA5B	54437	hgsc.bcm.edu	37	3	122631896	122631896	+	Missense_Mutation	SNP	A	A	T	rs2276782	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr3:122631896A>T	ENST00000357599.3	-	18	2905	c.2519T>A	c.(2518-2520)gTc>gAc	p.V840D	SEMA5B_ENST00000451055.2_Missense_Mutation_p.V894D|SEMA5B_ENST00000195173.4_Missense_Mutation_p.V839D	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	840			V -> D (in dbSNP:rs2276782). {ECO:0000269|PubMed:10819331, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.		cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		GCGCAGGAGGACCTCCACCAG	0.791													T|||	3010	0.601038	0.5348	0.621	5008	,	,		11243	0.3522		0.8082	False		,,,				2504	0.7198				p.V894D		.											.	SEMA5B-157	0			c.T2681A						.	T	ASP/VAL	2573,1477		827,919,279	4.0	5.0	5.0		2519	5.0	1.0	3	dbSNP_100	5	6625,1195		2828,969,113	no	missense	SEMA5B	NM_001031702.2	152	3655,1888,392	TT,TA,AA		15.2813,36.4691,22.5105	benign	840/1152	122631896	9198,2672	2025	3910	5935	SO:0001583	missense	54437	exon18			AGGAGGACCTCCA	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.2519T>A	3.37:g.122631896A>T	ENSP00000350215:p.Val840Asp	0	0		9	9	NM_001256347	0	0	0	0	0	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	1286	0.5888278388278388	247	0.5020325203252033	243	0.6712707182320442	193	0.3374125874125874	603	0.7955145118733509	T	5.344	0.248763	0.10130	0.635309	0.847187	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.34072	1.43;1.38;1.48;1.5	5.01	5.01	0.66863	.	0.161766	0.52532	N	0.000069	T	0.00012	0.0000	N	0.00246	-1.78	0.30182	P	0.8002819999999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39354	-0.9618	9	0.02654	T	1	.	10.6514	0.45651	0.1435:0.0:0.0:0.8565	rs2276782	782;840	D3YTI7;Q9P283	.;SEM5B_HUMAN	D	840;839;782;894;840	ENSP00000350215:V840D;ENSP00000195173:V839D;ENSP00000389588:V894D;ENSP00000377208:V840D	ENSP00000195173:V839D	V	-	2	0	SEMA5B	124114586	1.000000	0.71417	0.990000	0.47175	0.785000	0.44390	4.886000	0.63149	0.945000	0.37605	-0.257000	0.10917	GTC	T|0.412;A|0.588		0.791	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
VWA5B2	90113	broad.mit.edu;bcgsc.ca	37	3	183951431	183951431	+	Missense_Mutation	SNP	C	C	T	rs902417	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr3:183951431C>T	ENST00000426955.2	+	4	698	c.598C>T	c.(598-600)Cct>Tct	p.P200S	EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000273794.5_5'UTR	NM_138345.1	NP_612354.1	Q8N398	VW5B2_HUMAN	von Willebrand factor A domain containing 5B2	211								p.P200S(1)		breast(3)|endometrium(4)|kidney(1)|lung(1)|prostate(1)|skin(5)	15						GCTGGCTGCCCCTCGGGACGT	0.662													C|||	1088	0.217252	0.177	0.2075	5008	,	,		16546	0.2351		0.2485	False		,,,				2504	0.228				p.P200S		.											.	.	1	Substitution - Missense(1)	kidney(1)	c.C598T						.	C	SER/PRO	241,1143		25,191,476	30.0	37.0	35.0		598	2.0	1.0	3	dbSNP_92	35	724,2458		83,558,950	yes	missense	VWA5B2	NM_138345.1	74	108,749,1426	TT,TC,CC		22.753,17.4133,21.1345	benign	200/1243	183951431	965,3601	692	1591	2283	SO:0001583	missense	90113	exon4			GCTGCCCCTCGGG		CCDS54686.1	3q27.1	2008-07-25	2008-07-25		ENSG00000145198	ENSG00000145198			25144	protein-coding gene	gene with protein product						15231747	Standard	NM_138345		Approved	DKFZp761K032, LOC90113	uc011bra.2	Q8N398	OTTHUMG00000156820	ENST00000426955.2:c.598C>T	3.37:g.183951431C>T	ENSP00000398688:p.Pro200Ser	116	1		231	10	NM_138345	0	0	0	0	0	B9EGN7	Missense_Mutation	SNP	ENST00000426955.2	37	CCDS54686.1	444	0.2032967032967033	88	0.17886178861788618	74	0.20441988950276244	94	0.16433566433566432	188	0.24802110817941952	C	1.623	-0.521080	0.04171	0.174133	0.22753	ENSG00000145198	ENST00000426955	T	0.60424	0.19	3.84	1.99	0.26369	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999633179	B;B	0.27823	0.19;0.004	B;B	0.29267	0.1;0.006	T	0.19160	-1.0314	8	0.33141	T	0.24	-0.1148	4.7979	0.13281	0.2103:0.6742:0.0:0.1154	rs902417;rs1687244;rs3882317;rs59041042;rs902417	200;211	B9EGN7;C9JW99	.;.	S	200	ENSP00000398688:P200S	ENSP00000398688:P200S	P	+	1	0	VWA5B2	185434125	0.999000	0.42202	0.982000	0.44146	0.641000	0.38312	1.678000	0.37586	0.384000	0.24942	0.462000	0.41574	CCT	C|0.788;T|0.212		0.662	VWA5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346004.2	XM_291077	
MUC4	4585	hgsc.bcm.edu;mdanderson.org	37	3	195508187	195508187	+	Missense_Mutation	SNP	C	C	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr3:195508187C>T	ENST00000463781.3	-	2	10723	c.10264G>A	c.(10264-10266)Gcc>Acc	p.A3422T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3422T|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGGGTGGCGTGACCTGTG	0.582																																					p.A3422T		.											.	MUC4-90	0			c.G10264A						.						27.0	21.0	23.0					3																	195508187		688	1579	2267	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10264G>A	3.37:g.195508187C>T	ENSP00000417498:p.Ala3422Thr	36	0		46	8	NM_018406	0	0	0	0	0	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.361	-0.939430	0.02322	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.49;1.48	0.312	-0.624	0.11552	.	.	.	.	.	T	0.08891	0.0220	N	0.02539	-0.55	0.09310	N	1	B	0.19583	0.037	B	0.08055	0.003	T	0.27434	-1.0074	8	.	.	.	.	1.4254	0.02322	0.3411:0.3312:0.0:0.3277	.	3294	E7ESK3	.	T	3422	ENSP00000417498:A3422T;ENSP00000420243:A3422T	.	A	-	1	0	MUC4	196992966	0.000000	0.05858	0.004000	0.12327	0.012000	0.07955	-2.425000	0.01028	-0.890000	0.03945	0.089000	0.15464	GCC	.		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
IDUA	3425	broad.mit.edu	37	4	996204	996204	+	Missense_Mutation	SNP	A	A	C			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:996204A>C	ENST00000247933.4	+	8	1208	c.1120A>C	c.(1120-1122)Acc>Ccc	p.T374P	IDUA_ENST00000514224.1_Missense_Mutation_p.T242P|IDUA_ENST00000453894.1_Missense_Mutation_p.T396P	NM_000203.3	NP_000194.2	P35475	IDUA_HUMAN	iduronidase, alpha-L-	374					carbohydrate metabolic process (GO:0005975)|cell morphogenesis (GO:0000902)|chemical homeostasis (GO:0048878)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate catabolic process (GO:0030209)|disaccharide metabolic process (GO:0005984)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|limb morphogenesis (GO:0035108)|lysosome organization (GO:0007040)|skeletal system morphogenesis (GO:0048705)|small molecule metabolic process (GO:0044281)	coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	L-iduronidase activity (GO:0003940)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			GGTCAACAACACCCGCCCGCC	0.711																																					p.T374P		.											.	IDUA-91	0			c.A1120C						.						26.0	28.0	27.0					4																	996204		2185	4282	6467	SO:0001583	missense	3425	exon8			AACAACACCCGCC	M74715	CCDS3343.1	4p16.3	2012-10-02			ENSG00000127415	ENSG00000127415	3.2.1.76		5391	protein-coding gene	gene with protein product		252800				1832239	Standard	NM_000203		Approved	MPS1	uc003gby.3	P35475	OTTHUMG00000088901	ENST00000247933.4:c.1120A>C	4.37:g.996204A>C	ENSP00000247933:p.Thr374Pro	38	5		213	89	NM_000203	0	0	0	0	0	B3KWK6	Missense_Mutation	SNP	ENST00000247933.4	37	CCDS3343.1	.	.	.	.	.	.	.	.	.	.	A	21.2	4.117066	0.77323	.	.	ENSG00000127415	ENST00000247933;ENST00000453894;ENST00000514224	D;D;D	0.94280	-3.39;-3.39;-3.39	5.31	5.31	0.75309	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.156849	0.56097	D	0.000026	D	0.96611	0.8894	M	0.86178	2.8	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	D	0.96508	0.9376	10	0.46703	T	0.11	-7.29	13.2474	0.60029	1.0:0.0:0.0:0.0	.	396;374	B3KWK6;P35475	.;IDUA_HUMAN	P	374;396;242	ENSP00000247933:T374P;ENSP00000396458:T396P;ENSP00000425081:T242P	ENSP00000247933:T374P	T	+	1	0	IDUA	986204	1.000000	0.71417	0.995000	0.50966	0.426000	0.31534	5.967000	0.70403	2.024000	0.59613	0.454000	0.30748	ACC	.		0.711	IDUA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000201812.1	NM_000203	
TNIP2	79155	hgsc.bcm.edu	37	4	2757800	2757800	+	Missense_Mutation	SNP	G	G	C	rs74548850	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:2757800G>C	ENST00000315423.7	-	1	303	c.217C>G	c.(217-219)Cgc>Ggc	p.R73G	TNIP2_ENST00000503235.1_Missense_Mutation_p.R73G|TNIP2_ENST00000510267.1_5'UTR	NM_024309.3	NP_077285.3			TNFAIP3 interacting protein 2											breast(2)|central_nervous_system(1)|large_intestine(4)|lung(6)|prostate(1)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.168)		TCCCGGAAGCGCGCAACCTGC	0.756													G|||	210	0.0419329	0.025	0.0447	5008	,	,		6355	0.0288		0.0408	False		,,,				2504	0.0777				p.R73G		.											.	TNIP2-90	0			c.C217G						.	G	GLY/ARG	60,3592		0,60,1766	5.0	7.0	6.0		217	2.8	1.0	4	dbSNP_131	6	267,7455		4,259,3598	no	missense	TNIP2	NM_024309.3	125	4,319,5364	CC,CG,GG		3.4577,1.6429,2.875	probably-damaging	73/430	2757800	327,11047	1826	3861	5687	SO:0001583	missense	79155	exon1			GGAAGCGCGCAAC	BC002740	CCDS3362.1, CCDS54714.1, CCDS75093.1	4p16.3	2008-08-01			ENSG00000168884	ENSG00000168884			19118	protein-coding gene	gene with protein product		610669				11390377, 12933576	Standard	NM_024309		Approved	ABIN-2, MGC4289, KLIP, FLIP1	uc003gfg.2	Q8NFZ5	OTTHUMG00000090267	ENST00000315423.7:c.217C>G	4.37:g.2757800G>C	ENSP00000321203:p.Arg73Gly	0	0		6	4	NM_024309	0	0	0	0	0		Missense_Mutation	SNP	ENST00000315423.7	37	CCDS3362.1	94	0.04304029304029304	17	0.034552845528455285	18	0.049723756906077346	18	0.03146853146853147	41	0.05408970976253298	G	19.51	3.841781	0.71488	0.016429	0.034577	ENSG00000168884	ENST00000315423;ENST00000503235	T;T	0.48522	0.82;0.81	3.62	2.75	0.32379	.	0.480578	0.20050	N	0.100314	T	0.14399	0.0348	M	0.65975	2.015	0.27856	N	0.940558	D;P	0.62365	0.991;0.481	P;B	0.52217	0.693;0.071	T	0.11299	-1.0593	10	0.23302	T	0.38	-8.2753	9.2129	0.37328	0.0:0.0:0.7823:0.2177	.	73;73	D6RGJ2;Q8NFZ5	.;TNIP2_HUMAN	G	73	ENSP00000321203:R73G;ENSP00000426314:R73G	ENSP00000321203:R73G	R	-	1	0	TNIP2	2727598	0.882000	0.30256	1.000000	0.80357	0.927000	0.56198	1.083000	0.30815	0.689000	0.31550	0.498000	0.49722	CGC	G|0.957;C|0.043		0.756	TNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206589.5	NM_024309	
WDR1	9948	bcgsc.ca	37	4	10099340	10099340	+	Missense_Mutation	SNP	T	T	C	rs13441	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:10099340T>C	ENST00000499869.2	-	5	746	c.553A>G	c.(553-555)Att>Gtt	p.I185V	WDR1_ENST00000382451.2_Intron|WDR1_ENST00000502702.1_Intron|WDR1_ENST00000382452.2_Missense_Mutation_p.I185V			O75083	WDR1_HUMAN	WD repeat domain 1	185			I -> V (in dbSNP:rs13441). {ECO:0000269|PubMed:15489334}.		blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sensory perception of sound (GO:0007605)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				endometrium(3)|lung(5)|ovary(2)|pancreas(1)|urinary_tract(1)	12				STAD - Stomach adenocarcinoma(129;0.000703)|Colorectal(103;0.0057)|LUSC - Lung squamous cell carcinoma(721;0.0232)		CTTACGCCAATTGTGAACTTG	0.512													T|||	2881	0.57528	0.3941	0.7147	5008	,	,		20083	0.6538		0.7097	False		,,,				2504	0.502				p.I185V		.											.	WDR1-48	0			c.A553G						.	T	,VAL/ILE	1813,2119		434,945,587	64.0	68.0	67.0		,553	4.3	0.7	4	dbSNP_52	67	5804,2484		2040,1724,380	yes	intron,missense	WDR1	NM_005112.4,NM_017491.3	,29	2474,2669,967	CC,CT,TT		29.971,46.1089,37.6678	,benign	,185/607	10099340	7617,4603	1966	4144	6110	SO:0001583	missense	9948	exon5			CGCCAATTGTGAA	AF020260	CCDS54739.1, CCDS54740.1	4p16.1	2013-01-09			ENSG00000071127	ENSG00000071127		"""WD repeat domain containing"""	12754	protein-coding gene	gene with protein product		604734				10036186	Standard	NM_017491		Approved		uc021xlv.1	O75083	OTTHUMG00000160253	ENST00000499869.2:c.553A>G	4.37:g.10099340T>C	ENSP00000427687:p.Ile185Val	127	1		136	5	NM_017491	0	0	0	0	0	A8K6E9|A8MPU4|O75313|Q8N6E5|Q9UG05|Q9UG78|Q9UQE0	Missense_Mutation	SNP	ENST00000499869.2	37	CCDS54740.1	1347	0.6167582417582418	198	0.4024390243902439	266	0.7348066298342542	356	0.6223776223776224	527	0.6952506596306068	T	9.102	1.004302	0.19199	0.461089	0.70029	ENSG00000071127	ENST00000499869;ENST00000382452;ENST00000508079	T;T;T	0.60299	0.2;0.2;0.2	5.56	4.35	0.52113	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.258408	0.32785	N	0.005649	T	0.00012	0.0000	N	0.20845	0.615	0.47094	P	6.850000000000467E-4	B	0.16802	0.019	B	0.19666	0.026	T	0.35699	-0.9778	9	0.36615	T	0.2	-12.9695	10.3924	0.44181	0.0:0.0:0.3423:0.6577	rs13441;rs1131629;rs2241481;rs3191683;rs17844834;rs17857545;rs52825858;rs13441	185	O75083	WDR1_HUMAN	V	185;185;189	ENSP00000427687:I185V;ENSP00000371890:I185V;ENSP00000425481:I189V	ENSP00000371890:I185V	I	-	1	0	WDR1	9708438	0.871000	0.30034	0.741000	0.31004	0.736000	0.42039	1.162000	0.31786	0.917000	0.36895	0.460000	0.39030	ATT	T|0.401;C|0.599		0.512	WDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359877.1		
FAM184B	27146	hgsc.bcm.edu	37	4	17643848	17643848	+	Missense_Mutation	SNP	G	G	A	rs2286771	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:17643848G>A	ENST00000265018.3	-	13	2562	c.2350C>T	c.(2350-2352)Cgg>Tgg	p.R784W		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	784				R -> W (in Ref. 1; BAA86590). {ECO:0000305}.						NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						GGGCCGCCCCGCTCCTGAGGA	0.701													G|||	2697	0.538538	0.1725	0.6599	5008	,	,		10215	0.8522		0.6233	False		,,,				2504	0.5368				p.R784W		.											.	FAM184B-23	0			c.C2350T						.						1.0	2.0	2.0					4																	17643848		374	1044	1418	SO:0001583	missense	27146	exon13			CGCCCCGCTCCTG		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.2350C>T	4.37:g.17643848G>A	ENSP00000265018:p.Arg784Trp	0	0		10	7	NM_015688	0	0	0	0	0		Missense_Mutation	SNP	ENST00000265018.3	37	CCDS47033.1	1272	0.5824175824175825	75	0.1524390243902439	232	0.6408839779005525	493	0.8618881118881119	472	0.6226912928759895	G	13.83	2.354233	0.41700	.	.	ENSG00000047662	ENST00000265018	T	0.34072	1.38	3.29	-3.67	0.04476	.	3.541600	0.00901	N	0.002342	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D	0.56968	0.978	B	0.40741	0.339	T	0.48547	-0.9026	9	0.72032	D	0.01	2.0681	6.7491	0.23477	0.107:0.2547:0.5506:0.0877	rs2286771;rs58699512;rs2286771	784	Q9ULE4	F184B_HUMAN	W	784	ENSP00000265018:R784W	ENSP00000265018:R784W	R	-	1	2	FAM184B	17252946	0.000000	0.05858	0.000000	0.03702	0.516000	0.34256	-0.323000	0.07997	-1.014000	0.03379	-0.369000	0.07265	CGG	G|0.440;A|0.560		0.701	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
SLIT2	9353	broad.mit.edu	37	4	20525746	20525746	+	Missense_Mutation	SNP	C	C	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:20525746C>T	ENST00000504154.1	+	14	1636	c.1384C>T	c.(1384-1386)Cgc>Tgc	p.R462C	SLIT2_ENST00000503823.1_Missense_Mutation_p.R462C|SLIT2_ENST00000273739.5_Missense_Mutation_p.R466C|SLIT2_ENST00000503837.1_Missense_Mutation_p.R466C	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	462	LRRCT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CAGCCCCCGCCGCCTGGCAAA	0.483																																					p.R462C		.											.	SLIT2-521	0			c.C1384T						.						109.0	123.0	118.0					4																	20525746		2203	4300	6503	SO:0001583	missense	9353	exon14			CCCCGCCGCCTGG	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1384C>T	4.37:g.20525746C>T	ENSP00000422591:p.Arg462Cys	78	0		89	4	NM_004787	0	0	0	0	0	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	37	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	C	32	5.172718	0.94807	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	D;D;T;T	0.81579	-1.5;-1.51;-1.43;-1.48	5.93	5.93	0.95920	Cysteine-rich flanking region, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91119	0.7204	M	0.84326	2.69	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.977;1.0	D	0.91338	0.5095	10	0.87932	D	0	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	462;462	O94813-3;O94813	.;SLIT2_HUMAN	C	462;462;466;466;466	ENSP00000427548:R462C;ENSP00000422591:R462C;ENSP00000273739:R466C;ENSP00000422261:R466C	ENSP00000273739:R466C	R	+	1	0	SLIT2	20134844	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.770000	0.85390	2.805000	0.96524	0.655000	0.94253	CGC	.		0.483	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
SOD3	6649	hgsc.bcm.edu	37	4	24801354	24801354	+	Silent	SNP	C	C	T	rs8192291	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:24801354C>T	ENST00000382120.3	+	2	416	c.211C>T	c.(211-213)Ctg>Ttg	p.L71L		NM_003102.2	NP_003093.2	P08294	SODE_HUMAN	superoxide dismutase 3, extracellular	71					removal of superoxide radicals (GO:0019430)|response to copper ion (GO:0046688)|response to hypoxia (GO:0001666)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	copper ion binding (GO:0005507)|heparin binding (GO:0008201)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			prostate(1)|urinary_tract(1)	2		Breast(46;0.0503)				GTCGGCCACGCTGGACGCCGC	0.726													C|||	994	0.198482	0.0968	0.1585	5008	,	,		11823	0.3512		0.2028	False		,,,				2504	0.2025				p.L71L		.											.	SOD3-90	0			c.C211T						.	C		341,3293		12,317,1488	4.0	5.0	5.0		211	0.7	0.0	4	dbSNP_117	5	1103,6325		63,977,2674	no	coding-synonymous	SOD3	NM_003102.2		75,1294,4162	TT,TC,CC		14.8492,9.3836,13.0537		71/241	24801354	1444,9618	1817	3714	5531	SO:0001819	synonymous_variant	6649	exon2			GCCACGCTGGACG		CCDS3430.1	4p15.2	2012-09-20			ENSG00000109610	ENSG00000109610	1.15.1.1		11181	protein-coding gene	gene with protein product		185490					Standard	NM_003102		Approved	EC-SOD	uc003gqz.3	P08294	OTTHUMG00000128565	ENST00000382120.3:c.211C>T	4.37:g.24801354C>T		1	0		19	8	NM_003102	0	0	0	0	0	Q5U781|Q6FHA2	Silent	SNP	ENST00000382120.3	37	CCDS3430.1																																																																																			C|0.777;T|0.223		0.726	SOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250416.1		
SHROOM3	57619	hgsc.bcm.edu	37	4	77662309	77662309	+	Silent	SNP	C	C	T	rs344143	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:77662309C>T	ENST00000296043.6	+	5	3936	c.2983C>T	c.(2983-2985)Ctg>Ttg	p.L995L		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	995	ASD1. {ECO:0000255|PROSITE- ProRule:PRU00637}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			TGAGGGCGACCTGGCCAGGCC	0.741													C|||	1906	0.380591	0.4115	0.4078	5008	,	,		9710	0.2669		0.4245	False		,,,				2504	0.3916				p.L995L		.											.	SHROOM3-93	0			c.C2983T						.	C		1365,2227		322,721,753	3.0	4.0	4.0		2983	-0.1	0.0	4	dbSNP_79	4	3066,4302		771,1524,1389	no	coding-synonymous	SHROOM3	NM_020859.3		1093,2245,2142	TT,TC,CC		41.6124,38.0011,40.4288		995/1997	77662309	4431,6529	1796	3684	5480	SO:0001819	synonymous_variant	57619	exon5			GGCGACCTGGCCA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.2983C>T	4.37:g.77662309C>T		0	0		34	32	NM_020859	0	0	0	0	0	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			C|0.604;T|0.396		0.741	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
DSPP	1834	bcgsc.ca	37	4	88537027	88537027	+	Silent	SNP	C	C	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr4:88537027C>T	ENST00000282478.7	+	4	3246	c.3213C>T	c.(3211-3213)gaC>gaT	p.D1071D	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Silent_p.D1071D			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1071	Asp/Ser-rich.				biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		atagcagtgacagcagtgaca	0.542																																					p.D1071D		.											.	DSPP-90	0			c.C3213T						.						56.0	66.0	63.0					4																	88537027		1577	2848	4425	SO:0001819	synonymous_variant	1834	exon5			CAGTGACAGCAGT	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3213C>T	4.37:g.88537027C>T		574	12		806	30	NM_014208	0	0	0	0	0	A8MUI0|O95815	Silent	SNP	ENST00000282478.7	37	CCDS43248.1																																																																																			.		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
SRD5A1	6715	hgsc.bcm.edu	37	5	6633779	6633779	+	Silent	SNP	C	C	G	rs248793	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr5:6633779C>G	ENST00000274192.5	+	1	324	c.90C>G	c.(88-90)cgC>cgG	p.R30R	SRD5A1_ENST00000504286.1_3'UTR|NSUN2_ENST00000506139.1_5'Flank|SRD5A1_ENST00000537411.1_Missense_Mutation_p.A39G|SRD5A1_ENST00000538824.1_Missense_Mutation_p.A39G|NSUN2_ENST00000264670.6_5'Flank|NSUN2_ENST00000539938.1_5'Flank	NM_001047.2	NP_001038.1	P18405	S5A1_HUMAN	steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1)	30				Missing (in Ref. 4; AAF14869). {ECO:0000305}.	androgen biosynthetic process (GO:0006702)|cell differentiation (GO:0030154)|sex determination (GO:0007530)|sex differentiation (GO:0007548)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-oxo-5-alpha-steroid 4-dehydrogenase activity (GO:0003865)|cholestenone 5-alpha-reductase activity (GO:0047751)|electron carrier activity (GO:0009055)			endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19					Dutasteride(DB01126)|Finasteride(DB01216)|Levonorgestrel(DB00367)|Spironolactone(DB00421)	TCTTCGCGCGCAATCGTCAGA	0.746													G|||	2833	0.565695	0.6936	0.6816	5008	,	,		9293	0.3899		0.5537	False		,,,				2504	0.5041				p.R30R		.											.	SRD5A1-90	0			c.C90G						.	G		2367,1089		855,657,216	5.0	6.0	5.0		90	0.8	0.0	5	dbSNP_79	5	4176,3144		1277,1622,761	no	coding-synonymous	SRD5A1	NM_001047.2		2132,2279,977	GG,GC,CC		42.9508,31.5104,39.2817		30/260	6633779	6543,4233	1728	3660	5388	SO:0001819	synonymous_variant	6715	exon1			CGCGCGCAATCGT	M32313	CCDS3870.1	5p15.31	2008-02-05			ENSG00000145545	ENSG00000145545	1.3.99.5		11284	protein-coding gene	gene with protein product		184753				1686016	Standard	XR_427663		Approved		uc003jdw.3	P18405	OTTHUMG00000090456	ENST00000274192.5:c.90C>G	5.37:g.6633779C>G		0	0		9	8	NM_001047	0	0	0	0	0	B2R7Q1|Q9UHY4|Q9UP36|Q9UP37	Silent	SNP	ENST00000274192.5	37	CCDS3870.1	1204	0.5512820512820513	332	0.6747967479674797	242	0.6685082872928176	214	0.3741258741258741	416	0.5488126649076517	G	11.09	1.537057	0.27475	0.684896	0.570492	ENSG00000145545	ENST00000537411;ENST00000538824	T	0.23552	1.9	3.76	0.815	0.18763	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28073	-1.0055	7	0.87932	D	0	-7.7997	5.3187	0.15870	0.1814:0.3179:0.5008:0.0	rs248793;rs1691051;rs17850143;rs17850363;rs57936391	39	F5GXK9	.	G	39	ENSP00000440186:A39G	ENSP00000446275:A39G	A	+	2	0	SRD5A1	6686779	0.019000	0.18553	0.000000	0.03702	0.000000	0.00434	1.407000	0.34657	-0.193000	0.10415	-0.132000	0.14878	GCA	C|0.454;G|0.546		0.746	SRD5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206903.1	NM_001047	
FAM170A	340069	bcgsc.ca	37	5	118969960	118969960	+	Missense_Mutation	SNP	C	C	T	rs328694	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr5:118969960C>T	ENST00000515256.1	+	3	689	c.517C>T	c.(517-519)Ccc>Tcc	p.P173S				A1A519	F170A_HUMAN	family with sequence similarity 170, member A	173			P -> S (in dbSNP:rs328694).		positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P173S(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(7)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	24						AGGTACTCCCCCCTCTGATGT	0.542													C|||	2221	0.44349	0.3495	0.3876	5008	,	,		21739	0.495		0.4453	False		,,,				2504	0.5552				p.P173S		.											.	FAM170A-91	1	Substitution - Missense(1)	prostate(1)	c.C517T						.	C	SER/PRO,SER/PRO	1354,2620		238,878,871	91.0	95.0	94.0		376,517	2.1	0.1	5	dbSNP_79	94	3719,4641		851,2017,1312	yes	missense,missense	FAM170A	NM_001163991.1,NM_182761.3	74,74	1089,2895,2183	TT,TC,CC		44.4856,34.0715,41.1302	probably-damaging,probably-damaging	126/283,173/330	118969960	5073,7261	1987	4180	6167	SO:0001583	missense	340069	exon3			ACTCCCCCCTCTG	AF427126	CCDS43353.1, CCDS54889.1	5q23.1	2008-06-12			ENSG00000164334	ENSG00000164334			27963	protein-coding gene	gene with protein product						12477932	Standard	NM_182761		Approved		uc003ksn.3	A1A519	OTTHUMG00000162946	ENST00000515256.1:c.517C>T	5.37:g.118969960C>T	ENSP00000422684:p.Pro173Ser	178	2		211	7	NM_182761	0	0	0	0	0	Q66LM8|Q7Z4V2|Q8IW94	Missense_Mutation	SNP	ENST00000515256.1	37		936	0.42857142857142855	172	0.34959349593495936	144	0.39779005524861877	299	0.5227272727272727	321	0.4234828496042216	C	10.32	1.318429	0.23994	0.340715	0.444856	ENSG00000164334	ENST00000296787;ENST00000515256	T	0.42131	0.98	4.89	2.11	0.27256	.	0.000000	0.64402	D	0.000013	T	0.00012	0.0000	M	0.67953	2.075	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.47129	-0.9141	8	.	.	.	-10.0542	3.7305	0.08491	0.171:0.5741:0.165:0.0898	rs328694;rs52831294;rs60487150;rs328694	126;173	D6RIE9;A1A519	.;F170A_HUMAN	S	126;173	ENSP00000422684:P173S	.	P	+	1	0	FAM170A	118997859	0.002000	0.14202	0.077000	0.20336	0.131000	0.20780	0.813000	0.27225	0.357000	0.24183	-0.136000	0.14681	CCC	C|0.562;T|0.438		0.542	FAM170A-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000371126.1	NM_182761	
FBN2	2201	broad.mit.edu	37	5	127727722	127727722	+	Missense_Mutation	SNP	C	C	G	rs34450503		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr5:127727722C>G	ENST00000508053.1	-	17	2566	c.1592G>C	c.(1591-1593)gGa>gCa	p.G531A	FBN2_ENST00000262464.4_Missense_Mutation_p.G531A|FBN2_ENST00000508989.1_Missense_Mutation_p.G498A			P35556	FBN2_HUMAN	fibrillin 2	531	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		TATACAATCTCCATTTGCATC	0.328													C|||	1	0.000199681	0.0	0.0	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.001				p.G531A		.											.	FBN2-146	0			c.G1592C						.	C	ALA/GLY	0,4406		0,0,2203	124.0	118.0	120.0		1592	4.1	1.0	5	dbSNP_126	120	21,8579	15.3+/-51.7	0,21,4279	yes	missense	FBN2	NM_001999.3	60	0,21,6482	GG,GC,CC		0.2442,0.0,0.1615	possibly-damaging	531/2913	127727722	21,12985	2203	4300	6503	SO:0001583	missense	2201	exon11			CAATCTCCATTTG	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1592G>C	5.37:g.127727722C>G	ENSP00000424571:p.Gly531Ala	86	2		86	3	NM_001999	0	0	0	0	0	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840824	0.51057	0.0	0.002442	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.87809	-2.3;-2.3;-2.3	4.14	4.14	0.48551	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000012	D	0.89061	0.6608	M	0.77820	2.39	0.42961	D	0.994405	D;P	0.54964	0.969;0.956	P;B	0.48425	0.577;0.352	D	0.90748	0.4655	10	0.72032	D	0.01	.	13.4765	0.61312	0.0:0.8424:0.1576:0.0	rs34450503	498;531	D6RJI3;P35556	.;FBN2_HUMAN	A	531;531;498	ENSP00000262464:G531A;ENSP00000424571:G531A;ENSP00000425596:G498A	ENSP00000262464:G531A	G	-	2	0	FBN2	127755621	0.999000	0.42202	0.995000	0.50966	0.971000	0.66376	4.271000	0.58902	2.592000	0.87571	0.585000	0.79938	GGA	C|0.999;G|0.001		0.328	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
SOWAHA	134548	hgsc.bcm.edu	37	5	132149684	132149684	+	Missense_Mutation	SNP	G	G	C	rs40274	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr5:132149684G>C	ENST00000378693.2	+	1	652	c.371G>C	c.(370-372)cGg>cCg	p.R124P		NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	124	Pro-rich.		R -> P (in dbSNP:rs40274).														CCCTTGGTCCGGGTGCCGCGG	0.776																																					p.R124P		.											.	.	0			c.G371C						.	C	PRO/ARG	2599,13		1293,13,0	2.0	3.0	3.0		371	-0.3	0.0	5	dbSNP_76	3	6177,193		2993,191,1	no	missense	ANKRD43	NM_175873.4	103	4286,204,1	CC,CG,GG		3.0298,0.4977,2.2935	benign	124/550	132149684	8776,206	1306	3185	4491	SO:0001583	missense	134548	exon1			TGGTCCGGGTGCC	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"""Ankyrin repeat domain containing"""	27033	protein-coding gene	gene with protein product			"""ankyrin repeat domain 43"""	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.371G>C	5.37:g.132149684G>C	ENSP00000367965:p.Arg124Pro	0	0		7	7	NM_175873	0	0	0	0	0	Q8NAE7	Missense_Mutation	SNP	ENST00000378693.2	37	CCDS43361.1	2142	0.9807692307692307	482	0.9796747967479674	357	0.9861878453038674	562	0.9825174825174825	741	0.9775725593667546	c	9.833	1.188835	0.21954	0.995023	0.969702	ENSG00000198944	ENST00000378693	T	0.38077	1.16	4.27	-0.265	0.12946	.	2.345400	0.02245	N	0.066177	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.36261	-0.9755	9	0.30078	T	0.28	-5.2019	3.6102	0.08057	0.2245:0.4439:0.2467:0.085	rs40274	124	Q2M3V2	ANR43_HUMAN	P	124	ENSP00000367965:R124P	ENSP00000367965:R124P	R	+	2	0	ANKRD43	132177583	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.768000	0.01794	-0.003000	0.14444	-3.153000	0.00058	CGG	G|0.980;C|0.020		0.776	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873	
PPP1R3G	648791	hgsc.bcm.edu	37	6	5086070	5086070	+	Silent	SNP	A	A	G	rs667752		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:5086070A>G	ENST00000405617.2	+	1	351	c.351A>G	c.(349-351)gcA>gcG	p.A117A		NM_001145115.1	NP_001138587.1	B7ZBB8	PP13G_HUMAN	protein phosphatase 1, regulatory subunit 3G	117					glucose homeostasis (GO:0042593)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)	cytoplasm (GO:0005737)	glycogen binding (GO:2001069)			kidney(2)	2						CGGAGGACGCACAGCTCGGCC	0.692													G|||	5008	1.0	1.0	1.0	5008	,	,		12505	1.0		1.0	False		,,,				2504	1.0				p.A117A		.											.	PPP1R3G-136	0			c.A351G						.						1.0	2.0	2.0					6																	5086070		400	1062	1462	SO:0001819	synonymous_variant	648791	exon1			GGACGCACAGCTC		CCDS47366.1	6p25.1	2012-04-17	2011-10-04		ENSG00000219607	ENSG00000219607		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14945	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3G"""			11948623	Standard	NM_001145115		Approved		uc011dia.1	B7ZBB8	OTTHUMG00000014172	ENST00000405617.2:c.351A>G	6.37:g.5086070A>G		0	0		8	8	NM_001145115	0	0	0	0	0		Silent	SNP	ENST00000405617.2	37	CCDS47366.1																																																																																			A|0.006;G|0.994		0.692	PPP1R3G-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039740.3	NM_001145115	
RREB1	6239	hgsc.bcm.edu	37	6	7230680	7230680	+	Missense_Mutation	SNP	G	G	T	rs9502564	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:7230680G>T	ENST00000349384.6	+	10	2662	c.2348G>T	c.(2347-2349)gGc>gTc	p.G783V	RREB1_ENST00000379933.3_Missense_Mutation_p.G783V|RREB1_ENST00000334984.6_Missense_Mutation_p.G783V|RREB1_ENST00000379938.2_Missense_Mutation_p.G783V	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	783			G -> V (in dbSNP:rs9502564). {ECO:0000269|PubMed:15067362, ECO:0000269|PubMed:21703425}.		multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CTGGGCGGGGGCCACAAGGGC	0.697													G|||	2678	0.534744	0.5333	0.4063	5008	,	,		15583	0.7411		0.2893	False		,,,				2504	0.6677				p.G783V		.											.	RREB1-144	0			c.G2348T						.	G	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	2083,2197		552,979,609	9.0	9.0	9.0		2348,2348,2348,2348	5.3	1.0	6	dbSNP_119	9	2599,5719		488,1623,2048	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	109,109,109,109	1040,2602,2657	TT,TG,GG		31.2455,48.6682,37.1646	benign,benign,benign,benign	783/1688,783/1743,783/1477,783/1688	7230680	4682,7916	2140	4159	6299	SO:0001583	missense	6239	exon10			GCGGGGGCCACAA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.2348G>T	6.37:g.7230680G>T	ENSP00000305560:p.Gly783Val	0	0		8	8	NM_001003700	0	0	0	0	0	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	1014	0.4642857142857143	249	0.5060975609756098	148	0.4088397790055249	412	0.7202797202797203	205	0.2704485488126649	G	11.15	1.553554	0.27739	0.486682	0.312455	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.09163	3.07;3.07;3.07;3.01	5.32	5.32	0.75619	.	0.278837	0.31370	N	0.007766	T	0.02533	0.0077	N	0.14661	0.345	0.21915	P	0.999474401	B;B;B	0.32653	0.161;0.379;0.328	B;B;B	0.35182	0.079;0.197;0.178	T	0.45512	-0.9256	9	0.13108	T	0.6	-17.3998	11.4207	0.49980	0.0:0.0:0.8202:0.1797	rs9502564	783;783;783	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	V	783	ENSP00000369265:G783V;ENSP00000369270:G783V;ENSP00000305560:G783V;ENSP00000335574:G783V	ENSP00000335574:G783V	G	+	2	0	RREB1	7175679	1.000000	0.71417	0.996000	0.52242	0.833000	0.47200	5.477000	0.66799	2.760000	0.94817	0.655000	0.94253	GGC	G|0.546;T|0.454		0.697	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
HLA-A	3105	hgsc.bcm.edu	37	6	29911239	29911261	+	Frame_Shift_Del	DEL	TTGAGAGCCTACCTGGATGGCAC	TTGAGAGCCTACCTGGATGGCAC	-	rs41540012|rs199474558|rs199474559|rs543623321|rs199474562|rs41541015|rs41545519|rs9260155|rs1059542|rs9260157|rs9260156|rs45495505|rs41551921|rs199474561|rs199474560|rs199474564|rs41545516|rs199474563|rs72555401	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	TTGAGAGCCTACCTGGATGGCAC	TTGAGAGCCTACCTGGATGGCAC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:29911239_29911261delTTGAGAGCCTACCTGGATGGCAC	ENST00000396634.1	+	5	879_901	c.538_560delTTGAGAGCCTACCTGGATGGCAC	c.(538-561)ttgagagcctacctggatggcacgfs	p.LRAYLDGT180fs	HLA-A_ENST00000376806.5_Frame_Shift_Del_p.LRAYLDGT180fs|HLA-A_ENST00000376809.5_Frame_Shift_Del_p.LRAYLDGT180fs|HLA-A_ENST00000376802.2_Frame_Shift_Del_p.LRAYLDGT180fs			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	180	Alpha-2.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)	p.L180*(1)		central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GGCGGAGCAGTTGAGAGCCTACCTGGATGGCACGTGCGTGGAG	0.655									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)																											p.180_187del		.											.	HLA-A-92	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.538_560del						.																																			SO:0001589	frameshift_variant	3105	exon3	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	GAGCAGTTGAGAG	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.538_560delTTGAGAGCCTACCTGGATGGCAC	6.37:g.29911239_29911261delTTGAGAGCCTACCTGGATGGCAC	ENSP00000379873:p.Leu180fs	152	0		288	0	NM_001242758	0	0	0	0	0	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Frame_Shift_Del	DEL	ENST00000396634.1	37	CCDS34373.1																																																																																			.		0.655	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
HLA-B	3106	hgsc.bcm.edu	37	6	31324599	31324599	+	Missense_Mutation	SNP	T	T	G	rs1050538	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:31324599T>G	ENST00000412585.2	-	2	237	c.209A>C	c.(208-210)gAg>gCg	p.E70A		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	70	Alpha-1.				antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)			endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						CGCCCGCGGCTCCTCTCTCGG	0.677									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of				.|||	806	0.160942	0.056	0.1037	5008	,	,		8039	0.3363		0.1103	False		,,,				2504	0.2147				p.E70A		.											.	HLA-B-90	0			c.A209C						.						36.0	35.0	35.0					6																	31324599		2116	4094	6210	SO:0001583	missense	3106	exon2	Familial Cancer Database	;Lichen Sclerosis, Familial	CGCGGCTCCTCTC	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.209A>C	6.37:g.31324599T>G	ENSP00000399168:p.Glu70Ala	60	0		109	20	NM_005514	0	0	0	0	0	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	3.589	-0.084055	0.07097	.	.	ENSG00000234745	ENST00000412585;ENST00000434333	T;T	0.00864	5.6;5.6	3.2	3.2	0.36748	MHC class I, alpha chain, alpha1/alpha2 (2);MHC classes I/II-like antigen recognition protein (2);MHC class I-like antigen recognition (2);	0.526052	0.13970	U	0.350240	T	0.06690	0.0171	H	0.99565	4.63	0.38806	P	0.044686000000000003	D;B;B	0.67145	0.996;0.002;0.0	D;B;B	0.81914	0.995;0.035;0.004	T	0.05321	-1.0892	9	0.72032	D	0.01	.	9.7863	0.40677	0.0:0.0:0.0:1.0	rs1050538;rs3175993	70;70;45	P30480;P01889;Q92671	1B42_HUMAN;1B07_HUMAN;.	A	70;81	ENSP00000399168:E70A;ENSP00000405931:E81A	ENSP00000399168:E70A	E	-	2	0	HLA-B	31432578	0.272000	0.24172	0.678000	0.29963	0.007000	0.05969	0.519000	0.22862	1.476000	0.48215	0.368000	0.22195	GAG	T|0.972;G|0.028		0.677	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
GPR111	222611	broad.mit.edu	37	6	47624239	47624239	+	Missense_Mutation	SNP	A	A	G	rs1485784	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:47624239A>G	ENST00000296862.1	+	1	17	c.17A>G	c.(16-18)tAt>tGt	p.Y6C	GPR111_ENST00000507065.1_5'UTR			Q8IZF7	GP111_HUMAN	G protein-coupled receptor 111	6					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(1)|endometrium(1)|kidney(1)|large_intestine(2)|liver(2)|lung(15)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29						CTGACTGCCTATGGGAACCGC	0.572													G|||	2743	0.547724	0.5393	0.4697	5008	,	,		18538	0.3046		0.6759	False		,,,				2504	0.7331				.		.											.	GPR111-91	0			.						.																																			SO:0001583	missense	222611	.			CTGCCTATGGGAA	AB065684		6p12.3	2014-08-08			ENSG00000164393	ENSG00000164393		"""-"", ""GPCR / Class B : Orphans"""	18991	protein-coding gene	gene with protein product						12435584	Standard	NM_153839		Approved	hGPCR35, PGR20	uc003oyy.3	Q8IZF7	OTTHUMG00000046168	ENST00000296862.1:c.17A>G	6.37:g.47624239A>G	ENSP00000296862:p.Tyr6Cys	78	1		84	3	.	0	0	0	0	0	Q2PNZ1|Q86SL6|Q8NGU5|Q8TDT5	Missense_Mutation	SNP	ENST00000296862.1	37		1118	0.5119047619047619	253	0.5142276422764228	189	0.5220994475138122	170	0.2972027972027972	506	0.6675461741424802	G	11.34	1.610722	0.28712	.	.	ENSG00000164393	ENST00000296862	T	0.26373	1.74	4.2	4.2	0.49525	.	683.235000	0.00166	N	0.000006	T	0.09774	0.0240	.	.	.	0.53005	P	3.900000000001125E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.12553	-1.0543	8	0.87932	D	0	.	8.3352	0.32211	0.1051:0.0:0.8949:0.0	rs1485784;rs1485784	6	Q8IZF7	GP111_HUMAN	C	6	ENSP00000296862:Y6C	ENSP00000296862:Y6C	Y	+	2	0	GPR111	47732198	0.001000	0.12720	0.002000	0.10522	0.003000	0.03518	0.454000	0.21827	1.398000	0.46701	-0.119000	0.15052	TAT	A|0.462;G|0.538		0.572	GPR111-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000106423.2	NM_153839	
KCNQ5	56479	hgsc.bcm.edu	37	6	73332121	73332121	+	Silent	SNP	C	C	T	rs34821312	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:73332121C>T	ENST00000370398.1	+	1	313	c.204C>T	c.(202-204)ctC>ctT	p.L68L	KCNQ5_ENST00000403813.2_Silent_p.L68L|KCNQ5_ENST00000414165.2_Silent_p.L68L|KCNQ5_ENST00000370392.1_Silent_p.L68L|KCNQ5_ENST00000355194.4_Silent_p.L68L|KCNQ5_ENST00000342056.2_Silent_p.L68L|KCNQ5_ENST00000402622.2_Silent_p.L68L|KCNQ5_ENST00000355635.3_Silent_p.L68L	NM_019842.3	NP_062816.2	Q9NR82	KCNQ5_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 5	68					protein complex assembly (GO:0006461)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|inward rectifier potassium channel activity (GO:0005242)			breast(1)|cervix(1)|endometrium(6)|kidney(7)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	57		all_epithelial(107;0.116)|Lung NSC(302;0.219)		COAD - Colon adenocarcinoma(1;0.0107)|Colorectal(1;0.0583)	Ezogabine(DB04953)	CGGCCACGCTCGGTGGCGGCG	0.726													C|||	528	0.105431	0.056	0.1138	5008	,	,		9736	0.0099		0.2127	False		,,,				2504	0.1544				p.L68L	GBM(142;1375 1859 14391 23261 44706)	.											.	KCNQ5-158	0			c.C204T						.	C	,,,,	223,3429		5,213,1608	3.0	4.0	4.0		204,204,204,204,204	-0.3	0.0	6	dbSNP_126	4	1356,5856		128,1100,2378	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ5	NM_001160130.1,NM_001160132.1,NM_001160133.1,NM_001160134.1,NM_019842.3	,,,,	133,1313,3986	TT,TC,CC		18.802,6.1062,14.5342	,,,,	68/924,68/943,68/952,68/823,68/933	73332121	1579,9285	1826	3606	5432	SO:0001819	synonymous_variant	56479	exon1			CACGCTCGGTGGC	AF202977	CCDS4976.1, CCDS55034.1	6q14	2012-07-05			ENSG00000185760	ENSG00000185760		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6299	protein-coding gene	gene with protein product		607357				10787416, 10816588, 16382104	Standard	NM_019842		Approved	Kv7.5	uc011dyh.2	Q9NR82	OTTHUMG00000015020	ENST00000370398.1:c.204C>T	6.37:g.73332121C>T		1	0		12	9	NM_001160132	0	0	0	0	0	A6NKT6|A6PVT6|A8MSQ5|B4DS33|B5MC83|B7ZL37|F5GZV0|Q17RE1|Q5VVP3|Q86W40|Q9NRN0|Q9NYA6	Silent	SNP	ENST00000370398.1	37	CCDS4976.1																																																																																			C|0.884;T|0.116		0.726	KCNQ5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000041198.3	NM_019842	
MTHFD1L	25902	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	151293139	151293139	+	Silent	SNP	T	T	C			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:151293139T>C	ENST00000367321.3	+	20	2344	c.2070T>C	c.(2068-2070)tcT>tcC	p.S690S	MTHFD1L_ENST00000478643.1_3'UTR	NM_001242767.1|NM_001242768.1|NM_015440.4	NP_001229696.1|NP_001229697.1|NP_056255.2	Q6UB35	C1TM_HUMAN	methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like	690	Formyltetrahydrofolate synthetase.				folic acid-containing compound biosynthetic process (GO:0009396)|folic acid-containing compound metabolic process (GO:0006760)|formate metabolic process (GO:0015942)|one-carbon metabolic process (GO:0006730)|oxidation-reduction process (GO:0055114)|tetrahydrofolate interconversion (GO:0035999)|tetrahydrofolate metabolic process (GO:0046653)	membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|formate-tetrahydrofolate ligase activity (GO:0004329)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	29		Ovarian(120;0.128)		OV - Ovarian serous cystadenocarcinoma(155;8.7e-12)		ACGGCAACTCTTCAGTGTTGG	0.393																																					p.S691S		.											.	MTHFD1L-292	0			c.T2073C						.						125.0	117.0	120.0					6																	151293139		2203	4300	6503	SO:0001819	synonymous_variant	25902	exon20			CAACTCTTCAGTG	BC017477	CCDS5228.1, CCDS56457.1, CCDS75535.1, CCDS75536.1	6q25.1	2010-07-19	2004-12-13	2004-12-14	ENSG00000120254	ENSG00000120254	6.3.4.3		21055	protein-coding gene	gene with protein product	"""10-formyl-THF synthetase"", ""mitochondrial C1-tetrahydrofolate synthase"", ""monofunctional C1-tetrahydrofolate synthase, mitochondrial"""	611427	"""formyltetrahydrofolate synthetase domain containing 1"""	FTHFSDC1		18804703	Standard	NM_015440		Approved	DKFZP586G1517, FLJ21145	uc021zgs.1	Q6UB35	OTTHUMG00000015828	ENST00000367321.3:c.2070T>C	6.37:g.151293139T>C		102	0		115	14	NM_001242767	0	0	0	0	0	Q2TBF3|Q8WVW0|Q96HG8|Q9H789|Q9UFU8	Silent	SNP	ENST00000367321.3	37	CCDS5228.1																																																																																			.		0.393	MTHFD1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042699.1	NM_015440	
SP8	221833	broad.mit.edu	37	7	20824941	20824943	+	In_Frame_Del	DEL	GCC	GCC	-	rs372591893	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr7:20824941_20824943delGCC	ENST00000361443.4	-	3	676_678	c.439_441delGGC	c.(439-441)ggcdel	p.G147del	SP8_ENST00000418710.2_In_Frame_Del_p.G165del	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	147					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.G165delG(1)|p.G147delG(1)		NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						GCGCGGAGGAgccgccgccgccg	0.729														461	0.0920527	0.0098	0.1124	5008	,	,		5525	0.002		0.2664	False		,,,				2504	0.1022				p.165_165del		.											.	SP8-91	2	Deletion - In frame(2)	central_nervous_system(2)	c.493_495del						.		,	50,654		19,12,321					,	0.5	0.3			2	602,1424		217,168,628	no	coding,coding	SP8	NM_198956.2,NM_182700.4	,	236,180,949	A1A1,A1R,RR		29.7137,7.1023,23.8828	,	,		652,2078				SO:0001651	inframe_deletion	221833	exon2			GGAGGAGCCGCCG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.439_441delGGC	7.37:g.20824950_20824952delGCC	ENSP00000354482:p.Gly147del	10	0		26	7	NM_182700	0	0	0	0	0	Q7Z615|Q7Z616|Q96MJ1	In_Frame_Del	DEL	ENST00000361443.4	37	CCDS5372.1																																																																																			.		0.729	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
GARS	2617	hgsc.bcm.edu	37	7	30634661	30634661	+	Missense_Mutation	SNP	C	C	G	rs1049402	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr7:30634661C>G	ENST00000389266.3	+	1	365	c.124C>G	c.(124-126)Ccc>Gcc	p.P42A	AC005154.6_ENST00000584199.1_RNA|AC005154.6_ENST00000579174.1_RNA|AC005154.6_ENST00000583664.1_RNA|AC005154.6_ENST00000584372.1_RNA|AC005154.6_ENST00000581665.1_RNA|AC005154.6_ENST00000582549.1_RNA|AC005154.6_ENST00000578994.1_RNA|AC005154.6_ENST00000580440.1_RNA	NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	42			P -> A (in dbSNP:rs1049402). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:7753621, ECO:0000269|PubMed:7961834, ECO:0000269|PubMed:7962006}.		cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)	p.P42fs*20(1)		breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	GGCCTCCTGCCCCCCGATCTC	0.736													G|||	3252	0.649361	0.5219	0.7147	5008	,	,		13746	0.6677		0.7634	False		,,,				2504	0.6391				p.P42A		.											.	GARS-91	1	Insertion - Frameshift(1)	large_intestine(1)	c.C124G						.	G	ALA/PRO	2445,1427		776,893,267	5.0	8.0	7.0		124	-6.6	0.0	7	dbSNP_86	7	6367,1671		2577,1213,229	no	missense	GARS	NM_002047.2	27	3353,2106,496	GG,GC,CC		20.7888,36.8543,26.0118	benign	42/740	30634661	8812,3098	1936	4019	5955	SO:0001583	missense	2617	exon1			TCCTGCCCCCCGA	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"""Aminoacyl tRNA synthetases / Class II"""	4162	protein-coding gene	gene with protein product	"""glycine tRNA ligase"""	600287	"""Charcot-Marie-Tooth neuropathy 2D"""	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.124C>G	7.37:g.30634661C>G	ENSP00000373918:p.Pro42Ala	0	0		5	5	NM_002047	0	0	0	0	0	B3KQA2|B4DIA0|Q969Y1	Missense_Mutation	SNP	ENST00000389266.3	37	CCDS43564.1	1456	0.6666666666666666	278	0.5650406504065041	268	0.7403314917127072	337	0.5891608391608392	573	0.7559366754617414	G	0.005	-2.164835	0.00318	0.631457	0.792112	ENSG00000106105	ENST00000389266	T	0.80393	-1.37	3.31	-6.63	0.01807	.	1.037800	0.07609	N	0.925137	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.13575	-1.0504	9	0.08179	T	0.78	.	5.5596	0.17135	0.0726:0.2689:0.1197:0.5389	rs1049402;rs3189564;rs11553500;rs17856223;rs17856227;rs1049402	42	P41250	SYG_HUMAN	A	42	ENSP00000373918:P42A	ENSP00000373918:P42A	P	+	1	0	GARS	30601186	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-0.671000	0.05250	-2.551000	0.00479	-0.744000	0.03518	CCC	C|0.329;G|0.671		0.736	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047	
PON1	5444	bcgsc.ca	37	7	94937446	94937446	+	Missense_Mutation	SNP	T	T	C	rs662	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr7:94937446T>C	ENST00000222381.3	-	6	806	c.575A>G	c.(574-576)cAa>cGa	p.Q192R	PON1_ENST00000542556.1_Missense_Mutation_p.Q192R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	192			Q -> R (polymorphism important for activity; dbSNP:rs662). {ECO:0000269|PubMed:1657140, ECO:0000269|PubMed:18987736, ECO:0000269|PubMed:7916578, ECO:0000269|PubMed:8098250, ECO:0000269|PubMed:8393742, ECO:0000269|PubMed:8393745, ECO:0000269|Ref.8}.		aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.Q192R(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CTCCCAGGATTGTAAGTAGGG	0.398													C|||	2719	0.542931	0.7526	0.4986	5008	,	,		16184	0.6657		0.2903	False		,,,				2504	0.4243				p.Q192R	GBM(119;715 1622 17358 22490 33240)	.											.	PON1-91	1	Substitution - Missense(1)	stomach(1)	c.A575G	GRCh37	CM930596	PON1	M	rs662	.	C	ARG/GLN	2910,1496	475.5+/-357.3	958,994,251	130.0	108.0	116.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	575	-1.0	0.0	7	dbSNP_36	116	2451,6149	698.1+/-405.0	360,1731,2209	yes	missense	PON1	NM_000446.5	43	1318,2725,2460	CC,CT,TT		28.5,33.9537,41.2194	benign	192/356	94937446	5361,7645	2203	4300	6503	SO:0001583	missense	5444	exon6			CAGGATTGTAAGT	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.575A>G	7.37:g.94937446T>C	ENSP00000222381:p.Gln192Arg	106	1		131	6	NM_000446	0	0	0	0	0	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	1127	0.5160256410256411	368	0.7479674796747967	172	0.47513812154696133	367	0.6416083916083916	220	0.29023746701846964	C	0.090	-1.168995	0.01660	0.660463	0.285	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.45276	0.9;0.9	5.04	-1.02	0.10135	Six-bladed beta-propeller, TolB-like (1);	0.663414	0.14660	N	0.306026	T	0.00012	0.0000	N	0.03608	-0.345	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33189	-0.9878	9	0.09084	T	0.74	-0.0356	8.8215	0.35030	0.1205:0.2374:0.0:0.6421	rs662;rs11567868;rs13306697;rs17773773;rs60480675;rs662	192;192	F5H4W9;P27169	.;PON1_HUMAN	R	192	ENSP00000222381:Q192R;ENSP00000444854:Q192R	ENSP00000222381:Q192R	Q	-	2	0	PON1	94775382	0.000000	0.05858	0.001000	0.08648	0.185000	0.23345	-1.304000	0.02741	-0.587000	0.05890	-0.215000	0.12644	CAA	T|0.544;C|0.456		0.398	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
SLC26A3	1811	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	7	107408290	107408290	+	Missense_Mutation	SNP	A	A	C			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	A	A	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr7:107408290A>C	ENST00000340010.5	-	19	2310	c.2126T>G	c.(2125-2127)tTt>tGt	p.F709C	SLC26A3_ENST00000422236.2_Missense_Mutation_p.F596C	NM_000111.2	NP_000102.1	P40879	S26A3_HUMAN	solute carrier family 26 (anion exchanger), member 3	709	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				anion transport (GO:0006820)|cellular response to cAMP (GO:0071320)|excretion (GO:0007588)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|membrane hyperpolarization (GO:0060081)|regulation of RNA biosynthetic process (GO:2001141)|regulation of transcription, DNA-templated (GO:0006355)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(18)|ovary(4)|prostate(1)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	46						TGTTAAGAAAAATATTGAGCT	0.328																																					p.F709C		.											.	SLC26A3-94	0			c.T2126G						.						95.0	97.0	96.0					7																	107408290		2203	4300	6503	SO:0001583	missense	1811	exon19			AAGAAAAATATTG	L02785	CCDS5748.1	7q31	2014-09-17	2013-07-18		ENSG00000091138	ENSG00000091138		"""Solute carriers"""	3018	protein-coding gene	gene with protein product		126650	"""congenital chloride diarrhea"", ""solute carrier family 26, member 3"""	DRA, CLD		8020951, 11087667	Standard	NM_000111		Approved		uc003ver.2	P40879	OTTHUMG00000154812	ENST00000340010.5:c.2126T>G	7.37:g.107408290A>C	ENSP00000345873:p.Phe709Cys	118	0		92	20	NM_000111	0	0	0	0	0		Missense_Mutation	SNP	ENST00000340010.5	37	CCDS5748.1	.	.	.	.	.	.	.	.	.	.	A	16.18	3.050665	0.55218	.	.	ENSG00000091138	ENST00000422236;ENST00000340010	D;D	0.89270	-2.49;-2.49	5.1	5.1	0.69264	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.096020	0.64402	D	0.000001	D	0.92512	0.7622	M	0.71581	2.175	0.31052	N	0.715098	D;B	0.69078	0.997;0.109	P;B	0.59761	0.863;0.169	D	0.92039	0.5639	10	0.62326	D	0.03	.	14.2264	0.65863	1.0:0.0:0.0:0.0	.	596;709	G5E9U3;P40879	.;S26A3_HUMAN	C	596;709	ENSP00000415817:F596C;ENSP00000345873:F709C	ENSP00000345873:F709C	F	-	2	0	SLC26A3	107195526	1.000000	0.71417	0.999000	0.59377	0.432000	0.31715	8.265000	0.89869	2.135000	0.66039	0.383000	0.25322	TTT	.		0.328	SLC26A3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337190.1	NM_000111	
CYP7B1	9420	broad.mit.edu	37	8	65537031	65537031	+	Missense_Mutation	SNP	C	C	T	rs267601966		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr8:65537031C>T	ENST00000310193.3	-	2	361	c.188G>A	c.(187-189)cGa>cAa	p.R63Q		NM_004820.3	NP_004811.1	O75881	CP7B1_HUMAN	cytochrome P450, family 7, subfamily B, polypeptide 1	63					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cell death (GO:0008219)|cholesterol metabolic process (GO:0008203)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|positive regulation of epithelial cell proliferation (GO:0050679)|prostate gland epithelium morphogenesis (GO:0060740)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	25-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033783)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	28		all_cancers(86;0.217)|Lung NSC(129;0.0521)|all_lung(136;0.0906)|all_epithelial(80;0.215)				GGGGTCTTTTCGTAAGTTCAG	0.383																																					p.R63Q		.											.	CYP7B1-93	0			c.G188A						.						139.0	136.0	137.0					8																	65537031		2203	4300	6503	SO:0001583	missense	9420	exon2			TCTTTTCGTAAGT	AF029403	CCDS6180.1	8q21.3	2008-07-04	2003-01-14		ENSG00000172817	ENSG00000172817		"""Cytochrome P450s"""	2652	protein-coding gene	gene with protein product		603711	"""cytochrome P450, subfamily VIIB (oxysterol 7 alpha-hydroxylase), polypeptide 1"", ""spastic paraplegia 5A (autosomal recessive)"""	SPG5A		9802883, 18252231	Standard	NM_004820		Approved		uc003xvj.2	O75881	OTTHUMG00000164387	ENST00000310193.3:c.188G>A	8.37:g.65537031C>T	ENSP00000310721:p.Arg63Gln	102	0		110	5	NM_004820	0	0	0	0	0	B2RN07|Q9UNF5	Missense_Mutation	SNP	ENST00000310193.3	37	CCDS6180.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.280736	0.23392	.	.	ENSG00000172817	ENST00000310193	T	0.69306	-0.39	5.63	-3.19	0.05171	.	0.894258	0.10065	N	0.720425	T	0.32285	0.0824	N	0.02765	-0.5	0.09310	N	1	B	0.16396	0.017	B	0.14023	0.01	T	0.16867	-1.0388	10	0.21540	T	0.41	0.0053	3.557	0.07867	0.1122:0.3987:0.115:0.3741	.	63	O75881	CP7B1_HUMAN	Q	63	ENSP00000310721:R63Q	ENSP00000310721:R63Q	R	-	2	0	CYP7B1	65699585	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.599000	0.05700	-0.406000	0.07588	-0.469000	0.05056	CGA	.		0.383	CYP7B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378550.1		
E2F5	1875	hgsc.bcm.edu	37	8	86089787	86089787	+	Silent	SNP	C	C	G	rs12926	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr8:86089787C>G	ENST00000416274.2	+	1	166	c.132C>G	c.(130-132)gcC>gcG	p.A44A	RP11-219B4.7_ENST00000562577.1_RNA|E2F5_ENST00000418930.2_Silent_p.A44A|E2F5_ENST00000256117.5_Silent_p.A44A|RP11-219B4.7_ENST00000566000.1_RNA|RP11-219B4.3_ENST00000520129.1_RNA	NM_001083588.1|NM_001951.3	NP_001077057.1|NP_001942.2	Q15329	E2F5_HUMAN	E2F transcription factor 5, p130-binding	44					gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			NS(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	8						TCGGGGGCGCCGGGGGCGGCA	0.751													C|||	2815	0.562101	0.5545	0.549	5008	,	,		6370	0.4157		0.6928	False		,,,				2504	0.5982				p.A44A		.											.	E2F5-415	0			c.C132G						.	C	,	2392,1558		800,792,383	4.0	5.0	5.0		132,132	0.9	0.1	8	dbSNP_52	5	5668,2428		2076,1516,456	no	coding-synonymous,coding-synonymous	E2F5	NM_001083588.1,NM_001951.3	,	2876,2308,839	GG,GC,CC		29.9901,39.443,33.0898	,	44/346,44/347	86089787	8060,3986	1975	4048	6023	SO:0001819	synonymous_variant	1875	exon1			GGGCGCCGGGGGC	X86097	CCDS47885.1, CCDS47886.1, CCDS55254.1	8q21.2	2004-01-29			ENSG00000133740	ENSG00000133740			3119	protein-coding gene	gene with protein product		600967				7892279	Standard	NM_001083588		Approved		uc003ycz.4	Q15329	OTTHUMG00000164785	ENST00000416274.2:c.132C>G	8.37:g.86089787C>G		0	0		8	8	NM_001083588	0	0	0	0	0	E9PBN9|Q16601|Q92756	Silent	SNP	ENST00000416274.2	37	CCDS47885.1																																																																																			C|0.434;G|0.566		0.751	E2F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380274.1	NM_001951	
EPPK1	83481	bcgsc.ca	37	8	144940290	144940290	+	Missense_Mutation	SNP	C	C	G	rs201976887		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr8:144940290C>G	ENST00000525985.1	-	2	7203	c.7132G>C	c.(7132-7134)Gac>Cac	p.D2378H				P58107	EPIPL_HUMAN	epiplakin 1	2378						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCGCTGGGGTCGGCCAGGACG	0.682																																					p.D2378H		.											.	EPPK1-25	0			c.G7132C						.	C	HIS/ASP	51,4341	20.2+/-43.8	0,51,2145	315.0	292.0	300.0		7132	3.6	0.8	8		300	22,8530	7.1+/-27.0	0,22,4254	no	missense	EPPK1	NM_031308.1	81	0,73,6399	GG,GC,CC		0.2572,1.1612,0.564	probably-damaging	2378/2420	144940290	73,12871	2196	4276	6472	SO:0001583	missense	83481	exon1			TGGGGTCGGCCAG	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.7132G>C	8.37:g.144940290C>G	ENSP00000436337:p.Asp2378His	108	0		370	16	NM_031308	0	0	0	0	0	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		.	.	.	.	.	.	.	.	.	.	C	22.4	4.279155	0.80692	0.011612	0.002572	ENSG00000227184	ENST00000525985	T	0.74737	-0.87	4.43	3.56	0.40772	.	.	.	.	.	D	0.83133	0.5188	M	0.89785	3.06	0.42176	D	0.991666	D	0.89917	1.0	D	0.91635	0.999	D	0.86316	0.1689	9	0.62326	D	0.03	.	10.4012	0.44231	0.0:0.9038:0.0:0.0962	.	2378	E9PPU0	.	H	2378	ENSP00000436337:D2378H	ENSP00000436337:D2378H	D	-	1	0	EPPK1	145012278	1.000000	0.71417	0.773000	0.31616	0.942000	0.58702	7.555000	0.82223	1.223000	0.43536	0.591000	0.81541	GAC	.		0.682	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ERMP1	79956	hgsc.bcm.edu	37	9	5832728	5832728	+	Silent	SNP	G	G	C	rs1131727	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:5832728G>C	ENST00000339450.5	-	1	389	c.300C>G	c.(298-300)gcC>gcG	p.A100A	ERMP1_ENST00000381506.3_5'Flank|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	100						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		GGTGTCCAGCGGCCCCGCGTA	0.741													G|||	2021	0.403554	0.1309	0.428	5008	,	,		3601	0.7093		0.34	False		,,,				2504	0.5051				p.A100A		.											.	ERMP1-69	0			c.C300G						.						4.0	3.0	3.0					9																	5832728		1620	3326	4946	SO:0001819	synonymous_variant	79956	exon1			TCCAGCGGCCCCG	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.300C>G	9.37:g.5832728G>C		0	0		11	10	NM_024896	0	0	0	0	0	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Silent	SNP	ENST00000339450.5	37	CCDS34983.1																																																																																			G|0.572;C|0.428		0.741	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
MLLT3	4300	broad.mit.edu	37	9	20414340	20414340	+	Silent	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:20414340G>A	ENST00000380338.4	-	5	790	c.504C>T	c.(502-504)agC>agT	p.S168S	MLLT3_ENST00000355930.6_5'UTR|MLLT3_ENST00000429426.2_Silent_p.S165S|MLLT3_ENST00000475957.1_5'UTR	NM_004529.2	NP_004520.2	P42568	AF9_HUMAN	myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3	168	Poly-Ser.				anterior/posterior pattern specification (GO:0009952)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of transcription, DNA-templated (GO:0006355)|segment specification (GO:0007379)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)		p.S168S(5)		central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(6)|lung(24)|ovary(1)|prostate(4)|skin(1)|urinary_tract(7)	66				GBM - Glioblastoma multiforme(3;4.35e-105)|Lung(42;3.48e-06)|LUSC - Lung squamous cell carcinoma(42;7.92e-05)		tgctgctgctgctactgctgc	0.537			T	MLL	ALL																																p.S168S		.		Dom	yes		9	9p22	4300	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 (AF9)"""		L	.	MLLT3-660	5	Substitution - coding silent(5)	lung(2)|urinary_tract(1)|endometrium(1)|kidney(1)	c.C504T						.						9.0	16.0	13.0					9																	20414340		1646	3412	5058	SO:0001819	synonymous_variant	4300	exon5			GCTGCTGCTACTG	L13744	CCDS6494.1	9p22	2008-02-05	2001-11-28		ENSG00000171843	ENSG00000171843			7136	protein-coding gene	gene with protein product		159558	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog); translocated to, 3"""			8506309, 8414510	Standard	NM_001286691		Approved	AF-9, AF9, YEATS3	uc003zoe.2	P42568	OTTHUMG00000019650	ENST00000380338.4:c.504C>T	9.37:g.20414340G>A		41	1		58	3	NM_004529	0	0	0	0	0	B1AMQ2|B2R7B3|B7Z755|D3DRJ8|Q8IVB0	Silent	SNP	ENST00000380338.4	37	CCDS6494.1																																																																																			.		0.537	MLLT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051872.1	NM_004529	
DMRTA1	63951	hgsc.bcm.edu	37	9	22447523	22447523	+	Silent	SNP	C	C	T	rs34336274	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:22447523C>T	ENST00000325870.2	+	1	684	c.459C>T	c.(457-459)gcC>gcT	p.A153A		NM_022160.2	NP_071443.2	Q5VZB9	DMRTA_HUMAN	DMRT-like family A1	153					male mating behavior (GO:0060179)|ovarian follicle development (GO:0001541)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	15		all_cancers(5;4.09e-243)|Acute lymphoblastic leukemia(3;8.25e-150)|all_hematologic(3;4.25e-147)|Esophageal squamous(3;2.32e-09)|Renal(3;1.71e-07)|Breast(3;2.07e-06)|Hepatocellular(5;0.00563)		GBM - Glioblastoma multiforme(1;5.12e-278)|Lung(24;8.2e-52)|LUSC - Lung squamous cell carcinoma(38;1.46e-37)|OV - Ovarian serous cystadenocarcinoma(39;0.0517)		AGAGCGAAGCCCGGGGGCTAC	0.736													C|||	35	0.00698882	0.003	0.0043	5008	,	,		11256	0.0		0.0268	False		,,,				2504	0.001				p.A153A		.											.	DMRTA1-578	0			c.C459T						.	C		8,3812		0,8,1902	4.0	4.0	4.0		459	-1.2	0.9	9	dbSNP_126	4	125,7543		0,125,3709	no	coding-synonymous	DMRTA1	NM_022160.2		0,133,5611	TT,TC,CC		1.6302,0.2094,1.1577		153/505	22447523	133,11355	1910	3834	5744	SO:0001819	synonymous_variant	63951	exon1			CGAAGCCCGGGGG	AJ290954	CCDS6514.1	9p21.3	2008-05-15			ENSG00000176399	ENSG00000176399			13826	protein-coding gene	gene with protein product		614803					Standard	NM_022160		Approved		uc003zpp.1	Q5VZB9	OTTHUMG00000019693	ENST00000325870.2:c.459C>T	9.37:g.22447523C>T		0	0		14	10	NM_022160	0	0	0	0	0	A1L481|Q8N8Y9|Q9H4B9	Silent	SNP	ENST00000325870.2	37	CCDS6514.1																																																																																			C|0.987;T|0.013		0.736	DMRTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051935.2		
TUSC1	286319	hgsc.bcm.edu	37	9	25678122	25678122	+	Silent	SNP	G	G	C	rs72631814	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:25678122G>C	ENST00000358022.3	-	1	734	c.198C>G	c.(196-198)gcC>gcG	p.A66A		NM_001004125.2	NP_001004125.1	Q2TAM9	TUSC1_HUMAN	tumor suppressor candidate 1	66										kidney(1)	1	all_hematologic(1;0.197)	all_neural(3;5.42e-18)|Glioma(3;5.54e-17)		GBM - Glioblastoma multiforme(1;1.51e-108)|Lung(42;2.88e-14)|LUSC - Lung squamous cell carcinoma(38;3.16e-11)		CCGCCAGGTCGGCAAACCGCT	0.776													G|||	885	0.176717	0.1324	0.1772	5008	,	,		7019	0.1151		0.3002	False		,,,				2504	0.1728				p.A66A	Pancreas(19;648 672 25630 30820 31331)	.											.	TUSC1-90	0			c.C198G						.	G		389,3633		24,341,1646	6.0	6.0	6.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	198	0.6	1.0	9	dbSNP_130	6	1826,6086		225,1376,2355	no	coding-synonymous	TUSC1	NM_001004125.2		249,1717,4001	CC,CG,GG		23.0789,9.6718,18.5604		66/213	25678122	2215,9719	2011	3956	5967	SO:0001819	synonymous_variant	286319	exon1			CAGGTCGGCAAAC	AY168647	CCDS34999.1	9p21.2	2014-05-22			ENSG00000198680	ENSG00000198680			31010	protein-coding gene	gene with protein product		610529				15208665	Standard	NM_001004125		Approved	TSG-9	uc003zpx.3	Q2TAM9	OTTHUMG00000159591	ENST00000358022.3:c.198C>G	9.37:g.25678122G>C		0	0		22	12	NM_001004125	0	0	0	0	0	A0PJ78|Q67GI3|Q86SS1|Q8TAH8	Silent	SNP	ENST00000358022.3	37	CCDS34999.1																																																																																			G|0.807;C|0.193		0.776	TUSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356351.1	NM_001004125	
AQP7	364	ucsc.edu	37	9	33385287	33385287	+	3'UTR	SNP	T	T	C	rs74557595		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	T	T	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:33385287T>C	ENST00000537089.1	-	0	1145				AQP7_ENST00000377425.4_Intron			O14520	AQP7_HUMAN	aquaporin 7						excretion (GO:0007588)|generation of precursor metabolites and energy (GO:0006091)|glycerol transport (GO:0015793)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	glycerol channel activity (GO:0015254)|water channel activity (GO:0015250)			NS(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(4)|skin(2)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.191)		TTCTCCCCATTGCTGCAGGCA	0.612																																					p.N249D		.											.	AQP7-90	0			c.A745G						.						59.0	62.0	61.0					9																	33385287		2202	4298	6500	SO:0001624	3_prime_UTR_variant	364	exon8			CCCCATTGCTGCA	AB006190	CCDS6541.1	9p13	2008-02-05			ENSG00000165269	ENSG00000165269		"""Ion channels / Aquaporins"""	640	protein-coding gene	gene with protein product		602974		AQP7L		9252401	Standard	NM_001170		Approved	AQP9, AQPap	uc003zst.3	O14520	OTTHUMG00000019773	ENST00000537089.1:c.*329A>G	9.37:g.33385287T>C		47	2		41	14	NM_001170	0	0	0	0	0	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		.	.	.	.	.	.	.	.	.	.	c	9.798	1.179797	0.21787	.	.	ENSG00000165269	ENST00000379507;ENST00000297988;ENST00000439678	T;T;T	0.11063	2.81;2.81;2.81	4.27	3.35	0.38373	Aquaporin-like (2);	.	.	.	.	T	0.07683	0.0193	.	.	.	0.18873	N	0.999987	B	0.02656	0.0	B	0.01281	0.0	T	0.35301	-0.9794	8	0.39692	T	0.17	-1.4238	6.1852	0.20493	0.0:0.7595:0.0:0.2405	.	249	O14520	AQP7_HUMAN	D	248;249;157	ENSP00000368821:N248D;ENSP00000297988:N249D;ENSP00000410138:N157D	ENSP00000297988:N249D	N	-	1	0	AQP7	33375287	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.126000	0.15769	0.443000	0.26582	-0.251000	0.11542	AAT	.		0.612	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
SH2D3C	10044	broad.mit.edu	37	9	130504196	130504196	+	Silent	SNP	G	G	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:130504196G>T	ENST00000314830.8	-	9	2072	c.1959C>A	c.(1957-1959)ggC>ggA	p.G653G	SH2D3C_ENST00000373276.3_Silent_p.G585G|SH2D3C_ENST00000373277.4_Silent_p.G496G|SH2D3C_ENST00000420366.1_Silent_p.G495G|SH2D3C_ENST00000471939.1_5'Flank|SH2D3C_ENST00000373274.3_Silent_p.G493G|SH2D3C_ENST00000429553.1_Silent_p.G299G	NM_170600.2	NP_733745.1	Q8N5H7	SH2D3_HUMAN	SH2 domain containing 3C	653	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				JNK cascade (GO:0007254)|positive regulation of signal transduction (GO:0009967)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)|SH3/SH2 adaptor activity (GO:0005070)	p.G653G(2)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGCCGGTGCAGCCCAGGATGT	0.687																																					p.G653G		.											.	SH2D3C-228	2	Substitution - coding silent(2)	lung(2)	c.C1959A						.						25.0	23.0	24.0					9																	130504196		2201	4297	6498	SO:0001819	synonymous_variant	10044	exon9			GGTGCAGCCCAGG	AF124251	CCDS6877.1, CCDS6878.1, CCDS48026.1, CCDS48028.1, CCDS59145.1	9q33.1-q33.3	2013-02-14	2002-01-14		ENSG00000095370	ENSG00000095370		"""SH2 domain containing"""	16884	protein-coding gene	gene with protein product		604722	"""SH2 domain-containing 3C"""			10187783	Standard	NM_170600		Approved	NSP3	uc004bsc.3	Q8N5H7	OTTHUMG00000020717	ENST00000314830.8:c.1959C>A	9.37:g.130504196G>T		31	0		149	12	NM_170600	0	0	0	0	0	A8K5S8|E9PG48|Q5HYE5|Q5JU31|Q6UY42|Q8N6X3|Q9Y2X5	Silent	SNP	ENST00000314830.8	37	CCDS6877.1																																																																																			.		0.687	SH2D3C-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054264.1	NM_005489	
C9orf172	389813	hgsc.bcm.edu	37	9	139740630	139740630	+	Silent	SNP	C	C	A	rs551392747	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	C	C	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:139740630C>A	ENST00000436881.1	+	1	1764	c.1764C>A	c.(1762-1764)gtC>gtA	p.V588V	PHPT1_ENST00000371661.1_5'Flank|PHPT1_ENST00000545326.1_5'Flank|PHPT1_ENST00000247665.10_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	588										endometrium(2)|large_intestine(1)|lung(6)	9						CGGACCTGGTCATCGACTCGC	0.771													c|||	5	0.000998403	0.0008	0.0	5008	,	,		7141	0.0		0.004	False		,,,				2504	0.0				p.V588V		.											.	.	0			c.C1764A						.						2.0	2.0	2.0					9																	139740630		956	1945	2901	SO:0001819	synonymous_variant	389813	exon1			CCTGGTCATCGAC		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.1764C>A	9.37:g.139740630C>A		0	0		16	8	NM_001080482	0	0	0	0	0		Silent	SNP	ENST00000436881.1	37	CCDS48059.1																																																																																			.		0.771	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765408	27765408	+	Silent	SNP	G	G	A			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chrX:27765408G>A	ENST00000451261.2	+	5	795	c.396G>A	c.(394-396)gaG>gaA	p.E132E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	132	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aagaggaggaggaggaggagg	0.567																																					p.E132E		.											.	DCAF8L2-42	0			c.G396A						.						18.0	16.0	16.0					X																	27765408		692	1587	2279	SO:0001819	synonymous_variant	347442	exon1			GGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.396G>A	X.37:g.27765408G>A		37	0		53	6	NM_001136533	0	0	0	0	0	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.		0.567	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
FAM47C	442444	broad.mit.edu	37	X	37028425	37028425	+	Missense_Mutation	SNP	A	A	G	rs145580328		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chrX:37028425A>G	ENST00000358047.3	+	1	1994	c.1942A>G	c.(1942-1944)Aat>Gat	p.N648D		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	648								p.N648D(7)		breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						GGAGCCTCCCAATACTGGAGT	0.642																																					p.N648D		.											.	FAM47C-111	7	Substitution - Missense(7)	urinary_tract(2)|prostate(2)|lung(2)|skin(1)	c.A1942G						.						51.0	56.0	55.0					X																	37028425		2201	4299	6500	SO:0001583	missense	442444	exon1			CCTCCCAATACTG	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.1942A>G	X.37:g.37028425A>G	ENSP00000367913:p.Asn648Asp	132	1		111	4	NM_001013736	0	0	0	0	0	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	.	.	.	.	.	.	.	.	.	.	-	3.343	-0.134139	0.06711	.	.	ENSG00000198173	ENST00000358047	T	0.13196	2.61	1.61	-3.22	0.05125	.	.	.	.	.	T	0.04543	0.0124	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38993	-0.9635	9	0.20519	T	0.43	.	0.6811	0.00875	0.2356:0.2078:0.3498:0.2069	.	648	Q5HY64	FA47C_HUMAN	D	648	ENSP00000367913:N648D	ENSP00000367913:N648D	N	+	1	0	FAM47C	36938346	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.937000	0.01547	-1.437000	0.01967	-1.178000	0.01721	AAT	A|1.000;G|0.000		0.642	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
SRPX	8406	broad.mit.edu	37	X	38079976	38079978	+	In_Frame_Del	DEL	GCA	GCA	-	rs35523939|rs72249350|rs139109693		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chrX:38079976_38079978delGCA	ENST00000378533.3	-	1	174_176	c.68_70delTGC	c.(67-72)ctgcgc>cgc	p.L23del	SRPX_ENST00000343800.6_Intron|SRPX_ENST00000538295.1_In_Frame_Del_p.L23del|SRPX_ENST00000432886.2_In_Frame_Del_p.L23del|RP13-43E11.1_ENST00000423919.1_RNA|SRPX_ENST00000544439.1_In_Frame_Del_p.L23del|TM4SF2_ENST00000465127.1_Intron	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	23			Missing. {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:8634709, ECO:0000269|PubMed:9162095}.		autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)		p.L23delL(2)		autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						GGCGGGACGCgcagcagcagcag	0.729											OREG0019726	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		636	0.168477	0.1657	0.1398	3775	,	,		8591	0.0129		0.2028	False		,,,				2504	0.1053				p.23_24del		.											.	SRPX-130	2	Deletion - In frame(2)	prostate(2)	c.68_70del						.																																			SO:0001651	inframe_deletion	8406	exon1			GGACGCGCAGCAG	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.68_70delTGC	X.37:g.38079985_38079987delGCA	ENSP00000367794:p.Leu23del	5	0	875	36	15	NM_001170751	0	0	0	0	0	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	In_Frame_Del	DEL	ENST00000378533.3	37	CCDS14245.1																																																																																			-|1.000;|0.000		0.729	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307	
CCDC120	90060	broad.mit.edu;ucsc.edu;bcgsc.ca	37	X	48921925	48921925	+	Missense_Mutation	SNP	C	C	T			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chrX:48921925C>T	ENST00000376396.3	+	6	568	c.349C>T	c.(349-351)Cgc>Tgc	p.R117C	CCDC120_ENST00000496529.2_Missense_Mutation_p.R117C|CCDC120_ENST00000603986.1_Missense_Mutation_p.R152C|CCDC120_ENST00000597275.1_Missense_Mutation_p.R117C|CCDC120_ENST00000536628.2_Missense_Mutation_p.R105C|CCDC120_ENST00000422185.2_Missense_Mutation_p.R117C	NM_001271835.1|NM_001271836.1|NM_033626.2	NP_001258764.1|NP_001258765.1|NP_296375.1	Q96HB5	CC120_HUMAN	coiled-coil domain containing 120	117										breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14						GGCCCTGGAACGCGAGGTGTC	0.687																																					p.R152C		.											.	CCDC120-131	0			c.C454T						.						7.0	7.0	7.0					X																	48921925		2167	4216	6383	SO:0001583	missense	90060	exon6			CTGGAACGCGAGG	BC008769	CCDS14316.1, CCDS55413.1, CCDS55414.1, CCDS55414.2	Xp11.23	2008-02-05			ENSG00000147144	ENSG00000147144			28910	protein-coding gene	gene with protein product						12477932	Standard	NM_033626		Approved	JM11	uc011mmr.3	Q96HB5	OTTHUMG00000021509	ENST00000376396.3:c.349C>T	X.37:g.48921925C>T	ENSP00000365577:p.Arg117Cys	55	1		93	20	NM_001163321	0	0	0	0	0	B4DFC1|B4DTU2|F5GZU4	Missense_Mutation	SNP	ENST00000376396.3	37	CCDS14316.1	.	.	.	.	.	.	.	.	.	.	C	15.25	2.776444	0.49786	.	.	ENSG00000147144	ENST00000376396;ENST00000422185;ENST00000536628	.	.	.	4.81	2.76	0.32466	.	0.000000	0.46145	D	0.000306	T	0.53094	0.1775	L	0.43923	1.385	0.27899	N	0.939031	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.995;0.998;0.998;0.995	T	0.46582	-0.9181	9	0.49607	T	0.09	0.6292	11.7682	0.51943	0.328:0.672:0.0:0.0	.	105;152;105;117	B4DTU2;B4DFC1;B4DF24;Q96HB5	.;.;.;CC120_HUMAN	C	117;117;105	.	ENSP00000365577:R117C	R	+	1	0	CCDC120	48808869	0.994000	0.37717	0.366000	0.25914	0.642000	0.38348	1.468000	0.35332	0.816000	0.34421	0.468000	0.43344	CGC	.		0.687	CCDC120-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056528.1	NM_033626	
MECP2	4204	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca;mdanderson.org	37	X	153295874	153295874	+	Missense_Mutation	SNP	G	G	A	rs267608632		TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	G	G	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chrX:153295874G>A	ENST00000303391.6	-	4	1654	c.1405C>T	c.(1405-1407)Cca>Tca	p.P469S	MECP2_ENST00000453960.2_Missense_Mutation_p.P481S|MECP2_ENST00000460227.1_5'Flank	NM_004992.3	NP_004983.1	P51608	MECP2_HUMAN	methyl CpG binding protein 2	469					adult locomotory behavior (GO:0008344)|behavioral fear response (GO:0001662)|cardiolipin metabolic process (GO:0032048)|catecholamine secretion (GO:0050432)|cerebellum development (GO:0021549)|chromatin silencing (GO:0006342)|dendrite development (GO:0016358)|glucocorticoid metabolic process (GO:0008211)|glutamine metabolic process (GO:0006541)|histone acetylation (GO:0016573)|histone methylation (GO:0016571)|inositol metabolic process (GO:0006020)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|negative regulation of histone acetylation (GO:0035067)|negative regulation of histone methylation (GO:0031061)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurological system process involved in regulation of systemic arterial blood pressure (GO:0001976)|neuron maturation (GO:0042551)|pathogenesis (GO:0009405)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of cell proliferation (GO:0008284)|positive regulation of synapse assembly (GO:0051965)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|proprioception (GO:0019230)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|sensory perception of pain (GO:0019233)|social behavior (GO:0035176)|startle response (GO:0001964)|synapse assembly (GO:0007416)|transcription, DNA-templated (GO:0006351)|ventricular system development (GO:0021591)|visual learning (GO:0008542)	cytosol (GO:0005829)|extracellular space (GO:0005615)|heterochromatin (GO:0000792)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded methylated DNA binding (GO:0010385)|methyl-CpG binding (GO:0008327)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein domain specific binding (GO:0019904)|protein N-terminus binding (GO:0047485)|sequence-specific DNA binding transcription factor activity (GO:0003700)|siRNA binding (GO:0035197)|transcription corepressor activity (GO:0003714)			breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(8)|prostate(2)|urinary_tract(1)	23	all_cancers(53;3.7e-16)|all_epithelial(53;3.44e-10)|all_lung(58;2.06e-07)|Lung NSC(58;2.72e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					TCTCTGTTTGGCCTTGGCATG	0.572																																					p.P481S		.											.	MECP2-226	0			c.C1441T						.						239.0	209.0	219.0					X																	153295874		2203	4300	6503	SO:0001583	missense	4204	exon3			TGTTTGGCCTTGG	AF158180	CCDS14741.1, CCDS48193.1	Xq28	2014-09-17	2014-06-18		ENSG00000169057	ENSG00000169057			6990	protein-coding gene	gene with protein product		300005	"""mental retardation, X-linked 16"", ""mental retardation, X-linked 79"", ""Rett syndrome"", ""methyl CpG binding protein 2 (Rett syndrome)"""	RTT, MRX16, MRX79		1606614, 10508514	Standard	NM_004992		Approved		uc004fjw.2	P51608	OTTHUMG00000024229	ENST00000303391.6:c.1405C>T	X.37:g.153295874G>A	ENSP00000301948:p.Pro469Ser	152	0		188	44	NM_001110792	0	0	0	0	0	O15233|Q6QHH9|Q7Z384	Missense_Mutation	SNP	ENST00000303391.6	37	CCDS14741.1	.	.	.	.	.	.	.	.	.	.	G	16.94	3.260525	0.59431	.	.	ENSG00000169057	ENST00000303391;ENST00000453960	D;D	0.97924	-4.6;-4.61	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	D	0.97601	0.9214	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.992	D	0.99655	1.0992	10	0.87932	D	0	-2.7874	17.6415	0.88138	0.0:0.0:1.0:0.0	.	481;469	P51608-2;P51608	.;MECP2_HUMAN	S	469;481	ENSP00000301948:P469S;ENSP00000395535:P481S	ENSP00000301948:P469S	P	-	1	0	MECP2	152949068	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.438000	0.82558	0.600000	0.82982	CCA	.		0.572	MECP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000061144.1	NM_004992	
JPH4	84502	broad.mit.edu	37	14	24044983	24044984	+	Frame_Shift_Ins	INS	-	-	C			TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10			-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr14:24044983_24044984insC	ENST00000397118.3	-	4	1963_1964	c.1061_1062insG	c.(1060-1062)ggcfs	p.G354fs	JPH4_ENST00000356300.4_Frame_Shift_Ins_p.G354fs|JPH4_ENST00000544177.1_5'Flank	NM_032452.2	NP_115828.2	Q96JJ6	JPH4_HUMAN	junctophilin 4	354					calcium ion transport into cytosol (GO:0060402)|learning (GO:0007612)|neuromuscular process controlling balance (GO:0050885)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic plasticity (GO:0048167)	dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|smooth endoplasmic reticulum (GO:0005790)				endometrium(1)|large_intestine(2)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00654)		CCTTAACCTTGCCCCGCCGAAG	0.718																																					p.G354fs		.											.	JPH4-92	0			c.1062_1063insG						.																																			SO:0001589	frameshift_variant	84502	exon3			AACCTTGCCCCGC	AB058734	CCDS9603.1	14q11	2004-05-28	2004-05-28	2004-05-28	ENSG00000092051	ENSG00000092051			20156	protein-coding gene	gene with protein product			"""junctophilin like 1"""	JPHL1		11347906	Standard	NM_032452		Approved	KIAA1831	uc001wkr.2	Q96JJ6	OTTHUMG00000028769	ENST00000397118.3:c.1062dupG	14.37:g.24044987_24044987dupC	ENSP00000380307:p.Gly354fs	6	0		194	6	NM_001146028	0	0	0	0	0	D3DS53|Q8ND44|Q96DQ0	Frame_Shift_Ins	INS	ENST00000397118.3	37	CCDS9603.1																																																																																			.		0.718	JPH4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413853.1	NM_032452	
GAS8	2622	hgsc.bcm.edu	37	16	90095597	90095598	+	Intron	INS	-	-	GGGGCAGCCTACGGGGCAGGCTGC	rs61118444|rs141303781|rs71137702	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr16:90095597_90095598insGGGGCAGCCTACGGGGCAGGCTGC	ENST00000268699.4	+	2	212				GAS8_ENST00000536122.1_Intron|C16orf3_ENST00000408886.2_In_Frame_Ins_p.50_51insPAACPVGC|GAS8_ENST00000540721.1_Intron	NM_001481.2	NP_001472.1	O95995	GAS8_HUMAN	growth arrest-specific 8						cellular protein localization (GO:0034613)|negative regulation of cell proliferation (GO:0008285)|sperm motility (GO:0030317)	Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile cilium (GO:0031514)				endometrium(3)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	14		all_cancers(9;4.44e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.00118)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.029)		gggcaggctatggggcagccta	0.663																																					p.I52delinsAACPVGCPI		.											.	C16orf3-90	0			c.154_155insGCAGCCTGCCCCGTAGGCTGCCCC						.																																			SO:0001627	intron_variant	750	exon1			AGGCTATGGGGCA	AF050079	CCDS10992.1, CCDS67101.1, CCDS73932.1	16q24.3	2014-07-18	2003-01-16	2003-01-17	ENSG00000141013	ENSG00000141013			4166	protein-coding gene	gene with protein product		605178	"""growth arrest-specific 11"""	GAS11		9790751	Standard	NM_001481		Approved		uc002fqi.1	O95995	OTTHUMG00000138988	ENST00000268699.4:c.90+1467->GGGGCAGCCTACGGGGCAGGCTGC	16.37:g.90095597_90095598insGGGGCAGCCTACGGGGCAGGCTGC		68	0		157	0	NM_001214	0	0	0	0	0	B2RCT1|B7Z4U1|G3V1L5|Q2M234	In_Frame_Ins	INS	ENST00000268699.4	37	CCDS10992.1																																																																																			GGGGCAGCCTACGGGGCAGGCTGC|1.000;|0.000		0.663	GAS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272877.2		
ATXN1	6310	hgsc.bcm.edu	37	6	16327909	16327910	+	In_Frame_Ins	INS	-	-	TGC	rs59310777	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr6:16327909_16327910insTGC	ENST00000244769.4	-	8	1568_1569	c.632_633insGCA	c.(631-633)cat>caGCAt	p.210_211insQ	ATXN1_ENST00000436367.1_In_Frame_Ins_p.210_211insQ	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	210	Poly-Gln.			H -> HQ (in Ref. 1; CAA55793). {ECO:0000305}.	adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)	p.H209_H211delHQH(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				gctgctgctgatgctgatgctg	0.668																																					p.H211delinsQH		.											.	ATXN1-93	1	Deletion - In frame(1)	prostate(1)	c.633_634insGCA						.																																			SO:0001652	inframe_insertion	6310	exon7			CTGCTGATGCTGA	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.630_632dupGCA	6.37:g.16327910_16327912dupTGC	ENSP00000244769:p.Gln224_Gln225dup	12	0		52	39	NM_001128164	0	0	0	0	0	Q17S02|Q9UJG2|Q9Y4J1	In_Frame_Ins	INS	ENST00000244769.4	37	CCDS34342.1																																																																																			.		0.668	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
FZD1	8321	hgsc.bcm.edu	37	7	90894459	90894460	+	In_Frame_Ins	INS	-	-	CCG	rs71292991|rs139480179	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr7:90894459_90894460insCCG	ENST00000287934.2	+	1	677_678	c.264_265insCCG	c.(265-267)ccg>CCGccg	p.89_89P>PP		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	89	Poly-Pro.				autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.Q88_P89insP(2)|p.Q88_P89insA(1)		breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			cggggcAGCAACCGCCGCCGCC	0.743														1874	0.374201	0.4047	0.4625	5008	,	,		10872	0.2986		0.4294	False		,,,				2504	0.2914				p.Q88delinsQP		.											.	FZD1-658	3	Insertion - In frame(3)	breast(2)|liver(1)	c.264_265insCCG						.			1606,5,2563		359,2,886,0,3,837						0.6	1.0		dbSNP_134	11	3182,3,4959		703,0,1776,1,1,1591	no	codingComplex	FZD1	NM_003505.1		1062,2,2662,1,4,2428	A1A1,A1A2,A1R,A2A2,A2R,RR		39.1085,38.5961,38.9349				4788,8,7522				SO:0001652	inframe_insertion	8321	exon1			GCAGCAACCGCCG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"""GPCR / Class F : Frizzled receptors"""	4038	protein-coding gene	gene with protein product	"""Wnt receptor"", ""frizzled, Drosophila, homolog of, 1"""	603408	"""frizzled (Drosophila) homolog 1"", ""frizzled homolog 1 (Drosophila)"", ""frizzled 1, seven transmembrane spanning receptor"", ""frizzled family receptor 1"""			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.274_276dupCCG	7.37:g.90894466_90894468dupCCG	ENSP00000287934:p.Pro93dup	2	2		33	33	NM_003505	0	0	0	0	0	A4D1E8|O94815|Q549T8	In_Frame_Ins	INS	ENST00000287934.2	37	CCDS5620.1																																																																																			-|0.606;CCG|0.394		0.743	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505	
SPATA31C1	441452	hgsc.bcm.edu	37	9	90534192	90534193	+	RNA	INS	-	-	TCTTGTCTCCCAGCGTCA	rs567658963|rs536300617	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	-	-	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr9:90534192_90534193insTCTTGTCTCCCAGCGTCA	ENST00000602681.1	+	0	938_939							P0DKV0	S31C1_HUMAN	SPATA31 subfamily C, member 1						cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TCCCAGCGTCATCTTGTCTCCC	0.594																																					p.H71delinsHLVSQRH		.											.	.	0			c.212_213insTCTTGTCTCCCAGCGTCA						.																																					441452	exon2			AGCGTCATCTTGT	AK093374		9q22.1	2014-03-18	2012-10-12	2012-10-12	ENSG00000230246	ENSG00000230246			27846	other	unknown			"""family with sequence similarity 75, member C1"""	FAM75C1			Standard	NM_001145124		Approved	FLJ36055	uc010mqi.3	P0DKV0	OTTHUMG00000020160		9.37:g.90534192_90534193insTCTTGTCTCCCAGCGTCA		293	0		378	0	NM_001145124	0	0	0	0	0		In_Frame_Ins	INS	ENST00000602681.1	37																																																																																				.		0.594	SPATA31C1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000467313.1	NM_001145124	
OBSCN	84033	hgsc.bcm.edu	37	1	228504669	228504670	+	Missense_Mutation	DNP	GC	GC	AT	rs61825302|rs11810627	byFrequency	TCGA-OR-A5KQ-01A-11D-A30A-10	TCGA-OR-A5KQ-10A-01D-A30A-10	GC	GC	-	-	-	-	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	71ee860b-0b75-498c-a470-f1022b5155e0	c748e192-64b2-4316-bf62-5f40129b4743	g.chr1:228504669_228504670GC>AT	ENST00000422127.1	+	51	13589_13590	c.13545_13546GC>AT	c.(13543-13548)gcGCgg>gcATgg	p.R4516W	OBSCN_ENST00000570156.2_Missense_Mutation_p.R5473W|OBSCN_ENST00000366709.4_Missense_Mutation_p.R1635W|OBSCN_ENST00000366707.4_Missense_Mutation_p.R2150W|OBSCN_ENST00000284548.11_Missense_Mutation_p.R4516W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4516	Ig-like 46.		R -> W (in dbSNP:rs11810627).		apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGGCCTCTGCGCGGCTCACCGT	0.733																																					p.R5228W		.											.	OBSCN-403	0			c.C16417T						.																																			SO:0001583	missense	84033	exon62			TCTGCGCGGCTCA	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	Exception_encountered	1.37:g.228504669_228504670delinsAT	ENSP00000409493:p.Arg4516Trp	0	0		19	1	NM_001271223	0	0	0	0	0	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	DNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.643;T|0.357		0.733	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
