#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
NCL	4691	hgsc.bcm.edu	37	2	232325382	232325384	+	In_Frame_Del	DEL	TCC	TCC	-	rs140018754		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:232325382_232325384delTCC	ENST00000322723.4	-	4	1047_1049	c.807_809delGGA	c.(805-810)gaggaa>gaa	p.269_270EE>E	SNORD82_ENST00000365530.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	269	Asp/Glu-rich (acidic).				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		TTAAGTACCTTCCTCCTCCTCTT	0.409																																					p.270_270del		Pindel,Atlas-Indel	.											.	NCL	80	.	0			c.808_810del						PASS	.			1,0,4265		0,0,1,0,0,2132						4.7	0.3			220	4,5,8245		0,0,4,0,5,4118	no	codingComplex	NCL	NM_005381.2		0,0,5,0,5,6250	A1A1,A1A2,A1R,A2A2,A2R,RR		0.109,0.0234,0.0799				5,5,12510				SO:0001651	inframe_deletion	4691	exon4			.		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.807_809delGGA	2.37:g.232325388_232325390delTCC	ENSP00000318195:p.Glu271del	142.0	0.0	.		153.0	50.0	0.327	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	In_Frame_Del	DEL	ENST00000322723.4	37	CCDS33397.1																																																																																			.	.	none		0.409	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
PCDH7	5099	hgsc.bcm.edu	37	4	30725858	30725859	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:30725858_30725859insA	ENST00000361762.2	+	1	3822_3823	c.2814_2815insA	c.(2815-2817)aaafs	p.K939fs	PCDH7_ENST00000543491.1_Frame_Shift_Ins_p.K939fs	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	939					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						AAAAGGACAAGAAAAACAAAAA	0.401																																					p.K938fs		Pindel,Atlas-Indel	.											.	PCDH7	215	.	0			c.2814_2815insA						PASS	.																																			SO:0001589	frameshift_variant	5099	exon1			.	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.2819dupA	4.37:g.30725863_30725863dupA	ENSP00000355243:p.Lys939fs	60.0	0.0	.		91.0	38.0	0.418	NM_032457	O60246|O60247|Q4W5C4	Frame_Shift_Ins	INS	ENST00000361762.2	37	CCDS33971.1																																																																																			.	.	none		0.401	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589	
ZNF560	147741	hgsc.bcm.edu	37	19	9578512	9578513	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9578512_9578513delTG	ENST00000301480.4	-	10	1323_1324	c.1110_1111delCA	c.(1108-1113)cacattfs	p.I371fs		NM_152476.2	NP_689689.2	Q96MR9	ZN560_HUMAN	zinc finger protein 560	371					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)|breast(3)|endometrium(3)|kidney(2)|large_intestine(16)|liver(2)|lung(24)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	65						TTTATCCCAATGTGGGTTTGCA	0.386																																					p.371_371del		Pindel,Atlas-Indel	.											.	ZNF560	162	.	0			c.1111_1112del						PASS	.																																			SO:0001589	frameshift_variant	147741	exon10			.	AK056548	CCDS12214.1	19p13.2	2013-09-20			ENSG00000198028	ENSG00000198028		"""Zinc fingers, C2H2-type"", ""-"""	26484	protein-coding gene	gene with protein product							Standard	NM_152476		Approved	FLJ31986	uc002mlp.1	Q96MR9	OTTHUMG00000180130	ENST00000301480.4:c.1110_1111delCA	19.37:g.9578514_9578515delTG	ENSP00000301480:p.Ile371fs	233.0	0.0	.		238.0	62.0	0.261	NM_152476	Q495S9|Q495T1	Frame_Shift_Del	DEL	ENST00000301480.4	37	CCDS12214.1																																																																																			.	.	none		0.386	ZNF560-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449901.1	NM_152476	
SEC16A	9919	hgsc.bcm.edu	37	9	139370955	139370963	+	In_Frame_Del	DEL	AGCTCCTGA	AGCTCCTGA	-	rs545335424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGCTCCTGA	AGCTCCTGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139370955_139370963delAGCTCCTGA	ENST00000371706.3	-	1	604_612	c.571_579delTCAGGAGCT	c.(571-579)tcaggagctdel	p.SGA191del	SEC16A_ENST00000431893.2_In_Frame_Del_p.SGA191del|SEC16A_ENST00000313050.7_In_Frame_Del_p.SGA369del|SEC16A_ENST00000290037.6_In_Frame_Del_p.SGA191del			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	191					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)		p.S369_A371delSGA(1)		breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		ACATCGCCAGAGCTCCTGAAGCTCCTGAG	0.574														13	0.00259585	0.0008	0.0014	5008	,	,		18859	0.0		0.004	False		,,,				2504	0.0072				p.369_372del		Pindel,Atlas-Indel	.											.	SEC16A	249	.	1	Deletion - In frame(1)	breast(1)	c.1106_1114del						PASS	.			7,3561		0,7,1777						1.9	0.0			19	42,7812		1,40,3886	no	coding	SEC16A	NM_014866.1		1,47,5663	A1A1,A1R,RR		0.5348,0.1962,0.429				49,11373				SO:0001651	inframe_deletion	9919	exon3			.	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.571_579delTCAGGAGCT	9.37:g.139370964_139370972delAGCTCCTGA	ENSP00000360771:p.Ser191_Ala193del	110.0	0.0	.		118.0	32.0	0.271	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	In_Frame_Del	DEL	ENST00000371706.3	37																																																																																				.	.	none		0.574	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
SPATA31A7	26165	hgsc.bcm.edu	37	9	65504156	65504156	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:65504156delG	ENST00000355045.2	-	4	3432	c.3404delC	c.(3403-3405)ccafs	p.P1135fs	SPATA31A7_ENST00000491812.2_5'Flank	NM_015667.2	NP_056482.2	Q8IWB4	S31A7_HUMAN	SPATA31 subfamily A, member 7	1135					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTTCCTGACTGGGGTAAGTTG	0.458																																					p.P1135fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3405delA						PASS	.																																			SO:0001589	frameshift_variant	727905	exon4			.		CCDS75838.1	9q12	2014-04-11	2012-10-12	2012-10-12	ENSG00000234734	ENSG00000276040			32007	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A7"""	FAM75A7		20850414	Standard	NM_015667		Approved	OTTHUMG00000013196		Q8IWB4	OTTHUMG00000188536	ENST00000355045.2:c.3404delC	9.37:g.65504156delG	ENSP00000347153:p.Pro1135fs	376.0	0.0	.		263.0	49.0	0.186	NM_001113541	Q5TZK4|Q9Y4Q5	Frame_Shift_Del	DEL	ENST00000355045.2	37	CCDS43825.1																																																																																			.	.	none		0.458	SPATA31A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036952.1	NM_015667	
MPHOSPH9	10198	hgsc.bcm.edu	37	12	123678972	123678974	+	In_Frame_Del	DEL	TTT	TTT	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TTT	TTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:123678972_123678974delTTT	ENST00000606320.1	-	13	2406_2408	c.2200_2202delAAA	c.(2200-2202)aaadel	p.K734del	MPHOSPH9_ENST00000392425.3_In_Frame_Del_p.K582del|MPHOSPH9_ENST00000302349.5_In_Frame_Del_p.K582del|MPHOSPH9_ENST00000541076.2_In_Frame_Del_p.K704del			Q99550	MPP9_HUMAN	M-phase phosphoprotein 9	734						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(18)|prostate(2)|skin(1)	33	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000182)|Epithelial(86;0.00046)|BRCA - Breast invasive adenocarcinoma(302;0.169)		GTTGAGCTTCTTTATCATCTGAG	0.305																																					p.582_583del		Pindel,Atlas-Indel	.											.	MPHOSPH9	75	.	0			c.1745_1747del						PASS	.																																			SO:0001651	inframe_deletion	10198	exon9			.	X98258	CCDS9243.1, CCDS9243.2	12q24	2008-03-03			ENSG00000051825	ENSG00000051825			7215	protein-coding gene	gene with protein product		605501				8885239	Standard	NM_022782		Approved	MPP9	uc001uel.3	Q99550	OTTHUMG00000168849	ENST00000606320.1:c.2200_2202delAAA	12.37:g.123678972_123678974delTTT	ENSP00000475489:p.Lys734del	142.0	0.0	.		162.0	50.0	0.309	NM_022782	A1L486|A6NEE2|B3KR87|Q9H976|U3KQ28	In_Frame_Del	DEL	ENST00000606320.1	37																																																																																				.	.	none		0.305	MPHOSPH9-030	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000471390.2		
TMSB4X	7114	hgsc.bcm.edu	37	X	12994443	12994444	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:12994443_12994444delAG	ENST00000380635.1	+	2	279_280	c.63_64delAG	c.(61-66)acagagfs	p.E22fs	TMSB4X_ENST00000380633.1_Frame_Shift_Del_p.E22fs|TMSB4X_ENST00000451311.2_Frame_Shift_Del_p.E22fs|TMSB4X_ENST00000380636.1_Frame_Shift_Del_p.E22fs			P62328	TYB4_HUMAN	thymosin beta 4, X-linked	22					actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|sequestering of actin monomers (GO:0042989)	cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)	poly(A) RNA binding (GO:0044822)			upper_aerodigestive_tract(1)	1						TGAAGAAGACAGAGACGCAAGA	0.54																																					p.21_21del		Pindel,Atlas-Indel	.											.	TMSB4X	3	.	0			c.62_63del						PASS	.			0,3721		0,0,1592,537						4.7	1.0			58	1,6483		0,1,2356,1770	no	frameshift	TMSB4X	NM_021109.3		0,1,3948,2307	A1A1,A1R,RR,R		0.0154,0.0,0.0098				1,10204				SO:0001589	frameshift_variant	7114	exon2			.		CCDS35202.1	Xp22.2	2013-05-14	2008-02-25		ENSG00000205542	ENSG00000205542			11881	protein-coding gene	gene with protein product		300159	"""thymosin, beta 4, X chromosome"""	TMSB4		2677145, 9381176	Standard	NM_021109		Approved	TB4X	uc004cvf.3	P62328	OTTHUMG00000021144	ENST00000380635.1:c.63_64delAG	X.37:g.12994445_12994446delAG	ENSP00000370009:p.Glu22fs	177.0	0.0	.		186.0	81.0	0.435	NM_021109	P01253|P01254|Q546P5|Q63576|Q9UE55	Frame_Shift_Del	DEL	ENST00000380635.1	37	CCDS35202.1																																																																																			.	.	none		0.540	TMSB4X-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000055779.1	NM_021109	
PKD1	5310	hgsc.bcm.edu	37	16	2144160	2144161	+	In_Frame_Ins	INS	-	-	TGG			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2144160_2144161insTGG	ENST00000262304.4	-	35	10758_10759	c.10550_10551insCCA	c.(10549-10551)ggg>ggCCAg	p.3517_3518insQ	RP11-304L19.3_ENST00000565937.1_RNA|RP11-304L19.1_ENST00000570072.1_RNA|PKD1_ENST00000423118.1_In_Frame_Ins_p.3516_3517insQ	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	3517					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GCCCCAGCTCCCCCAGCCTCTG	0.663																																					p.G3517delinsGQ		Pindel,Atlas-Indel	.											.	PKD1	184	.	0			c.10551_10552insCCA						PASS	.																																			SO:0001652	inframe_insertion	5310	exon35			.	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.10550_10551insCCA	16.37:g.2144160_2144161insTGG	ENSP00000262304:p.Gly3517_Glu3518insGln	167.0	0.0	.		217.0	59.0	0.272	NM_001009944	Q15140|Q15141	In_Frame_Ins	INS	ENST00000262304.4	37	CCDS32369.1																																																																																			.	.	none		0.663	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
SPANXN4	441525	hgsc.bcm.edu	37	X	142121809	142121811	+	Splice_Site	DEL	AGA	AGA	-	rs368252596		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:142121809_142121811delAGA	ENST00000446864.1	+	2	175_176	c.78_79delAGA	c.(76-81)aaagaa>aaaa	p.E27del	SPANXN4_ENST00000370504.3_Intron	NM_001009613.2	NP_001009613.1	Q5MJ08	SPXN4_HUMAN	SPANX family, member N4	27										endometrium(2)|large_intestine(2)|lung(3)|ovary(1)	8	Acute lymphoblastic leukemia(192;6.56e-05)					TTTTTTTACCAGAAGAAGAAGAA	0.414																																					.		Pindel,Atlas-Indel	.											.	SPANXN4	10	.	0			.						PASS	.			28,3000		4,16,4,1234,516						0.8	0.0		dbSNP_131	21	265,5828		10,168,77,2059,1542	no	coding-near-splice	SPANXN4	NM_001009613.2		14,184,81,3293,2058	A1A1,A1R,A1,RR,R		4.3493,0.9247,3.2124				293,8828				SO:0001630	splice_region_variant	441525	.			.	DQ336126	CCDS48178.1	Xq27.3	2009-03-25			ENSG00000189326	ENSG00000189326			33177	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 9"""	300667				14973187, 17012309	Standard	NM_001009613		Approved	SPANX-N4, CT11.9	uc004fbv.4	Q5MJ08	OTTHUMG00000022575	ENST00000446864.1:c.79-1AGA>-	X.37:g.142121818_142121820delAGA		117.0	0.0	.		229.0	39.0	0.170	.	Q0ZNK6|Q5W0S6	Splice_Site	DEL	ENST00000446864.1	37	CCDS48178.1																																																																																			.	.	none		0.414	SPANXN4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377539.1	NM_001009613	In_Frame_Del
FCRL5	83416	hgsc.bcm.edu	37	1	157488567	157488567	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:157488567delG	ENST00000361835.3	-	14	2823	c.2666delC	c.(2665-2667)cctfs	p.P889fs	FCRL5_ENST00000461387.1_5'UTR|FCRL5_ENST00000356953.4_Frame_Shift_Del_p.P889fs	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	889					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				CGAGTCTGAAGGGCTCCTGTG	0.493																																					p.P889fs		Pindel,Atlas-Indel	.											FCRL5,NS,carcinoma,-1,1	FCRL5	177	1	0			c.2667delT						PASS	.						93.0	91.0	92.0					1																	157488567		2203	4300	6503	SO:0001589	frameshift_variant	83416	exon14			.	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.2666delC	1.37:g.157488567delG	ENSP00000354691:p.Pro889fs	171.0	0.0	.		209.0	52.0	0.249	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Frame_Shift_Del	DEL	ENST00000361835.3	37	CCDS1165.1																																																																																			.	.	none		0.493	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
CLVS1	157807	hgsc.bcm.edu	37	8	62412051	62412053	+	In_Frame_Del	DEL	GAG	GAG	-	rs35623706	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:62412051_62412053delGAG	ENST00000519846.1	+	7	1487_1489	c.1015_1017delGAG	c.(1015-1017)gagdel	p.E340del	CLVS1_ENST00000518592.1_In_Frame_Del_p.E61del|CLVS1_ENST00000325897.4_In_Frame_Del_p.E340del|CLVS1_ENST00000518858.1_3'UTR			Q8IUQ0	CLVS1_HUMAN	clavesin 1	340					lysosome organization (GO:0007040)	clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|transporter activity (GO:0005215)			endometrium(3)|kidney(4)|large_intestine(4)|lung(21)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	41						CCTGAAACATGAGGAGAAGGGAG	0.498														8	0.00159744	0.0	0.0014	5008	,	,		18651	0.0		0.006	False		,,,				2504	0.001				p.338_339del		Pindel,Atlas-Indel	.											.	CLVS1	74	.	0			c.1014_1016del						PASS	.			6,4258		0,6,2126						2.0	1.0		dbSNP_126	118	75,8179		1,73,4053	no	coding	CLVS1	NM_173519.2		1,79,6179	A1A1,A1R,RR		0.9087,0.1407,0.6471				81,12437				SO:0001651	inframe_deletion	157807	exon6			.	AY094971	CCDS6176.1	8q12.1	2009-10-14	2009-10-14	2009-10-14		ENSG00000177182			23139	protein-coding gene	gene with protein product		611292	"""retinaldehyde binding protein 1-like 1"""	RLBP1L1		16802092, 19651769	Standard	NM_173519		Approved	MGC34646, CRALBPL, C6orf212L	uc003xuh.3	Q8IUQ0		ENST00000519846.1:c.1015_1017delGAG	8.37:g.62412054_62412056delGAG	ENSP00000428402:p.Glu340del	129.0	0.0	.		136.0	50.0	0.368	NM_173519	B2R7M5|C8UZT3|Q8NB32	In_Frame_Del	DEL	ENST00000519846.1	37	CCDS6176.1																																																																																			GAG|0.500;-|0.500	0.500	weak		0.498	CLVS1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378323.1	NM_173519	
SPATA31A5	727905	hgsc.bcm.edu	37	9	41506129	41506129	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:41506129delC	ENST00000377621.1	+	4	3430	c.3401delC	c.(3400-3402)accfs	p.T1134fs	RP11-100J16.5_ENST00000429787.2_RNA	NM_001113541.1	NP_001107013.1	Q5VU36	S31A5_HUMAN	SPATA31 subfamily A, member 5	1134					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTCAACTTACCCCAGTCAGG	0.463																																					p.T1134fs		Atlas-Indel	.											.	.	.	.	0			c.3400delA						PASS	.																																			SO:0001589	frameshift_variant	727905	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000233788				32005	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A5"""	FAM75A5		20850414	Standard	NM_001113541		Approved	OTTHUMG00000013204	uc004abu.4	Q5VU36	OTTHUMG00000013204	ENST00000377621.1:c.3401delC	9.37:g.41506129delC	ENSP00000366847:p.Thr1134fs	295.0	0.0	0		290.0	101.0	0.348276	NM_001113541		Frame_Shift_Del	DEL	ENST00000377621.1	37	CCDS47970.1																																																																																			.	.	none		0.463	SPATA31A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036962.1	NM_001113541	
KRT4	3851	hgsc.bcm.edu	37	12	53207602	53207603	+	Frame_Shift_Ins	INS	-	-	G	rs7135148|rs71092788		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53207602_53207603insG	ENST00000551956.1	-	1	732_733	c.240_241insC	c.(238-243)tttggcfs	p.G81fs	KRT4_ENST00000293774.4_Frame_Shift_Ins_p.G155fs|KRT4_ENST00000458244.2_Frame_Shift_Ins_p.G61fs			P19013	K2C4_HUMAN	keratin 4	81	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCACCAGTGCCAAAGCCTCCAG	0.599																																					p.G81fs	Pancreas(190;284 2995 41444 45903)	Atlas-Indel	.											.	KRT4	110	.	0			c.241_242insC						PASS	.																																			SO:0001589	frameshift_variant	3851	exon1			.		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240_241insC	12.37:g.53207602_53207603insG	ENSP00000448220:p.Gly81fs	69.0	0.0	0		101.0	40.0	0.39604	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Frame_Shift_Ins	INS	ENST00000551956.1	37	CCDS41787.2																																																																																			.	.	none		0.599	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
MAN1A2	10905	hgsc.bcm.edu	37	1	117945057	117945067	+	Splice_Site	DEL	TAAAGAGGTAA	TAAAGAGGTAA	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	TAAAGAGGTAA	TAAAGAGGTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:117945057_117945067delTAAAGAGGTAA	ENST00000356554.3	+	2	1287_1293	c.552_558delTAAAGAGGTAA	c.(550-558)attaaagag>at	p.IKE184fs	MAN1A2_ENST00000482811.1_Intron	NM_006699.3	NP_006690.1	O60476	MA1A2_HUMAN	mannosidase, alpha, class 1A, member 2	184					cellular protein metabolic process (GO:0044267)|lung alveolus development (GO:0048286)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(17)|ovary(1)|skin(1)|urinary_tract(1)	27	Lung SC(450;0.225)	all_cancers(81;7.9e-06)|all_epithelial(167;7.39e-07)|all_lung(203;2.84e-06)|Lung NSC(69;1.99e-05)		Lung(183;0.0688)|Kidney(133;0.114)|LUSC - Lung squamous cell carcinoma(189;0.223)|KIRC - Kidney renal clear cell carcinoma(1967;0.237)|Colorectal(144;0.243)		GGGAAAAAATTAAAGAGGTAATAAGCTGAGT	0.36																																					p.184_186del	Ovarian(33;199 881 8228 13687 31538)	Pindel,Atlas-Indel	.											.	MAN1A2	50	.	0			c.551_558del						PASS	.																																			SO:0001630	splice_region_variant	10905	exon2			.	AF027156	CCDS895.1	1p13	2008-02-05			ENSG00000198162	ENSG00000198162			6822	protein-coding gene	gene with protein product		604345				9592125	Standard	NM_006699		Approved	MAN1B	uc001ehd.1	O60476	OTTHUMG00000012149	ENST00000356554.3:c.558+1TAAAGAGGTAA>-	1.37:g.117945057_117945067delTAAAGAGGTAA		114.0	0.0	.		95.0	30.0	0.316	NM_006699	Q9H510	Frame_Shift_Del	DEL	ENST00000356554.3	37	CCDS895.1																																																																																			.	.	none		0.360	MAN1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033593.1	NM_006699	Frame_Shift_Del
MED15	51586	hgsc.bcm.edu	37	22	20920813	20920814	+	In_Frame_Ins	INS	-	-	CAGCAGCAGCAG	rs67182670|rs361923|rs535773989|rs539945336	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:20920813_20920814insCAGCAGCAGCAG	ENST00000263205.7	+	7	819_820	c.750_751insCAGCAGCAGCAG	c.(751-753)cag>CAGCAGCAGCAGcag	p.251_251Q>QQQQQ	MED15_ENST00000425759.2_In_Frame_Ins_p.140_140Q>QQQQQ|MED15_ENST00000382974.2_In_Frame_Ins_p.180_180Q>QQQQQ|MED15_ENST00000542773.1_In_Frame_Ins_p.56_56Q>QQQQQ|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000541476.1_In_Frame_Ins_p.225_225Q>QQQQQ|MED15_ENST00000406969.1_In_Frame_Ins_p.225_225Q>QQQQQ|MED15_ENST00000292733.7_In_Frame_Ins_p.251_251Q>QQQQQ	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	251	Poly-Gln.			Missing (in Ref. 3; BAB85034). {ECO:0000305}.	gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)	p.Q250_Q251insQ(4)		central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			aacaacagcaacagcagcagca	0.589																																					p.Q250delinsQQQQQ		Atlas-Indel	.											PCQAP,caecum,carcinoma,0,2	MED15	68	2	4	Insertion - In frame(4)	ovary(2)|large_intestine(2)	c.750_751insCAGCAGCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	51586	exon7			.	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.775_786dupCAGCAGCAGCAG	22.37:g.20920813_20920814insCAGCAGCAGCAG	ENSP00000263205:p.GlnGlnGlnGln259dup	62.0	0.0	0		70.0	13.0	0.185714	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	In_Frame_Ins	INS	ENST00000263205.7	37	CCDS33602.1																																																																																			.	.	alt		0.589	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	
ALMS1	7840	hgsc.bcm.edu	37	2	73681184	73681184	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:73681184delA	ENST00000264448.6	+	8	7638	c.7527delA	c.(7525-7527)gtafs	p.V2509fs	ALMS1_ENST00000377715.1_Frame_Shift_Del_p.V2509fs|ALMS1_ENST00000409009.1_Frame_Shift_Del_p.V2467fs|ALMS1-IT1_ENST00000441587.2_RNA	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2509					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						AAAGCCGGGTACGAGCACATG	0.368																																					p.V2509fs		Pindel,Atlas-Indel	.											ALMS1,NS,carcinoma,0,1	ALMS1	384	1	0			c.7526delT						PASS	.						34.0	32.0	33.0					2																	73681184		1889	4102	5991	SO:0001589	frameshift_variant	7840	exon8			.	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7527delA	2.37:g.73681184delA	ENSP00000264448:p.Val2509fs	92.0	0.0	.		135.0	30.0	0.222	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Frame_Shift_Del	DEL	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.368	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
DYSF	8291	hgsc.bcm.edu	37	2	71871177	71871195	+	Splice_Site	DEL	ATTTTGACACCCTGAAGGT	ATTTTGACACCCTGAAGGT	-	rs7573406|rs199861501|rs200809348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	ATTTTGACACCCTGAAGGT	ATTTTGACACCCTGAAGGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:71871177_71871195delATTTTGACACCCTGAAGGT	ENST00000258104.3	+	41	4770_4786	c.4493_4509delATTTTGACACCCTGAAGGT	c.(4492-4509)gattttgacaccctgaag>g	p.DFDTLK1498fs	DYSF_ENST00000410020.3_Splice_Site_p.DFDTLK1537fs|DYSF_ENST00000429174.2_Splice_Site_p.DFDTLK1519fs|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000409744.1_Splice_Site_p.DFDTLK1506fs|DYSF_ENST00000409651.1_Splice_Site_p.DFDTLK1530fs|DYSF_ENST00000394120.2_Splice_Site_p.DFDTLK1499fs|DYSF_ENST00000413539.2_Splice_Site_p.DFDTLK1529fs|DYSF_ENST00000409582.3_Splice_Site_p.DFDTLK1536fs|DYSF_ENST00000410041.1_Splice_Site_p.DFDTLK1516fs|DYSF_ENST00000409762.1_Splice_Site_p.DFDTLK1515fs|DYSF_ENST00000409366.1_Splice_Site_p.DFDTLK1520fs	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1498					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CTGGAGAAGGATTTTGACACCCTGAAGGTAAGGCCTCTC	0.493																																					p.1537_1542del		Pindel,Atlas-Indel	.											.	DYSF	536	.	0			c.4609_4626del	GRCh37	CD031501	DYSF	D		PASS	.																																			SO:0001630	splice_region_variant	8291	exon42			.	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4509+1ATTTTGACACCCTGAAGGT>-	2.37:g.71871177_71871195delATTTTGACACCCTGAAGGT		180.0	0.0	.		211.0	57.0	0.270	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	In_Frame_Del	DEL	ENST00000258104.3	37	CCDS1918.1																																																																																			.	.	none		0.493	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	Frame_Shift_Del
SPATA31A3	727830	hgsc.bcm.edu	37	9	40705744	40705744	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:40705744delC	ENST00000356699.5	+	4	3430	c.3401delC	c.(3400-3402)accfs	p.T1134fs	RP11-395E19.5_ENST00000432614.1_lincRNA	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	1134					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CCTCAACTTACCCCAGTCAGG	0.463																																					p.T1134fs		Atlas-Indel	.											.	.	.	.	0			c.3400delA						PASS	.						24.0	20.0	21.0					9																	40705744		919	2111	3030	SO:0001589	frameshift_variant	727830	exon4			.			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A3"""	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.3401delC	9.37:g.40705744delC	ENSP00000349132:p.Thr1134fs	207.0	0.0	0		504.0	37.0	0.0734127	NM_001083124		Frame_Shift_Del	DEL	ENST00000356699.5	37	CCDS47969.1																																																																																			.	.	none		0.463	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124	
OR5B12	390191	hgsc.bcm.edu	37	11	58207035	58207036	+	Frame_Shift_Del	DEL	AT	AT	-	rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207035_58207036delAT	ENST00000302572.2	-	1	610_611	c.589_590delAT	c.(589-591)attfs	p.I197fs		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACAAAAAAAATAACCATCTCA	0.391																																					p.197_197del		Atlas-Indel	.											.	OR5B12	80	.	0			c.590_591del						PASS	.																																			SO:0001589	frameshift_variant	390191	exon1			.	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.589_590delAT	11.37:g.58207035_58207036delAT	ENSP00000306657:p.Ile197fs	109.0	0.0	0		146.0	14.0	0.0958904	NM_001004733	B2RNL2|Q6IEV5	Frame_Shift_Del	DEL	ENST00000302572.2	37	CCDS31551.1																																																																																			.	.	none		0.391	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
CUL9	23113	hgsc.bcm.edu	37	6	43174057	43174065	+	Splice_Site	DEL	AGGAGGAAG	AGGAGGAAG	-	rs542758187	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	AGGAGGAAG	AGGAGGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:43174057_43174065delAGGAGGAAG	ENST00000252050.4	+	26	5106_5113	c.5022_5029delAGGAGGAAG	c.(5020-5031)gaaggaggaaga>gaga	p.GGR1675del	CUL9_ENST00000372647.2_Splice_Site_p.GGR1675del|CUL9_ENST00000354495.3_Splice_Site_p.GGR1565del	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	1675	Glu-rich.				microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						TCTGTCCCTCAGGAGGAAGAGGAGGAAGA	0.517														9	0.00179712	0.0	0.0	5008	,	,		22978	0.0		0.004	False		,,,				2504	0.0051				p.1675_1676del		Pindel,Atlas-Indel	.											.	CUL9	248	.	0			c.5023_5028del						PASS	.			3,4261		0,3,2129						3.3	0.9			67	25,8229		0,25,4102	no	coding-near-splice	CUL9	NM_015089.2		0,28,6231	A1A1,A1R,RR		0.3029,0.0704,0.2237				28,12490				SO:0001630	splice_region_variant	23113	exon26			.	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.5023-1AGGAGGAAG>-	6.37:g.43174066_43174074delAGGAGGAAG		66.0	0.0	.		50.0	20.0	0.400	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	In_Frame_Del	DEL	ENST00000252050.4	37	CCDS4890.1																																																																																			.	.	none		0.517	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	In_Frame_Del
DNAJC9	23234	hgsc.bcm.edu	37	10	75005896	75005902	+	Frame_Shift_Del	DEL	GTATGTC	GTATGTC	-	rs36012375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	GTATGTC	GTATGTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75005896_75005902delGTATGTC	ENST00000372950.4	-	3	2026_2032	c.354_360delGACATAC	c.(352-360)aagacatacfs	p.KTY118fs	MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000513954.1_RNA|DNAJC9_ENST00000453189.2_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	118					social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					CCGAACCTTTGTATGTCTTTTCAAAAG	0.382																																					p.119_121del		Pindel,Atlas-Indel	.											.	DNAJC9	19	.	0			c.355_361del						PASS	.																																			SO:0001589	frameshift_variant	23234	exon3			.	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.354_360delGACATAC	10.37:g.75005896_75005902delGTATGTC	ENSP00000362041:p.Lys118fs	168.0	0.0	.		118.0	20.0	0.169	NM_015190	B2RMW6	Frame_Shift_Del	DEL	ENST00000372950.4	37	CCDS7322.1																																																																																			.	.	none		0.382	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
PDPK1	5170	hgsc.bcm.edu	37	16	2611896	2611899	+	Frame_Shift_Del	DEL	CGAC	CGAC	-			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	CGAC	CGAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2611896_2611899delCGAC	ENST00000342085.4	+	4	602_605	c.453_456delCGAC	c.(451-456)gacgacfs	p.DD151fs	PDPK1_ENST00000354836.5_Frame_Shift_Del_p.DD151fs|RP11-20I23.8_ENST00000569852.1_RNA|PDPK1_ENST00000268673.7_Intron|PDPK1_ENST00000441549.3_Frame_Shift_Del_p.DD151fs|PDPK1_ENST00000389224.3_Frame_Shift_Del_p.DD124fs	NM_002613.4	NP_002604.1	O15530	PDPK1_HUMAN	3-phosphoinositide dependent protein kinase 1	151	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton organization (GO:0030036)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|cell migration (GO:0016477)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|focal adhesion assembly (GO:0048041)|hyperosmotic response (GO:0006972)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-threonine phosphorylation (GO:0018107)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of endothelial cell migration (GO:0010594)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of mast cell degranulation (GO:0043304)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)|type B pancreatic cell development (GO:0003323)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	3-phosphoinositide-dependent protein kinase activity (GO:0004676)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)	7		Ovarian(90;0.17)			Celecoxib(DB00482)	CATTTCAGGACGACGAGAAGCTGT	0.52																																					p.151_152del		Atlas-Indel	.											.	PDPK1	37	.	0			c.452_455del	GRCh37	CD072462	PDPK1	D		PASS	.																																			SO:0001589	frameshift_variant	5170	exon4			.	AF017995	CCDS10472.1, CCDS10473.1, CCDS58411.1	16p13.3	2014-03-20	2014-03-20		ENSG00000140992	ENSG00000140992			8816	protein-coding gene	gene with protein product	"""PkB kinase"""	605213				9094314, 9445477	Standard	NM_002613		Approved	PDK1	uc002cqs.4	O15530	OTTHUMG00000128874	ENST00000342085.4:c.453_456delCGAC	16.37:g.2611896_2611899delCGAC	ENSP00000344220:p.Asp151fs	582.0	0.0	0		582.0	62.0	0.106529	NM_001261816	H0Y4Z0|Q59EH6|Q6FI20|Q8IV52|Q9BRD5	Frame_Shift_Del	DEL	ENST00000342085.4	37	CCDS10472.1																																																																																			.	.	none		0.520	PDPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250831.3		
TUT1	64852	hgsc.bcm.edu	37	11	62359061	62359061	+	5'UTR	DEL	G	G	-	rs577382133	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62359061delG	ENST00000476907.1	-	0	588				MIR3654_ENST00000496634.2_5'Flank|TUT1_ENST00000308436.7_Frame_Shift_Del_p.P4fs			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific						mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CGATCCGATAGGAAGTGACAT	0.572													GG|GG|G|deletion	4	0.000798722	0.0	0.0	5008	,	,		18693	0.0		0.003	False		,,,				2504	0.001				p.P4fs		Pindel,Atlas-Indel	.											.	TUT1	122	.	0			c.12delT						PASS	.			5,4215		0,5,2105	34.0	46.0	42.0			-4.7	0.0	11		42	32,8150		2,28,4061	no	frameshift	TUT1	NM_022830.2		2,33,6166	A1A1,A1R,RR		0.3911,0.1185,0.2983			62359061	37,12365	692	1591	2283	SO:0001623	5_prime_UTR_variant	64852	exon1			.	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.-104C>-	11.37:g.62359061delG		46.0	0.0	.		50.0	12.0	0.240	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Frame_Shift_Del	DEL	ENST00000476907.1	37																																																																																				.	.	none		0.572	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240791	39240791	+	Silent	SNP	C	C	G	rs553572799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240791C>G	ENST00000391417.4	+	1	333	c.333C>G	c.(331-333)cgC>cgG	p.R111R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	136	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						cctgctgccgccccagctgct	0.662																																					p.R111R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,3	KRTAP4-7	49	3	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.C333G						scavenged	.																																			SO:0001819	synonymous_variant	100132476	exon1			CTGCCGCCCCAGC	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.333C>G	17.37:g.39240791C>G		29.0	0.0	0		32.0	5.0	0.15625	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.662	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
AKAP9	10142	hgsc.bcm.edu	37	7	91730338	91730338	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:91730338C>T	ENST00000359028.2	+	45	11302	c.11077C>T	c.(11077-11079)Ctg>Ttg	p.L3693L	AKAP9_ENST00000358100.2_Silent_p.L3639L|AKAP9_ENST00000356239.3_Silent_p.L3689L			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	3693					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACTTCAAACTCTGAGCCCTGA	0.393			T	BRAF	papillary thyroid																																p.L3689L		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C11065T						PASS	.						69.0	69.0	69.0					7																	91730338		2203	4300	6503	SO:0001819	synonymous_variant	10142	exon45			CAAACTCTGAGCC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.11077C>T	7.37:g.91730338C>T		73.0	0.0	0		98.0	4.0	0.0408163	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Silent	SNP	ENST00000359028.2	37																																																																																				.	.	none		0.393	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA9_ENST00000532602.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66.0	73.0	71.0		,1525,,,,,,,,,,,1525,1525	3.6	1.0	5	dbSNP_134	71	477,8069		47,383,3843	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	202.0	0.0	0		123.0	66.0	0.536585	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
MET	4233	hgsc.bcm.edu	37	7	116339672	116339672	+	Silent	SNP	C	C	T	rs35775721	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116339672C>T	ENST00000318493.6	+	2	721	c.534C>T	c.(532-534)agC>agT	p.S178S	MET_ENST00000436117.2_Silent_p.S178S|MET_ENST00000397752.3_Silent_p.S178S			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGTGGTGAGCGCCCTGGGAG	0.473			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				C|||	443	0.0884585	0.1664	0.0303	5008	,	,		20901	0.0526		0.0417	False		,,,				2504	0.1094				p.S178S		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	0			c.C534T						scavenged	.	C	,	514,3416		29,456,1480	104.0	105.0	105.0		534,534	-2.6	0.7	7	dbSNP_126	105	337,7949		10,317,3816	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	39,773,5296	TT,TC,CC		4.0671,13.0789,6.9663	,	178/1391,178/1409	116339672	851,11365	1965	4143	6108	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	GGTGAGCGCCCTG	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.534C>T	7.37:g.116339672C>T		115.0	1.0	0.00869565		150.0	82.0	0.546667	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.935;T|0.065	0.065	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
BTK	695	hgsc.bcm.edu	37	X	100612565	100612565	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:100612565A>G	ENST00000308731.7	-	13	1272	c.1109T>C	c.(1108-1110)aTa>aCa	p.I370T	BTK_ENST00000372880.1_Intron	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	370	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.		I -> M (in XLA). {ECO:0000269|PubMed:7711734}.		adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|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)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GAGCCTGGATATGAGTCCTGA	0.498									Agammaglobulinemia, X-linked																												p.I370T		Atlas-SNP	.											.	BTK	87	.	0			c.T1109C						PASS	.						304.0	239.0	261.0					X																	100612565		2203	4300	6503	SO:0001583	missense	695	exon13	Familial Cancer Database	Bruton Type Agammaglobulinemia	CTGGATATGAGTC	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.1109T>C	X.37:g.100612565A>G	ENSP00000308176:p.Ile370Thr	124.0	0.0	0		150.0	140.0	0.933333	NM_000061	B2RAW1|Q32ML5	Missense_Mutation	SNP	ENST00000308731.7	37	CCDS14482.1	.	.	.	.	.	.	.	.	.	.	A	15.88	2.962940	0.53507	.	.	ENSG00000010671	ENST00000372855;ENST00000372859;ENST00000372860;ENST00000395179;ENST00000372869;ENST00000443591;ENST00000308731	D	0.92647	-3.08	5.76	5.76	0.90799	SH2 motif (2);	0.046830	0.85682	D	0.000000	D	0.88941	0.6574	L	0.42008	1.315	0.54753	D	0.999988	B;P;P	0.44734	0.227;0.645;0.842	B;B;B	0.39419	0.114;0.299;0.185	D	0.89837	0.4000	10	0.66056	D	0.02	.	14.7456	0.69488	1.0:0.0:0.0:0.0	.	41;370;370	Q3MS94;B2RAW1;Q06187	.;.;BTK_HUMAN	T	41;41;39;41;41;41;370	ENSP00000308176:I370T	ENSP00000308176:I370T	I	-	2	0	BTK	100499221	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.664000	0.83830	1.943000	0.56356	0.483000	0.47432	ATA	.	.	none		0.498	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	
TTLL3	26140	hgsc.bcm.edu	37	3	9874914	9874914	+	Nonsense_Mutation	SNP	C	C	T	rs115917139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:9874914C>T	ENST00000547186.1	+	11	1897	c.1681C>T	c.(1681-1683)Cga>Tga	p.R561*	ARPC4-TTLL3_ENST00000397256.1_Intron|TTLL3_ENST00000455274.1_Intron|TTLL3_ENST00000427853.3_Intron|TTLL3_ENST00000397241.1_Intron|TTLL3_ENST00000426895.4_Nonsense_Mutation_p.R704*|TTLL3_ENST00000430793.1_Nonsense_Mutation_p.R349*|TTLL3_ENST00000383827.1_Intron	NM_001025930.3	NP_001021100.3	Q9Y4R7	TTLL3_HUMAN	tubulin tyrosine ligase-like family, member 3	561					axoneme assembly (GO:0035082)|cilium assembly (GO:0042384)|protein polyglycylation (GO:0018094)	axoneme (GO:0005930)|cilium (GO:0005929)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	protein-glycine ligase activity (GO:0070735)|protein-glycine ligase activity, initiating (GO:0070736)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(2)|skin(1)	26	Medulloblastoma(99;0.227)					GCTGACCCAGCGAGGCTCTGG	0.647													C|||	115	0.0229633	0.0	0.0231	5008	,	,		16546	0.001		0.0408	False		,,,				2504	0.0583				p.R704X		Atlas-SNP	.											.	TTLL3	51	.	0			c.C2110T						PASS	.	C	stop/ARG,	28,3784		0,28,1878	29.0	31.0	30.0		2110,	3.6	0.3	3	dbSNP_132	30	360,7860		10,340,3760	yes	stop-gained,intron	TTLL3,ARPC4-TTLL3	NM_001025930.3,NM_001198793.1	,	10,368,5638	TT,TC,CC		4.3796,0.7345,3.2247	,	704/916,	9874914	388,11644	1906	4110	6016	SO:0001587	stop_gained	26140	exon11			ACCCAGCGAGGCT		CCDS43048.1, CCDS43048.2	3p25.3	2013-02-14			ENSG00000214021	ENSG00000214021		"""Tubulin tyrosine ligase-like family"""	24483	protein-coding gene	gene with protein product						11054573	Standard	NR_037162		Approved	DKFZP434B103, HOTTL	uc003btg.4	Q9Y4R7	OTTHUMG00000128439	ENST00000547186.1:c.1681C>T	3.37:g.9874914C>T	ENSP00000446659:p.Arg561*	87.0	0.0	0		92.0	50.0	0.543478	NM_001025930	Q4KMS8|Q6AWA3|Q6ZU95|Q8NDN8|Q96GG8|Q9H876|Q9UI99	Nonsense_Mutation	SNP	ENST00000547186.1	37		43	0.019688644688644688	0	0.0	11	0.03038674033149171	0	0.0	32	0.04221635883905013	C	38	6.974468	0.97975	0.007345	0.043796	ENSG00000214021	ENST00000426895;ENST00000547186;ENST00000443148;ENST00000430793	.	.	.	5.39	3.58	0.41010	.	0.000000	0.27782	U	0.017874	.	.	.	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6056	0.33771	0.3092:0.5413:0.1495:0.0	rs3208837;rs17407417	.	.	.	X	704;561;499;349	.	ENSP00000392549:R704X	R	+	1	2	TTLL3	9849914	0.009000	0.17119	0.270000	0.24601	0.659000	0.38960	0.677000	0.25262	0.639000	0.30564	-0.152000	0.13540	CGA	C|0.975;T|0.025	0.025	strong		0.647	TTLL3-203	KNOWN	basic	protein_coding	protein_coding		NM_001025930.2	
PDE1C	5137	hgsc.bcm.edu	37	7	32209524	32209524	+	Missense_Mutation	SNP	G	G	C	rs377587504		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:32209524G>C	ENST00000396193.1	-	3	774	c.181C>G	c.(181-183)Ctc>Gtc	p.L61V		NM_001191058.1	NP_001177987.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	0					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	TTCCCTGTGAGCCCATCGATG	0.522																																					p.L61V		Atlas-SNP	.											.	PDE1C	465	.	0			c.C181G						PASS	.						263.0	223.0	235.0					7																	32209524		876	1991	2867	SO:0001583	missense	5137	exon3			CTGTGAGCCCATC	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396193.1:c.181C>G	7.37:g.32209524G>C	ENSP00000379496:p.Leu61Val	188.0	0.0	0		204.0	104.0	0.509804	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396193.1	37	CCDS55100.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.717510	0.68844	.	.	ENSG00000154678	ENST00000396193	T	0.77489	-1.1	5.75	4.88	0.63580	.	.	.	.	.	T	0.64294	0.2585	N	0.14661	0.345	0.80722	D	1	B	0.25667	0.131	B	0.21546	0.035	T	0.63945	-0.6522	9	0.72032	D	0.01	.	14.3935	0.66996	0.0714:0.0:0.9286:0.0	.	61	E9PE92	.	V	61	ENSP00000379496:L61V	ENSP00000379496:L61V	L	-	1	0	PDE1C	32176049	1.000000	0.71417	0.992000	0.48379	0.998000	0.95712	3.073000	0.50057	1.456000	0.47831	0.655000	0.94253	CTC	.	.	weak		0.522	PDE1C-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000215075.1		
FBXW9	84261	hgsc.bcm.edu	37	19	12802009	12802009	+	Missense_Mutation	SNP	T	T	C	rs143596846	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12802009T>C	ENST00000380339.3	-	5	890	c.854A>G	c.(853-855)gAc>gGc	p.D285G	CTD-2659N19.2_ENST00000585742.1_RNA|FBXW9_ENST00000393261.3_Missense_Mutation_p.D285G|FBXW9_ENST00000544494.1_Missense_Mutation_p.D23G|FBXW9_ENST00000587955.1_Missense_Mutation_p.D275G			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	285					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CACCTTCTTGTCATAGGTGCC	0.607													T|||	2	0.000399361	0.0	0.0	5008	,	,		18570	0.0		0.002	False		,,,				2504	0.0				p.D285G		Atlas-SNP	.											.	FBXW9	30	.	0			c.A854G						PASS	.	T	GLY/ASP	1,4145		0,1,2072	127.0	128.0	127.0		854	4.7	1.0	19	dbSNP_134	127	16,8394		0,16,4189	yes	missense	FBXW9	NM_032301.2	94	0,17,6261	CC,CT,TT		0.1902,0.0241,0.1354	probably-damaging	285/459	12802009	17,12539	2073	4205	6278	SO:0001583	missense	84261	exon5			TTCTTGTCATAGG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.854A>G	19.37:g.12802009T>C	ENSP00000369696:p.Asp285Gly	87.0	0.0	0		107.0	52.0	0.485981	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	19.32	3.804178	0.70682	2.41E-4	0.001902	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	D;T;T	0.89270	-2.49;1.07;1.07	4.66	4.66	0.58398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.90665	0.7072	L	0.32530	0.975	0.58432	D	0.999997	D;P;D	0.89917	1.0;0.872;0.999	D;P;D	0.81914	0.995;0.759;0.96	D	0.91740	0.5403	10	0.87932	D	0	-31.5318	13.2197	0.59881	0.0:0.0:0.0:1.0	.	275;285;285	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	G	23;285;285	ENSP00000442714:D23G;ENSP00000376945:D285G;ENSP00000369696:D285G	ENSP00000369696:D285G	D	-	2	0	FBXW9	12663009	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	6.197000	0.72100	1.957000	0.56846	0.379000	0.24179	GAC	T|0.999;C|0.001	0.001	strong		0.607	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
REEP4	80346	hgsc.bcm.edu	37	8	21996453	21996453	+	Missense_Mutation	SNP	C	C	T	rs79793560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21996453C>T	ENST00000306306.3	-	6	1007	c.539G>A	c.(538-540)cGg>cAg	p.R180Q	REEP4_ENST00000523293.1_Missense_Mutation_p.R180Q|REEP4_ENST00000334530.5_Intron	NM_025232.2	NP_079508.2	Q9H6H4	REEP4_HUMAN	receptor accessory protein 4	180					mitotic nuclear division (GO:0007067)|mitotic nuclear envelope reassembly (GO:0007084)|nuclear envelope organization (GO:0006998)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)	microtubule binding (GO:0008017)			kidney(1)|lung(3)|ovary(1)|skin(1)|urinary_tract(1)	7				Colorectal(74;0.00187)|COAD - Colon adenocarcinoma(73;0.061)|READ - Rectum adenocarcinoma(644;0.0993)		GGGTGGCCTCCGGTGGGACAC	0.652													C|||	46	0.0091853	0.0053	0.0187	5008	,	,		17285	0.002		0.0209	False		,,,				2504	0.0031				p.R180Q		Atlas-SNP	.											.	REEP4	13	.	0			c.G539A						PASS	.	C	GLN/ARG	24,4382		0,24,2179	25.0	26.0	26.0		539	1.9	0.1	8	dbSNP_131	26	158,8430		1,156,4137	yes	missense	REEP4	NM_025232.2	43	1,180,6316	TT,TC,CC		1.8398,0.5447,1.4006	benign	180/258	21996453	182,12812	2203	4294	6497	SO:0001583	missense	80346	exon6			GGCCTCCGGTGGG	BC013048	CCDS6024.1	8p21.3	2008-05-02	2006-02-07	2006-02-07	ENSG00000168476	ENSG00000168476		"""Receptor accessory proteins"""	26176	protein-coding gene	gene with protein product		609349	"""chromosome 8 open reading frame 20"""	C8orf20		16271481, 15550249	Standard	NM_025232		Approved	FLJ22246, FLJ22277, PP432	uc003xau.1	Q9H6H4	OTTHUMG00000131491	ENST00000306306.3:c.539G>A	8.37:g.21996453C>T	ENSP00000303482:p.Arg180Gln	85.0	0.0	0		116.0	64.0	0.551724	NM_025232	D3DSQ9|Q86VL1|Q9H6I5|Q9HBP4	Missense_Mutation	SNP	ENST00000306306.3	37	CCDS6024.1	29	0.013278388278388278	5	0.01016260162601626	8	0.022099447513812154	2	0.0034965034965034965	14	0.018469656992084433	C	3.815	-0.038862	0.07497	0.005447	0.018398	ENSG00000168476	ENST00000306306;ENST00000523293;ENST00000518664	D;D;D	0.89617	-1.7;-2.39;-2.54	4.86	1.92	0.25849	.	0.768004	0.11073	N	0.602648	T	0.62405	0.2425	N	0.14661	0.345	0.29351	N	0.865351	B	0.10296	0.003	B	0.04013	0.001	T	0.57871	-0.7736	10	0.13853	T	0.58	-14.4627	6.2242	0.20698	0.0:0.6692:0.1536:0.1772	.	180	Q9H6H4	REEP4_HUMAN	Q	180	ENSP00000303482:R180Q;ENSP00000428709:R180Q;ENSP00000428160:R180Q	ENSP00000303482:R180Q	R	-	2	0	REEP4	22052398	0.000000	0.05858	0.147000	0.22382	0.291000	0.27294	-0.823000	0.04443	0.481000	0.27557	-0.749000	0.03505	CGG	C|0.985;T|0.015	0.015	strong		0.652	REEP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254337.2	NM_025232	
MYO6	4646	hgsc.bcm.edu	37	6	76542585	76542585	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:76542585G>A	ENST00000369977.3	+	6	557	c.418G>A	c.(418-420)Gtg>Atg	p.V140M	MYO6_ENST00000369985.4_Missense_Mutation_p.V140M|MYO6_ENST00000369981.3_Missense_Mutation_p.V140M|MYO6_ENST00000369975.1_Missense_Mutation_p.V140M	NM_004999.3	NP_004990.3	Q9UM54	MYO6_HUMAN	myosin VI	140	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell differentiation (GO:0042491)|cellular response to electrical stimulus (GO:0071257)|dendrite development (GO:0016358)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|endocytosis (GO:0006897)|glutamate secretion (GO:0014047)|inner ear morphogenesis (GO:0042472)|intracellular protein transport (GO:0006886)|locomotory behavior (GO:0007626)|membrane organization (GO:0061024)|metabolic process (GO:0008152)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein targeting (GO:0006605)|regulation of secretion (GO:0051046)|regulation of synaptic plasticity (GO:0048167)|response to drug (GO:0042493)|sensory perception of sound (GO:0007605)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell cortex (GO:0005938)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|microvillus (GO:0005902)|neuronal cell body (GO:0043025)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|ruffle membrane (GO:0032587)|unconventional myosin complex (GO:0016461)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|minus-end directed microfilament motor activity (GO:0060001)|motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(16)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	58		all_hematologic(105;0.189)		BRCA - Breast invasive adenocarcinoma(397;0.223)		AGACATGAAGGTGCTCAAGAT	0.333																																					p.V140M		Atlas-SNP	.											.	MYO6	124	.	0			c.G418A						PASS	.						85.0	90.0	88.0					6																	76542585		2203	4300	6503	SO:0001583	missense	4646	exon6			ATGAAGGTGCTCA	U90236, AB002387	CCDS34487.1, CCDS75481.1	6q14.1	2014-09-17	2004-05-19		ENSG00000196586	ENSG00000196586		"""Myosins / Myosin superfamily : Class VI"""	7605	protein-coding gene	gene with protein product		600970	"""deafness, autosomal recessive 37"""	DFNA22, DFNB37		9259267, 11468689	Standard	XM_005248719		Approved	KIAA0389	uc003pih.1	Q9UM54	OTTHUMG00000015061	ENST00000369977.3:c.418G>A	6.37:g.76542585G>A	ENSP00000358994:p.Val140Met	56.0	0.0	0		50.0	26.0	0.52	NM_004999	A6H8V4|E1P540|Q5TEM5|Q5TEM6|Q5TEM7|Q9BZZ7|Q9UEG2	Missense_Mutation	SNP	ENST00000369977.3	37	CCDS34487.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.914335	0.92178	.	.	ENSG00000196586	ENST00000428345;ENST00000369981;ENST00000369985;ENST00000369977;ENST00000369975	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	D	0.91002	0.7170	L	0.55990	1.75	0.80722	D	1	D;D	0.69078	0.997;0.996	D;D	0.79784	0.957;0.993	D	0.89801	0.3975	10	0.46703	T	0.11	.	19.6547	0.95831	0.0:0.0:1.0:0.0	.	140;140	Q9UM54-2;Q9UM54-1	.;.	M	140	ENSP00000358998:V140M;ENSP00000359002:V140M;ENSP00000358994:V140M;ENSP00000358992:V140M	ENSP00000358992:V140M	V	+	1	0	MYO6	76599305	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.388000	0.97237	2.717000	0.92951	0.650000	0.86243	GTG	.	.	none		0.333	MYO6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041279.2	NM_004999	
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:146993392A>G	ENST00000397944.3	+	8	952	c.876A>G	c.(874-876)aaA>aaG	p.K292K	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	292	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						AGCTCCTGAAAGAAATATTGC	0.378													A|||	111	0.0221645	0.003	0.0274	5008	,	,		17411	0.0		0.0437	False		,,,				2504	0.045				p.K292K		Atlas-SNP	.											.	ADGB	93	.	0			c.A876G						PASS	.	A		13,1371		0,13,679	57.0	51.0	53.0		876	1.3	1.0	6	dbSNP_132	53	206,2976		9,188,1394	no	coding-synonymous	C6orf103	NM_024694.3		9,201,2073	GG,GA,AA		6.4739,0.9393,4.7963		292/1668	146993392	219,4347	692	1591	2283	SO:0001819	synonymous_variant	79747	exon8			CCTGAAAGAAATA	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.876A>G	6.37:g.146993392A>G		154.0	0.0	0		182.0	94.0	0.516484	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.976;G|0.024	0.024	strong		0.378	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
PCM1	5108	hgsc.bcm.edu	37	8	17830005	17830005	+	Missense_Mutation	SNP	G	G	A	rs17514547	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17830005G>A	ENST00000519253.1	+	23	4003	c.3752G>A	c.(3751-3753)cGc>cAc	p.R1251H	PCM1_ENST00000524226.1_Missense_Mutation_p.R1252H|PCM1_ENST00000327578.8_5'Flank|PCM1_ENST00000325083.8_Missense_Mutation_p.R1251H			Q15154	PCM1_HUMAN	pericentriolar material 1	1251			R -> H (in dbSNP:rs17514547).		centrosome organization (GO:0051297)|cilium assembly (GO:0042384)|cytoplasmic microtubule organization (GO:0031122)|G2/M transition of mitotic cell cycle (GO:0000086)|interkinetic nuclear migration (GO:0022027)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|microtubule anchoring (GO:0034453)|microtubule anchoring at centrosome (GO:0034454)|mitotic cell cycle (GO:0000278)|negative regulation of neurogenesis (GO:0050768)|neuronal stem cell maintenance (GO:0097150)|positive regulation of intracellular protein transport (GO:0090316)|protein localization to centrosome (GO:0071539)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|pericentriolar material (GO:0000242)|protein complex (GO:0043234)	identical protein binding (GO:0042802)		PCM1/JAK2(30)	breast(4)|endometrium(8)|kidney(5)|large_intestine(16)|lung(11)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	48				Colorectal(111;0.0789)		GGAAGAAGACGCCAGTTTGAT	0.378			T	"""RET, JAK2"""	"""papillary thyroid, CML, MPD"""								G|||	51	0.0101837	0.0008	0.0086	5008	,	,		17700	0.0		0.0268	False		,,,				2504	0.0174				p.R1251H		Atlas-SNP	.		Dom	yes		8	8p22-p21.3	5108	pericentriolar material 1  (PTC4)		"""E, L"""	.	PCM1	120	.	0			c.G3752A						PASS	.	G	HIS/ARG	17,3709		0,17,1846	102.0	96.0	98.0		3752	2.0	1.0	8	dbSNP_123	98	250,7948		5,240,3854	yes	missense	PCM1	NM_006197.3	29	5,257,5700	AA,AG,GG		3.0495,0.4563,2.2392	probably-damaging	1251/2025	17830005	267,11657	1863	4099	5962	SO:0001583	missense	5108	exon23			GAAGACGCCAGTT		CCDS47812.1	8p22-p21.3	2008-08-08			ENSG00000078674	ENSG00000078674			8727	protein-coding gene	gene with protein product		600299				8120099, 15659651	Standard	NM_006197		Approved	PTC4	uc003wyi.4	Q15154	OTTHUMG00000163699	ENST00000519253.1:c.3752G>A	8.37:g.17830005G>A	ENSP00000431099:p.Arg1251His	163.0	0.0	0		172.0	81.0	0.47093	NM_006197	Q58F13|Q6P1K7|Q8NB85|Q9BWC1|Q9H4A2	Missense_Mutation	SNP	ENST00000519253.1	37		27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	G	12.33	1.904852	0.33628	0.004563	0.030495	ENSG00000078674	ENST00000325083;ENST00000519253;ENST00000524226	T;T;T	0.52983	0.64;0.64;0.64	4.81	2.01	0.26516	.	0.261491	0.45126	N	0.000386	T	0.25121	0.0610	N	0.25647	0.755	0.80722	D	1	B;D;B;D	0.89917	0.0;1.0;0.01;1.0	B;D;B;D	0.79784	0.001;0.993;0.007;0.993	T	0.13980	-1.0489	10	0.44086	T	0.13	-0.0745	7.4507	0.27237	0.3627:0.0:0.6373:0.0	rs17514547;rs52805963;rs56506649;rs17514547	113;1251;1252;1251	B4DJ00;E7ETA6;E7EV56;Q15154	.;.;.;PCM1_HUMAN	H	1251;1251;1252	ENSP00000327077:R1251H;ENSP00000431099:R1251H;ENSP00000430521:R1252H	ENSP00000327077:R1251H	R	+	2	0	PCM1	17874285	0.992000	0.36948	1.000000	0.80357	0.174000	0.22865	0.417000	0.21214	0.305000	0.22832	0.313000	0.20887	CGC	G|0.986;A|0.014	0.014	strong		0.378	PCM1-003	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374800.1	NM_006197	
PDGFRA	5156	hgsc.bcm.edu	37	4	55152040	55152040	+	Silent	SNP	C	C	T	rs2228230	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55152040C>T	ENST00000257290.5	+	18	2803	c.2472C>T	c.(2470-2472)gtC>gtT	p.V824V	FIP1L1_ENST00000507166.1_Silent_p.V584V	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	824	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.V824V(15)		NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	CTCGCAACGTCCTCCTGGCAC	0.498			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			C|||	1204	0.240415	0.3449	0.2767	5008	,	,		22168	0.1726		0.1451	False		,,,				2504	0.2413				p.V824V	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	PDGFRA,NS,carcinoma,0,17	PDGFRA	1583	17	15	Substitution - coding silent(15)	soft_tissue(11)|central_nervous_system(3)|endometrium(1)	c.C2472T						PASS	.	C		1381,3025	455.5+/-351.0	211,959,1033	186.0	168.0	174.0		2472	2.4	1.0	4	dbSNP_98	174	1198,7402	241.0+/-271.5	95,1008,3197	no	coding-synonymous	PDGFRA	NM_006206.4		306,1967,4230	TT,TC,CC		13.9302,31.3436,19.8293		824/1090	55152040	2579,10427	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon18	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	CAACGTCCTCCTG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.2472C>T	4.37:g.55152040C>T		66.0	0.0	0		64.0	24.0	0.375	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			C|0.801;T|0.199	0.199	strong		0.498	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
TNS1	7145	hgsc.bcm.edu	37	2	218758200	218758200	+	Missense_Mutation	SNP	T	T	G	rs61745748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:218758200T>G	ENST00000171887.4	-	8	756	c.304A>C	c.(304-306)Aat>Cat	p.N102H	TNS1_ENST00000419504.1_Missense_Mutation_p.N102H|TNS1_ENST00000310858.6_Missense_Mutation_p.N133H|TNS1_ENST00000430930.1_Missense_Mutation_p.N102H	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	102	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				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)		GGGTCTGCATTGAGCCATGTG	0.562													T|||	63	0.0125799	0.0023	0.0086	5008	,	,		19412	0.0		0.0199	False		,,,				2504	0.0348				p.N102H		Atlas-SNP	.											.	TNS1	251	.	0			c.A304C						PASS	.	T	HIS/ASN	19,4387	26.2+/-53.5	0,19,2184	144.0	113.0	123.0		304	5.1	1.0	2	dbSNP_129	123	190,8410	85.0+/-147.5	0,190,4110	yes	missense	TNS1	NM_022648.4	68	0,209,6294	GG,GT,TT		2.2093,0.4312,1.607	possibly-damaging	102/1736	218758200	209,12797	2203	4300	6503	SO:0001583	missense	7145	exon8			CTGCATTGAGCCA	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.304A>C	2.37:g.218758200T>G	ENSP00000171887:p.Asn102His	122.0	0.0	0		152.0	77.0	0.506579	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	T	18.57	3.652558	0.67472	0.004312	0.022093	ENSG00000079308	ENST00000171887;ENST00000419504;ENST00000430930;ENST00000446903;ENST00000413554;ENST00000310858;ENST00000413280	D;D;D;D;D;D;D	0.98617	-5.03;-5.03;-5.03;-5.03;-5.03;-5.03;-5.03	5.09	5.09	0.68999	Phosphatase tensin type (1);	0.098933	0.64402	D	0.000002	D	0.96361	0.8813	L	0.49350	1.555	0.54753	D	0.99998	D;B;D;D;D;D	0.89917	0.988;0.086;1.0;0.976;0.963;0.963	P;B;D;P;P;P	0.91635	0.819;0.112;0.999;0.867;0.498;0.498	D	0.92353	0.5891	10	0.72032	D	0.01	.	14.6945	0.69110	0.0:0.0:0.0:1.0	.	102;156;133;102;102;102	B2RU35;A1L0S7;Q6IPI5;Q9HBL0;E9PGF5;E9PF55	.;.;.;TENS1_HUMAN;.;.	H	102;102;102;227;170;133;102	ENSP00000171887:N102H;ENSP00000408724:N102H;ENSP00000406016:N102H;ENSP00000405460:N227H;ENSP00000400383:N170H;ENSP00000308321:N133H;ENSP00000395615:N102H	ENSP00000171887:N102H	N	-	1	0	TNS1	218466445	1.000000	0.71417	0.961000	0.40146	0.927000	0.56198	6.097000	0.71452	2.142000	0.66516	0.460000	0.39030	AAT	T|0.986;G|0.014	0.014	strong		0.562	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
ABCA7	10347	hgsc.bcm.edu	37	19	1054583	1054583	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1054583C>T	ENST00000263094.6	+	28	3972	c.3741C>T	c.(3739-3741)gcC>gcT	p.A1247A	ABCA7_ENST00000433129.1_Silent_p.A1247A|ABCA7_ENST00000435683.2_Silent_p.A1109A	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1247					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCTGCCTGCCCTCTTTGTGG	0.632																																					p.A1247A		Atlas-SNP	.											.	ABCA7	174	.	0			c.C3741T						PASS	.						93.0	70.0	78.0					19																	1054583		2203	4300	6503	SO:0001819	synonymous_variant	10347	exon28			GCCTGCCCTCTTT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3741C>T	19.37:g.1054583C>T		53.0	0.0	0		80.0	31.0	0.3875	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.	.	none		0.632	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
FADD	8772	hgsc.bcm.edu	37	11	70049752	70049752	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:70049752C>T	ENST00000301838.4	+	1	484	c.187C>T	c.(187-189)Ctg>Ttg	p.L63L	RP11-805J14.5_ENST00000526174.1_RNA|RP11-805J14.5_ENST00000527232.1_RNA	NM_003824.3	NP_003815.1	Q13158	FADD_HUMAN	Fas (TNFRSF6)-associated via death domain	63	DED. {ECO:0000255|PROSITE- ProRule:PRU00065}.				activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to mechanical stimulus (GO:0071260)|defense response to virus (GO:0051607)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|lymph node development (GO:0048535)|motor neuron apoptotic process (GO:0097049)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of activation-induced cell death of T cells (GO:0070236)|negative regulation of necroptotic process (GO:0060546)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of CD8-positive, alpha-beta cytotoxic T cell extravasation (GO:2000454)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of proteolysis (GO:0045862)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|protein heterooligomerization (GO:0051291)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAIL-activated apoptotic signaling pathway (GO:0036462)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral process (GO:0016032)	CD95 death-inducing signaling complex (GO:0031265)|cell body (GO:0044297)|cytosol (GO:0005829)|death-inducing signaling complex (GO:0031264)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|ripoptosome (GO:0097342)	death effector domain binding (GO:0035877)|death receptor binding (GO:0005123)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|tumor necrosis factor receptor superfamily binding (GO:0032813)			endometrium(1)|lung(4)|ovary(1)|pancreas(1)|urinary_tract(2)	9	Esophageal squamous(2;1.19e-45)		LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CACCGAGCTCCTGCGCGAGCT	0.736																																					p.L63L		Atlas-SNP	.											.	FADD	14	.	0			c.C187T						PASS	.						18.0	23.0	21.0					11																	70049752		2140	4217	6357	SO:0001819	synonymous_variant	8772	exon1			GAGCTCCTGCGCG	U24231	CCDS8196.1	11q13.3	2014-09-17			ENSG00000168040	ENSG00000168040			3573	protein-coding gene	gene with protein product	"""Fas-associating protein with death domain"", ""Fas-associating death domain-containing protein"", ""mediator of receptor-induced toxicity"", ""growth-inhibiting gene 3 protein"""	602457				7536190, 7538907	Standard	NM_003824		Approved	MORT1, GIG3	uc001opm.2	Q13158	OTTHUMG00000167264	ENST00000301838.4:c.187C>T	11.37:g.70049752C>T		65.0	0.0	0		62.0	33.0	0.532258	NM_003824	Q14866|Q6IBR4	Silent	SNP	ENST00000301838.4	37	CCDS8196.1																																																																																			.	.	none		0.736	FADD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393902.1	NM_003824	
PCDHGB1	56104	hgsc.bcm.edu	37	5	140730384	140730384	+	Missense_Mutation	SNP	G	G	T	rs62378414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140730384G>T	ENST00000523390.1	+	1	557	c.557G>T	c.(556-558)aGt>aTt	p.S186I	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	186	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCTGATGGAAGTAAATATCCG	0.468													.|||	118	0.0235623	0.0356	0.0288	5008	,	,		20557	0.001		0.0298	False		,,,				2504	0.0204				p.S186I		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.G557T						PASS	.	G	,,,ILE/SER,ILE/SER	118,3644		2,114,1765	151.0	148.0	149.0		,,,557,557	1.3	1.0	5	dbSNP_129	149	241,7983		3,235,3874	yes	intron,intron,intron,missense,missense	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,142,142	5,349,5639	TT,TG,GG		2.9304,3.1366,2.9952	,,,,	,,,186/928,186/811	140730384	359,11627	1881	4112	5993	SO:0001583	missense	56104	exon1			ATGGAAGTAAATA	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.557G>T	5.37:g.140730384G>T	ENSP00000429273:p.Ser186Ile	108.0	0.0	0		134.0	47.0	0.350746	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	53	0.024267399267399268	16	0.032520325203252036	16	0.04419889502762431	0	0.0	21	0.027704485488126648	.	12.14	1.849715	0.32699	0.031366	0.029304	ENSG00000254221	ENST00000523390	T	0.22336	1.96	5.36	1.34	0.21922	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.04452	0.0122	M	0.62088	1.915	0.09310	N	1	B;B	0.32467	0.125;0.372	B;B	0.35727	0.094;0.209	T	0.24764	-1.0151	9	0.40728	T	0.16	.	1.2756	0.02030	0.2205:0.1214:0.4089:0.2492	rs62378414	186;186	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	I	186	ENSP00000429273:S186I	ENSP00000429273:S186I	S	+	2	0	PCDHGB1	140710568	0.000000	0.05858	0.998000	0.56505	0.897000	0.52465	-0.393000	0.07305	0.019000	0.15079	-0.253000	0.11424	AGT	G|0.975;T|0.025	0.025	strong		0.468	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
CNDP1	84735	hgsc.bcm.edu	37	18	72228136	72228136	+	Missense_Mutation	SNP	G	G	A	rs150779486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:72228136G>A	ENST00000358821.3	+	4	577	c.349G>A	c.(349-351)Gaa>Aaa	p.E117K	CNDP1_ENST00000585136.1_Intron|RP11-231E4.3_ENST00000583702.1_RNA|CNDP1_ENST00000582365.1_Missense_Mutation_p.E74K	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	117						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		CATCCTGGCCGAACTGGGGAG	0.552													G|||	12	0.00239617	0.0091	0.0	5008	,	,		16481	0.0		0.0	False		,,,				2504	0.0				p.E117K	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											.	CNDP1	98	.	0			c.G349A						PASS	.	G	LYS/GLU	47,4359	48.9+/-83.8	0,47,2156	135.0	136.0	136.0		349	4.2	0.1	18	dbSNP_134	136	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CNDP1	NM_032649.5	56	0,49,6454	AA,AG,GG		0.0233,1.0667,0.3767	possibly-damaging	117/508	72228136	49,12957	2203	4300	6503	SO:0001583	missense	84735	exon4			CTGGCCGAACTGG		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.349G>A	18.37:g.72228136G>A	ENSP00000351682:p.Glu117Lys	120.0	0.0	0		117.0	62.0	0.529915	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	5.843	0.339732	0.11069	0.010667	2.33E-4	ENSG00000150656	ENST00000358821	T	0.08896	3.04	5.11	4.22	0.49857	.	0.189436	0.45606	D	0.000347	T	0.03564	0.0102	L	0.45228	1.405	0.19300	N	0.99998	P	0.36633	0.562	B	0.14578	0.011	T	0.37641	-0.9697	10	0.13853	T	0.58	-25.2873	9.5834	0.39501	0.0785:0.1446:0.7769:0.0	.	117	Q96KN2	CNDP1_HUMAN	K	117	ENSP00000351682:E117K	ENSP00000351682:E117K	E	+	1	0	CNDP1	70379116	0.997000	0.39634	0.058000	0.19502	0.362000	0.29581	3.719000	0.54926	1.116000	0.41820	0.655000	0.94253	GAA	G|0.996;A|0.004	0.004	strong		0.552	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
ZNF207	7756	hgsc.bcm.edu	37	17	30677325	30677325	+	Silent	SNP	G	G	A	rs140451700	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:30677325G>A	ENST00000321233.6	+	1	175	c.21G>A	c.(19-21)aaG>aaA	p.K7K	RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394670.4_Silent_p.K7K|ZNF207_ENST00000342555.6_5'UTR|ZNF207_ENST00000394673.2_Silent_p.K7K|ZNF207_ENST00000577908.1_Silent_p.K7K|MIR632_ENST00000385193.1_RNA|ZNF207_ENST00000341711.6_Silent_p.K7K	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	7	Microtubule-binding region.				attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			AGAAGAAGAAGCAGCTGAAGC	0.537													G|||	4	0.000798722	0.0	0.0043	5008	,	,		19354	0.0		0.001	False		,,,				2504	0.0				p.K7K		Atlas-SNP	.											.	ZNF207	32	.	0			c.G21A						PASS	.	G	,,	4,4402	8.1+/-20.4	0,4,2199	209.0	197.0	201.0		21,21,21	3.5	1.0	17	dbSNP_134	201	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF207	NM_001032293.2,NM_001098507.1,NM_003457.3	,,	0,69,6434	AA,AG,GG		0.7558,0.0908,0.5305	,,	7/464,7/495,7/479	30677325	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	7756	exon1			GAAGAAGCAGCTG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.21G>A	17.37:g.30677325G>A		298.0	0.0	0		322.0	172.0	0.534162	NM_003457	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Silent	SNP	ENST00000321233.6	37	CCDS11271.1																																																																																			G|0.996;A|0.004	0.004	strong		0.537	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2		
C4BPA	722	hgsc.bcm.edu	37	1	207287446	207287446	+	Splice_Site	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207287446C>G	ENST00000367070.3	+	3	338	c.144C>G	c.(142-144)ggC>ggG	p.G48G		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	48					complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GGTGTCCAGGCAATTGTGGTC	0.443																																					p.G48G		Atlas-SNP	.											.	C4BPA	70	.	0			c.C144G						PASS	.						182.0	169.0	174.0					1																	207287446		2203	4300	6503	SO:0001630	splice_region_variant	722	exon3			TCCAGGCAATTGT	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.143-1C>G	1.37:g.207287446C>G		137.0	0.0	0		144.0	69.0	0.479167	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																			.	.	none		0.443	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		Silent
NPHP3	27031	hgsc.bcm.edu	37	3	132401603	132401603	+	Missense_Mutation	SNP	G	G	C	rs143451766	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:132401603G>C	ENST00000337331.5	-	26	3842	c.3756C>G	c.(3754-3756)agC>agG	p.S1252R	NPHP3_ENST00000326682.8_3'UTR	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	1252			S -> R (in NPHP3; dbSNP:rs143451766). {ECO:0000269|PubMed:12872122}.		atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						TCCGACCCAGGCTATCTTCAT	0.348													G|||	2	0.000399361	0.0	0.0	5008	,	,		18145	0.0		0.002	False		,,,				2504	0.0				p.S1252R		Atlas-SNP	.											.	NPHP3	110	.	0			c.C3756G	GRCh37	CM032020	NPHP3	M	rs143451766	PASS	.	G	ARG/SER	3,4403	6.2+/-15.9	0,3,2200	109.0	115.0	113.0		3756	4.4	1.0	3	dbSNP_134	113	8,8592	6.4+/-24.3	0,8,4292	yes	missense	NPHP3	NM_153240.4	110	0,11,6492	CC,CG,GG		0.093,0.0681,0.0846	probably-damaging	1252/1331	132401603	11,12995	2203	4300	6503	SO:0001583	missense	27031	exon26			ACCCAGGCTATCT	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.3756C>G	3.37:g.132401603G>C	ENSP00000338766:p.Ser1252Arg	179.0	0.0	0		177.0	70.0	0.39548	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Missense_Mutation	SNP	ENST00000337331.5	37	CCDS3078.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.67	3.188670	0.57909	6.81E-4	9.3E-4	ENSG00000113971	ENST00000393144;ENST00000393156;ENST00000337331	T	0.76839	-1.05	6.16	4.38	0.52667	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.77267	0.4105	N	0.20881	0.62	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.83275	0.996;0.966	T	0.72057	-0.4405	10	0.21014	T	0.42	-24.6133	9.7792	0.40639	0.2093:0.0:0.7907:0.0	.	1252;134	Q7Z494;Q7Z491	NPHP3_HUMAN;.	R	532;314;1252	ENSP00000338766:S1252R	ENSP00000338766:S1252R	S	-	3	2	NPHP3	133884293	1.000000	0.71417	1.000000	0.80357	0.892000	0.51952	2.446000	0.44908	0.937000	0.37394	0.650000	0.86243	AGC	G|0.999;C|0.001	0.001	strong		0.348	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
IFNA17	3451	hgsc.bcm.edu	37	9	21227821	21227821	+	Missense_Mutation	SNP	T	T	C	rs141849715	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:21227821T>C	ENST00000413767.2	-	1	400	c.352A>G	c.(352-354)Aac>Gac	p.N118D		NM_021268.2	NP_067091.1	P01571	IFN17_HUMAN	interferon, alpha 17	118					adaptive immune response (GO:0002250)|B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|natural killer cell activation involved in immune response (GO:0002323)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|regulation of MHC class I biosynthetic process (GO:0045343)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|T cell activation involved in immune response (GO:0002286)|type I interferon signaling pathway (GO:0060337)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|type I interferon receptor binding (GO:0005132)			breast(1)|endometrium(2)|lung(4)|ovary(1)|skin(1)	9				Lung(24;2.13e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		GCTTCCAGGTTATTCAGTTGC	0.473																																					p.N118D		Atlas-SNP	.											.	IFNA17	17	.	0			c.A352G						PASS	.	T	ASP/ASN	4,4402	4.2+/-10.8	0,4,2199	149.0	155.0	153.0		352	-0.6	0.0	9	dbSNP_134	153	34,8566	17.9+/-57.8	1,32,4267	no	missense	IFNA17	NM_021268.2	23	1,36,6466	CC,CT,TT		0.3953,0.0908,0.2922	benign	118/190	21227821	38,12968	2203	4300	6503	SO:0001583	missense	3451	exon1			CCAGGTTATTCAG		CCDS6500.1	9p22	2010-12-10			ENSG00000234829	ENSG00000234829		"""Interferons"""	5422	protein-coding gene	gene with protein product		147583				1385305	Standard	NM_021268		Approved	LEIF2C1, IFN-alphaI	uc003zos.1	P01571	OTTHUMG00000019667	ENST00000413767.2:c.352A>G	9.37:g.21227821T>C	ENSP00000411940:p.Asn118Asp	454.0	0.0	0		365.0	127.0	0.347945	NM_021268	Q14639|Q4KMT4|Q5VZ53|Q7M4Q4	Missense_Mutation	SNP	ENST00000413767.2	37	CCDS6500.1	7	0.003205128205128205	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	t	0.009	-1.820432	0.00595	9.08E-4	0.003953	ENSG00000234829	ENST00000413767	T	0.02890	4.12	2.87	-0.61	0.11604	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.099480	0.06778	N	0.784835	T	0.00356	0.0011	N	0.00014	-2.915	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50013	-0.8877	10	0.02654	T	1	.	3.954	0.09382	0.0:0.356:0.3901:0.2539	.	118	P01571	IFN17_HUMAN	D	118	ENSP00000411940:N118D	ENSP00000411940:N118D	N	-	1	0	IFNA17	21217821	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.698000	0.05092	0.082000	0.17018	-0.702000	0.03669	AAC	T|0.997;C|0.003	0.003	strong		0.473	IFNA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051896.1	NM_021268	
GCC2	9648	hgsc.bcm.edu	37	2	109087167	109087167	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:109087167G>T	ENST00000309863.6	+	6	2096	c.1382G>T	c.(1381-1383)gGt>gTt	p.G461V		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	461					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						GAAATACAGGGTCTTAAGGAA	0.294																																					p.G461V		Atlas-SNP	.											GCC2,NS,carcinoma,-1,1	GCC2	129	1	0			c.G1382T						PASS	.						35.0	37.0	37.0					2																	109087167		2203	4289	6492	SO:0001583	missense	9648	exon6			TACAGGGTCTTAA	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.1382G>T	2.37:g.109087167G>T	ENSP00000307939:p.Gly461Val	124.0	0.0	0		153.0	58.0	0.379085	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Missense_Mutation	SNP	ENST00000309863.6	37	CCDS33268.1	.	.	.	.	.	.	.	.	.	.	G	9.716	1.158335	0.21454	.	.	ENSG00000135968	ENST00000309863;ENST00000409896;ENST00000393318	T	0.31247	1.5	5.41	4.51	0.55191	.	0.374008	0.26163	N	0.025964	T	0.25344	0.0616	L	0.57536	1.79	0.44330	D	0.99721	B	0.30763	0.294	B	0.30251	0.113	T	0.07770	-1.0755	10	0.30078	T	0.28	.	5.137	0.14939	0.1494:0.0:0.6492:0.2014	.	461	Q8IWJ2	GCC2_HUMAN	V	461;424;206	ENSP00000307939:G461V	ENSP00000307939:G461V	G	+	2	0	GCC2	108453599	1.000000	0.71417	1.000000	0.80357	0.601000	0.36947	2.328000	0.43867	2.688000	0.91661	0.655000	0.94253	GGT	.	.	none		0.294	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000524944.1_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000420247.2_Silent_p.K200K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16.0	19.0	18.0		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.600G>A	11.37:g.65293819G>A		86.0	0.0	0		111.0	52.0	0.468468	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
ISM2	145501	hgsc.bcm.edu	37	14	77944624	77944624	+	Missense_Mutation	SNP	T	T	C	rs149849326	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77944624T>C	ENST00000342219.4	-	6	1215	c.1159A>G	c.(1159-1161)Aag>Gag	p.K387E	ISM2_ENST00000412904.1_Missense_Mutation_p.K306E|ISM2_ENST00000493585.1_Silent_p.G271G|ISM2_ENST00000393684.3_Missense_Mutation_p.K299E|ISM2_ENST00000429906.1_Missense_Mutation_p.K306E	NM_199296.2	NP_954993.1	Q6H9L7	ISM2_HUMAN	isthmin 2	387						extracellular region (GO:0005576)				endometrium(3)|large_intestine(4)|lung(11)|prostate(1)|skin(1)|urinary_tract(1)	21						GCCAGGAGCTTCCACTCCTCA	0.637													T|||	41	0.0081869	0.003	0.0086	5008	,	,		19142	0.0		0.0159	False		,,,				2504	0.0153				p.K387E		Atlas-SNP	.											.	ISM2	68	.	0			c.A1159G						PASS	.	T	,GLU/LYS	12,4394	17.9+/-39.9	0,12,2191	160.0	139.0	146.0		813,1159	4.0	0.1	14	dbSNP_134	146	179,8421	81.8+/-144.4	4,171,4125	yes	coding-synonymous,missense	ISM2	NM_182509.3,NM_199296.2	,56	4,183,6316	CC,CT,TT		2.0814,0.2724,1.4686	,benign	271/293,387/572	77944624	191,12815	2203	4300	6503	SO:0001583	missense	145501	exon6			GGAGCTTCCACTC	AK056709	CCDS9864.1, CCDS45143.1	14q24.3	2013-05-15	2013-05-15	2008-12-23	ENSG00000100593	ENSG00000100593			23176	protein-coding gene	gene with protein product	"""thrombospondin and AMOP containing isthmin-like 1"""	612684	"""thrombospondin, type I domain-containing 3"", ""thrombospondin, type I, domain containing 3"", ""isthmin 2 homolog (zebrafish)"""	THSD3		15194193	Standard	NM_199296		Approved	FLJ32147, TAIL1	uc001xtz.3	Q6H9L7	OTTHUMG00000158563	ENST00000342219.4:c.1159A>G	14.37:g.77944624T>C	ENSP00000341490:p.Lys387Glu	141.0	0.0	0		156.0	72.0	0.461538	NM_199296	A8K6D5|O95432|Q495U5|Q68CN3|Q86TQ7|Q86TW3|Q86TW4|Q8N501|Q8NBL0	Missense_Mutation	SNP	ENST00000342219.4	37	CCDS9864.1	16	0.007326007326007326	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	10	0.013192612137203167	T	0.025	-1.384359	0.01194	0.002724	0.020814	ENSG00000100593	ENST00000342219;ENST00000412904;ENST00000429906;ENST00000393684	T;T;T;T	0.21734	1.99;2.0;2.0;2.31	4.91	4.02	0.46733	.	0.727256	0.11876	N	0.520968	T	0.07188	0.0182	.	.	.	0.09310	N	1	B;B	0.14012	0.009;0.005	B;B	0.11329	0.006;0.003	T	0.24119	-1.0169	9	0.23302	T	0.38	-16.3633	10.822	0.46610	0.0:0.0:0.8104:0.1896	.	306;387	Q6H9L7-5;Q6H9L7	.;ISM2_HUMAN	E	387;306;306;299	ENSP00000341490:K387E;ENSP00000416773:K306E;ENSP00000395387:K306E;ENSP00000377289:K299E	ENSP00000341490:K387E	K	-	1	0	ISM2	77014377	0.530000	0.26330	0.071000	0.20095	0.024000	0.10985	1.079000	0.30766	1.071000	0.40834	-0.384000	0.06662	AAG	T|0.987;C|0.013	0.013	strong		0.637	ISM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351309.1	NM_182509	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416994	105416994	+	Silent	SNP	A	A	G	rs191772734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105416994A>G	ENST00000333244.5	-	7	4913	c.4794T>C	c.(4792-4794)gtT>gtC	p.V1598V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1598						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGGCCCTTAACATCTATCT	0.602													.|||	51	0.0101837	0.0015	0.013	5008	,	,		15713	0.0		0.0268	False		,,,				2504	0.0133				p.V1598V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T4794C						PASS	.	G		12,3588		0,12,1788	105.0	116.0	113.0		4794	-3.1	0.0	14		113	131,7909		8,115,3897	no	coding-synonymous	AHNAK2	NM_138420.2		8,127,5685	GG,GA,AA		1.6294,0.3333,1.2285		1598/5796	105416994	143,11497	1800	4020	5820	SO:0001819	synonymous_variant	113146	exon7			GCCCTTAACATCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4794T>C	14.37:g.105416994A>G		169.0	0.0	0		165.0	81.0	0.490909	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.991;G|0.009	0.009	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
CR2	1380	hgsc.bcm.edu	37	1	207648456	207648456	+	Missense_Mutation	SNP	G	G	T	rs144572703	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:207648456G>T	ENST00000367058.3	+	13	2623	c.2434G>T	c.(2434-2436)Gtg>Ttg	p.V812L	CR2_ENST00000367057.3_Missense_Mutation_p.V871L|CR2_ENST00000367059.3_Missense_Mutation_p.V812L|CR2_ENST00000458541.2_Missense_Mutation_p.V785L	NM_001877.4	NP_001868.2	P20023	CR2_HUMAN	complement component (3d/Epstein Barr virus) receptor 2	812	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.				B cell differentiation (GO:0030183)|B cell proliferation (GO:0042100)|complement activation, classical pathway (GO:0006958)|immune response (GO:0006955)|innate immune response (GO:0045087)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	complement binding (GO:0001848)|complement receptor activity (GO:0004875)|DNA binding (GO:0003677)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|breast(3)|endometrium(4)|kidney(3)|large_intestine(12)|lung(26)|ovary(1)|pancreas(1)|prostate(1)|skin(12)|upper_aerodigestive_tract(3)|urinary_tract(1)	69						CAATGACATAGTGTATGTTGA	0.448													G|||	10	0.00199681	0.0008	0.0014	5008	,	,		23285	0.0		0.002	False		,,,				2504	0.0061				p.V871L		Atlas-SNP	.											.	CR2	164	.	0			c.G2611T						PASS	.	G	LEU/VAL,LEU/VAL	18,4388	26.2+/-53.5	0,18,2185	177.0	156.0	163.0		2611,2434	0.4	0.0	1	dbSNP_134	163	49,8551	32.3+/-84.9	0,49,4251	yes	missense,missense	CR2	NM_001006658.2,NM_001877.4	32,32	0,67,6436	TT,TG,GG		0.5698,0.4085,0.5151	benign,benign	871/1093,812/1034	207648456	67,12939	2203	4300	6503	SO:0001583	missense	1380	exon14			GACATAGTGTATG	M26004	CCDS1478.1, CCDS31007.1	1q32	2014-09-17			ENSG00000117322	ENSG00000117322		"""CD molecules"", ""Complement system"""	2336	protein-coding gene	gene with protein product		120650					Standard	NM_001006658		Approved	CD21	uc001hfv.3	P20023	OTTHUMG00000036307	ENST00000367058.3:c.2434G>T	1.37:g.207648456G>T	ENSP00000356025:p.Val812Leu	159.0	0.0	0		173.0	83.0	0.479769	NM_001006658	C9JHD2|Q13866|Q14212|Q53EL2|Q5BKT9|Q5SR46|Q5SR48	Missense_Mutation	SNP	ENST00000367058.3	37	CCDS1478.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	5.431	0.264713	0.10294	0.004085	0.005698	ENSG00000117322	ENST00000367058;ENST00000367057;ENST00000367059;ENST00000458541	T;T;T;T	0.68331	-0.32;-0.32;-0.32;-0.32	4.7	0.427	0.16489	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.49287	0.1548	L	0.60845	1.875	0.09310	N	1	B;B;B	0.21520	0.039;0.012;0.057	B;B;B	0.27796	0.083;0.027;0.05	T	0.52215	-0.8605	9	0.56958	D	0.05	.	2.2553	0.04053	0.1786:0.1505:0.516:0.1549	.	812;812;871	Q5SR47;P20023;P20023-3	.;CR2_HUMAN;.	L	812;871;812;785	ENSP00000356025:V812L;ENSP00000356024:V871L;ENSP00000356026:V812L;ENSP00000404222:V785L	ENSP00000356024:V871L	V	+	1	0	CR2	205715079	0.006000	0.16342	0.000000	0.03702	0.195000	0.23768	0.157000	0.16402	-0.007000	0.14345	0.655000	0.94253	GTG	G|0.996;T|0.004	0.004	strong		0.448	CR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000088274.1	NM_001877	
TLE1	7088	hgsc.bcm.edu	37	9	84302311	84302311	+	Silent	SNP	A	A	G	rs147523347	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:84302311A>G	ENST00000376499.3	-	2	1127	c.63T>C	c.(61-63)acT>acC	p.T21T	TLE1_ENST00000376472.1_5'UTR|RP11-154D17.1_ENST00000437181.1_lincRNA|TLE1_ENST00000376463.1_5'Flank	NM_005077.3	NP_005068.2	Q04724	TLE1_HUMAN	transducin-like enhancer of split 1 (E(sp1) homolog, Drosophila)	21	Gln-rich.				multicellular organismal development (GO:0007275)|negative regulation of anoikis (GO:2000811)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation of gene expression (GO:0010628)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription factor binding (GO:0008134)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	29						ACTCCGGGATAGTGAACTTGA	0.642											OREG0019267	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	30	0.00599042	0.0	0.0029	5008	,	,		13712	0.0		0.007	False		,,,				2504	0.0215				p.T21T	NSCLC(155;1437 1995 30668 39354 45875)|Melanoma(16;266 781 14000 47728 51870)	Atlas-SNP	.											TLE1,NS,haematopoietic_neoplasm,0,1	TLE1	81	1	0			c.T63C						scavenged	.	A		6,4396	9.9+/-24.2	0,6,2195	25.0	26.0	25.0		63	-3.5	1.0	9	dbSNP_134	25	55,8545	30.1+/-81.4	2,51,4247	no	coding-synonymous	TLE1	NM_005077.3		2,57,6442	GG,GA,AA		0.6395,0.1363,0.4692		21/771	84302311	61,12941	2201	4300	6501	SO:0001819	synonymous_variant	7088	exon2			CGGGATAGTGAAC		CCDS6661.1	9q21.32	2013-01-10	2001-11-28		ENSG00000196781	ENSG00000196781		"""WD repeat domain containing"""	11837	protein-coding gene	gene with protein product	"""enhancer of split groucho 1"""	600189	"""transducin-like enhancer of split 1, homolog of Drosophila E(sp1)"""			8365415, 8808280	Standard	NM_005077		Approved	ESG1, GRG1, ESG	uc004aly.3	Q04724	OTTHUMG00000021008	ENST00000376499.3:c.63T>C	9.37:g.84302311A>G		97.0	1.0	0.0103093	1228	132.0	61.0	0.462121	NM_005077	A8K495|Q5T3G4|Q969V9	Silent	SNP	ENST00000376499.3	37	CCDS6661.1																																																																																			A|0.995;G|0.005	0.005	strong		0.642	TLE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055407.1	NM_005077	
PXMP2	5827	hgsc.bcm.edu	37	12	133272590	133272590	+	Silent	SNP	G	G	T	rs145883118	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133272590G>T	ENST00000317479.3	+	3	422	c.357G>T	c.(355-357)ccG>ccT	p.P119P	PXMP2_ENST00000539093.1_Intron|PXMP2_ENST00000543589.1_Intron|RP13-672B3.2_ENST00000537262.1_Intron|PXMP2_ENST00000545677.1_Intron|PXMP2_ENST00000428960.2_Silent_p.P26P	NM_018663.1	NP_061133.1	Q9NR77	PXMP2_HUMAN	peroxisomal membrane protein 2, 22kDa	119						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|protein complex (GO:0043234)				large_intestine(1)|liver(2)|lung(1)	4	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.86e-08)|Epithelial(86;2.47e-07)|all cancers(50;6.85e-06)		TCTTTGCACCGGCCTTCCTCA	0.537													G|||	3	0.000599042	0.0	0.0	5008	,	,		16181	0.0		0.002	False		,,,				2504	0.001				p.P119P		Atlas-SNP	.											.	PXMP2	15	.	0			c.G357T						PASS	.						89.0	85.0	87.0					12																	133272590		2203	4300	6503	SO:0001819	synonymous_variant	5827	exon3			TGCACCGGCCTTC		CCDS9279.1	12q24	2010-08-18	2002-08-29		ENSG00000176894	ENSG00000176894			9716	protein-coding gene	gene with protein product			"""peroxisomal membrane protein 2 (22kD)"""			11590176	Standard	NM_018663		Approved	PMP22	uc001ukt.3	Q9NR77	OTTHUMG00000168019	ENST00000317479.3:c.357G>T	12.37:g.133272590G>T		108.0	0.0	0		122.0	57.0	0.467213	NM_018663		Silent	SNP	ENST00000317479.3	37	CCDS9279.1																																																																																			G|0.999;T|0.001	0.001	strong		0.537	PXMP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397553.1	NM_018663	
MYOM1	8736	hgsc.bcm.edu	37	18	3129297	3129297	+	Silent	SNP	C	C	T	rs72860212	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:3129297C>T	ENST00000356443.4	-	18	3060	c.2727G>A	c.(2725-2727)ccG>ccA	p.P909P	MYOM1_ENST00000400569.3_Silent_p.P909P|MYOM1_ENST00000261606.7_Intron|MYOM1_ENST00000582016.1_5'UTR	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	909					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						TCTGTGGTGGCGGGGTAAGCT	0.493											OREG0024838	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0.0	0.0014	5008	,	,		19213	0.0		0.002	False		,,,				2504	0.0				p.P909P		Atlas-SNP	.											MYOM1,bladder,carcinoma,-1,1	MYOM1	192	1	0			c.G2727A						PASS	.	C	,	0,3830		0,0,1915	112.0	118.0	116.0		2727,	-5.7	0.0	18	dbSNP_130	116	28,8192		0,28,4082	no	coding-synonymous,intron	MYOM1	NM_003803.3,NM_019856.1	,	0,28,5997	TT,TC,CC		0.3406,0.0,0.2324	,	909/1686,	3129297	28,12022	1915	4110	6025	SO:0001819	synonymous_variant	8736	exon18			TGGTGGCGGGGTA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2727G>A	18.37:g.3129297C>T		253.0	0.0	0	608	231.0	121.0	0.52381	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Silent	SNP	ENST00000356443.4	37	CCDS45824.1																																																																																			C|0.998;T|0.002	0.002	strong		0.493	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
NOL10	79954	hgsc.bcm.edu	37	2	10740989	10740989	+	Missense_Mutation	SNP	T	T	C	rs115424813	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:10740989T>C	ENST00000381685.5	-	17	1517	c.1412A>G	c.(1411-1413)aAg>aGg	p.K471R	AC092687.5_ENST00000414538.1_RNA|NOL10_ENST00000538384.1_Missense_Mutation_p.K445R|NOL10_ENST00000345985.3_Missense_Mutation_p.K421R|NOL10_ENST00000542668.1_Missense_Mutation_p.K421R	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	471						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CTTAACTTTCTTTTTCCATGT	0.303													T|||	5	0.000998403	0.0008	0.0	5008	,	,		14204	0.0		0.004	False		,,,				2504	0.0				p.K471R		Atlas-SNP	.											.	NOL10	22	.	0			c.A1412G						PASS	.	T	ARG/LYS	1,4363		0,1,2181	147.0	126.0	133.0		1412	5.4	1.0	2	dbSNP_133	133	34,8502		0,34,4234	yes	missense	NOL10	NM_024894.2	26	0,35,6415	CC,CT,TT		0.3983,0.0229,0.2713	benign	471/689	10740989	35,12865	2182	4268	6450	SO:0001583	missense	79954	exon17			ACTTTCTTTTTCC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1412A>G	2.37:g.10740989T>C	ENSP00000371101:p.Lys471Arg	150.0	0.0	0		140.0	71.0	0.507143	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	12.48	1.950627	0.34377	2.29E-4	0.003983	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.48522	0.81;2.21;1.42;2.21	5.39	5.39	0.77823	.	0.041560	0.85682	D	0.000000	T	0.35248	0.0925	L	0.41573	1.285	0.53688	D	0.999975	B;B;B	0.12630	0.001;0.003;0.006	B;B;B	0.15052	0.007;0.012;0.005	T	0.15492	-1.0435	10	0.11182	T	0.66	-7.9689	10.455	0.44546	0.0:0.0825:0.0:0.9174	.	445;471;421	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	R	421;471;421;445	ENSP00000263837:K421R;ENSP00000371101:K471R;ENSP00000437625:K421R;ENSP00000439663:K445R	ENSP00000263837:K421R	K	-	2	0	NOL10	10658440	1.000000	0.71417	1.000000	0.80357	0.404000	0.30871	4.072000	0.57563	2.170000	0.68504	0.460000	0.39030	AAG	T|0.998;C|0.002	0.002	strong		0.303	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
FAT4	79633	hgsc.bcm.edu	37	4	126412106	126412106	+	Missense_Mutation	SNP	C	C	G	rs147662558	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:126412106C>G	ENST00000394329.3	+	17	14142	c.14129C>G	c.(14128-14130)tCt>tGt	p.S4710C	FAT4_ENST00000335110.5_Missense_Mutation_p.S2951C	NM_024582.4	NP_078858.4	Q6V0I7	FAT4_HUMAN	FAT atypical cadherin 4	4710	Necessary and sufficient for interaction with MPDZ. {ECO:0000250}.				branching involved in ureteric bud morphogenesis (GO:0001658)|cerebral cortex development (GO:0021987)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|inner ear receptor stereocilium organization (GO:0060122)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|plasma membrane organization (GO:0007009)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(93)|liver(3)|lung(120)|ovary(9)|pancreas(2)|prostate(21)|skin(31)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(6)	355						TCCAAATCTTCTACGTTCTAT	0.483													C|||	30	0.00599042	0.0008	0.0058	5008	,	,		20671	0.0		0.0179	False		,,,				2504	0.0072				p.S4710C		Atlas-SNP	.											.	FAT4	1752	.	0			c.C14129G						PASS	.	C	CYS/SER	22,4384	30.8+/-60.4	0,22,2181	103.0	109.0	107.0		14129	4.9	0.3	4	dbSNP_134	107	177,8423	80.6+/-143.3	1,175,4124	yes	missense	FAT4	NM_024582.4	112	1,197,6305	GG,GC,CC		2.0581,0.4993,1.5301	probably-damaging	4710/4982	126412106	199,12807	2203	4300	6503	SO:0001583	missense	79633	exon17			AATCTTCTACGTT	AY356402	CCDS3732.3	4q28.1	2013-05-31	2013-05-31		ENSG00000196159	ENSG00000196159		"""Cadherins / Cadherin-related"""	23109	protein-coding gene	gene with protein product	"""cadherin-related family member 11"""	612411	"""FAT tumor suppressor homolog 4 (Drosophila)"""			15003449	Standard	NM_024582		Approved	CDHF14, FAT-J, CDHR11	uc003ifj.4	Q6V0I7	OTTHUMG00000133100	ENST00000394329.3:c.14129C>G	4.37:g.126412106C>G	ENSP00000377862:p.Ser4710Cys	95.0	0.0	0		117.0	56.0	0.478632	NM_024582	A8K5Z6|B5MDG4|Q3LIA6|Q8TCK7|Q9H5T6	Missense_Mutation	SNP	ENST00000394329.3	37	CCDS3732.3	20	0.009157509157509158	0	0.0	5	0.013812154696132596	0	0.0	15	0.01978891820580475	C	15.14	2.744809	0.49151	0.004993	0.020581	ENSG00000196159	ENST00000394329;ENST00000335110	T;D	0.82081	-1.36;-1.57	4.93	4.93	0.64822	.	0.000000	0.33732	U	0.004612	T	0.73760	0.3628	L	0.36672	1.1	0.41081	D	0.985527	D;D;D	0.61697	0.982;0.983;0.99	P;P;P	0.53313	0.639;0.533;0.723	T	0.82729	-0.0313	10	0.72032	D	0.01	.	17.1555	0.86791	0.0:1.0:0.0:0.0	.	2951;4710;4709	Q6V0I7-2;Q6V0I7;Q6V0I7-3	.;FAT4_HUMAN;.	C	4710;2951	ENSP00000377862:S4710C;ENSP00000335169:S2951C	ENSP00000335169:S2951C	S	+	2	0	FAT4	126631556	0.998000	0.40836	0.267000	0.24556	0.798000	0.45092	5.643000	0.67895	2.283000	0.76528	0.561000	0.74099	TCT	C|0.986;G|0.014	0.014	strong		0.483	FAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256765.2	NM_024582	
PITRM1	10531	hgsc.bcm.edu	37	10	3180288	3180288	+	Missense_Mutation	SNP	C	C	T	rs35779348	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:3180288C>T	ENST00000224949.4	-	27	3083	c.3049G>A	c.(3049-3051)Ggc>Agc	p.G1017S	PITRM1_ENST00000380994.1_Missense_Mutation_p.G575S|PITRM1_ENST00000451104.2_Missense_Mutation_p.G919S|PITRM1_ENST00000464395.1_5'UTR|PITRM1_ENST00000380989.2_Missense_Mutation_p.G1018S			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	1017					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						ATGGCCAGGCCGTGTGTGCTC	0.612													C|||	45	0.00898562	0.0008	0.0231	5008	,	,		17586	0.0		0.0268	False		,,,				2504	0.001				p.G1018S		Atlas-SNP	.											.	PITRM1	109	.	0			c.G3052A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	26,4230		1,24,2103	48.0	53.0	52.0		3052,2755,3049	3.0	0.0	10	dbSNP_126	52	266,8210		6,254,3978	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	56,56,56	7,278,6081	TT,TC,CC		3.1383,0.6109,2.2934	possibly-damaging,possibly-damaging,possibly-damaging	1018/1039,919/940,1017/1038	3180288	292,12440	2128	4238	6366	SO:0001583	missense	10531	exon27			CCAGGCCGTGTGT	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.3049G>A	10.37:g.3180288C>T	ENSP00000224949:p.Gly1017Ser	97.0	0.0	0		128.0	65.0	0.507812	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	29	0.013278388278388278	0	0.0	8	0.022099447513812154	0	0.0	21	0.027704485488126648	c	15.07	2.724507	0.48728	0.006109	0.031383	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104	T;T;T;T	0.55760	0.5;0.5;0.5;0.5	5.83	3.02	0.34903	Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.146245	0.64402	N	0.000007	T	0.29223	0.0727	M	0.61703	1.905	0.49798	D	0.99982	P;D;P	0.62365	0.898;0.991;0.87	B;P;B	0.50049	0.312;0.629;0.355	T	0.25187	-1.0139	10	0.23891	T	0.37	-27.4489	9.9005	0.41344	0.0:0.7891:0.0:0.2109	rs35779348	919;1017;952	E7ES23;Q5JRX3;E9PDX7	.;PREP_HUMAN;.	S	1017;1010;1018;575;919	ENSP00000224949:G1017S;ENSP00000370377:G1018S;ENSP00000370382:G575S;ENSP00000401201:G919S	ENSP00000224949:G1017S	G	-	1	0	PITRM1	3170288	0.938000	0.31826	0.006000	0.13384	0.000000	0.00434	3.590000	0.53979	0.394000	0.25230	-1.075000	0.02238	GGC	T|0.016;G|0.000;C|0.984	0.016	strong		0.612	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
GRIN2D	2906	hgsc.bcm.edu	37	19	48908597	48908597	+	Missense_Mutation	SNP	G	G	A	rs372406980		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:48908597G>A	ENST00000263269.3	+	3	1160	c.1072G>A	c.(1072-1074)Gag>Aag	p.E358K		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	358					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCACCGCGGCGAGAGTCTGCA	0.622																																					p.E358K		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G1072A						PASS	.						14.0	15.0	15.0					19																	48908597		2201	4295	6496	SO:0001583	missense	2906	exon3			CGCGGCGAGAGTC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1072G>A	19.37:g.48908597G>A	ENSP00000263269:p.Glu358Lys	22.0	0.0	0		40.0	25.0	0.625	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	37	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	G	15.44	2.833830	0.50951	.	.	ENSG00000105464	ENST00000263269	T	0.05319	3.46	4.32	4.32	0.51571	.	0.845492	0.10398	N	0.679577	T	0.06280	0.0162	L	0.31926	0.97	0.42288	D	0.992125	P	0.48230	0.907	B	0.33620	0.167	T	0.50285	-0.8846	10	0.54805	T	0.06	.	15.9622	0.79939	0.0:0.0:1.0:0.0	.	358	O15399	NMDE4_HUMAN	K	358	ENSP00000263269:E358K	ENSP00000263269:E358K	E	+	1	0	GRIN2D	53600409	0.989000	0.36119	0.999000	0.59377	0.911000	0.54048	3.506000	0.53364	2.116000	0.64780	0.561000	0.74099	GAG	.	.	alt		0.622	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
GRIN2A	2903	hgsc.bcm.edu	37	16	9862741	9862741	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9862741G>A	ENST00000396573.2	-	13	2871	c.2562C>T	c.(2560-2562)tcC>tcT	p.S854S	GRIN2A_ENST00000396575.2_Silent_p.S854S|GRIN2A_ENST00000404927.2_Silent_p.S854S|GRIN2A_ENST00000562109.1_Silent_p.S854S|GRIN2A_ENST00000535259.1_Silent_p.S697S|GRIN2A_ENST00000330684.3_Silent_p.S854S	NM_000833.3	NP_000824.1	Q12879	NMDE1_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2A	854					directional locomotion (GO:0033058)|dopamine metabolic process (GO:0042417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning or memory (GO:0007611)|memory (GO:0007613)|negative regulation of protein catabolic process (GO:0042177)|neurogenesis (GO:0022008)|positive regulation of apoptotic process (GO:0043065)|protein localization (GO:0008104)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic plasticity (GO:0048167)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to wounding (GO:0009611)|sensory perception of pain (GO:0019233)|serotonin metabolic process (GO:0042428)|sleep (GO:0030431)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|visual learning (GO:0008542)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(7)|breast(5)|cervix(1)|endometrium(11)|kidney(6)|large_intestine(36)|lung(71)|ovary(4)|prostate(9)|skin(45)|upper_aerodigestive_tract(2)|urinary_tract(1)	198					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAGGCCGGTCGGAGCACACGC	0.562																																					p.S854S		Atlas-SNP	.											.	GRIN2A	366	.	0			c.C2562T						PASS	.						89.0	91.0	91.0					16																	9862741		2197	4300	6497	SO:0001819	synonymous_variant	2903	exon13			CCGGTCGGAGCAC		CCDS10539.1, CCDS45407.1	16p13.2	2012-08-29			ENSG00000183454	ENSG00000183454		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4585	protein-coding gene	gene with protein product		138253		NMDAR2A		9480759	Standard	XM_005255267		Approved	GluN2A	uc002czo.4	Q12879	OTTHUMG00000129721	ENST00000396573.2:c.2562C>T	16.37:g.9862741G>A		50.0	0.0	0		68.0	28.0	0.411765	NM_000833	O00669|Q17RZ6	Silent	SNP	ENST00000396573.2	37	CCDS10539.1																																																																																			.	.	none		0.562	GRIN2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251930.3		
TEAD2	8463	hgsc.bcm.edu	37	19	49862722	49862722	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49862722C>T	ENST00000311227.2	-	3	357	c.267G>A	c.(265-267)ctG>ctA	p.L89L	TEAD2_ENST00000598397.1_5'Flank|TEAD2_ENST00000377214.4_Silent_p.L89L|AC010524.4_ENST00000596488.1_RNA|DKKL1_ENST00000594268.1_5'Flank|TEAD2_ENST00000539846.1_5'UTR|TEAD2_ENST00000598810.1_Silent_p.L89L|TEAD2_ENST00000601519.1_Silent_p.L89L|TEAD2_ENST00000593945.1_Silent_p.L89L	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	89					gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		TCCCCGTTCTCAGCTTGATGT	0.522																																					p.L89L		Atlas-SNP	.											.	TEAD2	70	.	0			c.G267A						PASS	.						254.0	214.0	228.0					19																	49862722		2203	4300	6503	SO:0001819	synonymous_variant	8463	exon3			CGTTCTCAGCTTG	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.267G>A	19.37:g.49862722C>T		145.0	0.0	0		197.0	86.0	0.436548	NM_001256658	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Silent	SNP	ENST00000311227.2	37	CCDS12761.1																																																																																			.	.	none		0.522	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598	
FAM160B2	64760	hgsc.bcm.edu	37	8	21954017	21954017	+	Silent	SNP	C	C	T	rs117838157|rs577506980	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21954017C>T	ENST00000289921.7	+	3	340	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_022749.5	NP_073586.5	Q86V87	F16B2_HUMAN	family with sequence similarity 160, member B2	98										endometrium(2)|kidney(1)|lung(2)|prostate(3)|urinary_tract(1)	9						TGGGCAAGGCCGAGGTGGGAG	0.716													c|||	50	0.00998403	0.0219	0.0072	5008	,	,		14888	0.0		0.0139	False		,,,				2504	0.002				p.A98A		Atlas-SNP	.											.	FAM160B2	35	.	0			c.C294T						PASS	.	T		95,3757		2,91,1833	13.0	16.0	15.0		294	-10.0	0.0	8	dbSNP_132	15	87,7943		1,85,3929	no	coding-synonymous	FAM160B2	NM_022749.5		3,176,5762	TT,TC,CC		1.0834,2.4663,1.5317		98/744	21954017	182,11700	1926	4015	5941	SO:0001819	synonymous_variant	64760	exon3			CAAGGCCGAGGTG	AK025454	CCDS6021.2	8p21.3	2012-11-30	2008-06-05	2008-06-05	ENSG00000158863	ENSG00000158863			16492	protein-coding gene	gene with protein product			"""retinoic acid induced 16"""	RAI16		22971576, 15626329	Standard	XR_247128		Approved	FLJ21801	uc011kyx.2	Q86V87	OTTHUMG00000097088	ENST00000289921.7:c.294C>T	8.37:g.21954017C>T		79.0	0.0	0		74.0	48.0	0.648649	NM_022749	B2RDQ5|B3KNX1|Q2M211|Q71JB5|Q7L3J6|Q969T0|Q9H6W4	Silent	SNP	ENST00000289921.7	37	CCDS6021.2																																																																																			C|0.990;T|0.010	0.010	strong		0.716	FAM160B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375334.2		
GAB1	2549	hgsc.bcm.edu	37	4	144359490	144359490	+	Missense_Mutation	SNP	C	C	T	rs28925904	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:144359490C>T	ENST00000262994.4	+	4	1234	c.932C>T	c.(931-933)cCa>cTa	p.P311L	GAB1_ENST00000262995.4_Missense_Mutation_p.P311L|GAB1_ENST00000505913.1_Missense_Mutation_p.P208L	NM_002039.3	NP_002030.2	Q13480	GAB1_HUMAN	GRB2-associated binding protein 1	311			P -> L (in dbSNP:rs28925904). {ECO:0000269|Ref.2}.		activation of JUN kinase activity (GO:0007257)|cell proliferation (GO:0008283)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis development (GO:0008544)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|interleukin-6-mediated signaling pathway (GO:0070102)|labyrinthine layer development (GO:0060711)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|regulation of cell migration (GO:0030334)|response to oxidative stress (GO:0006979)	cytosol (GO:0005829)	SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	30	all_hematologic(180;0.158)					GACATTCCTCCAACACCTGGT	0.423													C|||	39	0.00778754	0.0	0.0173	5008	,	,		15521	0.0		0.0249	False		,,,				2504	0.002				p.P311L		Atlas-SNP	.											.	GAB1	80	.	0			c.C932T						PASS	.	C	LEU/PRO,LEU/PRO	20,4386	28.1+/-56.4	0,20,2183	96.0	87.0	90.0		932,932	5.8	1.0	4	dbSNP_125	90	175,8425	80.4+/-143.0	0,175,4125	yes	missense,missense	GAB1	NM_002039.3,NM_207123.2	98,98	0,195,6308	TT,TC,CC		2.0349,0.4539,1.4993	probably-damaging,probably-damaging	311/695,311/725	144359490	195,12811	2203	4300	6503	SO:0001583	missense	2549	exon4			TTCCTCCAACACC	U43885	CCDS3759.1, CCDS3760.1	4q31.1	2013-01-10			ENSG00000109458	ENSG00000109458		"""Pleckstrin homology (PH) domain containing"""	4066	protein-coding gene	gene with protein product		604439				8596638	Standard	NM_207123		Approved		uc003ijd.3	Q13480	OTTHUMG00000161432	ENST00000262994.4:c.932C>T	4.37:g.144359490C>T	ENSP00000262994:p.Pro311Leu	115.0	0.0	0		117.0	56.0	0.478632	NM_207123	A8K152|Q4W5G2|Q6P1W2	Missense_Mutation	SNP	ENST00000262994.4	37	CCDS3759.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	33	5.225676	0.95173	0.004539	0.020349	ENSG00000109458	ENST00000262995;ENST00000262994;ENST00000505913	T;T;T	0.42131	0.98;0.98;0.98	5.8	5.8	0.92144	.	0.048415	0.85682	D	0.000000	T	0.35653	0.0939	M	0.65975	2.015	0.80722	D	1	P;P	0.52577	0.954;0.947	B;P	0.46320	0.439;0.512	T	0.48570	-0.9024	10	0.59425	D	0.04	1.2408	20.063	0.97692	0.0:1.0:0.0:0.0	rs28925904;rs28925904	311;311	Q13480;Q13480-2	GAB1_HUMAN;.	L	311;311;208	ENSP00000262995:P311L;ENSP00000262994:P311L;ENSP00000424554:P208L	ENSP00000262994:P311L	P	+	2	0	GAB1	144578940	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.564000	0.67359	2.735000	0.93741	0.655000	0.94253	CCA	C|0.986;T|0.014	0.014	strong		0.423	GAB1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364998.1	NM_002039	
TRIM3	10612	hgsc.bcm.edu	37	11	6486914	6486914	+	Silent	SNP	C	C	T	rs144521953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:6486914C>T	ENST00000525074.1	-	2	406	c.12G>A	c.(10-12)agG>agA	p.R4R	TRIM3_ENST00000359518.3_Silent_p.R4R|TRIM3_ENST00000345851.3_Silent_p.R4R|TRIM3_ENST00000536344.1_Intron|TRIM3_ENST00000537602.1_Silent_p.R4R	NM_001248006.1	NP_001234935.1	O75382	TRIM3_HUMAN	tripartite motif containing 3	4					nervous system development (GO:0007399)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)	protein C-terminus binding (GO:0008022)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(3)	27		all_lung(207;9.97e-06)|Lung NSC(207;1.74e-05)|Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;9.34e-10)|Lung(200;0.0234)|LUSC - Lung squamous cell carcinoma(625;0.133)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGCTGTCCTCCCTCTTTGCCA	0.602																																					p.R4R	Melanoma(6;5 510 1540 25169 29084)	Atlas-SNP	.											.	TRIM3	67	.	0			c.G12A						PASS	.	C	,	1,4401	2.1+/-5.4	0,1,2200	148.0	113.0	125.0		12,12	3.3	1.0	11	dbSNP_134	125	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	TRIM3	NM_006458.2,NM_033278.2	,	0,6,6491	TT,TC,CC		0.0582,0.0227,0.0462	,	4/745,4/745	6486914	6,12988	2201	4296	6497	SO:0001819	synonymous_variant	10612	exon2			GTCCTCCCTCTTT	AF045239	CCDS7764.1, CCDS58115.1	11p15.5	2013-01-09	2011-01-25	2001-11-23	ENSG00000110171	ENSG00000110171		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	10064	protein-coding gene	gene with protein product	"""ring finger protein 22"", ""brain expressed ring finger"", ""tripartite motif protein TRIM3"""	605493	"""tripartite motif-containing 3"""	RNF22		10391919	Standard	NM_006458		Approved	HAC1, BERP, RNF97	uc009yfd.3	O75382	OTTHUMG00000133405	ENST00000525074.1:c.12G>A	11.37:g.6486914C>T		92.0	0.0	0		106.0	45.0	0.424528	NM_001248006	B7Z5E6|F5H2Q8|Q4V9L4|Q9C038|Q9C039	Silent	SNP	ENST00000525074.1	37	CCDS7764.1																																																																																			C|0.999;T|0.001	0.001	strong		0.602	TRIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384224.2	NM_006458	
MTUS1	57509	hgsc.bcm.edu	37	8	17611924	17611924	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17611924G>A	ENST00000262102.6	-	2	1617	c.1393C>T	c.(1393-1395)Cca>Tca	p.P465S	MTUS1_ENST00000381862.3_Missense_Mutation_p.P465S|MTUS1_ENST00000519263.1_Missense_Mutation_p.P465S|MTUS1_ENST00000381869.3_Missense_Mutation_p.P465S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	465					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCGAGTCTGGTATGTTTTTA	0.418																																					p.P465S		Atlas-SNP	.											.	MTUS1	144	.	0			c.C1393T						PASS	.						155.0	147.0	149.0					8																	17611924		1868	4121	5989	SO:0001583	missense	57509	exon2			AGTCTGGTATGTT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1393C>T	8.37:g.17611924G>A	ENSP00000262102:p.Pro465Ser	180.0	0.0	0		244.0	48.0	0.196721	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	.	.	.	.	.	.	.	.	.	.	G	6.988	0.552322	0.13374	.	.	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.18960	3.16;3.17;3.16;2.18	5.0	-1.15	0.09709	.	0.579128	0.16128	N	0.228351	T	0.09598	0.0236	N	0.16656	0.425	0.09310	N	1	B;B;B	0.23377	0.084;0.041;0.041	B;B;B	0.21917	0.037;0.011;0.011	T	0.18745	-1.0327	10	0.52906	T	0.07	-0.6007	2.2436	0.04025	0.3516:0.1319:0.4048:0.1117	.	465;465;465	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	S	465	ENSP00000371293:P465S;ENSP00000262102:P465S;ENSP00000430167:P465S;ENSP00000371286:P465S	ENSP00000262102:P465S	P	-	1	0	MTUS1	17656204	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.204000	0.17335	-0.351000	0.08249	-1.623000	0.00790	CCA	.	.	none		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
MT-ND5	4540	hgsc.bcm.edu	37	M	13135	13135	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:13135G>A	ENST00000361567.2	+	1	799	c.799G>A	c.(799-801)Gca>Aca	p.A267T	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	267					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCCACCCCCTAGCAGAAAATA	0.498																																					p.A267T		Atlas-SNP	.											.	.	.	.	0			c.G799A						PASS	.																																			SO:0001583	missense	0	exon1			CCCCTAGCAGAAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.799G>A	M.37:g.13135G>A	ENSP00000354813:p.Ala267Thr	8.0	0.0	0		22.0	22.0	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.498	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
KIAA1614	57710	hgsc.bcm.edu	37	1	180897634	180897634	+	Missense_Mutation	SNP	G	G	A	rs140222211	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:180897634G>A	ENST00000367588.4	+	4	1185	c.1130G>A	c.(1129-1131)cGt>cAt	p.R377H	KIAA1614_ENST00000367587.1_5'UTR	NM_020950.1	NP_066001.1	Q5VZ46	K1614_HUMAN	KIAA1614	377										NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(5)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	33						CTGCTGCAGCGTGCCCGCATG	0.687													G|||	14	0.00279553	0.0	0.0029	5008	,	,		14999	0.001		0.005	False		,,,				2504	0.0061				p.R377H		Atlas-SNP	.											.	KIAA1614	75	.	0			c.G1130A						PASS	.	G	HIS/ARG	5,4137		0,5,2066	49.0	56.0	54.0		1130	1.1	1.0	1	dbSNP_134	54	54,8378		1,52,4163	yes	missense	KIAA1614	NM_020950.1	29	1,57,6229	AA,AG,GG		0.6404,0.1207,0.4692	probably-damaging	377/1191	180897634	59,12515	2071	4216	6287	SO:0001583	missense	57710	exon4			TGCAGCGTGCCCG	AB046834	CCDS41442.1	1q25.3	2008-02-05			ENSG00000135835	ENSG00000135835			29327	protein-coding gene	gene with protein product							Standard	NM_020950		Approved		uc001gok.2	Q5VZ46	OTTHUMG00000035183	ENST00000367588.4:c.1130G>A	1.37:g.180897634G>A	ENSP00000356560:p.Arg377His	177.0	0.0	0		202.0	95.0	0.470297	NM_020950	Q5VZ45|Q9HCF8	Missense_Mutation	SNP	ENST00000367588.4	37	CCDS41442.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.72	2.618956	0.46736	0.001207	0.006404	ENSG00000135835	ENST00000367588	T	0.22336	1.96	5.56	1.09	0.20402	.	0.498887	0.17274	N	0.180243	T	0.14874	0.0359	L	0.58101	1.795	0.37966	D	0.933112	B	0.13145	0.007	B	0.10450	0.005	T	0.13872	-1.0493	9	0.72032	D	0.01	-0.6487	9.816	0.40853	0.2886:0.0:0.7114:0.0	.	377	Q5VZ46	K1614_HUMAN	H	377	ENSP00000356560:R377H	ENSP00000356560:R377H	R	+	2	0	KIAA1614	179164257	0.993000	0.37304	0.971000	0.41717	0.997000	0.91878	2.386000	0.44380	0.254000	0.21573	0.650000	0.86243	CGT	G|0.997;A|0.003	0.003	strong		0.687	KIAA1614-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085151.1	XM_046531	
HTATIP2	10553	hgsc.bcm.edu	37	11	20403763	20403763	+	Missense_Mutation	SNP	C	C	T	rs376468659		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:20403763C>T	ENST00000451739.2	+	4	922	c.481C>T	c.(481-483)Cgt>Tgt	p.R161C	HTATIP2_ENST00000419348.2_Missense_Mutation_p.R195C|HTATIP2_ENST00000443524.2_Missense_Mutation_p.R161C|HTATIP2_ENST00000531058.1_Missense_Mutation_p.R115C|HTATIP2_ENST00000421577.2_Missense_Mutation_p.R161C	NM_001098522.1	NP_001091992.1			HIV-1 Tat interactive protein 2, 30kDa											large_intestine(2)|lung(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	8						AAAATTTGATCGTTACTCTGT	0.343																																					p.R195C		Atlas-SNP	.											.	HTATIP2	30	.	0			c.C583T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4404		0,0,2202	125.0	141.0	136.0		583,481,481,481	5.6	1.0	11		136	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	HTATIP2	NM_001098520.1,NM_001098521.1,NM_001098522.1,NM_006410.4	180,180,180,180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging	195/277,161/243,161/243,161/243	20403763	1,13003	2202	4300	6502	SO:0001583	missense	10553	exon5			TTTGATCGTTACT	AF039103	CCDS7852.1, CCDS44553.1, CCDS53613.1	11p15.1	2011-09-14	2002-08-29		ENSG00000109854	ENSG00000109854	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	16637	protein-coding gene	gene with protein product	"""Tat-interacting protein (30kD)"", ""short chain dehydrogenase/reductase family 44U, member 1"""	605628	"""HIV-1 Tat interactive protein 2, 30 kDa"""			9482853, 9174052, 19027726	Standard	NM_006410		Approved	TIP30, CC3, FLJ26963, SDR44U1	uc001mpx.2	Q9BUP3	OTTHUMG00000166015	ENST00000451739.2:c.481C>T	11.37:g.20403763C>T	ENSP00000394259:p.Arg161Cys	73.0	0.0	0		82.0	4.0	0.0487805	NM_001098520		Missense_Mutation	SNP	ENST00000451739.2	37	CCDS7852.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.666405	0.88251	0.0	1.16E-4	ENSG00000109854	ENST00000421577;ENST00000443524;ENST00000419348;ENST00000451739;ENST00000531058	T;T;T;T;T	0.32753	1.5;1.5;1.5;1.5;1.44	5.62	5.62	0.85841	NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.57007	0.2024	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.69654	0.939;0.965	T	0.55438	-0.8141	10	0.46703	T	0.11	-19.1679	17.5131	0.87765	0.0:1.0:0.0:0.0	.	161;195	Q9BUP3;Q9BUP3-3	HTAI2_HUMAN;.	C	161;161;195;161;115	ENSP00000397752:R161C;ENSP00000387876:R161C;ENSP00000392985:R195C;ENSP00000394259:R161C;ENSP00000436729:R115C	ENSP00000392985:R195C	R	+	1	0	HTATIP2	20360339	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	3.464000	0.53057	2.809000	0.96659	0.655000	0.94253	CGT	.	.	weak		0.343	HTATIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387445.2	NM_001098521	
NXPE4	54827	hgsc.bcm.edu	37	11	114453549	114453549	+	Silent	SNP	G	G	A	rs371147789		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:114453549G>A	ENST00000375478.3	-	3	471	c.291C>T	c.(289-291)gcC>gcT	p.A97A	NXPE4_ENST00000424261.2_5'UTR	NM_001077639.1	NP_001071107.1	Q6UWF7	NXPE4_HUMAN	neurexophilin and PC-esterase domain family, member 4	97						extracellular vesicular exosome (GO:0070062)											TGCTATGTGTGGCGCTGGTGG	0.537																																					p.A97A		Atlas-SNP	.											FAM55D,NS,carcinoma,-2,1	.	.	1	0			c.C291T						PASS	.	G	,	1,4331		0,1,2165	251.0	250.0	250.0		291,	-1.0	0.0	11		250	2,8546		0,2,4272	no	coding-synonymous,utr-5	FAM55D	NM_001077639.1,NM_017678.2	,	0,3,6437	AA,AG,GG		0.0234,0.0231,0.0233	,	97/545,	114453549	3,12877	2166	4274	6440	SO:0001819	synonymous_variant	54827	exon3			ATGTGTGGCGCTG	AK000134	CCDS41718.1, CCDS44737.1	11q23.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000137634	ENSG00000137634			23117	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 33"", ""family with sequence similarity 55, member D"""	C11orf33, FAM55D		20056006	Standard	NM_017678		Approved	FLJ20127	uc001ppc.3	Q6UWF7	OTTHUMG00000168291	ENST00000375478.3:c.291C>T	11.37:g.114453549G>A		251.0	0.0	0		325.0	142.0	0.436923	NM_001077639	Q6QDB4|Q9NXP5	Silent	SNP	ENST00000375478.3	37	CCDS41718.1																																																																																			.	.	weak		0.537	NXPE4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399179.1	NM_017678	
TAB1	10454	hgsc.bcm.edu	37	22	39813801	39813801	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39813801C>A	ENST00000216160.6	+	5	559	c.497C>A	c.(496-498)gCc>gAc	p.A166D	TAB1_ENST00000331454.3_Missense_Mutation_p.A166D	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	166	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|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)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						TCGGGAGGGGCCATGGCCGTT	0.577																																					p.A166D		Atlas-SNP	.											.	TAB1	36	.	0			c.C497A						PASS	.						86.0	73.0	77.0					22																	39813801		2203	4300	6503	SO:0001583	missense	10454	exon5			GAGGGGCCATGGC	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.497C>A	22.37:g.39813801C>A	ENSP00000216160:p.Ala166Asp	109.0	0.0	0		129.0	66.0	0.511628	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	C	29.0	4.967710	0.92855	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.10960	2.82;2.82	5.34	5.34	0.76211	Protein phosphatase 2C-like (4);	0.225313	0.44097	D	0.000492	T	0.36248	0.0960	M	0.76170	2.325	0.80722	D	1	P;P;D	0.89917	0.944;0.814;1.0	P;B;D	0.87578	0.531;0.393;0.998	T	0.10109	-1.0644	10	0.72032	D	0.01	.	19.0356	0.92976	0.0:1.0:0.0:0.0	.	166;166;310	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	D	166	ENSP00000216160:A166D;ENSP00000333049:A166D	ENSP00000216160:A166D	A	+	2	0	TAB1	38143747	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.726000	0.74758	2.496000	0.84212	0.655000	0.94253	GCC	.	.	none		0.577	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
ZNF287	57336	hgsc.bcm.edu	37	17	16455760	16455760	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:16455760A>G	ENST00000395824.1	-	6	2313	c.1696T>C	c.(1696-1698)Tgt>Cgt	p.C566R	ZNF287_ENST00000395825.3_Missense_Mutation_p.C566R			Q9HBT7	ZN287_HUMAN	zinc finger protein 287	559					positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(5)|prostate(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (92;0.083)		CATTCATTACATTTATAACAC	0.348																																					p.C566R		Atlas-SNP	.											.	ZNF287	60	.	0			c.T1696C						PASS	.						89.0	92.0	91.0					17																	16455760		2203	4300	6503	SO:0001583	missense	57336	exon6			CATTACATTTATA	AF217227	CCDS11179.2	17p11.2	2013-01-09			ENSG00000141040	ENSG00000141040		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13502	protein-coding gene	gene with protein product							Standard	NM_020653		Approved	ZKSCAN13, ZSCAN45	uc002gqi.2	Q9HBT7	OTTHUMG00000058993	ENST00000395824.1:c.1696T>C	17.37:g.16455760A>G	ENSP00000379168:p.Cys566Arg	65.0	0.0	0		96.0	4.0	0.0416667	NM_020653	Q6IAG1	Missense_Mutation	SNP	ENST00000395824.1	37	CCDS11179.2	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420080	0.62622	.	.	ENSG00000141040	ENST00000395825;ENST00000395824	D;D	0.99974	-10.2;-10.2	5.18	5.18	0.71444	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.56097	D	0.000025	D	0.99984	0.9995	H	0.99225	4.475	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.99087	1.0839	10	0.87932	D	0	.	13.3294	0.60477	1.0:0.0:0.0:0.0	.	559	Q9HBT7	ZN287_HUMAN	R	566	ENSP00000379169:C566R;ENSP00000379168:C566R	ENSP00000379168:C566R	C	-	1	0	ZNF287	16396485	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.014000	0.93635	2.317000	0.78254	0.459000	0.35465	TGT	.	.	none		0.348	ZNF287-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130504.1		
CCT4	10575	hgsc.bcm.edu	37	2	62103327	62103327	+	Silent	SNP	G	G	T	rs115496486	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:62103327G>T	ENST00000394440.3	-	8	1116	c.820C>A	c.(820-822)Cga>Aga	p.R274R	CCT4_ENST00000544079.1_Silent_p.R244R|CCT4_ENST00000538252.1_Silent_p.R218R|AC107081.5_ENST00000425779.1_RNA|CCT4_ENST00000544185.1_Silent_p.R124R|CCT4_ENST00000461540.2_5'UTR	NM_006430.3	NP_006421.2	P50991	TCPD_HUMAN	chaperonin containing TCP1, subunit 4 (delta)	274					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			breast(1)|large_intestine(2)|lung(6)|ovary(2)	11	Lung NSC(7;0.035)|all_lung(7;0.0691)		LUSC - Lung squamous cell carcinoma(7;6.5e-06)|Epithelial(17;0.0647)|all cancers(80;0.221)			CGCAGCACTCGGTCCATCTGG	0.328													G|||	14	0.00279553	0.0	0.0058	5008	,	,		16234	0.0		0.0099	False		,,,				2504	0.0				p.R274R		Atlas-SNP	.											.	CCT4	38	.	0			c.C820A						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	103.0	107.0	106.0		820	2.1	1.0	2	dbSNP_132	106	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	CCT4	NM_006430.2		0,50,6453	TT,TG,GG		0.5116,0.1362,0.3844		274/540	62103327	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	10575	exon8			GCACTCGGTCCAT		CCDS33206.1, CCDS58711.1	2p15	2011-09-02			ENSG00000115484	ENSG00000115484		"""Heat Shock Proteins / Chaperonins"""	1617	protein-coding gene	gene with protein product		605142				9819444	Standard	NM_001256721		Approved	Cctd	uc002sbo.4	P50991	OTTHUMG00000152166	ENST00000394440.3:c.820C>A	2.37:g.62103327G>T		150.0	0.0	0		231.0	87.0	0.376623	NM_006430	B2R6I3|B7Z8B1|F5H5W3|O14870|Q53QP9|Q96C51	Silent	SNP	ENST00000394440.3	37	CCDS33206.1																																																																																			G|0.996;T|0.004	0.004	strong		0.328	CCT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325548.2		
HDAC4	9759	hgsc.bcm.edu	37	2	240078400	240078400	+	Silent	SNP	G	G	A	rs148880349	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:240078400G>A	ENST00000345617.3	-	7	1472	c.681C>T	c.(679-681)caC>caT	p.H227H	HDAC4_ENST00000543185.1_5'Flank|HDAC4_ENST00000553145.1_5'Flank|HDAC4_ENST00000541256.1_Silent_p.H196H	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	227	Interaction with MEF2A.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		CCAGGACCGGGTGGTTATAGG	0.567																																					p.H227H		Atlas-SNP	.											.	HDAC4	127	.	0			c.C681T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	126.0	120.0	122.0		681	3.5	1.0	2	dbSNP_134	122	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	HDAC4	NM_006037.3		0,12,6491	AA,AG,GG		0.1047,0.0681,0.0923		227/1085	240078400	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon7			GACCGGGTGGTTA	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.681C>T	2.37:g.240078400G>A		57.0	0.0	0		77.0	42.0	0.545455	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.999;A|0.001	0.001	strong		0.567	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
ACP2	53	hgsc.bcm.edu	37	11	47261762	47261762	+	Missense_Mutation	SNP	A	A	G	rs145420520	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:47261762A>G	ENST00000256997.3	-	11	1293	c.1177T>C	c.(1177-1179)Ttc>Ctc	p.F393L	ACP2_ENST00000529444.1_Missense_Mutation_p.F330L|ACP2_ENST00000533929.1_Missense_Mutation_p.F365L|ACP2_ENST00000537863.1_Missense_Mutation_p.F206L|ACP2_ENST00000527256.1_Missense_Mutation_p.F361L|ACP2_ENST00000525230.1_5'UTR	NM_001610.2	NP_001601.1	P11117	PPAL_HUMAN	acid phosphatase 2, lysosomal	393					dephosphorylation (GO:0016311)|lysosome organization (GO:0007040)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)	acid phosphatase activity (GO:0003993)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|prostate(1)	10						ATGAGGAGGAAGAGGATGGAG	0.592													A|||	28	0.00559105	0.0015	0.0086	5008	,	,		22440	0.0		0.0149	False		,,,				2504	0.0051				p.F393L	Melanoma(90;262 1440 11488 44828 48531)	Atlas-SNP	.											.	ACP2	36	.	0			c.T1177C						PASS	.	A	LEU/PHE	9,4393	14.3+/-33.2	0,9,2192	121.0	83.0	96.0		1177	5.7	1.0	11	dbSNP_134	96	85,8511	49.8+/-109.6	1,83,4214	yes	missense	ACP2	NM_001610.2	22	1,92,6406	GG,GA,AA		0.9888,0.2045,0.7232	benign	393/424	47261762	94,12904	2201	4298	6499	SO:0001583	missense	53	exon11			GGAGGAAGAGGAT	X15525	CCDS7928.1, CCDS44583.1	11p11.2	2008-02-05			ENSG00000134575	ENSG00000134575	3.1.3.2		123	protein-coding gene	gene with protein product		171650				975882	Standard	NM_001610		Approved		uc001nei.3	P11117	OTTHUMG00000166949	ENST00000256997.3:c.1177T>C	11.37:g.47261762A>G	ENSP00000256997:p.Phe393Leu	63.0	0.0	0		63.0	29.0	0.460317	NM_001610	E9PCI1|Q561W5|Q9BTU7	Missense_Mutation	SNP	ENST00000256997.3	37	CCDS7928.1	19	0.0086996336996337	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	13	0.017150395778364115	A	11.49	1.654886	0.29425	0.002045	0.009888	ENSG00000134575	ENST00000256997;ENST00000529444;ENST00000527256;ENST00000537863;ENST00000540414;ENST00000533929	T;T;T;T;T	0.10288	3.17;3.08;3.2;2.89;3.05	5.66	5.66	0.87406	.	0.156460	0.64402	D	0.000019	T	0.02418	0.0074	N	0.08118	0	0.34188	D	0.67174	B;B;B;B	0.12013	0.001;0.005;0.001;0.005	B;B;B;B	0.08055	0.001;0.003;0.001;0.003	T	0.32188	-0.9916	10	0.25106	T	0.35	.	9.2012	0.37260	0.9119:0.0:0.0881:0.0	.	330;361;365;393	E9PHY0;B7Z7D2;E9PQY3;P11117	.;.;.;PPAL_HUMAN	L	393;330;361;206;383;365	ENSP00000256997:F393L;ENSP00000436658:F330L;ENSP00000432205:F361L;ENSP00000441933:F206L;ENSP00000432439:F365L	ENSP00000256997:F393L	F	-	1	0	ACP2	47218338	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.024000	0.57218	2.158000	0.67659	0.482000	0.46254	TTC	A|0.991;G|0.009	0.009	strong		0.592	ACP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392022.2	NM_001610	
NHSL1	57224	hgsc.bcm.edu	37	6	138745896	138745896	+	Silent	SNP	A	A	G	rs117203533	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:138745896A>G	ENST00000427025.2	-	7	4783	c.4155T>C	c.(4153-4155)caT>caC	p.H1385H	NHSL1_ENST00000343505.5_Silent_p.H1381H	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1385										breast(2)|endometrium(4)|kidney(1)	7						GGGAGGGAGAATGGTTTCGGG	0.527													A|||	57	0.0113818	0.0015	0.0504	5008	,	,		15079	0.0		0.0179	False		,,,				2504	0.002				p.H1385H		Atlas-SNP	.											.	NHSL1	99	.	0			c.T4155C						PASS	.	A	,	5,1379		0,5,687	42.0	43.0	43.0		4143,4155	-2.2	1.0	6	dbSNP_132	43	35,3147		2,31,1558	no	coding-synonymous,coding-synonymous	NHSL1	NM_001144060.1,NM_020464.1	,	2,36,2245	GG,GA,AA		1.0999,0.3613,0.876	,	1381/1607,1385/1611	138745896	40,4526	692	1591	2283	SO:0001819	synonymous_variant	57224	exon7			GGGAGAATGGTTT	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4155T>C	6.37:g.138745896A>G		82.0	0.0	0		117.0	55.0	0.470085	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Silent	SNP	ENST00000427025.2	37	CCDS55063.1																																																																																			A|0.989;G|0.011	0.011	strong		0.527	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
AASDHPPT	60496	hgsc.bcm.edu	37	11	105950335	105950335	+	Missense_Mutation	SNP	A	A	G	rs528924003		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:105950335A>G	ENST00000278618.4	+	2	547	c.325A>G	c.(325-327)Atc>Gtc	p.I109V	KBTBD3_ENST00000534815.1_5'Flank|KBTBD3_ENST00000531837.1_5'Flank|KBTBD3_ENST00000526793.1_5'Flank	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	109	Coenzyme A binding.				macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		CAACTTTAACATCTCTCATCA	0.393																																					p.I109V		Atlas-SNP	.											.	AASDHPPT	40	.	0			c.A325G						PASS	.						116.0	115.0	115.0					11																	105950335		2201	4299	6500	SO:0001583	missense	60496	exon2			TTTAACATCTCTC	AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.325A>G	11.37:g.105950335A>G	ENSP00000278618:p.Ile109Val	144.0	0.0	0		138.0	72.0	0.521739	NM_015423	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	A	2.118	-0.402119	0.04865	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.91	3.59	0.41128	4&apos (1);-phosphopantetheinyl transferase (1);	0.472007	0.24312	N	0.039629	T	0.16428	0.0395	N	0.01817	-0.705	0.36736	D	0.881978	B	0.02656	0.0	B	0.01281	0.0	T	0.20472	-1.0274	9	0.05620	T	0.96	.	7.3013	0.26422	0.6388:0.0:0.3612:0.0	.	109	Q9NRN7	ADPPT_HUMAN	V	44;44;109	.	ENSP00000278618:I109V	I	+	1	0	AASDHPPT	105455545	0.998000	0.40836	1.000000	0.80357	0.985000	0.73830	1.307000	0.33516	0.485000	0.27652	0.533000	0.62120	ATC	.	.	none		0.393	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423	
RNF135	84282	hgsc.bcm.edu	37	17	29326155	29326155	+	Missense_Mutation	SNP	G	G	T	rs61749868	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:29326155G>T	ENST00000328381.5	+	5	2118	c.1245G>T	c.(1243-1245)tgG>tgT	p.W415C	RNF135_ENST00000535306.2_3'UTR|RNF135_ENST00000443677.2_3'UTR|RNF135_ENST00000324689.4_3'UTR	NM_032322.3	NP_115698.3	Q8IUD6	RN135_HUMAN	ring finger protein 135	415	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		W -> C (in dbSNP:rs61749868). {ECO:0000269|PubMed:19291764}.		innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-beta production (GO:0032728)|protein ubiquitination (GO:0016567)|regulation of innate immune response (GO:0045088)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ligase activity (GO:0016874)|ribonucleoprotein complex binding (GO:0043021)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.?(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	10		all_cancers(10;8.65e-08)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Myeloproliferative disorder(56;0.0255)				CTGCCTTCTGGCTGTATGGCT	0.458													G|||	12	0.00239617	0.0015	0.0	5008	,	,		21128	0.0		0.0099	False		,,,				2504	0.0				p.W415C		Atlas-SNP	.											.	RNF135	19	.	1	Unknown(1)	central_nervous_system(1)	c.G1245T						PASS	.	G	,CYS/TRP,	10,4396	16.8+/-37.8	0,10,2193	104.0	106.0	105.0		,1245,	5.2	1.0	17	dbSNP_129	105	86,8514	49.4+/-109.1	0,86,4214	yes	utr-3,missense,utr-3	RNF135	NM_001184992.1,NM_032322.3,NM_197939.1	,215,	0,96,6407	TT,TG,GG		1.0,0.227,0.7381	,probably-damaging,	,415/433,	29326155	96,12910	2203	4300	6503	SO:0001583	missense	84282	exon5			CTTCTGGCTGTAT	AJ496729	CCDS11262.1, CCDS11263.1, CCDS54104.1	17q11.2	2013-01-09			ENSG00000181481	ENSG00000181481		"""RING-type (C3HC4) zinc fingers"""	21158	protein-coding gene	gene with protein product	"""riplet"""	611358				11468690, 19017631	Standard	NM_001184992		Approved	MGC13061	uc002hfz.3	Q8IUD6	OTTHUMG00000132867	ENST00000328381.5:c.1245G>T	17.37:g.29326155G>T	ENSP00000328340:p.Trp415Cys	78.0	0.0	0		102.0	40.0	0.392157	NM_032322	A0AVM5|B2R7G9|B6ZLM5|F5GX60|Q9BSE9	Missense_Mutation	SNP	ENST00000328381.5	37	CCDS11262.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	15.55	2.867158	0.51588	0.00227	0.01	ENSG00000181481	ENST00000328381;ENST00000535605	T	0.69926	-0.44	5.21	5.21	0.72293	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.176168	0.28072	N	0.016704	T	0.72244	0.3436	L	0.56280	1.765	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.73852	-0.3852	10	0.38643	T	0.18	-10.0145	16.6225	0.84934	0.0:0.0:1.0:0.0	rs61749868	415	Q8IUD6	RN135_HUMAN	C	415;234	ENSP00000328340:W415C	ENSP00000328340:W415C	W	+	3	0	RNF135	26350281	1.000000	0.71417	0.995000	0.50966	0.297000	0.27493	6.437000	0.73421	2.613000	0.88420	0.655000	0.94253	TGG	G|0.995;T|0.005	0.005	strong		0.458	RNF135-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256342.3	NM_032322	
ZFHX4	79776	hgsc.bcm.edu	37	8	77763355	77763355	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:77763355A>C	ENST00000521891.2	+	10	4646	c.4198A>C	c.(4198-4200)Aac>Cac	p.N1400H	ZFHX4_ENST00000050961.6_Missense_Mutation_p.N1355H|ZFHX4_ENST00000518282.1_Missense_Mutation_p.N1374H|ZFHX4_ENST00000455469.2_Missense_Mutation_p.N1355H	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	1355					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.N1400D(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			GTATCGCTGTAACCATTGTAG	0.453										HNSCC(33;0.089)																											p.N1400H		Atlas-SNP	.											ZFHX4,NS,carcinoma,0,1	ZFHX4	878	1	1	Substitution - Missense(1)	lung(1)	c.A4198C						PASS	.						87.0	82.0	83.0					8																	77763355		1894	4118	6012	SO:0001583	missense	79776	exon10			CGCTGTAACCATT		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.4198A>C	8.37:g.77763355A>C	ENSP00000430497:p.Asn1400His	166.0	0.0	0		238.0	108.0	0.453782	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	13.28	2.190004	0.38707	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	4.65	4.65	0.58169	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.000000	0.48286	U	0.000184	T	0.48077	0.1480	M	0.73962	2.25	0.40800	D	0.98333	P;P;P	0.50528	0.894;0.936;0.936	P;P;P	0.53809	0.548;0.735;0.735	T	0.56414	-0.7983	10	0.72032	D	0.01	.	14.5713	0.68213	1.0:0.0:0.0:0.0	.	1355;1355;1400	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	H	1400;1400;1355;1355;1374	ENSP00000430497:N1400H;ENSP00000399605:N1355H;ENSP00000050961:N1355H;ENSP00000430848:N1374H	ENSP00000050961:N1355H	N	+	1	0	ZFHX4	77925910	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	7.066000	0.76734	2.096000	0.63516	0.454000	0.30748	AAC	.	.	none		0.453	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
CDH19	28513	hgsc.bcm.edu	37	18	64176386	64176386	+	Silent	SNP	C	C	T	rs150353589	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:64176386C>T	ENST00000262150.2	-	11	1966	c.1674G>A	c.(1672-1674)ccG>ccA	p.P558P	CDH19_ENST00000540086.1_Intron	NM_021153.3	NP_066976.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	1833	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				TTGTAAGTGACGGGATTCCAT	0.448													c|||	21	0.00419329	0.0008	0.0086	5008	,	,		16460	0.0		0.0139	False		,,,				2504	0.0				p.P558P		Atlas-SNP	.											CDH19,mucosal,malignant_melanoma,-2,2	CDH19	141	2	0			c.G1674A						PASS	.	T		6,4400	11.4+/-27.6	0,6,2197	199.0	172.0	181.0		1674	1.3	0.1	18	dbSNP_134	181	58,8542	36.4+/-91.3	0,58,4242	no	coding-synonymous	CDH19	NM_021153.2		0,64,6439	TT,TC,CC		0.6744,0.1362,0.4921		558/773	64176386	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	28513	exon11			AAGTGACGGGATT	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000262150.2:c.1674G>A	18.37:g.64176386C>T		210.0	0.0	0		221.0	125.0	0.565611	NM_021153	O15098	Silent	SNP	ENST00000262150.2	37	CCDS11994.1																																																																																			A|0.000;C|0.996;T|0.004	0.004	strong		0.448	CDH19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256219.1	NM_021153	
PBRM1	55193	hgsc.bcm.edu	37	3	52676038	52676038	+	Missense_Mutation	SNP	C	C	G	rs200106731		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52676038C>G	ENST00000296302.7	-	10	1020	c.1019G>C	c.(1018-1020)gGt>gCt	p.G340A	PBRM1_ENST00000356770.4_Missense_Mutation_p.G308A|PBRM1_ENST00000409057.1_Missense_Mutation_p.G340A|PBRM1_ENST00000337303.4_Missense_Mutation_p.G340A|PBRM1_ENST00000409767.1_Missense_Mutation_p.G340A|PBRM1_ENST00000410007.1_Missense_Mutation_p.G340A|PBRM1_ENST00000394830.3_Missense_Mutation_p.G340A|PBRM1_ENST00000409114.3_Missense_Mutation_p.G340A			Q86U86	PB1_HUMAN	polybromo 1	340			G -> A (found in a malignant melanoma cell line). {ECO:0000269|PubMed:21248752}.		chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TGATAAACGACCTCCTTGTAC	0.363			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																p.G340A		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.G1019C						PASS	.	C	ALA/GLY,ALA/GLY,ALA/GLY	0,4406		0,0,2203	260.0	245.0	250.0		923,1019,1019	4.8	1.0	3		250	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	60,60,60	0,3,6500	GG,GC,CC		0.0349,0.0,0.0231	benign,benign,benign	308/1603,340/1583,340/1583	52676038	3,13003	2203	4300	6503	SO:0001583	missense	55193	exon11			AAACGACCTCCTT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1019G>C	3.37:g.52676038C>G	ENSP00000296302:p.Gly340Ala	97.0	0.0	0		102.0	54.0	0.529412	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Missense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	C	15.82	2.945034	0.53079	0.0	3.49E-4	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103	T;T;T;T;T;T;T;T;T;T	0.33216	1.45;1.43;1.46;1.42;1.43;1.42;1.89;1.42;1.43;1.44	5.71	4.83	0.62350	Bromodomain (1);	0.049850	0.85682	D	0.000000	T	0.13543	0.0328	N	0.08118	0	0.46113	D	0.998875	B;B;B;B;B;B;B;B;B	0.23377	0.03;0.03;0.058;0.066;0.017;0.082;0.084;0.066;0.066	B;B;B;B;B;B;B;B;B	0.29267	0.019;0.02;0.031;0.046;0.024;0.1;0.034;0.046;0.046	T	0.20806	-1.0264	10	0.11794	T	0.64	-18.8331	5.4588	0.16606	0.0:0.7329:0.0:0.2671	.	340;340;340;340;340;340;340;308;340	Q86U86-9;Q86U86-6;Q86U86-4;Q86U86-2;Q86U86-8;Q86U86-7;Q86U86;Q86U86-3;Q86U86-5	.;.;.;.;.;.;PB1_HUMAN;.;.	A	308;340;340;340;340;340;340;340;340;284	ENSP00000349213:G308A;ENSP00000378307:G340A;ENSP00000296302:G340A;ENSP00000338302:G340A;ENSP00000386593:G340A;ENSP00000386529:G340A;ENSP00000386643:G340A;ENSP00000386601:G340A;ENSP00000387775:G340A;ENSP00000397662:G284A	ENSP00000296302:G340A	G	-	2	0	PBRM1	52651078	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.354000	0.66040	2.700000	0.92200	0.650000	0.86243	GGT	C|0.999;G|0.001	0.001	weak		0.363	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
CFAP46	54777	hgsc.bcm.edu	37	10	134698678	134698678	+	Missense_Mutation	SNP	G	G	A	rs185087227		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:134698678G>A	ENST00000368586.5	-	27	3656	c.3556C>T	c.(3556-3558)Cgc>Tgc	p.R1186C	TTC40_ENST00000368582.2_Missense_Mutation_p.R1186C	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						AGGGCCAGGCGGTGCCACATG	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		15096	0.0		0.001	False		,,,				2504	0.0				p.R1186C		Atlas-SNP	.											.	TTC40	100	.	0			c.C3556T						PASS	.																																			SO:0001583	missense	54777	exon27			CCAGGCGGTGCCA																												ENST00000368586.5:c.3556C>T	10.37:g.134698678G>A	ENSP00000357575:p.Arg1186Cys	72.0	0.0	0		77.0	35.0	0.454545	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	15.93	2.977814	0.53720	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.50001	2.74;0.76	4.16	3.2	0.36748	.	.	.	.	.	T	0.55481	0.1923	.	.	.	0.32430	N	0.548168	.	.	.	.	.	.	T	0.67313	-0.5702	6	0.87932	D	0	.	12.0765	0.53647	0.0:0.0:0.8275:0.1725	.	.	.	.	C	1186	ENSP00000357575:R1186C;ENSP00000357571:R1186C	ENSP00000357571:R1186C	R	-	1	0	C10orf93	134548668	1.000000	0.71417	0.998000	0.56505	0.460000	0.32559	4.225000	0.58600	1.843000	0.53566	0.460000	0.39030	CGC	G|1.000;A|0.000	0.000	strong		0.582	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
CCPG1	9236	hgsc.bcm.edu	37	15	55652969	55652969	+	Missense_Mutation	SNP	C	C	G	rs200417770		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55652969C>G	ENST00000310958.6	-	8	1300	c.1002G>C	c.(1000-1002)caG>caC	p.Q334H	CCPG1_ENST00000569205.1_Missense_Mutation_p.Q334H|CCPG1_ENST00000425574.3_Intron|CCPG1_ENST00000442196.3_Missense_Mutation_p.Q334H|DYX1C1-CCPG1_ENST00000565113.1_RNA	NM_001204450.1|NM_001204451.1|NM_004748.4|NM_020739.3	NP_001191379.1|NP_001191380.1|NP_004739.3|NP_065790.2	Q9ULG6	CCPG1_HUMAN	cell cycle progression 1	334					cell cycle (GO:0007049)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of Rho guanyl-nucleotide exchange factor activity (GO:2001106)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|stomach(3)	30				all cancers(107;0.0354)		ATATTCTAATCTGTTCTCTTA	0.343																																					p.Q334H		Atlas-SNP	.											CCPG1,NS,carcinoma,0,1	CCPG1	74	1	0			c.G1002C						scavenged	.						124.0	115.0	118.0					15																	55652969		1815	4071	5886	SO:0001583	missense	9236	exon8			TCTAATCTGTTCT	AF212228	CCDS42039.1, CCDS55966.1, CCDS55967.1	15q21.1	2011-04-20				ENSG00000260916			24227	protein-coding gene	gene with protein product		611326				9383053, 10574462	Standard	NM_004748		Approved	KIAA1254, CPR8	uc010bfk.2	Q9ULG6		ENST00000310958.6:c.1002G>C	15.37:g.55652969C>G	ENSP00000311656:p.Gln334His	179.0	1.0	0.00558659		161.0	57.0	0.354037	NM_020739	A0PJH3|A8K9T0|O14712|Q05DG4|Q5U5S7|Q8IYV8|Q9BY53|Q9HA17	Missense_Mutation	SNP	ENST00000310958.6	37	CCDS42039.1	.	.	.	.	.	.	.	.	.	.	C	15.32	2.799689	0.50208	.	.	ENSG00000256061	ENST00000310958;ENST00000442196	T;T	0.36157	1.27;1.27	5.72	2.86	0.33363	.	0.153716	0.64402	D	0.000014	T	0.53546	0.1803	M	0.66939	2.045	0.47214	D	0.999356	D;D;D;D	0.76494	0.999;0.999;0.999;0.999	D;D;D;D	0.75484	0.986;0.976;0.986;0.979	T	0.52109	-0.8619	10	0.72032	D	0.01	.	9.2561	0.37584	0.0:0.6926:0.0:0.3074	.	334;334;334;190	A8K9T0;Q9ULG6-4;Q9ULG6;Q9ULG6-2	.;.;CCPG1_HUMAN;.	H	334	ENSP00000311656:Q334H;ENSP00000403400:Q334H	ENSP00000311656:Q334H	Q	-	3	2	DYX1C1	53440261	1.000000	0.71417	0.997000	0.53966	0.943000	0.58893	0.759000	0.26461	0.450000	0.26774	-0.145000	0.13849	CAG	C|0.999;G|0.001	0.001	weak		0.343	CCPG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419850.1	NM_004748	
SH2D4B	387694	hgsc.bcm.edu	37	10	82348395	82348395	+	Missense_Mutation	SNP	G	G	A	rs140909202		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82348395G>A	ENST00000470604.2	+	4	502	c.502G>A	c.(502-504)Gaa>Aaa	p.E168K	SH2D4B_ENST00000339284.2_Missense_Mutation_p.E169K|SH2D4B_ENST00000313455.4_Missense_Mutation_p.E120K			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	168	Glu-rich.									endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			GAGGAAAGAGGAAGAGGAGAG	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		20999	0.0		0.001	False		,,,				2504	0.0				p.E169K		Atlas-SNP	.											.	SH2D4B	44	.	0			c.G505A						PASS	.	G	LYS/GLU,LYS/GLU	3,4403	6.2+/-15.9	0,3,2200	78.0	73.0	75.0		358,505	4.2	1.0	10	dbSNP_134	75	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	SH2D4B	NM_001145719.1,NM_207372.2	56,56	0,7,6496	AA,AG,GG		0.0465,0.0681,0.0538	probably-damaging,probably-damaging	120/310,169/358	82348395	7,12999	2203	4300	6503	SO:0001583	missense	387694	exon4			AAAGAGGAAGAGG		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.502G>A	10.37:g.82348395G>A	ENSP00000417953:p.Glu168Lys	21.0	0.0	0		32.0	12.0	0.375	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Missense_Mutation	SNP	ENST00000470604.2	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.52	3.409626	0.62399	6.81E-4	4.65E-4	ENSG00000178217	ENST00000339284;ENST00000372147;ENST00000470604;ENST00000313455	T;T;T	0.13657	2.57;2.57;2.57	5.16	4.24	0.50183	.	0.062098	0.64402	D	0.000007	T	0.32194	0.0821	L	0.58669	1.825	0.45930	D	0.998765	D;D	0.89917	0.998;1.0	D;D	0.85130	0.919;0.997	T	0.01829	-1.1265	10	0.45353	T	0.12	-11.6747	13.3192	0.60424	0.0:0.1602:0.8398:0.0	.	120;169	Q5SQS7-3;Q5SQS7-2	.;.	K	169;168;168;120	ENSP00000345295:E169K;ENSP00000417953:E168K;ENSP00000314242:E120K	ENSP00000314242:E120K	E	+	1	0	SH2D4B	82338375	1.000000	0.71417	1.000000	0.80357	0.868000	0.49771	4.750000	0.62162	1.143000	0.42306	0.655000	0.94253	GAA	G|0.999;A|0.001	0.001	strong		0.507	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
AMY2B	280	hgsc.bcm.edu	37	1	104117892	104117892	+	Missense_Mutation	SNP	T	T	C	rs140209167	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:104117892T>C	ENST00000361355.4	+	8	1542	c.926T>C	c.(925-927)gTc>gCc	p.V309A	AMY2B_ENST00000491397.1_3'UTR	NM_020978.3	NP_066188.1	P19961	AMY2B_HUMAN	amylase, alpha 2B (pancreatic)	309					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)			breast(1)|endometrium(7)|kidney(4)|large_intestine(1)|lung(30)|prostate(1)|skin(1)|urinary_tract(1)	46		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0669)|all cancers(265;0.083)|Epithelial(280;0.094)|Lung(183;0.112)		AGAGCACTTGTCTTTGTGGAT	0.408													.|||	6	0.00119808	0.0	0.0014	5008	,	,		14681	0.0		0.005	False		,,,				2504	0.0				p.V309A		Atlas-SNP	.											.	AMY2B	80	.	0			c.T926C						PASS	.	T	ALA/VAL	2,4404	4.2+/-10.8	0,2,2201	275.0	274.0	275.0		926	4.1	1.0	1	dbSNP_134	275	30,8566	21.0+/-64.5	0,30,4268	no	missense	AMY2B	NM_020978.3	64	0,32,6469	CC,CT,TT		0.349,0.0454,0.2461	probably-damaging	309/512	104117892	32,12970	2203	4298	6501	SO:0001583	missense	280	exon8			CACTTGTCTTTGT	M24895	CCDS782.1	1p21	2010-08-02	2006-04-27		ENSG00000240038	ENSG00000240038	3.2.1.1		478	protein-coding gene	gene with protein product		104660	"""amylase, alpha 2B; pancreatic"""	AMY2		8268204	Standard	NM_020978		Approved		uc001duq.3	P19961	OTTHUMG00000011024	ENST00000361355.4:c.926T>C	1.37:g.104117892T>C	ENSP00000354610:p.Val309Ala	192.0	0.0	0		261.0	137.0	0.524904	NM_020978	B3KTI1|B3KXB7|D3DT76|Q9UBH3	Missense_Mutation	SNP	ENST00000361355.4	37	CCDS782.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	22.1	4.248687	0.80024	4.54E-4	0.00349	ENSG00000240038	ENST00000361355	D	0.98400	-4.91	5.26	4.12	0.48240	Glycoside hydrolase, subgroup, catalytic domain (1);Glycosyl hydrolase, family 13, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.98372	0.9459	M	0.82323	2.585	0.80722	D	1	P	0.40681	0.727	P	0.57204	0.815	D	0.99818	1.1045	10	0.66056	D	0.02	.	11.3322	0.49484	0.0:0.0734:0.0:0.9266	.	309	P19961	AMY2B_HUMAN	A	309	ENSP00000354610:V309A	ENSP00000354610:V309A	V	+	2	0	AMY2B	103919415	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.096000	0.64535	1.992000	0.58205	0.456000	0.33151	GTC	T|0.998;C|0.002	0.002	strong		0.408	AMY2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030318.1	NM_020978	
NAT1	9	hgsc.bcm.edu	37	8	18080128	18080128	+	Missense_Mutation	SNP	C	C	T	rs141552883		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:18080128C>T	ENST00000517492.1	+	3	1210	c.572C>T	c.(571-573)tCc>tTc	p.S191F	NAT1_ENST00000541942.1_Missense_Mutation_p.S191F|NAT1_ENST00000517441.1_3'UTR|NAT1_ENST00000518029.1_Missense_Mutation_p.S191F|NAT1_ENST00000307719.4_Missense_Mutation_p.S191F|NAT1_ENST00000545197.1_Missense_Mutation_p.S253F|NAT1_ENST00000535084.1_Missense_Mutation_p.S191F|NAT1_ENST00000520546.1_Missense_Mutation_p.S191F|NAT1_ENST00000539092.1_Missense_Mutation_p.S191F			Q8IZM9	S38A6_HUMAN	N-acetyltransferase 1 (arylamine N-acetyltransferase)	0					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				NS(1)|breast(1)|endometrium(3)|kidney(1)|lung(2)|urinary_tract(1)	9				Colorectal(111;0.0519)|COAD - Colon adenocarcinoma(73;0.208)		AAAATCTACTCCTTTACTCTT	0.358													C|||	1	0.000199681	0.0	0.0	5008	,	,		19441	0.0		0.001	False		,,,				2504	0.0				p.S253F		Atlas-SNP	.											.	NAT1	38	.	0			c.C758T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER,PHE/SER	0,4406		0,0,2203	112.0	115.0	114.0		572,572,572,572,572,572,758,758,572	3.1	0.5	8	dbSNP_134	114	1,8599		0,1,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense	NAT1	NM_000662.5,NM_001160170.1,NM_001160171.1,NM_001160172.1,NM_001160173.1,NM_001160174.1,NM_001160175.1,NM_001160176.1,NM_001160179.1	155,155,155,155,155,155,155,155,155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	191/291,191/291,191/291,191/291,191/291,191/291,253/353,253/353,191/291	18080128	1,13005	2203	4300	6503	SO:0001583	missense	9	exon4			TCTACTCCTTTAC	BC047666	CCDS6007.1, CCDS55205.1	8p22	2012-01-18			ENSG00000171428	ENSG00000171428	2.3.1.5		7645	protein-coding gene	gene with protein product		108345		AAC1		7773298	Standard	NM_001160174		Approved		uc003wyt.3	P18440	OTTHUMG00000097001	ENST00000517492.1:c.572C>T	8.37:g.18080128C>T	ENSP00000429407:p.Ser191Phe	116.0	0.0	0		138.0	62.0	0.449275	NM_001160176	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000517492.1	37	CCDS6007.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	7.210	0.595309	0.13875	0.0	1.16E-4	ENSG00000171428	ENST00000535084;ENST00000307719;ENST00000545197;ENST00000539092;ENST00000541942;ENST00000518029;ENST00000517492;ENST00000520546	T;T;T;T;T;T;T;T	0.02177	4.41;4.41;4.41;4.41;4.41;4.41;4.41;4.41	4.05	3.13	0.36017	.	0.492839	0.21479	N	0.073870	T	0.07279	0.0184	M	0.90252	3.1	0.32873	D	0.50949	P;P	0.47409	0.895;0.851	P;P	0.52909	0.713;0.658	T	0.12811	-1.0533	10	0.10111	T	0.7	.	5.0238	0.14374	0.2107:0.6782:0.0:0.1111	.	253;191	F5H5R8;P18440	.;ARY1_HUMAN	F	191;191;253;191;191;191;191;191	ENSP00000444609:S191F;ENSP00000307218:S191F;ENSP00000443194:S253F;ENSP00000440434:S191F;ENSP00000440900:S191F;ENSP00000428270:S191F;ENSP00000429407:S191F;ENSP00000429341:S191F	ENSP00000307218:S191F	S	+	2	0	NAT1	18124408	0.952000	0.32445	0.453000	0.27007	0.784000	0.44337	0.616000	0.24344	0.767000	0.33267	0.460000	0.39030	TCC	C|1.000;T|0.000	0.000	strong		0.358	NAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374828.1	NM_000662	
PLCG2	5336	hgsc.bcm.edu	37	16	81990441	81990441	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81990441A>T	ENST00000359376.3	+	32	3926	c.3712A>T	c.(3712-3714)Aat>Tat	p.N1238Y		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	1238					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						GTTCAGTGTTAATGAGAACCA	0.512																																					p.N1238Y		Atlas-SNP	.											.	PLCG2	276	.	0			c.A3712T						PASS	.						99.0	100.0	100.0					16																	81990441		1953	4145	6098	SO:0001583	missense	5336	exon32			AGTGTTAATGAGA		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.3712A>T	16.37:g.81990441A>T	ENSP00000352336:p.Asn1238Tyr	52.0	0.0	0		84.0	34.0	0.404762	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	.	.	.	.	.	.	.	.	.	.	A	18.00	3.525302	0.64747	.	.	ENSG00000197943	ENST00000359376	T	0.67171	-0.25	5.49	5.49	0.81192	.	0.250471	0.46758	D	0.000266	T	0.71082	0.3298	L	0.36672	1.1	0.52099	D	0.999942	D	0.67145	0.996	P	0.59703	0.862	T	0.74414	-0.3673	10	0.72032	D	0.01	.	13.83	0.63375	1.0:0.0:0.0:0.0	.	1238	P16885	PLCG2_HUMAN	Y	1238	ENSP00000352336:N1238Y	ENSP00000352336:N1238Y	N	+	1	0	PLCG2	80547942	1.000000	0.71417	0.990000	0.47175	0.448000	0.32197	6.593000	0.74100	2.078000	0.62432	0.413000	0.27773	AAT	.	.	none		0.512	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
WNT8B	7479	hgsc.bcm.edu	37	10	102241724	102241724	+	Silent	SNP	G	G	A	rs76078607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:102241724G>A	ENST00000343737.5	+	5	551	c.423G>A	c.(421-423)gcG>gcA	p.A141A		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	141					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		TCGGAGAGGCGATTTCCAAGC	0.607											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	9	0.00179712	0.0	0.0	5008	,	,		17905	0.0		0.008	False		,,,				2504	0.001				p.A141A		Atlas-SNP	.											.	WNT8B	31	.	0			c.G423A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	122.0	105.0	111.0		423	-10.4	0.9	10	dbSNP_132	111	32,8568	22.2+/-67.0	0,32,4268	no	coding-synonymous	WNT8B	NM_003393.3		0,37,6466	AA,AG,GG		0.3721,0.1135,0.2845		141/352	102241724	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	7479	exon5			AGAGGCGATTTCC	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"""Wingless-type MMTV integration sites"""	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.423G>A	10.37:g.102241724G>A		92.0	0.0	0	1365	68.0	7.0	0.102941	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	37	CCDS7494.1																																																																																			G|0.998;A|0.002	0.002	strong		0.607	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393	
RPGRIP1L	23322	hgsc.bcm.edu	37	16	53639448	53639448	+	Silent	SNP	G	G	A	rs144924117		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:53639448G>A	ENST00000379925.3	-	26	3830	c.3780C>T	c.(3778-3780)gtC>gtT	p.V1260V	RPGRIP1L_ENST00000563746.1_Silent_p.V1226V|RPGRIP1L_ENST00000262135.4_Silent_p.V1180V|RPGRIP1L_ENST00000564374.1_Silent_p.V1214V	NM_015272.2	NP_056087.2	Q68CZ1	FTM_HUMAN	RPGRIP1-like	1260					camera-type eye development (GO:0043010)|cerebellum development (GO:0021549)|cilium assembly (GO:0042384)|corpus callosum development (GO:0022038)|determination of left/right symmetry (GO:0007368)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|establishment or maintenance of cell polarity (GO:0007163)|head development (GO:0060322)|in utero embryonic development (GO:0001701)|kidney development (GO:0001822)|lateral ventricle development (GO:0021670)|liver development (GO:0001889)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|neural tube patterning (GO:0021532)|nose development (GO:0043584)|olfactory bulb development (GO:0021772)|pericardium development (GO:0060039)|regulation of smoothened signaling pathway (GO:0008589)	axoneme (GO:0005930)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|tight junction (GO:0005923)	thromboxane A2 receptor binding (GO:0031870)			endometrium(6)|kidney(3)|large_intestine(9)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(2)	46		all_cancers(37;0.0973)				CGGCAAGGTCGACGTGAGCCA	0.532													G|||	1	0.000199681	0.0	0.0	5008	,	,		18112	0.0		0.001	False		,,,				2504	0.0				p.V1260V		Atlas-SNP	.											.	RPGRIP1L	118	.	0			c.C3780T						PASS	.	G	,	2,4394	4.2+/-10.8	0,2,2196	181.0	134.0	150.0		3540,3780	-7.5	0.0	16	dbSNP_134	150	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	RPGRIP1L	NM_001127897.1,NM_015272.2	,	0,9,6489	AA,AG,GG		0.0814,0.0455,0.0693	,	1180/1236,1260/1316	53639448	9,12987	2198	4300	6498	SO:0001819	synonymous_variant	23322	exon26			AAGGTCGACGTGA		CCDS32447.1, CCDS45486.1	16q12.2	2014-09-17				ENSG00000103494			29168	protein-coding gene	gene with protein product	"""fantom homolog"", ""Meckel syndrome, type 5"", ""protein phosphatase 1, regulatory subunit 134"""	610937				10231032	Standard	NM_015272		Approved	KIAA1005, CORS3, JBTS7, MKS5, NPHP8, FTM, PPP1R134	uc002ehp.3	Q68CZ1		ENST00000379925.3:c.3780C>T	16.37:g.53639448G>A		86.0	0.0	0		105.0	65.0	0.619048	NM_015272	A0PJ88|Q9Y2K8	Silent	SNP	ENST00000379925.3	37	CCDS32447.1																																																																																			G|1.000;A|0.000	0.000	strong		0.532	RPGRIP1L-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422187.1	NM_015272	
ZNF667	63934	hgsc.bcm.edu	37	19	56952615	56952615	+	Silent	SNP	A	A	G	rs61740673	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:56952615A>G	ENST00000504904.3	-	7	2468	c.1749T>C	c.(1747-1749)taT>taC	p.Y583Y	ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000292069.6_Silent_p.Y583Y|ZNF667_ENST00000342634.3_Silent_p.Y711Y			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		TACTACATTCATAGGGTTTCT	0.398													A|||	158	0.0315495	0.0961	0.0159	5008	,	,		20645	0.0		0.0159	False		,,,				2504	0.0041				p.Y583Y		Atlas-SNP	.											ZNF667,NS,NS,-2,1	ZNF667	95	1	0			c.T1749C						PASS	.	A		393,4013	197.7+/-221.8	16,361,1826	120.0	115.0	117.0		1749	-0.7	0.4	19	dbSNP_129	117	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	ZNF667	NM_022103.3		16,457,6030	GG,GA,AA		1.1163,8.9197,3.7598		583/611	56952615	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			ACATTCATAGGGT		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1749T>C	19.37:g.56952615A>G		87.0	0.0	0		81.0	44.0	0.54321	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			A|0.965;G|0.035	0.035	strong		0.398	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
BRPF3	27154	hgsc.bcm.edu	37	6	36185759	36185759	+	Missense_Mutation	SNP	A	A	G	rs145016452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:36185759A>G	ENST00000357641.6	+	9	3308	c.3055A>G	c.(3055-3057)Agt>Ggt	p.S1019G	BRPF3_ENST00000543502.1_Missense_Mutation_p.S749G|BRPF3_ENST00000534694.1_Intron|BRPF3_ENST00000339717.7_Missense_Mutation_p.S749G|BRPF3_ENST00000443324.2_Intron|BRPF3_ENST00000534400.1_Missense_Mutation_p.S1019G	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	1019					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						TTTGGGTCTCAGTGGTGGACT	0.498													A|||	4	0.000798722	0.0008	0.0029	5008	,	,		21651	0.0		0.001	False		,,,				2504	0.0				p.S1019G		Atlas-SNP	.											.	BRPF3	93	.	0			c.A3055G						PASS	.	A	GLY/SER	3,4403	6.2+/-15.9	0,3,2200	183.0	146.0	159.0		3055	3.4	1.0	6	dbSNP_134	159	27,8573	19.2+/-60.6	0,27,4273	yes	missense	BRPF3	NM_015695.2	56	0,30,6473	GG,GA,AA		0.314,0.0681,0.2307	benign	1019/1206	36185759	30,12976	2203	4300	6503	SO:0001583	missense	27154	exon9			GGTCTCAGTGGTG	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.3055A>G	6.37:g.36185759A>G	ENSP00000350267:p.Ser1019Gly	174.0	0.0	0		243.0	99.0	0.407407	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Missense_Mutation	SNP	ENST00000357641.6	37	CCDS34437.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	14.27	2.484908	0.44147	6.81E-4	0.00314	ENSG00000096070	ENST00000357641;ENST00000339717;ENST00000543502;ENST00000534400	T;T;T;T	0.19394	2.27;2.28;2.28;2.15	6.05	3.37	0.38596	.	0.607803	0.19087	N	0.123094	T	0.05135	0.0137	N	0.24115	0.695	0.80722	D	1	B;B	0.17465	0.022;0.0	B;B	0.18263	0.021;0.0	T	0.17501	-1.0367	10	0.25751	T	0.34	.	8.2232	0.31554	0.7652:0.0:0.2348:0.0	.	749;1019	Q17RB6;Q9ULD4	.;BRPF3_HUMAN	G	1019;749;749;1019	ENSP00000350267:S1019G;ENSP00000345419:S749G;ENSP00000445352:S749G;ENSP00000436504:S1019G	ENSP00000345419:S749G	S	+	1	0	BRPF3	36293737	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.870000	0.39529	1.116000	0.41820	0.528000	0.53228	AGT	A|0.997;G|0.003	0.003	strong		0.498	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695	
KIAA0586	9786	hgsc.bcm.edu	37	14	58943847	58943847	+	Silent	SNP	G	G	A	rs373201020		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:58943847G>A	ENST00000556134.1	+	21	3061	c.2787G>A	c.(2785-2787)gaG>gaA	p.E929E	KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000354386.6_Silent_p.E997E|KIAA0586_ENST00000423743.3_Silent_p.E900E|KIAA0586_ENST00000261244.5_Silent_p.E868E	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	929					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCAGGGTAGAGCAAGAAATAA	0.388																																					p.E997E		Atlas-SNP	.											.	KIAA0586	180	.	0			c.G2991A						PASS	.	G		0,3666		0,0,1833	84.0	73.0	76.0		2604	-0.5	1.0	14		76	1,8181		0,1,4090	no	coding-synonymous	KIAA0586	NM_014749.3		0,1,5923	AA,AG,GG		0.0122,0.0,0.0084		868/1473	58943847	1,11847	1833	4091	5924	SO:0001819	synonymous_variant	9786	exon22			GGTAGAGCAAGAA	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.2787G>A	14.37:g.58943847G>A		72.0	0.0	0		88.0	39.0	0.443182	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Silent	SNP	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	weak		0.388	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
LYPD3	27076	hgsc.bcm.edu	37	19	43965594	43965594	+	Missense_Mutation	SNP	C	C	T	rs149095976	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:43965594C>T	ENST00000244333.3	-	5	1038	c.950G>A	c.(949-951)gGg>gAg	p.G317E		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	317					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CTGCTGGGGCCCCCCTTTTGC	0.622													C|||	4	0.000798722	0.0	0.0014	5008	,	,		16242	0.0		0.003	False		,,,				2504	0.0				p.G317E		Atlas-SNP	.											.	LYPD3	24	.	0			c.G950A						PASS	.	C	GLU/GLY	2,4404	4.2+/-10.8	0,2,2201	43.0	46.0	45.0		950	0.4	0.0	19	dbSNP_134	45	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LYPD3	NM_014400.2	98	0,13,6490	TT,TC,CC		0.1279,0.0454,0.1	benign	317/347	43965594	13,12993	2203	4300	6503	SO:0001583	missense	27076	exon5			TGGGGCCCCCCTT	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.950G>A	19.37:g.43965594C>T	ENSP00000244333:p.Gly317Glu	91.0	0.0	0		103.0	48.0	0.466019	NM_014400	Q9UJ74	Missense_Mutation	SNP	ENST00000244333.3	37	CCDS12620.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.42	1.345506	0.24426	4.54E-4	0.001279	ENSG00000124466	ENST00000244333;ENST00000377995	T	0.12879	2.64	5.13	0.434	0.16539	.	0.666605	0.13500	N	0.383293	T	0.07098	0.0180	N	0.14661	0.345	0.09310	N	1	B	0.20368	0.044	B	0.18263	0.021	T	0.31336	-0.9947	10	0.72032	D	0.01	.	4.5533	0.12124	0.3053:0.5268:0.0:0.1679	.	317	O95274	LYPD3_HUMAN	E	317;265	ENSP00000244333:G317E	ENSP00000244333:G317E	G	-	2	0	LYPD3	48657434	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.324000	0.07986	0.018000	0.15052	-0.143000	0.13931	GGG	C|0.999;T|0.001	0.001	strong		0.622	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
FXR2	9513	hgsc.bcm.edu	37	17	7497292	7497292	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7497292G>A	ENST00000250113.7	-	11	1385	c.1051C>T	c.(1051-1053)Cga>Tga	p.R351*	FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	351						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		ATGTTCTCTCGGGTGCCAACA	0.502																																					p.R351X		Atlas-SNP	.											FXR2,NS,carcinoma,+2,1	FXR2	44	1	0			c.C1051T						scavenged	.						68.0	67.0	67.0					17																	7497292		1905	4118	6023	SO:0001587	stop_gained	9513	exon11			TCTCTCGGGTGCC	U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1051C>T	17.37:g.7497292G>A	ENSP00000250113:p.Arg351*	55.0	0.0	0		73.0	3.0	0.0410959	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Nonsense_Mutation	SNP	ENST00000250113.7	37	CCDS45604.1	.	.	.	.	.	.	.	.	.	.	G	39	7.571676	0.98365	.	.	ENSG00000129245	ENST00000250113	.	.	.	5.52	4.54	0.55810	.	0.209774	0.41605	D	0.000848	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.21014	T	0.42	-0.0119	11.2846	0.49214	0.0:0.0:0.6676:0.3324	.	.	.	.	X	351	.	ENSP00000250113:R351X	R	-	1	2	FXR2	7438017	1.000000	0.71417	1.000000	0.80357	0.844000	0.47949	3.669000	0.54561	1.555000	0.49500	0.563000	0.77884	CGA	.	.	none		0.502	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
ERICH3	127254	hgsc.bcm.edu	37	1	75078423	75078423	+	Missense_Mutation	SNP	C	C	T	rs150709786	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75078423C>T	ENST00000326665.5	-	9	1289	c.1071G>A	c.(1069-1071)atG>atA	p.M357I	RP4-612J11.1_ENST00000416017.1_RNA|C1orf173_ENST00000420661.2_Missense_Mutation_p.M160I	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		357										NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						TGTTCACCTGCATCCCATTCA	0.423													C|||	7	0.00139776	0.0	0.0014	5008	,	,		18608	0.0		0.001	False		,,,				2504	0.0051				p.M357I		Atlas-SNP	.											C1orf173,NS,lymphoid_neoplasm,-2,1	C1orf173	380	1	0			c.G1071A						PASS	.	C	ILE/MET	2,4404	4.2+/-10.8	0,2,2201	99.0	95.0	97.0		1071	-6.5	0.9	1	dbSNP_134	97	14,8586	9.8+/-36.6	0,14,4286	yes	missense	C1orf173	NM_001002912.4	10	0,16,6487	TT,TC,CC		0.1628,0.0454,0.123	benign	357/1531	75078423	16,12990	2203	4300	6503	SO:0001583	missense	127254	exon9			CACCTGCATCCCA																												ENST00000326665.5:c.1071G>A	1.37:g.75078423C>T	ENSP00000322609:p.Met357Ile	64.0	0.0	0		72.0	38.0	0.527778	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	11.61	1.691085	0.30052	4.54E-4	0.001628	ENSG00000178965	ENST00000326665;ENST00000420661	T;T	0.16073	2.87;2.37	5.63	-6.51	0.01878	.	.	.	.	.	T	0.01287	0.0042	N	0.17474	0.49	0.30304	N	0.789207	B;B	0.16396	0.001;0.017	B;B	0.12837	0.003;0.008	T	0.33854	-0.9852	9	0.02654	T	1	-0.6393	1.2823	0.02043	0.2419:0.2826:0.0937:0.3818	.	160;357	Q5RHP9-3;Q5RHP9	.;CA173_HUMAN	I	357;160	ENSP00000322609:M357I;ENSP00000398581:M160I	ENSP00000322609:M357I	M	-	3	0	C1orf173	74851011	0.009000	0.17119	0.871000	0.34182	0.994000	0.84299	-0.981000	0.03766	-1.229000	0.02564	-0.140000	0.14226	ATG	C|0.999;T|0.001	0.001	strong		0.423	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
JAG1	182	hgsc.bcm.edu	37	20	10625624	10625624	+	Missense_Mutation	SNP	C	C	T	rs147809756	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:10625624C>T	ENST00000254958.5	-	18	2746	c.2231G>A	c.(2230-2232)cGa>cAa	p.R744Q	JAG1_ENST00000423891.2_Missense_Mutation_p.R585Q|JAG1_ENST00000488480.1_RNA	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	744	EGF-like 14. {ECO:0000255|PROSITE- ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						GCTACTGTTTCGGGCTATAAA	0.567									Alagille Syndrome				C|||	5	0.000998403	0.0	0.0029	5008	,	,		16903	0.0		0.002	False		,,,				2504	0.001				p.R744Q		Atlas-SNP	.											JAG1_ENST00000254958,NS,malignant_melanoma,-1,6	JAG1	213	6	0			c.G2231A						scavenged	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	149.0	156.0	154.0		2231	6.1	1.0	20	dbSNP_134	154	9,8591	7.1+/-27.0	0,9,4291	yes	missense	JAG1	NM_000214.2	43	0,10,6493	TT,TC,CC		0.1047,0.0227,0.0769	possibly-damaging	744/1219	10625624	10,12996	2203	4300	6503	SO:0001583	missense	182	exon18	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTGTTTCGGGCTA	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2231G>A	20.37:g.10625624C>T	ENSP00000254958:p.Arg744Gln	77.0	1.0	0.012987		116.0	63.0	0.543103	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Missense_Mutation	SNP	ENST00000254958.5	37	CCDS13112.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	18.43	3.623272	0.66901	2.27E-4	0.001047	ENSG00000101384	ENST00000254958;ENST00000423891	D;D	0.87256	-2.23;-2.23	6.07	6.07	0.98685	Epidermal growth factor-like, type 3 (1);	0.047287	0.85682	D	0.000000	D	0.83294	0.5223	L	0.49778	1.585	0.58432	D	0.999995	P	0.36768	0.569	B	0.26614	0.071	T	0.80915	-0.1169	10	0.29301	T	0.29	.	20.6439	0.99570	0.0:1.0:0.0:0.0	.	744	P78504	JAG1_HUMAN	Q	744;585	ENSP00000254958:R744Q;ENSP00000389519:R585Q	ENSP00000254958:R744Q	R	-	2	0	JAG1	10573624	0.994000	0.37717	0.999000	0.59377	0.872000	0.50106	4.742000	0.62103	2.884000	0.98904	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.567	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
UNC13B	10497	hgsc.bcm.edu	37	9	35398605	35398605	+	Missense_Mutation	SNP	G	G	A	rs41315995	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:35398605G>A	ENST00000378495.3	+	31	3862	c.3640G>A	c.(3640-3642)Gtt>Att	p.V1214I	UNC13B_ENST00000396787.1_Missense_Mutation_p.V1226I|UNC13B_ENST00000481299.1_3'UTR|UNC13B_ENST00000378496.4_Missense_Mutation_p.V1214I	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1214					apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			ACTGAATACGGTTCTGGATGA	0.527													G|||	40	0.00798722	0.0015	0.0101	5008	,	,		21287	0.0		0.0239	False		,,,				2504	0.0072				p.V1214I		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3640A						PASS	.	G	ILE/VAL	19,4387	26.2+/-53.5	0,19,2184	142.0	135.0	138.0		3640	5.7	1.0	9	dbSNP_127	138	151,8449	72.9+/-135.5	2,147,4151	yes	missense	UNC13B	NM_006377.3	29	2,166,6335	AA,AG,GG		1.7558,0.4312,1.3071	possibly-damaging	1214/1592	35398605	170,12836	2203	4300	6503	SO:0001583	missense	10497	exon31			AATACGGTTCTGG	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3640G>A	9.37:g.35398605G>A	ENSP00000367756:p.Val1214Ile	87.0	0.0	0		111.0	51.0	0.459459	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	19	0.0086996336996337	0	0.0	5	0.013812154696132596	0	0.0	14	0.018469656992084433	G	31	5.075214	0.94000	0.004312	0.017558	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.34472	1.36;1.36;1.36	5.7	5.7	0.88788	.	0.000000	0.85682	D	0.000000	T	0.45377	0.1339	M	0.86573	2.825	0.80722	D	1	B;D	0.58268	0.314;0.982	B;P	0.54924	0.068;0.764	T	0.61997	-0.6947	10	0.56958	D	0.05	-16.6564	19.8236	0.96607	0.0:0.0:1.0:0.0	rs41315995	1214;1214	F8W8M9;O14795	.;UN13B_HUMAN	I	1226;1214;1214;801	ENSP00000380006:V1226I;ENSP00000367756:V1214I;ENSP00000367757:V1214I	ENSP00000367756:V1214I	V	+	1	0	UNC13B	35388605	1.000000	0.71417	0.996000	0.52242	0.914000	0.54420	6.586000	0.74067	2.695000	0.91970	0.455000	0.32223	GTT	G|0.987;A|0.013	0.013	strong		0.527	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
DNAH17	8632	hgsc.bcm.edu	37	17	76503585	76503585	+	Silent	SNP	G	G	C	rs12943086	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:76503585G>C	ENST00000585328.1	-	28	4654	c.4530C>G	c.(4528-4530)ctC>ctG	p.L1510L	DNAH17_ENST00000389840.5_Silent_p.L1509L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	1509	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			AGTCCCCCGGGAGCTGGGTGC	0.597													G|||	60	0.0119808	0.0015	0.0317	5008	,	,		19330	0.0		0.0338	False		,,,				2504	0.002				p.L1513L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C4539G						PASS	.	G		19,4133		0,19,2057	45.0	50.0	48.0		4539	-1.1	0.9	17	dbSNP_121	48	286,8196		6,274,3961	no	coding-synonymous	DNAH17	NM_173628.3		6,293,6018	CC,CG,GG		3.3718,0.4576,2.4141		1513/4463	76503585	305,12329	2076	4241	6317	SO:0001819	synonymous_variant	8632	exon28			CCCCGGGAGCTGG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.4530C>G	17.37:g.76503585G>C		140.0	0.0	0		126.0	59.0	0.468254	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.977;C|0.023	0.023	strong		0.597	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
ZNF780B	163131	hgsc.bcm.edu	37	19	40541845	40541845	+	Silent	SNP	A	A	G	rs371876870		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40541845A>G	ENST00000434248.1	-	5	986	c.921T>C	c.(919-921)tgT>tgC	p.C307C	ZNF780B_ENST00000221355.6_Silent_p.C159C	NM_001005851.2	NP_001005851.1	Q9Y6R6	Z780B_HUMAN	zinc finger protein 780B	307					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	23	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CACATTCCCTACATACAAAGG	0.373																																					p.C307C		Atlas-SNP	.											.	ZNF780B	143	.	0			c.T921C						PASS	.	A		0,4406		0,0,2203	116.0	118.0	117.0		921	1.1	0.5	19		117	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF780B	NM_001005851.2		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		307/834	40541845	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	163131	exon5			TTCCCTACATACA	AK127063	CCDS46077.1	19q13.2	2013-01-08	2006-08-15	2006-08-15	ENSG00000128000	ENSG00000128000		"""Zinc fingers, C2H2-type"", ""-"""	33109	protein-coding gene	gene with protein product			"""zinc finger protein 779"""	ZNF779			Standard	NM_001005851		Approved		uc002omu.3	Q9Y6R6	OTTHUMG00000155118	ENST00000434248.1:c.921T>C	19.37:g.40541845A>G		94.0	0.0	0		99.0	38.0	0.383838	NM_001005851	B9EH00	Silent	SNP	ENST00000434248.1	37	CCDS46077.1																																																																																			.	.	weak		0.373	ZNF780B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338466.1	NM_001005851	
MAMLD1	10046	hgsc.bcm.edu	37	X	149639035	149639035	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:149639035C>A	ENST00000370401.2	+	4	1500	c.1190C>A	c.(1189-1191)gCt>gAt	p.A397D	MAMLD1_ENST00000426613.2_Missense_Mutation_p.A372D|MAMLD1_ENST00000432680.2_Missense_Mutation_p.A372D|MAMLD1_ENST00000262858.5_Missense_Mutation_p.A397D|MAMLD1_ENST00000455522.2_5'Flank			Q13495	MAMD1_HUMAN	mastermind-like domain containing 1	397					male gonad development (GO:0008584)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(3)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)	37	Acute lymphoblastic leukemia(192;6.56e-05)					AGCAGCAATGCTGCCCTGGGG	0.597																																					p.A397D		Atlas-SNP	.											.	MAMLD1	263	.	0			c.C1190A						PASS	.						107.0	102.0	104.0					X																	149639035		2203	4300	6503	SO:0001583	missense	10046	exon3			GCAATGCTGCCCT	U46023	CCDS14693.2, CCDS55525.1, CCDS55526.1	Xq28	2008-02-05	2008-01-03	2008-01-03	ENSG00000013619	ENSG00000013619			2568	protein-coding gene	gene with protein product		300120	"""chromosome X open reading frame 6"""	CXorf6		9169146, 17086185, 18162467	Standard	NM_001177465		Approved	CG1, F18	uc011mxu.2	Q13495	OTTHUMG00000024157	ENST00000370401.2:c.1190C>A	X.37:g.149639035C>A	ENSP00000359428:p.Ala397Asp	45.0	0.0	0		124.0	20.0	0.16129	NM_005491	B2RCQ4|B4DG93|B9EGA5	Missense_Mutation	SNP	ENST00000370401.2	37	CCDS14693.2	.	.	.	.	.	.	.	.	.	.	C	7.869	0.727815	0.15507	.	.	ENSG00000013619	ENST00000445612;ENST00000370401;ENST00000432680;ENST00000262858;ENST00000426613	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	5.03	3.2	0.36748	.	0.474459	0.21020	N	0.081532	T	0.76054	0.3934	L	0.47716	1.5	0.21290	N	0.999735	D;D;D;D	0.71674	0.996;0.96;0.998;0.96	P;B;D;P	0.66351	0.899;0.408;0.943;0.59	T	0.66228	-0.5976	9	.	.	.	-2.4414	11.1467	0.48434	0.1443:0.7201:0.1356:0.0	.	359;372;372;397	F6WVG1;Q13495-4;Q13495-3;Q13495	.;.;.;MAMD1_HUMAN	D	359;397;372;397;372	ENSP00000359428:A397D;ENSP00000414517:A372D;ENSP00000262858:A397D;ENSP00000397438:A372D	.	A	+	2	0	MAMLD1	149389693	0.101000	0.21875	0.000000	0.03702	0.046000	0.14306	4.214000	0.58527	0.358000	0.24211	0.529000	0.55759	GCT	.	.	none		0.597	MAMLD1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060844.2	NM_005491	
METTL7B	196410	hgsc.bcm.edu	37	12	56077599	56077599	+	Silent	SNP	A	A	T	rs73117273	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56077599A>T	ENST00000394252.3	+	2	710	c.501A>T	c.(499-501)ggA>ggT	p.G167G		NM_152637.2	NP_689850.2	Q6UX53	MET7B_HUMAN	methyltransferase like 7B	167							methyltransferase activity (GO:0008168)			kidney(1)|large_intestine(1)|lung(4)	6						CCTCCCAGGGAGGTGTGCTCT	0.527													A|||	25	0.00499201	0.0008	0.0043	5008	,	,		18463	0.0		0.0179	False		,,,				2504	0.0031				p.G167G		Atlas-SNP	.											.	METTL7B	35	.	0			c.A501T						PASS	.	A		12,4394	20.2+/-43.8	0,12,2191	129.0	127.0	128.0		501	2.8	1.0	12	dbSNP_130	128	67,8533	41.7+/-99.0	1,65,4234	no	coding-synonymous	METTL7B	NM_152637.2		1,77,6425	TT,TA,AA		0.7791,0.2724,0.6074		167/245	56077599	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	196410	exon2			CCAGGGAGGTGTG		CCDS8887.2	12q13.2	2012-06-12			ENSG00000170439	ENSG00000170439			28276	protein-coding gene	gene with protein product	"""associated with lipid droplets 1"""					17004324	Standard	NM_152637		Approved	MGC17301, ALDI	uc010spr.2	Q6UX53	OTTHUMG00000152665	ENST00000394252.3:c.501A>T	12.37:g.56077599A>T		265.0	0.0	0		250.0	126.0	0.504	NM_152637	A8K247|Q8WUI1	Silent	SNP	ENST00000394252.3	37	CCDS8887.2																																																																																			A|0.993;T|0.007	0.007	strong		0.527	METTL7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327271.1	NM_152637	
MET	4233	hgsc.bcm.edu	37	7	116340262	116340262	+	Missense_Mutation	SNP	A	A	G	rs33917957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116340262A>G	ENST00000318493.6	+	2	1311	c.1124A>G	c.(1123-1125)aAc>aGc	p.N375S	MET_ENST00000436117.2_Missense_Mutation_p.N375S|MET_ENST00000397752.3_Missense_Mutation_p.N375S			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.N375S(2)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GACTTCTTCAACAAGATCGTC	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	165	0.0329473	0.0053	0.0101	5008	,	,		19354	0.0526		0.0209	False		,,,				2504	0.0787				p.N375S		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,3	MET	412	3	2	Substitution - Missense(2)	upper_aerodigestive_tract(1)|kidney(1)	c.A1124G						PASS	.	A	SER/ASN,SER/ASN	26,3828		0,26,1901	101.0	93.0	96.0		1124,1124	4.9	1.0	7	dbSNP_126	96	151,8127		0,151,3988	yes	missense,missense	MET	NM_000245.2,NM_001127500.1	46,46	0,177,5889	GG,GA,AA		1.8241,0.6746,1.459	benign,benign	375/1391,375/1409	116340262	177,11955	1927	4139	6066	SO:0001583	missense	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCTTCAACAAGAT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1124A>G	7.37:g.116340262A>G	ENSP00000317272:p.Asn375Ser	39.0	0.0	0		56.0	33.0	0.589286	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Missense_Mutation	SNP	ENST00000318493.6	37	CCDS47689.1	46	0.021062271062271064	0	0.0	3	0.008287292817679558	27	0.0472027972027972	16	0.021108179419525065	A	10.97	1.502020	0.26949	0.006746	0.018241	ENSG00000105976	ENST00000397752;ENST00000318493;ENST00000436117	T;T;T	0.04551	3.6;3.6;3.6	6.04	4.91	0.64330	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.135646	0.64402	D	0.000003	T	0.00906	0.0030	L	0.52364	1.645	0.80722	D	1	B;B;B;B;B;B;B;B;B;B;B;B;B	0.21071	0.051;0.044;0.008;0.011;0.024;0.024;0.044;0.044;0.005;0.02;0.025;0.043;0.043	B;B;B;B;B;B;B;B;B;B;B;B;B	0.26310	0.018;0.026;0.047;0.034;0.047;0.026;0.068;0.038;0.007;0.015;0.026;0.026;0.026	T	0.36601	-0.9741	10	0.40728	T	0.16	.	9.6723	0.40019	0.869:0.0:0.131:0.0	rs33917957	375;375;375;375;375;375;375;375;375;375;375;375;375	B5A929;E7EQ94;B5A930;B5A934;B5A936;B5A937;B5A939;B5A941;B5A940;P08581-2;B5A942;P08581;A1L467	.;.;.;.;.;.;.;.;.;.;.;MET_HUMAN;.	S	375	ENSP00000380860:N375S;ENSP00000317272:N375S;ENSP00000410980:N375S	ENSP00000317272:N375S	N	+	2	0	MET	116127498	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	2.866000	0.48420	2.317000	0.78254	0.460000	0.39030	AAC	A|0.977;G|0.023	0.023	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
MET	4233	hgsc.bcm.edu	37	7	116436097	116436097	+	Silent	SNP	G	G	A	rs41737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116436097G>A	ENST00000318493.6	+	21	4333	c.4146G>A	c.(4144-4146)ccG>ccA	p.P1382P	MET_ENST00000539704.1_Silent_p.P234P|MET_ENST00000397752.3_Silent_p.P1364P			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.P1382P(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GTGTCGCTCCGTATCCTTCTC	0.468			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	1776	0.354633	0.0356	0.4726	5008	,	,		19834	0.4673		0.4433	False		,,,				2504	0.4949				p.P1382P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4146A						PASS	.	A	,	418,3602		15,388,1607	193.0	176.0	181.0		4092,4146	-3.1	1.0	7	dbSNP_76	181	3563,4817		777,2009,1404	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	792,2397,3011	AA,AG,GG		42.5179,10.398,32.1048	,	1364/1391,1382/1409	116436097	3981,8419	2010	4190	6200	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CGCTCCGTATCCT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.4146G>A	7.37:g.116436097G>A		173.0	0.0	0		192.0	88.0	0.458333	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.615;A|0.385	0.385	strong		0.468	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ZNF462	58499	hgsc.bcm.edu	37	9	109685748	109685748	+	Silent	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:109685748G>T	ENST00000277225.5	+	2	373	c.84G>T	c.(82-84)acG>acT	p.T28T	ZNF462_ENST00000457913.1_Silent_p.T28T|RP11-508N12.4_ENST00000451160.2_Silent_p.T28T			Q96JM2	ZN462_HUMAN	zinc finger protein 462	28					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						ATGTCCACACGGCATTTCTGC	0.498																																					p.T28T		Atlas-SNP	.											.	ZNF462	322	.	0			c.G84T						PASS	.						241.0	216.0	224.0					9																	109685748		2203	4300	6503	SO:0001819	synonymous_variant	58499	exon2			CCACACGGCATTT	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.84G>T	9.37:g.109685748G>T		204.0	0.0	0		231.0	81.0	0.350649	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			.	.	none		0.498	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
TMEM132D	121256	hgsc.bcm.edu	37	12	130184612	130184612	+	Silent	SNP	C	C	T	rs140064887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:130184612C>T	ENST00000422113.2	-	2	1037	c.711G>A	c.(709-711)ggG>ggA	p.G237G	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	237					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		TGACGCAGTCCCCTCTCTCAC	0.667													C|||	15	0.00299521	0.0015	0.0029	5008	,	,		15848	0.0		0.0099	False		,,,				2504	0.001				p.G237G		Atlas-SNP	.											.	TMEM132D	299	.	0			c.G711A						PASS	.	C		8,4398	12.9+/-30.5	0,8,2195	81.0	74.0	76.0		711	-7.6	0.0	12	dbSNP_134	76	66,8534	39.8+/-96.3	0,66,4234	no	coding-synonymous	TMEM132D	NM_133448.2		0,74,6429	TT,TC,CC		0.7674,0.1816,0.569		237/1100	130184612	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	121256	exon2			GCAGTCCCCTCTC	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.711G>A	12.37:g.130184612C>T		94.0	0.0	0		108.0	53.0	0.490741	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Silent	SNP	ENST00000422113.2	37	CCDS9266.1																																																																																			C|0.995;T|0.005	0.005	strong		0.667	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
SUMF1	285362	hgsc.bcm.edu	37	3	4508802	4508802	+	Missense_Mutation	SNP	G	G	A	rs200789939	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:4508802G>A	ENST00000272902.5	-	1	163	c.128C>T	c.(127-129)gCg>gTg	p.A43V	SUMF1_ENST00000534863.1_Missense_Mutation_p.A43V|SUMF1_ENST00000458465.2_Missense_Mutation_p.A43V|SUMF1_ENST00000383843.5_Missense_Mutation_p.A43V|SUMF1_ENST00000405420.2_Missense_Mutation_p.A43V	NM_182760.3	NP_877437.2	Q8NBK3	SUMF1_HUMAN	sulfatase modifying factor 1	43					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(3)	13		Melanoma(143;0.068)|Colorectal(144;0.233)		Epithelial(13;0.0147)|OV - Ovarian serous cystadenocarcinoma(96;0.0444)|all cancers(10;0.0549)		AAGGGACCCCGCGCCCGCACC	0.711													G|||	2	0.000399361	0.0	0.0	5008	,	,		13188	0.0		0.002	False		,,,				2504	0.0				p.A43V		Atlas-SNP	.											.	SUMF1	23	.	0			c.C128T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	0,4178		0,0,2089	5.0	7.0	6.0		128,128,128	2.7	0.0	3		6	3,8223		0,3,4110	no	missense,missense,missense	SUMF1	NM_001164674.1,NM_001164675.1,NM_182760.3	64,64,64	0,3,6199	AA,AG,GG		0.0365,0.0,0.0242	benign,benign,benign	43/350,43/355,43/375	4508802	3,12401	2089	4113	6202	SO:0001583	missense	285362	exon1			GACCCCGCGCCCG	BC017005	CCDS2564.1, CCDS54548.1, CCDS54549.1	3p26.1	2009-07-23			ENSG00000144455	ENSG00000144455			20376	protein-coding gene	gene with protein product		607939				12757705, 12757706	Standard	NM_182760		Approved	FGE, UNQ3037	uc003bpz.2	Q8NBK3	OTTHUMG00000090269	ENST00000272902.5:c.128C>T	3.37:g.4508802G>A	ENSP00000272902:p.Ala43Val	18.0	0.0	0		19.0	12.0	0.631579	NM_001164675	B4DXK5|B7XD05|E9PGL0|G5E9B0|Q0VAC6|Q0VAC7|Q2NL78|Q53ZE4|Q6UY39|Q96AK5|Q96DK8	Missense_Mutation	SNP	ENST00000272902.5	37	CCDS2564.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	11.94	1.790063	0.31685	0.0	3.65E-4	ENSG00000144455	ENST00000534982;ENST00000534863;ENST00000272902;ENST00000383843;ENST00000458465;ENST00000405420	D;D;D;D;D	0.92805	-2.68;-3.11;-3.09;-2.33;-3.11	4.54	2.71	0.32032	.	0.485588	0.20903	N	0.083614	D	0.87418	0.6172	L	0.59436	1.845	0.09310	N	1	B;B;B;B	0.19200	0.034;0.023;0.014;0.014	B;B;B;B	0.12156	0.003;0.007;0.005;0.005	T	0.75808	-0.3187	10	0.34782	T	0.22	-14.8698	5.3757	0.16164	0.1034:0.0:0.6962:0.2003	.	43;43;43;43	E9PF05;G5E9B0;E9PGL0;Q8NBK3	.;.;.;SUMF1_HUMAN	V	43	ENSP00000440421:A43V;ENSP00000272902:A43V;ENSP00000373355:A43V;ENSP00000410060:A43V;ENSP00000384977:A43V	ENSP00000272902:A43V	A	-	2	0	SUMF1	4483802	0.027000	0.19231	0.013000	0.15412	0.135000	0.20990	1.099000	0.31013	0.615000	0.30124	0.591000	0.81541	GCG	G|0.999;A|0.001	0.001	strong		0.711	SUMF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206591.2	NM_182760	
PCNT	5116	hgsc.bcm.edu	37	21	47841933	47841933	+	Silent	SNP	T	T	C	rs61735815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47841933T>C	ENST00000359568.5	+	32	7181	c.7074T>C	c.(7072-7074)ccT>ccC	p.P2358P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2358					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CAGGAGGCCCTGAGGCTCAAA	0.612													T|||	115	0.0229633	0.0151	0.0303	5008	,	,		15470	0.001		0.0686	False		,,,				2504	0.0041				p.P2358P		Atlas-SNP	.											.	PCNT	283	.	0			c.T7074C						PASS	.	T		137,4269	96.2+/-134.9	3,131,2069	74.0	79.0	77.0		7074	-8.4	0.0	21	dbSNP_129	77	532,8068	148.5+/-203.7	11,510,3779	no	coding-synonymous	PCNT	NM_006031.5		14,641,5848	CC,CT,TT		6.186,3.1094,5.1438		2358/3337	47841933	669,12337	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon32			AGGCCCTGAGGCT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7074T>C	21.37:g.47841933T>C		71.0	0.0	0		88.0	34.0	0.386364	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			T|0.952;C|0.048	0.048	strong		0.612	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
FLNA	2316	hgsc.bcm.edu	37	X	153594932	153594932	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:153594932T>G	ENST00000369850.3	-	7	1299	c.1063A>C	c.(1063-1065)Aag>Cag	p.K355Q	FLNA_ENST00000344736.4_Missense_Mutation_p.K355Q|FLNA_ENST00000360319.4_Missense_Mutation_p.K355Q|FLNA_ENST00000422373.1_Missense_Mutation_p.K355Q	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	355					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGGCTCACCTTATGAGTCCCC	0.632																																					p.K355Q		Atlas-SNP	.											.	FLNA	373	.	0			c.A1063C						PASS	.						89.0	91.0	91.0					X																	153594932		2009	4148	6157	SO:0001583	missense	2316	exon7			TCACCTTATGAGT	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1063A>C	X.37:g.153594932T>G	ENSP00000358866:p.Lys355Gln	98.0	0.0	0		231.0	126.0	0.545455	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	T	13.80	2.346167	0.41599	.	.	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.85171	-1.95;-1.95;-1.95;-1.95	4.87	4.87	0.63330	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.85605	0.5735	L	0.50993	1.605	0.80722	D	1	B;B	0.29612	0.251;0.18	B;B	0.42163	0.23;0.378	D	0.84661	0.0706	10	0.51188	T	0.08	.	13.3412	0.60545	0.0:0.0:0.0:1.0	.	355;355	P21333-2;P21333	.;FLNA_HUMAN	Q	355;328;355;355;355	ENSP00000353467:K355Q;ENSP00000416926:K355Q;ENSP00000358866:K355Q;ENSP00000358863:K355Q	ENSP00000358863:K355Q	K	-	1	0	FLNA	153248126	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.134000	0.71689	1.607000	0.50170	0.427000	0.28365	AAG	.	.	none		0.632	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
FERMT3	83706	hgsc.bcm.edu	37	11	63974995	63974995	+	Splice_Site	SNP	C	C	G	rs142815441	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:63974995C>G	ENST00000279227.5	+	2	254	c.159C>G	c.(157-159)atC>atG	p.I53M	FERMT3_ENST00000345728.5_Splice_Site_p.I53M	NM_178443.2	NP_848537.1	Q86UX7	URP2_HUMAN	fermitin family member 3	53					integrin activation (GO:0033622)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|platelet aggregation (GO:0070527)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|podosome (GO:0002102)	integrin binding (GO:0005178)			breast(1)|cervix(1)|endometrium(4)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	18						TGGAGCAGATCAGTGAGTGTC	0.657													C|||	7	0.00139776	0.0	0.0029	5008	,	,		12110	0.0		0.005	False		,,,				2504	0.0				p.I53M		Atlas-SNP	.											.	FERMT3	51	.	0			c.C159G						PASS	.	C	MET/ILE,MET/ILE	4,4398	8.1+/-20.4	0,4,2197	36.0	40.0	39.0		159,159	4.5	1.0	11	dbSNP_134	39	46,8548	29.6+/-80.5	0,46,4251	yes	missense-near-splice,missense-near-splice	FERMT3	NM_031471.5,NM_178443.2	10,10	0,50,6448	GG,GC,CC		0.5353,0.0909,0.3847	benign,benign	53/664,53/668	63974995	50,12946	2201	4297	6498	SO:0001630	splice_region_variant	83706	exon2			GCAGATCAGTGAG	L25343	CCDS8059.1, CCDS8060.1	11q13.1	2014-09-17	2010-06-24		ENSG00000149781	ENSG00000149781		"""Fermitins"", ""Pleckstrin homology (PH) domain containing"""	23151	protein-coding gene	gene with protein product	"""kindlin-3"""	607901	"""fermitin family homolog 3 (Drosophila)"""				Standard	NM_178443		Approved	URP2, KIND3, MIG2B, MGC10966, MIG-2, UNC112C	uc001nym.2	Q86UX7	OTTHUMG00000167790	ENST00000279227.5:c.160+1C>G	11.37:g.63974995C>G		96.0	0.0	0		123.0	52.0	0.422764	NM_031471	Q8IUA1|Q8N207|Q9BT48	Missense_Mutation	SNP	ENST00000279227.5	37	CCDS8060.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	12.17	1.857249	0.32791	9.09E-4	0.005353	ENSG00000149781	ENST00000544997;ENST00000345728;ENST00000279227	T;T;T	0.59083	1.55;0.29;0.29	4.48	4.48	0.54585	.	0.210781	0.37715	N	0.001977	T	0.39627	0.1085	L	0.54323	1.7	0.37691	D	0.923865	P;B	0.45011	0.848;0.031	B;B	0.36885	0.235;0.024	T	0.56183	-0.8021	10	0.49607	T	0.09	-30.3298	10.1956	0.43051	0.3098:0.6902:0.0:0.0	.	53;53	Q86UX7-2;Q86UX7	.;URP2_HUMAN	M	53	ENSP00000445778:I53M;ENSP00000339950:I53M;ENSP00000279227:I53M	ENSP00000279227:I53M	I	+	3	3	FERMT3	63731571	0.223000	0.23663	1.000000	0.80357	0.325000	0.28411	0.067000	0.14510	2.502000	0.84385	0.561000	0.74099	ATC	C|0.997;G|0.003	0.003	strong		0.657	FERMT3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396297.1	NM_031471	Missense_Mutation
KDR	3791	hgsc.bcm.edu	37	4	55946171	55946171	+	Silent	SNP	G	G	A	rs35961234	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55946171G>A	ENST00000263923.4	-	30	4303	c.4008C>T	c.(4006-4008)acC>acT	p.T1336T	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1336					angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.T1336T(1)		NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTGTGCTACCGGTTTGCACTC	0.532			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			G|||	48	0.00958466	0.0008	0.013	5008	,	,		17550	0.0		0.0348	False		,,,				2504	0.0031				p.T1336T		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	KDR,colon,carcinoma,0,5	KDR	307	5	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C4008T						PASS	.	G		26,4380	33.5+/-64.1	0,26,2177	220.0	204.0	209.0		4008	-5.9	0.0	4	dbSNP_126	209	228,8372	94.5+/-156.4	3,222,4075	no	coding-synonymous	KDR	NM_002253.2		3,248,6252	AA,AG,GG		2.6512,0.5901,1.9529		1336/1357	55946171	254,12752	2203	4300	6503	SO:0001819	synonymous_variant	3791	exon30			GCTACCGGTTTGC	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.4008C>T	4.37:g.55946171G>A		150.0	0.0	0		211.0	109.0	0.516588	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																			G|0.983;A|0.017	0.017	strong		0.532	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
PIKFYVE	200576	hgsc.bcm.edu	37	2	209190070	209190070	+	Silent	SNP	T	T	C	rs138885638	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:209190070T>C	ENST00000264380.4	+	20	2693	c.2535T>C	c.(2533-2535)tcT>tcC	p.S845S		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	845					cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GAGGAGGCTCTGATTATGAGC	0.378													T|||	3	0.000599042	0.0015	0.0	5008	,	,		20316	0.0		0.001	False		,,,				2504	0.0				p.S845S		Atlas-SNP	.											.	PIKFYVE	223	.	0			c.T2535C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	97.0	91.0	93.0		2535	1.9	1.0	2	dbSNP_134	93	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	PIKFYVE	NM_015040.3		0,15,6488	CC,CT,TT		0.1512,0.0454,0.1153		845/2099	209190070	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	200576	exon20			AGGCTCTGATTAT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.2535T>C	2.37:g.209190070T>C		104.0	0.0	0		101.0	51.0	0.504951	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Silent	SNP	ENST00000264380.4	37	CCDS2382.1																																																																																			T|0.999;C|0.001	0.001	strong		0.378	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
GALNT2	2590	hgsc.bcm.edu	37	1	230386238	230386238	+	Missense_Mutation	SNP	A	A	C	rs78164071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:230386238A>C	ENST00000366672.4	+	10	1013	c.941A>C	c.(940-942)gAt>gCt	p.D314A	GALNT2_ENST00000541865.1_Intron|GALNT2_ENST00000543760.1_Missense_Mutation_p.D276A	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	314	Catalytic subdomain B.				cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				TTTGTGATGGATAAGTTCTAT	0.488													A|||	6	0.00119808	0.0	0.0014	5008	,	,		19543	0.0		0.005	False		,,,				2504	0.0				p.D314A		Atlas-SNP	.											.	GALNT2	83	.	0			c.A941C						PASS	.	A	ALA/ASP	4,4402	9.9+/-24.2	0,4,2199	176.0	157.0	164.0		941	4.4	1.0	1	dbSNP_133	164	30,8570	22.2+/-67.0	0,30,4270	yes	missense	GALNT2	NM_004481.3	126	0,34,6469	CC,CA,AA		0.3488,0.0908,0.2614	benign	314/572	230386238	34,12972	2203	4300	6503	SO:0001583	missense	2590	exon10			TGATGGATAAGTT	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.941A>C	1.37:g.230386238A>C	ENSP00000355632:p.Asp314Ala	118.0	0.0	0		136.0	69.0	0.507353	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	CCDS1582.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	16.68	3.189190	0.57909	9.08E-4	0.003488	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291	T;T	0.59772	0.24;0.24	4.43	4.43	0.53597	.	0.000000	0.85682	D	0.000000	T	0.50514	0.1620	M	0.80746	2.51	0.80722	D	1	B;B	0.32573	0.376;0.213	B;B	0.28305	0.088;0.018	T	0.63479	-0.6628	10	0.66056	D	0.02	.	13.6391	0.62239	1.0:0.0:0.0:0.0	.	314;276	Q10471;G3V1S6	GALT2_HUMAN;.	A	276;314;195	ENSP00000445017:D276A;ENSP00000355632:D314A	ENSP00000355632:D314A	D	+	2	0	GALNT2	228452861	1.000000	0.71417	0.986000	0.45419	0.977000	0.68977	8.799000	0.91895	1.761000	0.52028	0.379000	0.24179	GAT	A|0.997;C|0.003	0.003	strong		0.488	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
PCNT	5116	hgsc.bcm.edu	37	21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	rs34500739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47766113T>G	ENST00000359568.5	+	4	818	c.711T>G	c.(709-711)caT>caG	p.H237Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	237	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CTGGCCTGCATCAGAGTCAGG	0.602													G|||	128	0.0255591	0.028	0.0303	5008	,	,		16755	0.001		0.0646	False		,,,				2504	0.0041				p.H237Q		Atlas-SNP	.											.	PCNT	283	.	0			c.T711G						PASS	.	G	GLN/HIS	192,4214	807.9+/-415.9	5,182,2016	83.0	74.0	77.0		711	3.3	1.0	21	dbSNP_126	77	528,8072	795.4+/-407.5	11,506,3783	yes	missense	PCNT	NM_006031.5	24	16,688,5799	GG,GT,TT		6.1395,4.3577,5.5359	benign	237/3337	47766113	720,12286	2203	4300	6503	SO:0001583	missense	5116	exon4			CCTGCATCAGAGT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.711T>G	21.37:g.47766113T>G	ENSP00000352572:p.His237Gln	122.0	0.0	0		150.0	80.0	0.533333	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	2.436	-0.329782	0.05314	0.043577	0.061395	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	3.27	3.27	0.37495	.	.	.	.	.	T	0.00073	0.0002	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45145	-0.9281	9	0.09084	T	0.74	.	8.0049	0.30319	0.0:0.0:0.7564:0.2436	rs34500739	119;237	O95613-2;O95613	.;PCNT_HUMAN	Q	237;224	ENSP00000352572:H237Q	ENSP00000338675:H224Q	H	+	3	2	PCNT	46590541	0.057000	0.20700	0.965000	0.40720	0.171000	0.22731	0.660000	0.25009	0.988000	0.38734	-0.648000	0.03929	CAT	T|0.949;G|0.051	0.051	strong		0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
SEMA3G	56920	hgsc.bcm.edu	37	3	52476246	52476246	+	Silent	SNP	G	G	A	rs34900551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:52476246G>A	ENST00000231721.2	-	4	413	c.414C>T	c.(412-414)gcC>gcT	p.A138A		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	138	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		TGGGCTGGAAGGCCCCAGTGC	0.657													G|||	49	0.00978435	0.0008	0.0101	5008	,	,		16416	0.0		0.0358	False		,,,				2504	0.0051				p.A138A		Atlas-SNP	.											.	SEMA3G	58	.	0			c.C414T						PASS	.	G		35,4371	40.0+/-72.8	0,35,2168	47.0	45.0	45.0		414	4.7	1.0	3	dbSNP_126	45	325,8275	112.0+/-172.2	3,319,3978	no	coding-synonymous	SEMA3G	NM_020163.1		3,354,6146	AA,AG,GG		3.7791,0.7944,2.768		138/783	52476246	360,12646	2203	4300	6503	SO:0001819	synonymous_variant	56920	exon4			CTGGAAGGCCCCA		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.414C>T	3.37:g.52476246G>A		183.0	0.0	0		211.0	109.0	0.516588	NM_020163	Q7L9D9|Q9H7Q3	Silent	SNP	ENST00000231721.2	37	CCDS2856.1																																																																																			G|0.978;A|0.022	0.022	strong		0.657	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
CEP162	22832	hgsc.bcm.edu	37	6	84884544	84884544	+	Missense_Mutation	SNP	T	T	G	rs149892489		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:84884544T>G	ENST00000403245.3	-	15	2041	c.1927A>C	c.(1927-1929)Aag>Cag	p.K643Q	KIAA1009_ENST00000257766.4_Missense_Mutation_p.K567Q|KIAA1009_ENST00000461137.1_5'UTR	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TCTTTCTCCTTTTCTGAGAAT	0.348																																					p.K643Q		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A1927C						PASS	.						78.0	70.0	72.0					6																	84884544		2203	4297	6500	SO:0001583	missense	22832	exon15			TCTCCTTTTCTGA																												ENST00000403245.3:c.1927A>C	6.37:g.84884544T>G	ENSP00000385215:p.Lys643Gln	174.0	0.0	0		205.0	17.0	0.0829268	NM_014895		Missense_Mutation	SNP	ENST00000403245.3	37	CCDS34494.2	.	.	.	.	.	.	.	.	.	.	T	21.8	4.205158	0.79127	.	.	ENSG00000135315	ENST00000257766;ENST00000403245	T;T	0.24723	1.84;1.85	5.42	5.42	0.78866	.	0.000000	0.85682	D	0.000000	T	0.44540	0.1298	M	0.77616	2.38	0.38548	D	0.949389	D	0.89917	1.0	D	0.85130	0.997	T	0.48222	-0.9054	10	0.52906	T	0.07	-30.2168	15.7393	0.77876	0.0:0.0:0.0:1.0	.	643	Q5TB80	QN1_HUMAN	Q	567;643	ENSP00000257766:K567Q;ENSP00000385215:K643Q	ENSP00000257766:K567Q	K	-	1	0	KIAA1009	84941263	1.000000	0.71417	0.993000	0.49108	0.784000	0.44337	5.561000	0.67339	2.184000	0.69523	0.460000	0.39030	AAG	.	.	weak		0.348	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
ICE2	79664	hgsc.bcm.edu	37	15	60745788	60745788	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:60745788A>G	ENST00000561114.1	-	9	1301	c.1139T>C	c.(1138-1140)tTt>tCt	p.F380S	NARG2_ENST00000261520.4_Intron|NARG2_ENST00000439632.1_Intron	NM_001276385.1	NP_001263314.1														breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	32						GGGGAAAAAAAAAGCATTACA	0.328																																					p.F380S		Atlas-SNP	.											.	NARG2	82	.	0			c.T1139C						PASS	.						54.0	55.0	55.0					15																	60745788		2203	4297	6500	SO:0001583	missense	79664	exon9			AAAAAAAAAGCAT																												ENST00000561114.1:c.1139T>C	15.37:g.60745788A>G	ENSP00000454162:p.Phe380Ser	151.0	0.0	0		163.0	74.0	0.453988	NM_001276385		Missense_Mutation	SNP	ENST00000561114.1	37																																																																																				.	.	none		0.328	NARG2-004	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000416605.1		
FAM103A1	83640	hgsc.bcm.edu	37	15	83657894	83657894	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:83657894G>A	ENST00000304191.3	+	3	345	c.124G>A	c.(124-126)Gaa>Aaa	p.E42K	C15orf40_ENST00000538348.2_Missense_Mutation_p.P128S|RP11-382A20.5_ENST00000566841.1_RNA	NM_031452.3	NP_113640.1	Q9BTL3	RAM_HUMAN	family with sequence similarity 103, member A1	42	Interaction with RNMT.				7-methylguanosine mRNA capping (GO:0006370)|methylation (GO:0032259)|recruitment of mRNA capping enzyme to RNA polymerase II holoenzyme complex (GO:0036031)	mRNA cap binding complex (GO:0005845)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			prostate(1)	1						AATTGTTGAGGAATGGAATAG	0.418																																					p.P128S		Atlas-SNP	.											.	C15orf40	18	.	0			c.C382T						PASS	.																																			SO:0001583	missense	123207	exon4			GTTGAGGAATGGA	CR597724	CCDS10321.1	15q25.2	2012-06-13			ENSG00000169612	ENSG00000169612			31022	protein-coding gene	gene with protein product	"""RNMT-activating mini protein"""	614547				22099306	Standard	NM_031452		Approved	HsT19360, C15orf18, MGC2560, RAM	uc002bjl.2	Q9BTL3	OTTHUMG00000147357	ENST00000304191.3:c.124G>A	15.37:g.83657894G>A	ENSP00000307181:p.Glu42Lys	274.0	0.0	0		352.0	151.0	0.428977	NM_001160116	Q2M1J8	Missense_Mutation	SNP	ENST00000304191.3	37	CCDS10321.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.4|25.4	4.630726|4.630726	0.87660|0.87660	.|.	.|.	ENSG00000169612|ENSG00000169609	ENST00000304191|ENST00000538348	.|.	.|.	.|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.167238|.	0.51477|.	D|.	0.000085|.	T|T	0.76659|0.76659	0.4018|0.4018	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	P|D	0.42692|0.67145	0.787|0.996	B|P	0.37601|0.61658	0.254|0.892	T|T	0.72350|0.72350	-0.4320|-0.4320	9|8	0.66056|0.29301	D|T	0.02|0.29	-9.1412|-9.1412	19.6657|19.6657	0.95891|0.95891	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	42|128	Q9BTL3|F5GX92	F103A_HUMAN|.	K|S	42|128	.|.	ENSP00000307181:E42K|ENSP00000441077:P128S	E|P	+|-	1|1	0|0	FAM103A1|C15orf40	81448898|81448898	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.984000|0.984000	0.73092|0.73092	7.848000|7.848000	0.86902|0.86902	2.744000|2.744000	0.94065|0.94065	0.655000|0.655000	0.94253|0.94253	GAA|CCT	.	.	none		0.418	FAM103A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304001.1	NM_031452	
PLCH1	23007	hgsc.bcm.edu	37	3	155203301	155203301	+	Missense_Mutation	SNP	C	C	T	rs143905522	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:155203301C>T	ENST00000340059.7	-	22	2841	c.2842G>A	c.(2842-2844)Gag>Aag	p.E948K	PLCH1_ENST00000334686.6_Missense_Mutation_p.E910K|PLCH1_ENST00000494598.1_Missense_Mutation_p.E928K|PLCH1_ENST00000460012.1_Missense_Mutation_p.E910K|PLCH1_ENST00000414191.1_Missense_Mutation_p.E910K|PLCH1_ENST00000447496.2_Missense_Mutation_p.E948K|PLCH1-AS2_ENST00000472913.1_RNA	NM_001130960.1	NP_001124432.1	Q4KWH8	PLCH1_HUMAN	phospholipase C, eta 1	948					inositol phosphate metabolic process (GO:0043647)|lipid catabolic process (GO:0016042)|phosphatidylinositol-mediated signaling (GO:0048015)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase C activity (GO:0050429)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			NS(3)|breast(3)|endometrium(9)|kidney(4)|large_intestine(20)|lung(45)|ovary(2)|prostate(5)|skin(8)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	107			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			CTTGTGGCCTCGGACACAGAA	0.517																																					p.E948K		Atlas-SNP	.											PLCH1_ENST00000340059,bladder,carcinoma,+1,2	PLCH1	406	2	0			c.G2842A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	154.0	144.0	147.0		2842,2842,2728	5.9	1.0	3	dbSNP_134	147	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	PLCH1	NM_001130960.1,NM_001130961.1,NM_014996.2	56,56,56	0,7,6496	TT,TC,CC		0.0581,0.0454,0.0538	benign,benign,benign	948/1694,948/1003,910/1656	155203301	7,12999	2203	4300	6503	SO:0001583	missense	23007	exon22			TGGCCTCGGACAC	AB028992	CCDS33881.1, CCDS46939.1, CCDS46940.1	3q25	2013-01-10	2006-03-16	2006-03-16	ENSG00000114805	ENSG00000114805	3.1.4.11	"""EF-hand domain containing"""	29185	protein-coding gene	gene with protein product		612835	"""phospholipase C-like 3"""	PLCL3		15702972	Standard	NM_014996		Approved	KIAA1069, MGC117152, DKFZp434C1372, PLCeta1	uc021xge.1	Q4KWH8	OTTHUMG00000158477	ENST00000340059.7:c.2842G>A	3.37:g.155203301C>T	ENSP00000345988:p.Glu948Lys	167.0	0.0	0		200.0	100.0	0.5	NM_001130960	Q29RV9|Q4KWH9|Q68CN0|Q86XK4|Q9H9U2|Q9UPT3	Missense_Mutation	SNP	ENST00000340059.7	37	CCDS46939.1	.	.	.	.	.	.	.	.	.	.	C	17.41	3.382670	0.61845	4.54E-4	5.81E-4	ENSG00000114805	ENST00000494598;ENST00000460012;ENST00000447496;ENST00000340059;ENST00000334686;ENST00000414191	T;T;T;T;T;T	0.34275	1.8;1.65;1.37;1.68;1.65;1.65	5.88	5.88	0.94601	.	0.244558	0.40385	N	0.001102	T	0.35941	0.0949	L	0.54323	1.7	0.80722	D	1	B;P;B	0.52061	0.222;0.95;0.039	B;B;B	0.37601	0.099;0.254;0.031	T	0.19679	-1.0298	10	0.39692	T	0.17	.	20.2228	0.98330	0.0:1.0:0.0:0.0	.	910;948;948	Q4KWH8-2;Q4KWH8;Q4KWH8-3	.;PLCH1_HUMAN;.	K	928;910;948;948;910;910	ENSP00000419100:E928K;ENSP00000417502:E910K;ENSP00000402759:E948K;ENSP00000345988:E948K;ENSP00000335469:E910K;ENSP00000412977:E910K	ENSP00000335469:E910K	E	-	1	0	PLCH1	156685995	0.993000	0.37304	0.975000	0.42487	0.446000	0.32137	3.168000	0.50801	2.789000	0.95967	0.655000	0.94253	GAG	C|1.000;T|0.000	0.000	strong		0.517	PLCH1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351125.1	NM_014996	
SPHKAP	80309	hgsc.bcm.edu	37	2	228855993	228855993	+	Missense_Mutation	SNP	C	C	T	rs61752221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:228855993C>T	ENST00000392056.3	-	10	4817	c.4771G>A	c.(4771-4773)Gag>Aag	p.E1591K	SPHKAP_ENST00000344657.5_Missense_Mutation_p.E1562K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	1591						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GGCTTACCCTCTGTGCTTTCT	0.418													C|||	24	0.00479233	0.0015	0.0086	5008	,	,		19744	0.0		0.0159	False		,,,				2504	0.0				p.E1591K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.G4771A						PASS	.	C	LYS/GLU,LYS/GLU	8,4398	14.3+/-33.2	0,8,2195	184.0	175.0	178.0		4771,4684	4.2	0.9	2	dbSNP_129	178	121,8479	63.5+/-125.6	0,121,4179	yes	missense,missense	SPHKAP	NM_001142644.1,NM_030623.3	56,56	0,129,6374	TT,TC,CC		1.407,0.1816,0.9918	benign,benign	1591/1701,1562/1672	228855993	129,12877	2203	4300	6503	SO:0001583	missense	80309	exon10			TACCCTCTGTGCT		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.4771G>A	2.37:g.228855993C>T	ENSP00000375909:p.Glu1591Lys	198.0	0.0	0		237.0	102.0	0.43038	NM_001142644	Q68DA3|Q68DR8|Q9C0I5	Missense_Mutation	SNP	ENST00000392056.3	37	CCDS46537.1	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	11	0.014511873350923483	C	12.78	2.039722	0.35989	0.001816	0.01407	ENSG00000153820	ENST00000392056;ENST00000344657	T;T	0.12147	2.73;2.71	6.17	4.25	0.50352	.	0.480270	0.24755	N	0.035878	T	0.05547	0.0146	N	0.22421	0.69	0.33424	D	0.580224	B;B	0.15473	0.011;0.013	B;B	0.18561	0.022;0.013	T	0.23940	-1.0174	10	0.19590	T	0.45	.	6.1421	0.20265	0.0:0.7401:0.0:0.2599	rs61752221	1591;1562	Q2M3C7;Q2M3C7-2	SPKAP_HUMAN;.	K	1591;1562	ENSP00000375909:E1591K;ENSP00000339886:E1562K	ENSP00000339886:E1562K	E	-	1	0	SPHKAP	228564237	0.988000	0.35896	0.850000	0.33497	0.996000	0.88848	2.406000	0.44557	0.778000	0.33520	0.655000	0.94253	GAG	C|0.991;T|0.009	0.009	strong		0.418	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
RERE	473	hgsc.bcm.edu	37	1	8421186	8421186	+	Missense_Mutation	SNP	G	G	A	rs201922249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:8421186G>A	ENST00000337907.3	-	19	3015	c.2381C>T	c.(2380-2382)cCt>cTt	p.P794L	RERE_ENST00000400907.2_Intron|RERE_ENST00000476556.1_Missense_Mutation_p.P240L|RERE_ENST00000377464.1_Missense_Mutation_p.P526L|RERE_ENST00000400908.2_Missense_Mutation_p.P794L	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	794	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GTGGGGAACAGGCGCTGTGGG	0.731													G|||	25	0.00499201	0.0	0.0101	5008	,	,		12737	0.0		0.0159	False		,,,				2504	0.002				p.P794L		Atlas-SNP	.											.	RERE	129	.	0			c.C2381T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	16,4116		0,16,2050	8.0	9.0	9.0		2381,719,2381	4.2	0.0	1		9	135,8059		1,133,3963	yes	missense,missense,missense	RERE	NM_012102.3,NM_001042682.1,NM_001042681.1	98,98,98	1,149,6013	AA,AG,GG		1.6475,0.3872,1.2251	benign,benign,benign	794/1567,240/1013,794/1567	8421186	151,12175	2066	4097	6163	SO:0001583	missense	473	exon19			GGAACAGGCGCTG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2381C>T	1.37:g.8421186G>A	ENSP00000338629:p.Pro794Leu	21.0	0.0	0		19.0	13.0	0.684211	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	20.8	4.057756	0.76074	0.003872	0.016475	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000476556;ENST00000400908	T;T;T	0.46063	0.88;0.89;0.88	5.15	4.24	0.50183	.	.	.	.	.	T	0.22513	0.0543	L	0.44542	1.39	0.37189	D	0.903842	B;B	0.27910	0.193;0.005	B;B	0.31390	0.129;0.038	T	0.35599	-0.9782	9	0.54805	T	0.06	-2.2502	12.4483	0.55664	0.0824:0.0:0.9176:0.0	.	526;794	B1AKN3;Q9P2R6	.;RERE_HUMAN	L	794;526;240;794	ENSP00000338629:P794L;ENSP00000366684:P526L;ENSP00000383700:P794L	ENSP00000338629:P794L	P	-	2	0	RERE	8343773	0.692000	0.27719	0.002000	0.10522	0.010000	0.07245	4.289000	0.59013	1.299000	0.44798	0.561000	0.74099	CCT	G|0.994;A|0.006	0.006	strong		0.731	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
SLC25A52	147407	hgsc.bcm.edu	37	18	29340051	29340051	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:29340051C>T	ENST00000579441.2	-	1	573	c.574G>A	c.(574-576)Ggc>Agc	p.G192S	SLC25A52_ENST00000269205.5_Missense_Mutation_p.G202S			Q3SY17	S2552_HUMAN	solute carrier family 25, member 52	192					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)											CCTCGAAGGCCGAAAAACAAG	0.473																																					p.G202S		Atlas-SNP	.											MCART2_ENST00000269205,NS,carcinoma,+1,2	.	.	2	0			c.G604A						scavenged	.						71.0	70.0	70.0					18																	29340051		2203	4297	6500	SO:0001583	missense	147407	exon1			GAAGGCCGAAAAA		CCDS32812.1, CCDS32812.2	18q12.1	2013-07-15	2012-03-29	2012-03-29	ENSG00000141437	ENSG00000141437		"""Solute carriers"""	23324	protein-coding gene	gene with protein product			"""mitochondrial carrier triple repeat 2"""	MCART2			Standard	NM_001034172		Approved		uc002kxa.3	Q3SY17	OTTHUMG00000179617	ENST00000579441.2:c.574G>A	18.37:g.29340051C>T	ENSP00000462754:p.Gly192Ser	211.0	1.0	0.00473934		292.0	19.0	0.0650685	NM_001034172		Missense_Mutation	SNP	ENST00000579441.2	37		.	.	.	.	.	.	.	.	.	.	C	13.46	2.243739	0.39697	.	.	ENSG00000141437	ENST00000269205;ENST00000535708	T	0.79141	-1.24	1.22	0.273	0.15650	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	T	0.65544	0.2701	L	0.54323	1.7	0.48511	D	0.999667	B	0.24483	0.104	B	0.19391	0.025	T	0.51052	-0.8754	10	0.26408	T	0.33	.	5.5522	0.17097	0.0:0.7844:0.0:0.2156	.	192	Q3SY17	MCAR2_HUMAN	S	202;192	ENSP00000372612:G202S	ENSP00000372612:G202S	G	-	1	0	MCART2	27594049	1.000000	0.71417	0.108000	0.21378	0.927000	0.56198	4.925000	0.63425	0.084000	0.17077	0.505000	0.49811	GGC	.	.	none		0.473	SLC25A52-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_084000	
CXCR1	3577	hgsc.bcm.edu	37	2	219029932	219029932	+	Start_Codon_SNP	SNP	C	C	T	rs55808468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:219029932C>T	ENST00000295683.2	-	2	123	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_000634.2	NP_000625.1	P25024	CXCR1_HUMAN	chemokine (C-X-C motif) receptor 1	1					cell surface receptor signaling pathway (GO:0007166)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|receptor internalization (GO:0031623)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)|G-protein coupled receptor activity (GO:0004930)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)			endometrium(1)|large_intestine(2)|lung(7)|prostate(3)	13					Ketoprofen(DB01009)	TAATATTTGACATGTCCTCTT	0.403													C|||	6	0.00119808	0.0008	0.0014	5008	,	,		25559	0.0		0.004	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	CXCR1	42	.	0			c.G3A						PASS	.	C	ILE/MET	9,4397	15.5+/-35.6	0,9,2194	107.0	104.0	105.0		3	-7.0	0.0	2	dbSNP_129	105	69,8531	42.2+/-99.7	2,65,4233	yes	missense	CXCR1	NM_000634.2	10	2,74,6427	TT,TC,CC		0.8023,0.2043,0.5997	benign	1/351	219029932	78,12928	2203	4300	6503	SO:0001582	initiator_codon_variant	3577	exon2			ATTTGACATGTCC	U11870	CCDS2409.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000163464	ENSG00000163464		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6026	protein-coding gene	gene with protein product		146929	"""interleukin 8 receptor, alpha"""	CMKAR1, IL8RA		1303245, 1427896	Standard	NM_000634		Approved	CKR-1, CDw128a, CD181	uc002vhc.3	P25024	OTTHUMG00000133108	ENST00000295683.2:c.3G>A	2.37:g.219029932C>T	ENSP00000295683:p.Met1Ile	69.0	0.0	0		85.0	38.0	0.447059	NM_000634	B2R6Q3|Q2YEF8|Q2YEG4|Q2YEG5|Q2YEG7|Q2YEG8|Q53R18|Q6IN95|Q8N6T6|Q9P2T8|Q9P2T9|Q9P2U0|Q9P2U1|Q9P2U2	Missense_Mutation	SNP	ENST00000295683.2	37	CCDS2409.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	10.73	1.433980	0.25813	0.002043	0.008023	ENSG00000163464	ENST00000295683;ENST00000421691	T	0.64085	-0.08	4.29	-7.02	0.01589	.	2.764150	0.01362	N	0.012266	T	0.31136	0.0787	.	.	.	0.21802	N	0.999532	B	0.19706	0.038	B	0.16722	0.016	T	0.10359	-1.0633	9	0.33141	T	0.24	.	2.2979	0.04154	0.1065:0.3398:0.1472:0.4066	rs55808468;rs61752207	1	P25024	CXCR1_HUMAN	I	1	ENSP00000295683:M1I	ENSP00000295683:M1I	M	-	3	0	CXCR1	218738177	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.941000	0.00329	-0.947000	0.03673	0.313000	0.20887	ATG	C|0.996;T|0.004	0.004	strong		0.403	CXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256773.2	NM_000634	Missense_Mutation
MUC17	140453	hgsc.bcm.edu	37	7	100679720	100679720	+	Missense_Mutation	SNP	G	G	A	rs140695064	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100679720G>A	ENST00000306151.4	+	3	5087	c.5023G>A	c.(5023-5025)Gct>Act	p.A1675T		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1675	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCCTACACCTGCTGAAGGTAC	0.493													G|||	4	0.000798722	0.0008	0.0	5008	,	,		26161	0.0		0.003	False		,,,				2504	0.0				p.A1675T		Atlas-SNP	.											.	MUC17	804	.	0			c.G5023A						PASS	.						208.0	220.0	216.0					7																	100679720		2203	4300	6503	SO:0001583	missense	140453	exon3			ACACCTGCTGAAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5023G>A	7.37:g.100679720G>A	ENSP00000302716:p.Ala1675Thr	78.0	0.0	0		52.0	32.0	0.615385	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	G	2.769	-0.256106	0.05829	.	.	ENSG00000169876	ENST00000306151	T	0.02085	4.46	0.932	-0.0747	0.13730	.	.	.	.	.	T	0.00998	0.0033	N	0.08118	0	0.09310	N	1	B	0.27286	0.174	B	0.16722	0.016	T	0.47114	-0.9142	9	0.08179	T	0.78	.	3.5105	0.07706	0.297:0.0:0.703:0.0	.	1675	Q685J3	MUC17_HUMAN	T	1675	ENSP00000302716:A1675T	ENSP00000302716:A1675T	A	+	1	0	MUC17	100466440	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-3.486000	0.00455	-0.003000	0.14444	0.134000	0.15878	GCT	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
NUDT18	79873	hgsc.bcm.edu	37	8	21965801	21965801	+	Silent	SNP	C	C	A	rs184414226	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21965801C>A	ENST00000309188.6	-	4	337	c.219G>T	c.(217-219)ctG>ctT	p.L73L	NUDT18_ENST00000522405.1_5'UTR|NUDT18_ENST00000521807.2_3'UTR	NM_024815.3	NP_079091.3	Q6ZVK8	NUD18_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 18	73	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				dADP catabolic process (GO:0046057)|dGDP catabolic process (GO:0046067)|GDP catabolic process (GO:0046712)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	8-hydroxy-dADP phosphatase activity (GO:0044717)|8-oxo-dGDP phosphatase activity (GO:0044715)|8-oxo-GDP phosphatase activity (GO:0044716)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|lung(2)	4				Colorectal(74;0.00185)|COAD - Colon adenocarcinoma(73;0.0608)|READ - Rectum adenocarcinoma(5;0.0986)		TCCCCGCAGGCAGGTACCACG	0.647													C|||	20	0.00399361	0.0015	0.0159	5008	,	,		17574	0.0		0.005	False		,,,				2504	0.002				p.L73L		Atlas-SNP	.											.	NUDT18	13	.	0			c.G219T						PASS	.	C		3,4253		0,3,2125	29.0	35.0	33.0		221	-6.9	0.4	8		33	74,8356		1,72,4142	yes	coding-synonymous	NUDT18	NM_024815.3		1,75,6267	AA,AC,CC		0.8778,0.0705,0.607		73/324	21965801	77,12609	2128	4215	6343	SO:0001819	synonymous_variant	79873	exon4			CGCAGGCAGGTAC		CCDS75706.1	8p21.3	2012-07-31				ENSG00000275074		"""Nudix motif containing"""	26194	protein-coding gene	gene with protein product	"""mutT human homolog 3"""	615791				22556419	Standard	NM_024815		Approved	FLJ22494, MTH3	uc003xaq.1	Q6ZVK8		ENST00000309188.6:c.219G>T	8.37:g.21965801C>A		65.0	0.0	0		81.0	48.0	0.592593	NM_024815	Q8IZ75|Q9H687	Silent	SNP	ENST00000309188.6	37		8	0.003663003663003663	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	0	0.0	C	9.689	1.151432	0.21371	7.05E-4	0.008778	ENSG00000173566	ENST00000522379	.	.	.	5.1	-6.89	0.01660	.	.	.	.	.	T	0.20981	0.0505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.36016	-0.9765	4	.	.	.	.	2.7266	0.05215	0.1919:0.4767:0.2185:0.113	.	.	.	.	S	109	.	.	A	-	1	0	NUDT18	22021746	0.082000	0.21442	0.361000	0.25849	0.984000	0.73092	-0.870000	0.04228	-1.380000	0.02115	0.561000	0.74099	GCC	C|0.996;A|0.004	0.004	strong		0.647	NUDT18-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_024815	
ARHGAP9	64333	hgsc.bcm.edu	37	12	57869681	57869681	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57869681G>A	ENST00000356411.2	-	10	1384	c.1246C>T	c.(1246-1248)Cag>Tag	p.Q416*	ARHGAP9_ENST00000393797.2_Nonsense_Mutation_p.Q487*|ARHGAP9_ENST00000550454.1_5'Flank|ARHGAP9_ENST00000424809.2_Nonsense_Mutation_p.Q416*|ARHGAP9_ENST00000550288.1_Nonsense_Mutation_p.Q495*|ARHGAP9_ENST00000393791.3_Nonsense_Mutation_p.Q416*|ARHGAP9_ENST00000430041.2_Nonsense_Mutation_p.Q232*			Q9BRR9	RHG09_HUMAN	Rho GTPase activating protein 9	416	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)			endometrium(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(1)	30			GBM - Glioblastoma multiforme(3;3.37e-34)			TGGTCCGACTGCAGCAGGAAC	0.647																																					p.Q416X		Atlas-SNP	.											.	ARHGAP9	79	.	0			c.C1246T						PASS	.						27.0	30.0	29.0					12																	57869681		2201	4296	6497	SO:0001587	stop_gained	64333	exon9			CCGACTGCAGCAG	AB051853	CCDS8941.2, CCDS44928.1, CCDS44929.1	12q13.3	2013-01-10			ENSG00000123329	ENSG00000123329		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	14130	protein-coding gene	gene with protein product		610576				11396949	Standard	NM_032496		Approved	MGC1295, 10C	uc001soc.3	Q9BRR9	OTTHUMG00000150147	ENST00000356411.2:c.1246C>T	12.37:g.57869681G>A	ENSP00000348782:p.Gln416*	120.0	0.0	0		117.0	47.0	0.401709	NM_001080157	B4DVI3|E9PDX9|Q8NAF3|Q8TCJ3|Q8WYR0|Q96EZ2|Q96S74	Nonsense_Mutation	SNP	ENST00000356411.2	37		.	.	.	.	.	.	.	.	.	.	G	40	7.946108	0.98574	.	.	ENSG00000123329	ENST00000393791;ENST00000356411;ENST00000423291;ENST00000424809;ENST00000393797;ENST00000340423;ENST00000430041;ENST00000548139	.	.	.	3.97	3.97	0.46021	.	0.139059	0.48767	D	0.000170	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	13.468	0.61266	0.0:0.0:1.0:0.0	.	.	.	.	X	416;416;86;416;487;465;232;232	.	ENSP00000344852:Q465X	Q	-	1	0	ARHGAP9	56155948	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	5.206000	0.65192	2.235000	0.73313	0.561000	0.74099	CAG	.	.	none		0.647	ARHGAP9-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_032496	
ALPP	250	hgsc.bcm.edu	37	2	233243796	233243796	+	Splice_Site	SNP	T	T	C	rs200958062|rs1130338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233243796T>C	ENST00000392027.2	+	2	461	c.192T>C	c.(190-192)gaT>gaC	p.D64D	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	64					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		TCCTGGGCGATGGTGAGTGAG	0.667													t|||	60	0.0119808	0.0008	0.0101	5008	,	,		17060	0.0		0.0258	False		,,,				2504	0.0266				p.D64D		Atlas-SNP	.											.	ALPP	53	.	0			c.T192C						PASS	.	C		9,4397		0,9,2194	72.0	79.0	77.0		192	-5.0	0.0	2		77	144,8456		4,136,4160	no	coding-synonymous-near-splice	ALPP	NM_001632.3		4,145,6354	CC,CT,TT		1.6744,0.2043,1.1764		64/536	233243796	153,12853	2203	4300	6503	SO:0001630	splice_region_variant	250	exon2			GGGCGATGGTGAG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.193+1T>C	2.37:g.233243796T>C		94.0	0.0	0		85.0	33.0	0.388235	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	37	CCDS2490.1																																																																																			T|0.989;C|0.011	0.011	strong		0.667	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	Silent
WDR90	197335	hgsc.bcm.edu	37	16	716494	716494	+	Missense_Mutation	SNP	G	G	A	rs373898012		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:716494G>A	ENST00000293879.4	+	38	4780	c.4780G>A	c.(4780-4782)Gct>Act	p.A1594T	RHOT2_ENST00000315082.4_5'Flank|WDR90_ENST00000549091.1_Missense_Mutation_p.A1596T|WDR90_ENST00000315764.4_Intron|WDR90_ENST00000547543.1_3'UTR|WDR90_ENST00000547944.1_Missense_Mutation_p.A193T			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1594										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCTATGGCTGGCTGCCAGTGG	0.632																																					p.A1594T		Atlas-SNP	.											.	WDR90	107	.	0			c.G4780A						PASS	.	G	THR/ALA	0,4066		0,0,2033	30.0	40.0	37.0		4780	4.5	1.0	16		37	2,8340		0,2,4169	no	missense	WDR90	NM_145294.4	58	0,2,6202	AA,AG,GG		0.024,0.0,0.0161	probably-damaging	1594/1749	716494	2,12406	2033	4171	6204	SO:0001583	missense	197335	exon38			TGGCTGGCTGCCA	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.4780G>A	16.37:g.716494G>A	ENSP00000293879:p.Ala1594Thr	98.0	0.0	0		106.0	51.0	0.481132	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.919032	0.92249	0.0	2.4E-4	ENSG00000161996	ENST00000549091;ENST00000293879;ENST00000547944	T;T;T	0.62788	1.43;1.4;-0.0	4.49	4.49	0.54785	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.235790	0.42420	D	0.000715	T	0.78534	0.4298	M	0.77486	2.375	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.981	T	0.78352	-0.2237	10	0.33141	T	0.24	.	16.1987	0.82053	0.0:0.0:1.0:0.0	.	193;1594	G3V201;Q96KV7	.;WDR90_HUMAN	T	1596;1594;193	ENSP00000448122:A1596T;ENSP00000293879:A1594T;ENSP00000449576:A193T	ENSP00000293879:A1594T	A	+	1	0	WDR90	656495	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	6.432000	0.73400	2.045000	0.60652	0.561000	0.74099	GCT	.	.	weak		0.632	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
UNC119	9094	hgsc.bcm.edu	37	17	26874803	26874803	+	Missense_Mutation	SNP	G	G	A	rs146916036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26874803G>A	ENST00000335765.4	-	4	612	c.502C>T	c.(502-504)Cgc>Tgc	p.R168C	UNC119_ENST00000484980.1_Missense_Mutation_p.R73C|UNC119_ENST00000470125.1_Missense_Mutation_p.R73C|UNC119_ENST00000301032.4_Missense_Mutation_p.R168C	NM_005148.3	NP_005139.1	Q13432	U119A_HUMAN	unc-119 homolog (C. elegans)	168	Required for centrosome localization.				cytokinesis, completion of separation (GO:0007109)|endocytosis (GO:0006897)|lipoprotein transport (GO:0042953)|negative regulation of caveolin-mediated endocytosis (GO:2001287)|negative regulation of clathrin-mediated endocytosis (GO:1900186)|phototransduction (GO:0007602)|positive regulation of protein tyrosine kinase activity (GO:0061098)|synaptic transmission (GO:0007268)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	lipid binding (GO:0008289)			breast(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	7	Lung NSC(42;0.00431)					AGCTGGTTGCGGAAGTAGTGC	0.537											OREG0024277	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R168C		Atlas-SNP	.											.	UNC119	27	.	0			c.C502T						PASS	.	G	CYS/ARG,CYS/ARG	0,4406		0,0,2203	173.0	156.0	162.0		502,502	4.8	1.0	17	dbSNP_134	162	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	UNC119	NM_005148.3,NM_054035.2	180,180	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	probably-damaging,probably-damaging	168/241,168/221	26874803	11,12995	2203	4300	6503	SO:0001583	missense	9094	exon4			GGTTGCGGAAGTA	U40998	CCDS11233.1, CCDS11234.1	17q11.2	2014-09-17	2001-11-28		ENSG00000109103	ENSG00000109103			12565	protein-coding gene	gene with protein product	"""POC7 centriolar protein homolog A (Chlamydomonas)"""	604011	"""unc119 (C.elegans) homolog"""			8576185, 9538874	Standard	NM_005148		Approved	HRG4, POC7, POC7A	uc002hbk.2	Q13432	OTTHUMG00000132606	ENST00000335765.4:c.502C>T	17.37:g.26874803G>A	ENSP00000337040:p.Arg168Cys	216.0	0.0	0	790	259.0	122.0	0.471042	NM_005148	A8K8G4|F1T095|O95126	Missense_Mutation	SNP	ENST00000335765.4	37	CCDS11233.1	.	.	.	.	.	.	.	.	.	.	G	21.9	4.221194	0.79464	0.0	0.001279	ENSG00000109103	ENST00000335765;ENST00000301032;ENST00000444148	D;D;D	0.82344	-1.51;-1.59;-1.6	5.81	4.83	0.62350	Immunoglobulin E-set (1);	0.000000	0.85682	D	0.000000	D	0.93259	0.7852	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.76575	0.988;0.988	D	0.95030	0.8168	10	0.87932	D	0	-19.9144	16.2568	0.82522	0.0:0.0:0.8662:0.1338	.	168;168	F1T095;Q13432	.;U119A_HUMAN	C	168;168;161	ENSP00000337040:R168C;ENSP00000301032:R168C;ENSP00000414639:R161C	ENSP00000301032:R168C	R	-	1	0	UNC119	23898930	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.862000	0.56009	1.437000	0.47472	0.462000	0.41574	CGC	G|0.999;A|0.001	0.001	strong		0.537	UNC119-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255842.2		
NBEAL2	23218	hgsc.bcm.edu	37	3	47033970	47033970	+	Silent	SNP	C	C	T	rs201015016	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:47033970C>T	ENST00000450053.3	+	10	1217	c.1038C>T	c.(1036-1038)taC>taT	p.Y346Y	NBEAL2_ENST00000292309.5_Silent_p.Y346Y|NBEAL2_ENST00000383740.2_5'UTR	NM_015175.2	NP_055990.1	Q6ZNJ1	NBEL2_HUMAN	neurobeachin-like 2	346					blood coagulation (GO:0007596)|megakaryocyte development (GO:0035855)|platelet alpha granule organization (GO:0070889)|platelet formation (GO:0030220)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(9)|lung(9)|ovary(4)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	51		Acute lymphoblastic leukemia(5;0.0534)		BRCA - Breast invasive adenocarcinoma(193;0.0012)|KIRC - Kidney renal clear cell carcinoma(197;0.00575)|Kidney(197;0.00656)		CACAGCTGTACCTGCAGTCCC	0.642													C|||	2	0.000399361	0.0	0.0014	5008	,	,		17796	0.0		0.001	False		,,,				2504	0.0				p.Y346Y		Atlas-SNP	.											.	NBEAL2	267	.	0			c.C1038T						PASS	.	C		3,3859		0,3,1928	26.0	28.0	27.0		1038	3.4	1.0	3		27	23,8219		0,23,4098	no	coding-synonymous	NBEAL2	NM_015175.1		0,26,6026	TT,TC,CC		0.2791,0.0777,0.2148		346/2755	47033970	26,12078	1931	4121	6052	SO:0001819	synonymous_variant	23218	exon10			GCTGTACCTGCAG	AB011112	CCDS46817.1	3p21.31	2014-09-17			ENSG00000160796	ENSG00000160796		"""WD repeat domain containing"""	31928	protein-coding gene	gene with protein product		614169					Standard	NM_015175		Approved	KIAA0540	uc003cqp.3	Q6ZNJ1	OTTHUMG00000156497	ENST00000450053.3:c.1038C>T	3.37:g.47033970C>T		96.0	0.0	0		88.0	37.0	0.420455	NM_015175	O60288|Q6P994|Q6UX91|Q8NAC9	Silent	SNP	ENST00000450053.3	37	CCDS46817.1																																																																																			C|0.998;T|0.002	0.002	weak		0.642	NBEAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344363.3	XM_291064	
EZH2	2146	hgsc.bcm.edu	37	7	148508727	148508727	+	Missense_Mutation	SNP	T	T	G	rs267601394		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:148508727T>G	ENST00000460911.1	-	16	2010	c.1922A>C	c.(1921-1923)tAc>tCc	p.Y641S	EZH2_ENST00000320356.2_Missense_Mutation_p.Y646S|EZH2_ENST00000541220.1_Missense_Mutation_p.Y590S|EZH2_ENST00000350995.2_Missense_Mutation_p.Y602S|EZH2_ENST00000478654.1_Missense_Mutation_p.Y590S|EZH2_ENST00000483967.1_Missense_Mutation_p.Y632S|EZH2_ENST00000476773.1_Missense_Mutation_p.Y590S			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	641	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.		Y -> C (in a patient with diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> F (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> H (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> N (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.|Y -> S (found in patients with follicular lymphoma; also in diffuse large B-cell lymphoma; somatic mutation). {ECO:0000269|PubMed:20081860}.		cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)	p.Y646F(59)|p.Y646S(22)|p.Y602F(8)|p.Y646C(6)|p.Y602S(4)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			CTCTCCACAGTATTCTGAGAT	0.378			Mis		DLBCL																																p.Y646S		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,face,carcinoma,-1,214	EZH2	823	214	99	Substitution - Missense(99)	haematopoietic_and_lymphoid_tissue(99)	c.A1937C						PASS	.						96.0	89.0	91.0					7																	148508727		2203	4300	6503	SO:0001583	missense	2146	exon16			CCACAGTATTCTG		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.1922A>C	7.37:g.148508727T>G	ENSP00000419711:p.Tyr641Ser	46.0	0.0	0		57.0	24.0	0.421053	NM_004456	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	.	.	.	.	.	.	.	.	.	.	t	25.3	4.619614	0.87460	.	.	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967	D;D;D;D;D;D;D	0.93307	-3.2;-1.94;-1.94;-1.94;-3.2;-3.2;-1.94	5.63	5.63	0.86233	SET domain (3);	0.000000	0.85682	D	0.000000	D	0.97654	0.9231	H	0.99516	4.605	0.80722	D	1	D;P;P;D;P	0.63880	0.986;0.918;0.543;0.993;0.688	P;P;B;P;B	0.52481	0.7;0.577;0.395;0.7;0.318	D	0.99066	1.0832	10	0.87932	D	0	.	15.87	0.79108	0.0:0.0:0.0:1.0	.	632;590;641;602;646	Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;EZH2_HUMAN;.;.	S	590;646;641;602;590;590;632	ENSP00000417062:Y590S;ENSP00000320147:Y646S;ENSP00000419711:Y641S;ENSP00000223193:Y602S;ENSP00000443219:Y590S;ENSP00000419050:Y590S;ENSP00000419856:Y632S	ENSP00000320147:Y646S	Y	-	2	0	EZH2	148139660	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.789000	0.85783	2.145000	0.66743	0.533000	0.62120	TAC	.	.	none		0.378	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
MUC2	4583	hgsc.bcm.edu	37	11	1103855	1103855	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1103855C>T	ENST00000441003.2	+	48	8181	c.8154C>T	c.(8152-8154)gtC>gtT	p.V2718V		NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	5080					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	CCGTCCCCGTCACCACGGAGG	0.642																																					p.V2714V		Atlas-SNP	.											.	MUC2	614	.	0			c.C8142T						PASS	.						22.0	25.0	24.0					11																	1103855		2048	4156	6204	SO:0001819	synonymous_variant	4583	exon49			CCCCGTCACCACG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.8154C>T	11.37:g.1103855C>T		97.0	0.0	0		106.0	62.0	0.584906	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
FAM189B	10712	hgsc.bcm.edu	37	1	155217614	155217614	+	Missense_Mutation	SNP	T	T	C	rs553505679		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:155217614T>C	ENST00000361361.2	-	12	2475	c.1966A>G	c.(1966-1968)Agc>Ggc	p.S656G	FAM189B_ENST00000368368.3_Missense_Mutation_p.S638G|FAM189B_ENST00000350210.2_Missense_Mutation_p.S560G|FAM189B_ENST00000472550.1_5'Flank	NM_006589.2	NP_006580.2	P81408	F189B_HUMAN	family with sequence similarity 189, member B	656						integral component of membrane (GO:0016021)	WW domain binding (GO:0050699)			breast(4)|central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23						AGGCTGAGGCTGTGGGGGCGG	0.647													T|||	1	0.000199681	0.0008	0.0	5008	,	,		14418	0.0		0.0	False		,,,				2504	0.0				p.S656G		Atlas-SNP	.											.	FAM189B	51	.	0			c.A1966G						PASS	.						11.0	11.0	11.0					1																	155217614		2144	4211	6355	SO:0001583	missense	10712	exon12			TGAGGCTGTGGGG	AF070550	CCDS1103.1, CCDS1104.1, CCDS58035.1	1q21	2009-07-09	2009-07-09	2009-07-09	ENSG00000160767	ENSG00000160767			1233	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 2"""	C1orf2		9331372	Standard	NM_006589		Approved	cote1	uc001fjm.3	P81408	OTTHUMG00000035844	ENST00000361361.2:c.1966A>G	1.37:g.155217614T>C	ENSP00000354958:p.Ser656Gly	373.0	0.0	0		400.0	205.0	0.5125	NM_006589	B1AVS5|Q8IXL3|Q9BR66	Missense_Mutation	SNP	ENST00000361361.2	37	CCDS1103.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.066640	0.76301	.	.	ENSG00000160767	ENST00000350210;ENST00000368368;ENST00000361361	T;T;T	0.03272	3.99;3.99;3.99	4.51	4.51	0.55191	.	0.000000	0.64402	D	0.000008	T	0.03959	0.0111	N	0.19112	0.55	0.31239	N	0.695389	D;P;P;P	0.59767	0.986;0.924;0.954;0.924	D;P;D;P	0.70935	0.971;0.878;0.916;0.827	T	0.21348	-1.0248	10	0.87932	D	0	.	12.1475	0.54031	0.0:0.0:0.0:1.0	.	421;638;560;656	B1AVS2;B1AVS5;P81408-2;P81408	.;.;.;F189B_HUMAN	G	560;638;656	ENSP00000307128:S560G;ENSP00000357352:S638G;ENSP00000354958:S656G	ENSP00000307128:S560G	S	-	1	0	FAM189B	153484238	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.099000	0.64554	2.037000	0.60232	0.529000	0.55759	AGC	.	.	none		0.647	FAM189B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087224.1	NM_006589	
ZNF688	146542	hgsc.bcm.edu	37	16	30582855	30582855	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30582855G>A	ENST00000223459.6	-	1	1200	c.96C>T	c.(94-96)gcC>gcT	p.A32A	AC002310.7_ENST00000486926.1_RNA|ZNF688_ENST00000395219.1_Intron|ZNF688_ENST00000563707.1_Silent_p.A32A|AC002310.7_ENST00000492040.1_RNA|ZNF688_ENST00000567855.1_Silent_p.A32A	NM_145271.3	NP_660314.1	P0C7X2	ZN688_HUMAN	zinc finger protein 688	32	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(2)|lung(2)|ovary(1)	8						AGAAGTACACGGCCACGTCCG	0.741																																					p.A32A		Atlas-SNP	.											.	ZNF688	37	.	0			c.C96T						PASS	.						12.0	14.0	13.0					16																	30582855		2187	4293	6480	SO:0001819	synonymous_variant	146542	exon1			GTACACGGCCACG	AK122680	CCDS10684.1	16p11.2	2013-01-08			ENSG00000229809	ENSG00000229809		"""Zinc fingers, C2H2-type"", ""-"""	30489	protein-coding gene	gene with protein product						10493829	Standard	XM_005255139		Approved		uc002dys.2	P0C7X2	OTTHUMG00000132408	ENST00000223459.6:c.96C>T	16.37:g.30582855G>A		109.0	0.0	0		103.0	41.0	0.398058	NM_145271	A8MV39|B3KV51|O75701|Q8IW91|Q8WV14|Q96MN0	Silent	SNP	ENST00000223459.6	37	CCDS10684.1																																																																																			.	.	none		0.741	ZNF688-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255544.2	NM_145271	
SLC11A2	4891	hgsc.bcm.edu	37	12	51386017	51386017	+	Missense_Mutation	SNP	G	G	T	rs144863268	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51386017G>T	ENST00000262051.7	-	13	1390	c.1303C>A	c.(1303-1305)Cta>Ata	p.L435I	SLC11A2_ENST00000541174.2_Missense_Mutation_p.L435I|SLC11A2_ENST00000547688.1_Missense_Mutation_p.L464I|SLC11A2_ENST00000546743.1_Missense_Mutation_p.L356I|SLC11A2_ENST00000262052.5_Missense_Mutation_p.L435I|SLC11A2_ENST00000547198.1_Missense_Mutation_p.L435I|SLC11A2_ENST00000394904.3_Missense_Mutation_p.L464I|SLC11A2_ENST00000545993.2_Missense_Mutation_p.L431I	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	435			L -> I (in dbSNP:rs144863268). {ECO:0000269|PubMed:9642100}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						ATCCCTGTTAGATGCTCTACA	0.468													G|||	3	0.000599042	0.0015	0.0	5008	,	,		21375	0.0		0.001	False		,,,				2504	0.0				p.L464I		Atlas-SNP	.											.	SLC11A2	51	.	0			c.C1390A						PASS	.	G	ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU,ILE/LEU	1,4405	2.1+/-5.4	0,1,2202	152.0	126.0	135.0		1303,1390,1303,1303,1303,1303,1291	4.7	0.9	12	dbSNP_134	135	25,8575	17.3+/-56.4	0,25,4275	yes	missense,missense,missense,missense,missense,missense,missense	SLC11A2	NM_000617.2,NM_001174125.1,NM_001174126.1,NM_001174127.1,NM_001174128.1,NM_001174129.1,NM_001174130.1	5,5,5,5,5,5,5	0,26,6477	TT,TG,GG		0.2907,0.0227,0.1999	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	435/562,464/591,435/569,435/569,435/562,435/562,431/558	51386017	26,12980	2203	4300	6503	SO:0001583	missense	4891	exon13			CTGTTAGATGCTC	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.1303C>A	12.37:g.51386017G>T	ENSP00000262051:p.Leu435Ile	101.0	0.0	0		93.0	39.0	0.419355	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	19.37	3.814690	0.70912	2.27E-4	0.002907	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.69561	-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41;-0.41	5.59	4.67	0.58626	.	0.000000	0.85682	D	0.000000	T	0.73361	0.3577	L	0.49256	1.55	0.58432	D	0.999993	D;D;D;D;D;P	0.64830	0.985;0.981;0.994;0.994;0.985;0.883	D;D;D;D;D;P	0.67382	0.951;0.919;0.919;0.919;0.951;0.665	T	0.72191	-0.4365	9	.	.	.	-6.39	9.6058	0.39632	0.1786:0.0:0.8214:0.0	.	398;431;464;435;284;435	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	I	435;435;435;464;464;435;431;356	ENSP00000262051:L435I;ENSP00000446769:L435I;ENSP00000262052:L435I;ENSP00000378364:L464I;ENSP00000449200:L464I;ENSP00000444542:L435I;ENSP00000442810:L431I;ENSP00000446914:L356I	.	L	-	1	2	SLC11A2	49672284	1.000000	0.71417	0.949000	0.38748	0.975000	0.68041	2.010000	0.40913	1.408000	0.46895	0.655000	0.94253	CTA	G|0.998;T|0.002	0.002	strong		0.468	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
PRUNE2	158471	hgsc.bcm.edu	37	9	79322711	79322711	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:79322711G>A	ENST00000376718.3	-	8	4602	c.4479C>T	c.(4477-4479)gaC>gaT	p.D1493D	PRUNE2_ENST00000428286.1_Silent_p.D1134D	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	1493					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						CTATAGGGACGTCCCCAAAAT	0.468																																					p.D1493D		Atlas-SNP	.											.	PRUNE2	331	.	0			c.C4479T						PASS	.						43.0	42.0	43.0					9																	79322711		1568	3582	5150	SO:0001819	synonymous_variant	158471	exon8			AGGGACGTCCCCA	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.4479C>T	9.37:g.79322711G>A		83.0	0.0	0		100.0	45.0	0.45	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Silent	SNP	ENST00000376718.3	37	CCDS47982.1	.	.	.	.	.	.	.	.	.	.	G	3.028	-0.200220	0.06219	.	.	ENSG00000106772	ENST00000426088	.	.	.	5.49	-1.57	0.08506	.	.	.	.	.	T	0.20129	0.0484	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	-1.5436	2.2159	0.03959	0.4355:0.2533:0.0685:0.2427	.	.	.	.	C	815	.	.	R	-	1	0	PRUNE2	78512531	0.011000	0.17503	0.001000	0.08648	0.002000	0.02628	0.261000	0.18442	-0.420000	0.07427	-0.238000	0.12139	CGT	.	.	none		0.468	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
SMIM8	57150	hgsc.bcm.edu	37	6	88046818	88046818	+	Silent	SNP	A	A	G	rs138902411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:88046818A>G	ENST00000392863.1	+	3	158	c.69A>G	c.(67-69)ccA>ccG	p.P23P	RP1-102H19.8_ENST00000448282.2_Silent_p.P23P|SMIM8_ENST00000608353.1_Silent_p.P23P|SMIM8_ENST00000608868.1_Silent_p.P23P|SMIM8_ENST00000608525.1_Silent_p.P23P|SMIM8_ENST00000229570.5_Silent_p.P23P	NM_001042493.1	NP_001035958.1	Q96KF7	SMIM8_HUMAN	small integral membrane protein 8	23						integral component of membrane (GO:0016021)											TTCAAAGCCCAGGGCTCAGAG	0.408													A|||	2	0.000399361	0.0	0.0	5008	,	,		14790	0.0		0.002	False		,,,				2504	0.0				p.P23P		Atlas-SNP	.											.	.	.	.	0			c.A69G						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	94.0	96.0	95.0		69,69	2.1	1.0	6	dbSNP_134	95	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous,coding-synonymous	C6orf162	NM_001042493.1,NM_020425.4	,	0,23,6480	GG,GA,AA		0.2093,0.1135,0.1768	,	23/98,23/98	88046818	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	57150	exon3			AAGCCCAGGGCTC	AL050201	CCDS34496.1, CCDS75493.1	6q15	2013-06-21	2012-11-20	2012-11-20	ENSG00000111850	ENSG00000111850			21401	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 162"""	C6orf162			Standard	NM_001287445		Approved	DKFZP586E1923, dJ102H19.2	uc003plq.1	Q96KF7	OTTHUMG00000015168	ENST00000392863.1:c.69A>G	6.37:g.88046818A>G		89.0	0.0	0		68.0	39.0	0.573529	NM_001042493	B2R4V6|E1P505|Q5TEZ3|Q6NSD2|Q8IZ10	Silent	SNP	ENST00000392863.1	37	CCDS34496.1																																																																																			A|0.998;G|0.002	0.002	strong		0.408	SMIM8-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472479.2	NM_020425	
CEMP1	752014	hgsc.bcm.edu	37	16	2580755	2580755	+	Missense_Mutation	SNP	G	G	C	rs76722821	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2580755G>C	ENST00000567119.1	-	1	654	c.320C>G	c.(319-321)gCg>gGg	p.A107G	AMDHD2_ENST00000413459.3_Missense_Mutation_p.A594P|AMDHD2_ENST00000565570.1_3'UTR|AMDHD2_ENST00000302956.4_3'UTR|CEMP1_ENST00000565480.1_Intron|CEMP1_ENST00000382350.1_Missense_Mutation_p.A107G|MIR3178_ENST00000581887.1_RNA	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	107						cytoplasm (GO:0005737)				lung(1)|skin(1)	2						GCAGGGCCTCGCCTGAGGGAG	0.627													G|||	40	0.00798722	0.0	0.0173	5008	,	,		18584	0.0		0.0258	False		,,,				2504	0.002				p.A594P		Atlas-SNP	.											.	AMDHD2	33	.	0			c.G1780C						PASS	.	G	PRO/ALA,GLY/ALA	12,3928		0,12,1958	31.0	36.0	35.0		1780,320	0.6	0.0	16	dbSNP_131	35	141,8143		5,131,4006	yes	missense,missense	AMDHD2,CEMP1	NM_001145815.1,NM_001048212.3	27,60	5,143,5964	CC,CG,GG		1.7021,0.3046,1.2516	probably-damaging,probably-damaging	594/595,107/248	2580755	153,12071	1970	4142	6112	SO:0001583	missense	51005	exon11			GGCCTCGCCTGAG	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"""cementum protein-23"""	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.320C>G	16.37:g.2580755G>C	ENSP00000457380:p.Ala107Gly	54.0	0.0	0		64.0	32.0	0.5	NM_001145815	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	37	CCDS42108.1	20|20	0.009157509157509158|0.009157509157509158	0|0	0.0|0.0	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	14|14	0.018469656992084433|0.018469656992084433	G|G	3.474|3.474	-0.107349|-0.107349	0.06924|0.06924	0.003046|0.003046	0.017021|0.017021	ENSG00000205923|ENSG00000162066	ENST00000382350|ENST00000413459	T|.	0.55234|.	0.53|.	0.559|0.559	0.559|0.559	0.17272|0.17272	.|.	.|.	.|.	.|.	.|.	T|T	0.38241|0.38241	0.1033|0.1033	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D|D	0.65815|0.56968	0.995|0.978	D|P	0.69142|0.61800	0.962|0.894	T|T	0.28618|0.28618	-1.0038|-1.0038	7|6	0.87932|0.87932	D|D	0|0	.|.	.|.	.|.	.|.	.|.	107|594	Q6PRD7|Q9Y303-3	CEMP1_HUMAN|.	G|P	107|594	ENSP00000371787:A107G|.	ENSP00000371787:A107G|ENSP00000391596:A594P	A|A	-|+	2|1	0|0	CEMP1|AMDHD2	2520756|2520756	0.005000|0.005000	0.15991|0.15991	0.001000|0.001000	0.08648|0.08648	0.002000|0.002000	0.02628|0.02628	-0.342000|-0.342000	0.07801|0.07801	0.556000|0.556000	0.29098|0.29098	0.561000|0.561000	0.74099|0.74099	GCG|GCC	G|0.990;C|0.010	0.010	strong		0.627	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212	
ZFPM2	23414	hgsc.bcm.edu	37	8	106814029	106814029	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:106814029C>A	ENST00000407775.2	+	8	1969	c.1719C>A	c.(1717-1719)agC>agA	p.S573R	ZFPM2_ENST00000378472.4_Missense_Mutation_p.S304R|RP11-152P17.2_ENST00000524045.2_RNA|RP11-152P17.2_ENST00000521622.1_RNA|ZFPM2_ENST00000517361.1_Missense_Mutation_p.S441R|RP11-152P17.2_ENST00000520594.1_RNA|RP11-152P17.2_ENST00000520433.1_RNA|ZFPM2_ENST00000522296.1_3'UTR|RP11-152P17.2_ENST00000509144.2_RNA|ZFPM2_ENST00000520492.1_Missense_Mutation_p.S441R|RP11-152P17.2_ENST00000518932.1_RNA	NM_012082.3	NP_036214.2	Q8WW38	FOG2_HUMAN	zinc finger protein, FOG family member 2	573					blood coagulation (GO:0007596)|embryonic organ development (GO:0048568)|gonadal mesoderm development (GO:0007506)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|negative regulation of cell death (GO:0060548)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of female gonad development (GO:2000195)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|vasculogenesis (GO:0001570)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|nucleic acid binding transcription factor activity (GO:0001071)|RNA polymerase II transcription coactivator activity (GO:0001105)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(4)|breast(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(11)|liver(2)|lung(48)|ovary(4)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	99			OV - Ovarian serous cystadenocarcinoma(57;8.28e-08)			ATTGCAGCAGCCGATGGCAGC	0.448																																					p.S573R		Atlas-SNP	.											.	ZFPM2	219	.	0			c.C1719A						PASS	.						128.0	131.0	130.0					8																	106814029		1929	4136	6065	SO:0001583	missense	23414	exon8			CAGCAGCCGATGG	AF119334	CCDS47908.1	8q23	2013-01-10	2012-11-27		ENSG00000169946	ENSG00000169946		"""Zinc fingers, C2H2-type"", ""Zinc fingers, C2HC-type containing"""	16700	protein-coding gene	gene with protein product		603693	"""zinc finger protein, multitype 2"""			9927675, 10438528	Standard	NM_012082		Approved	FOG2, hFOG-2, ZNF89B, ZC2HC11B	uc003ymd.3	Q8WW38	OTTHUMG00000164818	ENST00000407775.2:c.1719C>A	8.37:g.106814029C>A	ENSP00000384179:p.Ser573Arg	125.0	0.0	0		185.0	93.0	0.502703	NM_012082	Q32MA6|Q9NPL7|Q9NPS4|Q9UNI5	Missense_Mutation	SNP	ENST00000407775.2	37	CCDS47908.1	.	.	.	.	.	.	.	.	.	.	C	15.47	2.842831	0.51057	.	.	ENSG00000169946	ENST00000407775;ENST00000520492;ENST00000517361;ENST00000378472	T;T;T;T	0.25579	1.79;2.28;2.28;3.53	5.86	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.48059	0.1479	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.44711	-0.9310	10	0.44086	T	0.13	.	11.619	0.51106	0.0:0.8135:0.0:0.1865	.	573	Q8WW38	FOG2_HUMAN	R	573;441;441;304	ENSP00000384179:S573R;ENSP00000430757:S441R;ENSP00000428720:S441R;ENSP00000367733:S304R	ENSP00000367733:S304R	S	+	3	2	ZFPM2	106883205	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.698000	0.37794	1.485000	0.48380	0.655000	0.94253	AGC	.	.	none		0.448	ZFPM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380614.1		
NWD1	284434	hgsc.bcm.edu	37	19	16872794	16872794	+	Silent	SNP	C	C	T	rs61995711	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:16872794C>T	ENST00000552788.1	+	6	1978	c.1978C>T	c.(1978-1980)Ctg>Ttg	p.L660L	NWD1_ENST00000379808.3_Silent_p.L660L|NWD1_ENST00000523826.1_Silent_p.L454L|NWD1_ENST00000339803.6_Silent_p.L525L|NWD1_ENST00000524140.2_Silent_p.L660L|NWD1_ENST00000549814.1_Silent_p.L660L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	660	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CTGTAGACAGCTGGTCGAGGT	0.582													C|||	33	0.00658946	0.0008	0.0086	5008	,	,		16843	0.0		0.0229	False		,,,				2504	0.0031				p.L660L		Atlas-SNP	.											.	NWD1	303	.	0			c.C1978T						PASS	.	C		17,4389	24.3+/-50.5	0,17,2186	89.0	70.0	76.0		1978	3.3	1.0	19	dbSNP_129	76	198,8402	86.6+/-149.0	2,194,4104	no	coding-synonymous	NWD1	NM_001007525.3		2,211,6290	TT,TC,CC		2.3023,0.3858,1.6531		660/1433	16872794	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon8			AGACAGCTGGTCG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1978C>T	19.37:g.16872794C>T		75.0	0.0	0		98.0	44.0	0.44898	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				C|0.986;T|0.014	0.014	strong		0.582	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
RHPN2	85415	hgsc.bcm.edu	37	19	33517507	33517507	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:33517507C>T	ENST00000254260.3	-	3	252	c.217G>A	c.(217-219)Gtg>Atg	p.V73M	RHPN2_ENST00000400226.4_De_novo_Start_OutOfFrame	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	73					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)		p.V73M(2)		NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TCCAGCCGCACTTGCTCCCGC	0.552																																					p.V73M		Atlas-SNP	.											RHPN2,face,carcinoma,0,2	RHPN2	107	2	2	Substitution - Missense(2)	NS(1)|skin(1)	c.G217A						scavenged	.						84.0	83.0	83.0					19																	33517507		2203	4300	6503	SO:0001583	missense	85415	exon3			GCCGCACTTGCTC	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.217G>A	19.37:g.33517507C>T	ENSP00000254260:p.Val73Met	15.0	1.0	0.0666667		39.0	5.0	0.128205	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.542997	0.65198	.	.	ENSG00000131941	ENST00000254260	T	0.39787	1.06	3.88	3.88	0.44766	.	0.000000	0.85682	D	0.000000	T	0.64853	0.2636	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.71984	-0.4427	10	0.87932	D	0	11.9954	16.025	0.80536	0.0:1.0:0.0:0.0	.	73	Q8IUC4	RHPN2_HUMAN	M	73	ENSP00000254260:V73M	ENSP00000254260:V73M	V	-	1	0	RHPN2	38209347	1.000000	0.71417	1.000000	0.80357	0.343000	0.28985	7.267000	0.78462	2.167000	0.68274	0.557000	0.71058	GTG	.	.	none		0.552	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
PLEC	5339	hgsc.bcm.edu	37	8	144992552	144992552	+	Missense_Mutation	SNP	G	G	A	rs201666443		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144992552G>A	ENST00000322810.4	-	32	12017	c.11848C>T	c.(11848-11850)Cgc>Tgc	p.R3950C	PLEC_ENST00000354589.3_Missense_Mutation_p.R3813C|PLEC_ENST00000354958.2_Missense_Mutation_p.R3791C|PLEC_ENST00000527096.1_Missense_Mutation_p.R3836C|PLEC_ENST00000357649.2_Missense_Mutation_p.R3817C|PLEC_ENST00000436759.2_Missense_Mutation_p.R3840C|PLEC_ENST00000345136.3_Missense_Mutation_p.R3813C|PLEC_ENST00000356346.3_Missense_Mutation_p.R3799C|PLEC_ENST00000398774.2_Missense_Mutation_p.R3781C	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	3950	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						AAGCCCAGGCGGGGGTCCACG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		15094	0.0		0.0	False		,,,				2504	0.001				p.R3950C		Atlas-SNP	.											.	PLEC	1144	.	0			c.C11848T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4044		0,0,2022	12.0	17.0	16.0		11518,11395,11371,11848,11341,11437,11449,11437	3.8	0.6	8		16	2,8328		0,2,4163	yes	missense,missense,missense,missense,missense,missense,missense,missense	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	180,180,180,180,180,180,180,180	0,2,6185	AA,AG,GG		0.024,0.0,0.0162	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	3840/4575,3799/4534,3791/4526,3950/4685,3781/4516,3813/4548,3817/4552,3813/4548	144992552	2,12372	2022	4165	6187	SO:0001583	missense	5339	exon32			CCAGGCGGGGGTC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.11848C>T	8.37:g.144992552G>A	ENSP00000323856:p.Arg3950Cys	27.0	0.0	0		28.0	11.0	0.392857	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Missense_Mutation	SNP	ENST00000322810.4	37	CCDS43772.1	.	.	.	.	.	.	.	.	.	.	G	8.746	0.920155	0.17982	0.0	2.4E-4	ENSG00000178209	ENST00000345136;ENST00000357649;ENST00000354589;ENST00000398774;ENST00000322810;ENST00000354958;ENST00000356346;ENST00000436759;ENST00000527096	T;T;T;T;T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78;-0.78	3.78	3.78	0.43462	.	0.335440	0.24089	U	0.041652	T	0.67135	0.2861	L	0.46157	1.445	0.35517	D	0.801081	P;D;P;P;P;P;P;P	0.54772	0.894;0.968;0.894;0.913;0.894;0.894;0.894;0.894	B;B;B;B;B;B;B;B	0.43990	0.311;0.311;0.311;0.438;0.311;0.311;0.311;0.311	T	0.74300	-0.3710	10	0.38643	T	0.18	.	10.3245	0.43785	0.0:0.0:0.8027:0.1973	.	3840;3799;3791;3950;3781;3813;3817;3813	Q15149-2;Q15149-9;Q15149-8;Q15149;Q15149-7;Q15149-5;Q15149-6;Q15149-4	.;.;.;PLEC_HUMAN;.;.;.;.	C	3813;3817;3813;3781;3950;3791;3799;3840;3836	ENSP00000344848:R3813C;ENSP00000350277:R3817C;ENSP00000346602:R3813C;ENSP00000381756:R3781C;ENSP00000323856:R3950C;ENSP00000347044:R3791C;ENSP00000348702:R3799C;ENSP00000388180:R3840C;ENSP00000434583:R3836C	ENSP00000323856:R3950C	R	-	1	0	PLEC	145064540	0.957000	0.32711	0.639000	0.29394	0.951000	0.60555	2.993000	0.49425	2.103000	0.63969	0.297000	0.19635	CGC	.	.	weak		0.652	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
PGAP1	80055	hgsc.bcm.edu	37	2	197781288	197781288	+	Missense_Mutation	SNP	T	T	C	rs142320636	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:197781288T>C	ENST00000354764.4	-	3	445	c.331A>G	c.(331-333)Aaa>Gaa	p.K111E	PGAP1_ENST00000409188.1_Missense_Mutation_p.K69E|PGAP1_ENST00000409475.1_Missense_Mutation_p.K111E|PGAP1_ENST00000485830.1_5'UTR	NM_024989.3	NP_079265.2	Q75T13	PGAP1_HUMAN	post-GPI attachment to proteins 1	111					anterior/posterior axis specification (GO:0009948)|attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|embryonic pattern specification (GO:0009880)|forebrain regionalization (GO:0021871)|head development (GO:0060322)|intracellular protein transport (GO:0006886)|myo-inositol transport (GO:0015798)|post-translational protein modification (GO:0043687)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	nuclease activity (GO:0004518)|phosphoric ester hydrolase activity (GO:0042578)			breast(4)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(9)|lung(11)|ovary(6)|stomach(1)|urinary_tract(1)	40						TCCTCTGCTTTTCTAAGTGCA	0.388													T|||	4	0.000798722	0.0	0.0014	5008	,	,		18296	0.0		0.003	False		,,,				2504	0.0				p.K111E		Atlas-SNP	.											.	PGAP1	84	.	0			c.A331G						PASS	.	T	GLU/LYS	2,4404	4.2+/-10.8	0,2,2201	77.0	71.0	73.0		331	5.6	1.0	2	dbSNP_134	73	13,8587	9.8+/-36.6	0,13,4287	yes	missense	PGAP1	NM_024989.3	56	0,15,6488	CC,CT,TT		0.1512,0.0454,0.1153	possibly-damaging	111/923	197781288	15,12991	2203	4300	6503	SO:0001583	missense	80055	exon3			CTGCTTTTCTAAG		CCDS2318.1	2q33.1	2014-03-03			ENSG00000197121	ENSG00000197121			25712	protein-coding gene	gene with protein product	"""GPI inositol-deacylase"""	611655				14734546, 17711852, 24482476	Standard	XM_005246866		Approved	FLJ12377, Bst1, SPG67	uc002utw.3	Q75T13	OTTHUMG00000132743	ENST00000354764.4:c.331A>G	2.37:g.197781288T>C	ENSP00000346809:p.Lys111Glu	119.0	0.0	0		128.0	58.0	0.453125	NM_024989	Q4G0R8|Q4ZG47|Q53SM0|Q6AW92|Q6UWV4|Q9HA24	Missense_Mutation	SNP	ENST00000354764.4	37	CCDS2318.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	24.3	4.516548	0.85495	4.54E-4	0.001512	ENSG00000197121	ENST00000354764;ENST00000409475;ENST00000409188	D;D;D	0.85955	-2.05;-2.05;-2.05	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	D	0.91503	0.7317	M	0.79123	2.44	0.80722	D	1	P;D	0.76494	0.873;0.999	B;D	0.83275	0.403;0.996	D	0.89403	0.3697	10	0.18276	T	0.48	-17.7348	16.0983	0.81144	0.0:0.0:0.0:1.0	.	111;111	Q75T13-3;Q75T13	.;PGAP1_HUMAN	E	111;111;69	ENSP00000346809:K111E;ENSP00000387028:K111E;ENSP00000386802:K69E	ENSP00000346809:K111E	K	-	1	0	PGAP1	197489533	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.643000	0.83403	2.256000	0.74724	0.524000	0.50904	AAA	T|0.999;C|0.001	0.001	strong		0.388	PGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256103.5	NM_024989	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447512	110447512	+	Missense_Mutation	SNP	G	G	C	rs142972518	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110447512G>C	ENST00000378402.5	+	29	3538	c.3434G>C	c.(3433-3435)gGg>gCg	p.G1145A		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1145	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CAGAATGTAGGGGGTGAAGAG	0.443										HNSCC(38;0.096)			G|||	58	0.0115815	0.0015	0.0101	5008	,	,		18338	0.0		0.0268	False		,,,				2504	0.0225				p.G1145A		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3434C						PASS	.	G	ALA/GLY	15,3743		0,15,1864	197.0	197.0	197.0		3434	-2.3	0.0	8	dbSNP_134	197	167,8083		3,161,3961	yes	missense	PKHD1L1	NM_177531.4	60	3,176,5825	CC,CG,GG		2.0242,0.3991,1.5157	benign	1145/4244	110447512	182,11826	1879	4125	6004	SO:0001583	missense	93035	exon29			ATGTAGGGGGTGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3434G>C	8.37:g.110447512G>C	ENSP00000367655:p.Gly1145Ala	167.0	0.0	0		222.0	102.0	0.459459	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	27	0.012362637362637362	0	0.0	5	0.013812154696132596	0	0.0	22	0.029023746701846966	G	2.585	-0.296544	0.05532	0.003991	0.020242	ENSG00000205038	ENST00000378402	D	0.85702	-2.02	6.07	-2.3	0.06785	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.912531	0.09435	N	0.802529	T	0.53142	0.1778	L	0.34521	1.04	0.09310	N	1	B	0.16396	0.017	B	0.21360	0.034	T	0.50074	-0.8870	10	0.12103	T	0.63	.	12.0147	0.53307	0.3405:0.0:0.6595:0.0	.	1145	Q86WI1	PKHL1_HUMAN	A	1145	ENSP00000367655:G1145A	ENSP00000367655:G1145A	G	+	2	0	PKHD1L1	110516688	0.005000	0.15991	0.000000	0.03702	0.004000	0.04260	0.643000	0.24750	-0.303000	0.08856	-0.768000	0.03414	GGG	G|0.986;C|0.014	0.014	strong		0.443	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
TRIM67	440730	hgsc.bcm.edu	37	1	231344908	231344908	+	Missense_Mutation	SNP	A	A	G	rs114415891	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:231344908A>G	ENST00000366653.5	+	8	2035	c.2035A>G	c.(2035-2037)Atg>Gtg	p.M679V	TRIM67_ENST00000449018.3_Missense_Mutation_p.M617V|TRIM67_ENST00000444294.3_Missense_Mutation_p.M677V|TRIM67_ENST00000366652.2_Missense_Mutation_p.M679V			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	679	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.			M -> V (in Ref. 3; BAC86689). {ECO:0000305}.	negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)	p.M679V(1)		breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GGTCAAGGACATGATGCTGGG	0.617													A|||	30	0.00599042	0.0	0.0072	5008	,	,		20231	0.0		0.0229	False		,,,				2504	0.002				p.M679V		Atlas-SNP	.											TRIM67_ENST00000366653,colon,carcinoma,-1,7	TRIM67	160	7	1	Substitution - Missense(1)	breast(1)	c.A2035G						PASS	.	A	VAL/MET	20,4368	26.2+/-53.5	0,20,2174	91.0	99.0	96.0		2035	5.7	1.0	1	dbSNP_132	96	142,8458	68.7+/-131.2	1,140,4159	yes	missense	TRIM67	NM_001004342.3	21	1,160,6333	GG,GA,AA		1.6512,0.4558,1.2473	benign	679/784	231344908	162,12826	2194	4300	6494	SO:0001583	missense	440730	exon8			AAGGACATGATGC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.2035A>G	1.37:g.231344908A>G	ENSP00000355613:p.Met679Val	230.0	1.0	0.00434783		263.0	127.0	0.48289	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Missense_Mutation	SNP	ENST00000366653.5	37	CCDS44333.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	A	4.607	0.112797	0.08831	0.004558	0.016512	ENSG00000119283	ENST00000444294;ENST00000366652;ENST00000449018;ENST00000366653	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.73	5.73	0.89815	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.85682	D	0.000000	T	0.28400	0.0702	N	0.02721	-0.515	0.46981	D	0.999274	B	0.14012	0.009	B	0.17098	0.017	T	0.27739	-1.0065	10	0.28530	T	0.3	.	16.3197	0.82945	1.0:0.0:0.0:0.0	.	679	Q6ZTA4	TRI67_HUMAN	V	677;679;617;679	ENSP00000412124:M677V;ENSP00000355612:M679V;ENSP00000400163:M617V;ENSP00000355613:M679V	ENSP00000355612:M679V	M	+	1	0	TRIM67	229411531	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.313000	0.65798	2.302000	0.77476	0.533000	0.62120	ATG	A|0.990;G|0.010	0.010	strong		0.617	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
ATP8B3	148229	hgsc.bcm.edu	37	19	1783185	1783185	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1783185G>A	ENST00000310127.6	-	29	3983	c.3745C>T	c.(3745-3747)Cgt>Tgt	p.R1249C	ATP8B3_ENST00000539485.1_Missense_Mutation_p.R1259C|ATP8B3_ENST00000525591.1_Missense_Mutation_p.R1212C	NM_138813.3	NP_620168.1	O60423	AT8B3_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 3	1249					binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)	p.R1259C(1)		central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	23		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)		TAGCTGGAACGGCGGGCACGA	0.587																																					p.R1249C		Atlas-SNP	.											ATP8B3,caecum,carcinoma,0,1	ATP8B3	108	1	1	Substitution - Missense(1)	large_intestine(1)	c.C3745T						PASS	.						48.0	49.0	49.0					19																	1783185		1993	4151	6144	SO:0001583	missense	148229	exon29			TGGAACGGCGGGC	AA827939	CCDS45901.1, CCDS54196.1	19p13.3	2010-04-28	2010-04-28		ENSG00000130270	ENSG00000130270		"""ATPases / P-type"""	13535	protein-coding gene	gene with protein product	"""aminophospholipid translocase ATP8B3"", ""potential phospholipid-transporting ATPase IK"""	605866	"""ATPase, Class I, type 8B, member 3"", ""ATPase, class I, type 8B, member 3"""			11015572	Standard	NM_138813		Approved	ATPIK	uc002ltw.4	O60423	OTTHUMG00000166189	ENST00000310127.6:c.3745C>T	19.37:g.1783185G>A	ENSP00000311336:p.Arg1249Cys	136.0	0.0	0		145.0	67.0	0.462069	NM_138813	Q7Z485|Q8IVB8|Q8N4Y8|Q96M22	Missense_Mutation	SNP	ENST00000310127.6	37	CCDS45901.1	.	.	.	.	.	.	.	.	.	.	G	18.38	3.611889	0.66558	.	.	ENSG00000130270	ENST00000310127;ENST00000539485;ENST00000525591	T;T;T	0.65732	-0.17;-0.05;-0.07	4.57	4.57	0.56435	.	0.144065	0.47852	D	0.000201	T	0.78710	0.4326	M	0.76727	2.345	0.54753	D	0.999983	D;D	0.89917	1.0;1.0	D;D	0.79108	0.988;0.992	T	0.82323	-0.0514	10	0.87932	D	0	.	16.3466	0.83134	0.0:0.0:1.0:0.0	.	1249;1212	O60423;Q7Z485	AT8B3_HUMAN;.	C	1249;1259;1212	ENSP00000311336:R1249C;ENSP00000443574:R1259C;ENSP00000437115:R1212C	ENSP00000311336:R1249C	R	-	1	0	ATP8B3	1734185	1.000000	0.71417	0.937000	0.37676	0.253000	0.25986	7.161000	0.77505	2.088000	0.63022	0.549000	0.68633	CGT	.	.	none		0.587	ATP8B3-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388279.1	NM_138813	
RB1	5925	hgsc.bcm.edu	37	13	48947553	48947553	+	Silent	SNP	C	C	T	rs117865557		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:48947553C>T	ENST00000267163.4	+	12	1278	c.1140C>T	c.(1138-1140)aaC>aaT	p.N380N		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	380	Domain A.|Pocket; binds T and E1A.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(8)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	CTGTTATGAACACTATCCAAC	0.294		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)			C|||	1	0.000199681	0.0	0.0	5008	,	,		14986	0.001		0.0	False		,,,				2504	0.0				p.N380N		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	.	RB1	1068	.	23	Whole gene deletion(15)|Unknown(8)	bone(11)|breast(5)|central_nervous_system(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|haematopoietic_and_lymphoid_tissue(1)|endometrium(1)	c.C1140T						PASS	.	C		0,4406		0,0,2203	103.0	110.0	107.0		1140	4.3	1.0	13	dbSNP_132	107	3,8577	3.0+/-9.4	0,3,4287	no	coding-synonymous	RB1	NM_000321.2		0,3,6490	TT,TC,CC		0.035,0.0,0.0231		380/929	48947553	3,12983	2203	4290	6493	SO:0001819	synonymous_variant	5925	exon12	Familial Cancer Database		TATGAACACTATC	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1140C>T	13.37:g.48947553C>T		334.0	0.0	0		135.0	118.0	0.874074	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Silent	SNP	ENST00000267163.4	37	CCDS31973.1																																																																																			C|1.000;T|0.000	0.000	strong		0.294	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
PAIP2	51247	hgsc.bcm.edu	37	5	138700404	138700404	+	Missense_Mutation	SNP	G	G	A	rs151194423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:138700404G>A	ENST00000394795.2	+	3	1281	c.290G>A	c.(289-291)aGt>aAt	p.S97N	PAIP2_ENST00000511706.1_Intron|PAIP2_ENST00000510080.1_Missense_Mutation_p.S97N|PAIP2_ENST00000511381.1_3'UTR|CTB-43P18.1_ENST00000503553.3_RNA|PAIP2_ENST00000265192.4_Missense_Mutation_p.S97N			Q9BPZ3	PAIP2_HUMAN	poly(A) binding protein interacting protein 2	97					memory (GO:0007613)|negative regulation of translational initiation (GO:0045947)|regulation of long-term synaptic potentiation (GO:1900271)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mRNA binding (GO:0003729)|translation repressor activity (GO:0030371)			kidney(1)|large_intestine(2)|lung(2)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00325)			CTTGTTATCAGTGATGGCTCT	0.398													G|||	2	0.000399361	0.0	0.0029	5008	,	,		20179	0.0		0.0	False		,,,				2504	0.0				p.S97N		Atlas-SNP	.											.	PAIP2	10	.	0			c.G290A						PASS	.						108.0	94.0	99.0					5																	138700404		2203	4300	6503	SO:0001583	missense	51247	exon3			TTATCAGTGATGG	AF151052	CCDS4211.1	5q32	2008-02-05			ENSG00000120727	ENSG00000120727			17970	protein-coding gene	gene with protein product		605604				11172725, 16804161	Standard	NM_016480		Approved	PAIP2A	uc003led.3	Q9BPZ3	OTTHUMG00000129227	ENST00000394795.2:c.290G>A	5.37:g.138700404G>A	ENSP00000378275:p.Ser97Asn	123.0	0.0	0		143.0	66.0	0.461538	NM_001033112	B2RBI1|D3DQC6|Q49A06|Q9H0Y5|Q9P0Q8	Missense_Mutation	SNP	ENST00000394795.2	37	CCDS4211.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	13.16	2.153214	0.38021	.	.	ENSG00000120727	ENST00000265192;ENST00000394795;ENST00000510080	.	.	.	5.93	3.13	0.36017	.	0.483405	0.25916	N	0.027466	T	0.27629	0.0679	L	0.34521	1.04	0.35331	D	0.785643	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	8	.	.	.	-10.2094	6.1013	0.20049	0.2021:0.2583:0.5396:0.0	.	97	Q9BPZ3	PAIP2_HUMAN	N	97	.	.	S	+	2	0	PAIP2	138728303	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.347000	0.44036	0.381000	0.24851	-0.165000	0.13383	AGT	G|0.999;A|0.001	0.001	strong		0.398	PAIP2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373002.1	NM_016480	
EP400	57634	hgsc.bcm.edu	37	12	132445675	132445675	+	Missense_Mutation	SNP	G	G	A	rs61745448	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132445675G>A	ENST00000333577.4	+	2	620	c.511G>A	c.(511-513)Gtg>Atg	p.V171M	EP400_ENST00000332482.4_Missense_Mutation_p.V171M|EP400_ENST00000389561.2_Missense_Mutation_p.V171M|EP400_ENST00000330386.6_Missense_Mutation_p.V171M|EP400_ENST00000389562.2_Missense_Mutation_p.V171M			Q96L91	EP400_HUMAN	E1A binding protein p400	171					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)	NuA4 histone acetyltransferase complex (GO:0035267)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|Swr1 complex (GO:0000812)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			NS(1)|breast(6)|central_nervous_system(10)|cervix(1)|endometrium(21)|kidney(13)|large_intestine(25)|lung(56)|ovary(5)|prostate(8)|skin(6)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	161	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.198)		OV - Ovarian serous cystadenocarcinoma(86;3.01e-08)|Epithelial(86;3.43e-07)|all cancers(50;2.01e-06)		AGGGGGCTTCGTGGATGCCAG	0.672													G|||	61	0.0121805	0.0008	0.0231	5008	,	,		15923	0.0		0.0408	False		,,,				2504	0.0031				p.V171M		Atlas-SNP	.											.	EP400	370	.	0			c.G511A						PASS	.	G	MET/VAL	44,4360	43.8+/-77.6	0,44,2158	55.0	42.0	46.0		511	4.9	1.0	12	dbSNP_129	46	411,8187	121.7+/-180.7	15,381,3903	no	missense	EP400	NM_015409.4	21	15,425,6061	AA,AG,GG		4.7802,0.9991,3.4995	probably-damaging	171/3124	132445675	455,12547	2202	4299	6501	SO:0001583	missense	57634	exon2			GGCTTCGTGGATG	U80743	CCDS31929.1, CCDS31929.2	12q24.33	2008-02-01	2002-02-05	2002-02-08		ENSG00000183495			11958	protein-coding gene	gene with protein product		606265	"""trinucleotide repeat containing 12"""	TNRC12		9225980, 11509179	Standard	NM_015409		Approved	CAGH32, KIAA1498, P400, KIAA1818, DKFZP434I225	uc001ujn.3	Q96L91		ENST00000333577.4:c.511G>A	12.37:g.132445675G>A	ENSP00000333602:p.Val171Met	426.0	0.0	0		478.0	237.0	0.495816	NM_015409	O15411|Q6P2F5|Q8N8Q7|Q8NE05|Q96JK7|Q9P230	Missense_Mutation	SNP	ENST00000333577.4	37		42	0.019230769230769232	0	0.0	10	0.027624309392265192	0	0.0	32	0.04221635883905013	G	6.433	0.448071	0.12223	0.009991	0.047802	ENSG00000183495	ENST00000537902;ENST00000333577;ENST00000389561;ENST00000389562;ENST00000332482;ENST00000330386;ENST00000423130;ENST00000541296;ENST00000542457	D;D;D;D;D	0.94232	-3.23;-3.38;-3.38;-3.38;-3.38	5.79	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.83312	0.5227	M	0.75447	2.3	0.37260	D	0.906958	D;D;D;D;D	0.67145	0.996;0.996;0.996;0.995;0.996	P;P;P;P;P	0.59487	0.753;0.753;0.753;0.858;0.753	D	0.87512	0.2440	10	0.87932	D	0	.	15.0397	0.71781	0.0684:0.0:0.9316:0.0	rs61745448	171;171;171;171;171	Q96L91-2;Q96L91-4;Q96L91-5;F8WCN8;Q96L91-3	.;.;.;.;.	M	171	ENSP00000333602:V171M;ENSP00000374212:V171M;ENSP00000374213:V171M;ENSP00000331737:V171M;ENSP00000330620:V171M	ENSP00000330620:V171M	V	+	1	0	EP400	131011628	1.000000	0.71417	0.961000	0.40146	0.048000	0.14542	9.461000	0.97646	1.453000	0.47775	0.563000	0.77884	GTG	G|0.976;A|0.024	0.024	strong		0.672	EP400-203	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015409	
MAP3K1	4214	hgsc.bcm.edu	37	5	56177843	56177843	+	Missense_Mutation	SNP	C	C	G	rs45556841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:56177843C>G	ENST00000399503.3	+	14	2816	c.2816C>G	c.(2815-2817)tCt>tGt	p.S939C		NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	939					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		GTAGGACCTTCTAGTTcaaca	0.423													C|||	37	0.00738818	0.0015	0.0259	5008	,	,		20934	0.0		0.0139	False		,,,				2504	0.0031				p.S939C		Atlas-SNP	.											.	MAP3K1	355	.	0			c.C2816G						PASS	.	C	CYS/SER	20,3788		0,20,1884	73.0	70.0	71.0		2816	3.9	1.0	5	dbSNP_127	71	191,8093		5,181,3956	yes	missense	MAP3K1	NM_005921.1	112	5,201,5840	GG,GC,CC		2.3056,0.5252,1.745	benign	939/1513	56177843	211,11881	1904	4142	6046	SO:0001583	missense	4214	exon14			GACCTTCTAGTTC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.2816C>G	5.37:g.56177843C>G	ENSP00000382423:p.Ser939Cys	146.0	0.0	0		139.0	75.0	0.539568	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	23	0.010531135531135532	1	0.0020325203252032522	13	0.03591160220994475	0	0.0	9	0.011873350923482849	C	11.21	1.571845	0.28003	0.005252	0.023056	ENSG00000095015	ENST00000399503	T	0.32272	1.46	5.71	3.87	0.44632	.	0.150855	0.47093	D	0.000259	T	0.04182	0.0116	N	0.08118	0	0.26331	N	0.977519	B	0.24368	0.102	B	0.27262	0.078	T	0.15578	-1.0432	10	0.87932	D	0	.	13.0984	0.59206	0.1278:0.7495:0.1227:0.0	rs45556841	939	Q13233	M3K1_HUMAN	C	939	ENSP00000382423:S939C	ENSP00000382423:S939C	S	+	2	0	MAP3K1	56213600	0.989000	0.36119	0.986000	0.45419	0.965000	0.64279	2.061000	0.41403	1.414000	0.47017	0.655000	0.94253	TCT	C|0.985;G|0.015	0.015	strong		0.423	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
ASXL2	55252	hgsc.bcm.edu	37	2	25972936	25972936	+	Missense_Mutation	SNP	C	C	T	rs192716734	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25972936C>T	ENST00000435504.4	-	12	1782	c.1489G>A	c.(1489-1491)Gct>Act	p.A497T	ASXL2_ENST00000404843.1_Missense_Mutation_p.A237T|ASXL2_ENST00000336112.4_Missense_Mutation_p.A469T|ASXL2_ENST00000272341.4_Missense_Mutation_p.A237T			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	497					adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCCTGTTCAGCAGAGGTGACT	0.453													C|||	7	0.00139776	0.0	0.0058	5008	,	,		20730	0.0		0.003	False		,,,				2504	0.0				p.A497T		Atlas-SNP	.											.	ASXL2	217	.	0			c.G1489A						PASS	.	C	THR/ALA	2,3826		0,2,1912	173.0	158.0	163.0		1489	4.2	1.0	2		163	44,8222		1,42,4090	yes	missense	ASXL2	NM_018263.4	58	1,44,6002	TT,TC,CC		0.5323,0.0522,0.3804	benign	497/1436	25972936	46,12048	1914	4133	6047	SO:0001583	missense	55252	exon11			GTTCAGCAGAGGT			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.1489G>A	2.37:g.25972936C>T	ENSP00000391447:p.Ala497Thr	129.0	0.0	0		158.0	76.0	0.481013	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	C	11.46	1.644550	0.29246	5.22E-4	0.005323	ENSG00000143970	ENST00000435504;ENST00000336112;ENST00000404843;ENST00000272341	T;T;T;T	0.18338	2.24;2.24;2.22;2.22	6.01	4.22	0.49857	.	0.445872	0.26951	N	0.021661	T	0.10208	0.0250	L	0.48362	1.52	0.26143	N	0.980241	B;B	0.17852	0.006;0.024	B;B	0.13407	0.005;0.009	T	0.19811	-1.0294	10	0.14252	T	0.57	-2.402	11.1814	0.48631	0.0:0.8518:0.0:0.1482	.	237;497	Q76L83-2;Q76L83	.;ASXL2_HUMAN	T	497;469;237;237	ENSP00000391447:A497T;ENSP00000337250:A469T;ENSP00000383920:A237T;ENSP00000272341:A237T	ENSP00000272341:A237T	A	-	1	0	ASXL2	25826440	0.000000	0.05858	1.000000	0.80357	0.627000	0.37826	0.440000	0.21592	1.566000	0.49654	-0.142000	0.14014	GCT	C|0.997;T|0.003	0.003	strong		0.453	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
DNAH3	55567	hgsc.bcm.edu	37	16	20948142	20948142	+	Silent	SNP	A	A	G	rs140126023	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:20948142A>G	ENST00000261383.3	-	60	11687	c.11688T>C	c.(11686-11688)aaT>aaC	p.N3896N	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	3896					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CTCGGCCAAGATTGATGAGGC	0.562													A|||	2	0.000399361	0.0	0.0	5008	,	,		17157	0.0		0.001	False		,,,				2504	0.001				p.N3896N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T11688C						PASS	.	A		6,4396	11.4+/-27.6	0,6,2195	59.0	52.0	54.0		11688	2.0	0.6	16	dbSNP_134	54	29,8571	21.0+/-64.5	0,29,4271	no	coding-synonymous	DNAH3	NM_017539.1		0,35,6466	GG,GA,AA		0.3372,0.1363,0.2692		3896/4117	20948142	35,12967	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon60			GCCAAGATTGATG	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.11688T>C	16.37:g.20948142A>G		39.0	0.0	0		47.0	15.0	0.319149	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			A|0.998;G|0.002	0.002	strong		0.562	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ASB2	51676	hgsc.bcm.edu	37	14	94417531	94417531	+	Missense_Mutation	SNP	T	T	C	rs11555542	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:94417531T>C	ENST00000315988.4	-	4	1038	c.550A>G	c.(550-552)Aac>Gac	p.N184D	ASB2_ENST00000556337.1_Intron|ASB2_ENST00000555019.1_Missense_Mutation_p.N232D|MIR4506_ENST00000584693.1_RNA	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	184					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		CAGCGGTGGTTGGTGTCTGCA	0.632													T|||	104	0.0207668	0.0023	0.0605	5008	,	,		19972	0.001		0.0567	False		,,,				2504	0.001				p.N232D		Atlas-SNP	.											.	ASB2	71	.	0			c.A694G						PASS	.	T	ASP/ASN,ASP/ASN	50,4356	50.9+/-86.3	0,50,2153	76.0	63.0	67.0		694,550	5.6	1.0	14	dbSNP_120	67	469,8131	139.0+/-195.8	10,449,3841	yes	missense,missense	ASB2	NM_001202429.1,NM_016150.4	23,23	10,499,5994	CC,CT,TT		5.4535,1.1348,3.9905	possibly-damaging,possibly-damaging	232/636,184/588	94417531	519,12487	2203	4300	6503	SO:0001583	missense	51676	exon6			GGTGGTTGGTGTC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.550A>G	14.37:g.94417531T>C	ENSP00000320675:p.Asn184Asp	53.0	0.0	0		71.0	42.0	0.591549	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Missense_Mutation	SNP	ENST00000315988.4	37	CCDS9915.1	67	0.030677655677655676	2	0.0040650406504065045	25	0.06906077348066299	1	0.0017482517482517483	39	0.051451187335092345	T	27.5	4.840814	0.91197	0.011348	0.054535	ENSG00000100628	ENST00000555019;ENST00000434324;ENST00000315988;ENST00000543546;ENST00000555507;ENST00000556062	T;T;T;T	0.73789	-0.5;-0.5;-0.5;-0.78	5.62	5.62	0.85841	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.25044	0.0608	N	0.25201	0.72	0.54753	D	0.999986	P;D;P	0.76494	0.922;0.999;0.922	P;D;P	0.83275	0.841;0.996;0.677	T	0.60742	-0.7203	10	0.30078	T	0.28	-2.7607	15.8384	0.78818	0.0:0.0:0.0:1.0	rs11555542;rs11555542	200;232;184	B3KPZ6;B4E166;Q96Q27	.;.;ASB2_HUMAN	D	232;200;184;130;130;78	ENSP00000451575:N232D;ENSP00000320675:N184D;ENSP00000450940:N130D;ENSP00000451694:N78D	ENSP00000320675:N184D	N	-	1	0	ASB2	93487284	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.258000	0.72487	2.137000	0.66172	0.459000	0.35465	AAC	T|0.964;C|0.036	0.036	strong		0.632	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
ADAMTSL4	54507	hgsc.bcm.edu	37	1	150526270	150526270	+	Missense_Mutation	SNP	C	C	T	rs41317517	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150526270C>T	ENST00000369038.2	+	4	1004	c.803C>T	c.(802-804)tCc>tTc	p.S268F	ADAMTSL4_ENST00000271643.4_Missense_Mutation_p.S268F|ADAMTSL4_ENST00000369041.5_Missense_Mutation_p.S268F|MIR4257_ENST00000581735.1_RNA|ADAMTSL4_ENST00000369039.5_Missense_Mutation_p.S268F|RP11-54A4.2_ENST00000442435.2_RNA			Q6UY14	ATL4_HUMAN	ADAMTS-like 4	268					apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|positive regulation of apoptotic process (GO:0043065)	interstitial matrix (GO:0005614)	metalloendopeptidase activity (GO:0004222)|protease binding (GO:0002020)			breast(1)|cervix(1)|endometrium(6)|large_intestine(3)|lung(13)|ovary(2)|prostate(3)|skin(3)	32	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;3.18e-23)|all cancers(9;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(6;1.13e-14)|BRCA - Breast invasive adenocarcinoma(12;0.000503)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CCCACGCACTCCTTAGGAGAA	0.657													C|||	17	0.00339457	0.0015	0.0072	5008	,	,		15387	0.001		0.008	False		,,,				2504	0.001				p.S268F		Atlas-SNP	.											.	ADAMTSL4	101	.	0			c.C803T						PASS	.	C	PHE/SER,PHE/SER	16,4390	23.3+/-48.9	0,16,2187	50.0	49.0	49.0		803,803	0.4	0.0	1	dbSNP_127	49	100,8500	55.2+/-116.2	1,98,4201	yes	missense,missense	ADAMTSL4	NM_019032.4,NM_025008.3	155,155	1,114,6388	TT,TC,CC		1.1628,0.3631,0.8919	possibly-damaging,possibly-damaging	268/1075,268/878	150526270	116,12890	2203	4300	6503	SO:0001583	missense	54507	exon6			CGCACTCCTTAGG	BC027478	CCDS955.1, CCDS30852.1, CCDS72908.1	1q21.2	2008-02-05	2005-12-01	2005-12-01	ENSG00000143382	ENSG00000143382			19706	protein-coding gene	gene with protein product		610113	"""thrombospondin repeat containing 1"""	TSRC1		12706885	Standard	NM_019032		Approved	DKFZP434K1772	uc001eux.3	Q6UY14	OTTHUMG00000034863	ENST00000369038.2:c.803C>T	1.37:g.150526270C>T	ENSP00000358034:p.Ser268Phe	103.0	0.0	0		143.0	73.0	0.51049	NM_019032	B2RTT0|F8WAD0|Q5T5F7|Q6IPM6|Q8N643|Q9HBS6	Missense_Mutation	SNP	ENST00000369038.2	37	CCDS955.1	13	0.005952380952380952	1	0.0020325203252032522	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	C	8.618	0.890660	0.17613	0.003631	0.011628	ENSG00000143382	ENST00000369041;ENST00000271643;ENST00000369039;ENST00000369038	T;T;T;T	0.64085	0.02;-0.08;0.2;-0.08	4.73	0.378	0.16204	.	.	.	.	.	T	0.26304	0.0642	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.12013	0.001;0.005;0.002;0.005	B;B;B;B	0.09377	0.002;0.004;0.002;0.004	T	0.32851	-0.9891	9	0.72032	D	0.01	.	7.3289	0.26571	0.0:0.5416:0.0:0.4584	rs41317517	268;268;268;268	B7ZMJ3;F8WAD0;Q6UY14;Q6UY14-2	.;.;ATL4_HUMAN;.	F	268	ENSP00000358037:S268F;ENSP00000271643:S268F;ENSP00000358035:S268F;ENSP00000358034:S268F	ENSP00000271643:S268F	S	+	2	0	ADAMTSL4	148792894	0.000000	0.05858	0.000000	0.03702	0.064000	0.16182	-0.115000	0.10741	0.034000	0.15491	0.484000	0.47621	TCC	C|0.991;T|0.009	0.009	strong		0.657	ADAMTSL4-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084395.4	NM_019032	
ZNF268	10795	hgsc.bcm.edu	37	12	133780587	133780587	+	Missense_Mutation	SNP	G	G	A	rs373286359		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133780587G>A	ENST00000536435.2	+	6	2645	c.2315G>A	c.(2314-2316)cGa>cAa	p.R772Q	ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000537565.1_Missense_Mutation_p.R611Q|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000228289.5_Missense_Mutation_p.R772Q|ZNF268_ENST00000536899.2_3'UTR	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	772					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		TCACATCAGCGAACTCATGCA	0.423																																					p.R772Q		Atlas-SNP	.											ZNF268,NS,carcinoma,0,1	ZNF268	71	1	0			c.G2315A						PASS	.						31.0	31.0	31.0					12																	133780587		692	1590	2282	SO:0001583	missense	10795	exon6			ATCAGCGAACTCA	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.2315G>A	12.37:g.133780587G>A	ENSP00000444412:p.Arg772Gln	7.0	0.0	0		5.0	4.0	0.8	NM_001165881	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	.	.	.	.	.	.	.	.	.	.	G	16.68	3.191297	0.58017	.	.	ENSG00000090612	ENST00000541009;ENST00000228289;ENST00000537565;ENST00000541019	T;T	0.24723	1.84;1.84	3.98	0.988	0.19796	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.18130	0.0435	L	0.60957	1.885	0.21416	N	0.999694	B;P	0.36495	0.42;0.556	B;B	0.15484	0.01;0.013	T	0.10382	-1.0632	8	.	.	.	.	7.3383	0.26623	0.3109:0.0:0.6891:0.0	.	772;611	Q14587;Q14587-2	ZN268_HUMAN;.	Q	772;772;611;611	ENSP00000228289:R772Q;ENSP00000445713:R611Q	.	R	+	2	0	ZNF268	.	0.000000	0.05858	0.096000	0.21009	0.817000	0.46193	-0.126000	0.10563	0.332000	0.23536	0.650000	0.86243	CGA	.	.	alt		0.423	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
MORC1	27136	hgsc.bcm.edu	37	3	108677910	108677910	+	Missense_Mutation	SNP	C	C	T	rs78212601	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:108677910C>T	ENST00000483760.1	-	27	2837	c.2794G>A	c.(2794-2796)Gaa>Aaa	p.E932K	MORC1_ENST00000232603.5_Missense_Mutation_p.E953K					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						AGATTATCTTCTTTAAGCAAA	0.378													C|||	40	0.00798722	0.0	0.0101	5008	,	,		15018	0.001		0.0288	False		,,,				2504	0.0031				p.E953K		Atlas-SNP	.											.	MORC1	211	.	0			c.G2857A						PASS	.	C	LYS/GLU	18,4388	20.2+/-43.8	0,18,2185	46.0	48.0	47.0		2857	5.2	1.0	3	dbSNP_131	47	191,8407	78.4+/-141.0	2,187,4110	yes	missense	MORC1	NM_014429.3	56	2,205,6295	TT,TC,CC		2.2214,0.4085,1.6072	probably-damaging	953/985	108677910	209,12795	2203	4299	6502	SO:0001583	missense	27136	exon28			TATCTTCTTTAAG	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.2794G>A	3.37:g.108677910C>T	ENSP00000417282:p.Glu932Lys	87.0	0.0	0		105.0	44.0	0.419048	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		31	0.014194139194139194	0	0.0	8	0.022099447513812154	0	0.0	23	0.030343007915567283	C	22.9	4.346692	0.82022	0.004085	0.022214	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.10005	2.92;2.92	5.2	5.2	0.72013	.	0.143592	0.32640	N	0.005834	T	0.04092	0.0114	L	0.32530	0.975	0.29995	N	0.816578	P;P	0.46784	0.884;0.884	P;P	0.46419	0.516;0.516	T	0.01048	-1.1469	10	0.44086	T	0.13	-17.6497	14.1073	0.65099	0.0:1.0:0.0:0.0	.	932;953	E7ERX1;Q86VD1	.;MORC1_HUMAN	K	953;932	ENSP00000232603:E953K;ENSP00000417282:E932K	ENSP00000232603:E953K	E	-	1	0	MORC1	110160600	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	1.944000	0.40263	2.716000	0.92895	0.650000	0.86243	GAA	C|0.984;T|0.016	0.016	strong		0.378	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
FLG	2312	hgsc.bcm.edu	37	1	152283605	152283605	+	Nonsense_Mutation	SNP	C	C	A	rs199895224		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152283605C>A	ENST00000368799.1	-	3	3792	c.3757G>T	c.(3757-3759)Gga>Tga	p.G1253*	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1253	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGTTCCTGTCCCACCTGTGAG	0.557									Ichthyosis																												p.G1253X		Atlas-SNP	.											.	FLG	900	.	0			c.G3757T						PASS	.						276.0	263.0	267.0					1																	152283605		2203	4300	6503	SO:0001587	stop_gained	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCTGTCCCACCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3757G>T	1.37:g.152283605C>A	ENSP00000357789:p.Gly1253*	226.0	0.0	0		223.0	101.0	0.452915	NM_002016	Q01720|Q5T583|Q9UC71	Nonsense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	38	6.749215	0.97809	.	.	ENSG00000143631	ENST00000368799	.	.	.	2.72	0.669	0.17918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	.	5.0097	0.14306	0.0:0.6754:0.0:0.3246	.	.	.	.	X	1253	.	ENSP00000357789:G1253X	G	-	1	0	FLG	150550229	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.711000	0.05019	0.347000	0.23924	0.186000	0.17326	GGA	.	.	weak		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
WRN	7486	hgsc.bcm.edu	37	8	30999075	30999075	+	Missense_Mutation	SNP	C	C	T	rs143954702		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:30999075C>T	ENST00000298139.5	+	25	3346	c.3097C>T	c.(3097-3099)Cgg>Tgg	p.R1033W		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	1033					aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		AGAAGTTTCTCGGTATAACAA	0.423			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome																												p.R1033W	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.C3097T						PASS	.	C	TRP/ARG	3,4403	6.2+/-15.9	0,3,2200	106.0	104.0	105.0		3097	3.2	0.1	8	dbSNP_134	105	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WRN	NM_000553.4	101	0,5,6498	TT,TC,CC		0.0233,0.0681,0.0384	benign	1033/1433	30999075	5,13001	2203	4300	6503	SO:0001583	missense	7486	exon25	Familial Cancer Database	WS, Adult Progeria	GTTTCTCGGTATA		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.3097C>T	8.37:g.30999075C>T	ENSP00000298139:p.Arg1033Trp	108.0	0.0	0		145.0	77.0	0.531034	NM_000553	A1KYY9	Missense_Mutation	SNP	ENST00000298139.5	37	CCDS6082.1	.	.	.	.	.	.	.	.	.	.	C	13.66	2.304314	0.40795	6.81E-4	2.33E-4	ENSG00000165392	ENST00000298139	T	0.30448	1.53	5.9	3.15	0.36227	RQC domain (2);	0.406919	0.26176	N	0.025894	T	0.18841	0.0452	L	0.36672	1.1	0.21950	N	0.999455	B;P	0.38565	0.098;0.637	B;B	0.26614	0.044;0.071	T	0.11494	-1.0585	10	0.72032	D	0.01	-1.5776	8.5727	0.33578	0.1396:0.1272:0.7332:0.0	.	443;1033	Q59F09;Q14191	.;WRN_HUMAN	W	1033	ENSP00000298139:R1033W	ENSP00000298139:R1033W	R	+	1	2	WRN	31118617	0.089000	0.21612	0.091000	0.20842	0.002000	0.02628	0.474000	0.22148	0.400000	0.25396	-0.134000	0.14843	CGG	C|1.000;T|0.000	0.000	weak		0.423	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
BPIFA2	140683	hgsc.bcm.edu	37	20	31761919	31761919	+	Missense_Mutation	SNP	A	A	G	rs17304572	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:31761919A>G	ENST00000253362.2	+	4	483	c.337A>G	c.(337-339)Aaa>Gaa	p.K113E	BPIFA2_ENST00000354932.5_Missense_Mutation_p.K113E			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	113			K -> E (in dbSNP:rs17304572).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										CCTGGATGTCAAAGCTGAACC	0.507													A|||	36	0.0071885	0.0008	0.0447	5008	,	,		20651	0.0		0.003	False		,,,				2504	0.001				p.K113E		Atlas-SNP	.											.	.	.	.	0			c.A337G						PASS	.	A	GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	190.0	130.0	150.0		337	0.5	0.0	20	dbSNP_123	150	65,8535	39.3+/-95.6	0,65,4235	yes	missense	BPIFA2	NM_080574.2	56	0,74,6429	GG,GA,AA		0.7558,0.2043,0.569	possibly-damaging	113/250	31761919	74,12932	2203	4300	6503	SO:0001583	missense	140683	exon4			GATGTCAAAGCTG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.337A>G	20.37:g.31761919A>G	ENSP00000253362:p.Lys113Glu	118.0	0.0	0		111.0	62.0	0.558559	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	15	0.006868131868131868	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	4	0.005277044854881266	A	14.94	2.685424	0.47991	0.002043	0.007558	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.05580	3.42;3.42	4.11	0.538	0.17150	.	0.626240	0.15043	N	0.283766	T	0.02767	0.0083	L	0.50919	1.6	0.09310	N	1	P	0.41624	0.757	B	0.43728	0.429	T	0.30001	-0.9993	10	0.15952	T	0.53	-20.1787	3.5768	0.07937	0.5707:0.2098:0.2195:0.0	rs17304572;rs52835642;rs56630818;rs17304572	113	Q96DR5	BPIA2_HUMAN	E	113	ENSP00000253362:K113E;ENSP00000347012:K113E	ENSP00000253362:K113E	K	+	1	0	BPIFA2	31225580	0.000000	0.05858	0.000000	0.03702	0.039000	0.13416	0.427000	0.21379	0.060000	0.16281	0.459000	0.35465	AAA	A|0.994;G|0.006	0.006	strong		0.507	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
TCERG1	10915	hgsc.bcm.edu	37	5	145838647	145838647	+	Silent	SNP	C	C	T	rs187468589		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:145838647C>T	ENST00000296702.5	+	4	677	c.639C>T	c.(637-639)gcC>gcT	p.A213A	TCERG1_ENST00000394421.2_Silent_p.A213A	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	213	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			aggcccaggcccaggcccagg	0.731																																					p.A213A		Atlas-SNP	.											TCERG1,NS,neuroblastoma,0,1	TCERG1	148	1	0			c.C639T						scavenged	.						10.0	14.0	12.0					5																	145838647		2183	4260	6443	SO:0001819	synonymous_variant	10915	exon4			CCAGGCCCAGGCC	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.639C>T	5.37:g.145838647C>T		17.0	0.0	0		17.0	10.0	0.588235	NM_006706	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																			C|0.974;T|0.026	0.026	strong		0.731	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
ABLIM3	22885	hgsc.bcm.edu	37	5	148596546	148596546	+	Missense_Mutation	SNP	A	A	G	rs148615457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148596546A>G	ENST00000506113.1	+	7	1176	c.694A>G	c.(694-696)Acc>Gcc	p.T232A	ABLIM3_ENST00000309868.7_Missense_Mutation_p.T232A|ABLIM3_ENST00000504238.1_Missense_Mutation_p.T232A|RP11-331K21.1_ENST00000512647.2_RNA|ABLIM3_ENST00000508983.1_Missense_Mutation_p.T232A|ABLIM3_ENST00000356541.3_Missense_Mutation_p.T232A|ABLIM3_ENST00000326685.7_Missense_Mutation_p.T232A|RP11-331K21.1_ENST00000522685.1_RNA|AC012613.2_ENST00000523176.1_RNA			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	232	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACCACCCAACCTGTGCCAG	0.517																																					p.T232A		Atlas-SNP	.											.	ABLIM3	91	.	0			c.A694G						PASS	.	A	ALA/THR	1,4405	2.1+/-5.4	0,1,2202	94.0	80.0	85.0		694	2.8	1.0	5	dbSNP_134	85	9,8591	7.1+/-27.0	0,9,4291	yes	missense	ABLIM3	NM_014945.2	58	0,10,6493	GG,GA,AA		0.1047,0.0227,0.0769	benign	232/684	148596546	10,12996	2203	4300	6503	SO:0001583	missense	22885	exon8			CACCCAACCTGTG	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.694A>G	5.37:g.148596546A>G	ENSP00000425394:p.Thr232Ala	82.0	0.0	0		127.0	68.0	0.535433	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	.	.	.	.	.	.	.	.	.	.	A	15.03	2.710883	0.48517	2.27E-4	0.001047	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	D;D;D;D;D;D	0.86865	-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	5.49	2.84	0.33178	Zinc finger, LIM-type (5);	0.416904	0.28192	N	0.016242	T	0.80037	0.4550	L	0.38175	1.15	0.26146	N	0.980218	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.11329	0.0;0.0;0.006	T	0.72204	-0.4361	10	0.62326	D	0.03	.	9.5085	0.39062	0.8081:0.0:0.1919:0.0	.	232;232;232	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	A	232	ENSP00000315841:T232A;ENSP00000348938:T232A;ENSP00000310309:T232A;ENSP00000425394:T232A;ENSP00000421183:T232A;ENSP00000420855:T232A	ENSP00000310309:T232A	T	+	1	0	ABLIM3	148576739	0.953000	0.32496	0.990000	0.47175	0.990000	0.78478	3.238000	0.51352	1.013000	0.39391	-0.264000	0.10439	ACC	A|0.999;G|0.001	0.001	strong		0.517	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
ANO2	57101	hgsc.bcm.edu	37	12	5841701	5841701	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:5841701C>T	ENST00000356134.5	-	16	1604	c.1533G>A	c.(1531-1533)acG>acA	p.T511T	ANO2_ENST00000546188.1_Silent_p.T511T|ANO2_ENST00000327087.8_Silent_p.T510T|ANO2_ENST00000538154.1_5'UTR	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	515					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)			central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						CGCCACACTCCGTCGTGTTTG	0.463																																					p.T510T		Atlas-SNP	.											ANO2_ENST00000327087,NS,carcinoma,0,2	ANO2	309	2	0			c.G1530A						PASS	.						110.0	110.0	110.0					12																	5841701		2074	4205	6279	SO:0001819	synonymous_variant	57101	exon15			ACACTCCGTCGTG	AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.1533G>A	12.37:g.5841701C>T		155.0	0.0	0		185.0	89.0	0.481081	NM_020373	C4N787|Q9H847	Silent	SNP	ENST00000356134.5	37																																																																																				.	.	none		0.463	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4	NM_020373	
ZNF486	90649	hgsc.bcm.edu	37	19	20308149	20308149	+	Nonsense_Mutation	SNP	C	C	G	rs184976796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20308149C>G	ENST00000335117.8	+	4	687	c.630C>G	c.(628-630)taC>taG	p.Y210*	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	210					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						AGAAACCATACAAATGTGAAG	0.363													C|||	17	0.00339457	0.0	0.0058	5008	,	,		19254	0.0		0.0109	False		,,,				2504	0.002				p.Y210X		Atlas-SNP	.											.	ZNF486	74	.	0			c.C630G						PASS	.	C	stop/TYR	7,4291		0,7,2142	39.0	42.0	41.0		630	0.8	0.1	19		41	54,8492		0,54,4219	no	stop-gained	ZNF486	NM_052852.2		0,61,6361	GG,GC,CC		0.6319,0.1629,0.4749		210/464	20308149	61,12783	2149	4273	6422	SO:0001587	stop_gained	90649	exon4			ACCATACAAATGT	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.630C>G	19.37:g.20308149C>G	ENSP00000335042:p.Tyr210*	20.0	0.0	0		32.0	15.0	0.46875	NM_052852	Q0VG00	Nonsense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	8	0.003663003663003663	0	0.0	5	0.013812154696132596	0	0.0	3	0.00395778364116095	c	10.99	1.507634	0.27036	0.001629	0.006319	ENSG00000256229	ENST00000545779;ENST00000335117	.	.	.	0.814	0.814	0.18756	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	6.9774	0.24683	0.0:1.0:0.0:0.0	.	.	.	.	X	249;210	.	ENSP00000335042:Y210X	Y	+	3	2	ZNF486	20169149	0.000000	0.05858	0.057000	0.19452	0.056000	0.15407	-0.409000	0.07160	0.183000	0.20059	0.186000	0.17326	TAC	C|0.995;G|0.005	0.005	strong		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
B2M	567	hgsc.bcm.edu	37	15	45003770	45003770	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:45003770T>A	ENST00000558401.1	+	1	96	c.26T>A	c.(25-27)gTg>gAg	p.V9E	B2M_ENST00000559916.1_Missense_Mutation_p.V9E|B2M_ENST00000544417.1_Missense_Mutation_p.V9E|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	9					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 exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		GCCTTAGCTGTGCTCGCGCTA	0.617																																					p.V9E		Atlas-SNP	.											.	B2M	99	.	0			c.T26A						PASS	.						132.0	95.0	108.0					15																	45003770		2198	4298	6496	SO:0001583	missense	567	exon1			TAGCTGTGCTCGC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.26T>A	15.37:g.45003770T>A	ENSP00000452780:p.Val9Glu	98.0	0.0	0		57.0	52.0	0.912281	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.499636	0.44455	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01430	4.9	5.35	4.23	0.50019	.	0.532223	0.09808	U	0.753127	T	0.01976	0.0062	L	0.46157	1.445	0.09310	N	1	B;B;B	0.30973	0.302;0.201;0.201	B;B;B	0.26969	0.075;0.073;0.055	T	0.45775	-0.9238	10	0.87932	D	0	.	7.8636	0.29524	0.0:0.0912:0.0:0.9088	.	9;9;9	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	E	9	ENSP00000437604:V9E	ENSP00000340858:V9E	V	+	2	0	B2M	42791062	0.003000	0.15002	0.002000	0.10522	0.005000	0.04900	1.408000	0.34668	1.166000	0.42689	0.533000	0.62120	GTG	.	.	none		0.617	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	
MYH14	79784	hgsc.bcm.edu	37	19	50795617	50795617	+	Silent	SNP	C	C	T	rs147447646	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50795617C>T	ENST00000596571.1	+	34	5104	c.5104C>T	c.(5104-5106)Ctg>Ttg	p.L1702L	MYH14_ENST00000262269.8_Silent_p.L1743L|MYH14_ENST00000440075.2_Silent_p.L1743L|MYH14_ENST00000601313.1_Silent_p.L1743L|MYH14_ENST00000598205.1_Silent_p.L1710L|MYH14_ENST00000425460.1_Silent_p.L1710L|MYH14_ENST00000376970.2_Silent_p.L1735L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1702					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CCTCAAGGGCCTGGAGGCTGA	0.642													C|||	5	0.000998403	0.0	0.0014	5008	,	,		16103	0.0		0.004	False		,,,				2504	0.0				p.L1743L		Atlas-SNP	.											.	MYH14	261	.	0			c.C5227T						PASS	.	C	,,	4,4008		0,4,2002	14.0	17.0	16.0		5128,5227,5104	1.6	1.0	19	dbSNP_134	16	28,8352		0,28,4162	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	0,32,6164	TT,TC,CC		0.3341,0.0997,0.2582	,,	1710/2004,1743/2037,1702/1996	50795617	32,12360	2006	4190	6196	SO:0001819	synonymous_variant	79784	exon37			AAGGGCCTGGAGG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.5104C>T	19.37:g.50795617C>T		72.0	0.0	0		97.0	54.0	0.556701	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
MAP10	54627	hgsc.bcm.edu	37	1	232943775	232943775	+	Silent	SNP	C	C	T	rs147903928		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:232943775C>T	ENST00000418460.1	+	1	3133	c.3006C>T	c.(3004-3006)tcC>tcT	p.S1002S		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	860					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										CAAATGTGTCCGAACTTAATG	0.378													C|||	1	0.000199681	0.0	0.0	5008	,	,		17059	0.0		0.001	False		,,,				2504	0.0				p.S1002S		Atlas-SNP	.											.	.	.	.	0			c.C3006T						PASS	.	C		0,3776		0,0,1888	133.0	133.0	133.0		3006	-2.9	1.0	1	dbSNP_134	133	10,8194		0,10,4092	no	coding-synonymous	KIAA1383	NM_019090.2		0,10,5980	TT,TC,CC		0.1219,0.0,0.0835		1002/1048	232943775	10,11970	1888	4102	5990	SO:0001819	synonymous_variant	54627	exon1			TGTGTCCGAACTT	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.3006C>T	1.37:g.232943775C>T		249.0	1.0	0.00401606		294.0	138.0	0.469388	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Silent	SNP	ENST00000418460.1	37	CCDS44334.1																																																																																			C|0.999;T|0.001	0.001	strong		0.378	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
RAB11B	9230	hgsc.bcm.edu	37	19	8468322	8468322	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:8468322A>G	ENST00000328024.6	+	5	755	c.537A>G	c.(535-537)aaA>aaG	p.K179K		NM_004218.3	NP_004209.2	Q15907	RB11B_HUMAN	RAB11B, member RAS oncogene family	179					cellular response to acidic pH (GO:0071468)|constitutive secretory pathway (GO:0045054)|establishment of protein localization to membrane (GO:0090150)|GTP catabolic process (GO:0006184)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|melanosome transport (GO:0032402)|receptor recycling (GO:0001881)|regulated secretory pathway (GO:0045055)|regulation of anion transport (GO:0044070)|regulation of endocytic recycling (GO:2001135)|regulation of protein localization to cell surface (GO:2000008)|retrograde transport, endosome to plasma membrane (GO:1990126)|small GTPase mediated signal transduction (GO:0007264)|transferrin transport (GO:0033572)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|phagocytic vesicle (GO:0045335)|recycling endosome (GO:0055037)|recycling endosome membrane (GO:0055038)|synaptic vesicle (GO:0008021)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			large_intestine(2)|lung(1)|ovary(1)	4						TGTCACAGAAACAGATCGCAG	0.657																																					p.K179K		Atlas-SNP	.											.	RAB11B	15	.	0			c.A537G						PASS	.						134.0	109.0	117.0					19																	8468322		2203	4300	6503	SO:0001819	synonymous_variant	9230	exon5			ACAGAAACAGATC	X79780	CCDS12201.1	19p13.2	2012-07-02			ENSG00000185236	ENSG00000185236		"""RAB, member RAS oncogene"""	9761	protein-coding gene	gene with protein product		604198				7811277	Standard	NM_004218		Approved	H-YPT3	uc002mju.4	Q15907		ENST00000328024.6:c.537A>G	19.37:g.8468322A>G		114.0	0.0	0		126.0	65.0	0.515873	NM_004218	A5YM50|B2R7I4|B4DMK0|D6W671|Q2YDT2|Q5U0I1|Q6FHR0|Q6FI42|Q8NI07	Silent	SNP	ENST00000328024.6	37	CCDS12201.1																																																																																			.	.	none		0.657	RAB11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460343.2	NM_004218	
PTPRO	5800	hgsc.bcm.edu	37	12	15699555	15699555	+	Silent	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:15699555G>C	ENST00000281171.4	+	13	2547	c.2217G>C	c.(2215-2217)gtG>gtC	p.V739V	PTPRO_ENST00000442921.2_5'UTR|PTPRO_ENST00000348962.2_Silent_p.V739V|PTPRO_ENST00000445537.2_5'UTR|PTPRO_ENST00000544244.1_5'UTR|PTPRO_ENST00000542557.1_5'UTR	NM_030667.2	NP_109592.1	Q16827	PTPRO_HUMAN	protein tyrosine phosphatase, receptor type, O	739	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell morphogenesis (GO:0000902)|glomerular visceral epithelial cell differentiation (GO:0072112)|glomerulus development (GO:0032835)|lamellipodium assembly (GO:0030032)|monocyte chemotaxis (GO:0002548)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of glomerular filtration (GO:0003105)|negative regulation of neuron projection development (GO:0010977)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of glomerular filtration (GO:0003093)|slit diaphragm assembly (GO:0036060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)|Wnt-protein binding (GO:0017147)			NS(2)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(11)|lung(30)|ovary(2)|prostate(1)|skin(17)|upper_aerodigestive_tract(1)	74		Hepatocellular(102;0.244)				AGACTTCAGTGACTTTGCTGT	0.393																																					p.V739V		Atlas-SNP	.											.	PTPRO	148	.	0			c.G2217C						PASS	.						98.0	94.0	96.0					12																	15699555		2203	4300	6503	SO:0001819	synonymous_variant	5800	exon13			TTCAGTGACTTTG	U20489	CCDS8674.1, CCDS8675.1, CCDS44837.1, CCDS53754.1	12p13-p12	2013-02-11			ENSG00000151490	ENSG00000151490		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9678	protein-coding gene	gene with protein product	"""osteoclastic transmembrane protein-tyrosine phosphatase"""	600579				7519601, 7665166, 21722858	Standard	NM_030667		Approved	PTPU2, GLEPP1, PTP-U2, PTP-oc, NPHS6	uc001rcv.2	Q16827	OTTHUMG00000168786	ENST00000281171.4:c.2217G>C	12.37:g.15699555G>C		183.0	0.0	0		160.0	73.0	0.45625	NM_002848	A0AV39|Q13101|Q8IYG3|Q9UBF0|Q9UBT5	Silent	SNP	ENST00000281171.4	37	CCDS8675.1																																																																																			.	.	none		0.393	PTPRO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401079.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1263648	1263648	+	Silent	SNP	G	G	A	rs151293115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1263648G>A	ENST00000529681.1	+	31	5596	c.5538G>A	c.(5536-5538)gtG>gtA	p.V1846V	MUC5B_ENST00000447027.1_Silent_p.V1849V|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1846	7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		TCGGGCAGGTGCTGACCTGCA	0.592													g|||	3	0.000599042	0.0	0.0	5008	,	,		19439	0.0		0.003	False		,,,				2504	0.0				p.V1846V		Atlas-SNP	.											.	MUC5B	473	.	0			c.G5538A						PASS	.			0,4334		0,0,2167	59.0	72.0	68.0		5538	-1.6	0.0	11	dbSNP_134	68	28,8486		0,28,4229	no	coding-synonymous	MUC5B	NM_002458.2		0,28,6396	AA,AG,GG		0.3289,0.0,0.2179		1846/5763	1263648	28,12820	2167	4257	6424	SO:0001819	synonymous_variant	727897	exon31			GCAGGTGCTGACC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.5538G>A	11.37:g.1263648G>A		118.0	0.0	0		129.0	52.0	0.403101	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.999;A|0.001	0.001	strong		0.592	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
OR5P2	120065	hgsc.bcm.edu	37	11	7818165	7818165	+	Missense_Mutation	SNP	C	C	T	rs569926953	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:7818165C>T	ENST00000329434.2	-	1	355	c.325G>A	c.(325-327)Gtc>Atc	p.V109I	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	109						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.V109I(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		GCCAGAAGGACGCATTCGACT	0.483																																					p.V109I		Atlas-SNP	.											OR5P2,brain,glioma,0,2	OR5P2	68	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G325A						scavenged	.						96.0	111.0	106.0					11																	7818165		2105	4292	6397	SO:0001583	missense	120065	exon1			GAAGGACGCATTC	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.325G>A	11.37:g.7818165C>T	ENSP00000331823:p.Val109Ile	64.0	0.0	0		60.0	3.0	0.05	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	37	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	C	6.601	0.479294	0.12581	.	.	ENSG00000183303	ENST00000329434	T	0.01059	5.39	5.5	1.92	0.25849	GPCR, rhodopsin-like superfamily (1);	0.172021	0.42172	N	0.000756	T	0.00724	0.0024	N	0.11000	0.08	0.18873	N	0.999981	B	0.02656	0.0	B	0.04013	0.001	T	0.49214	-0.8963	10	0.49607	T	0.09	-40.3172	3.5462	0.07829	0.6539:0.1394:0.0739:0.1327	.	109	Q8WZ92	OR5P2_HUMAN	I	109	ENSP00000331823:V109I	ENSP00000331823:V109I	V	-	1	0	OR5P2	7774741	0.000000	0.05858	0.991000	0.47740	0.012000	0.07955	-0.165000	0.09968	0.161000	0.19458	-1.921000	0.00515	GTC	.	.	none		0.483	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
RASGEF1B	153020	hgsc.bcm.edu	37	4	82355804	82355804	+	Missense_Mutation	SNP	C	C	T	rs34211143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:82355804C>T	ENST00000264400.2	-	11	1340	c.1189G>A	c.(1189-1191)Gtc>Atc	p.V397I	RASGEF1B_ENST00000335927.7_Missense_Mutation_p.V355I|RASGEF1B_ENST00000509081.1_Missense_Mutation_p.V396I	NM_152545.1	NP_689758.1	Q0VAM2	RGF1B_HUMAN	RasGEF domain family, member 1B	397	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of Ras GTPase activity (GO:0032320)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)	Ras guanyl-nucleotide exchange factor activity (GO:0005088)			endometrium(2)|kidney(5)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	26						TCAAAATTGACATGGCCATTG	0.453													C|||	30	0.00599042	0.0008	0.0159	5008	,	,		17128	0.0		0.0179	False		,,,				2504	0.0				p.V397I		Atlas-SNP	.											RASGEF1B,NS,carcinoma,+2,1	RASGEF1B	44	1	0			c.G1189A						PASS	.	C	ILE/VAL	17,4389	24.3+/-50.5	0,17,2186	74.0	68.0	70.0		1189	3.7	1.0	4	dbSNP_126	70	131,8469	64.9+/-127.2	1,129,4170	yes	missense	RASGEF1B	NM_152545.1	29	1,146,6356	TT,TC,CC		1.5233,0.3858,1.1379	benign	397/474	82355804	148,12858	2203	4300	6503	SO:0001583	missense	153020	exon11			AATTGACATGGCC	AK056257	CCDS34022.1, CCDS75151.1, CCDS75152.1	4q21.21	2013-09-24				ENSG00000138670			24881	protein-coding gene	gene with protein product		614532				12488504	Standard	XM_005262776		Approved	GPIG4, FLJ31695	uc003hmi.1	Q0VAM2		ENST00000264400.2:c.1189G>A	4.37:g.82355804C>T	ENSP00000264400:p.Val397Ile	127.0	0.0	0		135.0	70.0	0.518519	NM_152545	Q0VAM1|Q4W5L7|Q4W5M3|Q96MY8	Missense_Mutation	SNP	ENST00000264400.2	37	CCDS34022.1	18	0.008241758241758242	0	0.0	6	0.016574585635359115	0	0.0	12	0.0158311345646438	C	4.202	0.036168	0.08148	0.003858	0.015233	ENSG00000138670	ENST00000509081;ENST00000264400;ENST00000335927	T;T;T	0.26373	1.74;1.74;1.74	4.62	3.69	0.42338	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine-nucleotide exchange factor, conserved site (1);Ras guanine nucleotide exchange factor, domain (1);	0.122271	0.53938	D	0.000046	T	0.03783	0.0107	N	0.01809	-0.71	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.19063	-1.0317	10	0.02654	T	1	.	12.9491	0.58389	0.0:0.9062:0.0:0.0938	rs34211143	355;396;397	Q0VAM2-2;Q0VAM2-3;Q0VAM2	.;.;RGF1B_HUMAN	I	396;397;355	ENSP00000425393:V396I;ENSP00000264400:V397I;ENSP00000338437:V355I	ENSP00000264400:V397I	V	-	1	0	RASGEF1B	82574828	0.941000	0.31946	0.997000	0.53966	0.997000	0.91878	1.302000	0.33459	2.413000	0.81919	0.585000	0.79938	GTC	C|0.989;T|0.011	0.011	strong		0.453	RASGEF1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362830.1	NM_152545	
HFE	3077	hgsc.bcm.edu	37	6	26093141	26093141	+	Missense_Mutation	SNP	G	G	A	rs1800562	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:26093141G>A	ENST00000357618.5	+	4	967	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	HFE_ENST00000461397.1_Missense_Mutation_p.C268Y|HFE_ENST00000470149.1_Missense_Mutation_p.C279Y|HFE_ENST00000317896.7_Missense_Mutation_p.C190Y|HFE_ENST00000336625.8_Missense_Mutation_p.C176Y|HFE_ENST00000397022.3_Missense_Mutation_p.C259Y|HFE_ENST00000353147.5_Missense_Mutation_p.C102Y|HFE_ENST00000352392.4_Intron|HFE_ENST00000309234.6_Missense_Mutation_p.C282Y|HFE_ENST00000488199.1_Missense_Mutation_p.C180Y|HFE_ENST00000349999.4_Missense_Mutation_p.C194Y	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	282	Alpha-3.|Ig-like C1-type.		C -> Y (in HFE1; associated with susceptibility to porphyria cutanea tarda; associated with increased serum transferrin levels; higher frequency in patients with type 2 diabetes than in controls; dbSNP:rs1800562). {ECO:0000269|PubMed:10094552, ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:11069625, ECO:0000269|PubMed:11423500, ECO:0000269|PubMed:12542741, ECO:0000269|PubMed:14633868, ECO:0000269|PubMed:18157833, ECO:0000269|PubMed:8696333, ECO:0000269|PubMed:9024376, ECO:0000269|PubMed:9106528, ECO:0000269|PubMed:9620340, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATATACGTGCCAGGTGGAG	0.547									Hemochromatosis				G|||	63	0.0125799	0.0023	0.0216	5008	,	,		19430	0.0		0.0427	False		,,,				2504	0.002				p.C282Y		Atlas-SNP	.											.	HFE	37	.	0			c.G845A	GRCh37	CM004391|CM960828	HFE	M	rs1800562	PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,	67,4339		1,65,2137	84.0	81.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	845,527,569,803,581,539,776,305,	5.3	1.0	6	dbSNP_89	82	551,8049		18,515,3767	yes	missense,missense,missense,missense,missense,missense,missense,missense,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	194,194,194,194,194,194,194,194,	19,580,5904	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.407,1.5207,4.7517	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	282/349,176/243,190/257,268/335,194/261,180/247,259/326,102/169,	26093141	618,12388	2203	4300	6503	SO:0001583	missense	3077	exon4	Familial Cancer Database		ATACGTGCCAGGT		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"""Immunoglobulin superfamily / C1-set domain containing"""	4886	protein-coding gene	gene with protein product	"""high Fe"""	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.845G>A	6.37:g.26093141G>A	ENSP00000417404:p.Cys282Tyr	228.0	0.0	0		192.0	87.0	0.453125	NM_000410	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	43	0.019688644688644688	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	35	0.04617414248021108	.	17.19	3.326013	0.60743	0.015207	0.06407	ENSG00000010704	ENST00000349999;ENST00000397022;ENST00000317896;ENST00000353147;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000488199;ENST00000309234	D;D;D;D;D;D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68	5.35	5.35	0.76521	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.98557	0.9518	H	0.99143	4.445	0.80722	A	1	D;D;D;D;D;P;D;D;D	0.89917	0.982;1.0;1.0;1.0;1.0;0.951;0.996;0.993;0.961	P;D;D;D;D;P;P;D;P	0.91635	0.756;0.999;0.999;0.999;0.999;0.56;0.826;0.917;0.667	D	0.98784	1.0733	9	0.87932	D	0	.	14.7506	0.69522	0.0:0.0:1.0:0.0	rs1800562;rs4134660;rs17530654;rs58044250;rs1800562	279;102;180;190;176;268;194;259;282	Q6B0J5;Q30201-6;Q30201-4;Q30201-7;Q30201-10;Q30201-3;Q30201-2;Q30201-5;Q30201	.;.;.;.;.;.;.;.;HFE_HUMAN	Y	194;259;190;102;282;279;176;268;180;282	ENSP00000259699:C194Y;ENSP00000380217:C259Y;ENSP00000313776:C190Y;ENSP00000312342:C102Y;ENSP00000417404:C282Y;ENSP00000419725:C279Y;ENSP00000337819:C176Y;ENSP00000420802:C268Y;ENSP00000420559:C180Y;ENSP00000311698:C282Y	ENSP00000311698:C282Y	C	+	2	0	HFE	26201120	1.000000	0.71417	0.993000	0.49108	0.351000	0.29236	4.282000	0.58971	2.941000	0.99782	0.655000	0.94253	TGC	G|0.966;A|0.034	0.034	strong		0.547	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1		
HIP1	3092	hgsc.bcm.edu	37	7	75187009	75187009	+	Silent	SNP	T	T	C	rs144294774	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:75187009T>C	ENST00000336926.6	-	16	1556	c.1530A>G	c.(1528-1530)aaA>aaG	p.K510K	HIP1_ENST00000434438.2_Silent_p.K510K	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	510					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CCAGCTCTTTTTTCTCTCGTT	0.537			T	PDGFRB	CMML								T|||	13	0.00259585	0.0098	0.0	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.K510K		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.A1530G						PASS	.	T		55,4351	54.2+/-90.2	0,55,2148	160.0	155.0	157.0		1530	-2.0	0.9	7	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous	HIP1	NM_005338.5		0,55,6448	CC,CT,TT		0.0,1.2483,0.4229		510/1038	75187009	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon16			CTCTTTTTTCTCT	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.1530A>G	7.37:g.75187009T>C		127.0	0.0	0		142.0	70.0	0.492958	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			T|0.996;C|0.004	0.004	strong		0.537	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240796	39240796	+	Missense_Mutation	SNP	G	G	C	rs553572799|rs199957151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240796G>C	ENST00000391417.4	+	1	338	c.338G>C	c.(337-339)aGc>aCc	p.S113T		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	138	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						tgccgccccagctgctgccgc	0.667																																					p.S113T		Atlas-SNP	.											KRTAP4-7,NS,carcinoma,+1,1	KRTAP4-7	49	1	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G338C						scavenged	.																																			SO:0001583	missense	100132476	exon1			GCCCCAGCTGCTG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.338G>C	17.37:g.39240796G>C	ENSP00000375236:p.Ser113Thr	28.0	1.0	0.0357143		41.0	19.0	0.463415	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.047	-1.263726	0.01433	.	.	ENSG00000240871	ENST00000391417	T	0.00627	6.12	2.73	1.66	0.24008	.	2.038930	0.02697	N	0.111300	T	0.00552	0.0018	.	.	.	0.21290	N	0.999731	B	0.13145	0.007	B	0.12837	0.008	T	0.47222	-0.9134	9	0.17832	T	0.49	.	5.1702	0.15107	0.0:0.2319:0.5315:0.2367	.	168	Q9BYR0	KRA47_HUMAN	T	113	ENSP00000375236:S113T	ENSP00000375236:S113T	S	+	2	0	KRTAP4-7	36494322	0.010000	0.17322	0.067000	0.19924	0.024000	0.10985	-0.517000	0.06275	0.191000	0.20236	0.289000	0.19496	AGC	.	.	weak		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
MYH11	4629	hgsc.bcm.edu	37	16	15818834	15818834	+	Missense_Mutation	SNP	C	C	T	rs151058774		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15818834C>T	ENST00000300036.5	-	29	3983	c.3874G>A	c.(3874-3876)Gtc>Atc	p.V1292I	MYH11_ENST00000396324.3_Missense_Mutation_p.V1299I|NDE1_ENST00000396354.1_3'UTR|MYH11_ENST00000576790.2_Missense_Mutation_p.V1292I|MYH11_ENST00000452625.2_Missense_Mutation_p.V1299I|NDE1_ENST00000342673.5_3'UTR|NDE1_ENST00000396355.1_3'UTR|AF001548.5_ENST00000574212.1_RNA|NDE1_ENST00000571896.1_3'UTR	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1292					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						ATCCCTGTGACGCTCTCAACT	0.542			T	CBFB	AML																																p.V1299I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G3895A						PASS	.						55.0	46.0	49.0					16																	15818834		2197	4300	6497	SO:0001583	missense	4629	exon30			CTGTGACGCTCTC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.3874G>A	16.37:g.15818834C>T	ENSP00000300036:p.Val1292Ile	80.0	0.0	0		100.0	48.0	0.48	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	C	16.35	3.099342	0.56183	.	.	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.75367	-0.93;-0.93;-0.93;-0.93	5.17	5.17	0.71159	Myosin tail (1);	0.069264	0.56097	D	0.000021	T	0.73164	0.3552	L	0.45470	1.425	0.80722	D	1	B;B;B;B;B	0.28439	0.104;0.212;0.212;0.104;0.212	B;B;B;B;B	0.35312	0.2;0.103;0.103;0.103;0.146	T	0.72714	-0.4210	10	0.52906	T	0.07	.	17.6819	0.88246	0.0:1.0:0.0:0.0	.	1299;1292;1299;1292;1299	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	I	1292;1292;1299;1299;1299	ENSP00000300036:V1292I;ENSP00000345136:V1292I;ENSP00000379616:V1299I;ENSP00000407821:V1299I	ENSP00000300036:V1292I	V	-	1	0	MYH11	15726335	1.000000	0.71417	1.000000	0.80357	0.694000	0.40290	7.818000	0.86416	2.409000	0.81822	0.650000	0.86243	GTC	C|0.999;G|0.001	.	alt		0.542	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
MUC21	394263	hgsc.bcm.edu	37	6	30954439	30954439	+	Missense_Mutation	SNP	A	A	G	rs147266731	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954439A>G	ENST00000376296.3	+	2	728	c.487A>G	c.(487-489)Agc>Ggc	p.S163G	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	163	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGTGAGGCCAGCACAGCCAC	0.617																																					p.S163G		Atlas-SNP	.											MUC21,NS,carcinoma,0,3	MUC21	98	3	0			c.A487G						scavenged	.	A	GLY/SER	5,4401	4.2+/-10.8	0,5,2198	145.0	136.0	139.0		487	2.5	0.0	6	dbSNP_134	139	8,8592	3.0+/-9.4	0,8,4292	no	missense	MUC21	NM_001010909.2	56	0,13,6490	GG,GA,AA		0.093,0.1135,0.1	benign	163/567	30954439	13,12993	2203	4300	6503	SO:0001583	missense	394263	exon2			GAGGCCAGCACAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.487A>G	6.37:g.30954439A>G	ENSP00000365473:p.Ser163Gly	62.0	2.0	0.0322581		107.0	8.0	0.0747664	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	A	12.76	2.033332	0.35893	0.001135	9.3E-4	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.03441	3.93	3.76	2.55	0.30701	.	.	.	.	.	T	0.00936	0.0031	N	0.20986	0.625	0.09310	N	1	B	0.27013	0.166	B	0.30782	0.12	T	0.48570	-0.9024	8	.	.	.	-5.3386	7.5189	0.27616	0.8914:0.0:0.1086:0.0	.	163	Q5SSG8	MUC21_HUMAN	G	163	ENSP00000365473:S163G	.	S	+	1	0	MUC21	31062418	0.000000	0.05858	0.006000	0.13384	0.067000	0.16453	1.000000	0.29770	0.599000	0.29845	0.397000	0.26171	AGC	A|0.996;G|0.004	0.004	strong		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
MUC21	394263	hgsc.bcm.edu	37	6	30954594	30954594	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954594G>C	ENST00000376296.3	+	2	883	c.642G>C	c.(640-642)gaG>gaC	p.E214D	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	214	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CCAACTCTGAGTCCAGAACGA	0.612																																					p.E214D		Atlas-SNP	.											.	MUC21	98	.	0			c.G642C						PASS	.						154.0	152.0	153.0					6																	30954594		2203	4300	6503	SO:0001583	missense	394263	exon2			CTCTGAGTCCAGA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.642G>C	6.37:g.30954594G>C	ENSP00000365473:p.Glu214Asp	95.0	0.0	0		120.0	6.0	0.05	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	G	3.066	-0.192132	0.06299	.	.	ENSG00000204544	ENST00000376296	T	0.01787	4.64	3.54	-7.08	0.01558	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.08055	0.003	T	0.43196	-0.9406	8	.	.	.	.	10.9515	0.47332	0.1259:0.5078:0.3663:0.0	.	214	Q5SSG8	MUC21_HUMAN	D	214	ENSP00000365473:E214D	.	E	+	3	2	MUC21	31062573	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.756000	0.04777	-2.750000	0.00375	-0.349000	0.07799	GAG	.	.	none		0.612	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
FAS	355	hgsc.bcm.edu	37	10	90768672	90768672	+	Missense_Mutation	SNP	C	C	T	rs121913078		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:90768672C>T	ENST00000355279.2	+	4	361	c.361C>T	c.(361-363)Cgg>Tgg	p.R121W	FAS_ENST00000355740.2_Missense_Mutation_p.R121W|FAS_ENST00000313771.5_3'UTR|FAS_ENST00000357339.2_Missense_Mutation_p.R121W|FAS_ENST00000352159.4_Missense_Mutation_p.R121W			P49327	FAS_HUMAN	Fas cell surface death receptor	0	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)	18		Colorectal(252;0.0161)		Colorectal(12;0.000136)|COAD - Colon adenocarcinoma(12;0.000193)	Cerulenin(DB01034)|Orlistat(DB01083)	AAACTGCACCCGGACCCAGAA	0.393																																					p.R121W		Atlas-SNP	.											FAS,caecum,carcinoma,-1,1	FAS	47	1	0			c.C361T	GRCh37	CM971493	FAS	M	rs121913078	PASS	.						247.0	274.0	265.0					10																	90768672		2203	4300	6503	SO:0001583	missense	355	exon4			TGCACCCGGACCC	M67454	CCDS7393.1, CCDS7394.1, CCDS7395.1	10q24.1	2014-09-17	2013-05-22	2005-01-07	ENSG00000026103	ENSG00000026103		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11920	protein-coding gene	gene with protein product	"""TNF receptor superfamily member 6"""	134637	"""tumor necrosis factor receptor superfamily, member 6"", ""Fas (TNF receptor superfamily, member 6)"""	FAS1, APT1, TNFRSF6		1385299, 1385309	Standard	NM_000043		Approved	CD95, APO-1	uc001kfr.3	P25445	OTTHUMG00000018701	ENST00000355279.2:c.361C>T	10.37:g.90768672C>T	ENSP00000347426:p.Arg121Trp	115.0	0.0	0		71.0	60.0	0.84507	NM_152872	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000355279.2	37	CCDS7395.1	.	.	.	.	.	.	.	.	.	.	C	13.43	2.235818	0.39498	.	.	ENSG00000026103	ENST00000540197;ENST00000355740;ENST00000352159;ENST00000357339;ENST00000355279;ENST00000371875	D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89	4.2	-2.74	0.05932	TNFR/CD27/30/40/95 cysteine-rich region (3);	2.803120	0.00964	N	0.003143	D	0.94879	0.8345	M	0.68593	2.085	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.77557	0.971;0.99;0.983	D	0.84814	0.0792	10	0.66056	D	0.02	0.1313	8.0344	0.30484	0.5264:0.2147:0.2589:0.0	.	121;121;121	P25445-6;Q5T9P3;P25445	.;.;TNR6_HUMAN	W	148;121;121;121;121;121	ENSP00000347979:R121W;ENSP00000345601:R121W;ENSP00000349896:R121W;ENSP00000347426:R121W	ENSP00000345601:R121W	R	+	1	2	FAS	90758652	0.000000	0.05858	0.000000	0.03702	0.502000	0.33828	-1.179000	0.03090	-0.519000	0.06444	0.650000	0.86243	CGG	.	.	weak		0.393	FAS-011	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000049280.2		
BMP1	649	hgsc.bcm.edu	37	8	22049596	22049596	+	Missense_Mutation	SNP	G	G	A	rs145284541	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22049596G>A	ENST00000306385.5	+	9	1782	c.1112G>A	c.(1111-1113)cGc>cAc	p.R371H	BMP1_ENST00000354870.5_3'UTR|BMP1_ENST00000397816.3_Missense_Mutation_p.R371H|BMP1_ENST00000306349.8_Missense_Mutation_p.R371H|BMP1_ENST00000397814.3_Missense_Mutation_p.R371H	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	371	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GACCTGTACCGCAGCCGCCTG	0.632													G|||	17	0.00339457	0.0008	0.0072	5008	,	,		18169	0.0		0.0109	False		,,,				2504	0.0				p.R371H		Atlas-SNP	.											BMP1_ENST00000306349,NS,carcinoma,+1,2	BMP1	131	2	0			c.G1112A						PASS	.	G	HIS/ARG,HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	179.0	142.0	155.0		1112,1112	5.8	1.0	8	dbSNP_134	155	61,8539	37.8+/-93.5	0,61,4239	yes	missense,missense	BMP1	NM_001199.3,NM_006129.4	29,29	0,67,6436	AA,AG,GG		0.7093,0.1362,0.5151	possibly-damaging,possibly-damaging	371/731,371/987	22049596	67,12939	2203	4300	6503	SO:0001583	missense	649	exon9			TGTACCGCAGCCG		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.1112G>A	8.37:g.22049596G>A	ENSP00000305714:p.Arg371His	53.0	0.0	0		54.0	18.0	0.333333	NM_001199	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Missense_Mutation	SNP	ENST00000306385.5	37	CCDS6026.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	26.4	4.738348	0.89573	0.001362	0.007093	ENSG00000168487	ENST00000306385;ENST00000397816;ENST00000306349;ENST00000397814	T;T;T;T	0.18960	2.18;2.18;2.18;2.18	5.77	5.77	0.91146	CUB (5);	0.000000	0.39274	U	0.001414	T	0.30166	0.0756	L	0.38175	1.15	0.80722	D	1	D;D;D;D	0.89917	0.99;1.0;0.999;0.999	P;D;D;P	0.91635	0.86;0.999;0.949;0.862	T	0.01249	-1.1406	10	0.44086	T	0.13	.	17.4922	0.87707	0.0:0.0:1.0:0.0	.	371;444;371;371	P13497;Q59F71;P13497-2;P13497-6	BMP1_HUMAN;.;.;.	H	371	ENSP00000305714:R371H;ENSP00000380917:R371H;ENSP00000306121:R371H;ENSP00000380915:R371H	ENSP00000306121:R371H	R	+	2	0	BMP1	22105541	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.535000	0.53575	2.724000	0.93272	0.561000	0.74099	CGC	G|0.995;A|0.005	0.005	strong		0.632	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
PEX11G	92960	hgsc.bcm.edu	37	19	7542168	7542168	+	Missense_Mutation	SNP	G	G	A	rs11668511	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:7542168G>A	ENST00000221480.1	-	5	654	c.646C>T	c.(646-648)Ctc>Ttc	p.L216F	PEX11G_ENST00000593942.1_Missense_Mutation_p.L146F|PEX11G_ENST00000599519.1_5'UTR	NM_001270539.1|NM_080662.3	NP_001257468.1|NP_542393.1	Q96HA9	PX11C_HUMAN	peroxisomal biogenesis factor 11 gamma	216					peroxisome fission (GO:0016559)|regulation of peroxisome size (GO:0044375)	integral component of peroxisomal membrane (GO:0005779)|intrinsic component of peroxisomal membrane (GO:0031231)|peroxisome (GO:0005777)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(1)|endometrium(1)|lung(1)|ovary(1)|prostate(1)|skin(1)	7						GTGCCCATGAGGCCCACTAGC	0.706													G|||	51	0.0101837	0.0008	0.0115	5008	,	,		14100	0.0		0.0358	False		,,,				2504	0.0061				p.L216F		Atlas-SNP	.											.	PEX11G	16	.	0			c.C646T						PASS	.	G	PHE/LEU	25,4313		0,25,2144	12.0	15.0	14.0		646	5.2	1.0	19	dbSNP_120	14	286,8238		4,278,3980	yes	missense	PEX11G	NM_080662.2	22	4,303,6124	AA,AG,GG		3.3552,0.5763,2.418	probably-damaging	216/242	7542168	311,12551	2169	4262	6431	SO:0001583	missense	92960	exon5			CCATGAGGCCCAC	BC008780	CCDS12178.1	19p13.2	2008-02-05				ENSG00000104883			20208	protein-coding gene	gene with protein product		607583				12417726	Standard	NM_080662		Approved		uc002mgk.2	Q96HA9		ENST00000221480.1:c.646C>T	19.37:g.7542168G>A	ENSP00000221480:p.Leu216Phe	33.0	0.0	0		32.0	16.0	0.5	NM_080662	Q8NDM0	Missense_Mutation	SNP	ENST00000221480.1	37	CCDS12178.1	31	0.014194139194139194	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	20.6	4.010285	0.75046	0.005763	0.033552	ENSG00000104883	ENST00000221480	T	0.52983	0.64	5.2	5.2	0.72013	.	0.065408	0.64402	D	0.000008	T	0.38321	0.1036	M	0.78223	2.4	0.58432	D	0.999999	D	0.71674	0.998	D	0.63113	0.911	T	0.53301	-0.8458	10	0.28530	T	0.3	-20.3419	9.8052	0.40789	0.094:0.0:0.906:0.0	rs11668511	216	Q96HA9	PX11C_HUMAN	F	216	ENSP00000221480:L216F	ENSP00000221480:L216F	L	-	1	0	PEX11G	7448168	1.000000	0.71417	1.000000	0.80357	0.688000	0.40055	4.977000	0.63792	2.405000	0.81733	0.563000	0.77884	CTC	G|0.985;A|0.015	0.015	strong		0.706	PEX11G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458965.1	NM_080662	
MEF2B	100271849	hgsc.bcm.edu	37	19	19260045	19260045	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19260045T>A	ENST00000602424.2	-	5	974	c.248A>T	c.(247-249)gAc>gTc	p.D83V	MEF2B_ENST00000409224.1_Missense_Mutation_p.D83V|MEF2B_ENST00000410050.1_Missense_Mutation_p.D83V|MEF2B_ENST00000409447.2_Missense_Mutation_p.D83V|MEF2BNB-MEF2B_ENST00000444486.3_Missense_Mutation_p.D83V|MEF2BNB-MEF2B_ENST00000514819.3_Missense_Mutation_p.D100V|MEF2BNB-MEF2B_ENST00000602276.1_5'UTR|MEF2B_ENST00000424583.2_Missense_Mutation_p.D83V|MEF2B_ENST00000162023.5_Missense_Mutation_p.D83V	NM_005919.3	NP_005910.1	Q02080	MEF2B_HUMAN	myocyte enhancer factor 2B	83					muscle organ development (GO:0007517)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase binding (GO:0042826)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D83V(11)|p.D83A(2)		breast(1)|haematopoietic_and_lymphoid_tissue(21)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	28			OV - Ovarian serous cystadenocarcinoma(5;0.00011)|Epithelial(12;0.00412)			CTCGAGGATGTCAGTGTTGGT	0.607																																					p.D83V		Atlas-SNP	.											MEF2BNB-MEF2B,NS,lymphoid_neoplasm,0,15	MEF2BNB-MEF2B	29	15	13	Substitution - Missense(13)	haematopoietic_and_lymphoid_tissue(13)	c.A248T						PASS	.						126.0	63.0	84.0					19																	19260045		2203	4300	6503	SO:0001583	missense	4207	exon5			AGGATGTCAGTGT	X63380	CCDS12394.1, CCDS46024.1	19p13.11	2010-05-12	2007-04-24					"""Myocyte enhancer factors"""	6995	protein-coding gene	gene with protein product		600661				1516833, 8575763	Standard	NM_001145785		Approved	RSRFR2	uc002nll.2	Q02080		ENST00000602424.2:c.248A>T	19.37:g.19260045T>A	ENSP00000473308:p.Asp83Val	120.0	0.0	0		122.0	53.0	0.434426	NM_005919	A0AV80|B4DVH7|B7ZVY1|G5E9M1	Missense_Mutation	SNP	ENST00000602424.2	37	CCDS12394.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.187318	0.78789	.	.	ENSG00000213999	ENST00000409224;ENST00000424583;ENST00000410050;ENST00000444486;ENST00000409447;ENST00000162023	D;D;D;D;D	0.83837	-1.77;-1.77;-1.77;-1.77;-1.77	5.33	5.33	0.75918	Transcription factor, MADS-box (1);	0.000000	0.85682	D	0.000000	D	0.90167	0.6927	M	0.74467	2.265	0.80722	D	1	D;D;D;D;D	0.89917	0.999;0.998;1.0;1.0;1.0	D;D;D;D;D	0.87578	0.963;0.92;0.997;0.997;0.998	D	0.91163	0.4962	10	0.72032	D	0.01	-31.0539	13.2359	0.59969	0.0:0.0:0.0:1.0	.	83;130;83;83;83	Q02080;B8ZZJ5;C9J4J4;G5E9M1;B3KQ23	MEF2B_HUMAN;.;.;.;.	V	83;83;83;83;130;83	ENSP00000386480:D83V;ENSP00000402154:D83V;ENSP00000386374:D83V;ENSP00000390762:D83V;ENSP00000162023:D83V	ENSP00000162023:D83V	D	-	2	0	MEF2B	19121045	1.000000	0.71417	0.999000	0.59377	0.518000	0.34316	7.923000	0.87546	2.024000	0.59613	0.459000	0.35465	GAC	.	.	none		0.607	MEF2B-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_005919	
MTRR	4552	hgsc.bcm.edu	37	5	7893005	7893005	+	Silent	SNP	C	C	T	rs34172797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7893005C>T	ENST00000264668.2	+	11	1647	c.1617C>T	c.(1615-1617)agC>agT	p.S539S	MTRR_ENST00000440940.2_Silent_p.S512S	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	539	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	ATGAAGACAGCGGGAAAGCCC	0.458													C|||	45	0.00898562	0.0045	0.0259	5008	,	,		18337	0.0		0.0189	False		,,,				2504	0.002				p.S539S		Atlas-SNP	.											.	MTRR	74	.	0			c.C1617T						PASS	.	C	,	66,4340	61.7+/-98.7	0,66,2137	84.0	71.0	75.0		1536,1617	0.2	0.0	5	dbSNP_126	75	207,8393	89.4+/-151.6	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,269,6232	TT,TC,CC		2.407,1.498,2.099	,	512/699,539/726	7893005	273,12733	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			AGACAGCGGGAAA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1617C>T	5.37:g.7893005C>T		89.0	0.0	0		118.0	58.0	0.491525	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			C|0.981;T|0.019	0.019	strong		0.458	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
SMO	6608	hgsc.bcm.edu	37	7	128843263	128843263	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128843263C>A	ENST00000249373.3	+	2	650	c.370C>A	c.(370-372)Ccc>Acc	p.P124T		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	124	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	AGTGATCCAGCCCCTGCTGTG	0.652			Mis		skin basal cell																																p.P124T		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.C370A						PASS	.						22.0	18.0	19.0					7																	128843263		2178	4271	6449	SO:0001583	missense	6608	exon2			ATCCAGCCCCTGC	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.370C>A	7.37:g.128843263C>A	ENSP00000249373:p.Pro124Thr	105.0	0.0	0		113.0	53.0	0.469027	NM_005631	A4D1K5	Missense_Mutation	SNP	ENST00000249373.3	37	CCDS5811.1	.	.	.	.	.	.	.	.	.	.	C	26.0	4.690771	0.88735	.	.	ENSG00000128602	ENST00000249373	T	0.79554	-1.28	5.5	5.5	0.81552	Frizzled domain (5);	0.000000	0.85682	D	0.000000	D	0.90321	0.6972	M	0.82630	2.6	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.90922	0.4784	10	0.56958	D	0.05	.	16.9188	0.86158	0.0:1.0:0.0:0.0	.	124	Q99835	SMO_HUMAN	T	124	ENSP00000249373:P124T	ENSP00000249373:P124T	P	+	1	0	SMO	128630499	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.695000	0.84257	2.584000	0.87258	0.563000	0.77884	CCC	.	.	none		0.652	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
MAGEB6	158809	hgsc.bcm.edu	37	X	26212334	26212334	+	Missense_Mutation	SNP	A	A	C	rs143802048	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:26212334A>C	ENST00000379034.1	+	2	520	c.371A>C	c.(370-372)tAt>tCt	p.Y124S		NM_173523.2	NP_775794.2	Q8N7X4	MAGB6_HUMAN	melanoma antigen family B, 6	124	Ser-rich.									breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(18)|ovary(3)|prostate(2)	33						GGCTCAAAATATGATGTGGCT	0.552													.|||	342	0.090596	0.0242	0.0706	3775	,	,		12620	0.0794		0.0646	False		,,,				2504	0.1186				p.Y124S		Atlas-SNP	.											.	MAGEB6	91	.	0			c.A371C						PASS	.	C	SER/TYR	21,3809		1,4,15,1626,553	85.0	77.0	80.0		371	-1.5	0.0	X	dbSNP_134	80	81,6624		6,7,62,2414,1789	no	missense	MAGEB6	NM_173523.2	144	7,11,77,4040,2342	CC,CA,C,AA,A		1.2081,0.5483,0.9682	benign	124/408	26212334	102,10433	2199	4278	6477	SO:0001583	missense	158809	exon2			CAAAATATGATGT	AF320514	CCDS14217.1	Xp22.12	2009-03-17			ENSG00000176746	ENSG00000176746			23796	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 4"""	300467				10861452	Standard	NM_173523		Approved	FLJ40242, MAGE-B6, MAGEB6A, CT3.4	uc004dbr.3	Q8N7X4	OTTHUMG00000021285	ENST00000379034.1:c.371A>C	X.37:g.26212334A>C	ENSP00000368320:p.Tyr124Ser	89.0	0.0	0		22.0	11.0	0.5	NM_173523	Q6GS19|Q9H219	Missense_Mutation	SNP	ENST00000379034.1	37	CCDS14217.1	.	.	.	.	.	.	.	.	.	.	C	0.003	-2.460724	0.00171	0.005483	0.012081	ENSG00000176746	ENST00000379034	T	0.01629	4.72	1.23	-1.47	0.08772	.	.	.	.	.	T	0.00468	0.0015	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42292	-0.9460	9	0.02654	T	1	.	2.6776	0.05084	0.2703:0.469:0.0:0.2607	.	124	Q8N7X4	MAGB6_HUMAN	S	124	ENSP00000368320:Y124S	ENSP00000368320:Y124S	Y	+	2	0	MAGEB6	26122255	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.070000	0.03440	-1.353000	0.02191	-2.567000	0.00172	TAT	A|0.980;C|0.020	0.020	strong		0.552	MAGEB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056123.1	NM_173523	
FCGBP	8857	hgsc.bcm.edu	37	19	40376811	40376811	+	Missense_Mutation	SNP	C	C	T	rs4802062	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:40376811C>T	ENST00000221347.6	-	24	11618	c.11611G>A	c.(11611-11613)Ggg>Agg	p.G3871R	FCGBP_ENST00000595713.1_5'Flank	NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3871	VWFD 9. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GACAGTGGCCCTGTGGGGCTG	0.602																																					p.G3871R		Atlas-SNP	.											FCGBP,NS,carcinoma,+2,1	FCGBP	416	1	0			c.G11611A						scavenged	.						9.0	14.0	12.0					19																	40376811		2097	4111	6208	SO:0001583	missense	8857	exon24			GTGGCCCTGTGGG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.11611G>A	19.37:g.40376811C>T	ENSP00000221347:p.Gly3871Arg	618.0	1.0	0.00161812		785.0	145.0	0.184713	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	c	19.42	3.823259	0.71143	.	.	ENSG00000090920	ENST00000221347	T	0.19806	2.12	3.75	3.75	0.43078	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.55049	0.1896	M	0.92649	3.33	0.43485	D	0.995715	D	0.89917	1.0	D	0.97110	1.0	T	0.69038	-0.5251	9	0.72032	D	0.01	.	14.6972	0.69132	0.0:1.0:0.0:0.0	rs4802062	3871	Q9Y6R7	FCGBP_HUMAN	R	3871	ENSP00000221347:G3871R	ENSP00000221347:G3871R	G	-	1	0	FCGBP	45068651	0.998000	0.40836	0.523000	0.27875	0.621000	0.37620	3.885000	0.56182	1.792000	0.52537	0.313000	0.20887	GGG	C|0.962;T|0.038	0.038	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50659025	50659025	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50659025G>T	ENST00000248846.5	-	16	3867	c.3763C>A	c.(3763-3765)Cct>Act	p.P1255T	TUBGCP6_ENST00000439308.2_Missense_Mutation_p.P1255T|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	1255	9 X 27 AA tandem repeats.				G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TCCGACACAGGCTCCCCCAAG	0.637																																					p.P1255T		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.C3763A						PASS	.						68.0	53.0	58.0					22																	50659025		2203	4300	6503	SO:0001583	missense	85378	exon16			ACACAGGCTCCCC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.3763C>A	22.37:g.50659025G>T	ENSP00000248846:p.Pro1255Thr	61.0	0.0	0		81.0	35.0	0.432099	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Missense_Mutation	SNP	ENST00000248846.5	37	CCDS14087.1	.	.	.	.	.	.	.	.	.	.	g	6.032	0.374231	0.11409	.	.	ENSG00000128159	ENST00000248846;ENST00000439308	T;T	0.11063	3.19;2.81	3.02	-0.545	0.11843	.	2.098260	0.03949	U	0.288172	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B;B;B	0.16166	0.016;0.004;0.012	B;B;B	0.18561	0.013;0.013;0.022	T	0.36890	-0.9729	10	0.07644	T	0.81	.	8.0715	0.30691	0.0:0.0962:0.5704:0.3334	.	1247;1255;1255	B2RWN4;Q96RT7;Q96RT7-3	.;GCP6_HUMAN;.	T	1255	ENSP00000248846:P1255T;ENSP00000397387:P1255T	ENSP00000248846:P1255T	P	-	1	0	TUBGCP6	49001152	0.000000	0.05858	0.002000	0.10522	0.010000	0.07245	-0.481000	0.06552	-0.178000	0.10672	-0.578000	0.04140	CCT	.	.	none		0.637	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
AKR1C3	8644	hgsc.bcm.edu	37	10	5141619	5141619	+	Missense_Mutation	SNP	A	A	G	rs61730879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5141619A>G	ENST00000380554.3	+	5	1200	c.548A>G	c.(547-549)aAg>aGg	p.K183R	AKR1C3_ENST00000439082.2_Missense_Mutation_p.K64R|AKR1C3_ENST00000605149.1_Missense_Mutation_p.K160R	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	183					arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	CCAGGACTCAAGTACAAGCCT	0.512													A|||	7	0.00139776	0.0008	0.0029	5008	,	,		17607	0.0		0.004	False		,,,				2504	0.0				p.K183R		Atlas-SNP	.											.	AKR1C3	21	.	0			c.A548G						PASS	.						145.0	130.0	135.0					10																	5141619		2203	4300	6503	SO:0001583	missense	8644	exon5			GACTCAAGTACAA	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.548A>G	10.37:g.5141619A>G	ENSP00000369927:p.Lys183Arg	135.0	0.0	0		123.0	65.0	0.528455	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	14.92	2.680782	0.47886	.	.	ENSG00000196139	ENST00000439082;ENST00000380554	T;T	0.25414	1.8;1.8	2.67	2.67	0.31697	NADP-dependent oxidoreductase domain (3);	0.000000	0.64402	D	0.000003	T	0.23846	0.0577	L	0.36672	1.1	0.42266	D	0.992032	B;B;B	0.22480	0.002;0.07;0.07	B;B;B	0.37239	0.018;0.244;0.244	T	0.08513	-1.0718	10	0.44086	T	0.13	.	8.7963	0.34881	1.0:0.0:0.0:0.0	.	64;183;183	B4DL37;P42330;Q2XPP3	.;AK1C3_HUMAN;.	R	64;183	ENSP00000401327:K64R;ENSP00000369927:K183R	ENSP00000369927:K183R	K	+	2	0	AKR1C3	5131619	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	5.877000	0.69675	0.992000	0.38840	0.402000	0.26972	AAG	A|0.997;G|0.001;T|0.002	0.001	strong		0.512	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
NAA15	80155	hgsc.bcm.edu	37	4	140278638	140278638	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140278638T>G	ENST00000296543.5	+	11	1509	c.1186T>G	c.(1186-1188)Tac>Gac	p.Y396D	NAA15_ENST00000398947.1_Missense_Mutation_p.Y396D	NM_057175.3	NP_476516.1	Q9BXJ9	NAA15_HUMAN	N(alpha)-acetyltransferase 15, NatA auxiliary subunit	396					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)	p.Y396H(1)		NS(1)|endometrium(3)|large_intestine(7)|liver(2)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29						TGCTTTGGAGTACATAAATAC	0.338																																					p.Y396D		Atlas-SNP	.											NAA15,NS,carcinoma,0,1	NAA15	88	1	1	Substitution - Missense(1)	endometrium(1)	c.T1186G						PASS	.						83.0	76.0	78.0					4																	140278638		1854	4087	5941	SO:0001583	missense	80155	exon11			TTGGAGTACATAA	AY039242	CCDS43270.1	4q31.1	2010-01-14	2010-01-14	2010-01-14	ENSG00000164134	ENSG00000164134		"""N(alpha)-acetyltransferase subunits"""	30782	protein-coding gene	gene with protein product		608000	"""NMDA receptor regulated 1"""	NARG1		12140756, 11478804, 19660095	Standard	XM_005263236		Approved	TBDN100, NATH, FLJ13340	uc003ihu.1	Q9BXJ9	OTTHUMG00000137363	ENST00000296543.5:c.1186T>G	4.37:g.140278638T>G	ENSP00000296543:p.Tyr396Asp	118.0	0.0	0		133.0	55.0	0.413534	NM_057175	D3DNY6|Q52LG9|Q8IWH4|Q8NEV2|Q9H8P6	Missense_Mutation	SNP	ENST00000296543.5	37	CCDS43270.1	.	.	.	.	.	.	.	.	.	.	T	27.0	4.795402	0.90453	.	.	ENSG00000164134	ENST00000296543;ENST00000544077;ENST00000398947	T;T	0.49720	0.77;0.77	5.71	5.71	0.89125	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.72518	0.3470	M	0.90082	3.085	0.80722	D	1	P	0.46220	0.874	P	0.59889	0.865	T	0.77327	-0.2629	10	0.54805	T	0.06	-6.2825	15.994	0.80228	0.0:0.0:0.0:1.0	.	396	Q9BXJ9	NAA15_HUMAN	D	396;270;396	ENSP00000296543:Y396D;ENSP00000381920:Y396D	ENSP00000296543:Y396D	Y	+	1	0	NAA15	140498088	1.000000	0.71417	0.996000	0.52242	0.990000	0.78478	5.959000	0.70339	2.168000	0.68352	0.528000	0.53228	TAC	.	.	none		0.338	NAA15-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000267839.2	NM_057175	
ATF7	11016	hgsc.bcm.edu	37	12	53925573	53925573	+	Silent	SNP	C	C	T	rs139241958	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:53925573C>T	ENST00000548446.2	-	9	1027	c.915G>A	c.(913-915)caG>caA	p.Q305Q	ATF7_ENST00000420353.2_Silent_p.Q294Q|ATF7_ENST00000328463.7_Silent_p.Q305Q|ATF7_ENST00000415113.1_Silent_p.Q273Q|RP11-793H13.10_ENST00000591834.1_Silent_p.Q294Q|ATF7_ENST00000456903.4_Silent_p.Q294Q			P17544	ATF7_HUMAN	activating transcription factor 7	305					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9					Pseudoephedrine(DB00852)	GGATGAGAATCTGGCTCTGCT	0.517													C|||	27	0.00539137	0.0008	0.0144	5008	,	,		14364	0.0		0.0149	False		,,,				2504	0.001				p.Q294Q		Atlas-SNP	.											.	ATF7	51	.	0			c.G882A						PASS	.	C	,,	14,4046		0,14,2016	68.0	76.0	73.0		915,819,882	5.4	1.0	12	dbSNP_134	73	131,8225		2,127,4049	no	coding-synonymous,coding-synonymous,coding-synonymous	ATF7	NM_001130059.1,NM_001130060.1,NM_006856.2	,,	2,141,6065	TT,TC,CC		1.5677,0.3448,1.1678	,,	305/495,273/463,294/484	53925573	145,12271	2030	4178	6208	SO:0001819	synonymous_variant	11016	exon9			GAGAATCTGGCTC	X52943	CCDS44906.1, CCDS58238.1	12q13	2013-01-10				ENSG00000170653		"""basic leucine zipper proteins"""	792	protein-coding gene	gene with protein product		606371				1694576, 11278933	Standard	NM_006856		Approved	ATFA	uc001sdz.3	P17544	OTTHUMG00000169776	ENST00000548446.2:c.915G>A	12.37:g.53925573C>T		52.0	0.0	0		63.0	34.0	0.539683	NM_006856	A5D6Y4|B2RMP1|B4DQL4|Q13814|Q8IVR8|Q9UD83	Silent	SNP	ENST00000548446.2	37																																																																																				C|0.991;T|0.009	0.009	strong		0.517	ATF7-007	KNOWN	NMD_exception|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000406302.2	NM_001130059	
FAM66B	100128890	hgsc.bcm.edu	37	8	7190935	7190935	+	lincRNA	SNP	G	G	A	rs117479685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:7190935G>A	ENST00000606573.1	-	0	703									family with sequence similarity 66, member B																		CAAAGCTCAAGAAGTCCAGTG	0.483													g|||	16	0.00319489	0.0008	0.0029	5008	,	,		18653	0.001		0.005	False		,,,				2504	0.0072				p.E343K		Atlas-SNP	.											.	.	.	.	0			c.G1027A						PASS	.																																					401447	exon1			GCTCAAGAAGTCC			8p23.1	2013-07-05			ENSG00000215374	ENSG00000215374		"""Long non-coding RNAs"""	28890	non-coding RNA	RNA, long non-coding							Standard	NR_027423		Approved				OTTHUMG00000165383		8.37:g.7190935G>A		151.0	0.0	0		169.0	88.0	0.52071	NM_001256873		Missense_Mutation	SNP	ENST00000606573.1	37																																																																																				G|0.996;A|0.004	0.004	strong		0.483	FAM66B-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000470344.1	NR_027423	
PLCG2	5336	hgsc.bcm.edu	37	16	81942028	81942028	+	Missense_Mutation	SNP	C	C	G	rs72824905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:81942028C>G	ENST00000359376.3	+	17	1779	c.1565C>G	c.(1564-1566)cCc>cGc	p.P522R		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	522					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CAGGATATACCCCCTACAGAA	0.537													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20275	0.0		0.0109	False		,,,				2504	0.001				p.P522R		Atlas-SNP	.											.	PLCG2	276	.	0			c.C1565G						PASS	.	C	ARG/PRO	3,3799		0,3,1898	56.0	56.0	56.0		1565	4.8	1.0	16	dbSNP_130	56	73,8147		0,73,4037	yes	missense	PLCG2	NM_002661.3	103	0,76,5935	GG,GC,CC		0.8881,0.0789,0.6322	benign	522/1266	81942028	76,11946	1901	4110	6011	SO:0001583	missense	5336	exon17			ATATACCCCCTAC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1565C>G	16.37:g.81942028C>G	ENSP00000352336:p.Pro522Arg	59.0	0.0	0		61.0	21.0	0.344262	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Missense_Mutation	SNP	ENST00000359376.3	37	CCDS42204.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	6.031	0.373996	0.11409	7.89E-4	0.008881	ENSG00000197943	ENST00000359376	T	0.65364	-0.15	4.85	4.85	0.62838	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);SH2 motif (1);	0.750593	0.12934	N	0.427117	T	0.36248	0.0960	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.25710	-1.0124	10	0.49607	T	0.09	.	11.0904	0.48113	0.2379:0.7621:0.0:0.0	.	389;522	B4E3H3;P16885	.;PLCG2_HUMAN	R	522	ENSP00000352336:P522R	ENSP00000352336:P522R	P	+	2	0	PLCG2	80499529	0.014000	0.17966	0.979000	0.43373	0.335000	0.28730	2.624000	0.46444	2.249000	0.74217	0.655000	0.94253	CCC	C|0.993;G|0.007	0.007	strong		0.537	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
DSCC1	79075	hgsc.bcm.edu	37	8	120850521	120850521	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120850521C>T	ENST00000313655.4	-	8	1265	c.1051G>A	c.(1051-1053)Gaa>Aaa	p.E351K		NM_024094.2	NP_076999.2	Q9BVC3	DCC1_HUMAN	DNA replication and sister chromatid cohesion 1	351					DNA replication (GO:0006260)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|post-translational protein acetylation (GO:0034421)|regulation of DNA replication (GO:0006275)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			NS(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(1)|pancreas(1)	9	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GCAATATCTTCTTCTGTCCAC	0.338																																					p.E351K		Atlas-SNP	.											.	DSCC1	40	.	0			c.G1051A						PASS	.						82.0	86.0	85.0					8																	120850521		2203	4300	6503	SO:0001583	missense	79075	exon8			TATCTTCTTCTGT		CCDS6330.1	8q24.12	2013-05-24	2013-05-24		ENSG00000136982	ENSG00000136982			24453	protein-coding gene	gene with protein product	"""defective in sister chromatid cohesion homolog 1 (S. cerevisiae)"""	613203	"""defective in sister chromatid cohesion 1 homolog (S. cerevisiae)"""			12766176, 20826785	Standard	NM_024094		Approved	DCC1, hDCC1, MGC5528	uc003yov.3	Q9BVC3	OTTHUMG00000165010	ENST00000313655.4:c.1051G>A	8.37:g.120850521C>T	ENSP00000322180:p.Glu351Lys	133.0	0.0	0		127.0	16.0	0.125984	NM_024094	Q969N5	Missense_Mutation	SNP	ENST00000313655.4	37	CCDS6330.1	.	.	.	.	.	.	.	.	.	.	C	19.67	3.870756	0.72065	.	.	ENSG00000136982	ENST00000313655	T	0.46819	0.86	4.82	4.82	0.62117	.	0.212150	0.48767	D	0.000170	T	0.38321	0.1036	L	0.41079	1.255	0.50039	D	0.99984	P	0.35468	0.503	B	0.30029	0.11	T	0.19976	-1.0289	10	0.19590	T	0.45	-21.7187	18.2534	0.90011	0.0:1.0:0.0:0.0	.	351	Q9BVC3	DCC1_HUMAN	K	351	ENSP00000322180:E351K	ENSP00000322180:E351K	E	-	1	0	DSCC1	120919702	1.000000	0.71417	0.999000	0.59377	0.880000	0.50808	5.923000	0.70045	2.372000	0.80975	0.563000	0.77884	GAA	.	.	none		0.338	DSCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381443.1	NM_024094	
TM9SF1	10548	hgsc.bcm.edu	37	14	24662296	24662296	+	Missense_Mutation	SNP	T	T	C	rs62621251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24662296T>C	ENST00000261789.4	-	3	883	c.525A>G	c.(523-525)atA>atG	p.I175M	TM9SF1_ENST00000556387.1_Missense_Mutation_p.I384M|TM9SF1_ENST00000528669.1_Missense_Mutation_p.I175M|RP11-468E2.2_ENST00000561419.1_5'Flank|TM9SF1_ENST00000530611.1_Missense_Mutation_p.I384M|TM9SF1_ENST00000396854.4_Missense_Mutation_p.I175M|TM9SF1_ENST00000524835.1_Missense_Mutation_p.I88M	NM_006405.5	NP_006396.2	O15321	TM9S1_HUMAN	transmembrane 9 superfamily member 1	175					autophagy (GO:0006914)	cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				NS(1)|breast(4)|endometrium(3)|large_intestine(11)|lung(4)|ovary(1)	24				GBM - Glioblastoma multiforme(265;0.0183)		CATTGGCAAATATAATTCGGT	0.522													T|||	19	0.00379393	0.0	0.0086	5008	,	,		20446	0.0		0.0129	False		,,,				2504	0.0				p.I175M		Atlas-SNP	.											.	TM9SF1	58	.	0			c.A525G						PASS	.	T	MET/ILE,MET/ILE	9,4397	16.8+/-37.8	0,9,2194	103.0	99.0	100.0		525,525	3.9	1.0	14	dbSNP_129	100	87,8513	49.4+/-109.1	0,87,4213	yes	missense,missense	TM9SF1	NM_001014842.1,NM_006405.5	10,10	0,96,6407	CC,CT,TT		1.0116,0.2043,0.7381	possibly-damaging,possibly-damaging	175/490,175/607	24662296	96,12910	2203	4300	6503	SO:0001583	missense	10548	exon3			GGCAAATATAATT	U94831	CCDS9617.1, CCDS41934.1, CCDS73623.1	14q11.2	2005-10-11			ENSG00000100926	ENSG00000100926			11864	protein-coding gene	gene with protein product						9332367	Standard	NM_006405		Approved	MP70, HMP70	uc010tob.1	O15321	OTTHUMG00000029322	ENST00000261789.4:c.525A>G	14.37:g.24662296T>C	ENSP00000261789:p.Ile175Met	131.0	0.0	0		180.0	82.0	0.455556	NM_001014842	D3DS65|Q86SZ6|Q96FI8	Missense_Mutation	SNP	ENST00000261789.4	37	CCDS9617.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	17.64	3.439673	0.63067	0.002043	0.010116	ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000100926;ENSG00000254692	ENST00000261789;ENST00000528669;ENST00000556387;ENST00000524835;ENST00000396854;ENST00000528895;ENST00000530563;ENST00000530468;ENST00000525592;ENST00000528010;ENST00000530611	T;T;T;T;T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.1	3.94	0.45596	.	0.052007	0.64402	D	0.000001	T	0.54498	0.1862	M	0.65320	2	0.58432	D	0.999998	P;P;B	0.51791	0.948;0.494;0.016	P;B;B	0.59643	0.861;0.297;0.101	T	0.62765	-0.6785	10	0.72032	D	0.01	-10.9909	9.0359	0.36287	0.0:0.0:0.2919:0.7081	rs62621251	175;175;175	E9PJM1;Q86SZ6;O15321	.;.;TM9S1_HUMAN	M	175;175;384;88;175;175;88;175;175;175;384	ENSP00000261789:I175M;ENSP00000432997:I175M;ENSP00000451949:I384M;ENSP00000434387:I88M;ENSP00000380063:I175M;ENSP00000431447:I175M;ENSP00000437127:I88M;ENSP00000435857:I175M;ENSP00000432435:I175M;ENSP00000433792:I175M;ENSP00000433967:I384M	ENSP00000433967:I384M	I	-	3	3	TM9SF1;RP11-468E2.1	23732136	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.136000	0.50554	2.137000	0.66172	0.533000	0.62120	ATA	T|0.994;C|0.006	0.006	strong		0.522	TM9SF1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000073136.2	NM_006405	
MT-ND4	4538	hgsc.bcm.edu	37	M	11869	11869	+	Silent	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:11869C>A	ENST00000361381.2	+	1	1110	c.1110C>A	c.(1108-1110)ccC>ccA	p.P370P	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	370					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CTCGCCTTACCCCCCACTATT	0.448																																					p.P370P		Atlas-SNP	.											.	.	.	.	0			c.C1110A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTTACCCCCCACT			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1110C>A	M.37:g.11869C>A		7.0	0.0	0		26.0	26.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.448	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
AIF1L	83543	hgsc.bcm.edu	37	9	133995669	133995669	+	Missense_Mutation	SNP	T	T	C	rs112778089	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:133995669T>C	ENST00000247291.3	+	6	501	c.413T>C	c.(412-414)gTt>gCt	p.V138A	AIF1L_ENST00000372302.1_Missense_Mutation_p.V130A|AIF1L_ENST00000372312.3_Missense_Mutation_p.V143A|AIF1L_ENST00000372301.2_Missense_Mutation_p.V82A|AIF1L_ENST00000372300.1_3'UTR|AIF1L_ENST00000372298.1_Intron|AIF1L_ENST00000372297.2_3'UTR|AIF1L_ENST00000372309.3_Missense_Mutation_p.V164A	NM_031426.3	NP_113614.1	Q9BQI0	AIF1L_HUMAN	allograft inflammatory factor 1-like	138						actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)			lung(2)	2						CCCAAGCCAGTTGGCCCCCCT	0.542													T|||	3	0.000599042	0.0	0.0014	5008	,	,		14018	0.0		0.002	False		,,,				2504	0.0				p.V164A	Esophageal Squamous(95;611 1423 5044 34794 42333)	Atlas-SNP	.											.	AIF1L	15	.	0			c.T491C						PASS	.	T	ALA/VAL,,ALA/VAL	0,4406		0,0,2203	64.0	66.0	65.0		491,,413	-9.0	0.0	9	dbSNP_132	65	23,8577	16.6+/-54.9	0,23,4277	yes	missense,utr-3,missense	AIF1L	NM_001185095.1,NM_001185096.1,NM_031426.3	64,,64	0,23,6480	CC,CT,TT		0.2674,0.0,0.1768	benign,,benign	164/177,,138/151	133995669	23,12983	2203	4300	6503	SO:0001583	missense	83543	exon7			AGCCAGTTGGCCC	AL136566	CCDS6939.1, CCDS55348.1, CCDS55349.1	9q34.13-q34.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000126878	ENSG00000126878		"""EF-hand domain containing"""	28904	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 58"""	C9orf58		11230166	Standard	NM_001185095		Approved	IBA2, FLJ12783	uc004cad.2	Q9BQI0	OTTHUMG00000020817	ENST00000247291.3:c.413T>C	9.37:g.133995669T>C	ENSP00000247291:p.Val138Ala	199.0	0.0	0		181.0	99.0	0.546961	NM_001185095	B2RBC4|Q6ZR40|Q8NAX7|Q8WU47|Q9H9G0	Missense_Mutation	SNP	ENST00000247291.3	37	CCDS6939.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	6.283	0.420255	0.11928	0.0	0.002674	ENSG00000126878	ENST00000372309;ENST00000247291;ENST00000372302;ENST00000372312;ENST00000372301	T;T;T;T;T	0.61040	0.46;0.3;0.6;0.14;0.44	5.72	-9.04	0.00734	.	1.715750	0.03111	N	0.162504	T	0.34250	0.0891	N	0.25890	0.77	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.21177	-1.0253	10	0.08599	T	0.76	-0.9621	6.5492	0.22423	0.1036:0.5225:0.2109:0.1631	.	143;164;138	F5GYC9;Q9BQI0-2;Q9BQI0	.;.;AIF1L_HUMAN	A	164;138;130;143;82	ENSP00000361383:V164A;ENSP00000247291:V138A;ENSP00000361376:V130A;ENSP00000361386:V143A;ENSP00000361375:V82A	ENSP00000247291:V138A	V	+	2	0	AIF1L	132985490	0.000000	0.05858	0.001000	0.08648	0.925000	0.55904	-0.339000	0.07832	-1.647000	0.01511	-2.617000	0.00157	GTT	T|0.998;C|0.002	0.002	strong		0.542	AIF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054703.2	NM_031426	
ATHL1	80162	hgsc.bcm.edu	37	11	290888	290888	+	Silent	SNP	G	G	A	rs150075556	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:290888G>A	ENST00000409548.2	+	4	796	c.681G>A	c.(679-681)ctG>ctA	p.L227L	ATHL1_ENST00000409479.1_Silent_p.L227L|RP11-326C3.2_ENST00000525217.1_RNA|ATHL1_ENST00000409655.1_Silent_p.L50L|RP11-326C3.2_ENST00000534742.1_RNA|RP11-326C3.2_ENST00000533924.1_RNA	NM_025092.4	NP_079368.3	Q32M88	ATHL1_HUMAN	ATH1, acid trehalase-like 1 (yeast)	227					carbohydrate metabolic process (GO:0005975)		hydrolase activity, acting on glycosyl bonds (GO:0016798)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(7)|prostate(1)|skin(3)	17		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;5.38e-28)|Epithelial(43;3.25e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GGGGAGCTCTGTATACGGCTC	0.682													G|||	26	0.00519169	0.0	0.0144	5008	,	,		19309	0.003		0.005	False		,,,				2504	0.0082				p.L227L		Atlas-SNP	.											.	ATHL1	88	.	0			c.G681A						PASS	.	G		5,4401		0,5,2198	45.0	49.0	48.0		681	2.8	0.6	11	dbSNP_134	48	26,8574	7.1+/-27.0	0,26,4274	no	coding-synonymous	ATHL1	NM_025092.4		0,31,6472	AA,AG,GG		0.3023,0.1135,0.2384		227/738	290888	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	80162	exon4			AGCTCTGTATACG	AK090428	CCDS31322.2	11p15.5	2005-10-27			ENSG00000142102	ENSG00000142102			26210	protein-coding gene	gene with protein product							Standard	NM_025092		Approved	FLJ22635	uc010qvu.2	Q32M88	OTTHUMG00000153218	ENST00000409548.2:c.681G>A	11.37:g.290888G>A		148.0	0.0	0		162.0	91.0	0.561728	NM_025092	Q658X8|Q8TEG9|Q9H635	Silent	SNP	ENST00000409548.2	37	CCDS31322.2																																																																																			G|0.995;A|0.005	0.005	strong		0.682	ATHL1-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330164.3	NM_025092	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140347902	140347902	+	Silent	SNP	A	A	T	rs144335538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140347902A>T	ENST00000289269.5	+	1	2083	c.1551A>T	c.(1549-1551)ccA>ccT	p.P517P	PCDHA6_ENST00000529310.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	517	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAGGGCTGCCAGTCACCTCCT	0.507													A|||	11	0.00219649	0.0015	0.0014	5008	,	,		22726	0.0		0.008	False		,,,				2504	0.0				p.P517P	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.A1551T						PASS	.	A	,,,,,,,,,,,,,,,,,,	15,4391	21.2+/-45.6	0,15,2188	92.0	88.0	89.0		,1551,,,,,,,,,,,,,,,,,1551	3.6	1.0	5	dbSNP_134	89	94,8506	54.0+/-114.7	1,92,4207	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	1,107,6395	TT,TA,AA		1.093,0.3404,0.8381	,,,,,,,,,,,,,,,,,,	,517/1008,,,,,,,,,,,,,,,,,517/885	140347902	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			GCTGCCAGTCACC	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.1551A>T	5.37:g.140347902A>T		130.0	0.0	0		167.0	86.0	0.51497	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			A|0.993;T|0.007	0.007	strong		0.507	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
CSF2RA	1438	hgsc.bcm.edu	37	X	1413300	1413300	+	Silent	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1413300C>A	ENST00000381524.3	+	8	912	c.726C>A	c.(724-726)acC>acA	p.T242T	BX649553.3_ENST00000581137.1_RNA|CSF2RA_ENST00000381500.1_Silent_p.T242T|BX649553.2_ENST00000578699.1_RNA|CSF2RA_ENST00000417535.2_Silent_p.T242T|CSF2RA_ENST00000498153.1_3'UTR|MIR3690_ENST00000580266.1_RNA|CSF2RA_ENST00000494969.2_Intron|CSF2RA_ENST00000355432.3_Silent_p.T242T|CSF2RA_ENST00000432318.2_Silent_p.T242T|CSF2RA_ENST00000355805.2_Intron|CSF2RA_ENST00000381529.3_Silent_p.T242T|BX649553.4_ENST00000580687.1_RNA|CSF2RA_ENST00000361536.3_Silent_p.T242T|CSF2RA_ENST00000501036.2_Silent_p.T109T|CSF2RA_ENST00000381509.3_Silent_p.T242T|BX649553.1_ENST00000583047.1_RNA			P15509	CSF2R_HUMAN	colony stimulating factor 2 receptor, alpha, low-affinity (granulocyte-macrophage)	242	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				response to ethanol (GO:0045471)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(6)|kidney(3)|large_intestine(6)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	45		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	AGCCCAGGACCTATCAGAAGC	0.597																																					p.T242T	Esophageal Squamous(131;723 1707 25334 40494 41806)	Atlas-SNP	.											.	CSF2RA	153	.	0			c.C726A						PASS	.						330.0	265.0	287.0					X																	1413300		2203	4296	6499	SO:0001819	synonymous_variant	1438	exon6			CAGGACCTATCAG	M64445	CCDS35190.1, CCDS35191.1, CCDS35192.1, CCDS35193.1, CCDS55359.1, CCDS55360.1, CCDS55361.1	Xp22.32 and Yp11.3	2014-09-17			ENSG00000198223	ENSG00000198223		"""CD molecules"", ""Pseudoautosomal regions / PAR1"""	2435	protein-coding gene	gene with protein product		306250, 425000		CSF2R		1702217	Standard	NM_006140		Approved	CD116	uc010ncv.2	P15509	OTTHUMG00000012533	ENST00000381524.3:c.726C>A	X.37:g.1413300C>A		464.0	0.0	0		263.0	13.0	0.0494297	NM_172247	A7J003|A8KAM1|B4DW68|J3JS76|J3JS77|O00207|Q14429|Q14430|Q14431|Q16564	Silent	SNP	ENST00000381524.3	37	CCDS35191.1																																																																																			.	.	none		0.597	CSF2RA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000035013.2		
DNASE1L2	1775	hgsc.bcm.edu	37	16	2287294	2287294	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2287294C>T	ENST00000564065.1	+	3	1310	c.309C>T	c.(307-309)ttC>ttT	p.F103F	RP11-304L19.12_ENST00000564055.1_lincRNA|DNASE1L2_ENST00000320700.5_Silent_p.F103F|DNASE1L2_ENST00000382437.4_Silent_p.F103F|DNASE1L2_ENST00000567494.1_Silent_p.F103F			Q92874	DNSL2_HUMAN	deoxyribonuclease I-like 2	103					corneocyte development (GO:0003335)|DNA metabolic process (GO:0006259)|hair follicle development (GO:0001942)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)			endometrium(1)|prostate(1)|skin(2)	4						TGTACCTGTTCGTGTACAGGT	0.692																																					p.F103F		Atlas-SNP	.											.	DNASE1L2	14	.	0			c.C309T						PASS	.						13.0	16.0	15.0					16																	2287294		1860	4078	5938	SO:0001819	synonymous_variant	1775	exon4			CCTGTTCGTGTAC	U62647	CCDS42105.1	16p13.3	2008-02-05				ENSG00000167968			2958	protein-coding gene	gene with protein product		602622				9205125, 1577479	Standard	NM_001374		Approved	DNAS1L2	uc002cpp.3	Q92874		ENST00000564065.1:c.309C>T	16.37:g.2287294C>T		33.0	0.0	0		17.0	6.0	0.352941	NM_001374	E9PBY4|Q6JVM2|Q6JVM3	Silent	SNP	ENST00000564065.1	37	CCDS42105.1																																																																																			.	.	none		0.692	DNASE1L2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435236.1	NM_001374	
IGSF10	285313	hgsc.bcm.edu	37	3	151161330	151161330	+	Missense_Mutation	SNP	T	T	A	rs35736581	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:151161330T>A	ENST00000282466.3	-	5	5404	c.5405A>T	c.(5404-5406)gAc>gTc	p.D1802V	IGSF10_ENST00000495443.1_5'Flank	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	1802	Ig-like C2-type 4.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			CAATGTTCCGTCAACCGTCAC	0.493													T|||	5	0.000998403	0.0	0.0014	5008	,	,		20951	0.0		0.004	False		,,,				2504	0.0				p.D1802V		Atlas-SNP	.											.	IGSF10	279	.	0			c.A5405T						PASS	.	T	VAL/ASP	9,4397	15.5+/-35.6	0,9,2194	93.0	83.0	87.0		5405	5.3	0.1	3	dbSNP_126	87	44,8556	29.0+/-79.6	0,44,4256	yes	missense	IGSF10	NM_178822.4	152	0,53,6450	AA,AT,TT		0.5116,0.2043,0.4075	probably-damaging	1802/2624	151161330	53,12953	2203	4300	6503	SO:0001583	missense	285313	exon5			GTTCCGTCAACCG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.5405A>T	3.37:g.151161330T>A	ENSP00000282466:p.Asp1802Val	222.0	0.0	0		238.0	128.0	0.537815	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	11.28	1.592435	0.28357	0.002043	0.005116	ENSG00000152580	ENST00000282466;ENST00000544042	T	0.79653	-1.29	5.26	5.26	0.73747	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.128349	0.34291	N	0.004098	D	0.84456	0.5476	M	0.79475	2.455	0.80722	D	1	P	0.50943	0.94	P	0.62885	0.908	D	0.86437	0.1764	9	.	.	.	.	12.3129	0.54938	0.0:0.0:0.1409:0.8591	rs35736581	1802	Q6WRI0	IGS10_HUMAN	V	1802;429	ENSP00000282466:D1802V	.	D	-	2	0	IGSF10	152644020	0.991000	0.36638	0.052000	0.19188	0.038000	0.13279	2.679000	0.46909	1.993000	0.58246	0.482000	0.46254	GAC	T|0.996;A|0.004	0.004	strong		0.493	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
HR	55806	hgsc.bcm.edu	37	8	21976710	21976710	+	Missense_Mutation	SNP	T	T	C	rs7014851	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21976710T>C	ENST00000381418.4	-	15	4544	c.3064A>G	c.(3064-3066)Aca>Gca	p.T1022A	HR_ENST00000312841.8_Missense_Mutation_p.T1022A	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	1022	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.		T -> A (in ALUNC; dbSNP:rs7014851). {ECO:0000269|PubMed:9445480}.		negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		GGCAGTGGTGTGTCGGCATGC	0.642													C|||	392	0.0782748	0.261	0.0418	5008	,	,		15589	0.0		0.0159	False		,,,				2504	0.002				p.T1022A		Atlas-SNP	.											.	HR	71	.	0			c.A3064G	GRCh37	CM983990	HR	M	rs7014851	PASS	.	C	ALA/THR,ALA/THR	1101,3305	718.9+/-408.9	131,839,1233	64.0	59.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3064,3064	4.3	0.0	8	dbSNP_116	61	138,8462	812.3+/-407.1	1,136,4163	yes	missense,missense	HR	NM_005144.4,NM_018411.4	58,58	132,975,5396	CC,CT,TT		1.6047,24.9887,9.5264	benign,benign	1022/1190,1022/1135	21976710	1239,11767	2203	4300	6503	SO:0001583	missense	55806	exon15			GTGGTGTGTCGGC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.3064A>G	8.37:g.21976710T>C	ENSP00000370826:p.Thr1022Ala	113.0	0.0	0		132.0	65.0	0.492424	NM_018411	Q6GS30|Q96H33|Q9NPE1	Missense_Mutation	SNP	ENST00000381418.4	37	CCDS6022.1	164	0.07509157509157509	140	0.2845528455284553	15	0.04143646408839779	0	0.0	9	0.011873350923482849	C	0.021	-1.420024	0.01136	0.249887	0.016047	ENSG00000168453	ENST00000381418;ENST00000312841	T;T	0.69806	-0.43;-0.43	5.18	4.29	0.51040	Transcription factor jumonji/aspartyl beta-hydroxylase (2);	0.000000	0.56097	N	0.000034	T	0.00012	0.0000	N	0.00210	-1.845	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16129	-1.0413	9	0.17832	T	0.49	-2.4672	7.2891	0.26356	0.0:0.7386:0.1695:0.0919	rs7014851;rs7014851	1022;1022	O43593-2;O43593	.;HAIR_HUMAN	A	1022	ENSP00000370826:T1022A;ENSP00000326765:T1022A	ENSP00000326765:T1022A	T	-	1	0	HR	22032655	0.965000	0.33210	0.010000	0.14722	0.026000	0.11368	1.953000	0.40352	0.571000	0.29365	-0.642000	0.03964	ACA	T|0.909;C|0.091	0.091	strong		0.642	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
SH3GLB1	51100	hgsc.bcm.edu	37	1	87170606	87170606	+	Silent	SNP	G	G	A	rs150324653	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:87170606G>A	ENST00000370558.4	+	1	348	c.24G>A	c.(22-24)gtG>gtA	p.V8V	SH3GLB1_ENST00000535010.1_5'UTR|RP4-612B15.3_ENST00000565575.1_RNA|SH3GLB1_ENST00000482504.1_Silent_p.V8V	NM_001206651.1|NM_001206653.1|NM_016009.4	NP_001193580.1|NP_001193582.1|NP_057093.1	Q9Y371	SHLB1_HUMAN	SH3-domain GRB2-like endophilin B1	8	Membrane-binding amphipathic helix.				'de novo' posttranslational protein folding (GO:0051084)|apoptotic process (GO:0006915)|phosphatidic acid biosynthetic process (GO:0006654)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial outer membrane (GO:0005741)|protein complex (GO:0043234)	fatty acid binding (GO:0005504)|identical protein binding (GO:0042802)|lysophosphatidic acid acyltransferase activity (GO:0042171)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(4)|lung(3)|stomach(1)	11		Lung NSC(277;0.209)		all cancers(265;0.0136)|Epithelial(280;0.0414)		ACTTCAACGTGAAGAAGCTGG	0.716													G|||	28	0.00559105	0.0008	0.0058	5008	,	,		12901	0.0		0.0179	False		,,,				2504	0.0051				p.V8V		Atlas-SNP	.											.	SH3GLB1	57	.	0			c.G24A						PASS	.	G	,,,	10,4384		0,10,2187	13.0	16.0	15.0		24,24,,24	1.6	1.0	1	dbSNP_134	15	87,8499		0,87,4206	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	SH3GLB1	NM_001206651.1,NM_001206652.1,NM_001206653.1,NM_016009.4	,,,	0,97,6393	AA,AG,GG		1.0133,0.2276,0.7473	,,,	8/395,8/387,,8/366	87170606	97,12883	2197	4293	6490	SO:0001819	synonymous_variant	51100	exon1			CAACGTGAAGAAG	AF263293	CCDS710.1, CCDS55612.1, CCDS55613.1, CCDS72819.1	1p22.3	2012-04-17	2001-12-04		ENSG00000097033	ENSG00000097033		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	10833	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 70"""	609287	"""SH3-domain, GRB2-like, endophilin B1"""			11161816, 11259440	Standard	NM_016009		Approved	CGI-61, KIAA0491, Bif-1, PPP1R70	uc001dly.3	Q9Y371	OTTHUMG00000010257	ENST00000370558.4:c.24G>A	1.37:g.87170606G>A		29.0	0.0	0		40.0	21.0	0.525	NM_001206652	B4E182|Q5H8U5|Q9H3Z0|Q9NR47|Q9NYA9	Silent	SNP	ENST00000370558.4	37	CCDS710.1																																																																																			G|0.993;A|0.007	0.007	strong		0.716	SH3GLB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028287.2	NM_016009	
SLC25A47	283600	hgsc.bcm.edu	37	14	100793603	100793603	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100793603C>T	ENST00000361529.3	+	4	301	c.223C>T	c.(223-225)Cgc>Tgc	p.R75C	SLC25A47_ENST00000557052.1_5'UTR	NM_207117.2	NP_997000.2	Q6Q0C1	S2547_HUMAN	solute carrier family 25, member 47	75					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|prostate(1)|skin(2)|urinary_tract(1)	13						TGGCACCTACCGCCACTGCCT	0.657																																					p.R75C	GBM(11;1289 1351)	Atlas-SNP	.											.	SLC25A47	36	.	0			c.C223T						PASS	.						102.0	101.0	101.0					14																	100793603		2203	4300	6503	SO:0001583	missense	283600	exon4			ACCTACCGCCACT		CCDS9959.1	14q32.2	2013-05-22	2010-07-19	2010-07-19	ENSG00000140107	ENSG00000140107		"""Solute carriers"""	20115	protein-coding gene	gene with protein product		609911	"""chromosome 14 open reading frame 68"""	C14orf68			Standard	NM_207117		Approved		uc001yhc.3	Q6Q0C1	OTTHUMG00000171571	ENST00000361529.3:c.223C>T	14.37:g.100793603C>T	ENSP00000354886:p.Arg75Cys	46.0	0.0	0		61.0	33.0	0.540984	NM_207117	B2RP39|Q68CL2|Q6PZD8|Q86U14	Missense_Mutation	SNP	ENST00000361529.3	37	CCDS9959.1	.	.	.	.	.	.	.	.	.	.	C	15.40	2.821452	0.50633	.	.	ENSG00000140107	ENST00000361529	T	0.79352	-1.26	4.7	3.73	0.42828	Mitochondrial carrier domain (2);	0.267820	0.33959	N	0.004392	T	0.78065	0.4225	M	0.85197	2.74	0.80722	D	1	B	0.20052	0.041	B	0.21546	0.035	T	0.78725	-0.2092	10	0.59425	D	0.04	2.8807	9.8376	0.40980	0.3148:0.6851:0.0:0.0	.	75	Q6Q0C1	S2547_HUMAN	C	75	ENSP00000354886:R75C	ENSP00000354886:R75C	R	+	1	0	SLC25A47	99863356	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	1.291000	0.33330	2.465000	0.83290	0.485000	0.47835	CGC	.	.	none		0.657	SLC25A47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414231.1		
CFAP58	159686	hgsc.bcm.edu	37	10	106214272	106214272	+	Missense_Mutation	SNP	C	C	A	rs74741614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:106214272C>A	ENST00000369704.3	+	18	2737	c.2603C>A	c.(2602-2604)aCc>aAc	p.T868N		NM_001008723.1	NP_001008723.1	Q5T655	CC147_HUMAN		868						extracellular space (GO:0005615)				NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(16)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	52		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;7.55e-10)|all cancers(201;3.37e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0189)		CTCAGGTCAACCAAAATGACG	0.458													C|||	26	0.00519169	0.0068	0.0144	5008	,	,		18670	0.0		0.007	False		,,,				2504	0.0				p.T868N		Atlas-SNP	.											.	CCDC147	137	.	0			c.C2603A						PASS	.	C	ASN/THR	36,4370	40.0+/-72.8	2,32,2169	130.0	122.0	124.0		2603	-0.6	0.0	10	dbSNP_131	124	122,8478	62.8+/-124.8	0,122,4178	yes	missense	CCDC147	NM_001008723.1	65	2,154,6347	AA,AC,CC		1.4186,0.8171,1.2148	benign	868/873	106214272	158,12848	2203	4300	6503	SO:0001583	missense	159686	exon18			GGTCAACCAAAAT																												ENST00000369704.3:c.2603C>A	10.37:g.106214272C>A	ENSP00000358718:p.Thr868Asn	150.0	0.0	0		87.0	7.0	0.0804598	NM_001008723	D3DRA6|Q8NA27	Missense_Mutation	SNP	ENST00000369704.3	37	CCDS31282.1	18	0.008241758241758242	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	5	0.006596306068601583	C	1.808	-0.475500	0.04414	0.008171	0.014186	ENSG00000120051	ENST00000369704	T	0.31769	1.48	5.47	-0.581	0.11713	.	1.145310	0.06302	N	0.701091	T	0.05090	0.0136	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24225	-1.0166	10	0.41790	T	0.15	6.1358	1.4035	0.02276	0.2731:0.4062:0.1339:0.1869	.	868	Q5T655	CC147_HUMAN	N	868	ENSP00000358718:T868N	ENSP00000358718:T868N	T	+	2	0	CCDC147	106204262	0.083000	0.21467	0.000000	0.03702	0.006000	0.05464	0.730000	0.26043	0.002000	0.14630	0.650000	0.86243	ACC	C|0.989;A|0.011	0.011	strong		0.458	CCDC147-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050216.1		
GGCX	2677	hgsc.bcm.edu	37	2	85783341	85783341	+	Silent	SNP	G	G	A	rs76767923	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:85783341G>A	ENST00000233838.4	-	5	662	c.582C>T	c.(580-582)caC>caT	p.H194H	GGCX_ENST00000473665.1_5'Flank|GGCX_ENST00000430215.3_Silent_p.H137H	NM_000821.5	NP_000812.2	P38435	VKGC_HUMAN	gamma-glutamyl carboxylase	194					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	gamma-glutamyl carboxylase activity (GO:0008488)			endometrium(3)|large_intestine(5)|lung(3)|ovary(1)|stomach(1)|urinary_tract(2)	15					Anisindione(DB01125)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Drotrecogin alfa(DB00055)|Menadione(DB00170)|Phylloquinone(DB01022)	AAAGGGGCACGTGGGCATTCC	0.557													G|||	7	0.00139776	0.0	0.0014	5008	,	,		14470	0.0		0.006	False		,,,				2504	0.0				p.H194H		Atlas-SNP	.											.	GGCX	44	.	0			c.C582T						PASS	.	G	,	7,4399	11.4+/-27.6	0,7,2196	127.0	93.0	104.0		582,411	-11.9	0.5	2	dbSNP_131	104	43,8557	27.9+/-77.7	0,43,4257	no	coding-synonymous,coding-synonymous	GGCX	NM_000821.5,NM_001142269.2	,	0,50,6453	AA,AG,GG		0.5,0.1589,0.3844	,	194/759,137/702	85783341	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	2677	exon5			GGGCACGTGGGCA		CCDS1978.1, CCDS46353.1	2p12	2008-05-21			ENSG00000115486	ENSG00000115486			4247	protein-coding gene	gene with protein product	"""vitamin K-dependent gamma-carboxylase"""	137167				1749935	Standard	NM_000821		Approved	VKCFD1	uc002sps.3	P38435	OTTHUMG00000130173	ENST00000233838.4:c.582C>T	2.37:g.85783341G>A		48.0	0.0	0		51.0	22.0	0.431373	NM_000821	B4DMC5|E9PEE1|Q14415|Q6GU45	Silent	SNP	ENST00000233838.4	37	CCDS1978.1																																																																																			G|0.996;A|0.004	0.004	strong		0.557	GGCX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252490.3	NM_000821	
WDR11	55717	hgsc.bcm.edu	37	10	122668181	122668181	+	Silent	SNP	T	T	C	rs34567350	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122668181T>C	ENST00000263461.6	+	29	3877	c.3631T>C	c.(3631-3633)Ttg>Ctg	p.L1211L	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CAAAGACTTATTGAATGAGCT	0.488													t|||	57	0.0113818	0.0408	0.0043	5008	,	,		18032	0.0		0.0	False		,,,				2504	0.0				p.L1211L		Atlas-SNP	.											.	WDR11	95	.	0			c.T3631C						PASS	.	C		143,4263	101.2+/-139.8	3,137,2063	99.0	101.0	100.0		3631	-7.0	0.0	10	dbSNP_126	100	0,8600		0,0,4300	no	coding-synonymous	WDR11	NM_018117.11		3,137,6363	CC,CT,TT		0.0,3.2456,1.0995		1211/1225	122668181	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	55717	exon29			GACTTATTGAATG	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.3631T>C	10.37:g.122668181T>C		141.0	0.0	0		153.0	73.0	0.477124	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			T|0.990;C|0.010	0.010	strong		0.488	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
ZNF341	84905	hgsc.bcm.edu	37	20	32376748	32376748	+	Silent	SNP	C	C	T	rs34260449	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32376748C>T	ENST00000375200.1	+	13	2297	c.1932C>T	c.(1930-1932)caC>caT	p.H644H	ZNF341_ENST00000342427.2_Silent_p.H637H|RP4-553F4.6_ENST00000443171.1_RNA|RP4-553F4.6_ENST00000439444.1_RNA|RP4-553F4.6_ENST00000423074.1_RNA	NM_001282933.1	NP_001269862.1	Q9BYN7	ZN341_HUMAN	zinc finger protein 341	644					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)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(3)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	31						TGTTGATCCACGAGCCCTTCA	0.552													C|||	60	0.0119808	0.0	0.0159	5008	,	,		17759	0.001		0.0318	False		,,,				2504	0.0164				p.H637H		Atlas-SNP	.											.	ZNF341	73	.	0			c.C1911T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	121.0	99.0	106.0		1911	-4.3	1.0	20	dbSNP_126	106	180,8420	82.6+/-145.2	2,176,4122	no	coding-synonymous	ZNF341	NM_032819.3		2,193,6308	TT,TC,CC		2.093,0.3858,1.5147		637/848	32376748	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	84905	exon13			GATCCACGAGCCC	AK027550	CCDS13227.1, CCDS74719.1	20q11.22	2013-01-08			ENSG00000131061	ENSG00000131061		"""Zinc fingers, C2H2-type"""	15992	protein-coding gene	gene with protein product							Standard	NM_001282933		Approved	dJ553F4.3	uc002wzx.3	Q9BYN7	OTTHUMG00000032275	ENST00000375200.1:c.1932C>T	20.37:g.32376748C>T		180.0	0.0	0		210.0	105.0	0.5	NM_032819	A2RUF4|B2RXE5|B7ZM09|Q5JXM8|Q96ST5	Silent	SNP	ENST00000375200.1	37																																																																																				C|0.985;T|0.015	0.015	strong		0.552	ZNF341-201	KNOWN	basic	protein_coding	protein_coding			
DIDO1	11083	hgsc.bcm.edu	37	20	61510849	61510849	+	Silent	SNP	C	C	T	rs373321839	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:61510849C>T	ENST00000266070.4	-	16	6784	c.6459G>A	c.(6457-6459)agG>agA	p.R2153R	DIDO1_ENST00000395343.1_Silent_p.R2153R	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	2153	Arg-rich.				apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					GGTTGGCGCTCCTCTcccggt	0.726													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		12926	0.0		0.002	False		,,,				2504	0.0				p.R2153R	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											.	DIDO1	321	.	0			c.G6459A						PASS	.	C	,	1,4315		0,1,2157	17.0	14.0	15.0		6459,6459	-0.3	0.0	20		15	5,8397		0,5,4196	no	coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_033081.2	,	0,6,6353	TT,TC,CC		0.0595,0.0232,0.0472	,	2153/2241,2153/2241	61510849	6,12712	2158	4201	6359	SO:0001819	synonymous_variant	11083	exon16			GGCGCTCCTCTCC	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.6459G>A	20.37:g.61510849C>T		33.0	0.0	0		13.0	5.0	0.384615	NM_001193369	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			.	.	weak		0.726	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
OR2T3	343173	hgsc.bcm.edu	37	1	248637447	248637447	+	Missense_Mutation	SNP	C	C	T	rs369769145		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:248637447C>T	ENST00000359594.2	+	1	821	c.796C>T	c.(796-798)Ctc>Ttc	p.L266F		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACCTACATGCTCCCGAGTTC	0.547																																					p.L266F		Atlas-SNP	.											.	OR2T3	79	.	0			c.C796T						PASS	.	C	PHE/LEU	0,4406		0,0,2203	363.0	338.0	347.0		796	1.4	0.0	1		347	1,8599	1.2+/-3.3	0,1,4299	no	missense	OR2T3	NM_001005495.1	22	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	266/319	248637447	1,13005	2203	4300	6503	SO:0001583	missense	343173	exon1			TACATGCTCCCGA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.796C>T	1.37:g.248637447C>T	ENSP00000352604:p.Leu266Phe	856.0	0.0	0		957.0	292.0	0.30512	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	.	.	.	.	.	.	.	.	.	.	c	11.19	1.565845	0.27915	0.0	1.16E-4	ENSG00000196539	ENST00000359594	T	0.37235	1.21	2.37	1.42	0.22433	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.31638	0.0803	L	0.33189	0.99	0.09310	N	1	P	0.41848	0.763	P	0.51016	0.656	T	0.17837	-1.0356	9	0.16420	T	0.52	.	3.9402	0.09323	0.0:0.593:0.2477:0.1593	.	266	Q8NH03	OR2T3_HUMAN	F	266	ENSP00000352604:L266F	ENSP00000352604:L266F	L	+	1	0	OR2T3	246704070	0.000000	0.05858	0.011000	0.14972	0.280000	0.26924	-1.065000	0.03458	0.109000	0.17891	0.186000	0.17326	CTC	.	.	none		0.547	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
ALPP	250	hgsc.bcm.edu	37	2	233243793	233243793	+	Silent	SNP	C	C	T	rs1130337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233243793C>T	ENST00000392027.2	+	2	458	c.189C>T	c.(187-189)ggC>ggT	p.G63G	AC068134.8_ENST00000439072.1_RNA|AC068134.8_ENST00000441266.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	63					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		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;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		TCTTCCTGGGCGATGGTGAGT	0.677													C|||	57	0.0113818	0.0008	0.0101	5008	,	,		17685	0.0		0.0249	False		,,,				2504	0.0245				p.G63G		Atlas-SNP	.											.	ALPP	53	.	0			c.C189T						PASS	.	T		10,4396		0,10,2193	71.0	79.0	76.0		189	-5.0	0.0	2	dbSNP_86	76	137,8463		3,131,4166	no	coding-synonymous	ALPP	NM_001632.3		3,141,6359	TT,TC,CC		1.593,0.227,1.1302		63/536	233243793	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	250	exon2			CCTGGGCGATGGT	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.189C>T	2.37:g.233243793C>T		95.0	0.0	0		88.0	36.0	0.409091	NM_001632	P05188|P06861|Q53S78|Q96DB7	Silent	SNP	ENST00000392027.2	37	CCDS2490.1																																																																																			C|0.996;G|0.001;T|0.003	0.003	strong		0.677	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
POMGNT2	84892	hgsc.bcm.edu	37	3	43122702	43122702	+	Silent	SNP	G	G	A	rs141040291		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:43122702G>A	ENST00000344697.2	-	2	567	c.222C>T	c.(220-222)caC>caT	p.H74H	POMGNT2_ENST00000441964.1_Silent_p.H74H	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	74					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										TGCGGTCTGTGTGCGTGCGGC	0.607																																					p.H74H		Atlas-SNP	.											.	.	.	.	0			c.C222T						PASS	.	G		0,4406		0,0,2203	83.0	73.0	76.0		222	4.9	1.0	3	dbSNP_134	76	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C3orf39	NM_032806.4		0,3,6500	AA,AG,GG		0.0349,0.0,0.0231		74/581	43122702	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	84892	exon2			GTCTGTGTGCGTG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.222C>T	3.37:g.43122702G>A		85.0	0.0	0		109.0	57.0	0.522936	NM_032806	B3KWC3|Q96SY3	Silent	SNP	ENST00000344697.2	37	CCDS2709.1																																																																																			G|1.000;A|0.000	0.000	weak		0.607	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
OR5H2	79310	hgsc.bcm.edu	37	3	98002527	98002527	+	Missense_Mutation	SNP	C	C	T	rs17787561	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:98002527C>T	ENST00000355273.2	+	1	796	c.796C>T	c.(796-798)Cgc>Tgc	p.R266C	RP11-325B23.2_ENST00000508616.1_lincRNA	NM_001005482.1	NP_001005482.1	Q8NGV7	OR5H2_HUMAN	olfactory receptor, family 5, subfamily H, member 2	266			R -> C (in dbSNP:rs17787561).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(5)|lung(13)|ovary(3)|upper_aerodigestive_tract(1)	24						CATGTATTTGCGCCCTGCATC	0.398													C|||	19	0.00379393	0.0	0.0058	5008	,	,		17042	0.0		0.0089	False		,,,				2504	0.0061				p.R266C		Atlas-SNP	.											.	OR5H2	63	.	0			c.C796T						PASS	.	C	CYS/ARG	6,4400	9.9+/-24.2	0,6,2197	87.0	83.0	84.0		796	-1.1	0.0	3	dbSNP_123	84	80,8520	47.2+/-106.3	1,78,4221	yes	missense	OR5H2	NM_001005482.1	180	1,84,6418	TT,TC,CC		0.9302,0.1362,0.6612	benign	266/315	98002527	86,12920	2203	4300	6503	SO:0001583	missense	79310	exon1			TATTTGCGCCCTG		CCDS33801.1	3q11.2	2013-09-23			ENSG00000197938	ENSG00000197938		"""GPCR / Class A : Olfactory receptors"""	14752	protein-coding gene	gene with protein product							Standard	NM_001005482		Approved		uc003dsj.1	Q8NGV7	OTTHUMG00000160080	ENST00000355273.2:c.796C>T	3.37:g.98002527C>T	ENSP00000347418:p.Arg266Cys	118.0	0.0	0		141.0	69.0	0.489362	NM_001005482	Q6IF87	Missense_Mutation	SNP	ENST00000355273.2	37	CCDS33801.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	0.635	-0.815604	0.02776	0.001362	0.009302	ENSG00000197938	ENST00000355273	T	0.35789	1.29	3.03	-1.07	0.09968	GPCR, rhodopsin-like superfamily (1);	0.410613	0.17855	U	0.159738	T	0.22742	0.0549	M	0.69523	2.12	0.09310	N	1	B	0.21688	0.059	B	0.19148	0.024	T	0.24728	-1.0152	10	0.62326	D	0.03	.	3.5217	0.07744	0.1797:0.3604:0.0:0.4599	rs17787561;rs52823927;rs17787561	266	Q8NGV7	OR5H2_HUMAN	C	266	ENSP00000347418:R266C	ENSP00000347418:R266C	R	+	1	0	OR5H2	99485217	0.000000	0.05858	0.003000	0.11579	0.006000	0.05464	-0.227000	0.09126	-0.440000	0.07211	-0.495000	0.04643	CGC	C|0.993;T|0.007	0.007	strong		0.398	OR5H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359113.2		
ZNF418	147686	hgsc.bcm.edu	37	19	58437629	58437629	+	Silent	SNP	T	T	A	rs147202003	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437629T>A	ENST00000396147.1	-	4	2211	c.1920A>T	c.(1918-1920)gtA>gtT	p.V640V	ZNF418_ENST00000595830.1_Silent_p.V640V|ZNF418_ENST00000599852.1_Silent_p.V555V|ZNF418_ENST00000425570.3_Silent_p.V661V|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	640					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		CTCCAGTGTGTACTCTCCTGT	0.438																																					p.V640V		Atlas-SNP	.											.	ZNF418	76	.	0			c.A1920T						PASS	.	A		11,4393		0,11,2191	120.0	122.0	121.0		1920	-3.1	0.0	19	dbSNP_134	121	120,8480		1,118,4181	no	coding-synonymous	ZNF418	NM_133460.1		1,129,6372	AA,AT,TT		1.3953,0.2498,1.0074		640/677	58437629	131,12873	2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			AGTGTGTACTCTC	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1920A>T	19.37:g.58437629T>A		114.0	0.0	0		88.0	13.0	0.147727	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			T|0.993;A|0.007	0.007	strong		0.438	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
MTMR7	9108	hgsc.bcm.edu	37	8	17157605	17157605	+	Missense_Mutation	SNP	A	A	C	rs145244130	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:17157605A>C	ENST00000180173.5	-	14	1783	c.1749T>G	c.(1747-1749)agT>agG	p.S583R	MTMR7_ENST00000398099.3_Missense_Mutation_p.S174R|VPS37A_ENST00000521162.1_3'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	583					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		TCATATTCCCACTGTAATCCT	0.453													A|||	6	0.00119808	0.0	0.0	5008	,	,		17679	0.0		0.003	False		,,,				2504	0.0031				p.S583R		Atlas-SNP	.											.	MTMR7	75	.	0			c.T1749G						PASS	.	A	ARG/SER	4,4402	8.1+/-20.4	0,4,2199	193.0	193.0	193.0		1749	-2.7	0.9	8	dbSNP_134	193	36,8564	24.6+/-71.5	1,34,4265	yes	missense	MTMR7	NM_004686.4	110	1,38,6464	CC,CA,AA		0.4186,0.0908,0.3076	possibly-damaging	583/661	17157605	40,12966	2203	4300	6503	SO:0001583	missense	9108	exon14			ATTCCCACTGTAA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1749T>G	8.37:g.17157605A>C	ENSP00000180173:p.Ser583Arg	242.0	0.0	0		286.0	141.0	0.493007	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	12.24	1.877751	0.33162	9.08E-4	0.004186	ENSG00000003987	ENST00000180173;ENST00000398099	D;T	0.92965	-3.14;-1.07	5.32	-2.65	0.06095	.	0.377447	0.33127	N	0.005259	T	0.79476	0.4452	L	0.36672	1.1	0.39153	D	0.96225	B	0.28128	0.201	B	0.19391	0.025	T	0.68507	-0.5390	10	0.15499	T	0.54	.	13.1914	0.59713	0.4371:0.0:0.5629:0.0	.	583	Q9Y216	MTMR7_HUMAN	R	583;174	ENSP00000180173:S583R;ENSP00000381171:S174R	ENSP00000180173:S583R	S	-	3	2	MTMR7	17201976	0.516000	0.26218	0.932000	0.37286	0.971000	0.66376	-0.103000	0.10940	-0.380000	0.07894	-0.326000	0.08463	AGT	A|0.997;C|0.003	0.003	strong		0.453	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
GALNS	2588	hgsc.bcm.edu	37	16	88893122	88893122	+	Missense_Mutation	SNP	C	C	T	rs150734270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:88893122C>T	ENST00000268695.5	-	10	1215	c.1127G>A	c.(1126-1128)cGg>cAg	p.R376Q	AC092384.1_ENST00000593752.1_5'Flank|GALNS_ENST00000542788.1_Missense_Mutation_p.R301Q	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	376	Catalytic domain.		R -> Q (in MPS4A; severe form; dbSNP:rs150734270). {ECO:0000269|PubMed:9521421}.		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		GTCCATCAGCCGGCCCTGCAG	0.662													C|||	7	0.00139776	0.0	0.0029	5008	,	,		14448	0.0		0.005	False		,,,				2504	0.0				p.R376Q	GBM(129;1929 2344 25209 33204)	Atlas-SNP	.											GALNS,bladder,carcinoma,0,1	GALNS	37	1	0			c.G1127A	GRCh37	CM980820	GALNS	M	rs150734270	PASS	.	C	GLN/ARG	1,4393	2.1+/-5.4	0,1,2196	28.0	29.0	28.0		1127	-2.8	0.2	16	dbSNP_134	28	16,8584	10.5+/-38.8	0,16,4284	yes	missense	GALNS	NM_000512.4	43	0,17,6480	TT,TC,CC		0.186,0.0228,0.1308	benign	376/523	88893122	17,12977	2197	4300	6497	SO:0001583	missense	2588	exon10			ATCAGCCGGCCCT	D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.1127G>A	16.37:g.88893122C>T	ENSP00000268695:p.Arg376Gln	113.0	0.0	0		135.0	70.0	0.518519	NM_000512	Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	37	CCDS10970.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	6.207	0.406403	0.11754	2.28E-4	0.00186	ENSG00000141012	ENST00000268695;ENST00000542788	D;D	0.93488	-3.23;-3.23	5.43	-2.81	0.05805	Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.908483	0.09491	N	0.794912	T	0.80358	0.4608	N	0.12853	0.265	0.09310	N	1	B;B	0.18310	0.007;0.027	B;B	0.08055	0.003;0.003	T	0.66064	-0.6016	10	0.31617	T	0.26	.	12.0153	0.53311	0.0:0.2983:0.0:0.7017	.	376;376	B2R6P1;P34059	.;GALNS_HUMAN	Q	376;301	ENSP00000268695:R376Q;ENSP00000438197:R301Q	ENSP00000268695:R376Q	R	-	2	0	GALNS	87420623	0.004000	0.15560	0.161000	0.22692	0.072000	0.16883	-0.448000	0.06820	-0.733000	0.04850	-0.755000	0.03482	CGG	C|0.999;T|0.001	0.001	strong		0.662	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1		
KIAA1462	57608	hgsc.bcm.edu	37	10	30318345	30318345	+	Silent	SNP	C	C	T	rs11813359	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:30318345C>T	ENST00000375377.1	-	3	833	c.732G>A	c.(730-732)acG>acA	p.T244T		NM_020848.2	NP_065899.1	Q9P266	JCAD_HUMAN	KIAA1462	244					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)				breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|lung(23)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	75						TGGGAATTTCCGTGCAACTCA	0.453													C|||	20	0.00399361	0.0023	0.0029	5008	,	,		21995	0.0		0.0139	False		,,,				2504	0.001				p.T244T		Atlas-SNP	.											KIAA1462,NS,carcinoma,-2,1	KIAA1462	162	1	0			c.G732A						scavenged	.	C		12,3910		0,12,1949	136.0	139.0	138.0		732	0.8	0.0	10	dbSNP_120	138	113,8169		0,113,4028	no	coding-synonymous	KIAA1462	NM_020848.2		0,125,5977	TT,TC,CC		1.3644,0.306,1.0243		244/1360	30318345	125,12079	1961	4141	6102	SO:0001819	synonymous_variant	57608	exon3			AATTTCCGTGCAA	AB040895	CCDS41500.1	10p12.1	2013-04-23			ENSG00000165757	ENSG00000165757			29283	protein-coding gene	gene with protein product	"""junctional protein associated with coronary artery disease"""	614398				10819331, 21884682	Standard	NM_020848		Approved	JCAD	uc001iux.3	Q9P266	OTTHUMG00000017885	ENST00000375377.1:c.732G>A	10.37:g.30318345C>T		148.0	1.0	0.00675676		175.0	75.0	0.428571	NM_020848	Q5HYA7|Q5T992|Q86WZ9|Q9BYJ2	Silent	SNP	ENST00000375377.1	37	CCDS41500.1																																																																																			C|0.994;T|0.006	0.006	strong		0.453	KIAA1462-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047409.1	NM_020848	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90572435	90572435	+	RNA	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90572435A>C	ENST00000551025.1	+	0	2444									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AGTCGAGTAGACTCTCAAAGT	0.348																																					p.D336A	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											.	CASP8AP2	108	.	0			c.A1007C						PASS	.																																					9994	exon7			GAGTAGACTCTCA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90572435A>C		26.0	0.0	0		38.0	14.0	0.368421	NM_001137667		Missense_Mutation	SNP	ENST00000551025.1	37																																																																																				.	.	none		0.348	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
WASL	8976	hgsc.bcm.edu	37	7	123332793	123332793	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123332793T>A	ENST00000223023.4	-	9	1287	c.955A>T	c.(955-957)Aca>Tca	p.T319S		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	319	Pro-rich.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						GGTGCAGCTGTGGGAGCTCTT	0.642																																					p.T319S		Atlas-SNP	.											.	WASL	70	.	0			c.A955T						PASS	.						78.0	76.0	77.0					7																	123332793		2203	4300	6503	SO:0001583	missense	8976	exon9			CAGCTGTGGGAGC	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.955A>T	7.37:g.123332793T>A	ENSP00000223023:p.Thr319Ser	61.0	0.0	0		73.0	5.0	0.0684932	NM_003941	A1JUI9|Q7Z746	Missense_Mutation	SNP	ENST00000223023.4	37	CCDS34743.1	.	.	.	.	.	.	.	.	.	.	T	8.371	0.835392	0.16820	.	.	ENSG00000106299	ENST00000223023	D	0.91180	-2.8	5.39	2.92	0.33932	.	0.235349	0.41938	N	0.000787	T	0.80352	0.4607	N	0.20881	0.62	0.44067	D	0.996816	B	0.06786	0.001	B	0.04013	0.001	T	0.67197	-0.5731	10	0.06625	T	0.88	-12.2313	10.6239	0.45495	0.2563:0.0:0.0:0.7437	.	319	O00401	WASL_HUMAN	S	319	ENSP00000223023:T319S	ENSP00000223023:T319S	T	-	1	0	WASL	123120029	0.958000	0.32768	0.997000	0.53966	0.999000	0.98932	1.689000	0.37700	0.315000	0.23110	0.524000	0.50904	ACA	.	.	none		0.642	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
BACH1	571	hgsc.bcm.edu	37	21	30699557	30699557	+	Missense_Mutation	SNP	G	G	C	rs35766001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:30699557G>C	ENST00000399921.1	+	3	1655	c.1412G>C	c.(1411-1413)gGc>gCc	p.G471A	BACH1_ENST00000286800.3_Missense_Mutation_p.G471A	NM_206866.1	NP_996749.1	Q9BX63	FANCJ_HUMAN	BTB and CNC homology 1, basic leucine zipper transcription factor 1	0					DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|urinary_tract(2)	27						AGTACTGAAGGCTGTTCAAGC	0.423													G|||	40	0.00798722	0.0015	0.0173	5008	,	,		20941	0.0		0.0119	False		,,,				2504	0.0143				p.G471A		Atlas-SNP	.											.	BACH1	66	.	0			c.G1412C						PASS	.	G	ALA/GLY,ALA/GLY	20,4386	26.2+/-53.5	0,20,2183	124.0	119.0	121.0		1412,1412	2.2	1.0	21	dbSNP_126	121	141,8459	71.0+/-133.6	1,139,4160	yes	missense,missense	BACH1	NM_001186.2,NM_206866.1	60,60	1,159,6343	CC,CG,GG		1.6395,0.4539,1.2379	benign,benign	471/737,471/737	30699557	161,12845	2203	4300	6503	SO:0001583	missense	571	exon3			CTGAAGGCTGTTC	AF026200	CCDS13585.1	21q22.1	2013-01-10			ENSG00000156273	ENSG00000156273		"""BTB/POZ domain containing"", ""basic leucine zipper proteins"""	935	protein-coding gene	gene with protein product		602751				9544839, 9479503	Standard	NR_027655		Approved	BACH-1, BTBD24	uc002ynj.3	O14867	OTTHUMG00000078878	ENST00000399921.1:c.1412G>C	21.37:g.30699557G>C	ENSP00000382805:p.Gly471Ala	194.0	0.0	0		190.0	98.0	0.515789	NM_206866	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000399921.1	37	CCDS13585.1	17|17	0.007783882783882784|0.007783882783882784	0|0	0.0|0.0	9|9	0.024861878453038673|0.024861878453038673	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	G|G	12.49|12.49	1.952889|1.952889	0.34471|0.34471	0.004539|0.004539	0.016395|0.016395	ENSG00000156273|ENSG00000156273	ENST00000286800;ENST00000399921|ENST00000422809	T;T|.	0.71461|.	-0.57;-0.57|.	5.48|5.48	2.16|2.16	0.27623|0.27623	.|.	0.249525|.	0.34853|.	N|.	0.003632|.	T|T	0.38931|0.38931	0.1059|0.1059	L|L	0.44542|0.44542	1.39|1.39	0.40301|0.40301	D|D	0.978604|0.978604	B|.	0.20052|.	0.041|.	B|.	0.15052|.	0.012|.	T|T	0.41161|0.41161	-0.9524|-0.9524	10|5	0.05436|.	T|.	0.98|.	-16.108|-16.108	10.9423|10.9423	0.47281|0.47281	0.0764:0.2453:0.6782:0.0|0.0764:0.2453:0.6782:0.0	rs35766001|rs35766001	471|.	O14867|.	BACH1_HUMAN|.	A|S	471|36	ENSP00000286800:G471A;ENSP00000382805:G471A|.	ENSP00000286800:G471A|.	G|R	+|+	2|3	0|2	BACH1|BACH1	29621428|29621428	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.990000|0.990000	0.78478|0.78478	1.712000|1.712000	0.37940|0.37940	0.648000|0.648000	0.30732|0.30732	-0.176000|-0.176000	0.13171|0.13171	GGC|AGG	G|0.989;C|0.011	0.011	strong		0.423	BACH1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171974.1	NM_206866	
GATA4	2626	hgsc.bcm.edu	37	8	11606438	11606438	+	Silent	SNP	C	C	T	rs192122549	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11606438C>T	ENST00000335135.4	+	3	1185	c.627C>T	c.(625-627)gaC>gaT	p.D209D	GATA4_ENST00000528712.1_Silent_p.D3D|GATA4_ENST00000532059.1_Silent_p.D210D	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	209					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		ATATGTTTGACGACTTCTCAG	0.517													C|||	2	0.000399361	0.0	0.0	5008	,	,		20917	0.0		0.002	False		,,,				2504	0.0				p.D209D		Atlas-SNP	.											.	GATA4	29	.	0			c.C627T						PASS	.	C		0,4406		0,0,2203	134.0	134.0	134.0		627	-10.2	0.2	8		134	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GATA4	NM_002052.3		0,3,6500	TT,TC,CC		0.0349,0.0,0.0231		209/443	11606438	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	2626	exon3			GTTTGACGACTTC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.627C>T	8.37:g.11606438C>T		132.0	0.0	0		224.0	105.0	0.46875	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	37	CCDS5983.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052	
MPP2	4355	hgsc.bcm.edu	37	17	41955315	41955315	+	Missense_Mutation	SNP	G	G	A	rs118165424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:41955315G>A	ENST00000461854.1	-	14	1676	c.1591C>T	c.(1591-1593)Cgc>Tgc	p.R531C	MPP2_ENST00000518766.1_Missense_Mutation_p.R552C|MPP2_ENST00000520305.1_Missense_Mutation_p.R368C|MPP2_ENST00000536246.1_Missense_Mutation_p.R496C|MPP2_ENST00000269095.4_Missense_Mutation_p.R507C|MPP2_ENST00000377184.3_Missense_Mutation_p.R524C|MPP2_ENST00000523501.1_Missense_Mutation_p.R496C			Q14168	MPP2_HUMAN	membrane protein, palmitoylated 2 (MAGUK p55 subfamily member 2)	531	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.			R -> C (in Ref. 3; BAG57760). {ECO:0000305}.	nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|liver(1)|lung(4)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.00314)		BRCA - Breast invasive adenocarcinoma(366;0.12)		CGCTGGATGCGGCTGCTCTCC	0.622													G|||	18	0.00359425	0.0008	0.0043	5008	,	,		18030	0.0		0.0139	False		,,,				2504	0.0				p.R507C		Atlas-SNP	.											MPP2,NS,carcinoma,+1,1	MPP2	67	1	0			c.C1519T						PASS	.	G	CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	68.0	55.0	60.0		1519	4.2	1.0	17	dbSNP_132	60	129,8471	66.0+/-128.3	3,123,4174	yes	missense	MPP2	NM_005374.3	180	3,138,6362	AA,AG,GG		1.5,0.3404,1.1072	probably-damaging	507/553	41955315	144,12862	2203	4300	6503	SO:0001583	missense	4355	exon13			GGATGCGGCTGCT		CCDS11471.1, CCDS62206.1, CCDS62207.1, CCDS62208.1, CCDS62209.1, CCDS62210.1	17q12-q21	2008-07-18			ENSG00000108852	ENSG00000108852			7220	protein-coding gene	gene with protein product	"""MAGUK p55 subfamily member 2"", ""discs large, homolog 2"""	600723		DLG2		7590743	Standard	NM_001278370		Approved	DKFZp761D0712	uc002ieo.1	Q14168	OTTHUMG00000133840	ENST00000461854.1:c.1591C>T	17.37:g.41955315G>A	ENSP00000428286:p.Arg531Cys	82.0	0.0	0		96.0	59.0	0.614583	NM_005374	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Missense_Mutation	SNP	ENST00000461854.1	37		13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	g	15.76	2.928029	0.52759	0.003404	0.015	ENSG00000108852	ENST00000377184;ENST00000269095;ENST00000461854;ENST00000520305;ENST00000523501;ENST00000536246;ENST00000518766	T;T;T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93;0.93;0.93	5.21	4.23	0.50019	.	.	.	.	.	T	0.37376	0.1001	M	0.79475	2.455	0.80722	D	1	P;P	0.42039	0.766;0.769	B;B	0.41271	0.288;0.352	T	0.39643	-0.9604	9	0.37606	T	0.19	.	11.8021	0.52133	0.0858:0.0:0.9142:0.0	.	552;524	E7EV80;Q14168-3	.;.	C	524;507;531;368;496;496;552	ENSP00000366389:R524C;ENSP00000269095:R507C;ENSP00000428286:R531C;ENSP00000428136:R368C;ENSP00000430540:R496C;ENSP00000438012:R496C;ENSP00000428182:R552C	ENSP00000269095:R507C	R	-	1	0	MPP2	39310841	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	5.339000	0.65953	1.203000	0.43233	0.555000	0.69702	CGC	G|0.991;A|0.009	0.009	strong		0.622	MPP2-003	KNOWN	non_canonical_polymorphism|basic	protein_coding	protein_coding	OTTHUMT00000258388.2	NM_005374	
NCKAP5	344148	hgsc.bcm.edu	37	2	133538703	133538703	+	Silent	SNP	G	G	A	rs61742426	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:133538703G>A	ENST00000409261.1	-	15	5344	c.4971C>T	c.(4969-4971)ggC>ggT	p.G1657G	NCKAP5_ENST00000405974.3_Intron|NCKAP5_ENST00000409213.1_Intron|NCKAP5_ENST00000317721.6_Silent_p.G1657G|NCKAP5_ENST00000473859.1_5'UTR	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	1657										NS(4)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(29)|lung(51)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	118						TGATAGAGCTGCCGATGAGAC	0.458													G|||	8	0.00159744	0.0	0.0	5008	,	,		17507	0.0		0.008	False		,,,				2504	0.0				p.G1657G		Atlas-SNP	.											.	NCKAP5	322	.	0			c.C4971T						PASS	.	G	,	5,3821		0,5,1908	94.0	97.0	96.0		4971,	5.3	0.0	2	dbSNP_129	96	55,8203		1,53,4075	no	coding-synonymous,intron	NCKAP5	NM_207363.2,NM_207481.3	,	1,58,5983	AA,AG,GG		0.666,0.1307,0.4965	,	1657/1910,	133538703	60,12024	1913	4129	6042	SO:0001819	synonymous_variant	344148	exon15			AGAGCTGCCGATG	AB005217	CCDS46417.1, CCDS46418.1	2q21.2	2010-02-17			ENSG00000176771	ENSG00000176771			29847	protein-coding gene	gene with protein product	"""Nck associated protein 5"", ""peripheral clock protein"""	608789				9344857	Standard	NM_207363		Approved	NAP5, ERIH1, ERIH2	uc002ttp.3	O14513	OTTHUMG00000153573	ENST00000409261.1:c.4971C>T	2.37:g.133538703G>A		358.0	0.0	0		434.0	219.0	0.504608	NM_207363	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Silent	SNP	ENST00000409261.1	37	CCDS46418.1																																																																																			G|0.996;A|0.004	0.004	strong		0.458	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
SPATA21	374955	hgsc.bcm.edu	37	1	16748432	16748432	+	Silent	SNP	C	C	T	rs114456729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16748432C>T	ENST00000335496.1	-	4	551	c.69G>A	c.(67-69)acG>acA	p.T23T	SPATA21_ENST00000540400.1_Intron|SPATA21_ENST00000466212.1_5'UTR	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	23							calcium ion binding (GO:0005509)	p.T23T(1)		breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		TAGGTCCAGGCGTGGATGGCA	0.562													C|||	122	0.024361	0.0015	0.036	5008	,	,		19316	0.001		0.0726	False		,,,				2504	0.0215				p.T23T		Atlas-SNP	.											SPATA21,NS,carcinoma,-1,2	SPATA21	47	2	1	Substitution - coding silent(1)	pancreas(1)	c.G69A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	219.0	207.0	211.0		69	-2.2	0.0	1	dbSNP_132	211	600,8000	158.9+/-212.3	23,554,3723	no	coding-synonymous	SPATA21	NM_198546.1		23,611,5869	TT,TC,CC		6.9767,1.2937,5.0515		23/470	16748432	657,12349	2203	4300	6503	SO:0001819	synonymous_variant	374955	exon4			TCCAGGCGTGGAT		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.69G>A	1.37:g.16748432C>T		96.0	0.0	0		129.0	73.0	0.565891	NM_198546	B9EK40|F5GXP5	Silent	SNP	ENST00000335496.1	37	CCDS172.1																																																																																			C|0.954;T|0.046	0.046	strong		0.562	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
UGT2B11	10720	hgsc.bcm.edu	37	4	70066306	70066306	+	Missense_Mutation	SNP	T	T	C	rs200852364	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:70066306T>C	ENST00000446444.1	-	6	1450	c.1442A>G	c.(1441-1443)cAt>cGt	p.H481R	RP11-704M14.1_ENST00000505646.1_RNA|RP11-704M14.1_ENST00000504301.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	481					estrogen metabolic process (GO:0008210)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	42						GGTGAGGTCATGGGCTGCAAC	0.463																																					p.H481R		Atlas-SNP	.											.	UGT2B11	92	.	0			c.A1442G						PASS	.						128.0	123.0	124.0					4																	70066306		2203	4300	6503	SO:0001583	missense	10720	exon6			AGGTCATGGGCTG	AF016492	CCDS3527.1	4q13.3	2008-02-05	2005-07-20		ENSG00000213759	ENSG00000213759		"""UDP glucuronosyltransferases"""	12545	protein-coding gene	gene with protein product		603064	"""UDP glycosyltransferase 2 family, polypeptide B11"""			9675083	Standard	NM_001073		Approved		uc003heh.3	O75310	OTTHUMG00000129395	ENST00000446444.1:c.1442A>G	4.37:g.70066306T>C	ENSP00000387683:p.His481Arg	116.0	0.0	0		154.0	16.0	0.103896	NM_001073	Q3KNV9	Missense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	.	.	.	.	.	.	.	.	.	.	-	2.143	-0.396340	0.04899	.	.	ENSG00000213759	ENST00000446444	T	0.61859	0.07	1.27	-0.615	0.11587	.	0.080367	0.49305	N	0.000142	T	0.52419	0.1733	M	0.73598	2.24	0.18873	N	0.999981	B	0.23185	0.081	B	0.28638	0.092	T	0.51220	-0.8733	10	0.66056	D	0.02	.	6.3349	0.21291	0.0:0.1865:0.0:0.8135	.	481	O75310	UDB11_HUMAN	R	481	ENSP00000387683:H481R	ENSP00000387683:H481R	H	-	2	0	UGT2B11	70100895	0.998000	0.40836	0.158000	0.22627	0.020000	0.10135	3.239000	0.51360	-0.460000	0.07003	-2.767000	0.00120	CAT	T|0.967;C|0.032	0.032	strong		0.463	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TNFRSF9	3604	hgsc.bcm.edu	37	1	7995152	7995152	+	Silent	SNP	G	G	A	rs373859958		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:7995152G>A	ENST00000377507.3	-	6	631	c.465C>T	c.(463-465)gaC>gaT	p.D155D		NM_001561.5	NP_001552.2	Q07011	TNR9_HUMAN	tumor necrosis factor receptor superfamily, member 9	155					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19	Ovarian(185;0.0634)|all_lung(157;0.151)	all_epithelial(116;9.63e-21)|all_lung(118;1.29e-06)|Lung NSC(185;7.5e-06)|Renal(390;0.000147)|Breast(348;0.000625)|Colorectal(325;0.000959)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;2.93e-71)|GBM - Glioblastoma multiforme(8;3.72e-37)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;7.71e-06)|Kidney(185;5.33e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000419)|KIRC - Kidney renal clear cell carcinoma(229;0.000979)|STAD - Stomach adenocarcinoma(132;0.00103)|READ - Rectum adenocarcinoma(331;0.0649)		CACAGACCACGTCCCTCTCCT	0.502																																					p.D155D		Atlas-SNP	.											.	TNFRSF9	50	.	0			c.C465T						PASS	.						105.0	88.0	94.0					1																	7995152		2203	4300	6503	SO:0001819	synonymous_variant	3604	exon7			GACCACGTCCCTC	L12964	CCDS92.1	1p36	2008-02-05			ENSG00000049249	ENSG00000049249		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11924	protein-coding gene	gene with protein product		602250		ILA		8262389, 8639902	Standard	NM_001561		Approved	CD137, 4-1BB	uc001aot.3	Q07011	OTTHUMG00000001223	ENST00000377507.3:c.465C>T	1.37:g.7995152G>A		137.0	0.0	0		130.0	56.0	0.430769	NM_001561		Silent	SNP	ENST00000377507.3	37	CCDS92.1																																																																																			.	.	none		0.502	TNFRSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003622.1		
MUC7	4589	hgsc.bcm.edu	37	4	71347050	71347050	+	Missense_Mutation	SNP	G	G	A	rs144679944	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:71347050G>A	ENST00000304887.5	+	3	779	c.589G>A	c.(589-591)Gca>Aca	p.A197T	MUC7_ENST00000413702.1_Missense_Mutation_p.A197T|MUC7_ENST00000456088.1_Missense_Mutation_p.A197T	NM_152291.2	NP_689504.2	Q8TAX7	MUC7_HUMAN	mucin 7, secreted	197	Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(2)|lung(23)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	42			Lung(101;0.211)			CACACCTTCTGCAACTACACA	0.592													G|||	7	0.00139776	0.0	0.0	5008	,	,		20060	0.0		0.007	False		,,,				2504	0.0				p.A197T		Atlas-SNP	.											.	MUC7	91	.	0			c.G589A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	428.0	344.0	372.0		589,589,589	-4.1	0.0	4	dbSNP_134	372	48,8552	31.2+/-83.2	0,48,4252	no	missense,missense,missense	MUC7	NM_152291.2,NM_001145007.1,NM_001145006.1	58,58,58	0,51,6452	AA,AG,GG		0.5581,0.0681,0.3921	benign,benign,benign	197/378,197/378,197/378	71347050	51,12955	2203	4300	6503	SO:0001583	missense	4589	exon4			CCTTCTGCAACTA	BC025688	CCDS3541.1	4q13.3	2008-02-05	2006-03-14		ENSG00000171195	ENSG00000171195		"""Mucins"""	7518	protein-coding gene	gene with protein product		158375	"""mucin 7, salivary"""			8838308	Standard	NM_152291		Approved	FLJ27047, MG2	uc003hfj.3	Q8TAX7	OTTHUMG00000129916	ENST00000304887.5:c.589G>A	4.37:g.71347050G>A	ENSP00000302021:p.Ala197Thr	270.0	0.0	0		359.0	149.0	0.415042	NM_001145007	Q9UCD7|Q9UCD8	Missense_Mutation	SNP	ENST00000304887.5	37	CCDS3541.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	5.104	0.204826	0.09704	6.81E-4	0.005581	ENSG00000171195	ENST00000413702;ENST00000456088;ENST00000304887	T;T;T	0.48836	0.8;0.8;0.8	2.05	-4.1	0.03940	.	.	.	.	.	T	0.19565	0.0470	L	0.27053	0.805	0.09310	N	1	B	0.16396	0.017	B	0.12837	0.008	T	0.14337	-1.0476	8	.	.	.	-1.511	4.8329	0.13449	0.4757:0.3088:0.2155:0.0	.	197	Q8TAX7	MUC7_HUMAN	T	197	ENSP00000407422:A197T;ENSP00000400585:A197T;ENSP00000302021:A197T	.	A	+	1	0	MUC7	71381639	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-6.631000	0.00059	-1.559000	0.01688	-0.136000	0.14681	GCA	G|0.996;A|0.004	0.004	strong		0.592	MUC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252168.2	NM_152291	
LRIT3	345193	hgsc.bcm.edu	37	4	110791290	110791290	+	Missense_Mutation	SNP	C	C	T	rs201097191		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:110791290C>T	ENST00000594814.1	+	4	1385	c.1385C>T	c.(1384-1386)cCt>cTt	p.P462L	LRIT3_ENST00000327908.3_Missense_Mutation_p.P279L|LRIT3_ENST00000409621.2_Missense_Mutation_p.P279L|LRIT3_ENST00000379920.3_Missense_Mutation_p.P417L	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	462					regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		AGTAAGCTTCCTCCAGCCAGC	0.468													C|||	1	0.000199681	0.0	0.0	5008	,	,		22471	0.0		0.001	False		,,,				2504	0.0				p.P462L		Atlas-SNP	.											.	LRIT3	107	.	0			c.C1385T						PASS	.						67.0	68.0	68.0					4																	110791290		2203	4300	6503	SO:0001583	missense	345193	exon4			AGCTTCCTCCAGC	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1385C>T	4.37:g.110791290C>T	ENSP00000469759:p.Pro462Leu	106.0	0.0	0		121.0	61.0	0.504132	NM_198506	C9J1C2|Q6ZTG1	Missense_Mutation	SNP	ENST00000594814.1	37	CCDS3688.3	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.59	1.982265	0.34942	.	.	ENSG00000183423	ENST00000327908;ENST00000379920;ENST00000409621	T;T;T	0.57752	0.38;0.55;0.38	5.06	4.22	0.49857	.	0.662798	0.13364	N	0.393444	T	0.42630	0.1211	L	0.43152	1.355	0.42468	D	0.992817	B;B	0.17667	0.006;0.023	B;B	0.16722	0.005;0.016	T	0.28996	-1.0026	10	0.36615	T	0.2	.	6.7454	0.23458	0.223:0.686:0.0:0.091	.	417;279	Q3SXY7;Q3SXY7-2	LRIT3_HUMAN;.	L	279;417;279	ENSP00000328222:P279L;ENSP00000369252:P417L;ENSP00000386734:P279L	ENSP00000328222:P279L	P	+	2	0	LRIT3	111010739	0.070000	0.21116	0.179000	0.23059	0.105000	0.19272	3.151000	0.50670	1.121000	0.41925	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	strong		0.468	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
LPHN1	22859	hgsc.bcm.edu	37	19	14261853	14261853	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14261853G>A	ENST00000340736.6	-	24	4554	c.4257C>T	c.(4255-4257)ccC>ccT	p.P1419P	CTB-55O6.12_ENST00000588387.1_RNA|CTB-55O6.12_ENST00000588658.1_RNA|LPHN1_ENST00000361434.3_Silent_p.P1414P	NM_001008701.2	NP_001008701.1	O94910	LPHN1_HUMAN	latrophilin 1	1419	Poly-Pro.				calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|heterophilic cell-cell adhesion (GO:0007157)|neuropeptide signaling pathway (GO:0007218)|positive regulation of synapse maturation (GO:0090129)	axon (GO:0030424)|cell junction (GO:0030054)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|G-protein coupled receptor activity (GO:0004930)|latrotoxin receptor activity (GO:0016524)			central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						AGATTTCGGGGGGGCCGGGGG	0.731																																					p.P1419P		Atlas-SNP	.											.	LPHN1	107	.	0			c.C4257T						PASS	.						2.0	3.0	3.0					19																	14261853		1382	3162	4544	SO:0001819	synonymous_variant	22859	exon24			TTCGGGGGGGCCG	AB020628	CCDS12307.1, CCDS32928.1	19p13.2	2014-08-08				ENSG00000072071		"""-"", ""GPCR / Class B : Orphans"""	20973	protein-coding gene	gene with protein product						10994649	Standard	NM_014921		Approved	KIAA0821, CIRL1, LEC2	uc010xnn.2	O94910		ENST00000340736.6:c.4257C>T	19.37:g.14261853G>A		48.0	0.0	0		33.0	23.0	0.69697	NM_001008701	Q96IE7|Q9BU07|Q9HAR3	Silent	SNP	ENST00000340736.6	37	CCDS32928.1																																																																																			.	.	none		0.731	LPHN1-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459696.1	NM_014921	
RIN2	54453	hgsc.bcm.edu	37	20	19915770	19915770	+	Missense_Mutation	SNP	G	G	A	rs78648341	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:19915770G>A	ENST00000255006.6	+	3	381	c.232G>A	c.(232-234)Gga>Aga	p.G78R	RIN2_ENST00000440354.2_Missense_Mutation_p.G29R|RIN2_ENST00000484638.1_3'UTR	NM_001242581.1|NM_018993.3	NP_001229510.1|NP_061866.1	Q8WYP3	RIN2_HUMAN	Ras and Rab interactor 2	29					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			autonomic_ganglia(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	27						CTCGGAGATCGGAGAACTGAA	0.532													G|||	37	0.00738818	0.0008	0.0101	5008	,	,		17562	0.0		0.0278	False		,,,				2504	0.001				p.G78R		Atlas-SNP	.											.	RIN2	126	.	0			c.G232A						PASS	.	G	ARG/GLY,ARG/GLY	4,3954		0,4,1975	70.0	68.0	69.0		232,85	5.7	1.0	20	dbSNP_131	69	99,8211		1,97,4057	yes	missense,missense	RIN2	NM_001242581.1,NM_018993.3	125,125	1,101,6032	AA,AG,GG		1.1913,0.1011,0.8396	probably-damaging,probably-damaging	78/945,29/896	19915770	103,12165	1979	4155	6134	SO:0001583	missense	54453	exon3			GAGATCGGAGAAC	AB060339	CCDS56182.1	20p11.22	2008-07-30			ENSG00000132669	ENSG00000132669			18750	protein-coding gene	gene with protein product		610222				11733506, 1849280, 16423831	Standard	NM_018993		Approved	RASSF4	uc002wro.2	Q8WYP3	OTTHUMG00000031996	ENST00000255006.6:c.232G>A	20.37:g.19915770G>A	ENSP00000255006:p.Gly78Arg	83.0	0.0	0		67.0	34.0	0.507463	NM_001242581	Q00425|Q5TFT8|Q9BQL3|Q9H071	Missense_Mutation	SNP	ENST00000255006.6	37	CCDS56182.1	25	0.011446886446886446	0	0.0	5	0.013812154696132596	0	0.0	20	0.026385224274406333	G	27.9	4.876983	0.91664	0.001011	0.011913	ENSG00000132669	ENST00000255006;ENST00000440354	T;T	0.06933	3.24;3.24	5.71	5.71	0.89125	.	0.059318	0.64402	D	0.000003	T	0.08846	0.0219	L	0.47716	1.5	0.33565	D	0.597839	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00834	-1.1547	9	.	.	.	-14.9319	18.6285	0.91350	0.0:0.0:1.0:0.0	.	29;29	E7EPJ1;Q8WYP3	.;RIN2_HUMAN	R	78;29	ENSP00000255006:G78R;ENSP00000391239:G29R	.	G	+	1	0	RIN2	19863770	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.995000	0.76257	2.703000	0.92315	0.655000	0.94253	GGA	G|0.987;A|0.013	0.013	strong		0.532	RIN2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078212.1		
GRHL2	79977	hgsc.bcm.edu	37	8	102585965	102585965	+	Silent	SNP	C	C	T	rs55682875	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:102585965C>T	ENST00000251808.3	+	6	1142	c.804C>T	c.(802-804)acC>acT	p.T268T	GRHL2_ENST00000395927.1_Silent_p.T252T	NM_024915.3	NP_079191.2	Q6ISB3	GRHL2_HUMAN	grainyhead-like 2 (Drosophila)	268					brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac ventricle morphogenesis (GO:0003208)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|face development (GO:0060324)|in utero embryonic development (GO:0001701)|lung lobe morphogenesis (GO:0060463)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(6)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	all_cancers(14;4.39e-08)|all_epithelial(15;4.09e-10)|Lung NSC(17;7.11e-06)|all_lung(17;1.44e-05)		Epithelial(11;5.81e-09)|all cancers(13;3.81e-07)|OV - Ovarian serous cystadenocarcinoma(57;0.000213)			GCCCCATGACCTACCTCAACA	0.527													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19445	0.0		0.002	False		,,,				2504	0.0				p.T268T		Atlas-SNP	.											.	GRHL2	68	.	0			c.C804T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	84.0	70.0	75.0		804	4.0	1.0	8	dbSNP_129	75	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	GRHL2	NM_024915.3		0,12,6491	TT,TC,CC		0.1163,0.0454,0.0923		268/626	102585965	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	79977	exon6			CATGACCTACCTC	AK023844	CCDS34931.1	8q22.3	2008-02-05	2005-07-11	2005-07-11	ENSG00000083307	ENSG00000083307			2799	protein-coding gene	gene with protein product		608576	"""deafness, autosomal dominant 28"", ""transcription factor CP2-like 3"""	DFNA28, TFCP2L3		12393799	Standard	NM_024915		Approved	FLJ13782, BOM	uc010mbu.3	Q6ISB3	OTTHUMG00000149915	ENST00000251808.3:c.804C>T	8.37:g.102585965C>T		62.0	0.0	0		68.0	36.0	0.529412	NM_024915	A1L303|Q6NT03|Q9H8B8	Silent	SNP	ENST00000251808.3	37	CCDS34931.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	GRHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313882.1	NM_024915	
PCDHGB1	56104	hgsc.bcm.edu	37	5	140731022	140731022	+	Missense_Mutation	SNP	A	A	G	rs77250251	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140731022A>G	ENST00000523390.1	+	1	1195	c.1195A>G	c.(1195-1197)Aag>Gag	p.K399E	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	399	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAATTATTACAAGCTGGTGAT	0.478													.|||	118	0.0235623	0.0356	0.0288	5008	,	,		20579	0.001		0.0298	False		,,,				2504	0.0204				p.K399E		Atlas-SNP	.											.	PCDHGB1	198	.	0			c.A1195G						PASS	.	A	,,,GLU/LYS,GLU/LYS	120,3818		2,116,1851	54.0	57.0	56.0		,,,1195,1195	3.0	0.6	5	dbSNP_132	56	243,8063		3,237,3913	yes	intron,intron,intron,missense,missense	PCDHGB1,PCDHGA3,PCDHGA2,PCDHGA1	NM_018912.2,NM_018915.2,NM_018916.3,NM_018922.2,NM_032095.1	,,,56,56	5,353,5764	GG,GA,AA		2.9256,3.0472,2.9647	,,,,	,,,399/928,399/811	140731022	363,11881	1969	4153	6122	SO:0001583	missense	56104	exon1			TATTACAAGCTGG	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.1195A>G	5.37:g.140731022A>G	ENSP00000429273:p.Lys399Glu	110.0	0.0	0		106.0	48.0	0.45283	NM_018922	Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	CCDS54923.1	53	0.024267399267399268	16	0.032520325203252036	16	0.04419889502762431	0	0.0	21	0.027704485488126648	.	10.77	1.444408	0.25987	0.030472	0.029256	ENSG00000254221	ENST00000523390	T	0.01705	4.68	5.49	2.97	0.34412	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.01156	0.0038	M	0.69463	2.115	0.19300	N	0.999972	P;P	0.48998	0.918;0.835	P;P	0.51385	0.668;0.612	T	0.20273	-1.0280	9	0.66056	D	0.02	.	12.1998	0.54319	0.7302:0.2698:0.0:0.0	.	399;399	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	E	399	ENSP00000429273:K399E	ENSP00000429273:K399E	K	+	1	0	PCDHGB1	140711206	0.000000	0.05858	0.646000	0.29493	0.241000	0.25554	0.720000	0.25896	0.406000	0.25560	0.460000	0.39030	AAG	A|0.975;G|0.025	0.025	strong		0.478	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
AS3MT	57412	hgsc.bcm.edu	37	10	104638211	104638211	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:104638211G>A	ENST00000369880.3	+	8	763	c.686G>A	c.(685-687)cGt>cAt	p.R229H	C10orf32-ASMT_ENST00000299353.6_3'UTR	NM_020682.3	NP_065733.2	Q9HBK9	AS3MT_HUMAN	arsenite methyltransferase	229					arsonoacetate metabolic process (GO:0018872)|toxin metabolic process (GO:0009404)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	arsenite methyltransferase activity (GO:0030791)|methylarsonite methyltransferase activity (GO:0030792)			large_intestine(1)|lung(6)	7		Colorectal(252;0.122)|all_hematologic(284;0.152)|Breast(234;0.198)		Epithelial(162;5.87e-09)|all cancers(201;1.58e-07)|BRCA - Breast invasive adenocarcinoma(275;0.223)		TGCCCTCCACGTTTGGTCACT	0.403																																					p.R229H		Atlas-SNP	.											.	AS3MT	17	.	0			c.G686A						PASS	.						181.0	173.0	176.0					10																	104638211		1886	4134	6020	SO:0001583	missense	57412	exon8			CTCCACGTTTGGT	AF226730	CCDS41567.1	10q24.33	2014-05-09	2014-05-09		ENSG00000214435	ENSG00000214435	2.1.1.137		17452	protein-coding gene	gene with protein product		611806	"""arsenic (+3 oxidation state) methyltransferase"""			11790780	Standard	NM_020682		Approved	CYT19	uc001kwk.3	Q9HBK9	OTTHUMG00000018972	ENST00000369880.3:c.686G>A	10.37:g.104638211G>A	ENSP00000358896:p.Arg229His	83.0	0.0	0		40.0	38.0	0.95	NM_020682	A6NP79|Q0VDK3|Q0VDK4|Q5PZ02	Missense_Mutation	SNP	ENST00000369880.3	37	CCDS41567.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376179	0.82682	.	.	ENSG00000214435	ENST00000369880	T	0.22945	1.93	5.48	3.61	0.41365	.	0.053428	0.64402	D	0.000001	T	0.41994	0.1183	M	0.74881	2.28	0.35290	D	0.782117	D;D;D	0.65815	0.965;0.995;0.995	P;P;P	0.56398	0.548;0.797;0.797	T	0.58042	-0.7706	9	0.40728	T	0.16	-15.267	11.7063	0.51599	0.1505:0.0:0.8495:0.0	.	229;229;229	Q0VDK3;Q9HBK9;Q0VDK4	.;AS3MT_HUMAN;.	H	229	ENSP00000358896:R229H	ENSP00000358896:R229H	R	+	2	0	AS3MT	104628201	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.613000	0.67688	1.314000	0.45095	-0.254000	0.11334	CGT	.	.	none		0.403	AS3MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050107.1	NM_020682	
PCDHB5	26167	hgsc.bcm.edu	37	5	140517034	140517034	+	Missense_Mutation	SNP	C	C	G	rs139801121	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140517034C>G	ENST00000231134.5	+	1	2235	c.2018C>G	c.(2017-2019)cCg>cGg	p.P673R		NM_015669.2	NP_056484.1	Q9Y5E4	PCDB5_HUMAN	protocadherin beta 5	673					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(12)|kidney(1)|large_intestine(18)|lung(25)|ovary(3)|prostate(6)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	81			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTGCCGCTGCCGGAGGCGGCC	0.692													C|||	46	0.0091853	0.0008	0.0159	5008	,	,		14307	0.0		0.0318	False		,,,				2504	0.002				p.P673R		Atlas-SNP	.											.	PCDHB5	184	.	0			c.C2018G						PASS	.	C	ARG/PRO	11,4325		0,11,2157	53.0	60.0	58.0		2018	4.7	0.1	5	dbSNP_134	58	155,8307		1,153,4077	no	missense	PCDHB5	NM_015669.2	103	1,164,6234	GG,GC,CC		1.8317,0.2537,1.2971	possibly-damaging	673/796	140517034	166,12632	2168	4231	6399	SO:0001583	missense	26167	exon1			CGCTGCCGGAGGC	AF152498	CCDS4247.1	5q31	2010-01-26			ENSG00000113209	ENSG00000113209		"""Cadherins / Protocadherins : Clustered"""	8690	other	protocadherin		606331				10380929	Standard	NM_015669		Approved	DKFZp586B0217, PCDH-BETA5	uc003liq.3	Q9Y5E4	OTTHUMG00000129616	ENST00000231134.5:c.2018C>G	5.37:g.140517034C>G	ENSP00000231134:p.Pro673Arg	28.0	0.0	0		18.0	9.0	0.5	NM_015669	Q549F4|Q9UFU9	Missense_Mutation	SNP	ENST00000231134.5	37	CCDS4247.1	40	0.018315018315018316	4	0.008130081300813009	11	0.03038674033149171	0	0.0	25	0.032981530343007916	C	14.58	2.579289	0.46006	0.002537	0.018317	ENSG00000113209	ENST00000231134	T	0.50277	0.75	4.71	4.71	0.59529	.	.	.	.	.	T	0.48589	0.1508	M	0.86028	2.79	0.09310	N	1	D	0.67145	0.996	D	0.69654	0.965	T	0.56902	-0.7902	9	0.72032	D	0.01	.	15.1203	0.72438	0.0:0.7833:0.2167:0.0	.	673	Q9Y5E4	PCDB5_HUMAN	R	673	ENSP00000231134:P673R	ENSP00000231134:P673R	P	+	2	0	PCDHB5	140497218	0.000000	0.05858	0.064000	0.19789	0.138000	0.21146	0.604000	0.24164	2.337000	0.79520	0.430000	0.28490	CCG	C|0.986;G|0.014	0.014	strong		0.692	PCDHB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251811.1	NM_015669	
MATN3	4148	hgsc.bcm.edu	37	2	20202930	20202930	+	Missense_Mutation	SNP	G	G	A	rs77245812	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20202930G>A	ENST00000407540.3	-	3	970	c.908C>T	c.(907-909)aCg>aTg	p.T303M	AC079145.4_ENST00000416575.1_RNA|MATN3_ENST00000421259.2_Intron	NM_002381.4	NP_002372.1	O15232	MATN3_HUMAN	matrilin 3	303	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.		T -> M (in dbSNP:rs28939676). {ECO:0000269|PubMed:12736871, ECO:0000269|PubMed:14729835, ECO:0000269|PubMed:15459972}.		extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|skin(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ACCTGAACACGTTTTCTTGTC	0.527													G|||	70	0.0139776	0.0	0.0101	5008	,	,		18855	0.001		0.0159	False		,,,				2504	0.047				p.T303M		Atlas-SNP	.											.	MATN3	28	.	0			c.C908T	GRCh37	CM031237	MATN3	M	rs77245812	PASS	.	G	MET/THR	20,4030		0,20,2005	127.0	118.0	121.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	908	5.5	0.4	2	dbSNP_131	121	122,8220		0,122,4049	yes	missense	MATN3	NM_002381.4	81	0,142,6054	AA,AG,GG		1.4625,0.4938,1.1459	probably-damaging	303/487	20202930	142,12250	2025	4171	6196	SO:0001583	missense	4148	exon3			GAACACGTTTTCT	AJ001047	CCDS46226.1	2p24-p23	2008-06-03			ENSG00000132031	ENSG00000132031			6909	protein-coding gene	gene with protein product		602109				9287130, 9350998	Standard	NM_002381		Approved	EDM5, HOA	uc002rdl.3	O15232	OTTHUMG00000151788	ENST00000407540.3:c.908C>T	2.37:g.20202930G>A	ENSP00000383894:p.Thr303Met	111.0	0.0	0		171.0	65.0	0.380117	NM_002381	B2CPU0|Q4ZG02	Missense_Mutation	SNP	ENST00000407540.3	37	CCDS46226.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	0	0.0	12	0.0158311345646438	G	22.5	4.298303	0.81025	0.004938	0.014625	ENSG00000132031	ENST00000407540	D	0.88201	-2.35	5.5	5.5	0.81552	Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.85682	D	0.000000	D	0.93106	0.7805	H	0.95539	3.685	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.93432	0.6786	10	0.72032	D	0.01	-21.4112	16.1448	0.81559	0.0:0.0:1.0:0.0	rs28939676;rs52790166	303	O15232	MATN3_HUMAN	M	303	ENSP00000383894:T303M	ENSP00000383894:T303M	T	-	2	0	MATN3	20066411	1.000000	0.71417	0.415000	0.26534	0.782000	0.44232	8.518000	0.90559	2.596000	0.87737	0.650000	0.86243	ACG	G|0.990;A|0.010	0.010	strong		0.527	MATN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323925.1	NM_002381	
LILRB2	10288	hgsc.bcm.edu	37	19	54780769	54780769	+	Missense_Mutation	SNP	G	G	C	rs139961541		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54780769G>C	ENST00000391749.4	-	10	1646	c.1375C>G	c.(1375-1377)Ctg>Gtg	p.L459V	LILRB2_ENST00000314446.5_Missense_Mutation_p.L458V|LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391746.1_Missense_Mutation_p.L459V|LILRB2_ENST00000391748.1_Missense_Mutation_p.L458V|LILRB2_ENST00000434421.1_Missense_Mutation_p.L343V	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	459					cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)	p.L459V(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAACCCCCAGGTGCCTTCCC	0.572																																					p.L459V		Atlas-SNP	.											LILRB2,right_upper_lobe,carcinoma,+2,1	LILRB2	94	1	1	Substitution - Missense(1)	lung(1)	c.C1375G						scavenged	.						160.0	108.0	126.0					19																	54780769		2203	4300	6503	SO:0001583	missense	10288	exon10			CCCCCAGGTGCCT	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1375C>G	19.37:g.54780769G>C	ENSP00000375629:p.Leu459Val	101.0	0.0	0		120.0	17.0	0.141667	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	G	5.506	0.278355	0.10403	.	.	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00507	7.04;7.04;7.05;6.92;6.95	1.5	1.5	0.22942	.	23.978700	0.00481	U	0.000134	T	0.00524	0.0017	L	0.43757	1.38	0.09310	N	1	B;B;B	0.21606	0.058;0.01;0.004	B;B;B	0.19391	0.025;0.014;0.004	T	0.48536	-0.9027	10	0.34782	T	0.22	.	6.574	0.22555	0.0:0.0:1.0:0.0	.	459;475;459	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	V	458;458;459;459;343	ENSP00000375628:L458V;ENSP00000319960:L458V;ENSP00000375629:L459V;ENSP00000375626:L459V;ENSP00000410117:L343V	ENSP00000319960:L458V	L	-	1	2	LILRB2	59472581	0.038000	0.19896	0.026000	0.17262	0.110000	0.19582	1.230000	0.32612	1.185000	0.42971	0.297000	0.19635	CTG	G|0.919;C|0.081	0.081	strong		0.572	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
FAT2	2196	hgsc.bcm.edu	37	5	150947162	150947162	+	Missense_Mutation	SNP	A	A	G	rs114337863	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150947162A>G	ENST00000261800.5	-	1	1343	c.1331T>C	c.(1330-1332)gTg>gCg	p.V444A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	444	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTCAATGACCACCACGGTGGA	0.542													A|||	39	0.00778754	0.0	0.0187	5008	,	,		18868	0.0		0.0209	False		,,,				2504	0.0051				p.V444A		Atlas-SNP	.											.	FAT2	465	.	0			c.T1331C						PASS	.	A	ALA/VAL	24,4382	31.7+/-61.6	0,24,2179	138.0	134.0	135.0		1331	5.7	0.1	5	dbSNP_132	135	222,8378	91.9+/-153.9	5,212,4083	yes	missense	FAT2	NM_001447.2	64	5,236,6262	GG,GA,AA		2.5814,0.5447,1.8914	probably-damaging	444/4350	150947162	246,12760	2203	4300	6503	SO:0001583	missense	2196	exon1			ATGACCACCACGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1331T>C	5.37:g.150947162A>G	ENSP00000261800:p.Val444Ala	165.0	0.0	0		213.0	90.0	0.422535	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	A	15.30	2.791763	0.50102	0.005447	0.025814	ENSG00000086570	ENST00000261800	T	0.69435	-0.4	5.72	5.72	0.89469	Cadherin (3);Cadherin-like (1);	0.000000	0.56097	D	0.000024	T	0.62171	0.2406	M	0.82132	2.575	0.58432	D	0.999999	D	0.67145	0.996	P	0.60473	0.875	T	0.76911	-0.2784	10	0.62326	D	0.03	.	16.0156	0.80439	1.0:0.0:0.0:0.0	.	444	Q9NYQ8	FAT2_HUMAN	A	444	ENSP00000261800:V444A	ENSP00000261800:V444A	V	-	2	0	FAT2	150927355	1.000000	0.71417	0.116000	0.21606	0.171000	0.22731	9.262000	0.95591	2.189000	0.69895	0.533000	0.62120	GTG	A|0.983;G|0.017	0.017	strong		0.542	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
RIC8A	60626	hgsc.bcm.edu	37	11	210660	210660	+	Missense_Mutation	SNP	C	C	G	rs34925440	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:210660C>G	ENST00000526104.1	+	4	2160	c.816C>G	c.(814-816)caC>caG	p.H272Q	RIC8A_ENST00000527696.1_Missense_Mutation_p.H266Q|RIC8A_ENST00000325207.5_Missense_Mutation_p.H272Q			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A	272					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		AGGAGTTCCACGGGTGAGAAT	0.587													C|||	30	0.00599042	0.0	0.0144	5008	,	,		19929	0.0		0.0159	False		,,,				2504	0.0041				p.H272Q		Atlas-SNP	.											.	RIC8A	45	.	0			c.C816G						PASS	.	C	GLN/HIS	7,4399	11.4+/-27.6	0,7,2196	81.0	78.0	79.0		816	-5.6	0.9	11	dbSNP_126	79	144,8456	68.4+/-130.8	2,140,4158	yes	missense	RIC8A	NM_021932.4	24	2,147,6354	GG,GC,CC		1.6744,0.1589,1.161	probably-damaging	272/538	210660	151,12855	2203	4300	6503	SO:0001583	missense	60626	exon4			GTTCCACGGGTGA	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069	ENST00000526104.1:c.816C>G	11.37:g.210660C>G	ENSP00000432008:p.His272Gln	125.0	0.0	0		125.0	70.0	0.56	NM_021932	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Missense_Mutation	SNP	ENST00000526104.1	37		21|21	0.009615384615384616|0.009615384615384616	0|0	0.0|0.0	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	15|15	0.01978891820580475|0.01978891820580475	C|C	16.14|16.14	3.038516|3.038516	0.55003|0.55003	0.001589|0.001589	0.016744|0.016744	ENSG00000177963|ENSG00000177963	ENST00000526104;ENST00000325207;ENST00000527696|ENST00000527728	T;T;T|.	0.42513|.	0.97;0.97;0.97|.	4.47|4.47	-5.57|-5.57	0.02521|0.02521	Armadillo-type fold (1);|.	0.047726|.	0.85682|.	N|.	0.000000|.	T|T	0.35624|0.35624	0.0938|0.0938	L|L	0.51853|0.51853	1.615|1.615	0.54753|0.54753	D|D	0.999985|0.999985	P;D;D|.	0.89917|.	0.548;1.0;1.0|.	B;D;D|.	0.97110|.	0.283;1.0;1.0|.	T|T	0.50866|0.50866	-0.8777|-0.8777	10|5	0.26408|.	T|.	0.33|.	-18.6535|-18.6535	8.7496|8.7496	0.34607|0.34607	0.0:0.5309:0.099:0.3701|0.0:0.5309:0.099:0.3701	rs34925440|rs34925440	266;272;272|.	Q9NPQ8-2;Q9NPQ8;Q9NPQ8-3|.	.;RIC8A_HUMAN;.|.	Q|R	272;272;266|167	ENSP00000432008:H272Q;ENSP00000325941:H272Q;ENSP00000434833:H266Q|.	ENSP00000325941:H272Q|.	H|T	+|+	3|2	2|0	RIC8A|RIC8A	200660|200660	0.002000|0.002000	0.14202|0.14202	0.872000|0.872000	0.34217|0.34217	0.678000|0.678000	0.39670|0.39670	-1.433000|-1.433000	0.02428|0.02428	-1.247000|-1.247000	0.02507|0.02507	-1.201000|-1.201000	0.01664|0.01664	CAC|ACG	C|0.988;G|0.012	0.012	strong		0.587	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
SLC38A1	81539	hgsc.bcm.edu	37	12	46622959	46622959	+	Silent	SNP	T	T	C	rs61928115	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:46622959T>C	ENST00000398637.5	-	5	985	c.291A>G	c.(289-291)gcA>gcG	p.A97A	SLC38A1_ENST00000549633.1_5'UTR|SLC38A1_ENST00000549049.1_Silent_p.A97A|SLC38A1_ENST00000552197.1_Silent_p.A97A|SLC38A1_ENST00000546893.1_Silent_p.A97A|SLC38A1_ENST00000439706.1_Silent_p.A97A	NM_001077484.1|NM_001278387.1|NM_001278388.1|NM_001278389.1|NM_030674.3	NP_001070952.1|NP_001265316.1|NP_001265317.1|NP_001265318.1|NP_109599.3	Q9H2H9	S38A1_HUMAN	solute carrier family 38, member 1	97					amino acid transmembrane transport (GO:0003333)|amino acid transport (GO:0006865)|ion transport (GO:0006811)|neurotransmitter uptake (GO:0001504)|neutral amino acid transport (GO:0015804)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neutral amino acid transmembrane transporter activity (GO:0015175)|sodium:amino acid symporter activity (GO:0005283)			NS(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(2)	23	Lung SC(27;0.137)|Renal(347;0.236)		all cancers(1;0.00805)|OV - Ovarian serous cystadenocarcinoma(5;0.0106)|Epithelial(2;0.0344)			TTCCAGTGTTTGCCAGGGCAA	0.408													T|||	42	0.00838658	0.0023	0.0101	5008	,	,		16884	0.0		0.0278	False		,,,				2504	0.0041				p.A97A		Atlas-SNP	.											.	SLC38A1	58	.	0			c.A291G						PASS	.	T	,	15,3751		0,15,1868	57.0	52.0	54.0		291,291	-1.7	1.0	12	dbSNP_129	54	215,7997		2,211,3893	no	coding-synonymous,coding-synonymous	SLC38A1	NM_001077484.1,NM_030674.3	,	2,226,5761	CC,CT,TT		2.6181,0.3983,1.9202	,	97/488,97/488	46622959	230,11748	1883	4106	5989	SO:0001819	synonymous_variant	81539	exon5			AGTGTTTGCCAGG	AF271070	CCDS41774.1, CCDS61106.1	12q13.11	2013-05-22				ENSG00000111371		"""Solute carriers"""	13447	protein-coding gene	gene with protein product		608490				10891391	Standard	NM_030674		Approved	ATA1, NAT2, SAT1	uc001rpc.3	Q9H2H9		ENST00000398637.5:c.291A>G	12.37:g.46622959T>C		47.0	0.0	0		44.0	20.0	0.454545	NM_030674	Q8NC61|Q8NCF8|Q96JX2|Q9H2Q2	Silent	SNP	ENST00000398637.5	37	CCDS41774.1																																																																																			T|0.985;C|0.015	0.015	strong		0.408	SLC38A1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404218.2		
NAGLU	4669	hgsc.bcm.edu	37	17	40695462	40695462	+	Missense_Mutation	SNP	G	G	A	rs147293270	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:40695462G>A	ENST00000225927.2	+	6	1539	c.1438G>A	c.(1438-1440)Gcc>Acc	p.A480T	RP11-400F19.8_ENST00000585572.1_RNA	NM_000263.3	NP_000254.2	P54802	ANAG_HUMAN	N-acetylglucosaminidase, alpha	480					carbohydrate metabolic process (GO:0005975)|cerebellar Purkinje cell layer development (GO:0021680)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|inner ear receptor cell development (GO:0060119)|locomotor rhythm (GO:0045475)|lysosome organization (GO:0007040)|middle ear morphogenesis (GO:0042474)|nervous system development (GO:0007399)|retinal rod cell development (GO:0046548)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)	alpha-N-acetylglucosaminidase activity (GO:0004561)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|ovary(2)|skin(1)	12		all_cancers(22;1.58e-05)|Breast(137;0.000153)|all_epithelial(22;0.000344)		BRCA - Breast invasive adenocarcinoma(366;0.13)	N-Acetyl-D-glucosamine(DB00141)	CAGCTTTGCCGCCCGGCGGTA	0.652													G|||	2	0.000399361	0.0008	0.0	5008	,	,		17281	0.0		0.001	False		,,,				2504	0.0				p.A480T		Atlas-SNP	.											.	NAGLU	36	.	0			c.G1438A						PASS	.	G	THR/ALA	3,4401		0,3,2199	21.0	19.0	19.0		1438	-0.8	0.0	17	dbSNP_134	19	13,8581		0,13,4284	yes	missense	NAGLU	NM_000263.3	58	0,16,6483	AA,AG,GG		0.1513,0.0681,0.1231	benign	480/744	40695462	16,12982	2202	4297	6499	SO:0001583	missense	4669	exon6			TTTGCCGCCCGGC		CCDS11427.1	17q21.2	2010-07-27	2010-07-27		ENSG00000108784	ENSG00000108784	3.2.1.50		7632	protein-coding gene	gene with protein product	"""Sanfilippo disease IIIB"""	609701					Standard	XM_006721920		Approved	NAG	uc002hzv.3	P54802		ENST00000225927.2:c.1438G>A	17.37:g.40695462G>A	ENSP00000225927:p.Ala480Thr	45.0	0.0	0		57.0	31.0	0.54386	NM_000263		Missense_Mutation	SNP	ENST00000225927.2	37	CCDS11427.1	.	.	.	.	.	.	.	.	.	.	G	0.011	-1.721599	0.00700	6.81E-4	0.001513	ENSG00000108784	ENST00000225927;ENST00000377405	D	0.98550	-4.99	4.37	-0.768	0.11013	Alpha-N-acetylglucosaminidase, C-terminal (1);	2.129420	0.01419	N	0.014306	D	0.94152	0.8124	N	0.25957	0.775	0.09310	N	1	B	0.19706	0.038	B	0.15870	0.014	D	0.89959	0.4085	10	0.08381	T	0.77	0.3738	4.8095	0.13337	0.3302:0.1519:0.518:0.0	.	480	P54802	ANAG_HUMAN	T	480;156	ENSP00000225927:A480T	ENSP00000225927:A480T	A	+	1	0	NAGLU	37948988	0.000000	0.05858	0.000000	0.03702	0.074000	0.17049	0.114000	0.15520	-0.174000	0.10743	0.205000	0.17691	GCC	G|0.999;A|0.001	0.001	strong		0.652	NAGLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450385.1	NM_000263	
LRP5	4041	hgsc.bcm.edu	37	11	68115631	68115631	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:68115631C>A	ENST00000294304.7	+	2	514	c.408C>A	c.(406-408)aaC>aaA	p.N136K		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	136	Beta-propeller 1.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGGTGGCCAACCTCAATGGCA	0.642																																					p.N136K		Atlas-SNP	.											.	LRP5	136	.	0			c.C408A						PASS	.						97.0	93.0	94.0					11																	68115631		2200	4294	6494	SO:0001583	missense	4041	exon2			GGCCAACCTCAAT	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.408C>A	11.37:g.68115631C>A	ENSP00000294304:p.Asn136Lys	50.0	0.0	0		52.0	22.0	0.423077	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	12.31	1.900963	0.33535	.	.	ENSG00000162337	ENST00000294304	D	0.83506	-1.73	3.71	2.78	0.32641	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.52532	U	0.000075	T	0.77772	0.4180	L	0.42632	1.34	0.50313	D	0.999863	P	0.45672	0.864	P	0.47376	0.545	T	0.71718	-0.4508	10	0.27785	T	0.31	.	7.2059	0.25907	0.0:0.7283:0.0:0.2717	.	136	O75197	LRP5_HUMAN	K	136	ENSP00000294304:N136K	ENSP00000294304:N136K	N	+	3	2	LRP5	67872207	0.792000	0.28813	0.998000	0.56505	0.307000	0.27823	-0.168000	0.09925	0.888000	0.36160	0.561000	0.74099	AAC	.	.	none		0.642	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
AGRN	375790	hgsc.bcm.edu	37	1	989207	989207	+	Missense_Mutation	SNP	G	G	C	rs74685771	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:989207G>C	ENST00000379370.2	+	34	5776	c.5726G>C	c.(5725-5727)aGt>aCt	p.S1909T	RP11-54O7.14_ENST00000418300.1_RNA	NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1931	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		GTGCTCTGGAGTGGCAAGGCC	0.652													G|||	45	0.00898562	0.0	0.0519	5008	,	,		19298	0.0089		0.0	False		,,,				2504	0.0				p.S1909T		Atlas-SNP	.											.	AGRN	110	.	0			c.G5726C						PASS	.	G	THR/SER	7,4393	9.9+/-24.2	0,7,2193	44.0	36.0	39.0		5726	-0.8	0.2	1	dbSNP_132	39	5,8587	5.0+/-18.6	0,5,4291	yes	missense	AGRN	NM_198576.3	58	0,12,6484	CC,CG,GG		0.0582,0.1591,0.0924	benign	1909/2046	989207	12,12980	2200	4296	6496	SO:0001583	missense	375790	exon34			TCTGGAGTGGCAA	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.5726G>C	1.37:g.989207G>C	ENSP00000368678:p.Ser1909Thr	205.0	0.0	0		237.0	123.0	0.518987	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	19|19	0.0086996336996337|0.0086996336996337	0|0	0.0|0.0	13|13	0.03591160220994475|0.03591160220994475	6|6	0.01048951048951049|0.01048951048951049	0|0	0.0|0.0	G|G	1.487|1.487	-0.555666|-0.555666	0.03967|0.03967	0.001591|0.001591	5.82E-4|5.82E-4	ENSG00000188157|ENSG00000188157	ENST00000419249|ENST00000379370;ENST00000379364	.|T	.|0.78595	.|-1.19	3.95|3.95	-0.779|-0.779	0.10973|0.10973	.|Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	.|0.141330	.|0.44902	.|D	.|0.000411	T|T	0.43166|0.43166	0.1235|0.1235	L|L	0.45285|0.45285	1.41|1.41	0.40815|0.40815	D|D	0.98345|0.98345	.|B	.|0.22346	.|0.068	.|B	.|0.42422	.|0.387	T|T	0.49495|0.49495	-0.8934|-0.8934	5|10	.|0.09338	.|T	.|0.73	-3.2936|-3.2936	12.7066|12.7066	0.57063|0.57063	0.0:0.0:0.4308:0.5692|0.0:0.0:0.4308:0.5692	.|.	.|1909	.|O00468	.|AGRIN_HUMAN	D|T	230|1909;271	.|ENSP00000368678:S1909T	.|ENSP00000368671:S271T	E|S	+|+	3|2	2|0	AGRN|AGRN	979070|979070	1.000000|1.000000	0.71417|0.71417	0.215000|0.215000	0.23724|0.23724	0.135000|0.135000	0.20990|0.20990	4.270000|4.270000	0.58896|0.58896	-0.358000|-0.358000	0.08162|0.08162	-0.521000|-0.521000	0.04368|0.04368	GAG|AGT	G|0.997;C|0.003	0.003	strong		0.652	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
EVL	51466	hgsc.bcm.edu	37	14	100613197	100613197	+	IGR	SNP	G	G	A	rs140696950	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100613197G>A	ENST00000402714.2	+	0	2353				DEGS2_ENST00000553834.1_Missense_Mutation_p.L44F|DEGS2_ENST00000305631.5_Silent_p.H291H|DEGS2_ENST00000557117.1_5'Flank			Q9UI08	EVL_HUMAN	Enah/Vasp-like						actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				TCACCCAGGAGTGGTGCTGCG	0.637													G|||	14	0.00279553	0.0008	0.0058	5008	,	,		18492	0.0		0.004	False		,,,				2504	0.0051				p.H291H		Atlas-SNP	.											.	DEGS2	25	.	0			c.C873T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	119.0	114.0	116.0		873	3.8	1.0	14	dbSNP_134	116	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous	DEGS2	NM_206918.2		0,22,6481	AA,AG,GG		0.2093,0.0908,0.1692		291/324	100613197	22,12984	2203	4300	6503	SO:0001628	intergenic_variant	123099	exon3			CCAGGAGTGGTGC	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530		14.37:g.100613197G>A		123.0	0.0	0		104.0	57.0	0.548077	NM_206918	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Silent	SNP	ENST00000402714.2	37		3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	14.12	2.441563	0.43326	9.08E-4	0.002093	ENSG00000168350	ENST00000553834	T	0.58210	0.35	4.86	3.75	0.43078	.	.	.	.	.	T	0.37183	0.0994	.	.	.	0.23519	N	0.997508	.	.	.	.	.	.	T	0.22906	-1.0203	5	.	.	.	-28.8619	8.174	0.31270	0.1037:0.2977:0.5986:0.0	.	.	.	.	F	44	ENSP00000450637:L44F	.	L	-	1	0	DEGS2	99682950	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	0.611000	0.24268	2.251000	0.74343	0.561000	0.74099	CTC	G|0.998;A|0.002	0.002	strong		0.637	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1		
KDM3B	51780	hgsc.bcm.edu	37	5	137766066	137766066	+	Silent	SNP	G	G	A	rs61749634	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:137766066G>A	ENST00000314358.5	+	22	5222	c.5022G>A	c.(5020-5022)gtG>gtA	p.V1674V	KDM3B_ENST00000542866.1_Silent_p.V706V|KDM3B_ENST00000394866.1_Silent_p.V1330V	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1674	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GGGCTATTGTGCAGTTCCTAG	0.532																																					p.V1674V		Atlas-SNP	.											.	KDM3B	177	.	0			c.G5022A						PASS	.	G		242,4164	143.1+/-178.2	8,226,1969	161.0	147.0	152.0		5022	3.9	1.0	5	dbSNP_129	152	279,8321	104.8+/-165.8	4,271,4025	yes	coding-synonymous	KDM3B	NM_016604.3		12,497,5994	AA,AG,GG		3.2442,5.4925,4.0058		1674/1762	137766066	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	51780	exon22			TATTGTGCAGTTC	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.5022G>A	5.37:g.137766066G>A		169.0	0.0	0		184.0	95.0	0.516304	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Silent	SNP	ENST00000314358.5	37	CCDS34242.1																																																																																			A|0.040;C|0.000;G|0.960;T|0.000	0.040	strong		0.532	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
NHSL2	340527	hgsc.bcm.edu	37	X	71359555	71359555	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:71359555G>A	ENST00000373677.1	+	2	2321	c.1059G>A	c.(1057-1059)tcG>tcA	p.S353S	NHSL2_ENST00000510661.1_Silent_p.S488S|NHSL2_ENST00000535692.1_Silent_p.S353S|NHSL2_ENST00000540800.1_Silent_p.S719S			Q5HYW2	NHSL2_HUMAN	NHS-like 2	353	Ser-rich.									NS(1)|breast(3)|endometrium(4)|kidney(2)|large_intestine(10)|lung(7)|stomach(1)	28	Renal(35;0.156)					CCAGCCAGTCGGAAACACCAA	0.592																																					p.S719S		Atlas-SNP	.											.	NHSL2	148	.	0			c.G2157A						PASS	.						70.0	52.0	58.0					X																	71359555		2203	4300	6503	SO:0001819	synonymous_variant	340527	exon6			CCAGTCGGAAACA			Xq13.1	2009-02-18			ENSG00000204131	ENSG00000204131			33737	protein-coding gene	gene with protein product							Standard	NM_001013627		Approved		uc011mqa.2	Q5HYW2	OTTHUMG00000021807	ENST00000373677.1:c.1059G>A	X.37:g.71359555G>A		60.0	0.0	0		84.0	6.0	0.0714286	NM_001013627	B2RN94	Silent	SNP	ENST00000373677.1	37																																																																																				.	.	none		0.592	NHSL2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000057170.1	NM_001013627	
HEPHL1	341208	hgsc.bcm.edu	37	11	93839219	93839219	+	Missense_Mutation	SNP	A	A	C	rs200078708		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:93839219A>C	ENST00000315765.9	+	17	2976	c.2968A>C	c.(2968-2970)Aac>Cac	p.N990H		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	990	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TACAATGACAAACTGGTATTT	0.348																																					p.N990H		Atlas-SNP	.											.	HEPHL1	144	.	0			c.A2968C						PASS	.	A	HIS/ASN	0,3770		0,0,1885	127.0	125.0	126.0		2968	4.8	1.0	11		126	5,8207		0,5,4101	yes	missense	HEPHL1	NM_001098672.1	68	0,5,5986	CC,CA,AA		0.0609,0.0,0.0417	possibly-damaging	990/1160	93839219	5,11977	1885	4106	5991	SO:0001583	missense	341208	exon17			ATGACAAACTGGT	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.2968A>C	11.37:g.93839219A>C	ENSP00000313699:p.Asn990His	189.0	0.0	0		203.0	122.0	0.600985	NM_001098672	Q3C1W7	Missense_Mutation	SNP	ENST00000315765.9	37	CCDS44710.1	.	.	.	.	.	.	.	.	.	.	A	16.31	3.088343	0.55968	0.0	6.09E-4	ENSG00000181333	ENST00000315765	D	0.99660	-6.32	5.95	4.84	0.62591	Cupredoxin (2);Multicopper oxidase, type 2 (1);	0.232485	0.50627	D	0.000102	D	0.99055	0.9676	L	0.38649	1.16	0.29801	N	0.832439	D	0.56968	0.978	D	0.64687	0.928	D	0.97256	0.9901	10	0.37606	T	0.19	-8.3966	11.4972	0.50415	0.9307:0.0:0.0693:0.0	.	990	Q6MZM0	HPHL1_HUMAN	H	990	ENSP00000313699:N990H	ENSP00000313699:N990H	N	+	1	0	HEPHL1	93478867	0.993000	0.37304	1.000000	0.80357	0.982000	0.71751	2.852000	0.48310	2.279000	0.76181	0.533000	0.62120	AAC	.	.	weak		0.348	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
SCYL2	55681	hgsc.bcm.edu	37	12	100732822	100732822	+	Missense_Mutation	SNP	G	G	A	rs117356610	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:100732822G>A	ENST00000360820.2	+	18	3099	c.2662G>A	c.(2662-2664)Gtg>Atg	p.V888M		NM_017988.4	NP_060458.3	Q6P3W7	SCYL2_HUMAN	SCY1-like 2 (S. cerevisiae)	888	Necessary for interaction with AP2 complex and clathrin, interaction with clathrin is necessary for its targeting to the TGN and endosomal membranes.				endosome to lysosome transport (GO:0008333)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of receptor internalization (GO:0002092)|receptor internalization involved in canonical Wnt signaling pathway (GO:2000286)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(4)|lung(15)|ovary(2)|skin(1)	41						ACAGATGAACGTGATAGGACA	0.438													G|||	6	0.00119808	0.0	0.0	5008	,	,		20321	0.001		0.004	False		,,,				2504	0.001				p.V888M		Atlas-SNP	.											SCYL2,NS,carcinoma,-2,1	SCYL2	99	1	0			c.G2662A						PASS	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	185.0	178.0	181.0		2662	-7.1	0.4	12	dbSNP_132	181	38,8562	26.3+/-74.7	0,38,4262	yes	missense	SCYL2	NM_017988.4	21	0,42,6461	AA,AG,GG		0.4419,0.0908,0.3229	benign	888/930	100732822	42,12964	2203	4300	6503	SO:0001583	missense	55681	exon18			ATGAACGTGATAG	AB037781	CCDS9076.1	12q23.1	2005-01-20				ENSG00000136021			19286	protein-coding gene	gene with protein product						10718198	Standard	NM_017988		Approved	KIAA1360	uc001thn.3	Q6P3W7	OTTHUMG00000170319	ENST00000360820.2:c.2662G>A	12.37:g.100732822G>A	ENSP00000354061:p.Val888Met	153.0	0.0	0		184.0	79.0	0.429348	NM_017988	A8KAB5|Q96EF4|Q96ST4|Q9H7V5|Q9NVH3|Q9P2I7	Missense_Mutation	SNP	ENST00000360820.2	37	CCDS9076.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	3.958	-0.010846	0.07727	9.08E-4	0.004419	ENSG00000136021	ENST00000360820	T	0.28454	1.61	5.8	-7.11	0.01542	.	0.675157	0.16660	N	0.204822	T	0.08891	0.0220	N	0.02916	-0.46	0.23314	N	0.99793	B	0.02656	0.0	B	0.01281	0.0	T	0.15983	-1.0418	10	0.30078	T	0.28	0.0271	7.2695	0.26248	0.3732:0.0:0.4283:0.1985	.	888	Q6P3W7	SCYL2_HUMAN	M	888	ENSP00000354061:V888M	ENSP00000354061:V888M	V	+	1	0	SCYL2	99256953	0.922000	0.31269	0.385000	0.26158	0.940000	0.58332	0.731000	0.26058	-1.435000	0.01972	-0.300000	0.09419	GTG	G|0.997;A|0.003	0.003	strong		0.438	SCYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408493.2	NM_017988	
SPEN	23013	hgsc.bcm.edu	37	1	16255799	16255799	+	Missense_Mutation	SNP	G	G	A	rs115566585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16255799G>A	ENST00000375759.3	+	11	3268	c.3064G>A	c.(3064-3066)Gtg>Atg	p.V1022M		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1022					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GCAGCCTGACGTGTCCTCTAG	0.423													G|||	12	0.00239617	0.0	0.0115	5008	,	,		20147	0.0		0.004	False		,,,				2504	0.0				p.V1022M		Atlas-SNP	.											.	SPEN	374	.	0			c.G3064A						PASS	.	G	MET/VAL	2,4404	2.1+/-5.4	0,2,2201	46.0	53.0	51.0		3064	-5.8	0.0	1	dbSNP_132	51	31,8569	18.5+/-59.3	0,31,4269	yes	missense	SPEN	NM_015001.2	21	0,33,6470	AA,AG,GG		0.3605,0.0454,0.2537	benign	1022/3665	16255799	33,12973	2203	4300	6503	SO:0001583	missense	23013	exon11			CCTGACGTGTCCT		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.3064G>A	1.37:g.16255799G>A	ENSP00000364912:p.Val1022Met	129.0	0.0	0		149.0	75.0	0.503356	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	5	0.0022893772893772895	0	0.0	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	0.012	-1.676123	0.00751	4.54E-4	0.003605	ENSG00000065526	ENST00000375759	T	0.09445	2.98	5.13	-5.85	0.02311	.	.	.	.	.	T	0.02304	0.0071	N	0.03608	-0.345	0.09310	N	1	B	0.11235	0.004	B	0.06405	0.002	T	0.41233	-0.9520	9	0.42905	T	0.14	6.4781	3.6799	0.08306	0.2371:0.3302:0.3421:0.0907	.	1022	Q96T58	MINT_HUMAN	M	1022	ENSP00000364912:V1022M	ENSP00000364912:V1022M	V	+	1	0	SPEN	16128386	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.308000	0.02730	-0.807000	0.04393	-0.150000	0.13652	GTG	G|0.998;A|0.002	0.002	strong		0.423	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
FAHD2B	151313	hgsc.bcm.edu	37	2	97749730	97749730	+	Silent	SNP	G	G	T	rs113222096	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:97749730G>T	ENST00000414820.1	-	8	1107	c.837C>A	c.(835-837)acC>acA	p.T279T	FAHD2B_ENST00000272610.3_Silent_p.T279T|FAHD2B_ENST00000468548.1_5'Flank|FAHD2B_ENST00000440566.2_Silent_p.T279T			Q6P2I3	FAH2B_HUMAN	fumarylacetoacetate hydrolase domain containing 2B	279							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			kidney(5)|large_intestine(2)|lung(3)|skin(2)	12						CACCTGGGGGGGTCCCAGTTA	0.557													g|||	25	0.00499201	0.0	0.0014	5008	,	,		21137	0.0		0.0209	False		,,,				2504	0.0031				p.T279T		Atlas-SNP	.											.	FAHD2B	34	.	0			c.C837A						PASS	.	G		22,4384	26.2+/-53.5	0,22,2181	31.0	32.0	32.0		837	-2.4	1.0	2	dbSNP_132	32	159,8437	73.8+/-136.5	0,159,4139	no	coding-synonymous	FAHD2B	NM_199336.1		0,181,6320	TT,TG,GG		1.8497,0.4993,1.3921		279/315	97749730	181,12821	2203	4298	6501	SO:0001819	synonymous_variant	151313	exon7			TGGGGGGGTCCCA		CCDS2030.1	2q11.2	2012-06-29			ENSG00000144199	ENSG00000144199			25318	protein-coding gene	gene with protein product							Standard	NM_199336		Approved	DKFZp434N062	uc002sxm.3	Q6P2I3	OTTHUMG00000130533	ENST00000414820.1:c.837C>A	2.37:g.97749730G>T		151.0	0.0	0		162.0	74.0	0.45679	NM_199336	D3DXH7|Q8NDK1	Silent	SNP	ENST00000414820.1	37	CCDS2030.1																																																																																			G|0.987;T|0.013	0.013	strong		0.557	FAHD2B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339482.1	NM_199336	
CWC22	57703	hgsc.bcm.edu	37	2	180835443	180835443	+	Missense_Mutation	SNP	C	C	G	rs143785942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:180835443C>G	ENST00000410053.3	-	10	1380	c.1081G>C	c.(1081-1083)Gaa>Caa	p.E361Q	CWC22_ENST00000295749.6_Missense_Mutation_p.E361Q	NM_020943.2	NP_065994.1	Q9HCG8	CWC22_HUMAN	CWC22 spliceosome-associated protein	361					mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(8)|stomach(1)	30						TCATCTTCTTCCACCAAATCA	0.403													C|||	4	0.000798722	0.0	0.0014	5008	,	,		14767	0.0		0.001	False		,,,				2504	0.002				p.E361Q		Atlas-SNP	.											.	CWC22	62	.	0			c.G1081C						PASS	.	C	GLN/GLU	0,3776		0,0,1888	96.0	91.0	92.0		1081	5.9	1.0	2	dbSNP_134	92	10,8210		0,10,4100	yes	missense	CWC22	NM_020943.2	29	0,10,5988	GG,GC,CC		0.1217,0.0,0.0834	possibly-damaging	361/909	180835443	10,11986	1888	4110	5998	SO:0001583	missense	57703	exon10			CTTCTTCCACCAA		CCDS46465.1	2q31.3	2014-07-03	2014-07-03		ENSG00000163510	ENSG00000163510			29322	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein b"""	615186	"""CWC22 spliceosome-associated protein homolog (S. cerevisiae)"""			9136012, 23236153	Standard	NM_020943		Approved	KIAA1604, EIF4GL, fSAPb, NCM	uc010frh.1	Q9HCG8	OTTHUMG00000154244	ENST00000410053.3:c.1081G>C	2.37:g.180835443C>G	ENSP00000387006:p.Glu361Gln	170.0	0.0	0		161.0	76.0	0.47205	NM_020943	Q05DC2|Q4G135|Q52LF0|Q6PEX2|Q7Z6I0|Q9H5L3|Q9H6Q6	Missense_Mutation	SNP	ENST00000410053.3	37	CCDS46465.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	27.9	4.873213	0.91664	0.0	0.001217	ENSG00000163510	ENST00000410053;ENST00000295749;ENST00000404136	T;T;T	0.30448	1.78;1.77;1.53	5.95	5.95	0.96441	Armadillo-type fold (1);	0.047002	0.85682	D	0.000000	T	0.62392	0.2424	M	0.88570	2.965	0.80722	D	1	D	0.76494	0.999	P	0.62649	0.905	T	0.67825	-0.5570	10	0.72032	D	0.01	-23.3839	19.3813	0.94536	0.0:1.0:0.0:0.0	.	361	Q9HCG8	CWC22_HUMAN	Q	361	ENSP00000387006:E361Q;ENSP00000295749:E361Q;ENSP00000384159:E361Q	ENSP00000295749:E361Q	E	-	1	0	CWC22	180543688	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.818000	0.86416	2.824000	0.97209	0.655000	0.94253	GAA	C|1.000;G|0.000	0.000	strong		0.403	CWC22-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334537.1	NM_020943	
HS3ST4	9951	hgsc.bcm.edu	37	16	25704441	25704441	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:25704441A>G	ENST00000331351.5	+	1	1095	c.703A>G	c.(703-705)Agg>Ggg	p.R235G		NM_006040.2	NP_006031.2	Q9Y661	HS3S4_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 4	235	Substrate binding. {ECO:0000250}.				heparan sulfate proteoglycan metabolic process (GO:0030201)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)			breast(2)|endometrium(3)|large_intestine(1)|lung(9)	15				GBM - Glioblastoma multiforme(48;0.0988)		CTTCTTCGACAGGAACTACGA	0.677																																					p.R235G		Atlas-SNP	.											.	HS3ST4	120	.	0			c.A703G						PASS	.						21.0	24.0	23.0					16																	25704441		1999	4138	6137	SO:0001583	missense	9951	exon1			TTCGACAGGAACT	AF105378	CCDS53995.1	16p11.2	2008-03-12			ENSG00000182601	ENSG00000182601	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5200	protein-coding gene	gene with protein product		604059				9988767	Standard	NM_006040		Approved	3OST4	uc002dof.3	Q9Y661	OTTHUMG00000059978	ENST00000331351.5:c.703A>G	16.37:g.25704441A>G	ENSP00000330606:p.Arg235Gly	116.0	0.0	0		76.0	40.0	0.526316	NM_006040	Q5QI42|Q8NDC2	Missense_Mutation	SNP	ENST00000331351.5	37	CCDS53995.1	.	.	.	.	.	.	.	.	.	.	.	22.4	4.279999	0.80692	.	.	ENSG00000182601	ENST00000331351	T	0.54866	0.55	4.29	4.29	0.51040	Sulfotransferase domain (1);	0.103409	0.56097	D	0.000029	T	0.72526	0.3471	M	0.86178	2.8	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.76299	-0.3010	10	0.72032	D	0.01	.	10.165	0.42875	0.8331:0.1669:0.0:0.0	.	235	Q9Y661	HS3S4_HUMAN	G	235	ENSP00000330606:R235G	ENSP00000330606:R235G	R	+	1	2	HS3ST4	25611942	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.496000	0.45346	1.560000	0.49568	0.460000	0.39030	AGG	.	.	none		0.677	HS3ST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133286.2	NM_006040	
ZFHX3	463	hgsc.bcm.edu	37	16	72992547	72992547	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992547C>A	ENST00000268489.5	-	2	2170	c.1498G>T	c.(1498-1500)Gat>Tat	p.D500Y	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	500					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AGTTCCTCATCCAACTCGCTT	0.552																																					p.D500Y		Atlas-SNP	.											ZFHX3,NS,carcinoma,+1,1	ZFHX3	404	1	0			c.G1498T						PASS	.						82.0	87.0	85.0					16																	72992547		2198	4300	6498	SO:0001583	missense	463	exon2			CCTCATCCAACTC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1498G>T	16.37:g.72992547C>A	ENSP00000268489:p.Asp500Tyr	76.0	0.0	0		90.0	44.0	0.488889	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	C	5.812	0.334030	0.11013	.	.	ENSG00000140836	ENST00000268489	T	0.78246	-1.16	5.01	5.01	0.66863	.	0.250248	0.27513	N	0.019037	T	0.60728	0.2291	N	0.08118	0	0.80722	D	1	P	0.34462	0.454	B	0.24974	0.057	T	0.67432	-0.5672	10	0.72032	D	0.01	.	18.6828	0.91553	0.0:1.0:0.0:0.0	.	500	Q15911	ZFHX3_HUMAN	Y	500	ENSP00000268489:D500Y	ENSP00000268489:D500Y	D	-	1	0	ZFHX3	71550048	1.000000	0.71417	0.991000	0.47740	0.641000	0.38312	1.580000	0.36547	2.487000	0.83934	0.650000	0.86243	GAT	.	.	none		0.552	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
SPAG5	10615	hgsc.bcm.edu	37	17	26911204	26911204	+	Silent	SNP	C	C	T	rs117510770	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:26911204C>T	ENST00000321765.5	-	13	2708	c.2376G>A	c.(2374-2376)ctG>ctA	p.L792L		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	792	Interaction with KNSTRN.				chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					CCTCTTTGGCCAGGACAGCTT	0.507													C|||	20	0.00399361	0.0008	0.0043	5008	,	,		23516	0.0		0.0159	False		,,,				2504	0.0				p.L792L		Atlas-SNP	.											.	SPAG5	92	.	0			c.G2376A						PASS	.	C		14,4392	22.3+/-47.3	0,14,2189	207.0	176.0	186.0		2376	3.8	1.0	17	dbSNP_132	186	132,8468	67.0+/-129.4	2,128,4170	no	coding-synonymous	SPAG5	NM_006461.3		2,142,6359	TT,TC,CC		1.5349,0.3177,1.1226		792/1194	26911204	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	10615	exon13			TTTGGCCAGGACA	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.2376G>A	17.37:g.26911204C>T		97.0	0.0	0		96.0	53.0	0.552083	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																			C|0.991;T|0.009	0.009	strong		0.507	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
ERICH3	127254	hgsc.bcm.edu	37	1	75037385	75037385	+	Missense_Mutation	SNP	C	C	T	rs200080388		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:75037385C>T	ENST00000326665.5	-	14	4227	c.4009G>A	c.(4009-4011)Gtt>Att	p.V1337I	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		1337	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						ACAGCCACAACCCTTCCTCCT	0.562																																					p.V1337I		Atlas-SNP	.											.	C1orf173	380	.	0			c.G4009A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	254.0	238.0	243.0		4009	2.1	0.0	1		243	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C1orf173	NM_001002912.4	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	1337/1531	75037385	1,13005	2203	4300	6503	SO:0001583	missense	127254	exon14			CCACAACCCTTCC																												ENST00000326665.5:c.4009G>A	1.37:g.75037385C>T	ENSP00000322609:p.Val1337Ile	130.0	0.0	0		134.0	72.0	0.537313	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	.	.	.	.	.	.	.	.	.	.	C	11.88	1.771644	0.31320	0.0	1.16E-4	ENSG00000178965	ENST00000326665	T	0.13901	2.55	4.1	2.14	0.27477	.	.	.	.	.	T	0.02727	0.0082	N	0.19112	0.55	0.09310	N	0.999999	P	0.36535	0.557	B	0.35971	0.215	T	0.42068	-0.9473	9	0.38643	T	0.18	.	7.5396	0.27731	0.0:0.734:0.1688:0.0972	.	1337	Q5RHP9	CA173_HUMAN	I	1337	ENSP00000322609:V1337I	ENSP00000322609:V1337I	V	-	1	0	C1orf173	74809973	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.090000	0.15025	0.187000	0.20147	0.462000	0.41574	GTT	.	.	weak		0.562	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
NCKIPSD	51517	hgsc.bcm.edu	37	3	48716537	48716537	+	Silent	SNP	C	C	A	rs76815705	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48716537C>A	ENST00000294129.2	-	10	1769	c.1650G>T	c.(1648-1650)ctG>ctT	p.L550L	NCKIPSD_ENST00000341520.4_Silent_p.L550L|NCKIPSD_ENST00000416649.2_Silent_p.L543L	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	550	Leu-rich.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AGAGGTCCGGCAGCTGCTCTG	0.652													C|||	26	0.00519169	0.0	0.0029	5008	,	,		17050	0.0		0.0139	False		,,,				2504	0.0102				p.L550L		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.G1650T						PASS	.	C	,	16,4390	22.3+/-47.3	0,16,2187	53.0	54.0	54.0		1650,1629	4.5	1.0	3	dbSNP_132	54	112,8488	52.3+/-112.8	0,112,4188	no	coding-synonymous,coding-synonymous	NCKIPSD	NM_016453.2,NM_184231.1	,	0,128,6375	AA,AC,CC		1.3023,0.3631,0.9842	,	550/723,543/716	48716537	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	51517	exon10			GTCCGGCAGCTGC	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1650G>T	3.37:g.48716537C>A		122.0	0.0	0		153.0	73.0	0.477124	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Silent	SNP	ENST00000294129.2	37	CCDS2776.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	C	7.195	0.592354	0.13812	0.003631	0.013023	ENSG00000213672	ENST00000415281	.	.	.	5.37	4.49	0.54785	.	.	.	.	.	T	0.47728	0.1461	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50406	-0.8832	4	.	.	.	.	6.1236	0.20167	0.1406:0.6518:0.1354:0.0721	.	.	.	.	S	259	.	.	A	-	1	0	NCKIPSD	48691541	0.999000	0.42202	1.000000	0.80357	0.841000	0.47740	0.710000	0.25748	1.236000	0.43740	0.650000	0.86243	GCC	C|0.989;A|0.011	0.011	strong		0.652	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
IL17B	27190	hgsc.bcm.edu	37	5	148754153	148754153	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:148754153C>T	ENST00000261796.3	-	3	372	c.322G>A	c.(322-324)Gac>Aac	p.D108N	RP11-394O4.3_ENST00000521756.1_RNA|IL17B_ENST00000505432.1_5'UTR	NM_014443.2	NP_055258.1	Q9UHF5	IL17B_HUMAN	interleukin 17B	108					cell-cell signaling (GO:0007267)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	extracellular space (GO:0005615)	cytokine activity (GO:0005125)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)|urinary_tract(1)	8			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGCTGGGGTCGTGGTTGATG	0.607																																					p.D108N		Atlas-SNP	.											.	IL17B	15	.	0			c.G322A						PASS	.						23.0	23.0	23.0					5																	148754153		2197	4291	6488	SO:0001583	missense	27190	exon3			TGGGGTCGTGGTT	AF184969	CCDS4297.1	5q33.1	2011-07-14			ENSG00000127743	ENSG00000127743		"""Interleukins and interleukin receptors"""	5982	protein-coding gene	gene with protein product	"""neuronal interleukin-17-related factor"""	604627				10639155	Standard	NM_014443		Approved	IL-17B, ZCYTO7, IL-20, MGC138900, MGC138901, NIRF	uc003lqo.3	Q9UHF5	OTTHUMG00000130051	ENST00000261796.3:c.322G>A	5.37:g.148754153C>T	ENSP00000261796:p.Asp108Asn	47.0	0.0	0		71.0	36.0	0.507042	NM_014443	Q14CE5	Missense_Mutation	SNP	ENST00000261796.3	37	CCDS4297.1	.	.	.	.	.	.	.	.	.	.	C	16.83	3.231424	0.58777	.	.	ENSG00000127743	ENST00000261796	T	0.64260	-0.09	4.68	4.68	0.58851	.	0.159823	0.42420	D	0.000720	T	0.76659	0.4018	L	0.58583	1.82	0.50813	D	0.999891	D	0.89917	1.0	D	0.91635	0.999	T	0.78851	-0.2041	10	0.62326	D	0.03	-20.8315	17.807	0.88604	0.0:1.0:0.0:0.0	.	108	Q9UHF5	IL17B_HUMAN	N	108	ENSP00000261796:D108N	ENSP00000261796:D108N	D	-	1	0	IL17B	148734346	1.000000	0.71417	1.000000	0.80357	0.092000	0.18411	5.794000	0.69067	2.423000	0.82170	0.561000	0.74099	GAC	.	.	none		0.607	IL17B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252330.1	NM_014443	
KIAA2018	205717	hgsc.bcm.edu	37	3	113376113	113376113	+	Silent	SNP	C	C	T	rs62265537|rs59601191|rs112313093|rs59990801|rs397990842|rs10606566		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:113376113C>T	ENST00000478658.1	-	5	4433	c.4416G>A	c.(4414-4416)caG>caA	p.Q1472Q	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Silent_p.Q1472Q			Q68DE3	K2018_HUMAN	KIAA2018	1472	Gln-rich.					membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						gttgctgttgctgctgctgct	0.502																																					p.Q1472Q		Atlas-SNP	.											KIAA2018,rectum,carcinoma,0,1	KIAA2018	180	1	0			c.G4416A						scavenged	.						68.0	71.0	70.0					3																	113376113		2188	4274	6462	SO:0001819	synonymous_variant	205717	exon7			CTGTTGCTGCTGC	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.4416G>A	3.37:g.113376113C>T		45.0	1.0	0.0222222		104.0	24.0	0.230769	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Silent	SNP	ENST00000478658.1	37	CCDS43133.1																																																																																			.	.	weak		0.502	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
ZFHX3	463	hgsc.bcm.edu	37	16	72992629	72992629	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992629C>T	ENST00000268489.5	-	2	2088	c.1416G>A	c.(1414-1416)gcG>gcA	p.A472A	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	472	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctcctcctccgcctcttcct	0.572																																					p.A472A		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1416A						PASS	.						39.0	43.0	42.0					16																	72992629		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCCTCCGCCTCT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1416G>A	16.37:g.72992629C>T		36.0	0.0	0		53.0	5.0	0.0943396	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.572	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
PDE6A	5145	hgsc.bcm.edu	37	5	149264117	149264117	+	Missense_Mutation	SNP	T	T	C	rs149380104	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149264117T>C	ENST00000255266.5	-	16	2071	c.1952A>G	c.(1951-1953)aAt>aGt	p.N651S		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	651					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	CTGTCGACGATTGAGGTTTTG	0.438													T|||	5	0.000998403	0.0	0.0029	5008	,	,		14804	0.0		0.0	False		,,,				2504	0.0031				p.N651S		Atlas-SNP	.											.	PDE6A	98	.	0			c.A1952G						PASS	.	T	SER/ASN	0,4406		0,0,2203	96.0	96.0	96.0		1952	4.6	1.0	5	dbSNP_134	96	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDE6A	NM_000440.2	46	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	benign	651/861	149264117	3,13003	2203	4300	6503	SO:0001583	missense	5145	exon16			CGACGATTGAGGT		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.1952A>G	5.37:g.149264117T>C	ENSP00000255266:p.Asn651Ser	165.0	1.0	0.00606061		227.0	161.0	0.709251	NM_000440	Q0P638	Missense_Mutation	SNP	ENST00000255266.5	37	CCDS4299.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	11.92	1.781228	0.31502	0.0	3.49E-4	ENSG00000132915	ENST00000255266	T	0.74737	-0.87	5.72	4.56	0.56223	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.096275	0.64402	N	0.000002	T	0.57257	0.2041	N	0.20328	0.56	0.44079	D	0.996839	P	0.36438	0.553	B	0.40782	0.34	T	0.55604	-0.8115	10	0.02654	T	1	.	9.7477	0.40457	0.0:0.0815:0.0:0.9185	.	651	P16499	PDE6A_HUMAN	S	651	ENSP00000255266:N651S	ENSP00000255266:N651S	N	-	2	0	PDE6A	149244310	1.000000	0.71417	0.997000	0.53966	0.971000	0.66376	3.597000	0.54031	1.011000	0.39340	0.455000	0.32223	AAT	T|1.000;C|0.000	0.000	strong		0.438	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
WASL	8976	hgsc.bcm.edu	37	7	123349251	123349251	+	Silent	SNP	T	T	C	rs3195229	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:123349251T>C	ENST00000223023.4	-	2	476	c.144A>G	c.(142-144)ttA>ttG	p.L48L		NM_003941.2	NP_003932.3	O00401	WASL_HUMAN	Wiskott-Aldrich syndrome-like	48	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cellular protein complex localization (GO:0034629)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|membrane budding (GO:0006900)|mitotic nuclear division (GO:0007067)|nitric oxide metabolic process (GO:0046209)|positive regulation of clathrin-mediated endocytosis (GO:2000370)|positive regulation of filopodium assembly (GO:0051491)|protein complex assembly (GO:0006461)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of protein localization (GO:0032880)|regulation of transcription, DNA-templated (GO:0006355)|response to bacterium (GO:0009617)|small molecule metabolic process (GO:0044281)|spindle localization (GO:0051653)|transcription, DNA-templated (GO:0006351)|vesicle organization (GO:0016050)|vesicle transport along actin filament (GO:0030050)	actin cap (GO:0030478)|actin cytoskeleton (GO:0015629)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	small GTPase regulator activity (GO:0005083)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CTGCTGCATATAACTGCACCA	0.368													T|||	4	0.000798722	0.0	0.0014	5008	,	,		16453	0.0		0.002	False		,,,				2504	0.001				p.L48L		Atlas-SNP	.											.	WASL	70	.	0			c.A144G						PASS	.	T		5,4401	11.4+/-27.6	0,5,2198	76.0	70.0	72.0		144	1.8	1.0	7	dbSNP_105	72	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	WASL	NM_003941.2		0,39,6464	CC,CT,TT		0.3953,0.1135,0.2999		48/506	123349251	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	8976	exon2			TGCATATAACTGC	D88460	CCDS34743.1	7q31.3	2008-02-01			ENSG00000106299	ENSG00000106299			12735	protein-coding gene	gene with protein product		605056				9422512, 9322739	Standard	NM_003941		Approved	N-WASP, NWASP	uc003vkz.3	O00401	OTTHUMG00000157346	ENST00000223023.4:c.144A>G	7.37:g.123349251T>C		292.0	0.0	0		322.0	143.0	0.444099	NM_003941	A1JUI9|Q7Z746	Silent	SNP	ENST00000223023.4	37	CCDS34743.1																																																																																			T|0.998;C|0.002	0.002	strong		0.368	WASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348522.1	NM_003941	
CHAT	1103	hgsc.bcm.edu	37	10	50830171	50830171	+	Missense_Mutation	SNP	C	C	T	rs8178990	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50830171C>T	ENST00000337653.2	+	5	880	c.727C>T	c.(727-729)Ctc>Ttc	p.L243F	CHAT_ENST00000455728.2_Missense_Mutation_p.L125F|CHAT_ENST00000339797.1_Missense_Mutation_p.L125F|CHAT_ENST00000460699.1_3'UTR|CHAT_ENST00000351556.3_Missense_Mutation_p.L125F|CHAT_ENST00000395559.2_Missense_Mutation_p.L125F|CHAT_ENST00000395562.2_Missense_Mutation_p.L161F	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase	243			L -> F (in dbSNP:rs8178990).		adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	CTCTGGTGTACTCAGCTACAA	0.622													C|||	126	0.0251597	0.0015	0.0202	5008	,	,		15265	0.0		0.0944	False		,,,				2504	0.0153				p.L243F		Atlas-SNP	.											.	CHAT	162	.	0			c.C727T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU,PHE/LEU	49,4357	50.2+/-85.5	1,47,2155	216.0	167.0	184.0		373,481,373,727,373,373,373	4.7	1.0	10	dbSNP_117	184	546,8054	150.3+/-205.2	29,488,3783	yes	missense,missense,missense,missense,missense,missense,missense	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	22,22,22,22,22,22,22	30,535,5938	TT,TC,CC		6.3488,1.1121,4.5748	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	125/631,161/667,125/631,243/749,125/631,125/631,125/631	50830171	595,12411	2203	4300	6503	SO:0001583	missense	1103	exon5			GGTGTACTCAGCT	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.727C>T	10.37:g.50830171C>T	ENSP00000337103:p.Leu243Phe	92.0	0.0	0		80.0	46.0	0.575	NM_020549	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	80	0.03663003663003663	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	72	0.09498680738786279	C	21.3	4.121133	0.77436	0.011121	0.063488	ENSG00000070748	ENST00000339797;ENST00000351556;ENST00000395559;ENST00000337653;ENST00000395562;ENST00000455728	D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	4.74	4.74	0.60224	.	0.245457	0.35096	N	0.003446	T	0.58104	0.2099	M	0.84156	2.68	0.43688	D	0.996133	P;D	0.67145	0.858;0.996	P;D	0.74348	0.637;0.983	T	0.76542	-0.2921	10	0.87932	D	0	-13.929	17.7116	0.88323	0.0:1.0:0.0:0.0	rs8178990;rs61678759;rs8178990	125;243	F8W8I2;P28329	.;CLAT_HUMAN	F	125;125;125;243;161;125	ENSP00000343486:L125F;ENSP00000345878:L125F;ENSP00000378926:L125F;ENSP00000337103:L243F;ENSP00000378929:L161F;ENSP00000390521:L125F	ENSP00000337103:L243F	L	+	1	0	CHAT	50500177	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.979000	0.56888	2.161000	0.67846	0.561000	0.74099	CTC	C|0.955;T|0.045	0.045	strong		0.622	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
TGS1	96764	hgsc.bcm.edu	37	8	56698365	56698365	+	Missense_Mutation	SNP	G	G	A	rs61753685	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:56698365G>A	ENST00000260129.5	+	3	731	c.254G>A	c.(253-255)aGt>aAt	p.S85N		NM_024831.6	NP_079107.6	Q96RS0	TGS1_HUMAN	trimethylguanosine synthase 1	85					7-methylguanosine cap hypermethylation (GO:0036261)|7-methylguanosine RNA capping (GO:0009452)|cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|regulation of transcription, DNA-templated (GO:0006355)|ribonucleoprotein complex biogenesis (GO:0022613)|ribonucleoprotein complex import into nucleus (GO:0071167)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)	RNA trimethylguanosine synthase activity (GO:0071164)			breast(3)|central_nervous_system(1)|endometrium(4)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		all_lung(136;0.119)|all_epithelial(80;0.125)|Lung NSC(129;0.147)	Epithelial(17;0.00027)|all cancers(17;0.00251)			CTGGATGAAAGTGAACTTGAT	0.418													G|||	7	0.00139776	0.0	0.0043	5008	,	,		17006	0.0		0.003	False		,,,				2504	0.001				p.S85N	Esophageal Squamous(34;275 823 4842 34837 48447)	Atlas-SNP	.											.	TGS1	66	.	0			c.G254A						PASS	.	G	ASN/SER	5,4401	11.4+/-27.6	0,5,2198	153.0	140.0	145.0		254	1.6	1.0	8	dbSNP_129	145	55,8545	34.8+/-89.0	1,53,4246	yes	missense	TGS1	NM_024831.6	46	1,58,6444	AA,AG,GG		0.6395,0.1135,0.4613	benign	85/854	56698365	60,12946	2203	4300	6503	SO:0001583	missense	96764	exon3			ATGAAAGTGAACT	AY028423	CCDS34894.1	8q11	2010-06-25	2010-06-25	2006-11-27	ENSG00000137574	ENSG00000137574	2.1.1.-		17843	protein-coding gene	gene with protein product		606461	"""nuclear receptor coactivator 6 interacting protein"", ""trimethylguanosine synthase homolog (S. cerevisiae)"""	NCOA6IP		11517327, 11983179, 19307714	Standard	NM_024831		Approved	PIMT	uc003xsj.4	Q96RS0	OTTHUMG00000164294	ENST00000260129.5:c.254G>A	8.37:g.56698365G>A	ENSP00000260129:p.Ser85Asn	201.0	0.0	0		226.0	112.0	0.495575	NM_024831	A6NJQ5|Q5GH23|Q8TDG9|Q96QU3|Q9H5V3	Missense_Mutation	SNP	ENST00000260129.5	37	CCDS34894.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	0.835	-0.743908	0.03088	0.001135	0.006395	ENSG00000137574	ENST00000260129	T	0.18338	2.22	5.8	1.61	0.23674	.	0.520508	0.22306	N	0.061787	T	0.06188	0.0160	N	0.25647	0.755	0.27538	N	0.950872	B	0.02656	0.0	B	0.01281	0.0	T	0.34850	-0.9812	10	0.13853	T	0.58	-5.7431	5.868	0.18786	0.3053:0.0:0.5326:0.1621	rs61753685	85	Q96RS0	TGS1_HUMAN	N	85	ENSP00000260129:S85N	ENSP00000260129:S85N	S	+	2	0	TGS1	56860919	0.976000	0.34144	0.996000	0.52242	0.006000	0.05464	0.183000	0.16919	0.382000	0.24878	-0.880000	0.02959	AGT	G|0.995;A|0.005	0.005	strong		0.418	TGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378152.1	NM_024831	
FRRS1	391059	hgsc.bcm.edu	37	1	100182997	100182997	+	Missense_Mutation	SNP	G	G	C	rs149801998		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:100182997G>C	ENST00000414213.1	-	11	1806	c.1205C>G	c.(1204-1206)gCt>gGt	p.A402G	FRRS1_ENST00000287474.5_Missense_Mutation_p.A402G|FRRS1_ENST00000492943.1_5'Flank			Q6ZNA5	FRRS1_HUMAN	ferric-chelate reductase 1	402	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.					integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	26		all_epithelial(167;2.09e-06)|all_lung(203;0.000435)|Lung NSC(277;0.00201)		Epithelial(280;0.0718)|all cancers(265;0.126)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.206)		AAGCAAGAAAGCTTTTGACCA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		22156	0.0		0.001	False		,,,				2504	0.0				p.A402G		Atlas-SNP	.											.	FRRS1	50	.	0			c.C1205G						PASS	.	G	GLY/ALA	0,4406		0,0,2203	163.0	157.0	159.0		1205	3.2	0.6	1	dbSNP_134	159	12,8588	9.1+/-34.3	0,12,4288	yes	missense	FRRS1	NM_001013660.2	60	0,12,6491	CC,CG,GG		0.1395,0.0,0.0923	benign	402/627	100182997	12,12994	2203	4300	6503	SO:0001583	missense	391059	exon11			AAGAAAGCTTTTG	AK131302	CCDS30780.1	1p21.3	2009-11-30	2006-02-22	2006-02-22	ENSG00000156869	ENSG00000156869			27622	protein-coding gene	gene with protein product		611578	"""stromal cell derived factor receptor 2 homolog (mouse)"""	SDFR2			Standard	NM_001013660		Approved	SDR2	uc001dsh.1	Q6ZNA5	OTTHUMG00000010768	ENST00000414213.1:c.1205C>G	1.37:g.100182997G>C	ENSP00000393884:p.Ala402Gly	87.0	0.0	0		96.0	39.0	0.40625	NM_001013660	A6NLN7	Missense_Mutation	SNP	ENST00000414213.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	G	11.14	1.550414	0.27739	0.0	0.001395	ENSG00000156869	ENST00000414213;ENST00000287474	.	.	.	5.03	3.16	0.36331	.	0.744958	0.13319	N	0.396864	T	0.23054	0.0557	L	0.54323	1.7	0.09310	N	0.99999	B	0.15930	0.015	B	0.19666	0.026	T	0.26538	-1.0100	9	0.40728	T	0.16	-1.6172	9.3248	0.37986	0.2357:0.0:0.7643:0.0	.	402	Q6ZNA5-2	.	G	402	.	ENSP00000287474:A402G	A	-	2	0	FRRS1	99955585	0.017000	0.18338	0.612000	0.29024	0.767000	0.43475	1.388000	0.34442	0.633000	0.30452	0.561000	0.74099	GCT	G|0.999;C|0.001	0.001	strong		0.398	FRRS1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001013660	
TAS2R5	54429	hgsc.bcm.edu	37	7	141490325	141490325	+	Missense_Mutation	SNP	G	G	A	rs147887777		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:141490325G>A	ENST00000247883.4	+	1	309	c.164G>A	c.(163-165)cGa>cAa	p.R55Q		NM_018980.2	NP_061853.1	Q9NYW4	TA2R5_HUMAN	taste receptor, type 2, member 5	55					chemosensory behavior (GO:0007635)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)	p.R55Q(1)		breast(1)|endometrium(1)|large_intestine(4)|lung(2)|skin(1)	9	Melanoma(164;0.0171)					GCTGGCTGCCGATTTCTCCTG	0.468													g|||	1	0.000199681	0.0	0.0014	5008	,	,		19581	0.0		0.0	False		,,,				2504	0.0				p.R55Q		Atlas-SNP	.											TAS2R5,colon,carcinoma,0,1	TAS2R5	33	1	1	Substitution - Missense(1)	large_intestine(1)	c.G164A						PASS	.	G	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	112.0	107.0	109.0		164	1.7	0.0	7	dbSNP_134	109	17,8583	12.6+/-44.7	0,17,4283	yes	missense	TAS2R5	NM_018980.2	43	0,20,6483	AA,AG,GG		0.1977,0.0681,0.1538	probably-damaging	55/300	141490325	20,12986	2203	4300	6503	SO:0001583	missense	54429	exon1			GCTGCCGATTTCT	AF227132	CCDS5869.1	7q31.3-q32	2012-08-22			ENSG00000127366	ENSG00000127366		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14912	protein-coding gene	gene with protein product		605062					Standard	NM_018980		Approved	T2R5	uc003vwr.1	Q9NYW4	OTTHUMG00000157632	ENST00000247883.4:c.164G>A	7.37:g.141490325G>A	ENSP00000247883:p.Arg55Gln	211.0	1.0	0.00473934		236.0	135.0	0.572034	NM_018980	Q645W0|Q75MV7	Missense_Mutation	SNP	ENST00000247883.4	37	CCDS5869.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	12.07	1.828778	0.32329	6.81E-4	0.001977	ENSG00000127366	ENST00000247883	T	0.37058	1.22	4.46	1.67	0.24075	.	.	.	.	.	T	0.57989	0.2091	M	0.84683	2.71	0.09310	N	1	D	0.76494	0.999	D	0.70716	0.97	T	0.45249	-0.9274	9	0.87932	D	0	.	6.4583	0.21942	0.3113:0.0:0.6887:0.0	.	55	Q9NYW4	TA2R5_HUMAN	Q	55	ENSP00000247883:R55Q	ENSP00000247883:R55Q	R	+	2	0	TAS2R5	141136794	0.130000	0.22417	0.009000	0.14445	0.033000	0.12548	1.820000	0.39032	0.162000	0.19483	0.561000	0.74099	CGA	G|0.999;A|0.001	0.001	strong		0.468	TAS2R5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349283.1		
ABCF1	23	hgsc.bcm.edu	37	6	30545879	30545879	+	Silent	SNP	A	A	G	rs113473909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30545879A>G	ENST00000326195.8	+	4	355	c.243A>G	c.(241-243)aaA>aaG	p.K81K	ABCF1_ENST00000376545.3_Silent_p.K81K|ABCF1_ENST00000396515.4_Silent_p.K81K	NM_001025091.1	NP_001020262.1	Q8NE71	ABCF1_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 1	81					inflammatory response (GO:0006954)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)|ribosome (GO:0005840)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|poly(A) RNA binding (GO:0044822)|ribosome binding (GO:0043022)|translation activator activity (GO:0008494)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(3)|skin(2)	21						ATACCCGAAAAGGCAGGCGGA	0.493													A|||	37	0.00738818	0.0	0.0043	5008	,	,		19009	0.006		0.004	False		,,,				2504	0.0245				p.K81K		Atlas-SNP	.											.	ABCF1	61	.	0			c.A243G						PASS	.	A	,	8,4398	14.3+/-33.2	0,8,2195	88.0	93.0	91.0		243,243	3.2	1.0	6	dbSNP_132	91	90,8510	42.6+/-100.3	1,88,4211	no	coding-synonymous,coding-synonymous	ABCF1	NM_001025091.1,NM_001090.2	,	1,96,6406	GG,GA,AA		1.0465,0.1816,0.7535	,	81/846,81/808	30545879	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	23	exon4			CCGAAAAGGCAGG	AF027302	CCDS34380.1, CCDS34381.1	6p21.33	2012-03-14			ENSG00000204574	ENSG00000204574		"""ATP binding cassette transporters / subfamily F"""	70	protein-coding gene	gene with protein product		603429		ABC50		9790762	Standard	NM_001025091		Approved	EST123147	uc003nql.3	Q8NE71	OTTHUMG00000031094	ENST00000326195.8:c.243A>G	6.37:g.30545879A>G		94.0	0.0	0		93.0	47.0	0.505376	NM_001090	A2BF75|O14897|Q69YP6	Silent	SNP	ENST00000326195.8	37	CCDS34380.1																																																																																			A|0.993;G|0.007	0.007	strong		0.493	ABCF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076137.3		
C17orf98	388381	hgsc.bcm.edu	37	17	36997503	36997503	+	Missense_Mutation	SNP	T	T	C	rs61752602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:36997503T>C	ENST00000398575.4	-	1	205	c.140A>G	c.(139-141)cAg>cGg	p.Q47R		NM_001080465.2	NP_001073934.1	A8MV24	CQ098_HUMAN	chromosome 17 open reading frame 98	47								p.Q47R(1)		endometrium(5)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(3)	14						GTGGTAGTCCTGCTGCGCGTT	0.617													T|||	64	0.0127796	0.0023	0.0144	5008	,	,		12922	0.0		0.0437	False		,,,				2504	0.0072				p.Q47R		Atlas-SNP	.											C17orf98,NS,carcinoma,0,1	C17orf98	34	1	1	Substitution - Missense(1)	pancreas(1)	c.A140G						PASS	.	T	ARG/GLN	25,3925		0,25,1950	55.0	55.0	55.0		140	1.4	1.0	17	dbSNP_129	55	343,7973		7,329,3822	yes	missense	C17orf98	NM_001080465.2	43	7,354,5772	CC,CT,TT		4.1246,0.6329,3.0002	benign	47/155	36997503	368,11898	1975	4158	6133	SO:0001583	missense	388381	exon1			TAGTCCTGCTGCG	AC006449, DY654789	CCDS42310.1	17q12	2014-05-06			ENSG00000214556	ENSG00000275489			34492	protein-coding gene	gene with protein product						16625196	Standard	NM_001080465		Approved	LOC388381	uc002hqv.2	A8MV24	OTTHUMG00000188506	ENST00000398575.4:c.140A>G	17.37:g.36997503T>C	ENSP00000381580:p.Gln47Arg	83.0	0.0	0		87.0	37.0	0.425287	NM_001080465		Missense_Mutation	SNP	ENST00000398575.4	37	CCDS42310.1	38	0.0173992673992674	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	31	0.040897097625329816	T	8.259	0.810759	0.16537	0.006329	0.041246	ENSG00000214556	ENST00000398575	T	0.43294	0.95	5.16	1.35	0.21983	.	1.362360	0.06396	U	0.717920	T	0.05364	0.0142	N	0.16790	0.44	0.23704	N	0.997064	B	0.12013	0.005	B	0.13407	0.009	T	0.16070	-1.0415	10	0.07175	T	0.84	-11.8449	4.455	0.11639	0.518:0.0925:0.0:0.3895	.	47	A8MV24	CQ098_HUMAN	R	47	ENSP00000381580:Q47R	ENSP00000381580:Q47R	Q	-	2	0	C17orf98	34251029	0.913000	0.31002	1.000000	0.80357	0.893000	0.52053	0.142000	0.16096	0.376000	0.24707	0.379000	0.24179	CAG	T|0.971;C|0.029	0.029	strong		0.617	C17orf98-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255469.2	NM_001080465	
H2AFV	94239	hgsc.bcm.edu	37	7	44874113	44874113	+	Missense_Mutation	SNP	T	T	C	rs1802437		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44874113T>C	ENST00000308153.4	-	5	465	c.374A>G	c.(373-375)cAg>cGg	p.Q125R	H2AFV_ENST00000437072.1_Intron|H2AFV_ENST00000350771.3_Missense_Mutation_p.Q99R|H2AFV_ENST00000222690.6_Intron|H2AFV_ENST00000381124.5_3'UTR|H2AFV_ENST00000521529.1_3'UTR|H2AFV_ENST00000349299.3_Missense_Mutation_p.Q87R	NM_012412.4	NP_036544.1	Q71UI9	H2AV_HUMAN	H2A histone family, member V	125			Q -> R (in dbSNP:rs1802437).			extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(1)|lung(4)|prostate(1)|urinary_tract(1)	9						AGCAGTTTTCTGCTGTCCCTT	0.373																																					p.Q125R		Atlas-SNP	.											.	H2AFV	14	.	0			c.A374G						PASS	.						90.0	79.0	83.0					7																	44874113		2203	4300	6503	SO:0001583	missense	94239	exon5			GTTTTCTGCTGTC	AF081192	CCDS5495.1, CCDS5496.1, CCDS5497.1, CCDS5498.1, CCDS47581.1	7p13	2011-01-27		2004-03-26	ENSG00000105968	ENSG00000105968		"""Histones / Replication-independent"""	20664	protein-coding gene	gene with protein product				H2AV			Standard	NM_012412		Approved	MGC10170, MGC10831, MGC1947	uc003tma.2	Q71UI9	OTTHUMG00000129217	ENST00000308153.4:c.374A>G	7.37:g.44874113T>C	ENSP00000308405:p.Gln125Arg	156.0	0.0	0		167.0	11.0	0.0658683	NM_012412	A6NFA8|A6NKY0|A6NN01|A8MQC5|Q59GV8|Q6PK98	Missense_Mutation	SNP	ENST00000308153.4	37	CCDS5496.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.461982	0.63513	.	.	ENSG00000105968	ENST00000349299;ENST00000308153;ENST00000350771	T;D;T	0.82619	0.93;-1.63;0.94	5.91	5.91	0.95273	Histone-fold (1);Histone H2A (1);	.	.	.	.	T	0.71600	0.3359	N	0.17474	0.49	0.80722	D	1	B;B;P	0.41673	0.0;0.029;0.759	B;B;B	0.37267	0.001;0.009;0.245	T	0.76405	-0.2971	9	0.59425	D	0.04	-19.8855	14.2973	0.66321	0.0:0.0:0.0:1.0	rs1802437	99;87;125	A6NKY0;A6NFA8;Q71UI9	.;.;H2AV_HUMAN	R	87;125;99	ENSP00000342714:Q87R;ENSP00000308405:Q125R;ENSP00000340708:Q99R	ENSP00000308405:Q125R	Q	-	2	0	H2AFV	44840638	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.465000	0.80898	2.261000	0.74972	0.533000	0.62120	CAG	T|0.999;C|0.001	0.001	weak		0.373	H2AFV-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251305.1	NM_012412	
HEATR4	399671	hgsc.bcm.edu	37	14	73961982	73961982	+	Missense_Mutation	SNP	C	C	T	rs76429074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:73961982C>T	ENST00000553558.1	-	16	3056	c.2735G>A	c.(2734-2736)gGa>gAa	p.G912E	HEATR4_ENST00000560393.1_Missense_Mutation_p.G865E|C14orf169_ENST00000531973.1_RNA|HEATR4_ENST00000334988.2_Missense_Mutation_p.G912E	NM_001220484.1	NP_001207413.1	Q86WZ0	HEAT4_HUMAN	HEAT repeat containing 4	912										breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28				BRCA - Breast invasive adenocarcinoma(234;0.00386)|OV - Ovarian serous cystadenocarcinoma(108;0.0719)		TCCTTGTTCTCCTTTGGGTTT	0.443													C|||	46	0.0091853	0.0015	0.0101	5008	,	,		18401	0.0		0.0258	False		,,,				2504	0.0112				p.G912E		Atlas-SNP	.											.	HEATR4	126	.	0			c.G2735A						PASS	.	C	GLU/GLY,GLU/GLY	24,4382	30.8+/-60.4	0,24,2179	235.0	195.0	209.0		2735,2735	1.1	0.0	14	dbSNP_131	209	254,8346	99.9+/-161.4	9,236,4055	yes	missense,missense	HEATR4	NM_001220484.1,NM_203309.2	98,98	9,260,6234	TT,TC,CC		2.9535,0.5447,2.1375	probably-damaging,probably-damaging	912/1027,912/1027	73961982	278,12728	2203	4300	6503	SO:0001583	missense	399671	exon15			TGTTCTCCTTTGG	BC047590	CCDS9815.1, CCDS9815.2	14q24.3	2013-09-20			ENSG00000187105	ENSG00000187105			16761	protein-coding gene	gene with protein product						15489334	Standard	NM_203309		Approved	MGC48595	uc021rwf.2	Q86WZ0	OTTHUMG00000171602	ENST00000553558.1:c.2735G>A	14.37:g.73961982C>T	ENSP00000450444:p.Gly912Glu	153.0	0.0	0		153.0	66.0	0.431373	NM_203309	B7Z7V9|E9KL41	Missense_Mutation	SNP	ENST00000553558.1	37	CCDS9815.2	27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	C	0.004	-2.369551	0.00209	0.005447	0.029535	ENSG00000187105	ENST00000553558;ENST00000334988	T	0.20332	2.08	4.96	1.12	0.20585	.	0.699661	0.12884	N	0.431159	T	0.01730	0.0055	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	10	0.02654	T	1	-2.6044	5.0448	0.14477	0.0:0.0995:0.3604:0.5401	.	912	Q86WZ0	HEAT4_HUMAN	E	912;865	ENSP00000450444:G912E	ENSP00000335447:G865E	G	-	2	0	HEATR4	73031735	0.000000	0.05858	0.045000	0.18777	0.010000	0.07245	-0.069000	0.11542	0.027000	0.15297	-0.302000	0.09304	GGA	C|0.982;T|0.018	0.018	strong		0.443	HEATR4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414422.2	NM_203309	
ABL1	25	hgsc.bcm.edu	37	9	133759686	133759686	+	Missense_Mutation	SNP	A	A	G	rs61746126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:133759686A>G	ENST00000318560.5	+	11	2390	c.2009A>G	c.(2008-2010)aAt>aGt	p.N670S		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	670					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GGGGTCCCCAATGGAGCCCTC	0.672			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								A|||	2	0.000399361	0.0008	0.0	5008	,	,		15138	0.0		0.001	False		,,,				2504	0.0				p.N689S		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A2066G						PASS	.	A	SER/ASN,SER/ASN	0,4366		0,0,2183	17.0	21.0	19.0		2009,2066	5.6	1.0	9	dbSNP_129	19	2,8516		0,2,4257	no	missense,missense	ABL1	NM_005157.4,NM_007313.2	46,46	0,2,6440	GG,GA,AA		0.0235,0.0,0.0155	possibly-damaging,possibly-damaging	670/1131,689/1150	133759686	2,12882	2183	4259	6442	SO:0001583	missense	25	exon11			TCCCCAATGGAGC	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2009A>G	9.37:g.133759686A>G	ENSP00000323315:p.Asn670Ser	31.0	0.0	0		28.0	19.0	0.678571	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	A	12.12	1.842721	0.32606	0.0	2.35E-4	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.12774	2.65;2.65	5.57	5.57	0.84162	.	0.093032	0.64402	D	0.000001	T	0.11495	0.0280	L	0.42245	1.32	0.54753	D	0.999987	B;B	0.33212	0.402;0.402	B;B	0.26864	0.074;0.074	T	0.10428	-1.0630	10	0.11182	T	0.66	.	14.9117	0.70761	1.0:0.0:0.0:0.0	rs61746126	670;707	P00519;Q59FK4	ABL1_HUMAN;.	S	485;689;670	ENSP00000361423:N689S;ENSP00000323315:N670S	ENSP00000323315:N670S	N	+	2	0	ABL1	132749507	0.999000	0.42202	0.997000	0.53966	0.985000	0.73830	4.109000	0.57824	2.117000	0.64856	0.459000	0.35465	AAT	A|0.999;G|0.001	0.001	strong		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
KY	339855	hgsc.bcm.edu	37	3	134322877	134322877	+	Silent	SNP	G	G	A	rs35316983	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:134322877G>A	ENST00000423778.2	-	11	1591	c.1530C>T	c.(1528-1530)cgC>cgT	p.R510R	KY_ENST00000503669.1_3'UTR|KY_ENST00000508956.1_Silent_p.R489R	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	510					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GGAAGATGTAGCGCCGCTGTG	0.592													G|||	25	0.00499201	0.0	0.0058	5008	,	,		19389	0.0		0.0209	False		,,,				2504	0.0				p.R510R		Atlas-SNP	.											KY_ENST00000423778,NS,carcinoma,-2,2	KY	92	2	0			c.C1530T						PASS	.	G		14,4172		0,14,2079	48.0	51.0	50.0		1530	4.6	1.0	3	dbSNP_126	50	191,8247		3,185,4031	yes	coding-synonymous	KY	NM_178554.4		3,199,6110	AA,AG,GG		2.2636,0.3344,1.6239		510/662	134322877	205,12419	2093	4219	6312	SO:0001819	synonymous_variant	339855	exon11			GATGTAGCGCCGC	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.1530C>T	3.37:g.134322877G>A		86.0	0.0	0		116.0	57.0	0.491379	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			G|0.989;A|0.011	0.011	strong		0.592	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
POLG	5428	hgsc.bcm.edu	37	15	89862237	89862237	+	Silent	SNP	C	C	T	rs61752780	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:89862237C>T	ENST00000268124.5	-	20	3531	c.3198G>A	c.(3196-3198)acG>acA	p.T1066T	POLG_ENST00000442287.2_Silent_p.T1066T	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	1066					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			GTATGTCAGACGTAGCAATGC	0.567								DNA polymerases (catalytic subunits)					C|||	29	0.00579073	0.0008	0.0043	5008	,	,		19589	0.0		0.0089	False		,,,				2504	0.0164				p.T1066T	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.G3198A						PASS	.	C	,	13,4387	20.2+/-43.8	0,13,2187	120.0	105.0	110.0		3198,3198	-0.2	0.0	15	dbSNP_129	110	67,8531	40.8+/-97.7	0,67,4232	no	coding-synonymous,coding-synonymous	POLG	NM_001126131.1,NM_002693.2	,	0,80,6419	TT,TC,CC		0.7793,0.2955,0.6155	,	1066/1240,1066/1240	89862237	80,12918	2200	4299	6499	SO:0001819	synonymous_variant	5428	exon20			GTCAGACGTAGCA	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.3198G>A	15.37:g.89862237C>T		117.0	0.0	0		143.0	69.0	0.482517	NM_002693	Q8NFM2|Q92515	Silent	SNP	ENST00000268124.5	37	CCDS10350.1																																																																																			C|0.994;T|0.006	0.006	strong		0.567	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
PCNT	5116	hgsc.bcm.edu	37	21	47841989	47841989	+	Missense_Mutation	SNP	C	C	T	rs61735814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47841989C>T	ENST00000359568.5	+	32	7237	c.7130C>T	c.(7129-7131)cCg>cTg	p.P2377L	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2377					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGGTTTCAGCCGCTGCCGGAA	0.627													C|||	94	0.01877	0.0008	0.0259	5008	,	,		16400	0.001		0.0676	False		,,,				2504	0.0061				p.P2377L		Atlas-SNP	.											PCNT,NS,carcinoma,+1,1	PCNT	283	1	0			c.C7130T						PASS	.	C	LEU/PRO	61,4345	57.4+/-93.9	1,59,2143	55.0	56.0	56.0		7130	-7.7	0.0	21	dbSNP_129	56	524,8076	147.1+/-202.6	11,502,3787	yes	missense	PCNT	NM_006031.5	98	12,561,5930	TT,TC,CC		6.093,1.3845,4.4979	benign	2377/3337	47841989	585,12421	2203	4300	6503	SO:0001583	missense	5116	exon32			TTCAGCCGCTGCC	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7130C>T	21.37:g.47841989C>T	ENSP00000352572:p.Pro2377Leu	53.0	0.0	0		73.0	29.0	0.39726	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	72	0.03296703296703297	2	0.0040650406504065045	13	0.03591160220994475	1	0.0017482517482517483	56	0.07387862796833773	C	10.31	1.315395	0.23908	0.013845	0.06093	ENSG00000160299	ENST00000359568	T	0.01464	4.86	4.05	-7.69	0.01263	.	.	.	.	.	T	0.00109	0.0003	L	0.40543	1.245	0.09310	N	1	B;P	0.41848	0.0;0.763	B;B	0.24155	0.001;0.051	T	0.45101	-0.9284	9	0.25751	T	0.34	.	0.2513	0.00206	0.3263:0.2474:0.2047:0.2216	rs61735814	2259;2377	O95613-2;O95613	.;PCNT_HUMAN	L	2377	ENSP00000352572:P2377L	ENSP00000352572:P2377L	P	+	2	0	PCNT	46666417	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.156000	0.03160	-1.441000	0.01958	-0.397000	0.06425	CCG	C|0.960;T|0.040	0.040	strong		0.627	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
TTN	7273	hgsc.bcm.edu	37	2	179582853	179582853	+	Missense_Mutation	SNP	T	T	C	rs72648982	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179582853T>C	ENST00000591111.1	-	84	24153	c.23929A>G	c.(23929-23931)Aga>Gga	p.R7977G	TTN_ENST00000589042.1_Missense_Mutation_p.R8294G|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.R7050G			Q8WZ42	TITIN_HUMAN	titin	12168	Ig-like 62.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CAAGAAATTCTAATTTCTGGA	0.378													T|||	61	0.0121805	0.0023	0.013	5008	,	,		21179	0.001		0.0278	False		,,,				2504	0.0204				p.R8294G		Atlas-SNP	.											.	TTN	18412	.	0			c.A24880G						PASS	.	T	,,,GLY/ARG	21,3687		0,21,1833	118.0	109.0	112.0		,,,21148	5.0	1.0	2	dbSNP_130	112	253,7959		2,249,3855	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,125	2,270,5688	CC,CT,TT		3.0809,0.5663,2.2987	,,,benign	,,,7050/33424	179582853	274,11646	1854	4106	5960	SO:0001583	missense	7273	exon86			AAATTCTAATTTC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.23929A>G	2.37:g.179582853T>C	ENSP00000465570:p.Arg7977Gly	45.0	0.0	0		50.0	30.0	0.6	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		28	0.01282051282051282	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	20	0.026385224274406333	T	9.326	1.059350	0.19987	0.005663	0.030809	ENSG00000155657	ENST00000342992	T	0.67523	-0.27	6.16	4.99	0.66335	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.42539	0.1207	M	0.70595	2.14	0.58432	D	0.999996	B	0.26577	0.153	B	0.24394	0.053	T	0.58725	-0.7586	9	0.87932	D	0	.	13.6119	0.62083	0.0:0.0:0.1293:0.8707	.	7977	Q8WZ42	TITIN_HUMAN	G	7050	ENSP00000343764:R7050G	ENSP00000343764:R7050G	R	-	1	2	TTN	179291098	0.010000	0.17322	0.992000	0.48379	0.963000	0.63663	1.356000	0.34079	1.113000	0.41760	0.528000	0.53228	AGA	T|0.981;C|0.019	0.019	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FAM184A	79632	hgsc.bcm.edu	37	6	119341211	119341211	+	Missense_Mutation	SNP	C	C	T	rs41292560	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:119341211C>T	ENST00000338891.7	-	4	1707	c.1264G>A	c.(1264-1266)Gct>Act	p.A422T	FAM184A_ENST00000368475.4_Missense_Mutation_p.A302T|FAM184A_ENST00000522284.1_Missense_Mutation_p.A302T|FAM184A_ENST00000521531.1_Missense_Mutation_p.A422T|FAM184A_ENST00000352896.5_Missense_Mutation_p.A302T|RP11-351A11.1_ENST00000518570.1_RNA	NM_024581.4	NP_078857.5	Q8NB25	F184A_HUMAN	family with sequence similarity 184, member A	422						extracellular space (GO:0005615)				breast(2)|central_nervous_system(2)|endometrium(2)|kidney(5)|large_intestine(19)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(5)	52						CGCAAAAAAGCTCTTTCCTCT	0.398													C|||	20	0.00399361	0.0	0.0029	5008	,	,		15929	0.0		0.0169	False		,,,				2504	0.001				p.A422T		Atlas-SNP	.											.	FAM184A	109	.	0			c.G1264A						PASS	.	C	THR/ALA,THR/ALA	11,3663		0,11,1826	156.0	142.0	146.0		904,1264	2.7	1.0	6	dbSNP_127	146	96,8068		1,94,3987	yes	missense,missense	FAM184A	NM_001100411.1,NM_024581.4	58,58	1,105,5813	TT,TC,CC		1.1759,0.2994,0.9039	benign,benign	302/972,422/1141	119341211	107,11731	1837	4082	5919	SO:0001583	missense	79632	exon4			AAAAAGCTCTTTC	BC009055	CCDS43499.1, CCDS43500.1, CCDS75508.1	6q22.31	2008-08-14	2008-08-14	2008-08-14	ENSG00000111879	ENSG00000111879			20991	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 60"""	C6orf60		11230166	Standard	NM_024581		Approved	FLJ13942	uc003pyj.3	Q8NB25	OTTHUMG00000015471	ENST00000338891.7:c.1264G>A	6.37:g.119341211C>T	ENSP00000342604:p.Ala422Thr	183.0	0.0	0		224.0	113.0	0.504464	NM_024581	B9DI75|F8W8D6|Q5TBS9|Q7Z323|Q96GY8|Q9H0J8|Q9H851	Missense_Mutation	SNP	ENST00000338891.7	37	CCDS43499.1	15	0.006868131868131868	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	12.19	1.862249	0.32884	0.002994	0.011759	ENSG00000111879	ENST00000338891;ENST00000352896;ENST00000368475;ENST00000521531;ENST00000522284	T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48	5.85	2.69	0.31865	.	0.416381	0.27831	N	0.017672	T	0.05960	0.0155	L	0.36672	1.1	0.27593	N	0.949223	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.11329	0.004;0.002;0.006	T	0.33471	-0.9867	10	0.15066	T	0.55	-3.7601	1.9962	0.03457	0.2501:0.3672:0.0:0.3827	rs41292560	422;302;422	Q8NB25-2;F8W8D6;Q8NB25	.;.;F184A_HUMAN	T	422;302;302;422;302	ENSP00000342604:A422T;ENSP00000326608:A302T;ENSP00000357460:A302T;ENSP00000430442:A422T;ENSP00000429826:A302T	ENSP00000342604:A422T	A	-	1	0	FAM184A	119382910	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.652000	0.46682	0.788000	0.33755	0.557000	0.71058	GCT	C|0.992;T|0.008	0.008	strong		0.398	FAM184A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042009.3	NM_024581	
NOL8	55035	hgsc.bcm.edu	37	9	95077289	95077289	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:95077289G>A	ENST00000535387.1	-	6	1617	c.1618C>T	c.(1618-1620)Cgt>Tgt	p.R540C	NOL8_ENST00000358855.4_Missense_Mutation_p.R472C|NOL8_ENST00000542053.1_Missense_Mutation_p.R472C|NOL8_ENST00000545558.1_Missense_Mutation_p.R540C|NOL8_ENST00000442668.2_Missense_Mutation_p.R540C					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TCCGCAGGACGAATACACTGT	0.498																																					p.R540C		Atlas-SNP	.											.	NOL8	118	.	0			c.C1618T						PASS	.						74.0	70.0	71.0					9																	95077289		1855	4090	5945	SO:0001583	missense	55035	exon7			CAGGACGAATACA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1618C>T	9.37:g.95077289G>A	ENSP00000441300:p.Arg540Cys	143.0	0.0	0		139.0	66.0	0.47482	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	G	6.026	0.373204	0.11409	.	.	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.44881	0.91;0.91;0.91;0.91;0.91;0.91	5.69	-5.16	0.02857	.	1.619260	0.02753	N	0.117648	T	0.20659	0.0497	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11591	-1.0581	10	0.40728	T	0.16	1.0458	2.1033	0.03685	0.3083:0.0914:0.1236:0.4767	.	540	Q76FK4	NOL8_HUMAN	C	540;542;472;540;540;472;540	ENSP00000401177:R540C;ENSP00000351723:R472C;ENSP00000441140:R540C;ENSP00000441300:R540C;ENSP00000440709:R472C;ENSP00000414112:R540C	ENSP00000351723:R472C	R	-	1	0	NOL8	94117110	0.000000	0.05858	0.004000	0.12327	0.118000	0.20060	-1.388000	0.02533	-0.487000	0.06735	-0.136000	0.14681	CGT	.	.	none		0.498	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
MET	4233	hgsc.bcm.edu	37	7	116435768	116435768	+	Silent	SNP	C	C	T	rs41736	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116435768C>T	ENST00000318493.6	+	20	4099	c.3912C>T	c.(3910-3912)gaC>gaT	p.D1304D	MET_ENST00000539704.1_Silent_p.D156D|MET_ENST00000397752.3_Silent_p.D1286D			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.D1304D(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			CTTATCCTGACGTAAACACCT	0.473			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)		OREG0003446	type=REGULATORY REGION|Gene=MET|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	c|||	1764	0.352236	0.034	0.464	5008	,	,		18610	0.4673		0.4414	False		,,,				2504	0.4928				p.D1304D		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.C3912T						scavenged	.	T	,	393,3383		15,363,1510	245.0	238.0	240.0		3858,3912	-10.9	0.0	7	dbSNP_76	240	3487,4731		756,1975,1378	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	771,2338,2888	TT,TC,CC		42.4312,10.4078,32.3495	,	1286/1391,1304/1409	116435768	3880,8114	1888	4109	5997	SO:0001819	synonymous_variant	4233	exon20	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCTGACGTAAAC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.3912C>T	7.37:g.116435768C>T		143.0	1.0	0.00699301	1473	147.0	79.0	0.537415	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.624;T|0.376	0.376	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
KDM4B	23030	hgsc.bcm.edu	37	19	5144411	5144411	+	Silent	SNP	T	T	C	rs10408767|rs57489512		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:5144411T>C	ENST00000159111.4	+	20	3107	c.2889T>C	c.(2887-2889)ccT>ccC	p.P963P	KDM4B_ENST00000536461.1_Silent_p.P997P	NM_015015.2	NP_055830	O94953	KDM4B_HUMAN	lysine (K)-specific demethylase 4B	963	Tudor 1.				chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(1)|liver(1)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	32						ACCTGTACCCTGAGAGCATCA	0.642																																					p.P963P		Atlas-SNP	.											KDM4B,rectum,carcinoma,0,6	KDM4B	120	6	0			c.T2889C						PASS	.						20.0	16.0	17.0					19																	5144411		2173	4262	6435	SO:0001819	synonymous_variant	23030	exon20			GTACCCTGAGAGC	AB020683	CCDS12138.1	19p13.3	2013-01-23	2009-04-06	2009-04-06		ENSG00000127663		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	29136	protein-coding gene	gene with protein product	"""tudor domain containing 14B"""	609765	"""jumonji domain containing 2B"""	JMJD2B		10048485, 15138608	Standard	NM_015015		Approved	KIAA0876, TDRD14B	uc002mbq.4	O94953		ENST00000159111.4:c.2889T>C	19.37:g.5144411T>C		54.0	0.0	0		72.0	9.0	0.125	NM_015015	B9EGN8|D6W631|O75274|Q6P3R5|Q9P1V1|Q9UF40	Silent	SNP	ENST00000159111.4	37	CCDS12138.1																																																																																			T|1.000;|0.000	.	weak		0.642	KDM4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450558.1	NM_015015	
TUBGCP2	10844	hgsc.bcm.edu	37	10	135106550	135106550	+	Silent	SNP	G	G	A	rs141042122	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:135106550G>A	ENST00000252936.3	-	6	1056	c.1017C>T	c.(1015-1017)gcC>gcT	p.A339A	TUBGCP2_ENST00000417178.2_Silent_p.A209A|TUBGCP2_ENST00000368562.1_5'Flank|RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000543663.1_Silent_p.A367A|TUBGCP2_ENST00000368563.2_Silent_p.A339A			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	339					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		CACCGAGGGAGGCCAGGATGT	0.652													G|||	5	0.000998403	0.0	0.0014	5008	,	,		17939	0.0		0.002	False		,,,				2504	0.002				p.A367A		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C1101T						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	45.0	45.0	45.0		1017	1.6	1.0	10	dbSNP_134	45	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	TUBGCP2	NM_006659.2		0,36,6467	AA,AG,GG		0.3721,0.0908,0.2768		339/903	135106550	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon8			GAGGGAGGCCAGG	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.1017C>T	10.37:g.135106550G>A		98.0	0.0	0		130.0	67.0	0.515385	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.997;A|0.003	0.003	strong		0.652	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
LRRC16B	90668	hgsc.bcm.edu	37	14	24534916	24534916	+	Missense_Mutation	SNP	G	G	T	rs79328356	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:24534916G>T	ENST00000342740.5	+	34	3636	c.3482G>T	c.(3481-3483)gGg>gTg	p.G1161V	LRRC16B_ENST00000334420.7_Intron	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1161						cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		GCCCTTCCCGGGTTGGAAAGA	0.617													G|||	98	0.0195687	0.003	0.0245	5008	,	,		17823	0.003		0.0616	False		,,,				2504	0.0123				p.G1161V		Atlas-SNP	.											LRRC16B,NS,carcinoma,+1,1	LRRC16B	120	1	0			c.G3482T						PASS	.	G	VAL/GLY	63,4343	58.7+/-95.3	1,61,2141	123.0	109.0	114.0		3482	4.5	1.0	14	dbSNP_131	114	574,8026	154.6+/-208.8	26,522,3752	yes	missense	LRRC16B	NM_138360.3	109	27,583,5893	TT,TG,GG		6.6744,1.4299,4.8977	probably-damaging	1161/1373	24534916	637,12369	2203	4300	6503	SO:0001583	missense	90668	exon34			TTCCCGGGTTGGA	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3482G>T	14.37:g.24534916G>T	ENSP00000340467:p.Gly1161Val	72.0	0.0	0		99.0	51.0	0.515152	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	60	0.027472527472527472	2	0.0040650406504065045	10	0.027624309392265192	1	0.0017482517482517483	47	0.06200527704485488	G	18.54	3.645209	0.67358	0.014299	0.066744	ENSG00000186648	ENST00000342740	T	0.17854	2.25	5.4	4.51	0.55191	.	0.141061	0.33161	N	0.005214	T	0.01835	0.0058	N	0.19112	0.55	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00950	-1.1503	10	0.72032	D	0.01	-15.7681	9.7564	0.40506	0.0947:0.0:0.9053:0.0	.	1161	Q8ND23	LR16B_HUMAN	V	1161	ENSP00000340467:G1161V	ENSP00000340467:G1161V	G	+	2	0	LRRC16B	23604756	0.964000	0.33143	0.972000	0.41901	0.867000	0.49689	1.806000	0.38892	1.272000	0.44329	0.655000	0.94253	GGG	G|0.958;T|0.042	0.042	strong		0.617	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
TTN	7273	hgsc.bcm.edu	37	2	179590329	179590329	+	Missense_Mutation	SNP	C	C	T	rs17355460	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179590329C>T	ENST00000591111.1	-	69	19875	c.19651G>A	c.(19651-19653)Gga>Aga	p.G6551R	TTN_ENST00000589042.1_Missense_Mutation_p.G6868R|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G5624R|RP11-171I2.1_ENST00000590024.1_RNA			Q8WZ42	TITIN_HUMAN	titin	12154	Ig-like 47.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCAGGCTCTCCGGCTACAACA	0.433													C|||	33	0.00658946	0.0008	0.0086	5008	,	,		20718	0.0		0.0209	False		,,,				2504	0.0051				p.G6868R		Atlas-SNP	.											.	TTN	18412	.	0			c.G20602A						PASS	.	C	ARG/GLY,,,	13,3713		0,13,1850	88.0	80.0	83.0		16870,,,	5.9	1.0	2	dbSNP_123	83	142,8056		2,138,3959	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	125,,,	2,151,5809	TT,TC,CC		1.7321,0.3489,1.2999	probably-damaging,,,	5624/33424,,,	179590329	155,11769	1863	4099	5962	SO:0001583	missense	7273	exon71			GCTCTCCGGCTAC	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.19651G>A	2.37:g.179590329C>T	ENSP00000465570:p.Gly6551Arg	133.0	0.0	0		150.0	65.0	0.433333	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	C	13.86	2.363340	0.41902	0.003489	0.017321	ENSG00000155657	ENST00000342992	T	0.81330	-1.48	5.86	5.86	0.93980	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.89515	0.6737	H	0.96748	3.875	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.92012	0.5619	9	0.87932	D	0	.	20.5632	0.99335	0.0:1.0:0.0:0.0	rs17355460;rs52829777;rs17355460	6551	Q8WZ42	TITIN_HUMAN	R	5624	ENSP00000343764:G5624R	ENSP00000343764:G5624R	G	-	1	0	TTN	179298574	0.989000	0.36119	0.998000	0.56505	0.450000	0.32258	3.002000	0.49496	2.937000	0.99478	0.650000	0.86243	GGA	C|0.991;T|0.009	0.009	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
LAMA5	3911	hgsc.bcm.edu	37	20	60898889	60898889	+	Missense_Mutation	SNP	C	C	T	rs372008452		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60898889C>T	ENST00000252999.3	-	44	5858	c.5792G>A	c.(5791-5793)cGa>cAa	p.R1931Q		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1931	Laminin EGF-like 18. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GCGGCCGCCTCGCAGGACACA	0.692																																					p.R1931Q		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5792A						PASS	.	C	GLN/ARG	1,4365		0,1,2182	22.0	24.0	23.0		5792	1.2	0.1	20		23	1,8575		0,1,4287	no	missense	LAMA5	NM_005560.3	43	0,2,6469	TT,TC,CC		0.0117,0.0229,0.0155	probably-damaging	1931/3696	60898889	2,12940	2183	4288	6471	SO:0001583	missense	3911	exon44			CCGCCTCGCAGGA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5792G>A	20.37:g.60898889C>T	ENSP00000252999:p.Arg1931Gln	75.0	0.0	0		72.0	41.0	0.569444	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.842202	0.32513	2.29E-4	1.17E-4	ENSG00000130702	ENST00000252999	T	0.63096	-0.02	3.63	1.17	0.20885	EGF-like, laminin (3);	0.328525	0.30101	U	0.010416	T	0.38241	0.1033	L	0.42008	1.315	0.09310	N	1	P	0.42993	0.797	B	0.32022	0.139	T	0.22906	-1.0203	10	0.15952	T	0.53	.	3.2772	0.06902	0.0:0.4524:0.2687:0.2789	.	1931	O15230	LAMA5_HUMAN	Q	1931	ENSP00000252999:R1931Q	ENSP00000252999:R1931Q	R	-	2	0	LAMA5	60332284	0.012000	0.17670	0.069000	0.20011	0.382000	0.30200	0.755000	0.26405	0.466000	0.27193	0.297000	0.19635	CGA	.	.	weak		0.692	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
USP40	55230	hgsc.bcm.edu	37	2	234433190	234433190	+	Missense_Mutation	SNP	C	C	G	rs200068889		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234433190C>G	ENST00000427112.2	-	14	1861	c.1826G>C	c.(1825-1827)tGt>tCt	p.C609S	USP40_ENST00000450966.1_Missense_Mutation_p.C621S|USP40_ENST00000251722.6_Missense_Mutation_p.C609S			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	609					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		TTCAGTTTCACACAGTGTCAG	0.378																																					p.C621S		Atlas-SNP	.											.	USP40	174	.	0			c.G1862C						PASS	.	C	SER/CYS	1,3723		0,1,1861	84.0	78.0	80.0		1862	2.4	0.1	2		80	2,8252		0,2,4125	yes	missense	USP40	NM_018218.2	112	0,3,5986	GG,GC,CC		0.0242,0.0269,0.025	benign	621/1248	234433190	3,11975	1862	4127	5989	SO:0001583	missense	55230	exon14			GTTTCACACAGTG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1826G>C	2.37:g.234433190C>G	ENSP00000387898:p.Cys609Ser	123.0	0.0	0		131.0	60.0	0.458015	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	6.767	0.510490	0.12883	2.69E-4	2.42E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.41065	1.01;1.01;1.01	5.68	2.38	0.29361	.	2.175690	0.01523	N	0.018456	T	0.31606	0.0802	L	0.27053	0.805	0.09310	N	0.999999	B;B	0.11235	0.002;0.004	B;B	0.11329	0.002;0.006	T	0.14254	-1.0479	10	0.21014	T	0.42	.	6.3009	0.21111	0.1483:0.6338:0.0:0.2179	.	609;621	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	S	621;609;609	ENSP00000415434:C621S;ENSP00000251722:C609S;ENSP00000387898:C609S	ENSP00000251722:C609S	C	-	2	0	USP40	234097929	0.190000	0.23276	0.056000	0.19401	0.988000	0.76386	0.707000	0.25704	0.709000	0.31976	0.563000	0.77884	TGT	.	.	weak		0.378	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
DAAM1	23002	hgsc.bcm.edu	37	14	59792755	59792755	+	Silent	SNP	G	G	A	rs61755642	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:59792755G>A	ENST00000395125.1	+	9	1157	c.1134G>A	c.(1132-1134)ccG>ccA	p.P378P	DAAM1_ENST00000360909.3_Silent_p.P378P|DAAM1_ENST00000351081.1_Silent_p.P378P	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	378	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	identical protein binding (GO:0042802)			breast(3)|cervix(3)|endometrium(5)|kidney(5)|large_intestine(4)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	37				OV - Ovarian serous cystadenocarcinoma(108;0.165)		AAGCTTACCCGCATTTCATGT	0.443													G|||	9	0.00179712	0.0	0.0014	5008	,	,		19975	0.0		0.007	False		,,,				2504	0.001				p.P378P		Atlas-SNP	.											.	DAAM1	95	.	0			c.G1134A						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	161.0	122.0	135.0		1134	-0.9	1.0	14	dbSNP_129	135	54,8546	35.3+/-89.8	0,54,4246	no	coding-synonymous	DAAM1	NM_014992.1		0,59,6444	AA,AG,GG		0.6279,0.1135,0.4536		378/1079	59792755	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon10			TTACCCGCATTTC	AB014566	CCDS9737.1, CCDS58323.1	14q22.3	2008-08-11			ENSG00000100592	ENSG00000100592			18142	protein-coding gene	gene with protein product		606626				11779461, 18162551	Standard	NM_014992		Approved	KIAA0666	uc031qou.1	Q9Y4D1	OTTHUMG00000140326	ENST00000395125.1:c.1134G>A	14.37:g.59792755G>A		153.0	0.0	0		192.0	101.0	0.526042	NM_001270520	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			G|0.995;A|0.005	0.005	strong		0.443	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
RAD54B	25788	hgsc.bcm.edu	37	8	95470507	95470507	+	Missense_Mutation	SNP	G	G	A	rs148525625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:95470507G>A	ENST00000336148.5	-	3	417	c.293C>T	c.(292-294)cCa>cTa	p.P98L	RAD54B_ENST00000297592.5_Missense_Mutation_p.P98L	NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	98					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			TGTATGAGGTGGATCTAATGT	0.308								Direct reversal of damage;Homologous recombination																													p.P98L		Atlas-SNP	.											RAD54B,NS,carcinoma,+1,1	RAD54B	88	1	0			c.C293T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	163.0	154.0	157.0		293,293	1.4	0.0	8	dbSNP_134	157	2,8594	2.2+/-6.3	0,2,4296	no	missense,missense	RAD54B	NM_001205262.1,NM_012415.3	98,98	0,2,6499	AA,AG,GG		0.0233,0.0,0.0154	benign,benign	98/118,98/911	95470507	2,13000	2203	4298	6501	SO:0001583	missense	25788	exon3			TGAGGTGGATCTA	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.293C>T	8.37:g.95470507G>A	ENSP00000336606:p.Pro98Leu	133.0	0.0	0		148.0	73.0	0.493243	NM_001205262	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.989826	0.54041	0.0	2.33E-4	ENSG00000197275	ENST00000336148;ENST00000523839;ENST00000297592	D;T;T	0.87966	-2.32;1.57;1.54	5.44	1.42	0.22433	.	1.455470	0.03871	N	0.275599	D	0.82435	0.5036	L	0.48642	1.525	0.09310	N	1	B;B	0.11235	0.004;0.0	B;B	0.11329	0.006;0.001	T	0.60321	-0.7286	10	0.15066	T	0.55	-28.8344	7.8043	0.29193	0.366:0.0:0.634:0.0	.	98;98	F6WBS8;Q9Y620	.;RA54B_HUMAN	L	98	ENSP00000336606:P98L;ENSP00000428554:P98L;ENSP00000430153:P98L	ENSP00000430153:P98L	P	-	2	0	RAD54B	95539683	0.000000	0.05858	0.000000	0.03702	0.525000	0.34531	-0.063000	0.11655	0.123000	0.18342	0.650000	0.86243	CCA	G|1.000;A|0.000	0.000	strong		0.308	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79058986	79058986	+	Silent	SNP	C	C	T	rs150434082	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:79058986C>T	ENST00000388820.4	-	19	3477	c.3267G>A	c.(3265-3267)gcG>gcA	p.A1089A	ADAMTS7_ENST00000566303.1_5'Flank	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	1089					cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CCCCTGTCCCCGCCAGGTCTA	0.627													c|||	4	0.000798722	0.0	0.0	5008	,	,		14692	0.0		0.004	False		,,,				2504	0.0				p.A1089A		Atlas-SNP	.											ADAMTS7,NS,carcinoma,-1,1	ADAMTS7	142	1	0			c.G3267A						PASS	.	C		5,4369		0,5,2182	18.0	24.0	22.0		3267	-4.2	0.0	15	dbSNP_134	22	48,8500		1,46,4227	no	coding-synonymous	ADAMTS7	NM_014272.3		1,51,6409	TT,TC,CC		0.5615,0.1143,0.4102		1089/1687	79058986	53,12869	2187	4274	6461	SO:0001819	synonymous_variant	11173	exon19			TGTCCCCGCCAGG	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.3267G>A	15.37:g.79058986C>T		86.0	0.0	0		106.0	63.0	0.59434	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			C|0.996;T|0.004	0.004	strong		0.627	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
TMPRSS3	64699	hgsc.bcm.edu	37	21	43809092	43809092	+	Missense_Mutation	SNP	C	C	T	rs45598239	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:43809092C>T	ENST00000291532.3	-	4	1223	c.268G>A	c.(268-270)Gct>Act	p.A90T	TMPRSS3_ENST00000398405.1_Missense_Mutation_p.A88T|TMPRSS3_ENST00000433957.2_Missense_Mutation_p.A90T|TMPRSS3_ENST00000474596.1_5'UTR|TMPRSS3_ENST00000398397.3_Missense_Mutation_p.A90T|TMPRSS3_ENST00000380399.1_Missense_Mutation_p.A174T	NM_032404.2	NP_115780.1	P57727	TMPS3_HUMAN	transmembrane protease, serine 3	90	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.			A -> T (in Ref. 1; AAG37012). {ECO:0000305}.	cellular sodium ion homeostasis (GO:0006883)|proteolysis (GO:0006508)|sensory perception of sound (GO:0007605)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(4)|skin(1)	13						TCACATCGAGCTATCAGCTCG	0.527													C|||	51	0.0101837	0.0038	0.0086	5008	,	,		21045	0.0		0.0358	False		,,,				2504	0.0041				p.A90T		Atlas-SNP	.											.	TMPRSS3	40	.	0			c.G268A	GRCh37	CM054156	TMPRSS3	M	rs45598239	PASS	.	C	THR/ALA,THR/ALA	40,4366	43.8+/-77.6	0,40,2163	93.0	79.0	83.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	268,268	5.2	0.1	21	dbSNP_127	83	415,8185	130.3+/-188.3	8,399,3893	yes	missense,missense	TMPRSS3	NM_024022.2,NM_032405.1	58,58	8,439,6056	TT,TC,CC		4.8256,0.9079,3.4984	probably-damaging,probably-damaging	90/455,90/345	43809092	455,12551	2203	4300	6503	SO:0001583	missense	64699	exon4			ATCGAGCTATCAG	AF201380	CCDS13686.1, CCDS42939.1, CCDS58790.1	21q22.3	2010-04-13			ENSG00000160183	ENSG00000160183		"""Serine peptidases / Transmembrane"""	11877	protein-coding gene	gene with protein product		605511		DFNB10, DFNB8		11462234, 11907649	Standard	NM_032405		Approved		uc002zbc.3	P57727	OTTHUMG00000086796	ENST00000291532.3:c.268G>A	21.37:g.43809092C>T	ENSP00000291532:p.Ala90Thr	54.0	0.0	0		78.0	38.0	0.487179	NM_001256317	D3DSJ6|Q5USC7|Q6ZMC3	Missense_Mutation	SNP	ENST00000291532.3	37	CCDS13686.1	36	0.016483516483516484	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	28	0.036939313984168866	C	14.53	2.562692	0.45694	0.009079	0.048256	ENSG00000160183	ENST00000291532;ENST00000433957;ENST00000398405;ENST00000380399;ENST00000398397	D;D;D;D;D	0.95412	-3.7;-3.7;-3.7;-3.7;-3.7	5.23	5.23	0.72850	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.138905	0.48286	D	0.000189	D	0.87529	0.6200	M	0.75447	2.3	0.38709	D	0.953168	D;D;D	0.56746	0.967;0.977;0.96	P;P;P	0.57244	0.765;0.787;0.816	D	0.87660	0.2534	9	.	.	.	.	18.8283	0.92127	0.0:1.0:0.0:0.0	rs45598239	90;90;90	P57727-3;P57727-5;P57727	.;.;TMPS3_HUMAN	T	90;90;88;174;90	ENSP00000291532:A90T;ENSP00000411013:A90T;ENSP00000381442:A88T;ENSP00000369762:A174T;ENSP00000381434:A90T	.	A	-	1	0	TMPRSS3	42682161	0.992000	0.36948	0.079000	0.20413	0.008000	0.06430	4.157000	0.58144	2.443000	0.82685	0.561000	0.74099	GCT	C|0.969;T|0.031	0.031	strong		0.527	TMPRSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195347.1		
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012259	46012259	+	Missense_Mutation	SNP	T	T	G	rs201362069	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46012259T>G	ENST00000400368.1	-	1	127	c.107A>C	c.(106-108)gAc>gCc	p.D36A	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	36						keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CTCTGGGCAGTCGTCCACCTG	0.687													.|||	62	0.0123802	0.0295	0.0029	5008	,	,		14636	0.002		0.0109	False		,,,				2504	0.0082				p.D36A		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.A107C						PASS	.	T	ALA/ASP,	103,3931		1,101,1915	46.0	45.0	45.0		107,	2.2	1.0	21		45	117,8165		2,113,4026	no	missense,intron	TSPEAR,KRTAP10-6	NM_198688.2,NM_144991.2	126,	3,214,5941	GG,GT,TT		1.4127,2.5533,1.7863	possibly-damaging,	36/366,	46012259	220,12096	2017	4141	6158	SO:0001583	missense	386674	exon1			GGGCAGTCGTCCA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.107A>C	21.37:g.46012259T>G	ENSP00000383219:p.Asp36Ala	78.0	0.0	0		80.0	23.0	0.2875	NM_198688		Missense_Mutation	SNP	ENST00000400368.1	37	CCDS42959.1	23	0.010531135531135532	13	0.026422764227642278	3	0.008287292817679558	1	0.0017482517482517483	6	0.0079155672823219	t	10.71	1.425617	0.25639	0.025533	0.014127	ENSG00000188155	ENST00000400368	T	0.14893	2.47	3.49	2.18	0.27775	.	.	.	.	.	T	0.05640	0.0148	M	0.63843	1.955	0.26990	N	0.965169	P	0.51791	0.948	B	0.41332	0.354	T	0.09729	-1.0661	9	0.38643	T	0.18	.	7.2248	0.26010	0.0:0.0:0.4041:0.5959	.	36	P60371	KR106_HUMAN	A	36	ENSP00000383219:D36A	ENSP00000383219:D36A	D	-	2	0	KRTAP10-6	44836687	0.979000	0.34478	0.997000	0.53966	0.407000	0.30961	1.226000	0.32563	1.354000	0.45846	0.334000	0.21626	GAC	T|0.993;G|0.007	0.007	strong		0.687	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
USP24	23358	hgsc.bcm.edu	37	1	55563349	55563349	+	Silent	SNP	G	G	A	rs75297697	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:55563349G>A	ENST00000294383.6	-	48	5636	c.5637C>T	c.(5635-5637)agC>agT	p.S1879S	USP24_ENST00000407756.1_Silent_p.S1719S	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1879	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						TTACCAAGACGCTAGGTAAAG	0.333													G|||	10	0.00199681	0.0045	0.0029	5008	,	,		17063	0.0		0.002	False		,,,				2504	0.0				p.S1879S		Atlas-SNP	.											.	USP24	323	.	0			c.C5637T						PASS	.	G		27,3571		0,27,1772	38.0	34.0	35.0		5637	-2.3	1.0	1	dbSNP_132	35	18,8108		0,18,4045	no	coding-synonymous	USP24	NM_015306.2		0,45,5817	AA,AG,GG		0.2215,0.7504,0.3838		1879/2621	55563349	45,11679	1799	4063	5862	SO:0001819	synonymous_variant	23358	exon48			CAAGACGCTAGGT	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.5637C>T	1.37:g.55563349G>A		132.0	0.0	0		132.0	69.0	0.522727	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			G|0.997;A|0.003	0.003	strong		0.333	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
ATP11A	23250	hgsc.bcm.edu	37	13	113481026	113481026	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:113481026G>A	ENST00000487903.1	+	12	1130	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	ATP11A_ENST00000375630.2_Missense_Mutation_p.D348N|ATP11A_ENST00000375645.3_Missense_Mutation_p.D348N|ATP11A_ENST00000283558.8_Missense_Mutation_p.D348N			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	348					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.134)|all_epithelial(44;0.141)				GGCATTCACGGACTTCCTGGC	0.547																																					p.D348N		Atlas-SNP	.											.	ATP11A	225	.	0			c.G1042A						PASS	.						118.0	104.0	109.0					13																	113481026		2203	4300	6503	SO:0001583	missense	23250	exon12			TTCACGGACTTCC	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.1042G>A	13.37:g.113481026G>A	ENSP00000420387:p.Asp348Asn	197.0	0.0	0		259.0	132.0	0.509652	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.006318	0.74932	.	.	ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558	D;D;D;D	0.90620	-2.7;-2.7;-2.7;-2.7	5.05	5.05	0.67936	ATPase, P-type, ATPase-associated domain (1);	0.000000	0.85682	D	0.000000	D	0.93048	0.7787	L	0.45744	1.44	0.80722	D	1	D;P;B	0.89917	1.0;0.887;0.217	D;P;B	0.97110	1.0;0.733;0.444	D	0.90323	0.4346	10	0.15499	T	0.54	.	18.4296	0.90620	0.0:0.0:1.0:0.0	.	348;348;348	E9PCW5;E9PEJ6;P98196	.;.;AT11A_HUMAN	N	348	ENSP00000420387:D348N;ENSP00000364781:D348N;ENSP00000364796:D348N;ENSP00000283558:D348N	ENSP00000283558:D348N	D	+	1	0	ATP11A	112529027	1.000000	0.71417	0.933000	0.37362	0.121000	0.20230	9.445000	0.97587	2.341000	0.79615	0.557000	0.71058	GAC	.	.	none		0.547	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
HLA-B	3106	hgsc.bcm.edu	37	6	31323286	31323286	+	Missense_Mutation	SNP	C	C	T	rs146555925		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:31323286C>T	ENST00000412585.2	-	4	731	c.703G>A	c.(703-705)Gcg>Acg	p.A235T		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	235	Alpha-3.|Ig-like C1-type.				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						GTGATCTCCGCAGGGTAGAAA	0.592									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A235T		Atlas-SNP	.											.	HLA-B	54	.	0			c.G703A						PASS	.						83.0	81.0	82.0					6																	31323286		2203	4298	6501	SO:0001583	missense	3106	exon4	Familial Cancer Database	;Lichen Sclerosis, Familial	TCTCCGCAGGGTA	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.703G>A	6.37:g.31323286C>T	ENSP00000399168:p.Ala235Thr	112.0	0.0	0		162.0	10.0	0.0617284	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	11.65	1.701624	0.30142	.	.	ENSG00000234745	ENST00000412585;ENST00000428231;ENST00000452596;ENST00000434333	T;T	0.14766	2.48;2.48	3.06	-1.02	0.10135	Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.402479	0.17716	U	0.164428	T	0.16727	0.0402	H	0.95780	3.72	0.09310	N	1	B	0.28820	0.224	B	0.41619	0.361	T	0.25847	-1.0120	10	0.87932	D	0	.	6.9863	0.24731	0.0:0.3733:0.0:0.6267	rs1050335;rs3190627	235	P01889	1B07_HUMAN	T	235;114;114;246	ENSP00000399168:A235T;ENSP00000405931:A246T	ENSP00000399168:A235T	A	-	1	0	HLA-B	31431265	0.000000	0.05858	0.023000	0.16930	0.855000	0.48748	-0.862000	0.04263	-0.113000	0.11958	0.442000	0.29010	GCG	C|0.999;T|0.001	0.001	weak		0.592	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
ALX1	8092	hgsc.bcm.edu	37	12	85674221	85674221	+	Missense_Mutation	SNP	A	A	G	rs115440539	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:85674221A>G	ENST00000316824.3	+	1	337	c.182A>G	c.(181-183)cAt>cGt	p.H61R		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	61					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		CGCGCCGAGCATCACGTGCGC	0.637													A|||	24	0.00479233	0.0	0.0043	5008	,	,		14543	0.0		0.0169	False		,,,				2504	0.0041				p.H61R		Atlas-SNP	.											.	ALX1	61	.	0			c.A182G						PASS	.	A	ARG/HIS	10,4396	16.8+/-37.8	0,10,2193	34.0	36.0	35.0		182	5.5	1.0	12	dbSNP_132	35	95,8505	51.5+/-111.7	1,93,4206	yes	missense	ALX1	NM_006982.2	29	1,103,6399	GG,GA,AA		1.1047,0.227,0.8073	benign	61/327	85674221	105,12901	2203	4300	6503	SO:0001583	missense	8092	exon1			CCGAGCATCACGT	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"""Homeoboxes / PRD class"""	1494	protein-coding gene	gene with protein product		601527	"""cartilage paired-class homeoprotein 1"""	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.182A>G	12.37:g.85674221A>G	ENSP00000315417:p.His61Arg	66.0	0.0	0		60.0	33.0	0.55	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	16	0.007326007326007326	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	A	16.30	3.084377	0.55861	0.00227	0.011047	ENSG00000180318	ENST00000316824	D	0.91686	-2.89	5.47	5.47	0.80525	.	0.165804	0.53938	D	0.000051	T	0.75642	0.3877	N	0.19112	0.55	0.50467	D	0.999873	B	0.24186	0.099	B	0.19946	0.027	T	0.77474	-0.2574	10	0.31617	T	0.26	.	12.1271	0.53922	0.8569:0.143:0.0:0.0	.	61	Q15699	ALX1_HUMAN	R	61	ENSP00000315417:H61R	ENSP00000315417:H61R	H	+	2	0	ALX1	84198352	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.410000	0.52664	2.069000	0.61940	0.528000	0.53228	CAT	A|0.991;G|0.009	0.009	strong		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982	
CPZ	8532	hgsc.bcm.edu	37	4	8621167	8621167	+	Silent	SNP	G	G	A	rs9342	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:8621167G>A	ENST00000360986.4	+	11	1956	c.1782G>A	c.(1780-1782)ggG>ggA	p.G594G	CPZ_ENST00000429646.2_Silent_p.G202G|CPZ_ENST00000315782.6_Silent_p.G583G|CPZ_ENST00000382480.2_Silent_p.G457G	NM_001014447.2	NP_001014447	Q66K79	CBPZ_HUMAN	carboxypeptidase Z	594					proteolysis (GO:0006508)|Wnt signaling pathway (GO:0016055)	extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(23)|ovary(3)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46						TTATTCATGGGCTGCGGAGGA	0.652													G|||	300	0.0599042	0.1354	0.0331	5008	,	,		14230	0.0288		0.0507	False		,,,				2504	0.0184				p.G594G		Atlas-SNP	.											.	CPZ	95	.	0			c.G1782A						PASS	.	G	,,	498,3908	230.4+/-244.6	36,426,1741	49.0	50.0	49.0		1782,1371,1749	-0.6	0.0	4	dbSNP_52	49	413,8187	129.8+/-187.9	8,397,3895	no	coding-synonymous,coding-synonymous,coding-synonymous	CPZ	NM_001014447.2,NM_001014448.2,NM_003652.3	,,	44,823,5636	AA,AG,GG		4.8023,11.3028,7.0045	,,	594/653,457/516,583/642	8621167	911,12095	2203	4300	6503	SO:0001819	synonymous_variant	8532	exon11			TCATGGGCTGCGG	U83411	CCDS3404.1, CCDS33953.1, CCDS43212.1	4p16.1	2012-02-10			ENSG00000109625	ENSG00000109625			2333	protein-coding gene	gene with protein product	"""metallocarboxypeptidase Z"""	603105				9099699	Standard	NM_001014447		Approved		uc003glm.3	Q66K79	OTTHUMG00000090513	ENST00000360986.4:c.1782G>A	4.37:g.8621167G>A		204.0	1.0	0.00490196		255.0	136.0	0.533333	NM_001014447	O00520|Q96MX2	Silent	SNP	ENST00000360986.4	37	CCDS33953.1																																																																																			G|0.936;A|0.064	0.064	strong		0.652	CPZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207001.4	NM_003652	
SCLT1	132320	hgsc.bcm.edu	37	4	129864289	129864289	+	Silent	SNP	T	T	C	rs144333168	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:129864289T>C	ENST00000281142.5	-	17	1997	c.1494A>G	c.(1492-1494)gtA>gtG	p.V498V	SCLT1_ENST00000502495.1_5'UTR|SCLT1_ENST00000503215.1_Intron|SCLT1_ENST00000434680.1_Intron|SCLT1_ENST00000439369.2_Intron	NM_144643.2	NP_653244.2	Q96NL6	SCLT1_HUMAN	sodium channel and clathrin linker 1	498					cilium assembly (GO:0042384)|clustering of voltage-gated sodium channels (GO:0045162)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|clathrin complex (GO:0071439)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule cytoskeleton (GO:0015630)	sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|stomach(1)	29						CAGACTCCAATACATTTTGAA	0.348													T|||	3	0.000599042	0.0	0.0	5008	,	,		17091	0.0		0.002	False		,,,				2504	0.001				p.V498V		Atlas-SNP	.											.	SCLT1	136	.	0			c.A1494G						PASS	.	T		2,4402	4.2+/-10.8	0,2,2200	79.0	75.0	76.0		1494	-10.6	0.0	4	dbSNP_134	76	22,8574	16.0+/-53.3	0,22,4276	no	coding-synonymous	SCLT1	NM_144643.2		0,24,6476	CC,CT,TT		0.2559,0.0454,0.1846		498/689	129864289	24,12976	2202	4298	6500	SO:0001819	synonymous_variant	132320	exon17			CTCCAATACATTT	AK055217	CCDS3740.1	4q28.2	2008-05-02			ENSG00000151466	ENSG00000151466			26406	protein-coding gene	gene with protein product		611399				15797711	Standard	XM_005262732		Approved	hCAP-1A, FLJ30655	uc003igp.2	Q96NL6	OTTHUMG00000133346	ENST00000281142.5:c.1494A>G	4.37:g.129864289T>C		127.0	0.0	0		132.0	66.0	0.5	NM_144643	A4QN04|Q0VAH2|Q6P2M4	Silent	SNP	ENST00000281142.5	37	CCDS3740.1																																																																																			T|0.999;C|0.001	0.001	strong		0.348	SCLT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257176.2	NM_144643	
SENP3	26168	hgsc.bcm.edu	37	17	7474729	7474729	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7474729C>T	ENST00000429205.2	+	12	1702	c.1653C>T	c.(1651-1653)ttC>ttT	p.F551F	SENP3_ENST00000321337.7_Silent_p.F550F|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000577269.1_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|SENP3_ENST00000578868.1_3'UTR|EIF4A1_ENST00000582746.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	551						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				CATTCAGCTTCACCCAGCAGG	0.542																																					p.F551F		Atlas-SNP	.											.	SENP3	18	.	0			c.C1653T						PASS	.						101.0	101.0	101.0					17																	7474729		1991	4189	6180	SO:0001819	synonymous_variant	26168	exon12			CAGCTTCACCCAG	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1653C>T	17.37:g.7474729C>T		120.0	0.0	0		120.0	59.0	0.491667	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	37																																																																																				.	.	none		0.542	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41105942	41105942	+	Missense_Mutation	SNP	G	G	A	rs34516375	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41105942G>A	ENST00000355341.4	+	9	1643	c.1142G>A	c.(1141-1143)aGt>aAt	p.S381N	ZFYVE19_ENST00000570108.1_Missense_Mutation_p.S358N|ZFYVE19_ENST00000299173.10_Missense_Mutation_p.S313N|ZFYVE19_ENST00000564258.1_Missense_Mutation_p.S206N|ZFYVE19_ENST00000336455.5_Missense_Mutation_p.S371N	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	381					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GATGAGGCAAGTGGCTTTAAC	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20274	0.0		0.006	False		,,,				2504	0.001				p.S381N		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.G1142A						PASS	.	G	ASN/SER	2,4120		0,2,2059	50.0	56.0	54.0		1142	5.3	1.0	15	dbSNP_126	54	32,8382		0,32,4175	yes	missense	ZFYVE19	NM_001077268.1	46	0,34,6234	AA,AG,GG		0.3803,0.0485,0.2712	possibly-damaging	381/472	41105942	34,12502	2061	4207	6268	SO:0001583	missense	84936	exon9			AGGCAAGTGGCTT	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1142G>A	15.37:g.41105942G>A	ENSP00000347498:p.Ser381Asn	87.0	0.0	0		52.0	51.0	0.980769	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Missense_Mutation	SNP	ENST00000355341.4	37	CCDS42025.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	32	5.125010	0.94429	4.85E-4	0.003803	ENSG00000166140	ENST00000355341;ENST00000299173;ENST00000336455	T;T;T	0.35048	1.33;1.33;1.33	5.27	5.27	0.74061	.	0.078430	0.85682	D	0.000000	T	0.51890	0.1701	M	0.72894	2.215	0.49389	D	0.999784	D;D;P	0.89917	1.0;0.981;0.753	D;P;B	0.87578	0.998;0.725;0.352	T	0.52631	-0.8550	10	0.36615	T	0.2	-14.0194	17.8147	0.88628	0.0:0.0:1.0:0.0	rs34516375	371;313;381	Q96K21-2;Q96K21-3;Q96K21	.;.;ZFY19_HUMAN	N	381;313;371	ENSP00000347498:S381N;ENSP00000299173:S313N;ENSP00000337824:S371N	ENSP00000299173:S313N	S	+	2	0	ZFYVE19	38893234	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	8.753000	0.91637	2.742000	0.94016	0.455000	0.32223	AGT	G|0.997;A|0.003	0.003	strong		0.597	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
DFFA	1676	hgsc.bcm.edu	37	1	10529326	10529326	+	Missense_Mutation	SNP	A	A	G	rs138842024	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:10529326A>G	ENST00000377038.3	-	2	273	c.206T>C	c.(205-207)aTa>aCa	p.I69T	DFFA_ENST00000377036.2_Missense_Mutation_p.I69T	NM_004401.2	NP_004392.1	O00273	DFFA_HUMAN	DNA fragmentation factor, 45kDa, alpha polypeptide	69	CIDE-N. {ECO:0000255|PROSITE- ProRule:PRU00447}.				apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|negative regulation of apoptotic DNA fragmentation (GO:1902511)|negative regulation of execution phase of apoptosis (GO:1900118)|positive regulation of apoptotic process (GO:0043065)|thymocyte apoptotic process (GO:0070242)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				large_intestine(3)|lung(2)	5	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.19e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.25e-07)|COAD - Colon adenocarcinoma(227;7.25e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000296)|Kidney(185;0.00074)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(132;0.0167)|READ - Rectum adenocarcinoma(331;0.0487)		ATCATCCACTATGGTGCCATC	0.423													A|||	11	0.00219649	0.0	0.0043	5008	,	,		21849	0.0		0.006	False		,,,				2504	0.002				p.I69T		Atlas-SNP	.											.	DFFA	24	.	0			c.T206C						PASS	.	A	THR/ILE,THR/ILE	5,4401	9.9+/-24.2	0,5,2198	152.0	132.0	139.0		206,206	5.5	1.0	1	dbSNP_134	139	38,8562	25.7+/-73.6	0,38,4262	yes	missense,missense	DFFA	NM_004401.2,NM_213566.1	89,89	0,43,6460	GG,GA,AA		0.4419,0.1135,0.3306	probably-damaging,probably-damaging	69/332,69/269	10529326	43,12963	2203	4300	6503	SO:0001583	missense	1676	exon2			TCCACTATGGTGC	AF087573	CCDS118.1, CCDS119.1	1p36.3-p36.2	2008-07-18	2002-08-29		ENSG00000160049	ENSG00000160049			2772	protein-coding gene	gene with protein product	"""DNA fragmentation factor, 45 kD, alpha subunit"""	601882	"""DNA fragmentation factor, 45 kD, alpha polypeptide"""			9605855, 9108473	Standard	NM_004401		Approved	DFF-45, DFF45, ICAD, DFF1	uc001arj.3	O00273	OTTHUMG00000001909	ENST00000377038.3:c.206T>C	1.37:g.10529326A>G	ENSP00000366237:p.Ile69Thr	225.0	0.0	0		272.0	135.0	0.496324	NM_004401	Q5T6G5|Q5T6G6|Q96I97|Q9Y6C6	Missense_Mutation	SNP	ENST00000377038.3	37	CCDS118.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	19.98	3.927190	0.73327	0.001135	0.004419	ENSG00000160049	ENST00000377038;ENST00000377036	.	.	.	5.49	5.49	0.81192	Caspase-activated nuclease CIDE-N (3);	0.000000	0.85682	D	0.000000	T	0.66752	0.2821	L	0.48362	1.52	0.58432	D	0.999998	D;D	0.89917	0.999;1.0	D;D	0.97110	0.991;1.0	T	0.69639	-0.5091	9	0.37606	T	0.19	-14.8227	15.6132	0.76744	1.0:0.0:0.0:0.0	.	69;69	O00273-2;O00273	.;DFFA_HUMAN	T	69	.	ENSP00000366235:I69T	I	-	2	0	DFFA	10451913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.677000	0.84024	2.076000	0.62316	0.533000	0.62120	ATA	A|0.997;G|0.003	0.003	strong		0.423	DFFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005418.1	NM_004401	
ACACB	32	hgsc.bcm.edu	37	12	109577344	109577344	+	Missense_Mutation	SNP	A	A	G	rs139767464	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:109577344A>G	ENST00000338432.7	+	2	253	c.134A>G	c.(133-135)cAg>cGg	p.Q45R	ACACB_ENST00000377848.3_Missense_Mutation_p.Q45R|ACACB_ENST00000377854.5_Missense_Mutation_p.Q45R			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	45					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	ATCCCGAGCCAGGAGCCCTTT	0.557													A|||	3	0.000599042	0.0	0.0014	5008	,	,		15671	0.0		0.002	False		,,,				2504	0.0				p.Q45R		Atlas-SNP	.											.	ACACB	330	.	0			c.A134G						PASS	.	A	ARG/GLN	4,4402	6.2+/-15.9	0,4,2199	76.0	80.0	79.0		134	0.2	0.9	12	dbSNP_134	79	23,8577	17.3+/-56.4	0,23,4277	yes	missense	ACACB	NM_001093.3	43	0,27,6476	GG,GA,AA		0.2674,0.0908,0.2076	benign	45/2459	109577344	27,12979	2203	4300	6503	SO:0001583	missense	32	exon1			CGAGCCAGGAGCC	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.134A>G	12.37:g.109577344A>G	ENSP00000341044:p.Gln45Arg	101.0	0.0	0		132.0	66.0	0.5	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	9.803	1.181034	0.21787	9.08E-4	0.002674	ENSG00000076555	ENST00000338432;ENST00000539864;ENST00000377848;ENST00000377854	D;D;D	0.95307	-3.67;-3.67;-3.67	5.53	0.147	0.14838	.	0.427648	0.19984	N	0.101719	D	0.83737	0.5319	N	0.14661	0.345	0.44579	D	0.997548	B	0.02656	0.0	B	0.04013	0.001	T	0.69172	-0.5215	10	0.15499	T	0.54	.	4.3681	0.11233	0.4845:0.3353:0.1802:0.0	.	45	O00763	ACACB_HUMAN	R	45;20;45;45	ENSP00000341044:Q45R;ENSP00000367079:Q45R;ENSP00000367085:Q45R	ENSP00000341044:Q45R	Q	+	2	0	ACACB	108061727	0.310000	0.24527	0.936000	0.37596	0.137000	0.21094	0.076000	0.14712	0.361000	0.24292	0.528000	0.53228	CAG	A|0.998;G|0.002	0.002	strong		0.557	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
LRRC48	83450	hgsc.bcm.edu	37	17	17919414	17919414	+	Missense_Mutation	SNP	G	G	A	rs200381151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:17919414G>A	ENST00000399187.1	+	13	1581	c.1363G>A	c.(1363-1365)Ggg>Agg	p.G455R	LRRC48_ENST00000583995.1_3'UTR|ATPAF2_ENST00000469327.1_5'Flank|LRRC48_ENST00000313838.8_Missense_Mutation_p.G455R	NM_031294.3	NP_112584.3	Q9H069	LRC48_HUMAN	leucine rich repeat containing 48	455						cytoplasm (GO:0005737)				breast(1)|large_intestine(2)|lung(2)|pancreas(1)|urinary_tract(1)	7	all_neural(463;0.228)					TAATGCTGTCGGGGCATCGCA	0.443													G|||	14	0.00279553	0.0038	0.0043	5008	,	,		21102	0.0		0.004	False		,,,				2504	0.002				p.G455R		Atlas-SNP	.											.	LRRC48	49	.	0			c.G1363A						PASS	.	G	ARG/GLY,ARG/GLY	28,3894		0,28,1933	153.0	145.0	147.0		1363,1363	5.5	0.9	17		147	67,8235		0,67,4084	yes	missense,missense	LRRC48	NM_001130090.1,NM_031294.3	125,125	0,95,6017	AA,AG,GG		0.807,0.7139,0.7772	,	455/524,455/524	17919414	95,12129	1961	4151	6112	SO:0001583	missense	83450	exon13			GCTGTCGGGGCAT	AK093317	CCDS45622.1, CCDS45623.1	17p11.2	2014-07-18			ENSG00000171962	ENSG00000171962			25384	protein-coding gene	gene with protein product						11997338, 23354437	Standard	NM_001130090		Approved	DKFZP586M1120	uc021trk.1	Q9H069	OTTHUMG00000059355	ENST00000399187.1:c.1363G>A	17.37:g.17919414G>A	ENSP00000382140:p.Gly455Arg	59.0	0.0	0		100.0	41.0	0.41	NM_031294	A8KAE6|Q86SF9|Q86W73|Q8IWG0	Missense_Mutation	SNP	ENST00000399187.1	37	CCDS45622.1	4	0.0018315018315018315	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	0	0.0	G	20.0	3.931107	0.73327	0.007139	0.00807	ENSG00000171962	ENST00000313838;ENST00000448396;ENST00000399187;ENST00000399185	T;T	0.52526	0.66;0.66	5.47	5.47	0.80525	.	0.412797	0.28724	N	0.014349	T	0.47581	0.1453	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	P	0.55871	0.786	T	0.53380	-0.8447	10	0.45353	T	0.12	-51.1913	8.5414	0.33395	0.1643:0.0:0.8357:0.0	.	455	Q9H069	LRC48_HUMAN	R	455	ENSP00000326870:G455R;ENSP00000382140:G455R	ENSP00000326870:G455R	G	+	1	0	LRRC48	17860139	0.998000	0.40836	0.932000	0.37286	0.749000	0.42624	3.102000	0.50291	2.557000	0.86248	0.563000	0.77884	GGG	G|0.997;A|0.003	0.003	strong		0.443	LRRC48-001	KNOWN	non_canonical_conserved|non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131945.3	NM_031294	
SLC25A40	55972	hgsc.bcm.edu	37	7	87483585	87483585	+	Silent	SNP	T	T	A	rs150511221	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87483585T>A	ENST00000341119.5	-	5	544	c.198A>T	c.(196-198)ctA>ctT	p.L66L		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	66					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					CACAGACACATAGATGATCCA	0.343													T|||	36	0.0071885	0.0015	0.0375	5008	,	,		16226	0.0		0.005	False		,,,				2504	0.0031				p.L66L		Atlas-SNP	.											.	SLC25A40	32	.	0			c.A198T						PASS	.	T		7,4399	14.3+/-33.2	0,7,2196	161.0	150.0	154.0		198	-7.1	0.1	7	dbSNP_134	154	106,8494	56.8+/-118.0	0,106,4194	no	coding-synonymous	SLC25A40	NM_018843.3		0,113,6390	AA,AT,TT		1.2326,0.1589,0.8688		66/339	87483585	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	55972	exon5			GACACATAGATGA	AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"""Solute carriers"""	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.198A>T	7.37:g.87483585T>A		101.0	0.0	0		83.0	32.0	0.385542	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Silent	SNP	ENST00000341119.5	37	CCDS5610.1																																																																																			T|0.994;A|0.006	0.006	strong		0.343	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843	
CDKL5	6792	hgsc.bcm.edu	37	X	18664128	18664128	+	Splice_Site	SNP	C	C	T	rs201714912		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:18664128C>T	ENST00000379989.3	+	20	3000	c.2715C>T	c.(2713-2715)gaC>gaT	p.D905D	CDKL5_ENST00000379996.3_Splice_Site_p.D905D|RS1_ENST00000379984.3_Intron|RS1_ENST00000476595.1_Intron	NM_001037343.1	NP_001032420.1	O76039	CDKL5_HUMAN	cyclin-dependent kinase-like 5	905					neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of Rac GTPase activity (GO:0032855)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of dendrite development (GO:0050773)	cytoplasm (GO:0005737)|dendrite cytoplasm (GO:0032839)|dendritic growth cone (GO:0044294)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)	p.D905D(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(12)|ovary(4)|skin(5)|stomach(1)	44	Hepatocellular(33;0.183)					actaactagacggtggatgtg	0.493													A|||	1	0.000264901	0.0	0.0	3775	,	,		14324	0.0		0.001	False		,,,				2504	0.0				p.D905D		Atlas-SNP	.											.	CDKL5	124	.	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C2715T						PASS	.	A	,,	1,3834		0,1,1631,571	140.0	112.0	122.0		,2715,2715	0.6	0.1	X		122	0,6728		0,0,2428,1872	no	intron,coding-synonymous-near-splice,coding-synonymous-near-splice	RS1,CDKL5	NM_000330.3,NM_001037343.1,NM_003159.2	,,	0,1,4059,2443	TT,TC,CC,C		0.0,0.0261,0.0095	,,	,905/1031,905/1031	18664128	1,10562	2203	4300	6503	SO:0001630	splice_region_variant	6792	exon19			ACTAGACGGTGGA	Y15057	CCDS14186.1	Xp22	2011-11-04	2002-11-26	2002-11-29	ENSG00000008086	ENSG00000008086		"""Cyclin-dependent kinases"""	11411	protein-coding gene	gene with protein product		300203	"""serine/threonine kinase 9"""	STK9		9721213, 16935860	Standard	XM_005274584		Approved	EIEE2	uc004cym.3	O76039	OTTHUMG00000021214	ENST00000379989.3:c.2714-1C>T	X.37:g.18664128C>T		39.0	0.0	0		49.0	5.0	0.102041	NM_003159	G9B9X4|Q14198|Q5H985|Q8IYC7|Q9UJL6	Silent	SNP	ENST00000379989.3	37	CCDS14186.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	CDKL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055945.2	NM_003159	Silent
STARD3	10948	hgsc.bcm.edu	37	17	37815305	37815305	+	Splice_Site	SNP	G	G	A	rs144713925		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37815305G>A	ENST00000336308.5	+	8	866	c.648G>A	c.(646-648)ggG>ggA	p.G216G	STARD3_ENST00000578232.1_3'UTR|STARD3_ENST00000394250.4_Splice_Site_p.G198G|STARD3_ENST00000580611.1_Splice_Site_p.G190G|STARD3_ENST00000544210.2_Splice_Site_p.G216G	NM_001165937.1|NM_006804.3	NP_001159409.1|NP_006795.3	Q14849	STAR3_HUMAN	StAR-related lipid transfer (START) domain containing 3	216	MENTAL. {ECO:0000255|PROSITE- ProRule:PRU00770}.		G -> A (in dbSNP:rs11556624). {ECO:0000269|PubMed:15489334}.		cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|mitochondrial transport (GO:0006839)|progesterone biosynthetic process (GO:0006701)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	cholesterol binding (GO:0015485)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|pancreas(1)|prostate(2)|stomach(1)	14	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			TTTCTGCAGGGTCTGACAATG	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		16693	0.0		0.0	False		,,,				2504	0.0				p.G216G		Atlas-SNP	.											.	STARD3	33	.	0			c.G648A						PASS	.	G	,,	1,4405		0,1,2202	221.0	216.0	218.0		648,594,648	2.7	1.0	17	dbSNP_134	218	10,8590	3.7+/-12.6	0,10,4290	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	STARD3	NM_001165937.1,NM_001165938.1,NM_006804.3	,,	0,11,6492	AA,AG,GG		0.1163,0.0227,0.0846	,,	216/446,198/428,216/446	37815305	11,12995	2203	4300	6503	SO:0001630	splice_region_variant	10948	exon8			TGCAGGGTCTGAC		CCDS11341.1, CCDS54117.1, CCDS54118.1	17q11-q12	2011-09-12	2007-08-16		ENSG00000131748	ENSG00000131748		"""StAR-related lipid transfer (START) domain containing"""	17579	protein-coding gene	gene with protein product		607048	"""START domain containing 3"""				Standard	NM_006804		Approved	es64, MLN64	uc002hsd.3	Q14849	OTTHUMG00000133213	ENST00000336308.5:c.647-1G>A	17.37:g.37815305G>A		220.0	0.0	0		203.0	92.0	0.453202	NM_006804	A8MXA4|B4DUY1|F5H0G2|Q53Y53|Q96HM9	Silent	SNP	ENST00000336308.5	37	CCDS11341.1																																																																																			G|0.999;A|0.001	0.001	strong		0.527	STARD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256933.1		Silent
DNAJC17	55192	hgsc.bcm.edu	37	15	41068771	41068771	+	Missense_Mutation	SNP	T	T	G	rs79709714	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:41068771T>G	ENST00000220496.4	-	5	380	c.350A>C	c.(349-351)gAg>gCg	p.E117A		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	117	Poly-Glu.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		GCTCCGGCTCTCCTCTTCCTC	0.622													T|||	42	0.00838658	0.0	0.0173	5008	,	,		14514	0.0		0.0258	False		,,,				2504	0.0041				p.E117A		Atlas-SNP	.											.	DNAJC17	18	.	0			c.A350C						PASS	.	T	ALA/GLU	26,4380	34.3+/-65.2	1,24,2178	156.0	128.0	138.0		350	4.5	1.0	15	dbSNP_131	138	239,8361	95.9+/-157.7	1,237,4062	yes	missense	DNAJC17	NM_018163.2	107	2,261,6240	GG,GT,TT		2.7791,0.5901,2.0375	benign	117/305	41068771	265,12741	2203	4300	6503	SO:0001583	missense	55192	exon5			CGGCTCTCCTCTT	AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"""Heat shock proteins / DNAJ (HSP40)"", ""RNA binding motif (RRM) containing"""	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.350A>C	15.37:g.41068771T>G	ENSP00000220496:p.Glu117Ala	114.0	0.0	0		69.0	57.0	0.826087	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	30	0.013736263736263736	0	0.0	6	0.016574585635359115	0	0.0	24	0.0316622691292876	T	10.51	1.369675	0.24771	0.005901	0.027791	ENSG00000104129	ENST00000220496	T	0.21191	2.02	4.46	4.46	0.54185	.	0.262954	0.42548	D	0.000681	T	0.06096	0.0158	L	0.55481	1.735	0.39777	D	0.972244	B	0.12630	0.006	B	0.10450	0.005	T	0.05550	-1.0878	10	0.10377	T	0.69	.	10.0697	0.42325	0.0:0.0:0.0:1.0	.	117	Q9NVM6	DJC17_HUMAN	A	117	ENSP00000220496:E117A	ENSP00000220496:E117A	E	-	2	0	DNAJC17	38856063	1.000000	0.71417	0.964000	0.40570	0.954000	0.61252	6.100000	0.71473	1.889000	0.54706	0.459000	0.35465	GAG	T|0.984;G|0.016	0.016	strong		0.622	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163	
ALPK3	57538	hgsc.bcm.edu	37	15	85382307	85382307	+	Missense_Mutation	SNP	G	G	A	rs34407151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:85382307G>A	ENST00000258888.5	+	4	1174	c.1007G>A	c.(1006-1008)cGc>cAc	p.R336H		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	336	Ig-like 1.		R -> H (in dbSNP:rs34407151). {ECO:0000269|PubMed:17344846}.		heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			CAGGGCAACCGCCACACACTG	0.582													G|||	27	0.00539137	0.0015	0.0058	5008	,	,		16839	0.0		0.0129	False		,,,				2504	0.0082				p.R336H		Atlas-SNP	.											.	ALPK3	289	.	0			c.G1007A						PASS	.	G	HIS/ARG	17,4389	22.3+/-47.3	0,17,2186	49.0	39.0	42.0		1007	4.9	1.0	15	dbSNP_126	42	120,8478	62.4+/-124.4	1,118,4180	yes	missense	ALPK3	NM_020778.4	29	1,135,6366	AA,AG,GG		1.3957,0.3858,1.0535	probably-damaging	336/1908	85382307	137,12867	2203	4299	6502	SO:0001583	missense	57538	exon4			GCAACCGCCACAC	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.1007G>A	15.37:g.85382307G>A	ENSP00000258888:p.Arg336His	73.0	0.0	0		103.0	45.0	0.436893	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	15	0.006868131868131868	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	18.96	3.732990	0.69189	0.003858	0.013957	ENSG00000136383	ENST00000258888	T	0.68025	-0.3	4.89	4.89	0.63831	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.308968	0.31438	N	0.007658	T	0.68513	0.3009	L	0.45228	1.405	0.32666	N	0.517502	D	0.89917	1.0	D	0.67231	0.95	T	0.78770	-0.2074	10	0.56958	D	0.05	-8.4768	15.5548	0.76184	0.0:0.0:1.0:0.0	rs34407151	336	Q96L96	ALPK3_HUMAN	H	336	ENSP00000258888:R336H	ENSP00000258888:R336H	R	+	2	0	ALPK3	83183311	0.443000	0.25641	0.990000	0.47175	0.998000	0.95712	2.146000	0.42216	2.266000	0.75297	0.491000	0.48974	CGC	G|0.990;A|0.010	0.010	strong		0.582	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
ZNF521	25925	hgsc.bcm.edu	37	18	22805218	22805218	+	Silent	SNP	G	G	A	rs35535552	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:22805218G>A	ENST00000361524.3	-	4	2812	c.2664C>T	c.(2662-2664)tgC>tgT	p.C888C	ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000538137.2_Silent_p.C888C|ZNF521_ENST00000584787.1_Silent_p.C668C	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	888					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					CACAAATGTCGCAGCCGTACA	0.522			T	PAX5	ALL								g|||	10	0.00199681	0.0	0.0072	5008	,	,		19940	0.0		0.004	False		,,,				2504	0.001				p.C888C		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,caecum,carcinoma,0,1	ZNF521	269	1	0			c.C2664T						scavenged	.	A		4,4402	8.1+/-20.4	0,4,2199	121.0	113.0	115.0		2664	-11.7	0.0	18	dbSNP_126	115	42,8558	27.9+/-77.7	0,42,4258	no	coding-synonymous	ZNF521	NM_015461.2		0,46,6457	AA,AG,GG		0.4884,0.0908,0.3537		888/1312	22805218	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			AATGTCGCAGCCG	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2664C>T	18.37:g.22805218G>A		192.0	1.0	0.00520833		285.0	128.0	0.449123	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			G|0.995;A|0.005	0.005	strong		0.522	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
ISX	91464	hgsc.bcm.edu	37	22	35478529	35478529	+	Missense_Mutation	SNP	G	G	A	rs8140287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:35478529G>A	ENST00000308700.6	+	2	1200	c.248G>A	c.(247-249)cGg>cAg	p.R83Q	ISX_ENST00000404699.2_Missense_Mutation_p.R83Q	NM_001008494.1	NP_001008494.1	Q2M1V0	ISX_HUMAN	intestine-specific homeobox	83			R -> Q (in dbSNP:rs8140287).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin A metabolic process (GO:1901738)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(12)|ovary(3)|prostate(1)|skin(4)	26						AAGAGCAAGCGGAGGGTTCGT	0.557													G|||	154	0.0307508	0.0023	0.0317	5008	,	,		20015	0.003		0.0557	False		,,,				2504	0.0716				p.R83Q		Atlas-SNP	.											.	ISX	62	.	0			c.G248A						PASS	.	G	GLN/ARG	51,4355	52.9+/-88.7	0,51,2152	142.0	115.0	124.0		248	4.9	0.7	22	dbSNP_116	124	462,8138	137.6+/-194.5	13,436,3851	yes	missense	ISX	NM_001008494.1	43	13,487,6003	AA,AG,GG		5.3721,1.1575,3.9443	probably-damaging	83/246	35478529	513,12493	2203	4300	6503	SO:0001583	missense	91464	exon2			GCAAGCGGAGGGT	AK025181	CCDS33640.1	22q12.3	2011-06-20			ENSG00000175329	ENSG00000175329		"""Homeoboxes / PRD class"""	28084	protein-coding gene	gene with protein product		612019					Standard	NM_001008494		Approved	RAXLX	uc003anj.3	Q2M1V0	OTTHUMG00000150962	ENST00000308700.6:c.248G>A	22.37:g.35478529G>A	ENSP00000311492:p.Arg83Gln	42.0	0.0	0		81.0	45.0	0.555556	NM_001008494	Q68DJ5	Missense_Mutation	SNP	ENST00000308700.6	37	CCDS33640.1	56	0.02564102564102564	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	47	0.06200527704485488	G	28.4	4.916181	0.92249	0.011575	0.053721	ENSG00000175329	ENST00000308700;ENST00000404699	D;D	0.97209	-4.29;-4.29	4.94	4.94	0.65067	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.47852	D	0.000205	D	0.91878	0.7429	M	0.93898	3.47	0.54753	D	0.99998	D	0.89917	1.0	D	0.91635	0.999	D	0.85305	0.1075	10	0.40728	T	0.16	.	15.6832	0.77388	0.0:0.0:1.0:0.0	rs8140287;rs52820185;rs8140287	83	Q2M1V0	ISX_HUMAN	Q	83	ENSP00000311492:R83Q;ENSP00000386037:R83Q	ENSP00000311492:R83Q	R	+	2	0	ISX	33808529	1.000000	0.71417	0.702000	0.30337	0.788000	0.44548	8.758000	0.91663	2.545000	0.85829	0.650000	0.86243	CGG	G|0.965;A|0.035	0.035	strong		0.557	ISX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320662.1	NM_001008494	
SLC4A7	9497	hgsc.bcm.edu	37	3	27436597	27436597	+	Missense_Mutation	SNP	G	G	A	rs114662202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:27436597G>A	ENST00000295736.5	-	19	2756	c.2686C>T	c.(2686-2688)Cca>Tca	p.P896S	SLC4A7_ENST00000437179.1_Missense_Mutation_p.P777S|SLC4A7_ENST00000455077.1_Missense_Mutation_p.P777S|SLC4A7_ENST00000446700.1_Missense_Mutation_p.P888S|SLC4A7_ENST00000388777.4_Missense_Mutation_p.P446S|SLC4A7_ENST00000428386.1_Missense_Mutation_p.P772S|SLC4A7_ENST00000454389.1_Missense_Mutation_p.P905S|SLC4A7_ENST00000435667.2_Missense_Mutation_p.P781S|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000445684.1_Missense_Mutation_p.P892S|SLC4A7_ENST00000440156.1_Missense_Mutation_p.P892S	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	896					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	CCTCTCTCTGGATGAGTAGGC	0.358													G|||	35	0.00698882	0.0106	0.0086	5008	,	,		17732	0.0		0.0129	False		,,,				2504	0.002				p.P896S		Atlas-SNP	.											SLC4A7,rectum,carcinoma,+2,4	SLC4A7	119	4	0			c.C2686T						scavenged	.	G	SER/PRO	50,4356	51.6+/-87.1	0,50,2153	60.0	59.0	59.0		2686	3.0	1.0	3	dbSNP_132	59	144,8456	66.7+/-129.0	2,140,4158	yes	missense	SLC4A7	NM_003615.3	74	2,190,6311	AA,AG,GG		1.6744,1.1348,1.4916	benign	896/1215	27436597	194,12812	2203	4300	6503	SO:0001583	missense	9497	exon19			TCTCTGGATGAGT	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2686C>T	3.37:g.27436597G>A	ENSP00000295736:p.Pro896Ser	179.0	1.0	0.00558659		154.0	64.0	0.415584	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	13	0.005952380952380952	4	0.008130081300813009	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	10.88	1.475427	0.26511	0.011348	0.016744	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	T;T;T;T;T;T;T;T;T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19;-1.19	6.06	2.95	0.34219	Bicarbonate transporter, C-terminal (1);	0.308279	0.38217	N	0.001764	T	0.49406	0.1555	N	0.25890	0.77	0.80722	D	1	B;B;B;B;B;B;B;B;B	0.19445	0.033;0.033;0.014;0.036;0.033;0.005;0.026;0.033;0.033	B;B;B;B;B;B;B;B;B	0.29176	0.099;0.04;0.04;0.099;0.099;0.015;0.06;0.099;0.04	T	0.53556	-0.8422	10	0.36615	T	0.2	.	9.3212	0.37966	0.0:0.1003:0.3472:0.5525	.	892;777;888;892;905;446;772;896;777	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	S	447;896;772;905;892;777;888;777;892;781;446;792	ENSP00000411031:P447S;ENSP00000295736:P896S;ENSP00000416368:P772S;ENSP00000390394:P905S;ENSP00000414797:P892S;ENSP00000394252:P777S;ENSP00000406605:P888S;ENSP00000407382:P777S;ENSP00000406804:P892S;ENSP00000395336:P781S;ENSP00000373429:P446S;ENSP00000388703:P792S	ENSP00000295736:P896S	P	-	1	0	SLC4A7	27411601	1.000000	0.71417	0.992000	0.48379	0.649000	0.38597	1.998000	0.40796	0.842000	0.35045	0.655000	0.94253	CCA	G|0.988;A|0.012	0.012	strong		0.358	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
MUC16	94025	hgsc.bcm.edu	37	19	9074697	9074697	+	Missense_Mutation	SNP	G	G	A	rs202216364		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9074697G>A	ENST00000397910.4	-	3	12952	c.12749C>T	c.(12748-12750)aCg>aTg	p.T4250M		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	4252	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						CTCCATATTCGTCACTGCTGT	0.478													G|||	1	0.000199681	0.0008	0.0	5008	,	,		24112	0.0		0.0	False		,,,				2504	0.0				p.T4250M		Atlas-SNP	.											.	MUC16	4315	.	0			c.C12749T						PASS	.	G	MET/THR	2,4014		0,2,2006	116.0	113.0	114.0		12749	1.6	0.0	19		114	11,8319		0,11,4154	yes	missense	MUC16	NM_024690.2	81	0,13,6160	AA,AG,GG		0.1321,0.0498,0.1053	probably-damaging	4250/14508	9074697	13,12333	2008	4165	6173	SO:0001583	missense	94025	exon3			ATATTCGTCACTG	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.12749C>T	19.37:g.9074697G>A	ENSP00000381008:p.Thr4250Met	136.0	0.0	0		157.0	70.0	0.44586	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	g	3.052	-0.195075	0.06259	4.98E-4	0.001321	ENSG00000181143	ENST00000397910	T	0.33654	1.4	1.63	1.63	0.23807	.	.	.	.	.	T	0.43809	0.1264	L	0.48642	1.525	.	.	.	D	0.89917	1.0	P	0.61070	0.883	T	0.54430	-0.8295	8	0.87932	D	0	.	6.6867	0.23148	0.0:0.0:1.0:0.0	.	4250	B5ME49	.	M	4250	ENSP00000381008:T4250M	ENSP00000381008:T4250M	T	-	2	0	MUC16	8935697	0.000000	0.05858	0.002000	0.10522	0.043000	0.13939	0.138000	0.16016	1.205000	0.43262	0.205000	0.17691	ACG	.	.	weak		0.478	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CC2D1A	54862	hgsc.bcm.edu	37	19	14040420	14040420	+	Missense_Mutation	SNP	G	G	A	rs201921029		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14040420G>A	ENST00000318003.7	+	26	2898	c.2657G>A	c.(2656-2658)cGc>cAc	p.R886H	CC2D1A_ENST00000589606.1_Missense_Mutation_p.R885H	NM_017721.4	NP_060191.3	Q6P1N0	C2D1A_HUMAN	coiled-coil and C2 domain containing 1A	886					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	27			OV - Ovarian serous cystadenocarcinoma(19;3.49e-23)			ATCATGCAACGCAGCCAGTGG	0.657																																					p.R886H		Atlas-SNP	.											.	CC2D1A	67	.	0			c.G2657A						PASS	.	G	HIS/ARG	1,4027		0,1,2013	10.0	14.0	12.0		2657	2.3	1.0	19		12	11,8333		0,11,4161	yes	missense	CC2D1A	NM_017721.4	29	0,12,6174	AA,AG,GG		0.1318,0.0248,0.097	benign	886/952	14040420	12,12360	2014	4172	6186	SO:0001583	missense	54862	exon26			TGCAACGCAGCCA	AF536205	CCDS42512.1	19p13.12	2007-01-08				ENSG00000132024			30237	protein-coding gene	gene with protein product	"""mental retardation, nonsyndromic, autosomal recessive, 3"""	610055				12761501, 16033914	Standard	NM_017721		Approved	FLJ20241, MRT3	uc002mxo.2	Q6P1N0		ENST00000318003.7:c.2657G>A	19.37:g.14040420G>A	ENSP00000313601:p.Arg886His	79.0	0.0	0		98.0	51.0	0.520408	NM_017721	Q7Z435|Q86XV0|Q8NF89|Q9H603|Q9NXI1	Missense_Mutation	SNP	ENST00000318003.7	37	CCDS42512.1	.	.	.	.	.	.	.	.	.	.	G	12.67	2.008455	0.35415	2.48E-4	0.001318	ENSG00000132024	ENST00000318003;ENST00000254346	T	0.20738	2.05	4.89	2.33	0.28932	.	0.066900	0.56097	D	0.000037	T	0.11879	0.0289	L	0.29908	0.895	0.41298	D	0.987024	B;B;B	0.29232	0.088;0.017;0.238	B;B;B	0.18561	0.015;0.005;0.022	T	0.10636	-1.0621	10	0.49607	T	0.09	-17.143	5.6295	0.17501	0.0919:0.1409:0.6232:0.144	.	507;885;886	Q9NX28;Q6P1N0-2;Q6P1N0	.;.;C2D1A_HUMAN	H	886;508	ENSP00000313601:R886H	ENSP00000254346:R508H	R	+	2	0	CC2D1A	13901420	1.000000	0.71417	1.000000	0.80357	0.679000	0.39708	3.033000	0.49743	1.044000	0.40200	-0.440000	0.05779	CGC	.	.	weak		0.657	CC2D1A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457954.1	NM_017721	
FREM2	341640	hgsc.bcm.edu	37	13	39263218	39263218	+	Silent	SNP	C	C	T	rs144811771		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:39263218C>T	ENST00000280481.7	+	1	1953	c.1737C>T	c.(1735-1737)atC>atT	p.I579I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	579					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CAGTGCCCATCCTGCCCCTTT	0.532																																					p.I579I		Atlas-SNP	.											.	FREM2	385	.	0			c.C1737T						PASS	.	C		0,4406		0,0,2203	126.0	122.0	123.0		1737	3.5	1.0	13	dbSNP_134	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FREM2	NM_207361.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		579/3170	39263218	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GCCCATCCTGCCC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1737C>T	13.37:g.39263218C>T		51.0	0.0	0		18.0	17.0	0.944444	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|1.000;T|0.000	0.000	weak		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ZNF486	90649	hgsc.bcm.edu	37	19	20308488	20308488	+	Silent	SNP	G	G	T	rs181719180	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:20308488G>T	ENST00000335117.8	+	4	1026	c.969G>T	c.(967-969)acG>acT	p.T323T	CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	323					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						AACCGTACACGTGTGATAAAT	0.388													G|||	17	0.00339457	0.0	0.0058	5008	,	,		21939	0.0		0.0109	False		,,,				2504	0.002				p.T323T		Atlas-SNP	.											ZNF486_ENST00000335117,NS,carcinoma,+1,4	ZNF486	74	4	0			c.G969T						PASS	.	G		6,4348		0,6,2171	47.0	52.0	50.0		969	-1.7	0.1	19		50	53,8525		0,53,4236	no	coding-synonymous	ZNF486	NM_052852.2		0,59,6407	TT,TG,GG		0.6179,0.1378,0.4562		323/464	20308488	59,12873	2177	4289	6466	SO:0001819	synonymous_variant	90649	exon4			GTACACGTGTGAT	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.969G>T	19.37:g.20308488G>T		25.0	0.0	0		24.0	9.0	0.375	NM_052852	Q0VG00	Silent	SNP	ENST00000335117.8	37	CCDS46029.1																																																																																			G|0.995;T|0.005	0.005	strong		0.388	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
ATG4C	84938	hgsc.bcm.edu	37	1	63299751	63299751	+	Missense_Mutation	SNP	A	A	C	rs146422144	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:63299751A>C	ENST00000317868.4	+	8	1183	c.976A>C	c.(976-978)Aaa>Caa	p.K326Q	ATG4C_ENST00000371120.3_Missense_Mutation_p.K326Q	NM_032852.3	NP_116241.2	Q96DT6	ATG4C_HUMAN	autophagy related 4C, cysteine peptidase	326					autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|protein targeting to membrane (GO:0006612)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)	cysteine-type endopeptidase activity (GO:0004197)|peptidase activity (GO:0008233)		ATG4C/FBXO38(2)	NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(3)|ovary(1)|prostate(2)	19						TATTGGTGGCAAACCTAAACA	0.299													A|||	5	0.000998403	0.0	0.0014	5008	,	,		17562	0.0		0.004	False		,,,				2504	0.0				p.K326Q		Atlas-SNP	.											.	ATG4C	96	.	0			c.A976C						PASS	.	A	GLN/LYS,GLN/LYS	4,4402	8.1+/-20.4	0,4,2199	186.0	196.0	193.0		976,976	6.0	1.0	1	dbSNP_134	193	21,8579	14.6+/-50.1	0,21,4279	yes	missense,missense	ATG4C	NM_032852.3,NM_178221.2	53,53	0,25,6478	CC,CA,AA		0.2442,0.0908,0.1922	probably-damaging,probably-damaging	326/459,326/459	63299751	25,12981	2203	4300	6503	SO:0001583	missense	84938	exon8			GGTGGCAAACCTA	AK027773	CCDS623.1	1p31.3	2014-02-12	2012-06-06	2005-09-11	ENSG00000125703	ENSG00000125703			16040	protein-coding gene	gene with protein product		611339	"""AUT (S. cerevisiae)-like 1, cysteine endopeptidase; AUT-like 1, cysteine endopeptidase (S. cerevisiae)"", ""APG4 autophagy 4 homolog C (S. cerevisiae)"", ""ATG4 autophagy related 4 homolog C (S. cerevisiae)"""	AUTL1, APG4C		12446702	Standard	NM_032852		Approved	FLJ14867, AUTL3	uc001dau.3	Q96DT6	OTTHUMG00000009142	ENST00000317868.4:c.976A>C	1.37:g.63299751A>C	ENSP00000322159:p.Lys326Gln	95.0	0.0	0		94.0	43.0	0.457447	NM_178221	A6NLR8|D3DQ58|Q96K04	Missense_Mutation	SNP	ENST00000317868.4	37	CCDS623.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	21.5	4.159289	0.78226	9.08E-4	0.002442	ENSG00000125703	ENST00000317868;ENST00000371120;ENST00000540025;ENST00000414558	T;T	0.48836	0.8;0.8	5.97	5.97	0.96955	.	0.042802	0.85682	D	0.000000	T	0.67683	0.2919	M	0.87547	2.89	0.80722	D	1	D	0.67145	0.996	D	0.70716	0.97	T	0.74562	-0.3624	10	0.72032	D	0.01	-20.3301	16.4534	0.84003	1.0:0.0:0.0:0.0	.	326	Q96DT6	ATG4C_HUMAN	Q	326;326;326;70	ENSP00000322159:K326Q;ENSP00000360161:K326Q	ENSP00000322159:K326Q	K	+	1	0	ATG4C	63072339	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.962000	0.93254	2.285000	0.76669	0.477000	0.44152	AAA	A|0.998;C|0.002	0.002	strong		0.299	ATG4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025332.2	NM_032852	
TMTC1	83857	hgsc.bcm.edu	37	12	29671406	29671406	+	Splice_Site	SNP	G	G	A	rs192684476		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:29671406G>A	ENST00000539277.1	-	13	2081	c.2023C>T	c.(2023-2025)Cgc>Tgc	p.R675C	TMTC1_ENST00000319685.8_5'UTR|TMTC1_ENST00000256062.5_Splice_Site_p.R567C|TMTC1_ENST00000551659.1_Splice_Site_p.R737C|TMTC1_ENST00000552618.1_Splice_Site_p.R699C|RP11-310I24.1_ENST00000549070.1_RNA	NM_001193451.1	NP_001180380.1	Q8IUR5	TMTC1_HUMAN	transmembrane and tetratricopeptide repeat containing 1	675						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)				breast(1)|endometrium(4)|kidney(3)|large_intestine(17)|lung(45)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Lung NSC(12;7.61e-10)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.032)					GAACTTTACCGCTTGTACCAT	0.458													G|||	1	0.000199681	0.0	0.0	5008	,	,		18068	0.001		0.0	False		,,,				2504	0.0				p.R675C		Atlas-SNP	.											.	TMTC1	147	.	0			c.C2023T						PASS	.						170.0	155.0	160.0					12																	29671406		2203	4300	6503	SO:0001630	splice_region_variant	83857	exon13			TTTACCGCTTGTA		CCDS8718.1, CCDS53772.1	12p11.22	2014-06-09	2006-01-06			ENSG00000133687		"""Tetratricopeptide (TTC) repeat domain containing"""	24099	protein-coding gene	gene with protein product		615855				24764305	Standard	NM_001193451		Approved	ARG99, OLF, FLJ31400, FLJ41625	uc021qwi.1	Q8IUR5	OTTHUMG00000169324	ENST00000539277.1:c.2024+1C>T	12.37:g.29671406G>A		172.0	0.0	0		204.0	88.0	0.431373	NM_001193451	D0EP37|F5H8B5|Q6PIU4|Q6ZSM5|Q96N52|Q9BXM2	Missense_Mutation	SNP	ENST00000539277.1	37	CCDS53772.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.48	3.135053	0.56828	.	.	ENSG00000133687	ENST00000540901;ENST00000256062;ENST00000551659;ENST00000552618;ENST00000539277	T;T;T;T	0.59638	0.25;0.25;0.46;0.25	4.79	3.89	0.44902	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.059624	0.64402	D	0.000007	T	0.80287	0.4595	H	0.94620	3.56	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.81914	0.995;0.993	D	0.84100	0.0395	9	.	.	.	-18.2441	10.3987	0.44216	0.0:0.0:0.6447:0.3553	.	675;737	Q8IUR5;F8VTQ9	TMTC1_HUMAN;.	C	438;567;737;699;675	ENSP00000256062:R567C;ENSP00000448112:R737C;ENSP00000449043:R699C;ENSP00000442046:R675C	.	R	-	1	0	TMTC1	29562673	1.000000	0.71417	1.000000	0.80357	0.602000	0.36980	1.784000	0.38674	1.370000	0.46153	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.458	TMTC1-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403509.1	NM_031920	Missense_Mutation
EPHA2	1969	hgsc.bcm.edu	37	1	16456763	16456763	+	Missense_Mutation	SNP	C	C	T	rs35903225	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:16456763C>T	ENST00000358432.5	-	15	2781	c.2627G>A	c.(2626-2628)cGt>cAt	p.R876H		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	876	Mediates interaction with ARHGEF16 and ELMO2.		R -> H (in dbSNP:rs35903225). {ECO:0000269|PubMed:17344846}.		activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	GTCAGGGGCACGAATGAGCTT	0.582													C|||	39	0.00778754	0.0015	0.0144	5008	,	,		17836	0.002		0.0239	False		,,,				2504	0.001				p.R876H		Atlas-SNP	.											.	EPHA2	102	.	0			c.G2627A						PASS	.	C	HIS/ARG	34,4372	39.2+/-71.8	0,34,2169	99.0	93.0	95.0		2627	5.6	1.0	1	dbSNP_126	95	220,8380	92.8+/-154.8	0,220,4080	yes	missense	EPHA2	NM_004431.3	29	0,254,6249	TT,TC,CC		2.5581,0.7717,1.9529	probably-damaging	876/977	16456763	254,12752	2203	4300	6503	SO:0001583	missense	1969	exon15			GGGGCACGAATGA	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.2627G>A	1.37:g.16456763C>T	ENSP00000351209:p.Arg876His	253.0	0.0	0		309.0	148.0	0.478964	NM_004431	B5A968|Q8N3Z2	Missense_Mutation	SNP	ENST00000358432.5	37	CCDS169.1	23	0.010531135531135532	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	29.2	4.986612	0.93106	0.007717	0.025581	ENSG00000142627	ENST00000358432	T	0.62364	0.03	5.63	5.63	0.86233	Protein kinase-like domain (1);	0.000000	0.49305	D	0.000155	T	0.56775	0.2008	M	0.84326	2.69	0.80722	D	1	D	0.76494	0.999	P	0.55112	0.769	T	0.74671	-0.3587	10	0.87932	D	0	.	18.2443	0.89979	0.0:1.0:0.0:0.0	rs35903225;rs61731099	876	P29317	EPHA2_HUMAN	H	876	ENSP00000351209:R876H	ENSP00000351209:R876H	R	-	2	0	EPHA2	16329350	1.000000	0.71417	0.962000	0.40283	0.926000	0.56050	4.709000	0.61867	2.670000	0.90874	0.655000	0.94253	CGT	C|0.983;T|0.017	0.017	strong		0.582	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
MUC21	394263	hgsc.bcm.edu	37	6	30954552	30954552	+	Silent	SNP	C	C	T	rs144720609		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954552C>T	ENST00000376296.3	+	2	841	c.600C>T	c.(598-600)tcC>tcT	p.S200S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	200	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACTCTGAGTCCAGCACAACCT	0.607																																					p.S200S		Atlas-SNP	.											.	MUC21	98	.	0			c.C600T						PASS	.						163.0	157.0	159.0					6																	30954552		2203	4300	6503	SO:0001819	synonymous_variant	394263	exon2			TGAGTCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.600C>T	6.37:g.30954552C>T		88.0	0.0	0		135.0	12.0	0.0888889	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.999;T|0.001	0.001	weak		0.607	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
DCAF10	79269	hgsc.bcm.edu	37	9	37861380	37861380	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:37861380C>T	ENST00000377724.3	+	7	1920	c.1555C>T	c.(1555-1557)Cgg>Tgg	p.R519W	DCAF10_ENST00000242323.7_Missense_Mutation_p.R482W|RP11-613M10.9_ENST00000540557.1_Intron|DCAF10_ENST00000483167.1_3'UTR	NM_024345.3	NP_077321.3	Q5QP82	DCA10_HUMAN	DDB1 and CUL4 associated factor 10	519					protein ubiquitination (GO:0016567)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)				central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|skin(1)	12						CAGTCCCCTGCGGGTGATCCG	0.483																																					p.R519W		Atlas-SNP	.											DCAF10,NS,carcinoma,0,1	DCAF10	31	1	0			c.C1555T						PASS	.						103.0	97.0	99.0					9																	37861380		2203	4300	6503	SO:0001583	missense	79269	exon7			CCCCTGCGGGTGA	BC003520	CCDS6613.2, CCDS75835.1	9p13.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000122741	ENSG00000122741		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	23686	protein-coding gene	gene with protein product			"""WD repeat domain 32"""	WDR32			Standard	NM_001286810		Approved	MGC10765, FLJ23201	uc004aao.3	Q5QP82	OTTHUMG00000019934	ENST00000377724.3:c.1555C>T	9.37:g.37861380C>T	ENSP00000366953:p.Arg519Trp	202.0	0.0	0		236.0	107.0	0.45339	NM_024345	A4VCJ5|Q32NE2|Q8N2Q5|Q96ET5|Q9BTQ5|Q9H5P6	Missense_Mutation	SNP	ENST00000377724.3	37	CCDS6613.2	.	.	.	.	.	.	.	.	.	.	C	18.69	3.677247	0.68042	.	.	ENSG00000122741	ENST00000377724;ENST00000242323	T;T	0.01388	4.95;4.95	6.06	6.06	0.98353	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.161766	0.56097	D	0.000033	T	0.03783	0.0107	N	0.22421	0.69	0.47698	D	0.99949	P;D	0.65815	0.894;0.995	B;P	0.59703	0.312;0.862	T	0.59862	-0.7374	10	0.56958	D	0.05	.	18.1147	0.89549	0.0:1.0:0.0:0.0	.	482;519	Q5QP82-2;Q5QP82	.;DCA10_HUMAN	W	519;482	ENSP00000366953:R519W;ENSP00000242323:R482W	ENSP00000242323:R482W	R	+	1	2	DCAF10	37851380	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	1.548000	0.36201	2.882000	0.98803	0.655000	0.94253	CGG	.	.	none		0.483	DCAF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052485.2	NM_024345	
GRIK1	2897	hgsc.bcm.edu	37	21	30926024	30926024	+	Splice_Site	SNP	G	G	A	rs363503	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:30926024G>A	ENST00000399907.1	-	17	3020	c.2609C>T	c.(2608-2610)gCt>gTt	p.A870V	GRIK1_ENST00000535441.1_Intron|GRIK1_ENST00000399909.1_Splice_Site_p.A855V|GRIK1_ENST00000399914.1_Intron|GRIK1_ENST00000389125.3_Intron|GRIK1_ENST00000399913.1_Intron|GRIK1_ENST00000389124.2_Intron|GRIK1_ENST00000309434.7_Splice_Site_p.A872V|GRIK1_ENST00000327783.4_Intron	NM_000830.3	NP_000821.1	P39086	GRIK1_HUMAN	glutamate receptor, ionotropic, kainate 1	870			A -> V (in dbSNP:rs363503).		adult behavior (GO:0030534)|behavioral response to pain (GO:0048266)|central nervous system development (GO:0007417)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|nervous system development (GO:0007399)|positive regulation of gamma-aminobutyric acid secretion (GO:0014054)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(11)|lung(18)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	45					Topiramate(DB00273)	GAAACAAAAAGCCTTGCATGC	0.313													G|||	31	0.0061901	0.0015	0.0072	5008	,	,		16981	0.001		0.005	False		,,,				2504	0.0184				p.A870V		Atlas-SNP	.											.	GRIK1	293	.	0			c.C2609T						PASS	.	G	VAL/ALA,	9,3601		0,9,1796	96.0	98.0	97.0		2609,	4.5	1.0	21	dbSNP_79	97	58,8104		0,58,4023	yes	missense-near-splice,intron	GRIK1	NM_000830.3,NM_175611.2	64,	0,67,5819	AA,AG,GG		0.7106,0.2493,0.5691	benign,	870/919,	30926024	67,11705	1805	4081	5886	SO:0001630	splice_region_variant	2897	exon17			CAAAAAGCCTTGC		CCDS33530.1, CCDS42913.1	21q22	2012-08-29			ENSG00000171189	ENSG00000171189		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4579	protein-coding gene	gene with protein product		138245		GLUR5		8468067	Standard	XM_005260942		Approved	GluK1	uc002yno.1	P39086	OTTHUMG00000078879	ENST00000399907.1:c.2608-1C>T	21.37:g.30926024G>A		90.0	0.0	0		73.0	32.0	0.438356	NM_000830	Q13001|Q86SU9	Missense_Mutation	SNP	ENST00000399907.1	37	CCDS42913.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	0	0.0	2	0.002638522427440633	G	17.20	3.327836	0.60743	0.002493	0.007106	ENSG00000171189	ENST00000399907;ENST00000399909;ENST00000309434	T;T;T	0.11277	2.8;2.79;2.8	5.4	4.52	0.55395	.	.	.	.	.	T	0.04182	0.0116	N	0.08118	0	0.31142	N	0.706501	B	0.20261	0.043	B	0.17433	0.018	T	0.16041	-1.0416	9	0.19147	T	0.46	.	13.6508	0.62310	0.0746:0.0:0.9254:0.0	rs363503	870	P39086	GRIK1_HUMAN	V	870;855;872	ENSP00000382791:A870V;ENSP00000382793:A855V;ENSP00000311646:A872V	ENSP00000311646:A872V	A	-	2	0	GRIK1	29847895	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.782000	0.68973	1.503000	0.48686	0.655000	0.94253	GCT	G|0.997;A|0.003	0.003	strong		0.313	GRIK1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171979.1		Missense_Mutation
ZNF768	79724	hgsc.bcm.edu	37	16	30536798	30536798	+	Silent	SNP	C	C	T	rs138236969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:30536798C>T	ENST00000380412.5	-	2	838	c.663G>A	c.(661-663)ggG>ggA	p.G221G	ZNF768_ENST00000562803.1_Silent_p.G190G	NM_024671.3	NP_078947.3	Q9H5H4	ZN768_HUMAN	zinc finger protein 768	221					regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	DNA-directed RNA polymerase II, core complex (GO:0005665)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						ACAGCAGGGCCCCTGTGGGCA	0.642													C|||	11	0.00219649	0.0	0.0014	5008	,	,		14345	0.0		0.0099	False		,,,				2504	0.0				p.G221G		Atlas-SNP	.											.	ZNF768	28	.	0			c.G663A						PASS	.	C		7,4387	11.4+/-27.6	0,7,2190	65.0	70.0	68.0		663	2.2	1.0	16	dbSNP_134	68	77,8523	41.2+/-98.3	0,77,4223	no	coding-synonymous	ZNF768	NM_024671.3		0,84,6413	TT,TC,CC		0.8953,0.1593,0.6465		221/541	30536798	84,12910	2197	4300	6497	SO:0001819	synonymous_variant	79724	exon2			CAGGGCCCCTGTG	BC013760	CCDS10681.2	16p11.2	2013-01-08			ENSG00000169957	ENSG00000169957		"""Zinc fingers, C2H2-type"""	26273	protein-coding gene	gene with protein product						12477932	Standard	NM_024671		Approved	FLJ23436	uc002dyk.4	Q9H5H4	OTTHUMG00000132392	ENST00000380412.5:c.663G>A	16.37:g.30536798C>T		112.0	0.0	0		124.0	64.0	0.516129	NM_024671	Q569L7|Q96CX4	Silent	SNP	ENST00000380412.5	37	CCDS10681.2																																																																																			C|0.995;T|0.005	0.005	strong		0.642	ZNF768-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255522.2	NM_024671	
SYNPO2L	79933	hgsc.bcm.edu	37	10	75406952	75406952	+	Missense_Mutation	SNP	A	A	G	rs200429699		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75406952A>G	ENST00000394810.2	-	4	2607	c.2458T>C	c.(2458-2460)Ttt>Ctt	p.F820L	SYNPO2L_ENST00000372873.4_Missense_Mutation_p.F596L	NM_001114133.1	NP_001107605.1	Q9H987	SYP2L_HUMAN	synaptopodin 2-like	820	Pro-rich.					cytoskeleton (GO:0005856)|nucleus (GO:0005634)|Z disc (GO:0030018)				breast(2)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	26	Prostate(51;0.0112)					TGGGGGAAAAAGGGAGAGAGC	0.577													A|||	1	0.000199681	0.0	0.0	5008	,	,		15267	0.0		0.001	False		,,,				2504	0.0				p.F820L		Atlas-SNP	.											SYNPO2L_ENST00000394810,NS,carcinoma,+1,4	SYNPO2L	118	4	0			c.T2458C						scavenged	.						62.0	74.0	70.0					10																	75406952		2202	4300	6502	SO:0001583	missense	79933	exon4			GGAAAAAGGGAGA	AK022983	CCDS7331.1, CCDS44438.1	10q22.3	2007-12-19			ENSG00000166317	ENSG00000166317			23532	protein-coding gene	gene with protein product							Standard	XM_005270158		Approved	FLJ12921	uc001jut.4	Q9H987	OTTHUMG00000018471	ENST00000394810.2:c.2458T>C	10.37:g.75406952A>G	ENSP00000378289:p.Phe820Leu	62.0	1.0	0.016129		91.0	48.0	0.527473	NM_001114133	A5PKV9|Q68A20	Missense_Mutation	SNP	ENST00000394810.2	37	CCDS44438.1	.	.	.	.	.	.	.	.	.	.	A	19.36	3.813125	0.70912	.	.	ENSG00000166317	ENST00000372873;ENST00000394810	T;T	0.22539	1.95;2.26	4.98	4.98	0.66077	.	0.119748	0.64402	D	0.000019	T	0.23766	0.0575	L	0.54323	1.7	0.44500	D	0.997447	P;P	0.45531	0.666;0.86	B;P	0.44561	0.162;0.453	T	0.03597	-1.1021	10	0.12103	T	0.63	-5.368	14.8374	0.70194	1.0:0.0:0.0:0.0	.	820;596	Q9H987;Q9H987-2	SYP2L_HUMAN;.	L	596;820	ENSP00000361964:F596L;ENSP00000378289:F820L	ENSP00000361964:F596L	F	-	1	0	SYNPO2L	75076958	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.139000	0.94554	2.090000	0.63153	0.402000	0.26972	TTT	.	.	weak		0.577	SYNPO2L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316562.2	NM_024875	
GPR162	27239	hgsc.bcm.edu	37	12	6934804	6934804	+	Silent	SNP	C	C	T	rs148277722	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6934804C>T	ENST00000311268.3	+	3	1810	c.1023C>T	c.(1021-1023)tgC>tgT	p.C341C	GPR162_ENST00000428545.2_Silent_p.C57C|LEPREL2_ENST00000606935.1_RNA|GPR162_ENST00000382315.3_Silent_p.C37C|LEPREL2_ENST00000396725.2_RNA|LEPREL2_ENST00000251761.8_RNA	NM_019858.1	NP_062832.1	Q16538	GP162_HUMAN	G protein-coupled receptor 162	341						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|pancreas(2)|skin(1)	18						GGGAGCAATGCGTGGCCATCA	0.607											OREG0021636	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	4	0.000798722	0.0015	0.0	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.002				p.C341C		Atlas-SNP	.											.	GPR162	55	.	0			c.C1023T						PASS	.	C	,	2,4400		0,2,2199	92.0	56.0	68.0		171,1023	0.7	1.0	12	dbSNP_134	68	17,8577		0,17,4280	no	coding-synonymous,coding-synonymous	GPR162	NM_014449.1,NM_019858.1	,	0,19,6479	TT,TC,CC		0.1978,0.0454,0.1462	,	57/305,341/589	6934804	19,12977	2201	4297	6498	SO:0001819	synonymous_variant	27239	exon3			GCAATGCGTGGCC	U47928, U47929, U47924, U47925	CCDS8563.1, CCDS44819.1	12p13	2012-08-21						"""GPCR / Class A : Orphans"""	16693	protein-coding gene	gene with protein product						15777626	Standard	NM_014449		Approved	A-2, GRCA	uc001qqw.1	Q16538		ENST00000311268.3:c.1023C>T	12.37:g.6934804C>T		97.0	0.0	0	637	140.0	71.0	0.507143	NM_019858	Q16664|Q59EH5|Q66K56	Silent	SNP	ENST00000311268.3	37	CCDS8563.1																																																																																			C|0.999;T|0.001	0.001	strong		0.607	GPR162-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399478.1	NM_019858	
MAFA	389692	hgsc.bcm.edu	37	8	144512157	144512157	+	Silent	SNP	C	C	T	rs373992315		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:144512157C>T	ENST00000333480.2	-	1	419	c.420G>A	c.(418-420)gaG>gaA	p.E140E	MAFA_ENST00000528185.1_5'Flank	NM_201589.3	NP_963883.2	Q8NHW3	MAFA_HUMAN	v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog A	140					insulin secretion (GO:0030073)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|lung(1)|upper_aerodigestive_tract(2)	4	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.237)			CGATGAGCGCCTCCACCGCGT	0.741										HNSCC(29;0.082)			.|||	1	0.000199681	0.0	0.0	5008	,	,		4841	0.0		0.001	False		,,,				2504	0.0				p.E140E		Atlas-SNP	.											.	MAFA	9	.	0			c.G420A						PASS	.	C		0,4076		0,0,2038	7.0	5.0	6.0		420	2.9	1.0	8		6	10,7996		0,10,3993	no	coding-synonymous	MAFA	NM_201589.3		0,10,6031	TT,TC,CC		0.1249,0.0,0.0828		140/354	144512157	10,12072	2038	4003	6041	SO:0001819	synonymous_variant	389692	exon1			GAGCGCCTCCACC	AY083269	CCDS34955.1	8q24.3	2013-07-09	2013-07-09			ENSG00000182759			23145	protein-coding gene	gene with protein product		610303					Standard	NM_201589		Approved	RIPE3b1, hMafA	uc003yyc.2	Q8NHW3		ENST00000333480.2:c.420G>A	8.37:g.144512157C>T		11.0	0.0	0		7.0	5.0	0.714286	NM_201589		Silent	SNP	ENST00000333480.2	37	CCDS34955.1																																																																																			.	.	weak		0.741	MAFA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381511.2	NM_201589	
HS1BP3	64342	hgsc.bcm.edu	37	2	20840851	20840851	+	Silent	SNP	C	C	T	rs148915944		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:20840851C>T	ENST00000304031.3	-	3	313	c.288G>A	c.(286-288)aaG>aaA	p.K96K	HS1BP3_ENST00000402541.1_Silent_p.K96K|HS1BP3_ENST00000406618.3_Silent_p.K96K	NM_022460.3	NP_071905.3	Q53T59	H1BP3_HUMAN	HCLS1 binding protein 3	96	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.						phosphatidylinositol binding (GO:0035091)			endometrium(4)|large_intestine(1)|lung(7)|ovary(1)|skin(2)	15	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAAACAGGACCTTCCTGGGTA	0.552													C|||	1	0.000199681	0.0	0.0014	5008	,	,		20113	0.0		0.0	False		,,,				2504	0.0				p.K96K		Atlas-SNP	.											.	HS1BP3	33	.	0			c.G288A						PASS	.	C		0,4406		0,0,2203	166.0	168.0	167.0		288	3.7	1.0	2	dbSNP_134	167	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	HS1BP3	NM_022460.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		96/393	20840851	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	64342	exon3			CAGGACCTTCCTG		CCDS1700.1	2p24.1	2006-08-15			ENSG00000118960	ENSG00000118960			24979	protein-coding gene	gene with protein product		609359				10590261, 15699368	Standard	NM_022460		Approved	HS1-BP3,FLJ14249	uc002rdw.1	Q53T59	OTTHUMG00000122099	ENST00000304031.3:c.288G>A	2.37:g.20840851C>T		43.0	0.0	0		41.0	19.0	0.463415	NM_022460	B2RAW2|D6W529|Q86VC2|Q8N367	Silent	SNP	ENST00000304031.3	37	CCDS1700.1																																																																																			C|0.999;T|0.001	0.001	strong		0.552	HS1BP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242863.1	NM_022460	
MTMR12	54545	hgsc.bcm.edu	37	5	32263316	32263316	+	Missense_Mutation	SNP	C	C	T	rs61748194	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:32263316C>T	ENST00000382142.3	-	7	786	c.616G>A	c.(616-618)Gac>Aac	p.D206N	MTMR12_ENST00000280285.5_Missense_Mutation_p.D206N|MTMR12_ENST00000264934.5_Missense_Mutation_p.D206N	NM_001040446.1	NP_001035536.1	Q9C0I1	MTMRC_HUMAN	myotubularin related protein 12	206	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.					cytoplasm (GO:0005737)	phosphatase activity (GO:0016791)			breast(3)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	34						TTAAGTGTGTCAAACATTACG	0.398													C|||	37	0.00738818	0.0008	0.0173	5008	,	,		21370	0.0		0.0219	False		,,,				2504	0.002				p.D206N		Atlas-SNP	.											.	MTMR12	76	.	0			c.G616A						PASS	.	C	ASN/ASP	21,4385	29.0+/-57.7	0,21,2182	274.0	225.0	241.0		616	5.5	1.0	5	dbSNP_129	241	196,8404	86.1+/-148.5	3,190,4107	yes	missense	MTMR12	NM_001040446.1	23	3,211,6289	TT,TC,CC		2.2791,0.4766,1.6685	possibly-damaging	206/748	32263316	217,12789	2203	4300	6503	SO:0001583	missense	54545	exon7			GTGTGTCAAACAT	AB051469	CCDS34138.1, CCDS75230.1	5p15.33	2011-06-09	2005-04-07	2005-04-07	ENSG00000150712	ENSG00000150712		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	18191	protein-coding gene	gene with protein product		606501	"""phosphatidylinositol-3-phosphate associated protein"""	PIP3AP		11504939, 12495846	Standard	XM_005248313		Approved	3-PAP, FLJ20476, KIAA1682, 3PAP	uc003jhq.3	Q9C0I1	OTTHUMG00000161978	ENST00000382142.3:c.616G>A	5.37:g.32263316C>T	ENSP00000371577:p.Asp206Asn	370.0	1.0	0.0027027		348.0	151.0	0.433908	NM_001040446	Q69YJ4|Q6PFW3|Q96QU2|Q9NX27	Missense_Mutation	SNP	ENST00000382142.3	37	CCDS34138.1	25	0.011446886446886446	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	20	0.026385224274406333	C	19.09	3.760426	0.69763	0.004766	0.022791	ENSG00000150712	ENST00000280285;ENST00000382142;ENST00000264934	D;D;D	0.89681	-2.55;-2.55;-2.55	5.47	5.47	0.80525	Myotubularin phosphatase domain (1);	0.343414	0.29087	N	0.013200	T	0.78233	0.4251	M	0.62723	1.935	0.51767	D	0.999935	P;P;P	0.37370	0.592;0.592;0.457	B;B;B	0.42959	0.403;0.403;0.227	T	0.81867	-0.0735	10	0.19147	T	0.46	.	19.3518	0.94392	0.0:1.0:0.0:0.0	rs61748194	206;206;206	Q9C0I1-3;Q9C0I1-2;Q9C0I1	.;.;MTMRC_HUMAN	N	206	ENSP00000280285:D206N;ENSP00000371577:D206N;ENSP00000264934:D206N	ENSP00000264934:D206N	D	-	1	0	MTMR12	32299073	1.000000	0.71417	1.000000	0.80357	0.790000	0.44656	2.746000	0.47467	2.571000	0.86741	0.650000	0.86243	GAC	C|0.985;T|0.015	0.015	strong		0.398	MTMR12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366579.1	NM_019061	
STAG2	10735	hgsc.bcm.edu	37	X	123184082	123184082	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:123184082A>G	ENST00000371160.1	+	11	1230	c.940A>G	c.(940-942)Att>Gtt	p.I314V	STAG2_ENST00000354548.5_Missense_Mutation_p.I245V|STAG2_ENST00000469481.1_Intron|STAG2_ENST00000218089.9_Missense_Mutation_p.I314V|STAG2_ENST00000371157.3_Missense_Mutation_p.I314V|STAG2_ENST00000371144.3_Missense_Mutation_p.I314V|STAG2_ENST00000371145.3_Missense_Mutation_p.I314V	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	314	SCD. {ECO:0000255|PROSITE- ProRule:PRU00750}.				meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AGAGATTGGCATTTGGATGAA	0.378																																					p.I314V		Atlas-SNP	.											.	STAG2	309	.	0			c.A940G						PASS	.						283.0	235.0	252.0					X																	123184082		2203	4300	6503	SO:0001583	missense	10735	exon11			ATTGGCATTTGGA	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.940A>G	X.37:g.123184082A>G	ENSP00000360202:p.Ile314Val	121.0	0.0	0		231.0	78.0	0.337662	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	5.398	0.258667	0.10239	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	5.54	5.54	0.83059	Stromalin conservative domain (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.149337	0.64402	D	0.000013	T	0.10078	0.0247	N	0.01771	-0.73	0.42561	D	0.993144	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18304	-1.0341	10	0.02654	T	1	-9.3005	9.4174	0.38530	0.9193:0.0:0.0807:0.0	.	314;314	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	V	314;314;245;314;314;314;314	ENSP00000218089:I314V;ENSP00000397265:I314V;ENSP00000346555:I245V;ENSP00000360202:I314V;ENSP00000360199:I314V;ENSP00000360187:I314V;ENSP00000360186:I314V	ENSP00000218089:I314V	I	+	1	0	STAG2	123011763	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.344000	0.65981	1.952000	0.56665	0.486000	0.48141	ATT	.	.	none		0.378	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
KCNJ1	3758	hgsc.bcm.edu	37	11	128709126	128709126	+	Missense_Mutation	SNP	A	A	G	rs59172778	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128709126A>G	ENST00000392664.2	-	2	1186	c.1070T>C	c.(1069-1071)aTg>aCg	p.M357T	KCNJ1_ENST00000392666.1_Missense_Mutation_p.M338T|KCNJ1_ENST00000392665.2_Missense_Mutation_p.M338T|KCNJ1_ENST00000324036.3_Missense_Mutation_p.M338T|KCNJ1_ENST00000440599.2_Missense_Mutation_p.M338T	NM_000220.4	NP_000211.1	P48048	KCNJ1_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 1	357			M -> T (in BS2; dbSNP:rs59172778). {ECO:0000269|PubMed:8841184}.		cardiovascular system development (GO:0072358)|excretion (GO:0007588)|kidney development (GO:0001822)|post-embryonic development (GO:0009791)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of G-protein activated inward rectifier potassium channel activity (GO:1900128)|renal sodium ion absorption (GO:0070294)|synaptic transmission (GO:0007268)|tissue homeostasis (GO:0001894)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|inward rectifier potassium channel activity (GO:0005242)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			breast(2)|endometrium(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)	23	all_hematologic(175;0.0641)	all_lung(97;4.89e-06)|Lung NSC(97;9.34e-06)|Breast(109;0.00123)|all_hematologic(192;0.00793)|Renal(330;0.0112)|all_neural(223;0.0189)|Medulloblastoma(222;0.0425)		OV - Ovarian serous cystadenocarcinoma(99;4.05e-06)|LUSC - Lung squamous cell carcinoma(976;0.008)|Lung(977;0.00942)	Bethanidine(DB00217)|Glimepiride(DB00222)|Glyburide(DB01016)|Glycodiazine(DB01382)|Minoxidil(DB00350)|Tolazamide(DB00839)|Tolbutamide(DB01124)|Yohimbine(DB01392)	ATAAAGGCACATGGCACAGTG	0.438													A|||	14	0.00279553	0.0	0.0029	5008	,	,		21343	0.0		0.0119	False		,,,				2504	0.0				p.M357T		Atlas-SNP	.											.	KCNJ1	68	.	0			c.T1070C	GRCh37	CM960893	KCNJ1	M	rs59172778	PASS	.	A	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	8,4394	14.3+/-33.2	0,8,2193	119.0	114.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1070,1013,1013,1013,1013	5.9	1.0	11	dbSNP_129	115	81,8513	46.7+/-105.8	1,79,4217	yes	missense,missense,missense,missense,missense	KCNJ1	NM_000220.2,NM_153764.1,NM_153765.1,NM_153766.1,NM_153767.2	81,81,81,81,81	1,87,6410	GG,GA,AA		0.9425,0.1817,0.6848	benign,benign,benign,benign,benign	357/392,338/373,338/373,338/373,338/373	128709126	89,12907	2201	4297	6498	SO:0001583	missense	3758	exon2			AGGCACATGGCAC	BC063109	CCDS8476.1, CCDS8477.1	11q24	2011-07-05			ENSG00000151704	ENSG00000151704		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6255	protein-coding gene	gene with protein product		600359				7680431, 8190102, 16382105	Standard	NM_153765		Approved	Kir1.1, ROMK1	uc001qeo.2	P48048	OTTHUMG00000048247	ENST00000392664.2:c.1070T>C	11.37:g.128709126A>G	ENSP00000376432:p.Met357Thr	100.0	0.0	0		126.0	64.0	0.507937	NM_000220	B2RMR4|Q6LD67	Missense_Mutation	SNP	ENST00000392664.2	37	CCDS8476.1	11	0.005036630036630037	0	0.0	1	0.0027624309392265192	0	0.0	10	0.013192612137203167	A	8.138	0.784569	0.16189	0.001817	0.009425	ENSG00000151704	ENST00000392665;ENST00000392666;ENST00000440599;ENST00000324036;ENST00000392664	D;D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23;-3.23	5.9	5.9	0.94986	Immunoglobulin E-set (1);Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);Potassium channel, inwardly rectifying, Kir, cytoplasmic (1);	0.432611	0.29212	N	0.012803	D	0.86280	0.5895	N	0.24115	0.695	0.25998	N	0.982157	B	0.11235	0.004	B	0.22753	0.041	T	0.80714	-0.1259	10	0.72032	D	0.01	.	16.3245	0.82970	1.0:0.0:0.0:0.0	rs59172778;rs62625013	357	P48048	IRK1_HUMAN	T	338;338;338;338;357	ENSP00000376433:M338T;ENSP00000376434:M338T;ENSP00000406320:M338T;ENSP00000316233:M338T;ENSP00000376432:M357T	ENSP00000316233:M338T	M	-	2	0	KCNJ1	128214336	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.870000	0.63035	2.254000	0.74563	0.460000	0.39030	ATG	A|0.993;G|0.007	0.007	strong		0.438	KCNJ1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386233.1	NM_000220	
RNF213	57674	hgsc.bcm.edu	37	17	78338305	78338305	+	Silent	SNP	C	C	T	rs148958011	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78338305C>T	ENST00000582970.1	+	42	11966	c.11823C>T	c.(11821-11823)gtC>gtT	p.V3941V	CTD-2047H16.4_ENST00000572151.1_RNA|RNF213_ENST00000508628.2_Silent_p.V3990V|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000336301.6_Silent_p.V2014V	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	3941					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AGAGCCGCGTCCCCGAGTTAC	0.582													C|||	4	0.000798722	0.0	0.0014	5008	,	,		17383	0.0		0.001	False		,,,				2504	0.002				p.V3941V		Atlas-SNP	.											.	RNF213	766	.	0			c.C11823T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	74.0	70.0	71.0		11970	-3.7	0.0	17	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	RNF213	NM_020914.4		0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384		3990/5257	78338305	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon42			CCGCGTCCCCGAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.11823C>T	17.37:g.78338305C>T		102.0	0.0	0		137.0	79.0	0.576642	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
FCGR3A	2214	hgsc.bcm.edu	37	1	161512873	161512873	+	Missense_Mutation	SNP	T	T	A	rs115866423	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:161512873T>A	ENST00000436743.1	-	6	848	c.694A>T	c.(694-696)Aac>Tac	p.N232Y	RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'Flank|FCGR3A_ENST00000443193.1_Missense_Mutation_p.N267Y|FCGR3A_ENST00000367969.3_Missense_Mutation_p.N268Y|FCGR3A_ENST00000540048.1_Missense_Mutation_p.N232Y	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	232					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTTCGAATGTTTGTCTTCACA	0.443													T|||	29	0.00579073	0.0	0.0086	5008	,	,		22717	0.0		0.0099	False		,,,				2504	0.0133				p.N268Y		Atlas-SNP	.											.	FCGR3A	38	.	0			c.A802T						PASS	.	T	TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN,TYR/ASN	11,4395	19.1+/-41.9	0,11,2192	151.0	149.0	150.0		691,694,694,799,802	-2.9	0.0	1	dbSNP_132	150	100,8500	56.4+/-117.6	2,96,4202	no	missense,missense,missense,missense,missense	FCGR3A	NM_001127596.1,NM_001127595.1,NM_001127593.1,NM_001127592.1,NM_000569.6	143,143,143,143,143	2,107,6394	AA,AT,TT		1.1628,0.2497,0.8535	benign,benign,benign,benign,benign	231/254,232/255,232/255,267/290,268/291	161512873	111,12895	2203	4300	6503	SO:0001583	missense	2214	exon5			GAATGTTTGTCTT	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.694A>T	1.37:g.161512873T>A	ENSP00000416607:p.Asn232Tyr	417.0	0.0	0		407.0	196.0	0.481572	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Missense_Mutation	SNP	ENST00000436743.1	37	CCDS44266.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	T|T	9.319|9.319	1.057646|1.057646	0.19907|0.19907	0.002497|0.002497	0.011628|0.011628	ENSG00000203747|ENSG00000203747	ENST00000367969;ENST00000443193;ENST00000436743;ENST00000367967;ENST00000540048|ENST00000426740	T;T;T;T;T|.	0.01484|.	4.84;4.84;4.89;4.89;4.89|.	3.88|3.88	-2.9|-2.9	0.05648|0.05648	.|.	14.258800|.	0.00166|.	U|.	0.000000|.	T|T	0.12860|0.12860	0.0312|0.0312	L|L	0.38175|0.38175	1.15|1.15	0.09310|0.09310	N|N	1|1	B;P;P|.	0.37864|.	0.087;0.61;0.49|.	B;B;B|.	0.31812|.	0.029;0.101;0.136|.	T|T	0.33979|0.33979	-0.9847|-0.9847	10|5	0.66056|.	D|.	0.02|.	.|.	4.9176|4.9176	0.13853|0.13853	0.0:0.3545:0.157:0.4885|0.0:0.3545:0.157:0.4885	.|.	232;267;232|.	P08637;E9PG94;Q9UPY7|.	FCG3A_HUMAN;.;.|.	Y|H	268;267;232;232;232|248	ENSP00000356946:N268Y;ENSP00000392047:N267Y;ENSP00000416607:N232Y;ENSP00000356944:N232Y;ENSP00000444971:N232Y|.	ENSP00000356944:N232Y|.	N|Q	-|-	1|3	0|2	FCGR3A|FCGR3A	159779497|159779497	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-1.623000|-1.623000	0.02040|0.02040	-0.510000|-0.510000	0.06523|0.06523	0.482000|0.482000	0.46254|0.46254	AAC|CAA	T|0.993;A|0.007	0.007	strong		0.443	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
PPP3CC	5533	hgsc.bcm.edu	37	8	22390522	22390522	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:22390522A>G	ENST00000240139.5	+	12	1639	c.1312A>G	c.(1312-1314)Atc>Gtc	p.I438V	PPP3CC_ENST00000289963.8_Missense_Mutation_p.I438V|PPP3CC_ENST00000397775.3_Missense_Mutation_p.I447V	NM_005605.4	NP_005596.2	P48454	PP2BC_HUMAN	protein phosphatase 3, catalytic subunit, gamma isozyme	438					apoptotic process (GO:0006915)|intrinsic apoptotic signaling pathway (GO:0097193)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Prostate(55;0.104)		BRCA - Breast invasive adenocarcinoma(99;0.00756)|Colorectal(74;0.0238)|COAD - Colon adenocarcinoma(73;0.0835)		CAAGCAGACTATCGAGACAGG	0.542																																					p.I447V		Atlas-SNP	.											.	PPP3CC	39	.	0			c.A1339G						PASS	.						84.0	66.0	72.0					8																	22390522		2203	4300	6503	SO:0001583	missense	5533	exon13			CAGACTATCGAGA		CCDS34859.1, CCDS59094.1, CCDS59093.1	8p21.3	2010-03-17	2010-03-05		ENSG00000120910	ENSG00000120910	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9316	protein-coding gene	gene with protein product	"""calcineurin A gamma"", ""protein phosphatase 2B, catalytic subunit, gamma isoform"""	114107	"""protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform (calcineurin A gamma)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, gamma isoform"""			1339277	Standard	NM_005605		Approved	CALNA3, PP2Bgamma	uc011kzi.2	P48454	OTTHUMG00000163802	ENST00000240139.5:c.1312A>G	8.37:g.22390522A>G	ENSP00000240139:p.Ile438Val	60.0	0.0	0		103.0	48.0	0.466019	NM_001243974	B4DRT5|Q9BSS6|Q9H4M5	Missense_Mutation	SNP	ENST00000240139.5	37	CCDS34859.1	.	.	.	.	.	.	.	.	.	.	A	8.509	0.866175	0.17250	.	.	ENSG00000120910	ENST00000240139;ENST00000289963;ENST00000397775	T;T;T	0.05382	3.45;3.45;3.45	5.74	1.72	0.24424	.	0.185247	0.47455	D	0.000236	T	0.04588	0.0125	N	0.15975	0.35	0.34146	D	0.667017	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.12837	0.004;0.008;0.005	T	0.18745	-1.0327	10	0.45353	T	0.12	-16.5588	13.6583	0.62352	0.386:0.614:0.0:0.0	.	447;438;438	B4DRT5;P48454-2;P48454	.;.;PP2BC_HUMAN	V	438;438;447	ENSP00000240139:I438V;ENSP00000289963:I438V;ENSP00000380878:I447V	ENSP00000240139:I438V	I	+	1	0	PPP3CC	22446467	0.826000	0.29277	0.849000	0.33467	0.006000	0.05464	1.656000	0.37355	0.401000	0.25424	-0.313000	0.08912	ATC	.	.	none		0.542	PPP3CC-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375652.1	NM_005605	
GOT1L1	137362	hgsc.bcm.edu	37	8	37797467	37797467	+	Silent	SNP	A	A	G	rs151011886	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:37797467A>G	ENST00000307599.4	-	1	180	c.81T>C	c.(79-81)gaT>gaC	p.D27D		NM_152413.2	NP_689626.2	Q8NHS2	AATC2_HUMAN	glutamic-oxaloacetic transaminase 1-like 1	27					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)	cytoplasm (GO:0005737)	pyridoxal phosphate binding (GO:0030170)|transaminase activity (GO:0008483)			central_nervous_system(1)|endometrium(3)|lung(8)|ovary(1)|prostate(1)	14	Colorectal(12;0.00627)	Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;1.37e-11)			TCGGGTAATCATCTTGTTTGT	0.458													A|||	4	0.000798722	0.0	0.0	5008	,	,		21029	0.0		0.003	False		,,,				2504	0.001				p.D27D		Atlas-SNP	.											.	GOT1L1	87	.	0			c.T81C						PASS	.	A		2,3874		0,2,1936	141.0	127.0	132.0		81	-10.2	0.0	8	dbSNP_134	132	35,8205		0,35,4085	no	coding-synonymous	GOT1L1	NM_152413.2		0,37,6021	GG,GA,AA		0.4248,0.0516,0.3054		27/422	37797467	37,12079	1938	4120	6058	SO:0001819	synonymous_variant	137362	exon1			GTAATCATCTTGT	BC029504	CCDS47839.1	8p12	2005-09-22			ENSG00000169154	ENSG00000169154			28487	protein-coding gene	gene with protein product						12477932	Standard	NM_152413		Approved	MGC33309	uc011lbj.1	Q8NHS2	OTTHUMG00000164027	ENST00000307599.4:c.81T>C	8.37:g.37797467A>G		224.0	0.0	0		196.0	96.0	0.489796	NM_152413	A8MWL4	Silent	SNP	ENST00000307599.4	37	CCDS47839.1																																																																																			A|0.999;G|0.001	0.001	strong		0.458	GOT1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376823.1	NM_152413	
Unknown	0	hgsc.bcm.edu	37	11	5989180	5989180	+	IGR	SNP	C	C	T	rs147979628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:5989180C>T								OR56A3 (19589 upstream) : OR52L1 (17941 downstream)																							CACGTTAGTACAGATGCAGTT	0.458													.|||	6	0.00119808	0.0	0.0	5008	,	,		23124	0.0		0.006	False		,,,				2504	0.0				p.C182Y		Atlas-SNP	.											.	.	.	.	0			c.G545A						PASS	.	C	TYR/CYS	0,1384		0,0,692	105.0	86.0	92.0		545	2.9	0.9	11	dbSNP_134	92	7,3175		0,7,1584	yes	missense	OR56A5	NM_001146033.1	194	0,7,2276	TT,TC,CC		0.22,0.0,0.1533	possibly-damaging	182/314	5989180	7,4559	692	1591	2283	SO:0001628	intergenic_variant	390084	exon1			TTAGTACAGATGC																													11.37:g.5989180C>T		87.0	0.0	0		125.0	58.0	0.464	NM_001146033		Missense_Mutation	SNP		37																																																																																				C|0.998;T|0.002	0.002	strong	0	0.458								
EZH2	2146	hgsc.bcm.edu	37	7	148525904	148525904	+	Missense_Mutation	SNP	C	C	G	rs2302427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:148525904C>G	ENST00000460911.1	-	6	641	c.553G>C	c.(553-555)Gac>Cac	p.D185H	EZH2_ENST00000320356.2_Missense_Mutation_p.D185H|EZH2_ENST00000541220.1_Missense_Mutation_p.D176H|EZH2_ENST00000350995.2_Missense_Mutation_p.D146H|EZH2_ENST00000478654.1_Missense_Mutation_p.D176H|EZH2_ENST00000483967.1_Missense_Mutation_p.D176H|EZH2_ENST00000536783.1_Missense_Mutation_p.D76H|EZH2_ENST00000476773.1_Missense_Mutation_p.D176H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	185	Interaction with DNMT1, DNMT3A and DNMT3B.		D -> H (in dbSNP:rs2302427).		cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			tcatcatcgtcatcatcatta	0.393			Mis		DLBCL								C|||	400	0.0798722	0.0038	0.0461	5008	,	,		19098	0.2063		0.0696	False		,,,				2504	0.0869				p.D185H		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,NS,carcinoma,+2,2	EZH2	823	2	0			c.G553C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	66,4340	60.5+/-97.4	0,66,2137	178.0	146.0	157.0		553,526,526,553,436	5.7	0.9	7	dbSNP_100	157	719,7881	175.3+/-225.4	30,659,3611	yes	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	81,81,81,81,81	30,725,5748	GG,GC,CC		8.3605,1.498,6.0357	benign,benign,benign,benign,benign	185/747,176/738,176/696,185/752,146/708	148525904	785,12221	2203	4300	6503	SO:0001583	missense	2146	exon6			CATCGTCATCATC		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.553G>C	7.37:g.148525904C>G	ENSP00000419711:p.Asp185His	202.0	0.0	0		203.0	103.0	0.507389	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	161	0.07371794871794872	3	0.006097560975609756	21	0.058011049723756904	83	0.1451048951048951	54	0.0712401055408971	C	19.43	3.826662	0.71143	0.01498	0.083605	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94828	-3.46;-3.5;-3.46;-3.5;-3.46;-3.46;-3.53;0.81	5.69	5.69	0.88448	SANT domain, DNA binding (1);	0.168733	0.49916	D	0.000127	T	0.08980	0.0222	L	0.34521	1.04	0.09310	P	0.99999641944	P;B;B;B;P;P	0.47604	0.898;0.348;0.348;0.41;0.659;0.676	P;B;B;B;B;P	0.49226	0.553;0.393;0.393;0.299;0.393;0.603	T	0.59161	-0.7506	9	0.72032	D	0.01	.	19.4235	0.94732	0.0:1.0:0.0:0.0	rs2302427;rs52833659	185;176;176;185;146;185	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	176;185;185;146;176;176;176;76	ENSP00000417062:D176H;ENSP00000320147:D185H;ENSP00000419711:D185H;ENSP00000223193:D146H;ENSP00000443219:D176H;ENSP00000419050:D176H;ENSP00000419856:D176H;ENSP00000439305:D76H	ENSP00000320147:D185H	D	-	1	0	EZH2	148156837	1.000000	0.71417	0.919000	0.36401	0.821000	0.46438	7.538000	0.82048	2.682000	0.91365	0.585000	0.79938	GAC	C|0.926;G|0.074	0.074	strong		0.393	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
DNAH9	1770	hgsc.bcm.edu	37	17	11687721	11687721	+	Silent	SNP	G	G	A	rs16945337	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11687721G>A	ENST00000262442.4	+	41	7994	c.7926G>A	c.(7924-7926)gcG>gcA	p.A2642A	DNAH9_ENST00000454412.2_Silent_p.A2642A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	AAA 3. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ACTTCCCGGCGTCCCTGCAGA	0.542													G|||	239	0.0477236	0.0877	0.0058	5008	,	,		17425	0.002		0.0348	False		,,,				2504	0.0838				p.A2642A		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G7926A						PASS	.	G		358,4048	185.0+/-212.2	14,330,1859	177.0	169.0	172.0		7926	-2.6	0.0	17	dbSNP_123	172	195,8405	86.1+/-148.5	0,195,4105	no	coding-synonymous	DNAH9	NM_001372.3		14,525,5964	AA,AG,GG		2.2674,8.1253,4.2519		2642/4487	11687721	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon41			CCCGGCGTCCCTG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.7926G>A	17.37:g.11687721G>A		190.0	0.0	0		219.0	107.0	0.488584	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.956;A|0.044	0.044	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
SLC25A29	123096	hgsc.bcm.edu	37	14	100759690	100759690	+	Missense_Mutation	SNP	C	C	T	rs200054689		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:100759690C>T	ENST00000359232.3	-	3	403	c.103G>A	c.(103-105)Gag>Aag	p.E35K	SLC25A29_ENST00000556505.1_5'UTR|SLC25A29_ENST00000392908.3_Missense_Mutation_p.G20E|AL157871.2_ENST00000553954.1_RNA|SLC25A29_ENST00000539621.1_5'UTR|SLC25A29_ENST00000555927.1_5'UTR|RP11-638I2.6_ENST00000556458.1_lincRNA|SLC25A29_ENST00000554912.1_5'UTR	NM_001039355.1	NP_001034444.1	Q8N8R3	MCATL_HUMAN	solute carrier family 25 (mitochondrial carnitine/acylcarnitine carrier), member 29	35						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	acyl carnitine transmembrane transporter activity (GO:0015227)			NS(1)|endometrium(1)|ovary(1)	3		Melanoma(154;0.152)			L-Carnitine(DB00583)	TGAGGCTTCTCCACGCTCTGG	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		17380	0.0		0.001	False		,,,				2504	0.0				p.E35K		Atlas-SNP	.											.	SLC25A29	14	.	0			c.G103A						PASS	.						73.0	49.0	57.0					14																	100759690		2202	4300	6502	SO:0001583	missense	123096	exon3			GCTTCTCCACGCT	AK095532	CCDS32156.1	14q32.2	2013-05-22	2012-03-29	2004-01-21	ENSG00000197119	ENSG00000197119		"""Solute carriers"""	20116	protein-coding gene	gene with protein product		615064	"""chromosome 14 open reading frame 69"", ""solute carrier family 25, member 29"""	C14orf69			Standard	XM_005267343		Approved	FLJ38975	uc010twx.2	Q8N8R3	OTTHUMG00000171569	ENST00000359232.3:c.103G>A	14.37:g.100759690C>T	ENSP00000352167:p.Glu35Lys	64.0	0.0	0		96.0	57.0	0.59375	NM_001039355	A3KMR5|Q541V0	Missense_Mutation	SNP	ENST00000359232.3	37	CCDS32156.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	7.062|7.062	0.566669|0.566669	0.13560|0.13560	.|.	.|.	ENSG00000197119|ENSG00000197119	ENST00000359232|ENST00000392908;ENST00000554060	T|.	0.78595|.	-1.19|.	4.41|4.41	4.41|4.41	0.53225|0.53225	Mitochondrial carrier domain (2);|.	0.175049|.	0.49305|.	D|.	0.000143|.	T|T	0.34135|0.34135	0.0887|0.0887	N|N	0.02334|0.02334	-0.595|-0.595	0.80722|0.80722	D|D	1|1	B|.	0.11235|.	0.004|.	B|.	0.15052|.	0.012|.	T|T	0.48536|0.48536	-0.9027|-0.9027	10|6	0.09590|0.87932	T|D	0.72|0	-26.801|-26.801	12.1754|12.1754	0.54182|0.54182	0.1709:0.8291:0.0:0.0|0.1709:0.8291:0.0:0.0	.|.	35|.	Q8N8R3|.	MCATL_HUMAN|.	K|E	35|20	ENSP00000352167:E35K|.	ENSP00000352167:E35K|ENSP00000376640:G20E	E|G	-|-	1|2	0|0	SLC25A29|SLC25A29	99829443|99829443	1.000000|1.000000	0.71417|0.71417	0.669000|0.669000	0.29828|0.29828	0.005000|0.005000	0.04900|0.04900	3.411000|3.411000	0.52672|0.52672	2.020000|2.020000	0.59435|0.59435	0.591000|0.591000	0.81541|0.81541	GAG|GGA	C|1.000;T|0.000	0.000	strong		0.632	SLC25A29-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000072449.3		
MYO18B	84700	hgsc.bcm.edu	37	22	26304363	26304363	+	Silent	SNP	G	G	A	rs58609797	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:26304363G>A	ENST00000407587.2	+	32	5395	c.5226G>A	c.(5224-5226)gaG>gaA	p.E1742E	MYO18B_ENST00000335473.7_Silent_p.E1741E|MYO18B_ENST00000536101.1_Silent_p.E1741E			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1741	Gln-rich.|Tail.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ACCAGGAGGAGGAACTGGAGG	0.607													G|||	259	0.0517173	0.1589	0.0159	5008	,	,		19484	0.0		0.0219	False		,,,				2504	0.0164				p.E1741E		Atlas-SNP	.											.	MYO18B	322	.	0			c.G5223A						PASS	.	G		439,3823		21,397,1713	54.0	66.0	62.0		5223	-0.9	1.0	22	dbSNP_129	62	122,8348		2,118,4115	no	coding-synonymous	MYO18B	NM_032608.5		23,515,5828	AA,AG,GG		1.4404,10.3003,4.4062		1741/2568	26304363	561,12171	2131	4235	6366	SO:0001819	synonymous_variant	84700	exon32			GGAGGAGGAACTG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.5226G>A	22.37:g.26304363G>A		67.0	0.0	0		84.0	40.0	0.47619	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				G|0.952;A|0.048	0.048	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
AKT1	207	hgsc.bcm.edu	37	14	105239894	105239894	+	Silent	SNP	C	C	T	rs1130233	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:105239894C>T	ENST00000554581.1	-	8	2206	c.726G>A	c.(724-726)gaG>gaA	p.E242E	AKT1_ENST00000544168.1_Silent_p.E180E|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000554192.1_5'Flank|AKT1_ENST00000555528.1_Silent_p.E242E|AKT1_ENST00000554848.1_Silent_p.E242E|AKT1_ENST00000402615.2_Silent_p.E242E|AKT1_ENST00000407796.2_Silent_p.E242E|AKT1_ENST00000349310.3_Silent_p.E242E			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	AGAACACACGCTCCCGGGACA	0.652		1	Mis		"""breast, colorectal, ovarian, NSCLC"""								C|||	1615	0.322484	0.0787	0.4222	5008	,	,		14497	0.6002		0.2425	False		,,,				2504	0.3773				p.E242E		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.G726A	GRCh37	CM081515	AKT1	M	rs1130233	PASS	.	C	,,	507,3897	216.1+/-234.9	33,441,1728	31.0	26.0	28.0		726,726,726	4.8	0.9	14	dbSNP_86	28	2115,6485	334.9+/-321.2	269,1577,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	302,2018,4182	TT,TC,CC		24.593,11.5123,20.163	,,	242/481,242/481,242/481	105239894	2622,10382	2202	4300	6502	SO:0001819	synonymous_variant	207	exon9			CACACGCTCCCGG	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.726G>A	14.37:g.105239894C>T		149.0	0.0	0		138.0	56.0	0.405797	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			C|0.769;T|0.231	0.231	strong		0.652	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
PRKD3	23683	hgsc.bcm.edu	37	2	37505108	37505108	+	Silent	SNP	C	C	T	rs116096831	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:37505108C>T	ENST00000379066.1	-	9	1959	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P	PRKD3_ENST00000234179.2_Silent_p.P399P			O94806	KPCD3_HUMAN	protein kinase D3	399					intracellular signal transduction (GO:0035556)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase C activity (GO:0004697)			breast(3)|central_nervous_system(2)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33		all_hematologic(82;0.21)				CCCTCATTAGCGGAATATTAT	0.368													C|||	10	0.00199681	0.0	0.0029	5008	,	,		16204	0.0		0.005	False		,,,				2504	0.0031				p.P399P	Melanoma(80;621 1355 8613 11814 51767)	Atlas-SNP	.											.	PRKD3	170	.	0			c.G1197A						PASS	.	C		3,4403	8.1+/-20.4	0,3,2200	191.0	157.0	168.0		1197	-6.0	0.9	2	dbSNP_132	168	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	PRKD3	NM_005813.3		0,49,6454	TT,TC,CC		0.5349,0.0681,0.3767		399/891	37505108	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	23683	exon8			CATTAGCGGAATA	AB015982	CCDS1789.1	2p21	2013-01-10	2004-10-28	2004-10-30	ENSG00000115825	ENSG00000115825		"""Pleckstrin homology (PH) domain containing"""	9408	protein-coding gene	gene with protein product		607077	"""protein kinase C, nu"""	PRKCN		10231560	Standard	NM_005813		Approved	EPK2	uc002rqd.3	O94806	OTTHUMG00000100961	ENST00000379066.1:c.1197G>A	2.37:g.37505108C>T		155.0	0.0	0		140.0	82.0	0.585714	NM_005813	D6W587|Q53TR7|Q8NEL8	Silent	SNP	ENST00000379066.1	37	CCDS1789.1																																																																																			C|0.996;T|0.004	0.004	strong		0.368	PRKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218570.3	NM_005813	
CDH15	1013	hgsc.bcm.edu	37	16	89245884	89245884	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:89245884C>T	ENST00000289746.2	+	2	168	c.103C>T	c.(103-105)Cgc>Tgc	p.R35C	CDH15_ENST00000521087.1_3'UTR	NM_004933.2	NP_004924.1	P55291	CAD15_HUMAN	cadherin 15, type 1, M-cadherin (myotubule)	35					adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	caveola (GO:0005901)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	18				BRCA - Breast invasive adenocarcinoma(80;0.0261)		GTACCCCTGGCGCCGGGCGCC	0.657																																					p.R35C		Atlas-SNP	.											CDH15,NS,carcinoma,-1,2	CDH15	54	2	0			c.C103T						PASS	.						83.0	82.0	82.0					16																	89245884		2198	4300	6498	SO:0001583	missense	1013	exon2			CCCTGGCGCCGGG	D83542	CCDS10976.1	16q24.3	2010-01-26	2008-10-30		ENSG00000129910	ENSG00000129910		"""Cadherins / Major cadherins"""	1754	protein-coding gene	gene with protein product		114019	"""cadherin 15, M-cadherin (myotubule)"""	CDH3, CDH14		1427864	Standard	NM_004933		Approved		uc002fmt.3	P55291	OTTHUMG00000138045	ENST00000289746.2:c.103C>T	16.37:g.89245884C>T	ENSP00000289746:p.Arg35Cys	125.0	0.0	0		147.0	82.0	0.557823	NM_004933		Missense_Mutation	SNP	ENST00000289746.2	37	CCDS10976.1	.	.	.	.	.	.	.	.	.	.	C	15.04	2.713980	0.48622	.	.	ENSG00000129910	ENST00000289746	T	0.58940	0.3	4.58	3.57	0.40892	.	0.454073	0.15889	N	0.239671	T	0.49643	0.1569	N	0.14661	0.345	0.58432	D	0.999997	D	0.69078	0.997	P	0.52343	0.696	T	0.54655	-0.8261	10	0.66056	D	0.02	.	11.1776	0.48610	0.1834:0.8166:0.0:0.0	.	35	P55291	CAD15_HUMAN	C	35	ENSP00000289746:R35C	ENSP00000289746:R35C	R	+	1	0	CDH15	87773385	0.038000	0.19896	0.916000	0.36221	0.077000	0.17291	0.119000	0.15626	2.104000	0.64026	0.407000	0.27541	CGC	.	.	none		0.657	CDH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269920.1	NM_004933	
UTRN	7402	hgsc.bcm.edu	37	6	144898276	144898276	+	Missense_Mutation	SNP	C	C	T	rs367807203		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:144898276C>T	ENST00000367545.3	+	50	7331	c.7331C>T	c.(7330-7332)aCg>aTg	p.T2444M		NM_007124.2	NP_009055.2	P46939	UTRO_HUMAN	utrophin	2444					aging (GO:0007568)|muscle cell differentiation (GO:0042692)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|neuron projection morphogenesis (GO:0048812)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane (GO:0016020)|membrane raft (GO:0045121)|myofibril (GO:0030016)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|cervix(2)|endometrium(21)|kidney(10)|large_intestine(29)|lung(56)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	148		Ovarian(120;0.218)		OV - Ovarian serous cystadenocarcinoma(155;5.72e-07)|GBM - Glioblastoma multiforme(68;4.9e-05)|Colorectal(48;0.213)		GAGTGGAGGACGGTGCAGGCC	0.493																																					p.T2444M		Atlas-SNP	.											.	UTRN	327	.	0			c.C7331T						PASS	.	C	MET/THR	0,4406		0,0,2203	105.0	86.0	93.0		7331	1.1	0.0	6		93	1,8599	1.2+/-3.3	0,1,4299	no	missense	UTRN	NM_007124.2	81	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	2444/3434	144898276	1,13005	2203	4300	6503	SO:0001583	missense	7402	exon50			GGAGGACGGTGCA	AK023675	CCDS34547.1	6q24	2008-02-05	2006-12-13		ENSG00000152818	ENSG00000152818			12635	protein-coding gene	gene with protein product		128240	"""utrophin (homologous to dystrophin)"""	DMDL		1426262	Standard	NM_007124		Approved	DRP, DRP1	uc003qkt.3	P46939	OTTHUMG00000015746	ENST00000367545.3:c.7331C>T	6.37:g.144898276C>T	ENSP00000356515:p.Thr2444Met	139.0	0.0	0		179.0	89.0	0.497207	NM_007124	Q5SYY1|Q5SZ57|Q9UJ40	Missense_Mutation	SNP	ENST00000367545.3	37	CCDS34547.1	.	.	.	.	.	.	.	.	.	.	C	13.76	2.333825	0.41297	0.0	1.16E-4	ENSG00000152818	ENST00000367545	T	0.60299	0.2	6.03	1.14	0.20703	.	0.371682	0.22724	N	0.056418	T	0.20088	0.0483	L	0.33485	1.01	0.09310	N	1	B	0.20261	0.043	B	0.25291	0.059	T	0.19910	-1.0291	10	0.48119	T	0.1	.	2.8168	0.05458	0.1134:0.528:0.11:0.2486	.	2444	P46939	UTRO_HUMAN	M	2444	ENSP00000356515:T2444M	ENSP00000356515:T2444M	T	+	2	0	UTRN	144939969	0.006000	0.16342	0.001000	0.08648	0.663000	0.39108	0.115000	0.15540	0.134000	0.18681	-0.137000	0.14449	ACG	.	.	weak		0.493	UTRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042551.1		
ARHGEF12	23365	hgsc.bcm.edu	37	11	120317731	120317731	+	Missense_Mutation	SNP	G	G	A	rs138160103	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:120317731G>A	ENST00000397843.2	+	18	1692	c.1526G>A	c.(1525-1527)cGa>cAa	p.R509Q	ARHGEF12_ENST00000532993.1_Missense_Mutation_p.R406Q|ARHGEF12_ENST00000356641.3_Missense_Mutation_p.R490Q	NM_015313.2	NP_056128.1	Q9NZN5	ARHGC_HUMAN	Rho guanine nucleotide exchange factor (GEF) 12	509	RGSL.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(5)|endometrium(6)|kidney(5)|large_intestine(13)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(2)	61		Breast(109;0.000813)|Medulloblastoma(222;0.0425)|Hepatocellular(160;0.0831)|all_hematologic(192;0.107)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.231)		GACAAGGACCGATTGACTTTG	0.443			T	MLL	AML								G|||	4	0.000798722	0.0	0.0	5008	,	,		22212	0.0		0.003	False		,,,				2504	0.001				p.R509Q		Atlas-SNP	.		Dom	yes		11	11q23.3	23365	RHO guanine nucleotide exchange factor (GEF) 12 (LARG)		L	.	ARHGEF12	133	.	0			c.G1526A						PASS	.	G	GLN/ARG,GLN/ARG	2,3952		0,2,1975	137.0	128.0	131.0		1469,1526	5.4	1.0	11	dbSNP_134	131	18,8334		0,18,4158	yes	missense,missense	ARHGEF12	NM_001198665.1,NM_015313.2	43,43	0,20,6133	AA,AG,GG		0.2155,0.0506,0.1625	probably-damaging,probably-damaging	490/1526,509/1545	120317731	20,12286	1977	4176	6153	SO:0001583	missense	23365	exon18			AGGACCGATTGAC	AF180681	CCDS41727.1, CCDS55794.1	11q23.3	2011-11-16			ENSG00000196914	ENSG00000196914		"""Rho guanine nucleotide exchange factors"""	14193	protein-coding gene	gene with protein product		604763				10681437, 9205841	Standard	NM_001198665		Approved	KIAA0382, LARG	uc001pxl.2	Q9NZN5	OTTHUMG00000166143	ENST00000397843.2:c.1526G>A	11.37:g.120317731G>A	ENSP00000380942:p.Arg509Gln	166.0	0.0	0		180.0	96.0	0.533333	NM_015313	O15086|Q6P526	Missense_Mutation	SNP	ENST00000397843.2	37	CCDS41727.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	37	6.004474	0.97195	5.06E-4	0.002155	ENSG00000196914	ENST00000397843;ENST00000356641;ENST00000532993	D;D;D	0.83837	-1.77;-1.77;-1.77	5.44	5.44	0.79542	Regulator of G protein signalling superfamily (1);Regulator of G protein signalling-like fold (1);	0.000000	0.41712	D	0.000824	D	0.90086	0.6903	M	0.76328	2.33	0.58432	D	0.999997	D;D;D	0.71674	0.998;0.987;0.989	P;P;P	0.60173	0.87;0.742;0.832	D	0.90454	0.4441	10	0.62326	D	0.03	-16.9171	19.6363	0.95735	0.0:0.0:1.0:0.0	.	406;490;509	B4DGW2;Q9NZN5-2;Q9NZN5	.;.;ARHGC_HUMAN	Q	509;490;406	ENSP00000380942:R509Q;ENSP00000349056:R490Q;ENSP00000432984:R406Q	ENSP00000349056:R490Q	R	+	2	0	ARHGEF12	119822941	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.416000	0.80143	2.714000	0.92807	0.650000	0.86243	CGA	G|0.998;A|0.002	0.002	strong		0.443	ARHGEF12-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388052.1	NM_015313	
RIPK2	8767	hgsc.bcm.edu	37	8	90770393	90770393	+	Silent	SNP	C	C	T	rs200258974		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:90770393C>T	ENST00000220751.4	+	1	419	c.105C>T	c.(103-105)gcC>gcT	p.A35A	RP11-37B2.1_ENST00000504145.1_lincRNA|RIPK2_ENST00000540020.1_5'UTR	NM_003821.5	NP_003812.1	O43353	RIPK2_HUMAN	receptor-interacting serine-threonine kinase 2	35	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|defense response to Gram-positive bacterium (GO:0050830)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of immature T cell proliferation (GO:0033091)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T-helper 1 cell differentiation (GO:0045627)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|response to exogenous dsRNA (GO:0043330)|response to interleukin-1 (GO:0070555)|response to interleukin-12 (GO:0070671)|response to interleukin-18 (GO:0070673)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|T cell proliferation (GO:0042098)|T cell receptor signaling pathway (GO:0050852)|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)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|LIM domain binding (GO:0030274)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(2)	10			BRCA - Breast invasive adenocarcinoma(11;0.0474)			TGTCGTCCGCCCGCCACGCAG	0.677																																					p.A35A		Atlas-SNP	.											RIPK2,NS,malignant_melanoma,+2,1	RIPK2	37	1	0			c.C105T						PASS	.																																			SO:0001819	synonymous_variant	8767	exon1			GTCCGCCCGCCAC	AC004003	CCDS6247.1	8q21	2008-05-02			ENSG00000104312	ENSG00000104312			10020	protein-coding gene	gene with protein product		603455				9575181, 9705938	Standard	XM_005251092		Approved	RICK, RIP2, CARDIAK, CARD3	uc003yee.3	O43353	OTTHUMG00000163809	ENST00000220751.4:c.105C>T	8.37:g.90770393C>T		66.0	0.0	0		86.0	55.0	0.639535	NM_003821	B7Z748|Q6UWF0	Silent	SNP	ENST00000220751.4	37	CCDS6247.1																																																																																			.	.	weak		0.677	RIPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375686.1		
IL6ST	3572	hgsc.bcm.edu	37	5	55248135	55248135	+	Missense_Mutation	SNP	C	C	T	rs34417936	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:55248135C>T	ENST00000381298.2	-	12	1807	c.1495G>A	c.(1495-1497)Gta>Ata	p.V499I	IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381287.4_3'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.V499I|IL6ST_ENST00000502326.3_Missense_Mutation_p.V499I|IL6ST_ENST00000381294.3_Missense_Mutation_p.V438I|IL6ST_ENST00000381293.2_Intron	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	499	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs34417936).		ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				TCAGCATATACTGGAGTAACT	0.363			O		hepatocellular ca								C|||	54	0.0107827	0.003	0.0259	5008	,	,		18030	0.0		0.0258	False		,,,				2504	0.0061				p.V499I		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.G1495A						PASS	.	C	ILE/VAL,ILE/VAL,	25,4381	29.9+/-59.1	0,25,2178	97.0	94.0	95.0		1312,1495,	5.9	0.8	5	dbSNP_126	95	259,8341	101.0+/-162.3	4,251,4045	yes	missense,missense,utr-3	IL6ST	NM_001190981.1,NM_002184.3,NM_175767.2	29,29,	4,276,6223	TT,TC,CC		3.0116,0.5674,2.1836	benign,benign,	438/858,499/919,	55248135	284,12722	2203	4300	6503	SO:0001583	missense	3572	exon12			CATATACTGGAGT	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1495G>A	5.37:g.55248135C>T	ENSP00000370698:p.Val499Ile	144.0	0.0	0		113.0	59.0	0.522124	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	30	0.013736263736263736	2	0.0040650406504065045	14	0.03867403314917127	0	0.0	14	0.018469656992084433	C	11.85	1.761705	0.31228	0.005674	0.030116	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.55234	0.53;0.53;1.12	5.93	5.93	0.95920	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.131931	0.53938	D	0.000041	T	0.11623	0.0283	L	0.31926	0.97	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.07578	-1.0765	10	0.12766	T	0.61	.	10.6199	0.45474	0.1248:0.6405:0.2347:0.0	rs34417936	499;438;499	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	I	499;499;438	ENSP00000370698:V499I;ENSP00000338799:V499I;ENSP00000370694:V438I	ENSP00000338799:V499I	V	-	1	0	IL6ST	55283892	0.919000	0.31177	0.836000	0.33094	0.996000	0.88848	0.610000	0.24253	2.826000	0.97356	0.655000	0.94253	GTA	C|0.980;T|0.020	0.020	strong		0.363	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
PLCB3	5331	hgsc.bcm.edu	37	11	64031241	64031241	+	Missense_Mutation	SNP	C	C	T	rs35169799	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64031241C>T	ENST00000540288.1	+	21	2637	c.2534C>T	c.(2533-2535)tCg>tTg	p.S845L	PLCB3_ENST00000279230.6_Missense_Mutation_p.S845L|PLCB3_ENST00000325234.5_Missense_Mutation_p.S778L	NM_000932.2	NP_000923.1	Q01970	PLCB3_HUMAN	phospholipase C, beta 3 (phosphatidylinositol-specific)	845				S -> L (in Ref. 6; CAA78903). {ECO:0000305}.	inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|regulation of systemic arterial blood pressure (GO:0003073)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|urinary_tract(1)	33						ACCGAAGCCTCGGACTACATT	0.667													C|||	114	0.0227636	0.0023	0.0303	5008	,	,		16910	0.0		0.0666	False		,,,				2504	0.0235				p.S845L		Atlas-SNP	.											PLCB3,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	PLCB3	103	1	0			c.C2534T						scavenged	.	C	LEU/SER,LEU/SER	67,4335	59.9+/-96.7	3,61,2137	89.0	87.0	88.0		2534,2333	5.2	1.0	11	dbSNP_126	88	578,8016	155.5+/-209.5	22,534,3741	yes	missense,missense	PLCB3	NM_000932.2,NM_001184883.1	145,145	25,595,5878	TT,TC,CC		6.7256,1.522,4.9631	benign,benign	845/1235,778/1168	64031241	645,12351	2201	4297	6498	SO:0001583	missense	5331	exon21			AAGCCTCGGACTA	Z26649	CCDS8064.1, CCDS53654.1	11q13	2008-03-18			ENSG00000149782	ENSG00000149782	3.1.4.11		9056	protein-coding gene	gene with protein product		600230				7849701	Standard	NM_000932		Approved		uc009ypg.2	Q01970	OTTHUMG00000167816	ENST00000540288.1:c.2534C>T	11.37:g.64031241C>T	ENSP00000443631:p.Ser845Leu	109.0	1.0	0.00917431		96.0	42.0	0.4375	NM_000932	A5PKZ6|G5E960|Q8N1A4	Missense_Mutation	SNP	ENST00000540288.1	37	CCDS8064.1	67	0.030677655677655676	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	50	0.06596306068601583	C	15.73	2.918361	0.52546	0.01522	0.067256	ENSG00000149782	ENST00000279230;ENST00000540288;ENST00000325234	T;T;T	0.21932	2.11;2.11;1.98	5.25	5.25	0.73442	C2 calcium/lipid-binding domain, CaLB (1);	0.184175	0.48767	D	0.000167	T	0.01156	0.0038	N	0.25647	0.755	0.36001	D	0.837379	D;P	0.58268	0.982;0.838	B;B	0.42138	0.377;0.177	T	0.05084	-1.0907	10	0.72032	D	0.01	.	13.2818	0.60219	0.1592:0.8407:0.0:0.0	rs35169799;rs61755083;rs35169799	778;845	G5E960;Q01970	.;PLCB3_HUMAN	L	845;845;778	ENSP00000279230:S845L;ENSP00000443631:S845L;ENSP00000324660:S778L	ENSP00000279230:S845L	S	+	2	0	PLCB3	63787817	0.637000	0.27216	0.952000	0.39060	0.334000	0.28698	2.527000	0.45615	2.462000	0.83206	0.561000	0.74099	TCG	C|0.957;T|0.043	0.043	strong		0.667	PLCB3-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396405.1		
ZNF418	147686	hgsc.bcm.edu	37	19	58437791	58437791	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437791A>G	ENST00000396147.1	-	4	2049	c.1758T>C	c.(1756-1758)acT>acC	p.T586T	ZNF418_ENST00000595830.1_Silent_p.T586T|ZNF418_ENST00000599852.1_Silent_p.T501T|ZNF418_ENST00000425570.3_Silent_p.T607T|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	586					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		GCCTTTCTCCAGTGTGAACTC	0.438																																					p.T586T		Atlas-SNP	.											.	ZNF418	76	.	0			c.T1758C						PASS	.						78.0	81.0	80.0					19																	58437791		2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			TTCTCCAGTGTGA	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1758T>C	19.37:g.58437791A>G		93.0	0.0	0		85.0	20.0	0.235294	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			.	.	none		0.438	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
GIGYF2	26058	hgsc.bcm.edu	37	2	233712223	233712223	+	Missense_Mutation	SNP	T	T	A	rs114013774|rs527464858	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:233712223T>A	ENST00000409547.1	+	29	3937	c.3626T>A	c.(3625-3627)cTg>cAg	p.L1209Q	GIGYF2_ENST00000409196.3_Missense_Mutation_p.L1203Q|GIGYF2_ENST00000373563.4_Missense_Mutation_p.L1209Q|GIGYF2_ENST00000373566.3_Missense_Mutation_p.L1231Q|GIGYF2_ENST00000409480.1_Missense_Mutation_p.L1231Q|GIGYF2_ENST00000409451.3_Missense_Mutation_p.L1230Q	NM_015575.3	NP_056390.2	Q6Y7W6	PERQ2_HUMAN	GRB10 interacting GYF protein 2	1209	Gln-rich.				adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|feeding behavior (GO:0007631)|homeostasis of number of cells within a tissue (GO:0048873)|insulin-like growth factor receptor signaling pathway (GO:0048009)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|musculoskeletal movement (GO:0050881)|negative regulation of translation (GO:0017148)|neuromuscular process controlling balance (GO:0050885)|post-embryonic development (GO:0009791)|spinal cord motor neuron differentiation (GO:0021522)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(17)|lung(11)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	63		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0271)|Lung NSC(271;0.0839)		Epithelial(121;7.37e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000472)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Lung(119;0.0118)|GBM - Glioblastoma multiforme(43;0.0145)		cagcagcagctgccacagcag	0.557																																					p.L1230Q		Atlas-SNP	.											.	GIGYF2	288	.	0			c.T3689A						PASS	.						14.0	16.0	15.0					2																	233712223		2161	4224	6385	SO:0001583	missense	26058	exon29			AGCAGCTGCCACA	U80751	CCDS33401.1, CCDS46542.1, CCDS46543.1	2q37.1	2011-07-06	2008-02-11	2008-02-11	ENSG00000204120	ENSG00000204120		"""Trinucleotide (CAG) repeat containing"""	11960	protein-coding gene	gene with protein product	"""GYF domain containing 2"""	612003	"""PERQ amino acid rich, with GYF domain 2"", ""PERQ amino acid rich, with GYF domain 3"", ""trinucleotide repeat containing 15"", ""Parkinson disease (autosomal recessive, early onset) 11"""	PERQ2, PERQ3, TNRC15, PARK11		9225980, 9734811, 12771153, 18358451, 19279319	Standard	NM_015575		Approved	KIAA0642, GYF2	uc002vtk.4	Q6Y7W6	OTTHUMG00000153237	ENST00000409547.1:c.3626T>A	2.37:g.233712223T>A	ENSP00000386537:p.Leu1209Gln	42.0	0.0	0		38.0	9.0	0.236842	NM_001103147	A6H8W4|B9EG55|E9PBB0|O75137|Q7Z2Z8|Q7Z3I2|Q96HU4|Q9NV82	Missense_Mutation	SNP	ENST00000409547.1	37	CCDS33401.1	.	.	.	.	.	.	.	.	.	.	T	0.021	-1.427088	0.01117	.	.	ENSG00000204120	ENST00000373566;ENST00000373563;ENST00000409480;ENST00000409547;ENST00000409196;ENST00000409451	T;T;T;T;T;T	0.61859	0.07;0.07;0.07;0.07;0.07;0.07	1.39	-2.77	0.05877	.	.	.	.	.	T	0.25344	0.0616	N	0.04959	-0.14	0.39400	D	0.966566	B;B;B	0.12630	0.0;0.006;0.0	B;B;B	0.08055	0.0;0.003;0.0	T	0.32322	-0.9911	9	0.13108	T	0.6	-0.0091	3.5635	0.07890	0.3937:0.4039:0.0:0.2024	.	1230;1209;1203	A6H8W4;Q6Y7W6;E9PBB0	.;PERQ2_HUMAN;.	Q	1231;1209;1231;1209;1203;1230	ENSP00000362667:L1231Q;ENSP00000362664:L1209Q;ENSP00000386765:L1231Q;ENSP00000386537:L1209Q;ENSP00000387070:L1203Q;ENSP00000387170:L1230Q	ENSP00000362664:L1209Q	L	+	2	0	GIGYF2	233420467	0.003000	0.15002	0.361000	0.25849	0.026000	0.11368	0.028000	0.13644	-2.729000	0.00385	-2.797000	0.00114	CTG	T|0.966;A|0.034	0.034	strong		0.557	GIGYF2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330316.2	NM_001103146	
ZBED1	9189	hgsc.bcm.edu	37	X	2408434	2408434	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:2408434C>T	ENST00000381223.4	-	2	530	c.327G>A	c.(325-327)gcG>gcA	p.A109A	ZBED1_ENST00000381218.3_Silent_p.A109A|DHRSX_ENST00000334651.5_Intron|ZBED1_ENST00000381222.2_Silent_p.A109A|ZBED1_ENST00000515319.1_5'Flank	NM_001171135.1|NM_001171136.1|NM_004729.3	NP_001164606.1|NP_001164607.1|NP_004720.1	O96006	ZBED1_HUMAN	zinc finger, BED-type containing 1	109					metabolic process (GO:0008152)	nuclear chromosome (GO:0000228)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|transposase activity (GO:0004803)			endometrium(8)|kidney(1)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	25		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TGACGGCCAGCGCGTCCTGCC	0.672																																					p.A109A		Atlas-SNP	.											.	ZBED1	64	.	0			c.G327A						PASS	.						59.0	59.0	59.0					X																	2408434		2203	4296	6499	SO:0001819	synonymous_variant	9189	exon2			GGCCAGCGCGTCC	AB018328	CCDS14118.1	Xp22.33 and Yp11	2013-05-03	2004-01-14	2004-01-16	ENSG00000214717	ENSG00000214717		"""Pseudoautosomal regions / PAR1"", ""Zinc fingers, BED-type"""	447	protein-coding gene	gene with protein product		300178	"""Ac-like transposable element"""	ALTE		9872452, 9887332, 23533661	Standard	NM_001171135		Approved	TRAMP, KIAA0785, DREF, hDREF	uc004cqh.2	O96006	OTTHUMG00000021069	ENST00000381223.4:c.327G>A	X.37:g.2408434C>T		139.0	0.0	0		87.0	79.0	0.908046	NM_001171135	Q96BY4	Silent	SNP	ENST00000381223.4	37	CCDS14118.1																																																																																			C|0.999;G|0.001	.	alt		0.672	ZBED1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000144310.3	NM_004729	
MYH11	4629	hgsc.bcm.edu	37	16	15814100	15814100	+	Missense_Mutation	SNP	T	T	G	rs34321232		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15814100T>G	ENST00000300036.5	-	34	4970	c.4861A>C	c.(4861-4863)Aag>Cag	p.K1621Q	MYH11_ENST00000396324.3_Missense_Mutation_p.K1628Q|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000576790.2_Missense_Mutation_p.K1621Q|MYH11_ENST00000452625.2_Missense_Mutation_p.K1628Q|NDE1_ENST00000342673.5_Intron|NDE1_ENST00000396355.1_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1621					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						CCTTCCAGCTTCTTCTTTGCT	0.577			T	CBFB	AML								T|||	1	0.000199681	0.0	0.0	5008	,	,		20791	0.0		0.0	False		,,,				2504	0.001				p.K1628Q		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.A4882C						PASS	.	T	GLN/LYS,GLN/LYS,,GLN/LYS,,GLN/LYS	0,4394		0,0,2197	121.0	104.0	110.0		4882,4882,,4861,,4861	4.9	1.0	16	dbSNP_126	110	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,intron,missense,intron,missense	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	53,53,,53,,53	0,3,6494	GG,GT,TT		0.0349,0.0,0.0231	probably-damaging,probably-damaging,,probably-damaging,,probably-damaging	1628/1946,1628/1980,,1621/1973,,1621/1939	15814100	3,12991	2197	4300	6497	SO:0001583	missense	4629	exon35			CCAGCTTCTTCTT	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.4861A>C	16.37:g.15814100T>G	ENSP00000300036:p.Lys1621Gln	147.0	0.0	0		190.0	98.0	0.515789	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.056096	0.76074	0.0	3.49E-4	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	D;D;D;D	0.85955	-2.05;-2.05;-2.05;-2.05	4.95	4.95	0.65309	Myosin tail (1);	0.000000	0.85682	D	0.000000	D	0.92176	0.7519	M	0.87827	2.91	0.80722	D	1	D;P;P;P;P	0.61697	0.99;0.893;0.893;0.742;0.893	D;P;P;P;P	0.63283	0.913;0.732;0.732;0.732;0.732	D	0.93505	0.6848	10	0.87932	D	0	.	13.7947	0.63164	0.0:0.0:0.0:1.0	rs34321232	1628;1621;1628;1621;1628	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	Q	1621;1621;1628;1628;1628	ENSP00000300036:K1621Q;ENSP00000345136:K1621Q;ENSP00000379616:K1628Q;ENSP00000407821:K1628Q	ENSP00000300036:K1621Q	K	-	1	0	MYH11	15721601	1.000000	0.71417	1.000000	0.80357	0.573000	0.36030	7.950000	0.87804	1.864000	0.54056	0.528000	0.53228	AAG	T|0.987;G|0.013	0.013	weak		0.577	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
MRPL51	51258	hgsc.bcm.edu	37	12	6601475	6601475	+	Missense_Mutation	SNP	G	G	A	rs11380	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:6601475G>A	ENST00000229238.3	-	3	810	c.349C>T	c.(349-351)Ctc>Ttc	p.L117F	NCAPD2_ENST00000545962.1_5'Flank|MRPL51_ENST00000543703.1_Missense_Mutation_p.L21F|NCAPD2_ENST00000315579.5_5'Flank|MRPL51_ENST00000543164.1_5'UTR	NM_016497.3	NP_057581.2	Q4U2R6	RM51_HUMAN	mitochondrial ribosomal protein L51	117					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			kidney(2)|large_intestine(1)|lung(3)	6						TGTTTGTAGAGATAGCGGATG	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		21574	0.0		0.002	False		,,,				2504	0.0				p.L117F		Atlas-SNP	.											MRPL51,NS,carcinoma,0,1	MRPL51	17	1	0			c.C349T						PASS	.	G	PHE/LEU	2,4404	4.2+/-10.8	0,2,2201	232.0	220.0	224.0		349	5.3	1.0	12	dbSNP_52	224	9,8591	7.1+/-27.0	0,9,4291	yes	missense	MRPL51	NM_016497.3	22	0,11,6492	AA,AG,GG		0.1047,0.0454,0.0846	probably-damaging	117/129	6601475	11,12995	2203	4300	6503	SO:0001583	missense	51258	exon3			TGTAGAGATAGCG	AB051355	CCDS8547.1	12p13.3-p13.1	2014-02-19	2002-01-07	2002-01-11		ENSG00000111639		"""Mitochondrial ribosomal proteins / large subunits"""	14044	protein-coding gene	gene with protein product		611855	"""mitochondrial ribosomal protein 64"""	MRP64		11551941, 11543634	Standard	NM_016497		Approved	CDA09, HSPC241, bMRP64	uc001qom.2	Q4U2R6		ENST00000229238.3:c.349C>T	12.37:g.6601475G>A	ENSP00000229238:p.Leu117Phe	326.0	0.0	0		331.0	166.0	0.501511	NM_016497	Q96Q57|Q9BQ36|Q9P0N7	Missense_Mutation	SNP	ENST00000229238.3	37	CCDS8547.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	26.9	4.780307	0.90195	4.54E-4	0.001047	ENSG00000111639	ENST00000229238	T	0.63255	-0.03	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.81128	0.4758	M	0.90483	3.12	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.84217	0.0459	10	0.87932	D	0	-15.4554	10.5659	0.45173	0.1242:0.0:0.8758:0.0	rs11380;rs52796309	117	Q4U2R6	RM51_HUMAN	F	117	ENSP00000229238:L117F	ENSP00000229238:L117F	L	-	1	0	MRPL51	6471736	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	5.291000	0.65667	2.478000	0.83669	0.462000	0.41574	CTC	G|0.999;A|0.001	0.001	strong		0.433	MRPL51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399956.1	NM_016497	
USP3	9960	hgsc.bcm.edu	37	15	63855190	63855190	+	Silent	SNP	G	G	A	rs61751106	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:63855190G>A	ENST00000380324.3	+	8	873	c.744G>A	c.(742-744)aaG>aaA	p.K248K	USP3-AS1_ENST00000560350.1_RNA|USP3_ENST00000268049.7_Silent_p.K226K|USP3_ENST00000559711.1_Silent_p.K159K|USP3-AS1_ENST00000559861.1_RNA|USP3_ENST00000539772.1_5'UTR|USP3_ENST00000536001.1_3'UTR|USP3-AS1_ENST00000559357.1_RNA|USP3_ENST00000558285.1_Silent_p.K231K|USP3_ENST00000540797.1_Silent_p.K204K	NM_006537.3	NP_006528.2	Q9Y6I4	UBP3_HUMAN	ubiquitin specific peptidase 3	248	USP.				DNA repair (GO:0006281)|histone deubiquitination (GO:0016578)|mitotic cell cycle (GO:0000278)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	nuclear chromatin (GO:0000790)	histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(7)|lung(4)	14				GBM - Glioblastoma multiforme(80;0.0187)		TTGTTTGGAAGATTATGCCAA	0.338													G|||	26	0.00519169	0.0008	0.0086	5008	,	,		18673	0.0		0.0119	False		,,,				2504	0.0072				p.K248K		Atlas-SNP	.											.	USP3	37	.	0			c.G744A						PASS	.	G		11,4395	16.8+/-37.8	0,11,2192	111.0	112.0	111.0		744	4.0	1.0	15	dbSNP_129	111	133,8467	62.1+/-124.0	2,129,4169	no	coding-synonymous	USP3	NM_006537.2		2,140,6361	AA,AG,GG		1.5465,0.2497,1.1072		248/521	63855190	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	9960	exon8			TTGGAAGATTATG	AF073344	CCDS32265.1, CCDS58370.1	15q22.3	2008-04-11	2005-08-08			ENSG00000140455		"""Ubiquitin-specific peptidases"""	12626	protein-coding gene	gene with protein product		604728	"""ubiquitin specific protease 3"""			12838346	Standard	NM_006537		Approved		uc002amf.4	Q9Y6I4		ENST00000380324.3:c.744G>A	15.37:g.63855190G>A		75.0	0.0	0		68.0	31.0	0.455882	NM_006537	B4DVU5|F5H1A6|Q8WVD0	Silent	SNP	ENST00000380324.3	37	CCDS32265.1																																																																																			G|0.990;A|0.010	0.010	strong		0.338	USP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417773.1		
OR4A15	81328	hgsc.bcm.edu	37	11	55136157	55136157	+	Silent	SNP	C	C	T	rs147678504	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55136157C>T	ENST00000314706.3	+	1	798	c.798C>T	c.(796-798)taC>taT	p.Y266Y		NM_001005275.1	NP_001005275.1	Q8NGL6	O4A15_HUMAN	olfactory receptor, family 4, subfamily A, member 15	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(2)|endometrium(2)|kidney(2)|large_intestine(7)|lung(48)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	71						AAGCTTTCTACACCTGTGCAT	0.423													.|||	7	0.00139776	0.0008	0.0	5008	,	,		20139	0.0		0.005	False		,,,				2504	0.001				p.Y266Y		Atlas-SNP	.											.	OR4A15	161	.	0			c.C798T						PASS	.	C		2,4400		0,2,2199	211.0	189.0	197.0		798	-0.7	0.0	11	dbSNP_134	197	29,8563		0,29,4267	no	coding-synonymous	OR4A15	NM_001005275.1		0,31,6466	TT,TC,CC		0.3375,0.0454,0.2386		266/345	55136157	31,12963	2201	4296	6497	SO:0001819	synonymous_variant	81328	exon1			TTTCTACACCTGT	AB065776	CCDS31500.1	11q11	2012-08-09			ENSG00000181958	ENSG00000181958		"""GPCR / Class A : Olfactory receptors"""	15152	protein-coding gene	gene with protein product							Standard	NM_001005275		Approved		uc010rif.2	Q8NGL6	OTTHUMG00000166711	ENST00000314706.3:c.798C>T	11.37:g.55136157C>T		205.0	0.0	0		236.0	107.0	0.45339	NM_001005275	Q6IFL4|Q96R65	Silent	SNP	ENST00000314706.3	37	CCDS31500.1																																																																																			C|0.997;T|0.003	0.003	strong		0.423	OR4A15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391161.1	NM_001005275	
KDM3B	51780	hgsc.bcm.edu	37	5	137754808	137754808	+	Missense_Mutation	SNP	G	G	A	rs7706614	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:137754808G>A	ENST00000314358.5	+	14	3802	c.3602G>A	c.(3601-3603)aGc>aAc	p.S1201N	KDM3B_ENST00000508386.1_3'UTR|KDM3B_ENST00000542866.1_Missense_Mutation_p.S233N|KDM3B_ENST00000394866.1_Missense_Mutation_p.S857N	NM_016604.3	NP_057688	Q7LBC6	KDM3B_HUMAN	lysine (K)-specific demethylase 3B	1201			S -> N (in dbSNP:rs7706614).		chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(15)|liver(2)|lung(18)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	65						GCATCAAATAGCAATAGTGAA	0.532													G|||	299	0.0597045	0.0764	0.0187	5008	,	,		17731	0.0208		0.0318	False		,,,				2504	0.135				p.S1201N		Atlas-SNP	.											.	KDM3B	177	.	0			c.G3602A						PASS	.	G	ASN/SER	242,4164	143.1+/-178.2	8,226,1969	83.0	78.0	79.0		3602	5.6	1.0	5	dbSNP_116	79	279,8321	104.8+/-165.8	4,271,4025	yes	missense	KDM3B	NM_016604.3	46	12,497,5994	AA,AG,GG		3.2442,5.4925,4.0058	benign	1201/1762	137754808	521,12485	2203	4300	6503	SO:0001583	missense	51780	exon14			CAAATAGCAATAG	AF251039	CCDS34242.1	5q31	2011-07-01	2009-04-06	2009-04-06	ENSG00000120733	ENSG00000120733		"""Chromatin-modifying enzymes / K-demethylases"""	1337	protein-coding gene	gene with protein product		609373	"""chromosome 5 open reading frame 7"", ""jumonji domain containing 1B"""	C5orf7, JMJD1B		15138608	Standard	NM_016604		Approved	KIAA1082, NET22	uc003lcy.1	Q7LBC6	OTTHUMG00000163469	ENST00000314358.5:c.3602G>A	5.37:g.137754808G>A	ENSP00000326563:p.Ser1201Asn	239.0	0.0	0		289.0	142.0	0.491349	NM_016604	A6H8X7|Q9BVH6|Q9BW93|Q9BZ52|Q9NYF4|Q9UPS0	Missense_Mutation	SNP	ENST00000314358.5	37	CCDS34242.1	84	0.038461538461538464	39	0.07926829268292683	6	0.016574585635359115	10	0.017482517482517484	29	0.03825857519788918	G	13.74	2.328710	0.41197	0.054925	0.032442	ENSG00000120733	ENST00000314358;ENST00000545151;ENST00000394866;ENST00000542866	T;T;T	0.71341	0.03;-0.56;-0.54	5.63	5.63	0.86233	.	0.216515	0.56097	D	0.000039	T	0.06050	0.0157	L	0.27053	0.805	0.39818	D	0.972792	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.002	T	0.13791	-1.0496	10	0.19147	T	0.46	-5.3037	13.3783	0.60752	0.0814:0.0:0.9186:0.0	rs7706614;rs17460129;rs56548578;rs57723304;rs7706614	857;1201	Q7LBC6-2;Q7LBC6	.;KDM3B_HUMAN	N	1201;991;857;233	ENSP00000326563:S1201N;ENSP00000378335:S857N;ENSP00000439462:S233N	ENSP00000326563:S1201N	S	+	2	0	KDM3B	137782707	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.336000	0.52113	2.665000	0.90641	0.650000	0.86243	AGC	G|0.953;A|0.047	0.047	strong		0.532	KDM3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373597.1	NM_016604	
POLD3	10714	hgsc.bcm.edu	37	11	74347244	74347244	+	Silent	SNP	C	C	T	rs35745457	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:74347244C>T	ENST00000263681.2	+	11	1251	c.1122C>T	c.(1120-1122)agC>agT	p.S374S	POLD3_ENST00000527458.1_Silent_p.S335S|POLD3_ENST00000532497.1_Silent_p.S268S	NM_006591.2	NP_006582.1	Q15054	DPOD3_HUMAN	polymerase (DNA-directed), delta 3, accessory subunit	374					base-excision repair (GO:0006284)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|mismatch repair (GO:0006298)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	delta DNA polymerase complex (GO:0043625)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|stomach(1)	18	Breast(11;3.21e-06)					CCTTTTAGAGCTCAAGTGGAG	0.343													C|||	20	0.00399361	0.0015	0.0014	5008	,	,		20618	0.0		0.0159	False		,,,				2504	0.001				p.S374S		Atlas-SNP	.											.	POLD3	87	.	0			c.C1122T						PASS	.	C		9,4391	15.5+/-35.6	0,9,2191	70.0	67.0	68.0		1122	2.0	1.0	11	dbSNP_126	68	110,8476	57.9+/-119.4	1,108,4184	no	coding-synonymous	POLD3	NM_006591.1		1,117,6375	TT,TC,CC		1.2812,0.2045,0.9164		374/467	74347244	119,12867	2200	4293	6493	SO:0001819	synonymous_variant	10714	exon11			TTAGAGCTCAAGT	D26018	CCDS8233.1	11q14	2014-06-13			ENSG00000077514	ENSG00000077514		"""DNA polymerases"""	20932	protein-coding gene	gene with protein product	"""DNA polymerase delta subunit p66"", ""Pol delta C subunit (p66)"", ""protein phosphatase 1, regulatory subunit 128"""	611415				10219083	Standard	NM_006591		Approved	P66, KIAA0039, P68, PPP1R128	uc001ovf.2	Q15054	OTTHUMG00000165621	ENST00000263681.2:c.1122C>T	11.37:g.74347244C>T		139.0	0.0	0		159.0	73.0	0.459119	NM_006591	B7ZAI6|Q32MZ9|Q32N00	Silent	SNP	ENST00000263681.2	37	CCDS8233.1	13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	12.52	1.961262	0.34565	0.002045	0.012812	ENSG00000077514	ENST00000524752	.	.	.	5.92	1.96	0.26148	.	.	.	.	.	T	0.41465	0.1160	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37033	-0.9723	4	.	.	.	-38.8421	8.8571	0.35234	0.0:0.7328:0.0:0.2672	rs35745457;rs61749198	.	.	.	V	98	.	.	A	+	2	0	POLD3	74024892	0.626000	0.27120	0.979000	0.43373	0.990000	0.78478	0.375000	0.20518	0.113000	0.18004	0.561000	0.74099	GCT	C|0.990;T|0.010	0.010	strong		0.343	POLD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385376.1	NM_006591	
SFSWAP	6433	hgsc.bcm.edu	37	12	132240010	132240010	+	Missense_Mutation	SNP	G	G	A	rs34541796	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:132240010G>A	ENST00000261674.4	+	10	1675	c.1534G>A	c.(1534-1536)Ggc>Agc	p.G512S	SFSWAP_ENST00000541286.1_Missense_Mutation_p.G512S|RP11-495K9.5_ENST00000537032.1_lincRNA	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	512			G -> S (in dbSNP:rs34541796).		mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						GAAAGAAGGGGGCGATAGCAT	0.473											OREG0022261	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	14	0.00279553	0.0	0.0029	5008	,	,		20123	0.0		0.0119	False		,,,				2504	0.0				p.G512S		Atlas-SNP	.											SFSWAP,colon,carcinoma,-2,1	SFSWAP	69	1	0			c.G1534A						PASS	.	G	SER/GLY	23,4383	29.9+/-59.1	0,23,2180	84.0	82.0	83.0		1534	2.7	0.0	12	dbSNP_126	83	222,8378	92.1+/-154.2	3,216,4081	yes	missense	SFSWAP	NM_004592.2	56	3,239,6261	AA,AG,GG		2.5814,0.522,1.8837	benign	512/952	132240010	245,12761	2203	4300	6503	SO:0001583	missense	6433	exon10			GAAGGGGGCGATA	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1534G>A	12.37:g.132240010G>A	ENSP00000261674:p.Gly512Ser	35.0	0.0	0	1593	45.0	22.0	0.488889	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Missense_Mutation	SNP	ENST00000261674.4	37	CCDS9273.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	G	5.528	0.282302	0.10458	0.00522	0.025814	ENSG00000061936	ENST00000261674;ENST00000544623;ENST00000535236;ENST00000541286	T;T;T	0.24538	2.84;1.85;2.87	5.49	2.69	0.31865	.	0.412335	0.27946	N	0.017203	T	0.03220	0.0094	N	0.12746	0.255	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.34153	-0.9840	10	0.09084	T	0.74	-12.0835	5.7966	0.18389	0.3482:0.1294:0.5224:0.0	rs34541796	512;512	F5H6B8;Q12872	.;SFSWA_HUMAN	S	512;449;305;512	ENSP00000261674:G512S;ENSP00000443045:G305S;ENSP00000437738:G512S	ENSP00000261674:G512S	G	+	1	0	SFSWAP	130805963	0.000000	0.05858	0.007000	0.13788	0.312000	0.27988	0.482000	0.22276	0.294000	0.22547	0.561000	0.74099	GGC	G|0.987;A|0.013	0.013	strong		0.473	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
URGCP	55665	hgsc.bcm.edu	37	7	43917604	43917604	+	Silent	SNP	C	C	T	rs2232098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43917604C>T	ENST00000453200.1	-	6	1951	c.1458G>A	c.(1456-1458)tcG>tcA	p.S486S	URGCP_ENST00000443736.1_Silent_p.S443S|URGCP_ENST00000497914.1_5'UTR|URGCP_ENST00000447717.3_Silent_p.S443S|URGCP_ENST00000402306.3_Silent_p.S477S|URGCP_ENST00000336086.6_Silent_p.S443S|URGCP_ENST00000223341.7_Silent_p.S443S|URGCP-MRPS24_ENST00000603700.1_Intron			Q8TCY9	URGCP_HUMAN	upregulator of cell proliferation	486					cell cycle (GO:0007049)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|liver(1)|lung(13)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGTAGGCATCCGAGTCTTTGA	0.587													C|||	92	0.0183706	0.0673	0.0043	5008	,	,		19017	0.0		0.0	False		,,,				2504	0.0				p.S486S		Atlas-SNP	.											.	URGCP	170	.	0			c.G1458A						PASS	.	C	,,,	214,3798		7,200,1799	136.0	141.0	140.0		1458,1329,,1431	-7.3	0.0	7	dbSNP_98	140	5,8311		0,5,4153	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	URGCP,URGCP-MRPS24	NM_001077663.1,NM_001077664.1,NM_001204871.1,NM_017920.3	,,,	7,205,5952	TT,TC,CC		0.0601,5.334,1.7764	,,,	486/932,443/889,,477/923	43917604	219,12109	2006	4158	6164	SO:0001819	synonymous_variant	55665	exon6			GGCATCCGAGTCT		CCDS43572.1, CCDS47577.1, CCDS47578.1	7p13	2010-02-17			ENSG00000106608	ENSG00000106608			30890	protein-coding gene	gene with protein product	"""up-regulated gene 4"""	610337				10819331, 12082552	Standard	NM_017920		Approved	URG4, KIAA1507, FLJ20654, DKFZp666G166, DKFZp686O0457	uc003tiw.3	Q8TCY9	OTTHUMG00000155245	ENST00000453200.1:c.1458G>A	7.37:g.43917604C>T		157.0	0.0	0		164.0	82.0	0.5	NM_001077663	E9PFF6|Q658M4|Q68DH6|Q6MZZ5|Q8WV98|Q9NWR7|Q9P221	Silent	SNP	ENST00000453200.1	37	CCDS47578.1																																																																																			C|0.972;T|0.028	0.028	strong		0.587	URGCP-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000338995.1	NM_001077664	
MEGF6	1953	hgsc.bcm.edu	37	1	3418428	3418428	+	Missense_Mutation	SNP	G	G	A	rs200472001	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:3418428G>A	ENST00000356575.4	-	18	2472	c.2246C>T	c.(2245-2247)gCc>gTc	p.A749V	MEGF6_ENST00000294599.4_Missense_Mutation_p.A644V	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	749	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		GTGGCAGGGGGCCCCCCCACA	0.697													G|||	9	0.00179712	0.0	0.0	5008	,	,		14048	0.0		0.001	False		,,,				2504	0.0082				p.A749V	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C2246T						PASS	.	G	VAL/ALA	0,3974		0,0,1987	21.0	30.0	27.0		2246	2.6	0.1	1		27	8,8250		0,8,4121	yes	missense	MEGF6	NM_001409.3	64	0,8,6108	AA,AG,GG		0.0969,0.0,0.0654	probably-damaging	749/1542	3418428	8,12224	1987	4129	6116	SO:0001583	missense	1953	exon18			CAGGGGGCCCCCC	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.2246C>T	1.37:g.3418428G>A	ENSP00000348982:p.Ala749Val	251.0	1.0	0.00398406		250.0	137.0	0.548	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	G	12.47	1.947341	0.34377	0.0	9.69E-4	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.33438	1.41;1.41	3.58	2.61	0.31194	EGF-like, laminin (1);Epidermal growth factor-like, type 3 (1);	0.071934	0.53938	U	0.000043	T	0.59702	0.2213	M	0.91038	3.17	0.32858	D	0.507526	D;D	0.76494	0.999;0.999	D;D	0.72982	0.979;0.979	T	0.73177	-0.4065	10	0.66056	D	0.02	-11.9588	11.1649	0.48537	0.0:0.1871:0.8129:0.0	.	749;644	O75095;O75095-2	MEGF6_HUMAN;.	V	644;749	ENSP00000294599:A644V;ENSP00000348982:A749V	ENSP00000294599:A644V	A	-	2	0	MEGF6	3408288	0.993000	0.37304	0.112000	0.21494	0.318000	0.28184	4.377000	0.59562	0.548000	0.28955	0.455000	0.32223	GCC	G|0.996;A|0.004	0.004	strong		0.697	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
ZNF578	147660	hgsc.bcm.edu	37	19	53015366	53015366	+	Missense_Mutation	SNP	C	C	T	rs376297084		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:53015366C>T	ENST00000421239.2	+	6	1976	c.1732C>T	c.(1732-1734)Cac>Tac	p.H578Y	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	578					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GGCTCACAATCACTTGATTGA	0.393																																					p.H578Y		Atlas-SNP	.											.	.	.	.	0			c.C1732T						PASS	.	C	TYR/HIS	1,4397		0,1,2198	55.0	57.0	56.0		1732	0.1	0.0	19		56	5,8591		0,5,4293	no	missense	ZNF578	NM_001099694.1	83	0,6,6491	TT,TC,CC		0.0582,0.0227,0.0462	possibly-damaging	578/591	53015366	6,12988	2199	4298	6497	SO:0001583	missense	147660	exon6			CACAATCACTTGA	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.1732C>T	19.37:g.53015366C>T	ENSP00000459216:p.His578Tyr	72.0	0.0	0		48.0	25.0	0.520833	NM_001099694	B4DR51|I3L1Y6	Missense_Mutation	SNP	ENST00000421239.2	37	CCDS54310.1	.	.	.	.	.	.	.	.	.	.	-	0.389	-0.924629	0.02377	2.27E-4	5.82E-4	ENSG00000258405	ENST00000553364	.	.	.	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.15825	0.0381	N	0.13098	0.295	0.09310	N	1	B	0.31485	0.325	B	0.20767	0.031	T	0.18777	-1.0326	6	.	.	.	.	.	.	.	.	578	G3V4F6	.	Y	578	.	.	H	+	1	0	ZNF578	57707178	0.033000	0.19621	0.009000	0.14445	0.011000	0.07611	0.000000	0.12993	0.132000	0.18615	0.134000	0.15878	CAC	.	.	weak		0.393	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
YBEY	54059	hgsc.bcm.edu	37	21	47717493	47717493	+	Missense_Mutation	SNP	G	G	T	rs61736728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47717493G>T	ENST00000329319.3	+	5	847	c.449G>T	c.(448-450)cGa>cTa	p.R150L	YBEY_ENST00000397692.1_Missense_Mutation_p.R62L|YBEY_ENST00000339195.6_Missense_Mutation_p.R107L|YBEY_ENST00000397691.1_Missense_Mutation_p.R150L|YBEY_ENST00000397694.1_Missense_Mutation_p.R105L|YBEY_ENST00000397701.4_Missense_Mutation_p.R150L	NM_058181.1	NP_478061.1	P58557	YBEY_HUMAN	ybeY metallopeptidase (putative)	150					rRNA processing (GO:0006364)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			endometrium(2)|large_intestine(1)|lung(4)|ovary(2)	9						GAGCTGGGCCGACGCACGGGG	0.701													G|||	87	0.0173722	0.0015	0.0245	5008	,	,		10890	0.001		0.0626	False		,,,				2504	0.0041				p.R150L		Atlas-SNP	.											YBEY,NS,carcinoma,0,1	YBEY	23	1	0			c.G449T						PASS	.	G	LEU/ARG	49,4099		1,47,2026	6.0	7.0	7.0		449	0.1	0.0	21	dbSNP_129	7	459,7799		8,443,3678	yes	missense	YBEY	NM_058181.1	102	9,490,5704	TT,TG,GG		5.5582,1.1813,4.0948	probably-damaging	150/168	47717493	508,11898	2074	4129	6203	SO:0001583	missense	54059	exon5			TGGGCCGACGCAC	AK294975	CCDS33591.1	21q22.3	2010-12-08	2010-12-08	2010-12-08	ENSG00000182362	ENSG00000182362			1299	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 57"""	C21orf57			Standard	XM_005261155		Approved		uc002ziv.3	P58557	OTTHUMG00000090632	ENST00000329319.3:c.449G>T	21.37:g.47717493G>T	ENSP00000329614:p.Arg150Leu	94.0	0.0	0		82.0	51.0	0.621951	NM_058181	B7WPA9|B7WPF7|D3DSN2	Missense_Mutation	SNP	ENST00000329319.3	37	CCDS33591.1	70	0.03205128205128205	3	0.006097560975609756	13	0.03591160220994475	1	0.0017482517482517483	53	0.06992084432717678	G	9.562	1.118668	0.20877	0.011813	0.055582	ENSG00000182362	ENST00000397701;ENST00000397694;ENST00000329319;ENST00000339195;ENST00000397692;ENST00000397691	.	.	.	4.96	0.0754	0.14399	.	0.158082	0.35838	N	0.002954	T	0.01029	0.0034	N	0.17594	0.5	0.09310	N	1	P;P;P;P	0.44044	0.462;0.825;0.804;0.704	B;B;B;B	0.43950	0.151;0.437;0.28;0.197	T	0.16364	-1.0405	9	0.02654	T	1	-8.7638	7.6929	0.28577	0.4468:0.0:0.5532:0.0	rs61736728	62;107;105;150	P58557-4;P58557-2;P58557-3;P58557	.;.;.;YBEY_HUMAN	L	150;105;150;107;62;150	.	ENSP00000329614:R150L	R	+	2	0	YBEY	46541921	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.015000	0.13355	-0.096000	0.12329	-1.036000	0.02392	CGA	G|0.968;T|0.032	0.032	strong		0.701	YBEY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207265.1	NM_058181	
B4GALNT3	283358	hgsc.bcm.edu	37	12	644351	644351	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:644351A>G	ENST00000266383.5	+	2	202	c.189A>G	c.(187-189)gaA>gaG	p.E63E		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	63					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			GCTGGAGAGAACTGGCCAAGG	0.567																																					p.E63E		Atlas-SNP	.											.	B4GALNT3	64	.	0			c.A189G						PASS	.						50.0	46.0	47.0					12																	644351		2203	4300	6503	SO:0001819	synonymous_variant	283358	exon2			GAGAGAACTGGCC	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.189A>G	12.37:g.644351A>G		43.0	0.0	0		46.0	4.0	0.0869565	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			.	.	none		0.567	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
CCDC68	80323	hgsc.bcm.edu	37	18	52605279	52605279	+	Missense_Mutation	SNP	C	C	T	rs72928889	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:52605279C>T	ENST00000591504.1	-	5	528	c.254G>A	c.(253-255)tGt>tAt	p.C85Y	CCDC68_ENST00000432185.1_Missense_Mutation_p.C85Y|CCDC68_ENST00000337363.4_Missense_Mutation_p.C85Y	NM_025214.2	NP_079490.1	Q9H2F9	CCD68_HUMAN	coiled-coil domain containing 68	85										breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|stomach(1)	14				Colorectal(16;0.0256)|READ - Rectum adenocarcinoma(59;0.21)		CAAACTGCAACAAGAAGGATC	0.358													C|||	65	0.0129792	0.003	0.0173	5008	,	,		18079	0.0		0.0417	False		,,,				2504	0.0072				p.C85Y		Atlas-SNP	.											.	CCDC68	38	.	0			c.G254A						PASS	.	C	TYR/CYS,TYR/CYS	31,4375	37.6+/-69.7	1,29,2173	98.0	90.0	93.0		254,254	1.1	0.0	18	dbSNP_130	93	309,8291	111.8+/-172.0	5,299,3996	yes	missense,missense	CCDC68	NM_001143829.1,NM_025214.2	194,194	6,328,6169	TT,TC,CC		3.593,0.7036,2.6142	benign,benign	85/336,85/336	52605279	340,12666	2203	4300	6503	SO:0001583	missense	80323	exon5			CTGCAACAAGAAG		CCDS11959.1	18q21	2006-02-07			ENSG00000166510	ENSG00000166510			24350	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma associated antigen"""					11149944, 15142679	Standard	NM_025214		Approved	SE57-1	uc002lft.3	Q9H2F9	OTTHUMG00000132708	ENST00000591504.1:c.254G>A	18.37:g.52605279C>T	ENSP00000466690:p.Cys85Tyr	182.0	0.0	0		188.0	89.0	0.473404	NM_025214	B2R9I3	Missense_Mutation	SNP	ENST00000591504.1	37	CCDS11959.1	37	0.01694139194139194	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	25	0.032981530343007916	C	14.87	2.663408	0.47572	0.007036	0.03593	ENSG00000166510	ENST00000337363;ENST00000432185	T;T	0.21361	2.01;2.01	5.18	1.09	0.20402	.	0.935721	0.09027	N	0.859369	T	0.03263	0.0095	L	0.46157	1.445	0.09310	N	1	P	0.51351	0.944	B	0.41036	0.346	T	0.14227	-1.0480	10	0.22109	T	0.4	2.9925	2.645	0.04981	0.1348:0.4379:0.2634:0.1639	.	85	Q9H2F9	CCD68_HUMAN	Y	85	ENSP00000337209:C85Y;ENSP00000413406:C85Y	ENSP00000337209:C85Y	C	-	2	0	CCDC68	50756277	0.000000	0.05858	0.009000	0.14445	0.868000	0.49771	-0.460000	0.06720	0.563000	0.29222	-0.181000	0.13052	TGT	C|0.975;T|0.025	0.025	strong		0.358	CCDC68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256006.1	NM_025214	
ARVCF	421	hgsc.bcm.edu	37	22	19969495	19969495	+	Silent	SNP	G	G	T	rs33992092	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19969495G>T	ENST00000263207.3	-	4	621	c.330C>A	c.(328-330)gtC>gtA	p.V110V	ARVCF_ENST00000406522.1_Silent_p.V47V|ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000401994.1_Silent_p.V47V|ARVCF_ENST00000344269.3_Silent_p.V47V|ARVCF_ENST00000406259.1_Silent_p.V110V	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	110					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CTTCGGATGTGACAATAGACA	0.652													G|||	108	0.0215655	0.0711	0.0086	5008	,	,		17773	0.0		0.008	False		,,,				2504	0.0				p.V110V		Atlas-SNP	.											.	ARVCF	54	.	0			c.C330A						PASS	.	G		239,4167	138.8+/-174.5	7,225,1971	123.0	94.0	104.0		330	1.3	1.0	22	dbSNP_126	104	38,8562	26.3+/-74.7	0,38,4262	no	coding-synonymous	ARVCF	NM_001670.2		7,263,6233	TT,TG,GG		0.4419,5.4244,2.1298		110/963	19969495	277,12729	2203	4300	6503	SO:0001819	synonymous_variant	421	exon4			GGATGTGACAATA		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.330C>A	22.37:g.19969495G>T		194.0	0.0	0		229.0	108.0	0.471616	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			G|0.979;T|0.021	0.021	strong		0.652	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
OS9	10956	hgsc.bcm.edu	37	12	58114677	58114677	+	Silent	SNP	C	C	T	rs564358823		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:58114677C>T	ENST00000315970.7	+	15	2030	c.1989C>T	c.(1987-1989)gaC>gaT	p.D663D	OS9_ENST00000552285.1_Silent_p.D608D|OS9_ENST00000413095.2_Silent_p.D402D|RP11-571M6.8_ENST00000548410.2_RNA|OS9_ENST00000389142.5_Silent_p.D593D|OS9_ENST00000389146.6_Silent_p.D648D|OS9_ENST00000439210.2_Silent_p.D534D|RP11-571M6.7_ENST00000549477.1_RNA|OS9_ENST00000435406.2_Silent_p.D556D|OS9_ENST00000551035.1_Silent_p.D576D|OS9_ENST00000257966.8_Silent_p.D609D	NM_001017958.2|NM_006812.3	NP_001017958.1|NP_006803.1	Q13438	OS9_HUMAN	osteosarcoma amplified 9, endoplasmic reticulum lectin	663					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|protein retention in ER lumen (GO:0006621)|protein targeting (GO:0006605)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum lumen (GO:0005788)|Hrd1p ubiquitin ligase complex (GO:0000836)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	21	all_neural(12;0.00548)|Glioma(12;0.0126)|Melanoma(17;0.122)		BRCA - Breast invasive adenocarcinoma(9;0.109)			GGGACCTGGACGAATTTGACT	0.607																																					p.D663D		Atlas-SNP	.											.	OS9	55	.	0			c.C1989T						PASS	.						74.0	78.0	77.0					12																	58114677		2203	4300	6503	SO:0001819	synonymous_variant	10956	exon15			CCTGGACGAATTT	AB002806	CCDS31843.1, CCDS31844.1, CCDS31845.1, CCDS31846.1, CCDS58246.1, CCDS58247.1, CCDS58248.1, CCDS58249.1	12q13	2009-08-26	2009-08-26						16994	protein-coding gene	gene with protein product	"""endoplasmic reticulum lectin 2"", ""erlectin 2"""	609677				8634085, 9498564, 19346256, 18264092	Standard	NM_006812		Approved	OS-9, ERLEC2	uc001spj.3	Q13438	OTTHUMG00000170284	ENST00000315970.7:c.1989C>T	12.37:g.58114677C>T		111.0	0.0	0		112.0	59.0	0.526786	NM_006812	A6NDD1|A6NFR7|A6NLB2|A8K5Q9|B4DE28|B4DPX1|B4E1I6|E7ENT8|E7EW91|F8VUH2|G3XA88|O00579|Q6IBL2|Q8IZ58|Q9BW99	Silent	SNP	ENST00000315970.7	37	CCDS31843.1																																																																																			.	.	none		0.607	OS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408344.1	NM_006812	
ARHGAP35	2909	hgsc.bcm.edu	37	19	47422388	47422388	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47422388C>T	ENST00000404338.3	+	1	456	c.456C>T	c.(454-456)gaC>gaT	p.D152D		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	152					axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										AAATGCCAGACGGAAAGCTGC	0.473																																					p.D152D		Atlas-SNP	.											GRLF1_ENST00000317082,NS,carcinoma,+1,2	.	.	2	0			c.C456T						PASS	.						81.0	76.0	78.0					19																	47422388		1933	4138	6071	SO:0001819	synonymous_variant	2909	exon1			GCCAGACGGAAAG	M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.456C>T	19.37:g.47422388C>T		110.0	0.0	0		104.0	56.0	0.538462	NM_004491	A7E2A4|Q14452|Q9C0E1	Silent	SNP	ENST00000404338.3	37	CCDS46127.1																																																																																			.	.	none		0.473	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466652.1	NM_004491	
WDR81	124997	hgsc.bcm.edu	37	17	1636950	1636950	+	Missense_Mutation	SNP	C	C	A	rs11657394	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1636950C>A	ENST00000409644.1	+	7	4619	c.4619C>A	c.(4618-4620)cCc>cAc	p.P1540H	WDR81_ENST00000309182.5_Missense_Mutation_p.P489H|WDR81_ENST00000545662.1_Missense_Mutation_p.P171H|WDR81_ENST00000446363.1_Missense_Mutation_p.P179H|WDR81_ENST00000419248.1_Missense_Mutation_p.P313H|WDR81_ENST00000437219.2_Missense_Mutation_p.P337H|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1540				P -> H (in Ref. 1; BAB84937). {ECO:0000305}.	negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GGCACCGGGCCCGAGTGGGAC	0.677													C|||	165	0.0329473	0.0295	0.0331	5008	,	,		15625	0.0		0.0716	False		,,,				2504	0.0317				p.P1540H		Atlas-SNP	.											.	WDR81	180	.	0			c.C4619A						PASS	.	C	HIS/PRO,HIS/PRO,HIS/PRO,HIS/PRO	170,4230		6,158,2036	27.0	31.0	30.0		1010,4619,938,1466	3.0	0.4	17	dbSNP_120	30	646,7940		23,600,3670	yes	missense,missense,missense,missense	WDR81	NM_001163673.1,NM_001163809.1,NM_001163811.1,NM_152348.3	77,77,77,77	29,758,5706	AA,AC,CC		7.5239,3.8636,6.2837	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	337/739,1540/1942,313/715,489/891	1636950	816,12170	2200	4293	6493	SO:0001583	missense	124997	exon7			CCGGGCCCGAGTG	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.4619C>A	17.37:g.1636950C>A	ENSP00000386609:p.Pro1540His	111.0	0.0	0		74.0	42.0	0.567568	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	80	0.03663003663003663	18	0.036585365853658534	10	0.027624309392265192	0	0.0	52	0.06860158311345646	C	9.979	1.227684	0.22542	0.038636	0.075239	ENSG00000167716	ENST00000437219;ENST00000309182;ENST00000446363;ENST00000419248;ENST00000418841;ENST00000409644;ENST00000354680;ENST00000545662	T;T;T;T;T;T;T	0.79940	-1.32;-1.32;-1.32;-1.32;-1.32;-1.32;-1.32	4.99	2.99	0.34606	.	0.416547	0.23768	N	0.044749	T	0.12050	0.0293	L	0.38531	1.155	0.09310	N	0.999998	P;P;P	0.39624	0.681;0.681;0.681	B;B;B	0.39971	0.315;0.315;0.215	T	0.10800	-1.0614	9	.	.	.	.	8.0582	0.30617	0.0:0.7513:0.0:0.2487	rs11657394	171;337;489	B7Z6V3;B7Z579;Q562E7	.;.;WDR81_HUMAN	H	337;489;179;313;125;1540;291;171	ENSP00000391074:P337H;ENSP00000312074:P489H;ENSP00000401560:P179H;ENSP00000407845:P313H;ENSP00000395198:P125H;ENSP00000386609:P1540H;ENSP00000442726:P171H	.	P	+	2	0	WDR81	1583700	0.000000	0.05858	0.424000	0.26647	0.467000	0.32768	0.449000	0.21744	0.519000	0.28406	0.563000	0.77884	CCC	C|0.946;A|0.054	0.054	strong		0.677	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
CGB8	94115	hgsc.bcm.edu	37	19	49551573	49551573	+	Silent	SNP	C	C	T	rs151241744	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49551573C>T	ENST00000448456.3	-	2	438	c.72G>A	c.(70-72)ccG>ccA	p.P24P	CGB8_ENST00000355414.2_Silent_p.P22P|CGB1_ENST00000391869.3_Intron	NM_033183.2	NP_149439.1	P01233	CGHB_HUMAN	chorionic gonadotropin, beta polypeptide 8	24			P -> M (requires 2 nucleotide substitutions). {ECO:0000269|PubMed:11861891, ECO:0000269|PubMed:6194155}.		apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|female gamete generation (GO:0007292)|peptide hormone processing (GO:0016486)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			pancreas(1)	1		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		GTGGCCGAAGCGGCTCCTTGG	0.657																																					p.P24P		Atlas-SNP	.											CGB8,NS,carcinoma,0,1	CGB8	2	1	0			c.G72A						scavenged	.						1.0	1.0	1.0					19																	49551573		258	679	937	SO:0001819	synonymous_variant	94115	exon2			CCGAAGCGGCTCC	BG435249	CCDS12753.1	19q13.32	2011-05-26							16453	protein-coding gene	gene with protein product		608827				6194155	Standard	NM_033183		Approved		uc002pmb.4	P01233		ENST00000448456.3:c.72G>A	19.37:g.49551573C>T		127.0	0.0	0		135.0	25.0	0.185185	NM_033183	A1A5E0|B9ZVP5|Q13991|Q14000|Q3KPI3|Q3SY41|Q8WTT5|Q8WXL1|Q8WXL2|Q8WXL3|Q8WXL4	Silent	SNP	ENST00000448456.3	37	CCDS12753.1																																																																																			T|1.000;|0.000	1.000	weak		0.657	CGB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452168.1	NM_033183	
SP8	221833	hgsc.bcm.edu	37	7	20825271	20825271	+	Silent	SNP	C	C	T	rs145875827		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:20825271C>T	ENST00000361443.4	-	3	348	c.111G>A	c.(109-111)tcG>tcA	p.S37S	SP8_ENST00000418710.2_Silent_p.S55S	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	37	Ser-rich.				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)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						AAGAAGAGGACGAGGAGCGTT	0.632																																					p.S55S		Atlas-SNP	.											.	SP8	43	.	0			c.G165A						PASS	.	C	,	1,4405		0,1,2202	46.0	47.0	47.0		165,111	-4.4	1.0	7	dbSNP_134	47	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SP8	NM_182700.4,NM_198956.2	,	0,4,6499	TT,TC,CC		0.0349,0.0227,0.0308	,	55/509,37/491	20825271	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	221833	exon2			AGAGGACGAGGAG		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.111G>A	7.37:g.20825271C>T		54.0	0.0	0		62.0	34.0	0.548387	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			C|1.000;T|0.000	0.000	weak		0.632	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
PDXDC1	23042	hgsc.bcm.edu	37	16	15111265	15111265	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:15111265G>A	ENST00000396410.4	+	11	1046	c.949G>A	c.(949-951)Gat>Aat	p.D317N	PDXDC1_ENST00000455313.2_Missense_Mutation_p.D294N|PDXDC1_ENST00000569715.1_Missense_Mutation_p.D290N|PDXDC1_ENST00000563679.1_Missense_Mutation_p.D335N|RP11-680G24.5_ENST00000565178.1_RNA|PDXDC1_ENST00000325823.7_Missense_Mutation_p.D302N|PDXDC1_ENST00000447912.2_Missense_Mutation_p.D226N|PDXDC1_ENST00000535621.2_Missense_Mutation_p.D317N|PDXDC1_ENST00000450288.2_Missense_Mutation_p.D289N	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	317					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GTATAAACACGATGACCCTGC	0.502																																					p.D317N		Atlas-SNP	.											.	PDXDC1	59	.	0			c.G949A						PASS	.						112.0	114.0	113.0					16																	15111265		2197	4300	6497	SO:0001583	missense	23042	exon11			AAACACGATGACC	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.949G>A	16.37:g.15111265G>A	ENSP00000379691:p.Asp317Asn	110.0	0.0	0		147.0	34.0	0.231293	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.526001	0.85600	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000537781;ENST00000455313	T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0	5.45	5.45	0.79879	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.044008	0.85682	D	0.000000	T	0.26629	0.0651	L	0.36672	1.1	0.47374	D	0.999404	P;P;P;P;P;P	0.51240	0.88;0.943;0.94;0.88;0.88;0.625	B;P;P;B;B;B	0.49597	0.288;0.463;0.616;0.288;0.288;0.2	T	0.00827	-1.1550	10	0.23891	T	0.37	-11.8011	18.2726	0.90073	0.0:0.0:1.0:0.0	.	289;226;317;289;317;294	E7EPL4;E7EMH5;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;PDXD1_HUMAN;.	N	302;226;317;317;289;23;294	ENSP00000322807:D302N;ENSP00000400310:D226N;ENSP00000437835:D317N;ENSP00000379691:D317N;ENSP00000391147:D289N;ENSP00000406703:D294N	ENSP00000322807:D302N	D	+	1	0	PDXDC1	15018766	1.000000	0.71417	0.619000	0.29118	0.845000	0.48019	8.666000	0.91149	2.546000	0.85860	0.542000	0.68232	GAT	.	.	none		0.502	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
WSCD1	23302	hgsc.bcm.edu	37	17	5984001	5984001	+	Missense_Mutation	SNP	T	T	C	rs199969111	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:5984001T>C	ENST00000574946.1	+	2	413	c.23T>C	c.(22-24)cTc>cCc	p.L8P	WSCD1_ENST00000574232.1_Missense_Mutation_p.L8P|WSCD1_ENST00000573634.1_Intron|WSCD1_ENST00000317744.5_Missense_Mutation_p.L8P|WSCD1_ENST00000539421.1_Missense_Mutation_p.L8P			Q658N2	WSCD1_HUMAN	WSC domain containing 1	8						integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						TTCTTCCGACTCCAGAAGTTT	0.662													T|||	10	0.00199681	0.0	0.0	5008	,	,		16288	0.0		0.002	False		,,,				2504	0.0082				p.L8P		Atlas-SNP	.											.	WSCD1	84	.	0			c.T23C						PASS	.	T	PRO/LEU	0,4242		0,0,2121	42.0	41.0	41.0		23	5.1	1.0	17		41	6,8158		0,6,4076	yes	missense	WSCD1	NM_015253.1	98	0,6,6197	CC,CT,TT		0.0735,0.0,0.0484	probably-damaging	8/576	5984001	6,12400	2121	4082	6203	SO:0001583	missense	23302	exon2			TCCGACTCCAGAA		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.23T>C	17.37:g.5984001T>C	ENSP00000460825:p.Leu8Pro	176.0	0.0	0		186.0	93.0	0.5	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Missense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	T	16.23	3.064321	0.55432	0.0	7.35E-4	ENSG00000179314	ENST00000317744;ENST00000539421	D;D	0.83163	-1.69;-1.69	5.07	5.07	0.68467	.	0.088957	0.46145	D	0.000303	D	0.86665	0.5987	L	0.39898	1.24	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	D	0.87073	0.2161	10	0.52906	T	0.07	-33.0853	12.7983	0.57571	0.0:0.0:0.0:1.0	.	8	Q658N2	WSCD1_HUMAN	P	8	ENSP00000323087:L8P;ENSP00000446032:L8P	ENSP00000323087:L8P	L	+	2	0	WSCD1	5924725	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.853000	0.62911	1.904000	0.55121	0.455000	0.32223	CTC	T|0.999;C|0.001	0.001	weak		0.662	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141381103	141381103	+	Silent	SNP	G	G	A	rs3735804	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:141381103G>A	ENST00000438773.2	-	8	1444	c.1311C>T	c.(1309-1311)ccC>ccT	p.P437P	TRAPPC9_ENST00000389328.4_Silent_p.P535P|TRAPPC9_ENST00000389327.3_Silent_p.P428P	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	437					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						GACTGTAGCCGGGCAGCGTTT	0.597													G|||	5	0.000998403	0.0	0.0	5008	,	,		17975	0.005		0.0	False		,,,				2504	0.0				p.P535P		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C1605T						PASS	.						83.0	83.0	83.0					8																	141381103		2203	4300	6503	SO:0001819	synonymous_variant	83696	exon8			GTAGCCGGGCAGC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.1311C>T	8.37:g.141381103G>A		98.0	0.0	0		122.0	57.0	0.467213	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	5	0.0022893772893772895	0	0.0	0	0.0	5	0.008741258741258742	0	0.0	G	7.589	0.670340	0.14776	.	.	ENSG00000167632	ENST00000520857	.	.	.	5.5	-6.88	0.01665	.	.	.	.	.	T	0.43478	0.1249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55471	-0.8136	4	.	.	.	.	10.8351	0.46683	0.6972:0.0949:0.2079:0.0	rs3735804;rs3735804	.	.	.	W	281	.	.	R	-	1	2	TRAPPC9	141450285	0.044000	0.20184	0.707000	0.30419	0.576000	0.36127	-0.575000	0.05861	-1.330000	0.02255	-0.391000	0.06502	CGG	G|0.996;A|0.004	0.004	strong		0.597	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
ZNF426	79088	hgsc.bcm.edu	37	19	9639710	9639710	+	Silent	SNP	T	T	C	rs45489098	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:9639710T>C	ENST00000535489.1	-	6	1347	c.1011A>G	c.(1009-1011)gtA>gtG	p.V337V	ZNF426_ENST00000253115.2_Silent_p.V337V|ZNF426_ENST00000593003.1_Silent_p.V299V			Q9BUY5	ZN426_HUMAN	zinc finger protein 426	337					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(3)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	20						ATTCCTTACATACATAGGGTT	0.433													T|||	10	0.00199681	0.0015	0.0043	5008	,	,		22000	0.0		0.005	False		,,,				2504	0.0				p.V337V		Atlas-SNP	.											.	ZNF426	56	.	0			c.A1011G						PASS	.	T		6,4400	12.9+/-30.5	0,6,2197	96.0	96.0	96.0		1011	-0.1	0.0	19	dbSNP_127	96	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	ZNF426	NM_024106.1		0,61,6442	CC,CT,TT		0.6395,0.1362,0.469		337/555	9639710	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	79088	exon8			CTTACATACATAG	AK095759	CCDS12215.1, CCDS74279.1	19p13.2	2013-01-08				ENSG00000130818		"""Zinc fingers, C2H2-type"", ""-"""	20725	protein-coding gene	gene with protein product							Standard	NM_024106		Approved	MGC2663	uc002mlq.3	Q9BUY5		ENST00000535489.1:c.1011A>G	19.37:g.9639710T>C		70.0	0.0	0		110.0	54.0	0.490909	NM_024106	B3KTL2	Silent	SNP	ENST00000535489.1	37	CCDS12215.1																																																																																			T|0.995;C|0.005	0.005	strong		0.433	ZNF426-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449905.1	NM_024106	
OGDHL	55753	hgsc.bcm.edu	37	10	50953406	50953406	+	Missense_Mutation	SNP	G	G	T	rs145957744		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:50953406G>T	ENST00000374103.4	-	12	1698	c.1613C>A	c.(1612-1614)aCc>aAc	p.T538N	OGDHL_ENST00000419399.1_Missense_Mutation_p.T481N|OGDHL_ENST00000432695.1_Missense_Mutation_p.T329N	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	538					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						CTCCTGCAGGGTGACTGTGCC	0.592																																					p.T538N		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1613A						PASS	.						72.0	64.0	67.0					10																	50953406		2203	4300	6503	SO:0001583	missense	55753	exon12			TGCAGGGTGACTG	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1613C>A	10.37:g.50953406G>T	ENSP00000363216:p.Thr538Asn	62.0	0.0	0		88.0	49.0	0.556818	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Missense_Mutation	SNP	ENST00000374103.4	37	CCDS7234.1	.	.	.	.	.	.	.	.	.	.	G	14.93	2.682876	0.47991	.	.	ENSG00000197444	ENST00000374103;ENST00000419399;ENST00000432695	T;T;D	0.95690	2.45;2.45;-3.78	5.4	5.4	0.78164	Dehydrogenase, E1 component (1);	0.051680	0.85682	D	0.000000	D	0.93903	0.8049	L	0.52011	1.625	0.58432	D	0.999999	B;B;B	0.12013	0.004;0.001;0.005	B;B;B	0.20577	0.012;0.007;0.03	D	0.90070	0.4162	10	0.37606	T	0.19	.	19.5511	0.95322	0.0:0.0:1.0:0.0	.	481;329;538	Q9ULD0-2;Q9ULD0-3;Q9ULD0	.;.;OGDHL_HUMAN	N	538;481;329	ENSP00000363216:T538N;ENSP00000401356:T481N;ENSP00000390240:T329N	ENSP00000363216:T538N	T	-	2	0	OGDHL	50623412	1.000000	0.71417	1.000000	0.80357	0.873000	0.50193	4.517000	0.60503	2.704000	0.92352	0.650000	0.86243	ACC	G|1.000;T|0.000	0.000	weak		0.592	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
WDR81	124997	hgsc.bcm.edu	37	17	1634183	1634183	+	Missense_Mutation	SNP	C	C	T	rs375054918		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1634183C>T	ENST00000409644.1	+	3	3910	c.3910C>T	c.(3910-3912)Cgc>Tgc	p.R1304C	WDR81_ENST00000309182.5_Missense_Mutation_p.R253C|WDR81_ENST00000545662.1_5'UTR|WDR81_ENST00000446363.1_5'UTR|WDR81_ENST00000419248.1_Missense_Mutation_p.R77C|WDR81_ENST00000437219.2_Missense_Mutation_p.R101C|RP11-961A15.1_ENST00000576540.1_RNA	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	1304					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CCACATCGCCCGCCTGTATGG	0.652																																					p.R1304C		Atlas-SNP	.											.	WDR81	180	.	0			c.C3910T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	68.0	68.0	68.0		757,229,3910,301	-0.5	1.0	17		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	WDR81	NM_152348.3,NM_001163811.1,NM_001163809.1,NM_001163673.1	180,180,180,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign,benign	253/891,77/715,1304/1942,101/739	1634183	1,13005	2203	4300	6503	SO:0001583	missense	124997	exon3			ATCGCCCGCCTGT	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.3910C>T	17.37:g.1634183C>T	ENSP00000386609:p.Arg1304Cys	98.0	0.0	0		117.0	49.0	0.418803	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	37	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	13.13	2.146331	0.37923	0.0	1.16E-4	ENSG00000167716	ENST00000455636;ENST00000437219;ENST00000309182;ENST00000419248;ENST00000409644	T;T;T;T	0.50813	2.45;2.45;2.45;0.73	5.69	-0.476	0.12100	.	0.474665	0.24649	N	0.036728	T	0.19967	0.0480	N	0.02011	-0.69	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.04840	-1.0923	10	0.38643	T	0.18	.	12.3797	0.55299	0.0:0.5955:0.0:0.4045	.	101;431;253	B7Z579;Q8TEL1;Q562E7	.;.;WDR81_HUMAN	C	101;101;253;77;1304	ENSP00000391074:R101C;ENSP00000312074:R253C;ENSP00000407845:R77C;ENSP00000386609:R1304C	ENSP00000312074:R253C	R	+	1	0	WDR81	1580933	0.804000	0.28969	0.983000	0.44433	0.645000	0.38454	1.280000	0.33202	0.064000	0.16427	0.655000	0.94253	CGC	.	.	weak		0.652	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
ZNF519	162655	hgsc.bcm.edu	37	18	14104957	14104957	+	Missense_Mutation	SNP	G	G	A	rs149267105	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:14104957G>A	ENST00000590202.1	-	3	1734	c.1582C>T	c.(1582-1584)Cgc>Tgc	p.R528C	RP11-411B10.3_ENST00000592926.1_RNA|ZNF519_ENST00000589498.1_Intron|ZNF519_ENST00000589203.1_Intron	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	528					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						AGGGTTGAGCGTCTGTTAAAA	0.398													G|||	3	0.000599042	0.0008	0.0	5008	,	,		19567	0.0		0.002	False		,,,				2504	0.0				p.R528C		Atlas-SNP	.											.	ZNF519	53	.	0			c.C1582T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	134.0	137.0	136.0		1582	-2.4	0.0	18	dbSNP_134	136	29,8571	21.6+/-65.8	0,29,4271	yes	missense	ZNF519	NM_145287.3	180	0,35,6468	AA,AG,GG		0.3372,0.1362,0.2691	probably-damaging	528/541	14104957	35,12971	2203	4300	6503	SO:0001583	missense	162655	exon3			TTGAGCGTCTGTT	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.1582C>T	18.37:g.14104957G>A	ENSP00000464872:p.Arg528Cys	49.0	0.0	0		70.0	38.0	0.542857	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	3	0.0013736263736263737	2	0.0040650406504065045	0	0.0	0	0.0	1	0.0013192612137203166	G	5.238	0.229427	0.09916	0.001362	0.003372	ENSG00000175322	ENST00000309305	.	.	.	1.2	-2.4	0.06583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.30510	0.0767	M	0.64404	1.975	0.09310	N	1	B	0.32829	0.386	B	0.26416	0.069	T	0.11717	-1.0576	8	0.45353	T	0.12	.	2.7452	0.05264	0.232:0.0:0.2362:0.5318	.	528	Q8TB69	ZN519_HUMAN	C	528	.	ENSP00000307908:R528C	R	-	1	0	ZNF519	14094957	0.000000	0.05858	0.000000	0.03702	0.509000	0.34042	-1.143000	0.03200	-1.216000	0.02607	0.089000	0.15464	CGC	G|0.998;A|0.002	0.002	strong		0.398	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
ADCY3	109	hgsc.bcm.edu	37	2	25062875	25062875	+	Missense_Mutation	SNP	C	C	T	rs201606553	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:25062875C>T	ENST00000260600.5	-	6	2073	c.1222G>A	c.(1222-1224)Ggg>Agg	p.G408R	ADCY3_ENST00000405392.1_Missense_Mutation_p.G19R	NM_004036.3	NP_004027.2	O60266	ADCY3_HUMAN	adenylate cyclase 3	408					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			NS(1)|breast(5)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(4)|skin(2)	44	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.203)					ATGTCCACCCCAGTCTTGGTC	0.642													C|||	4	0.000798722	0.0	0.0058	5008	,	,		18860	0.0		0.0	False		,,,				2504	0.0				p.G408R		Atlas-SNP	.											.	ADCY3	114	.	0			c.G1222A						PASS	.	C	ARG/GLY	0,4406		0,0,2203	94.0	100.0	98.0		1222	5.1	0.5	2		98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADCY3	NM_004036.3	125	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	408/1145	25062875	1,13005	2203	4300	6503	SO:0001583	missense	109	exon6			CCACCCCAGTCTT	AF033861	CCDS1715.1	2p23.3	2013-02-04			ENSG00000138031	ENSG00000138031	4.6.1.1	"""Adenylate cyclases"""	234	protein-coding gene	gene with protein product		600291				9920776	Standard	NM_004036		Approved	AC3	uc002rfs.4	O60266	OTTHUMG00000094765	ENST00000260600.5:c.1222G>A	2.37:g.25062875C>T	ENSP00000260600:p.Gly408Arg	93.0	0.0	0		125.0	60.0	0.48	NM_004036	B3KT86|Q53T54|Q9UDB1	Missense_Mutation	SNP	ENST00000260600.5	37	CCDS1715.1	.	.	.	.	.	.	.	.	.	.	C	17.55	3.417937	0.62622	0.0	1.16E-4	ENSG00000138031	ENST00000260600;ENST00000405392;ENST00000415879;ENST00000454027;ENST00000427849;ENST00000435135	D;D;D;D;D	0.84589	-1.87;-1.87;-1.87;-1.87;-1.87	5.05	5.05	0.67936	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.248631	0.39759	N	0.001263	D	0.83188	0.5200	N	0.20986	0.625	0.22827	N	0.998681	P;P;D	0.52996	0.843;0.843;0.957	P;P;P	0.55455	0.673;0.673;0.776	T	0.76016	-0.3113	10	0.44086	T	0.13	.	12.4747	0.55807	0.0:0.9179:0.0:0.0821	.	408;408;19	B7ZLX9;O60266;B3KT86	.;ADCY3_HUMAN;.	R	408;19;383;34;164;358	ENSP00000260600:G408R;ENSP00000384484:G19R;ENSP00000410120:G34R;ENSP00000399275:G164R;ENSP00000389799:G358R	ENSP00000260600:G408R	G	-	1	0	ADCY3	24916379	0.021000	0.18746	0.474000	0.27266	0.995000	0.86356	1.371000	0.34250	2.325000	0.78763	0.549000	0.68633	GGG	.	.	weak		0.642	ADCY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211574.2		
OR5B12	390191	hgsc.bcm.edu	37	11	58207036	58207036	+	Missense_Mutation	SNP	T	T	A	rs201567144|rs148519730	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:58207036T>A	ENST00000302572.2	-	1	610	c.589A>T	c.(589-591)Att>Ttt	p.I197F		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	197						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				ACAAAAAAAATAACCATCTCA	0.393																																					p.I197F		Atlas-SNP	.											.	OR5B12	80	.	0			c.A589T						PASS	.						69.0	65.0	66.0					11																	58207036		2201	4295	6496	SO:0001583	missense	390191	exon1			AAAAAATAACCAT	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.589A>T	11.37:g.58207036T>A	ENSP00000306657:p.Ile197Phe	112.0	0.0	0		136.0	59.0	0.433824	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	.	.	.	.	.	.	.	.	.	.	T	8.659	0.900137	0.17686	.	.	ENSG00000172362	ENST00000302572	T	0.00137	8.68	4.3	3.15	0.36227	GPCR, rhodopsin-like superfamily (1);	0.422268	0.20017	N	0.100981	T	0.00178	0.0005	L	0.52573	1.65	0.09310	N	1	B	0.14012	0.009	B	0.17979	0.02	T	0.28038	-1.0056	10	0.54805	T	0.06	-24.7022	9.4514	0.38727	0.1587:0.0:0.0:0.8413	.	197	Q96R08	OR5BC_HUMAN	F	197	ENSP00000306657:I197F	ENSP00000306657:I197F	I	-	1	0	OR5B12	57963612	0.000000	0.05858	0.617000	0.29091	0.689000	0.40095	-5.918000	0.00090	0.772000	0.33382	0.379000	0.24179	ATT	T|0.996;A|0.004	0.004	strong		0.393	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
STK10	6793	hgsc.bcm.edu	37	5	171523513	171523513	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:171523513C>A	ENST00000176763.5	-	8	1265	c.922G>T	c.(922-924)Gct>Tct	p.A308S	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	308					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			TTGGCCTCAGCCACCAGCTCC	0.622																																					p.A308S		Atlas-SNP	.											.	STK10	100	.	0			c.G922T						PASS	.						109.0	105.0	106.0					5																	171523513		2203	4300	6503	SO:0001583	missense	6793	exon8			CCTCAGCCACCAG	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.922G>T	5.37:g.171523513C>A	ENSP00000176763:p.Ala308Ser	46.0	0.0	0		62.0	7.0	0.112903	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	C	19.94	3.920058	0.73098	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.68479	-0.33	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.061568	0.64402	N	0.000005	T	0.72495	0.3467	M	0.74647	2.275	0.80722	D	1	B	0.27140	0.169	B	0.41510	0.359	T	0.67492	-0.5657	10	0.14656	T	0.56	.	15.7705	0.78164	0.0:1.0:0.0:0.0	.	308	O94804	STK10_HUMAN	S	308	ENSP00000176763:A308S	ENSP00000176763:A308S	A	-	1	0	STK10	171456118	1.000000	0.71417	0.997000	0.53966	0.953000	0.61014	7.791000	0.85805	2.320000	0.78422	0.485000	0.47835	GCT	.	.	none		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
POLE	5426	hgsc.bcm.edu	37	12	133233812	133233812	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:133233812G>A	ENST00000320574.5	-	29	3535	c.3492C>T	c.(3490-3492)ccC>ccT	p.P1164P	POLE_ENST00000535270.1_Silent_p.P1137P	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1164					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	GCAGCCAGTCGGGGTGTTTGA	0.532								DNA polymerases (catalytic subunits)																													p.P1164P		Atlas-SNP	.											.	POLE	416	.	0			c.C3492T						PASS	.						100.0	98.0	99.0					12																	133233812		2203	4300	6503	SO:0001819	synonymous_variant	5426	exon29			CCAGTCGGGGTGT		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.3492C>T	12.37:g.133233812G>A		160.0	0.0	0		201.0	101.0	0.502488	NM_006231	Q13533|Q86VH9	Silent	SNP	ENST00000320574.5	37	CCDS9278.1																																																																																			.	.	none		0.532	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
SH3BP1	23616	hgsc.bcm.edu	37	22	38044341	38044341	+	Silent	SNP	C	C	T	rs118183308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38044341C>T	ENST00000357436.4	+	14	1528	c.1215C>T	c.(1213-1215)ttC>ttT	p.F405F	Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000442465.2_Silent_p.F405F|SH3BP1_ENST00000599616.1_Silent_p.F341F|SH3BP1_ENST00000336738.5_Silent_p.F405F	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	405	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					TGATGAAGTTCCTGGCACGGC	0.582													C|||	45	0.00898562	0.0008	0.0274	5008	,	,		17464	0.0		0.0239	False		,,,				2504	0.001				p.F405F		Atlas-SNP	.											SH3BP1,NS,haematopoietic_neoplasm,0,1	SH3BP1	41	1	0			c.C1215T						PASS	.	C		14,4384		0,14,2185	42.0	34.0	37.0		1215	4.2	1.0	22	dbSNP_132	37	161,8435		0,161,4137	no	coding-synonymous	SH3BP1	NM_018957.3		0,175,6322	TT,TC,CC		1.873,0.3183,1.3468		405/702	38044341	175,12819	2199	4298	6497	SO:0001819	synonymous_variant	23616	exon14			GAAGTTCCTGGCA		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1215C>T	22.37:g.38044341C>T		26.0	0.0	0		23.0	13.0	0.565217	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			C|0.986;T|0.014	0.014	strong		0.582	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
CNTNAP5	129684	hgsc.bcm.edu	37	2	125660582	125660582	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:125660582C>T	ENST00000431078.1	+	22	3921	c.3557C>T	c.(3556-3558)gCg>gTg	p.A1186V		NM_130773.2	NP_570129.1	Q8WYK1	CNTP5_HUMAN	contactin associated protein-like 5	1186	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(24)|lung(100)|ovary(10)|prostate(12)|skin(4)|upper_aerodigestive_tract(3)	176				BRCA - Breast invasive adenocarcinoma(221;0.248)		GCCACTGTCGCGCCTGTGACT	0.537																																					p.A1186V		Atlas-SNP	.											CNTNAP5,caecum,carcinoma,-1,1	CNTNAP5	405	1	0			c.C3557T						PASS	.						62.0	62.0	62.0					2																	125660582		2131	4255	6386	SO:0001583	missense	129684	exon22			CTGTCGCGCCTGT	AB077881	CCDS46401.1	2q14.1	2008-02-05			ENSG00000155052	ENSG00000155052			18748	protein-coding gene	gene with protein product		610519					Standard	NM_130773		Approved	caspr5, FLJ31966	uc002tno.3	Q8WYK1	OTTHUMG00000153356	ENST00000431078.1:c.3557C>T	2.37:g.125660582C>T	ENSP00000399013:p.Ala1186Val	144.0	0.0	0		127.0	62.0	0.488189	NM_130773	Q4ZFW2|Q4ZG21|Q53R09|Q53RX1|Q53SG3|Q584P3|Q96MS7	Missense_Mutation	SNP	ENST00000431078.1	37	CCDS46401.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.578109	0.28180	.	.	ENSG00000155052	ENST00000431078	D	0.88354	-2.37	5.5	3.64	0.41730	Laminin G domain (1);	0.279884	0.24698	N	0.036332	D	0.86932	0.6052	M	0.69248	2.105	0.36478	D	0.867685	P	0.52842	0.956	B	0.40782	0.34	D	0.87606	0.2500	10	0.46703	T	0.11	.	13.6352	0.62219	0.2828:0.7172:0.0:0.0	.	1186	Q8WYK1	CNTP5_HUMAN	V	1186	ENSP00000399013:A1186V	ENSP00000399013:A1186V	A	+	2	0	CNTNAP5	125377052	0.980000	0.34600	0.439000	0.26833	0.015000	0.08874	3.047000	0.49854	0.652000	0.30806	-0.181000	0.13052	GCG	.	.	none		0.537	CNTNAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330864.3		
KIF21B	23046	hgsc.bcm.edu	37	1	200978422	200978422	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:200978422T>C	ENST00000422435.2	-	2	552	c.236A>G	c.(235-237)tAt>tGt	p.Y79C	KIF21B_ENST00000332129.2_Missense_Mutation_p.Y79C|KIF21B_ENST00000461742.2_Missense_Mutation_p.Y79C|KIF21B_ENST00000360529.5_Missense_Mutation_p.Y79C	NM_001252100.1	NP_001239029.1	O75037	KI21B_HUMAN	kinesin family member 21B	79	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(4)|large_intestine(8)|liver(1)|lung(27)|ovary(3)|pancreas(1)|prostate(5)|skin(8)|stomach(2)|urinary_tract(2)	83						CGTGGCATTATAGCCCTCGAA	0.557																																					p.Y79C		Atlas-SNP	.											.	KIF21B	208	.	0			c.A236G						PASS	.						106.0	96.0	99.0					1																	200978422		2203	4300	6503	SO:0001583	missense	23046	exon2			GCATTATAGCCCT	BC031927	CCDS30965.1, CCDS58054.1, CCDS58055.1, CCDS58056.1	1q32.1	2013-01-10			ENSG00000116852	ENSG00000116852		"""Kinesins"", ""WD repeat domain containing"""	29442	protein-coding gene	gene with protein product		608322				9455484	Standard	NM_001252100		Approved	DKFZP434J212, KIAA0449	uc001gvs.2	O75037	OTTHUMG00000035787	ENST00000422435.2:c.236A>G	1.37:g.200978422T>C	ENSP00000411831:p.Tyr79Cys	170.0	0.0	0		211.0	116.0	0.549763	NM_017596	B2RP62|B7ZMI0|Q5T4J3	Missense_Mutation	SNP	ENST00000422435.2	37	CCDS58056.1	.	.	.	.	.	.	.	.	.	.	T	22.5	4.296788	0.81025	.	.	ENSG00000116852	ENST00000332129;ENST00000360529;ENST00000461742;ENST00000422435;ENST00000539858	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	4.67	4.67	0.58626	Kinesin, motor domain (5);	0.000000	0.85682	D	0.000000	D	0.86497	0.5947	M	0.82630	2.6	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.998;0.998	D	0.88783	0.3272	10	0.87932	D	0	.	14.2798	0.66202	0.0:0.0:0.0:1.0	.	79;79;79;79	B7ZMI0;B2RP62;O75037;O75037-2	.;.;KI21B_HUMAN;.	C	79	ENSP00000328494:Y79C;ENSP00000353724:Y79C;ENSP00000433808:Y79C;ENSP00000411831:Y79C	ENSP00000328494:Y79C	Y	-	2	0	KIF21B	199245045	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.841000	0.86834	1.967000	0.57214	0.528000	0.53228	TAT	.	.	none		0.557	KIF21B-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382635.1	XM_371332	
KIF23	9493	hgsc.bcm.edu	37	15	69729049	69729049	+	Missense_Mutation	SNP	T	T	C	rs17310879	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:69729049T>C	ENST00000260363.4	+	14	1660	c.1543T>C	c.(1543-1545)Ttt>Ctt	p.F515L	KIF23_ENST00000558585.1_Missense_Mutation_p.F332L|KIF23_ENST00000395392.2_Missense_Mutation_p.F515L|KIF23_ENST00000537891.1_Missense_Mutation_p.F332L|KIF23_ENST00000352331.4_Missense_Mutation_p.F515L|KIF23_ENST00000559279.1_Missense_Mutation_p.F515L	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	515			F -> L (in dbSNP:rs17310879).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						GATTGATGAGTTTAACAAACA	0.338													T|||	32	0.00638978	0.0	0.0101	5008	,	,		17842	0.0		0.0199	False		,,,				2504	0.0051				p.F515L		Atlas-SNP	.											.	KIF23	57	.	0			c.T1543C						PASS	.	T	LEU/PHE,LEU/PHE	12,4386	17.9+/-39.9	0,12,2187	68.0	59.0	62.0		1543,1543	4.0	0.9	15	dbSNP_123	62	126,8470	61.0+/-122.8	2,122,4174	yes	missense,missense	KIF23	NM_004856.5,NM_138555.2	22,22	2,134,6361	CC,CT,TT		1.4658,0.2729,1.062	benign,benign	515/857,515/961	69729049	138,12856	2199	4298	6497	SO:0001583	missense	9493	exon14			GATGAGTTTAACA	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.1543T>C	15.37:g.69729049T>C	ENSP00000260363:p.Phe515Leu	58.0	0.0	0		73.0	37.0	0.506849	NM_138555	Q8WVP0	Missense_Mutation	SNP	ENST00000260363.4	37	CCDS32278.1	21	0.009615384615384616	0	0.0	5	0.013812154696132596	0	0.0	16	0.021108179419525065	T	6.643	0.487087	0.12641	0.002729	0.014658	ENSG00000137807	ENST00000260363;ENST00000352331;ENST00000395392;ENST00000537891	T;T;T;T	0.62364	0.03;0.03;0.03;0.03	5.11	3.99	0.46301	.	0.276826	0.41500	N	0.000878	T	0.19565	0.0470	N	0.08118	0	0.38724	D	0.953517	B;B;B	0.14012	0.001;0.009;0.0	B;B;B	0.15484	0.001;0.013;0.001	T	0.18209	-1.0344	10	0.02654	T	1	.	9.3049	0.37870	0.0:0.0866:0.0:0.9134	rs17310879;rs52817803;rs17310879	332;515;515	B4E1K0;Q02241-2;Q02241	.;.;KIF23_HUMAN	L	515;515;515;332	ENSP00000260363:F515L;ENSP00000304978:F515L;ENSP00000378790:F515L;ENSP00000442969:F332L	ENSP00000260363:F515L	F	+	1	0	KIF23	67516103	1.000000	0.71417	0.877000	0.34402	0.953000	0.61014	4.650000	0.61440	0.798000	0.33994	0.459000	0.35465	TTT	T|0.988;C|0.012	0.012	strong		0.338	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
ZZEF1	23140	hgsc.bcm.edu	37	17	4017695	4017695	+	Missense_Mutation	SNP	T	T	C	rs138134000	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4017695T>C	ENST00000381638.2	-	4	888	c.764A>G	c.(763-765)tAt>tGt	p.Y255C	ZZEF1_ENST00000574474.1_5'UTR|snoU13_ENST00000459263.1_RNA	NM_015113.3	NP_055928.3	O43149	ZZEF1_HUMAN	zinc finger, ZZ-type with EF-hand domain 1	255	DOC. {ECO:0000255|PROSITE- ProRule:PRU00614}.						calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(19)|ovary(3)|pancreas(1)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	84						TGTTTCTATATAAGCATAGCA	0.438													T|||	11	0.00219649	0.0	0.0	5008	,	,		17608	0.0		0.005	False		,,,				2504	0.0061				p.Y255C		Atlas-SNP	.											ZZEF1,NS,lymphoid_neoplasm,0,1	ZZEF1	195	1	0			c.A764G						PASS	.	T	CYS/TYR	5,4401	9.9+/-24.2	0,5,2198	180.0	158.0	166.0		764	5.1	1.0	17	dbSNP_134	166	56,8544	35.9+/-90.5	0,56,4244	yes	missense	ZZEF1	NM_015113.3	194	0,61,6442	CC,CT,TT		0.6512,0.1135,0.469	probably-damaging	255/2962	4017695	61,12945	2203	4300	6503	SO:0001583	missense	23140	exon4			TCTATATAAGCAT	BC035319	CCDS11043.1	17p13.3	2013-01-10	2004-11-03		ENSG00000074755	ENSG00000074755		"""Zinc fingers, ZZ-type"", ""EF-hand domain containing"""	29027	protein-coding gene	gene with protein product			"""zinc finger, ZZ-type with EF hand domain 1"""			9455477	Standard	XM_005256560		Approved	KIAA0399, ZZZ4, FLJ10821	uc002fxe.3	O43149	OTTHUMG00000090741	ENST00000381638.2:c.764A>G	17.37:g.4017695T>C	ENSP00000371051:p.Tyr255Cys	195.0	0.0	0		234.0	111.0	0.474359	NM_015113	A7MBM5|Q6NXG0|Q6ZRA1|Q6ZSF4|Q9NVB9	Missense_Mutation	SNP	ENST00000381638.2	37	CCDS11043.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	16.80	3.223085	0.58668	0.001135	0.006512	ENSG00000074755	ENST00000381638	T	0.63580	-0.05	5.12	5.12	0.69794	Anaphase-promoting complex, subunit 10/DOC domain (1);Galactose-binding domain-like (1);	0.367468	0.29028	N	0.013371	T	0.48370	0.1496	N	0.08118	0	0.27369	N	0.955744	D;D	0.63880	0.993;0.967	P;P	0.56788	0.687;0.806	T	0.53892	-0.8374	10	0.41790	T	0.15	-11.0054	14.927	0.70887	0.0:0.0:0.0:1.0	.	255;255	O43149-3;O43149	.;ZZEF1_HUMAN	C	255	ENSP00000371051:Y255C	ENSP00000371051:Y255C	Y	-	2	0	ZZEF1	3964444	1.000000	0.71417	0.981000	0.43875	0.970000	0.65996	3.945000	0.56637	1.912000	0.55364	0.455000	0.32223	TAT	T|0.996;C|0.004	0.004	strong		0.438	ZZEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207480.1	NM_015113	
MOG	4340	hgsc.bcm.edu	37	6	29638101	29638101	+	Silent	SNP	T	T	C	rs112913018	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:29638101T>C	ENST00000376917.3	+	6	865	c.636T>C	c.(634-636)ttT>ttC	p.F212F	MOG_ENST00000376902.3_3'UTR|MOG_ENST00000396701.2_Intron|MOG_ENST00000376888.2_Silent_p.F96F|MOG_ENST00000376894.4_Silent_p.F212F|MOG_ENST00000533330.2_3'UTR|MOG_ENST00000494692.1_Intron|MOG_ENST00000490427.1_Intron|MOG_ENST00000396704.3_Intron|MOG_ENST00000416766.2_Silent_p.F174F|MOG_ENST00000376891.4_Intron|MOG_ENST00000376898.3_Silent_p.F212F|MOG_ENST00000431798.2_Intron|MOG_ENST00000483013.1_Intron	NM_002433.4|NM_206809.3	NP_002424.3|NP_996532.2	Q16653	MOG_HUMAN	myelin oligodendrocyte glycoprotein	212					cell adhesion (GO:0007155)|central nervous system development (GO:0007417)|positive regulation of MyD88-dependent toll-like receptor signaling pathway (GO:0034126)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|skin(2)	19						TAACCCTGTTTGTAATTGTGC	0.527													T|||	5	0.000998403	0.0	0.0014	5008	,	,		18756	0.0		0.004	False		,,,				2504	0.0				p.F212F		Atlas-SNP	.											.	MOG	47	.	0			c.T636C						PASS	.						220.0	211.0	214.0					6																	29638101		2203	4300	6503	SO:0001819	synonymous_variant	4340	exon6			CCTGTTTGTAATT		CCDS4667.1, CCDS34366.1, CCDS34367.1, CCDS34368.1, CCDS34369.1, CCDS34370.1, CCDS47394.1, CCDS47395.1, CCDS47395.2, CCDS54977.1	6p22.1	2014-01-16			ENSG00000204655	ENSG00000204655		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	7197	protein-coding gene	gene with protein product		159465					Standard	NM_002433		Approved	BTN6, BTNL11	uc003nne.3	Q16653	OTTHUMG00000031099	ENST00000376917.3:c.636T>C	6.37:g.29638101T>C		406.0	0.0	0		423.0	209.0	0.49409	NM_002433	A6NDR4|A6NNJ9|A8MY31|B0UZR9|E9PGF0|F8W9D5|O00713|O00714|O00715|Q13054|Q13055|Q14855|Q29ZN8|Q56UY0|Q5JNX7|Q5JNY1|Q5JNY2|Q5JNY4|Q5SSB5|Q5SSB6|Q5STL9|Q5STM0|Q5STM1|Q5STM2|Q5STM5|Q5SUK5|Q5SUK7|Q5SUK8|Q5SUK9|Q5SUL0|Q5SUL1|Q8IYG5|Q92891|Q92892|Q92893|Q92894|Q92895|Q93053|Q96KU9|Q96KV0|Q96KV1|Q99605	Silent	SNP	ENST00000376917.3	37	CCDS34370.1																																																																																			A|0.002;C|0.001;T|0.997	0.001	strong		0.527	MOG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076160.3	NM_002433	
HR	55806	hgsc.bcm.edu	37	8	21978734	21978734	+	Silent	SNP	G	G	A	rs77689228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:21978734G>A	ENST00000381418.4	-	10	3691	c.2211C>T	c.(2209-2211)ccC>ccT	p.P737P	HR_ENST00000312841.8_Silent_p.P737P	NM_005144.4	NP_005135.2	O43593	HAIR_HUMAN	hair growth associated	737					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	27		Breast(100;0.000162)|Acute lymphoblastic leukemia(644;0.0775)|Prostate(55;0.116)		KIRC - Kidney renal clear cell carcinoma(542;1.19e-05)|BRCA - Breast invasive adenocarcinoma(99;3.56e-05)|Colorectal(74;0.00191)|COAD - Colon adenocarcinoma(73;0.0615)|READ - Rectum adenocarcinoma(644;0.1)		CAGCGGAATCGGGGGTCTCTG	0.632													G|||	33	0.00658946	0.0083	0.0101	5008	,	,		16735	0.0		0.0129	False		,,,				2504	0.002				p.P737P		Atlas-SNP	.											.	HR	71	.	0			c.C2211T						PASS	.	G	,	42,4364	44.6+/-78.6	0,42,2161	59.0	72.0	67.0		2211,2211	-5.9	0.9	8	dbSNP_132	67	120,8480	61.3+/-123.2	0,120,4180	no	coding-synonymous,coding-synonymous	HR	NM_005144.4,NM_018411.4	,	0,162,6341	AA,AG,GG		1.3953,0.9532,1.2456	,	737/1190,737/1135	21978734	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	55806	exon10			GGAATCGGGGGTC	AF039196	CCDS6022.1, CCDS6023.1	8p12	2012-12-07	2012-12-07		ENSG00000168453	ENSG00000168453			5172	protein-coding gene	gene with protein product		602302	"""hairless (mouse) homolog"", ""hairless homolog (mouse)"""	ALUNC		10051399, 9463324	Standard	NM_018411		Approved	AU	uc003xas.3	O43593	OTTHUMG00000097089	ENST00000381418.4:c.2211C>T	8.37:g.21978734G>A		105.0	0.0	0		131.0	70.0	0.534351	NM_018411	Q6GS30|Q96H33|Q9NPE1	Silent	SNP	ENST00000381418.4	37	CCDS6022.1																																																																																			G|0.988;A|0.012	0.012	strong		0.632	HR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214213.1		
EPHX2	2053	hgsc.bcm.edu	37	8	27358509	27358509	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27358509A>G	ENST00000521400.1	+	2	598	c.168A>G	c.(166-168)ggA>ggG	p.G56G	EPHX2_ENST00000380476.3_Silent_p.G3G|EPHX2_ENST00000520666.1_3'UTR|EPHX2_ENST00000518379.1_Silent_p.G56G|EPHX2_ENST00000521780.1_Intron|EPHX2_ENST00000517536.1_Silent_p.G56G	NM_001979.5	NP_001970.2	P34913	HYES_HUMAN	epoxide hydrolase 2, cytoplasmic	56	Phosphatase.				arachidonic acid metabolic process (GO:0019369)|cellular calcium ion homeostasis (GO:0006874)|cholesterol homeostasis (GO:0042632)|dephosphorylation (GO:0016311)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|inflammatory response (GO:0006954)|phospholipid dephosphorylation (GO:0046839)|positive regulation of gene expression (GO:0010628)|positive regulation of vasodilation (GO:0045909)|reactive oxygen species metabolic process (GO:0072593)|regulation of blood pressure (GO:0008217)|regulation of cholesterol metabolic process (GO:0090181)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|stilbene catabolic process (GO:0046272)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)	10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity (GO:0033885)|epoxide hydrolase activity (GO:0004301)|lipid phosphatase activity (GO:0042577)|magnesium ion binding (GO:0000287)|phosphatase activity (GO:0016791)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|toxic substance binding (GO:0015643)			cervix(1)|endometrium(8)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(5)|stomach(1)|urinary_tract(1)	27		Ovarian(32;2.61e-05)|all_epithelial(46;0.207)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0226)|Epithelial(17;1.12e-09)|Colorectal(74;0.157)		TTATGAAAGGAGAGATCACAC	0.527																																					p.G56G		Atlas-SNP	.											EPHX2,scalp,carcinoma,+2,1	EPHX2	57	1	0			c.A168G						PASS	.						101.0	94.0	97.0					8																	27358509		2203	4300	6503	SO:0001819	synonymous_variant	2053	exon2			GAAAGGAGAGATC	L05779	CCDS6060.1, CCDS59097.1, CCDS59098.1	8p21	2010-04-23			ENSG00000120915	ENSG00000120915	3.3.2.10		3402	protein-coding gene	gene with protein product		132811					Standard	NM_001979		Approved		uc003xfu.4	P34913	OTTHUMG00000102115	ENST00000521400.1:c.168A>G	8.37:g.27358509A>G		67.0	0.0	0		72.0	36.0	0.5	NM_001979	B2Z3B1|B3KTU8|B3KUA0|G3V134|J3KPH7|Q16764|Q9HBJ1|Q9HBJ2	Silent	SNP	ENST00000521400.1	37	CCDS6060.1	.	.	.	.	.	.	.	.	.	.	A	6.193	0.403741	0.11754	.	.	ENSG00000120915	ENST00000521684	.	.	.	4.33	0.328	0.15918	.	.	.	.	.	T	0.45418	0.1341	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.24404	-1.0161	4	.	.	.	-4.3771	3.8982	0.09149	0.6131:0.1839:0.203:0.0	.	.	.	.	G	56	.	.	E	+	2	0	EPHX2	27414426	0.994000	0.37717	0.854000	0.33618	0.579000	0.36224	0.349000	0.20055	-0.024000	0.13941	0.383000	0.25322	GAG	.	.	none		0.527	EPHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219954.4		
TAS2R31	259290	hgsc.bcm.edu	37	12	11183035	11183035	+	Nonsense_Mutation	SNP	C	C	T	rs78820764	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:11183035C>T	ENST00000390675.2	-	1	971	c.900G>A	c.(898-900)tgG>tgA	p.W300*	PRR4_ENST00000536668.1_Intron|TAS2R14_ENST00000381852.4_Intron	NM_176885.2	NP_795366.2	P59538	T2R31_HUMAN	taste receptor, type 2, member 31	300					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			kidney(1)|lung(6)	7						CTCCTTTCACCCAGTACCTCA	0.408																																					p.W300X		Atlas-SNP	.											.	TAS2R31	24	.	0			c.G900A						PASS	.																																			SO:0001587	stop_gained	259290	exon1			TTTCACCCAGTAC	AX097748, AF494228	CCDS53747.1	12p13.2	2012-08-22				ENSG00000256436		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19113	protein-coding gene	gene with protein product		612669	"""taste receptor, type 2, member 44"""	TAS2R44			Standard	NM_176885		Approved	T2R31, T2R53	uc001qzo.1	P59538		ENST00000390675.2:c.900G>A	12.37:g.11183035C>T	ENSP00000375093:p.Trp300*	314.0	0.0	0		263.0	16.0	0.0608365	NM_176885	P59547|Q17R84|Q645X5	Nonsense_Mutation	SNP	ENST00000390675.2	37	CCDS53747.1	.	.	.	.	.	.	.	.	.	.	.	10.72	1.429329	0.25726	.	.	ENSG00000256436	ENST00000390675	.	.	.	2.5	-1.35	0.09114	.	.	.	.	.	.	.	.	.	.	.	0.20196	N	0.99993	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.4522	0.16570	0.2085:0.3805:0.4109:0.0	rs3759247	.	.	.	X	300	.	ENSP00000375093:W300X	W	-	3	0	TAS2R31	11074302	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-2.133000	0.01308	-0.040000	0.13580	-1.271000	0.01417	TGG	C|0.989;T|0.011	0.011	strong		0.408	TAS2R31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400233.1	NM_176885	
TLR2	7097	hgsc.bcm.edu	37	4	154625042	154625042	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154625042T>G	ENST00000260010.6	+	1	2391	c.983T>G	c.(982-984)cTg>cGg	p.L328R		NM_003264.3	NP_003255.2	O60603	TLR2_HUMAN	toll-like receptor 2	328					apoptotic process (GO:0006915)|cell surface pattern recognition receptor signaling pathway (GO:0002752)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to peptidoglycan (GO:0071224)|cellular response to triacyl bacterial lipopeptide (GO:0071727)|central nervous system myelin formation (GO:0032289)|chloramphenicol transport (GO:0042892)|defense response to Gram-positive bacterium (GO:0050830)|detection of diacyl bacterial lipopeptide (GO:0042496)|detection of triacyl bacterial lipopeptide (GO:0042495)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|induction by symbiont of defense-related host nitric oxide production (GO:0052063)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|leukotriene metabolic process (GO:0006691)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-17 production (GO:0032700)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-18 production (GO:0032741)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of oligodendrocyte differentiation (GO:0048714)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of Wnt signaling pathway (GO:0030177)|response to fatty acid (GO:0070542)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to molecule of fungal origin (GO:0002238)|response to progesterone (GO:0032570)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|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)	cell body (GO:0044297)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopolysaccharide receptor activity (GO:0001875)|lipoteichoic acid binding (GO:0070891)|peptidoglycan binding (GO:0042834)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|signaling pattern recognition receptor activity (GO:0008329)|transmembrane signaling receptor activity (GO:0004888)|triacyl lipopeptide binding (GO:0042497)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	29	all_hematologic(180;0.093)	Renal(120;0.117)			OspA lipoprotein(DB00045)	TTTTATGATCTGAGCACTTTA	0.323																																					p.L328R		Atlas-SNP	.											.	TLR2	84	.	0			c.T983G						PASS	.						58.0	63.0	61.0					4																	154625042		2203	4299	6502	SO:0001583	missense	7097	exon3			ATGATCTGAGCAC	U88878	CCDS3784.1	4q32	2008-02-05				ENSG00000137462		"""CD molecules"""	11848	protein-coding gene	gene with protein product		603028				9435236	Standard	XM_005263193		Approved	TIL4, CD282	uc003inq.3	O60603		ENST00000260010.6:c.983T>G	4.37:g.154625042T>G	ENSP00000260010:p.Leu328Arg	80.0	0.0	0		115.0	57.0	0.495652	NM_003264	B3Y612|D1CS45|D1CS48|D1CS49|O15454|Q8NI00	Missense_Mutation	SNP	ENST00000260010.6	37	CCDS3784.1	.	.	.	.	.	.	.	.	.	.	T	18.84	3.708432	0.68615	.	.	ENSG00000137462	ENST00000260010	T	0.60424	0.19	6.06	4.88	0.63580	.	0.583671	0.16992	N	0.191252	T	0.72382	0.3453	M	0.77103	2.36	0.09310	N	0.999999	P	0.48407	0.91	P	0.57244	0.816	T	0.65726	-0.6098	10	0.87932	D	0	.	12.394	0.55374	0.0:0.0653:0.0:0.9347	.	328	O60603	TLR2_HUMAN	R	328	ENSP00000260010:L328R	ENSP00000260010:L328R	L	+	2	0	TLR2	154844492	0.709000	0.27886	0.013000	0.15412	0.020000	0.10135	5.184000	0.65070	1.116000	0.41820	-0.263000	0.10527	CTG	.	.	none		0.323	TLR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365205.1		
GPRASP2	114928	hgsc.bcm.edu	37	X	101970123	101970123	+	Missense_Mutation	SNP	G	G	A	rs139789934	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:101970123G>A	ENST00000535209.1	+	4	1157	c.326G>A	c.(325-327)cGt>cAt	p.R109H	GPRASP2_ENST00000332262.5_Missense_Mutation_p.R109H|GPRASP2_ENST00000543253.1_Missense_Mutation_p.R109H			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	109						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						GGTGGCGCTCGTTCTAAAACT	0.572													.|||	2	0.000529801	0.0	0.0	3775	,	,		14704	0.0		0.002	False		,,,				2504	0.0				p.R109H		Atlas-SNP	.											.	GPRASP2	89	.	0			c.G326A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	0,3835		0,0,1632,571	84.0	85.0	84.0		326,326,326,326,326,326	3.9	0.9	X	dbSNP_134	84	12,6716		0,12,2416,1872	yes	missense,missense,missense,missense,missense,missense	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	29,29,29,29,29,29	0,12,4048,2443	AA,AG,GG,G		0.1784,0.0,0.1136	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	109/839,109/839,109/839,109/839,109/839,109/839	101970123	12,10551	2203	4300	6503	SO:0001583	missense	114928	exon4			GCGCTCGTTCTAA	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.326G>A	X.37:g.101970123G>A	ENSP00000437394:p.Arg109His	37.0	0.0	0		80.0	73.0	0.9125	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	2	0.0012055455093429777	0	0.0	0	0.0	0	0.0	1	0.0013227513227513227	G	11.74	1.729796	0.30684	0.0	0.001784	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.08008	3.14;3.14;3.14	4.76	3.89	0.44902	.	0.000000	0.44483	D	0.000442	T	0.05502	0.0145	N	0.14661	0.345	0.18873	N	0.999989	P	0.51240	0.943	B	0.43990	0.438	T	0.28681	-1.0036	10	0.45353	T	0.12	.	6.4019	0.21642	0.1059:0.1825:0.7116:0.0	.	109	Q96D09	GASP2_HUMAN	H	109	ENSP00000437872:R109H;ENSP00000437394:R109H;ENSP00000339057:R109H	ENSP00000339057:R109H	R	+	2	0	GPRASP2	101856779	0.993000	0.37304	0.927000	0.36925	0.006000	0.05464	3.248000	0.51430	1.078000	0.41014	0.600000	0.82982	CGT	G|0.999;A|0.001	0.001	strong		0.572	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
STX16	8675	hgsc.bcm.edu	37	20	57242602	57242602	+	Silent	SNP	G	G	A	rs376636519		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:57242602G>A	ENST00000371141.4	+	3	925	c.201G>A	c.(199-201)gcG>gcA	p.A67A	STX16_ENST00000359617.4_Silent_p.A14A|STX16-NPEPL1_ENST00000530122.1_Silent_p.A67A|STX16_ENST00000358029.4_Silent_p.A63A|STX16_ENST00000361830.3_Silent_p.A67A|STX16_ENST00000361770.5_Silent_p.A50A|STX16_ENST00000496003.1_3'UTR|STX16_ENST00000371132.4_Silent_p.A46A|STX16_ENST00000355957.5_Silent_p.A50A	NM_001001433.2	NP_001001433.1	O14662	STX16_HUMAN	syntaxin 16	67					intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|SNARE complex (GO:0031201)	SNAP receptor activity (GO:0005484)			breast(1)|cervix(1)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|urinary_tract(1)	17	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;3.73e-09)|Epithelial(14;8.54e-06)|all cancers(14;6.89e-05)			CAGAAGCAGCGATTGGTGTGA	0.413																																					p.A67A		Atlas-SNP	.											.	STX16	36	.	0			c.G201A						PASS	.	G	,,,,	0,4406		0,0,2203	146.0	135.0	139.0		201,189,150,42,138	-4.6	0.6	20		139	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STX16	NM_001001433.2,NM_001134772.2,NM_001134773.2,NM_001204868.1,NM_003763.5	,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,	67/326,63/322,50/309,14/273,46/305	57242602	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8675	exon3			AGCAGCGATTGGT	AF038897	CCDS13468.1, CCDS13469.1, CCDS46619.1, CCDS46620.1, CCDS56199.1	20q13.32	2008-07-02			ENSG00000124222	ENSG00000124222			11431	protein-coding gene	gene with protein product		603666				9464276, 9587053, 15800843	Standard	NM_003763		Approved	hsyn16, SYN16	uc002xzi.3	O14662	OTTHUMG00000033084	ENST00000371141.4:c.201G>A	20.37:g.57242602G>A		108.0	0.0	0		105.0	54.0	0.514286	NM_001001433	A6NK32|A6NN69|A8MPP0|B7ZBN1|B7ZBN2|B7ZBN3|E1P5M0|E1P607|O14661|O14663|O60517|Q5W084|Q5W086|Q5W087|Q5XKI6|Q6GMS8|Q9H0Z0|Q9H1T7|Q9H1T8|Q9UIX5	Silent	SNP	ENST00000371141.4	37	CCDS13468.1																																																																																			.	.	weak		0.413	STX16-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080517.2	NM_001001433	
HEMGN	55363	hgsc.bcm.edu	37	9	100692330	100692330	+	Silent	SNP	A	A	G	rs35223978	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:100692330A>G	ENST00000259456.3	-	4	1490	c.1347T>C	c.(1345-1347)taT>taC	p.Y449Y		NM_018437.3|NM_197978.2	NP_060907.2|NP_932095.1	Q9BXL5	HEMGN_HUMAN	hemogen	449					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)	nucleus (GO:0005634)				NS(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|skin(2)|urinary_tract(1)	27		Acute lymphoblastic leukemia(62;0.0559)				GAGGAAAAGTATAAGCATCTT	0.468													A|||	19	0.00379393	0.0	0.0058	5008	,	,		18466	0.0		0.0109	False		,,,				2504	0.0041				p.Y449Y		Atlas-SNP	.											.	HEMGN	55	.	0			c.T1347C						PASS	.	A	,	5,4401	8.1+/-20.4	0,5,2198	221.0	201.0	208.0		1347,1347	0.6	0.0	9	dbSNP_126	208	69,8531	42.2+/-99.7	1,67,4232	no	coding-synonymous,coding-synonymous	HEMGN	NM_018437.3,NM_197978.1	,	1,72,6430	GG,GA,AA		0.8023,0.1135,0.569	,	449/485,449/485	100692330	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	55363	exon3			AAAAGTATAAGCA	AF228713	CCDS6731.1	9q22.33	2014-01-21			ENSG00000136929	ENSG00000136929			17509	protein-coding gene	gene with protein product		610715					Standard	NM_018437		Approved	EDAG, CT155, NDR	uc004axy.4	Q9BXL5	OTTHUMG00000020336	ENST00000259456.3:c.1347T>C	9.37:g.100692330A>G		176.0	0.0	0		205.0	89.0	0.434146	NM_197978	Q6XAR3|Q86XY5|Q9NPC0	Silent	SNP	ENST00000259456.3	37	CCDS6731.1																																																																																			A|0.995;G|0.005	0.005	strong		0.468	HEMGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053344.2	NM_197978	
NOTCH1	4851	hgsc.bcm.edu	37	9	139418260	139418260	+	Silent	SNP	A	A	G	rs4489420	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:139418260A>G	ENST00000277541.6	-	3	387	c.312T>C	c.(310-312)aaT>aaC	p.N104N	NOTCH1_ENST00000491649.1_5'UTR	NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	104	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGAGGCAGGCATTGTCCAGGG	0.687			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3706	0.740016	0.9523	0.6037	5008	,	,		12414	0.8363		0.505	False		,,,				2504	0.6922				p.N104N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.T312C						PASS	.	G		3779,511		1671,437,37	20.0	32.0	28.0		312	-4.3	0.0	9	dbSNP_111	28	4001,4491		956,2089,1201	yes	coding-synonymous	NOTCH1	NM_017617.3		2627,2526,1238	GG,GA,AA		47.1149,11.9114,39.1332		104/2556	139418260	7780,5002	2145	4246	6391	SO:0001819	synonymous_variant	4851	exon3			GCAGGCATTGTCC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.312T>C	9.37:g.139418260A>G		112.0	0.0	0		137.0	50.0	0.364964	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.323;G|0.677	0.677	strong		0.687	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
MRPS21	54460	hgsc.bcm.edu	37	1	150280546	150280546	+	Missense_Mutation	SNP	C	C	T	rs10480	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:150280546C>T	ENST00000369084.5	+	2	595	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	MRPS21_ENST00000309092.7_Missense_Mutation_p.R50C	NM_018997.3	NP_061870.1	P82921	RT21_HUMAN	mitochondrial ribosomal protein S21	50			R -> C (in dbSNP:rs10480).		translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(1)|pancreas(1)	4	Lung NSC(24;5.57e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAAGCCATGCCGCCGGCGACA	0.493													C|||	48	0.00958466	0.0008	0.0216	5008	,	,		17027	0.0		0.0249	False		,,,				2504	0.0072				p.R50C		Atlas-SNP	.											.	MRPS21	8	.	0			c.C148T						PASS	.	C	CYS/ARG,CYS/ARG	28,4378	35.2+/-66.4	0,28,2175	50.0	47.0	48.0		148,148	4.9	1.0	1	dbSNP_52	48	289,8311	106.6+/-167.4	8,273,4019	no	missense,missense	MRPS21	NM_018997.2,NM_031901.4	180,180	8,301,6194	TT,TC,CC		3.3605,0.6355,2.4373	benign,benign	50/88,50/88	150280546	317,12689	2203	4300	6503	SO:0001583	missense	54460	exon2			CCATGCCGCCGGC	AB051353	CCDS950.1	1q21	2012-09-13			ENSG00000187145			"""Mitochondrial ribosomal proteins / small subunits"""	14046	protein-coding gene	gene with protein product		611984					Standard	NM_031901		Approved		uc001euk.3	P82921	OTTHUMG00000012544	ENST00000369084.5:c.148C>T	1.37:g.150280546C>T	ENSP00000358080:p.Arg50Cys	203.0	1.0	0.00492611		202.0	108.0	0.534653	NM_018997	Q5TB11|Q9BST6	Missense_Mutation	SNP	ENST00000369084.5	37	CCDS950.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	14.33	2.504529	0.44558	0.006355	0.033605	ENSG00000187145	ENST00000309092;ENST00000369084	T;T	0.30182	1.54;1.54	4.93	4.93	0.64822	.	.	.	.	.	T	0.12732	0.0309	.	.	.	0.53005	D	0.999962	B	0.20780	0.048	B	0.15484	0.013	T	0.02991	-1.1085	8	0.36615	T	0.2	.	12.9741	0.58529	0.1618:0.8382:0.0:0.0	rs10480;rs10480	50	P82921	RT21_HUMAN	C	50	ENSP00000312395:R50C;ENSP00000358080:R50C	ENSP00000312395:R50C	R	+	1	0	MRPS21	148547170	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.309000	0.43699	2.567000	0.86603	0.650000	0.86243	CGC	C|0.979;T|0.021	0.021	strong		0.493	MRPS21-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035813.1	NM_018997	
FAM102A	399665	hgsc.bcm.edu	37	9	130710489	130710489	+	Silent	SNP	G	G	A	rs144841491	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130710489G>A	ENST00000373095.1	-	6	852	c.477C>T	c.(475-477)gcC>gcT	p.A159A	FAM102A_ENST00000373084.4_Silent_p.A17A|FAM102A_ENST00000300434.3_Intron	NM_001035254.2	NP_001030331.1	Q5T9C2	F102A_HUMAN	family with sequence similarity 102, member A	159	Ser-rich.									breast(1)|cervix(1)|large_intestine(3)|lung(1)|ovary(4)	10						AGATGGACTTGGCAGTCGATG	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20006	0.0		0.007	False		,,,				2504	0.0				p.A159A		Atlas-SNP	.											.	FAM102A	32	.	0			c.C477T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	92.0	82.0	85.0		477,51	3.2	1.0	9	dbSNP_134	85	33,8567	23.4+/-69.3	0,33,4267	no	coding-synonymous,coding-synonymous	FAM102A	NM_001035254.2,NM_203305.2	,	0,37,6466	AA,AG,GG		0.3837,0.0908,0.2845	,	159/385,17/243	130710489	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	399665	exon6			GGACTTGGCAGTC		CCDS6888.1, CCDS35150.1	9q34.11	2012-11-05	2005-11-17	2005-11-17	ENSG00000167106	ENSG00000167106			31419	protein-coding gene	gene with protein product	"""sym-3 homolog A (C. elegans)"""	610891	"""chromosome 9 open reading frame 132"""	C9orf132			Standard	NM_001035254		Approved	Eeig1, bA203J24.7, SYM-3A	uc004bsx.2	Q5T9C2	OTTHUMG00000020720	ENST00000373095.1:c.477C>T	9.37:g.130710489G>A		75.0	0.0	0		67.0	38.0	0.567164	NM_001035254	A2A329|Q8TEL4	Silent	SNP	ENST00000373095.1	37	CCDS35150.1																																																																																			G|0.997;A|0.003	0.003	strong		0.597	FAM102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054298.2		
ATG2B	55102	hgsc.bcm.edu	37	14	96769560	96769560	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:96769560G>C	ENST00000359933.4	-	33	5768	c.4875C>G	c.(4873-4875)tgC>tgG	p.C1625W	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1625					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		AATCAGGTTTGCATGGCGGGT	0.438																																					p.C1625W		Atlas-SNP	.											.	ATG2B	169	.	0			c.C4875G						PASS	.						88.0	89.0	89.0					14																	96769560		2203	4300	6503	SO:0001583	missense	55102	exon33			AGGTTTGCATGGC	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4875C>G	14.37:g.96769560G>C	ENSP00000353010:p.Cys1625Trp	104.0	0.0	0		117.0	52.0	0.444444	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	.	.	.	.	.	.	.	.	.	.	G	12.66	2.005762	0.35415	.	.	ENSG00000066739	ENST00000359933	T	0.09445	2.98	5.74	3.72	0.42706	.	0.435774	0.22296	N	0.061922	T	0.04227	0.0117	N	0.08118	0	0.23896	N	0.996539	P	0.49358	0.923	B	0.36289	0.221	T	0.33599	-0.9862	10	0.66056	D	0.02	.	4.7681	0.13142	0.3198:0.1534:0.5267:0.0	.	1625	Q96BY7	ATG2B_HUMAN	W	1625	ENSP00000353010:C1625W	ENSP00000261834:C269W	C	-	3	2	ATG2B	95839313	0.002000	0.14202	0.011000	0.14972	0.693000	0.40251	1.215000	0.32431	0.742000	0.32697	0.563000	0.77884	TGC	.	.	none		0.438	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
MXRA5	25878	hgsc.bcm.edu	37	X	3241591	3241591	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:3241591C>T	ENST00000217939.6	-	5	2289	c.2135G>A	c.(2134-2136)aGg>aAg	p.R712K		NM_015419.3	NP_056234.2	Q9NR99	MXRA5_HUMAN	matrix-remodelling associated 5	712						extracellular vesicular exosome (GO:0070062)				NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(3)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(32)|lung(81)|ovary(6)|prostate(3)|skin(9)|stomach(3)|urinary_tract(2)	157		all_lung(23;0.00031)|Lung NSC(23;0.000946)				CAGAAGTCTCCTTGAAGTGTT	0.498																																					p.R712K		Atlas-SNP	.											.	MXRA5	815	.	0			c.G2135A						PASS	.						81.0	72.0	75.0					X																	3241591		2203	4300	6503	SO:0001583	missense	25878	exon5			AGTCTCCTTGAAG	AF245505	CCDS14124.1	Xp22.33	2013-01-29			ENSG00000101825	ENSG00000101825		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	7539	protein-coding gene	gene with protein product	"""adlican"""					12101425	Standard	NM_015419		Approved	DKFZp564I1922	uc004crg.4	Q9NR99	OTTHUMG00000021083	ENST00000217939.6:c.2135G>A	X.37:g.3241591C>T	ENSP00000217939:p.Arg712Lys	66.0	0.0	0		81.0	73.0	0.901235	NM_015419	Q6P1M7|Q9Y3Y8	Missense_Mutation	SNP	ENST00000217939.6	37	CCDS14124.1	.	.	.	.	.	.	.	.	.	.	c	2.192	-0.385056	0.04966	.	.	ENSG00000101825	ENST00000381114;ENST00000217939	T	0.62639	0.01	3.49	-0.704	0.11256	.	0.543747	0.15356	N	0.266696	T	0.37598	0.1009	N	0.17082	0.46	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.13845	-1.0494	10	0.23891	T	0.37	.	5.8602	0.18743	0.0:0.5307:0.2897:0.1795	.	712	Q9NR99	MXRA5_HUMAN	K	712	ENSP00000217939:R712K	ENSP00000217939:R712K	R	-	2	0	MXRA5	3251591	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.256000	0.18351	-0.388000	0.07797	0.529000	0.55759	AGG	.	.	none		0.498	MXRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055655.2	NM_015419	
TBC1D4	9882	hgsc.bcm.edu	37	13	76055726	76055726	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76055726C>T	ENST00000377636.3	-	1	524	c.178G>A	c.(178-180)Gcc>Acc	p.A60T	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000431480.2_Missense_Mutation_p.A60T|TBC1D4_ENST00000377625.2_Missense_Mutation_p.A60T	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	60	PID 1. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		CGGATCTCGGCCATGAGCCAG	0.716																																					p.A60T		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G178A						PASS	.						9.0	11.0	11.0					13																	76055726		1891	4103	5994	SO:0001583	missense	9882	exon1			TCTCGGCCATGAG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.178G>A	13.37:g.76055726C>T	ENSP00000366863:p.Ala60Thr	63.0	0.0	0		52.0	4.0	0.0769231	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	.	.	.	.	.	.	.	.	.	.	C	34	5.373372	0.95923	.	.	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625	T;T;T	0.55930	0.49;0.49;0.49	3.95	3.95	0.45737	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.000000	0.49916	D	0.000138	T	0.70386	0.3218	M	0.68593	2.085	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.998;0.996	T	0.75459	-0.3310	10	0.72032	D	0.01	-9.0239	16.1706	0.81812	0.0:1.0:0.0:0.0	.	60;60;60	O60343-2;O60343-3;O60343	.;.;TBCD4_HUMAN	T	60	ENSP00000366863:A60T;ENSP00000395986:A60T;ENSP00000366852:A60T	ENSP00000366852:A60T	A	-	1	0	TBC1D4	74953727	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	6.673000	0.74482	2.017000	0.59298	0.561000	0.74099	GCC	.	.	none		0.716	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
HSPG2	3339	hgsc.bcm.edu	37	1	22200998	22200998	+	Missense_Mutation	SNP	C	C	T	rs2229481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22200998C>T	ENST00000374695.3	-	28	3636	c.3557G>A	c.(3556-3558)cGg>cAg	p.R1186Q		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1186	Laminin EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00460}.		R -> Q (in dbSNP:rs2229481).		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	CTGCTCACACCGAGGGCCCTC	0.682													C|||	320	0.0638978	0.1967	0.0432	5008	,	,		17120	0.0		0.0219	False		,,,				2504	0.0082				p.R1186Q		Atlas-SNP	.											.	HSPG2	311	.	0			c.G3557A						PASS	.	C	GLN/ARG	768,3638	290.1+/-280.8	57,654,1492	31.0	31.0	31.0		3557	0.2	1.0	1	dbSNP_98	31	256,8344	96.1+/-157.9	4,248,4048	yes	missense	HSPG2	NM_005529.5	43	61,902,5540	TT,TC,CC		2.9767,17.4308,7.8733	benign	1186/4392	22200998	1024,11982	2203	4300	6503	SO:0001583	missense	3339	exon28			TCACACCGAGGGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.3557G>A	1.37:g.22200998C>T	ENSP00000363827:p.Arg1186Gln	133.0	0.0	0		188.0	91.0	0.484043	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	152	0.0695970695970696	97	0.19715447154471544	22	0.06077348066298342	6	0.01048951048951049	27	0.03562005277044855	C	11.48	1.651776	0.29336	0.174308	0.029767	ENSG00000142798	ENST00000374695	T	0.61859	0.07	4.93	0.185	0.15096	EGF-like, laminin (4);	0.899723	0.09017	N	0.860725	T	0.00039	0.0001	N	0.04768	-0.165	0.44966	P	0.0020120000000000138	B	0.09022	0.002	B	0.10450	0.005	T	0.14476	-1.0471	9	0.25106	T	0.35	.	8.6369	0.33953	0.0:0.242:0.0:0.758	rs2229481;rs58148193;rs2229481	1186	P98160	PGBM_HUMAN	Q	1186	ENSP00000363827:R1186Q	ENSP00000363827:R1186Q	R	-	2	0	HSPG2	22073585	0.005000	0.15991	0.982000	0.44146	0.734000	0.41952	-0.080000	0.11339	-0.211000	0.10124	-0.480000	0.04831	CGG	C|0.915;T|0.085	0.085	strong		0.682	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
CCDC141	285025	hgsc.bcm.edu	37	2	179749720	179749720	+	Missense_Mutation	SNP	G	G	C	rs199718873		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:179749720G>C	ENST00000409284.1	-	11	1744	c.1627C>G	c.(1627-1629)Cta>Gta	p.L543V	CCDC141_ENST00000295723.5_5'Flank|CCDC141_ENST00000420890.2_Missense_Mutation_p.L543V			Q6ZP82	CC141_HUMAN	coiled-coil domain containing 141	543										NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(37)|ovary(8)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)	78			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.0531)|all cancers(119;0.147)			TCTTCTGCTAGCCATCTAGCT	0.393													G|||	1	0.000199681	0.0	0.0	5008	,	,		20422	0.0		0.001	False		,,,				2504	0.0				p.L543V		Atlas-SNP	.											.	CCDC141	362	.	0			c.C1627G						PASS	.																																			SO:0001583	missense	285025	exon11			CTGCTAGCCATCT	AK096821		2q31.2	2013-01-14			ENSG00000163492	ENSG00000163492		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26821	protein-coding gene	gene with protein product	"""coiled-coil protein associated with myosin II and DISC1"""					20956536	Standard	NM_173648		Approved	FLJ39502, CAMDI	uc002une.2	Q6ZP82	OTTHUMG00000132578	ENST00000409284.1:c.1627C>G	2.37:g.179749720G>C	ENSP00000386503:p.Leu543Val	226.0	0.0	0		266.0	145.0	0.545113	NM_173648	H7C0P1|J3KNW6|Q8N8H3	Missense_Mutation	SNP	ENST00000409284.1	37		.	.	.	.	.	.	.	.	.	.	G	15.06	2.721922	0.48728	.	.	ENSG00000163492	ENST00000420890;ENST00000443758;ENST00000446116;ENST00000409284	T;T	0.63096	-0.02;0.36	5.33	4.42	0.53409	.	.	.	.	.	T	0.53965	0.1829	L	0.59436	1.845	0.80722	D	1	P	0.48294	0.908	B	0.36922	0.236	T	0.58645	-0.7600	8	.	.	.	.	12.621	0.56603	0.0:0.0:0.8349:0.1651	.	543	B8ZZB3	.	V	543;543;478;543	ENSP00000395995:L543V;ENSP00000390190:L543V	.	L	-	1	2	CCDC141	179457965	0.990000	0.36364	0.998000	0.56505	0.327000	0.28475	1.785000	0.38684	2.489000	0.83994	0.591000	0.81541	CTA	G|0.999;C|0.001	0.001	weak		0.393	CCDC141-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000335873.1	NM_173648	
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117359	46117359	+	Silent	SNP	G	G	A	rs183770957	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:46117359G>A	ENST00000400365.3	+	1	273	c.243G>A	c.(241-243)acG>acA	p.T81T	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	81	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						GCTCCTGCACGCCCTCGTGCT	0.672													g|||	11	0.00219649	0.0008	0.0	5008	,	,		17438	0.0		0.0089	False		,,,				2504	0.001				p.T81T		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.G243A						PASS	.	A	,	4,4396		0,4,2196	62.0	71.0	68.0		,243	-6.1	0.0	21		68	70,8514		0,70,4222	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	0,74,6418	AA,AG,GG		0.8155,0.0909,0.5699	,	,81/246	46117359	74,12910	2200	4292	6492	SO:0001819	synonymous_variant	386685	exon1			CTGCACGCCCTCG	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.243G>A	21.37:g.46117359G>A		91.0	0.0	0		115.0	54.0	0.469565	NM_198699	B2RPA3	Silent	SNP	ENST00000400365.3	37	CCDS42967.1																																																																																			G|0.994;A|0.006	0.006	strong		0.672	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
GSTZ1	2954	hgsc.bcm.edu	37	14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	rs7972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R|GSTZ1_ENST00000361389.4_5'UTR			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43.0	35.0	37.0		,124,124	5.6	1.0	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"""Glutathione S-transferases / Soluble"""	4643	protein-coding gene	gene with protein product	"""maleylacetoacetate isomerase"""	603758	"""glutathione transferase zeta 1"""			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	59.0	0.0	0		69.0	27.0	0.391304	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870	
MUC21	394263	hgsc.bcm.edu	37	6	30954560	30954560	+	Missense_Mutation	SNP	C	C	T	rs531044924	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954560C>T	ENST00000376296.3	+	2	849	c.608C>T	c.(607-609)aCc>aTc	p.T203I	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	203	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						TCCAGCACAACCTCCAGTGGG	0.617													c|||	192	0.0383387	0.0401	0.0533	5008	,	,		25680	0.0337		0.0308	False		,,,				2504	0.0378				p.T203I		Atlas-SNP	.											.	MUC21	98	.	0			c.C608T						PASS	.						160.0	154.0	156.0					6																	30954560		2203	4300	6503	SO:0001583	missense	394263	exon2			GCACAACCTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.608C>T	6.37:g.30954560C>T	ENSP00000365473:p.Thr203Ile	94.0	0.0	0		142.0	13.0	0.0915493	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	c	9.167	1.020156	0.19433	.	.	ENSG00000204544	ENST00000376296	T	0.11385	2.78	4.1	1.24	0.21308	.	.	.	.	.	T	0.03095	0.0091	L	0.27053	0.805	0.09310	N	1	P	0.44044	0.825	P	0.44897	0.463	T	0.42292	-0.9460	8	.	.	.	.	7.7906	0.29119	0.0:0.7057:0.0:0.2943	.	203	Q5SSG8	MUC21_HUMAN	I	203	ENSP00000365473:T203I	.	T	+	2	0	MUC21	31062539	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.733000	0.04898	0.127000	0.18452	0.491000	0.48974	ACC	.	.	none		0.617	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
NCOA1	8648	hgsc.bcm.edu	37	2	24980955	24980955	+	Missense_Mutation	SNP	A	A	G	rs150066931	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:24980955A>G	ENST00000406961.1	+	21	4647	c.3995A>G	c.(3994-3996)aAc>aGc	p.N1332S	NCOA1_ENST00000395856.3_Missense_Mutation_p.N1332S|NCOA1_ENST00000405141.1_Missense_Mutation_p.N1332S|NCOA1_ENST00000348332.3_Missense_Mutation_p.N1332S|NCOA1_ENST00000538539.1_Missense_Mutation_p.N1332S|NCOA1_ENST00000288599.5_Missense_Mutation_p.N1332S|NCOA1_ENST00000407230.1_Missense_Mutation_p.N1181S			Q15788	NCOA1_HUMAN	nuclear receptor coactivator 1	1332					androgen receptor signaling pathway (GO:0030521)|cellular lipid metabolic process (GO:0044255)|cellular response to hormone stimulus (GO:0032870)|cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|estrous cycle phase (GO:0060206)|hippocampus development (GO:0021766)|histone H4 acetylation (GO:0043967)|hypothalamus development (GO:0021854)|labyrinthine layer morphogenesis (GO:0060713)|lactation (GO:0007595)|male gonad development (GO:0008584)|male mating behavior (GO:0060179)|ovulation cycle (GO:0042698)|positive regulation of apoptotic process (GO:0043065)|positive regulation of female receptivity (GO:0045925)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by galactose (GO:0000435)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular response to drug (GO:2001038)|response to estradiol (GO:0032355)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region DNA binding (GO:0001012)|RNA polymerase II transcription coactivator activity (GO:0001105)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)		PAX3/NCOA1(8)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(26)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	53	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CAGAACATGAACCCAATGATG	0.527			T	PAX3	alveolar rhadomyosarcoma								A|||	29	0.00579073	0.0	0.0072	5008	,	,		15823	0.0		0.001	False		,,,				2504	0.0235				p.N1332S		Atlas-SNP	.		Dom	yes		2	2p23	8648	nuclear receptor coactivator 1		M	.	NCOA1	210	.	0			c.A3995G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	161.0	132.0	142.0		3995,3995,3995	3.8	1.0	2	dbSNP_134	142	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense	NCOA1	NM_003743.4,NM_147223.2,NM_147233.2	46,46,46	0,9,6494	GG,GA,AA		0.1047,0.0,0.0692	probably-damaging,probably-damaging,probably-damaging	1332/1442,1332/1400,1332/1441	24980955	9,12997	2203	4300	6503	SO:0001583	missense	8648	exon19			ACATGAACCCAAT	U40396	CCDS1712.1, CCDS1713.1, CCDS42660.1	2p23	2011-07-01			ENSG00000084676	ENSG00000084676		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7668	protein-coding gene	gene with protein product		602691				7481822, 9575154	Standard	XM_005264625		Approved	SRC1, F-SRC-1, NCoA-1, KAT13A, RIP160, bHLHe74	uc002rfk.3	Q15788	OTTHUMG00000125523	ENST00000406961.1:c.3995A>G	2.37:g.24980955A>G	ENSP00000385216:p.Asn1332Ser	226.0	0.0	0		272.0	130.0	0.477941	NM_147223	O00150|O43792|O43793|Q13071|Q13420|Q2T9G5|Q53SX3|Q6GVI5|Q7KYV3	Missense_Mutation	SNP	ENST00000406961.1	37	CCDS1712.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	19.15	3.771069	0.69992	0.0	0.001047	ENSG00000084676	ENST00000406961;ENST00000405141;ENST00000407230;ENST00000538539;ENST00000348332;ENST00000288599;ENST00000395856	T;T;T;T;T;T;T	0.02369	4.44;4.42;4.32;4.42;4.44;4.42;4.44	5.01	3.82	0.43975	.	0.165920	0.53938	D	0.000052	T	0.06872	0.0175	L	0.47716	1.5	0.41217	D	0.986487	D;D;P;D;D	0.61697	0.982;0.99;0.586;0.99;0.982	P;P;B;P;P	0.54889	0.584;0.763;0.28;0.763;0.584	T	0.18085	-1.0348	10	0.62326	D	0.03	.	10.6256	0.45506	0.9228:0.0:0.0771:0.0	.	1332;1332;1332;1332;1181	A8K1V4;Q15788-3;Q15788;Q15788-2;B5MCN7	.;.;NCOA1_HUMAN;.;.	S	1332;1332;1181;1332;1332;1332;1332	ENSP00000385216:N1332S;ENSP00000385097:N1332S;ENSP00000385195:N1181S;ENSP00000444039:N1332S;ENSP00000320940:N1332S;ENSP00000288599:N1332S;ENSP00000379197:N1332S	ENSP00000288599:N1332S	N	+	2	0	NCOA1	24834459	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.694000	0.61760	0.897000	0.36392	0.477000	0.44152	AAC	A|0.999;G|0.001	0.001	strong		0.527	NCOA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246852.3	NM_147223	
MUM1	84939	hgsc.bcm.edu	37	19	1370742	1370742	+	Missense_Mutation	SNP	G	G	A	rs34502536	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1370742G>A	ENST00000415183.3	+	11	1680	c.1654G>A	c.(1654-1656)Ggg>Agg	p.G552R	MUM1_ENST00000591806.1_Missense_Mutation_p.G552R|MUM1_ENST00000311401.5_Missense_Mutation_p.G483R|MUM1_ENST00000344663.3_Missense_Mutation_p.G552R			Q2TAK8	MUM1_HUMAN	melanoma associated antigen (mutated) 1	551					chromatin organization (GO:0006325)|DNA repair (GO:0006281)	nucleus (GO:0005634)	nucleosome binding (GO:0031491)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;0.000172)|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)		GTGCCCCCTGGGGCAGAGGCA	0.662													G|||	35	0.00698882	0.0008	0.013	5008	,	,		13894	0.0		0.0239	False		,,,				2504	0.001				p.G552R		Atlas-SNP	.											.	MUM1	54	.	0			c.G1654A						PASS	.	G	ARG/GLY	17,4093		0,17,2038	7.0	8.0	8.0		1654	2.6	0.0	19	dbSNP_126	8	131,7971		0,131,3920	no	missense	MUM1	NM_032853.3	125	0,148,5958	AA,AG,GG		1.6169,0.4136,1.2119	possibly-damaging	552/712	1370742	148,12064	2055	4051	6106	SO:0001583	missense	84939	exon12			CCCCTGGGGCAGA	AK075241	CCDS12062.1	19p13.3	2008-02-05				ENSG00000160953			29641	protein-coding gene	gene with protein product						11042152, 7644523	Standard	NM_032853		Approved	MUM-1	uc002lrz.2	Q2TAK8		ENST00000415183.3:c.1654G>A	19.37:g.1370742G>A	ENSP00000394925:p.Gly552Arg	54.0	0.0	0		79.0	43.0	0.544304	NM_032853	A1L489|B5ME02|B7ZLY8|J3KQD6|Q13109|Q5XKB9|Q8N2I4|Q96A67	Missense_Mutation	SNP	ENST00000415183.3	37		26	0.011904761904761904	0	0.0	8	0.022099447513812154	0	0.0	18	0.023746701846965697	G	18.07	3.541037	0.65085	0.004136	0.016169	ENSG00000160953	ENST00000344663;ENST00000311401;ENST00000415183	T;T;T	0.40756	1.02;1.02;1.02	5.07	2.57	0.30868	.	0.460401	0.23351	N	0.049132	T	0.37945	0.1022	M	0.66939	2.045	0.09310	N	1	D;D;D;P	0.89917	0.999;1.0;0.993;0.954	D;D;P;P	0.69307	0.946;0.963;0.898;0.548	T	0.21211	-1.0252	10	0.72032	D	0.01	.	5.3578	0.16071	0.2867:0.0:0.7133:0.0	rs34502536	552;552;483;551	B7ZLY8;D6W5Y8;Q2TAK8-2;Q2TAK8	.;.;.;MUM1_HUMAN	R	552;483;552	ENSP00000345789:G552R;ENSP00000309135:G483R;ENSP00000394925:G552R	ENSP00000309135:G483R	G	+	1	0	MUM1	1321742	0.412000	0.25392	0.009000	0.14445	0.086000	0.17979	2.031000	0.41117	1.253000	0.44018	0.561000	0.74099	GGG	G|0.988;A|0.012	0.012	strong		0.662	MUM1-016	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000449510.1	NM_032853	
PKHD1	5314	hgsc.bcm.edu	37	6	51892977	51892977	+	Silent	SNP	A	A	G	rs141574387	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:51892977A>G	ENST00000371117.3	-	30	3812	c.3537T>C	c.(3535-3537)aaT>aaC	p.N1179N	PKHD1_ENST00000340994.4_Silent_p.N1179N	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	1179	IPT/TIG 6; atypical.				cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					TGCTGACCCCATTGATAGAGA	0.498													A|||	4	0.000798722	0.0	0.0029	5008	,	,		19364	0.0		0.001	False		,,,				2504	0.001				p.N1179N		Atlas-SNP	.											.	PKHD1	927	.	0			c.T3537C						PASS	.	A	,	0,4406		0,0,2203	144.0	158.0	154.0		3537,3537	2.0	1.0	6	dbSNP_134	154	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,15,6488	GG,GA,AA		0.1744,0.0,0.1153	,	1179/4075,1179/3397	51892977	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon30			GACCCCATTGATA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.3537T>C	6.37:g.51892977A>G		81.0	0.0	0		96.0	58.0	0.604167	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			A|0.999;G|0.001	0.001	strong		0.498	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
GTF2I	2969	hgsc.bcm.edu	37	7	74105424	74105424	+	Silent	SNP	A	A	G	rs143931854	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:74105424A>G	ENST00000324896.4	+	3	608	c.219A>G	c.(217-219)caA>caG	p.Q73Q	GTF2I_ENST00000416070.1_Silent_p.Q73Q|AC083884.8_ENST00000450426.2_RNA|GTF2I_ENST00000353920.4_Silent_p.Q73Q|GTF2I_ENST00000443166.1_Silent_p.Q73Q|GTF2I_ENST00000346152.4_Silent_p.Q73Q	NM_032999.2	NP_127492.1	P78347	GTF2I_HUMAN	general transcription factor IIi	73					negative regulation of angiogenesis (GO:0016525)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19						AGGATTTTCAAAAAGATTTTG	0.328													A|||	5	0.000998403	0.0	0.0043	5008	,	,		17800	0.0		0.002	False		,,,				2504	0.0				p.Q73Q		Atlas-SNP	.											.	GTF2I	40	.	0			c.A219G						PASS	.	A	,,,,	2,4404		0,2,2201	68.0	69.0	69.0		219,219,219,219,219	-1.2	1.0	7	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTF2I	NM_001163636.1,NM_001518.3,NM_032999.2,NM_033000.2,NM_033001.2	,,,,	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	,,,,	73/977,73/958,73/999,73/979,73/978	74105424	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	2969	exon3			TTTTCAAAAAGAT	U77948	CCDS5573.1, CCDS5574.1, CCDS5575.1, CCDS47614.1, CCDS64680.1	7q11.23	2011-05-25	2009-07-23			ENSG00000263001		"""General transcription factors"""	4659	protein-coding gene	gene with protein product		601679	"""general transcription factor II, i"""	WBSCR6		9334314, 9012831	Standard	NM_032999		Approved	TFII-I, BAP-135, SPIN, BTKAP1, DIWS, IB291	uc003uau.3	P78347		ENST00000324896.4:c.219A>G	7.37:g.74105424A>G		206.0	0.0	0		213.0	97.0	0.455399	NM_032999	O14743|O15359|O43546|O43588|O43589|Q75M85|Q75M86|Q75M87|Q75M88|Q86U51|Q9BSZ4	Silent	SNP	ENST00000324896.4	37	CCDS5573.1																																																																																			A|0.999;G|0.001	0.001	strong		0.328	GTF2I-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252708.1	NM_032999	
POTEE	445582	hgsc.bcm.edu	37	2	132020976	132020976	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:132020976A>G	ENST00000356920.5	+	15	2042	c.1948A>G	c.(1948-1950)Acg>Gcg	p.T650A	PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	650					retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											TGAAAATAGTACGTTGCGGGA	0.353																																					p.T650A		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,-1,1	.	.	1	0			c.A1948G						scavenged	.						25.0	26.0	26.0					2																	132020976		1927	4158	6085	SO:0001583	missense	445582	exon15			AATAGTACGTTGC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.1948A>G	2.37:g.132020976A>G	ENSP00000439189:p.Thr650Ala	428.0	1.0	0.00233645		404.0	162.0	0.40099	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	2.826	-0.243795	0.05906	.	.	ENSG00000188219	ENST00000356920	T	0.14144	2.53	0.993	0.993	0.19825	.	.	.	.	.	T	0.07999	0.0200	N	0.19112	0.55	0.09310	N	0.999999	B	0.10296	0.003	B	0.01281	0.0	T	0.31336	-0.9947	9	0.72032	D	0.01	.	4.2424	0.10654	1.0:0.0:0.0:0.0	.	650	Q6S8J3	POTEE_HUMAN	A	650	ENSP00000439189:T650A	ENSP00000439189:T650A	T	+	1	0	AC131180.1	131737446	0.001000	0.12720	0.030000	0.17652	0.008000	0.06430	1.083000	0.30815	0.705000	0.31890	0.155000	0.16302	ACG	.	.	none		0.353	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
TMEM109	79073	hgsc.bcm.edu	37	11	60689534	60689534	+	Missense_Mutation	SNP	C	C	T	rs75070807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:60689534C>T	ENST00000227525.3	+	4	1032	c.629C>T	c.(628-630)gCc>gTc	p.A210V	TMEM132A_ENST00000005286.4_5'Flank|RP11-881M11.4_ENST00000543907.1_RNA|TMEM132A_ENST00000453848.2_5'Flank|TMEM109_ENST00000536171.1_Missense_Mutation_p.A210V	NM_024092.2	NP_076997.1	Q9BVC6	TM109_HUMAN	transmembrane protein 109	210					cellular response to gamma radiation (GO:0071480)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of cell death (GO:0060548)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8						GCCTCTGGGGCCCAACTCGAG	0.706													C|||	48	0.00958466	0.0023	0.0173	5008	,	,		15459	0.0		0.0229	False		,,,				2504	0.0102				p.A210V		Atlas-SNP	.											.	TMEM109	24	.	0			c.C629T						PASS	.	C	VAL/ALA	31,4359		0,31,2164	21.0	25.0	24.0		629	2.8	1.0	11	dbSNP_131	24	237,8333		2,233,4050	yes	missense	TMEM109	NM_024092.2	64	2,264,6214	TT,TC,CC		2.7655,0.7062,2.0679	benign	210/244	60689534	268,12692	2195	4285	6480	SO:0001583	missense	79073	exon4			CTGGGGCCCAACT		CCDS7996.1	11q12.2	2005-12-22				ENSG00000110108			28771	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_024092		Approved	MGC5508	uc001nqg.3	Q9BVC6		ENST00000227525.3:c.629C>T	11.37:g.60689534C>T	ENSP00000227525:p.Ala210Val	25.0	0.0	0		60.0	37.0	0.616667	NM_024092		Missense_Mutation	SNP	ENST00000227525.3	37	CCDS7996.1	27	0.012362637362637362	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	19	0.025065963060686015	C	14.68	2.608134	0.46527	0.007062	0.027655	ENSG00000110108	ENST00000227525;ENST00000536171	.	.	.	4.75	2.82	0.32997	.	0.530146	0.18218	N	0.147992	T	0.11452	0.0279	L	0.34521	1.04	0.26459	N	0.975476	B	0.11235	0.004	B	0.14578	0.011	T	0.09314	-1.0680	9	0.39692	T	0.17	-13.8635	8.6821	0.34214	0.0:0.7661:0.1493:0.0847	.	210	Q9BVC6	TM109_HUMAN	V	210	.	ENSP00000227525:A210V	A	+	2	0	TMEM109	60446110	0.001000	0.12720	1.000000	0.80357	0.164000	0.22412	0.816000	0.27267	0.969000	0.38237	0.555000	0.69702	GCC	C|0.983;T|0.017	0.017	strong		0.706	TMEM109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396343.1	NM_024092	
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121432117G>C	ENST00000257555.6	+	4	1090	c.864G>C	c.(862-864)ggG>ggC	p.G288G	HNF1A_ENST00000400024.2_Silent_p.G288G|HNF1A_ENST00000544413.1_Silent_p.G288G|HNF1A_ENST00000541395.1_Silent_p.G288G|HNF1A_ENST00000543427.1_Silent_p.G171G|HNF1A_ENST00000538626.1_Intron|HNF1A_ENST00000402929.1_Silent_p.G288G			P20823	HNF1A_HUMAN	HNF1 homeobox A	288					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGTACAGCGGGCCCCCCCCAG	0.667									Hepatic Adenoma, Familial Clustering of				g|||	907	0.18111	0.1778	0.415	5008	,	,		17094	0.005		0.3032	False		,,,				2504	0.0757				p.G288G		Atlas-SNP	.											HNF1A,brain,glioma,0,1	HNF1A	302	1	0			c.G864C	GRCh37	CI064741|CM067044	HNF1A	I|M	rs56348580	PASS	.	G		802,3604		95,612,1496	24.0	24.0	24.0		864	2.3	1.0	12	dbSNP_129	24	2264,6334		374,1516,2409	no	coding-synonymous	HNF1A	NM_000545.5		469,2128,3905	CC,CG,GG		26.3317,18.2025,23.5774		288/632	121432117	3066,9938	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CAGCGGGCCCCCC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.864G>C	12.37:g.121432117G>C		25.0	0.0	0		45.0	22.0	0.488889	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.754;C|0.246	0.246	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
USP29	57663	hgsc.bcm.edu	37	19	57642413	57642413	+	Missense_Mutation	SNP	C	C	A	rs35394887	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:57642413C>A	ENST00000254181.4	+	4	2824	c.2370C>A	c.(2368-2370)gaC>gaA	p.D790E	USP29_ENST00000598197.1_Missense_Mutation_p.D790E	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	790	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		TGGGTTCTGACAACCCAGGAA	0.468													C|||	23	0.00459265	0.0	0.0072	5008	,	,		20144	0.0		0.006	False		,,,				2504	0.0123				p.D790E		Atlas-SNP	.											.	USP29	186	.	0			c.C2370A						PASS	.	C	GLU/ASP	5,4401	9.9+/-24.2	0,5,2198	50.0	43.0	46.0		2370	-1.5	0.0	19	dbSNP_126	46	62,8538	37.8+/-93.5	0,62,4238	yes	missense	USP29	NM_020903.2	45	0,67,6436	AA,AC,CC		0.7209,0.1135,0.5151	probably-damaging	790/923	57642413	67,12939	2203	4300	6503	SO:0001583	missense	57663	exon4			TTCTGACAACCCA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.2370C>A	19.37:g.57642413C>A	ENSP00000254181:p.Asp790Glu	105.0	0.0	0		128.0	60.0	0.46875	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	10.17	1.276210	0.23307	0.001135	0.007209	ENSG00000131864	ENST00000254181	T	0.72942	-0.7	2.05	-1.45	0.08828	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.57110	0.2031	L	0.54323	1.7	0.09310	N	1	P	0.47545	0.897	P	0.45946	0.498	T	0.55496	-0.8132	9	0.72032	D	0.01	.	5.8011	0.18414	0.0:0.5297:0.0:0.4703	rs35394887	790	Q9HBJ7	UBP29_HUMAN	E	790	ENSP00000254181:D790E	ENSP00000254181:D790E	D	+	3	2	USP29	62334225	0.862000	0.29867	0.001000	0.08648	0.010000	0.07245	-0.726000	0.04936	-0.484000	0.06763	-0.483000	0.04790	GAC	C|0.996;A|0.004	0.004	strong		0.468	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
LCE1F	353137	hgsc.bcm.edu	37	1	152748962	152748962	+	Missense_Mutation	SNP	C	C	T	rs116630978		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152748962C>T	ENST00000334371.2	+	1	115	c.115C>T	c.(115-117)Cct>Tct	p.P39S		NM_178354.2	NP_848131.1	Q5T754	LCE1F_HUMAN	late cornified envelope 1F	39	Pro-rich.				keratinization (GO:0031424)			p.P39A(1)		kidney(1)|large_intestine(2)|lung(7)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			taagtgccctccTGTCTCTTC	0.677													.|||	1	0.000199681	0.0008	0.0	5008	,	,		14646	0.0		0.0	False		,,,				2504	0.0				p.P39S		Atlas-SNP	.											LCE1F,NS,carcinoma,0,2	LCE1F	42	2	1	Substitution - Missense(1)	prostate(1)	c.C115T						PASS	.	C	SER/PRO	1,4405	2.1+/-5.4	0,1,2202	58.0	60.0	59.0		115	4.6	0.9	1	dbSNP_132	59	0,8600		0,0,4300	no	missense	LCE1F	NM_178354.2	74	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	39/119	152748962	1,13005	2203	4300	6503	SO:0001583	missense	353137	exon1			TGCCCTCCTGTCT		CCDS1023.1	1q21.3	2008-02-05			ENSG00000240386	ENSG00000240386		"""Late cornified envelopes"""	29467	protein-coding gene	gene with protein product		612608				11698679	Standard	NM_178354		Approved	LEP6	uc010pdv.2	Q5T754	OTTHUMG00000012403	ENST00000334371.2:c.115C>T	1.37:g.152748962C>T	ENSP00000334187:p.Pro39Ser	132.0	0.0	0		145.0	7.0	0.0482759	NM_178354		Missense_Mutation	SNP	ENST00000334371.2	37	CCDS1023.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	10.13	1.264799	0.23136	2.27E-4	0.0	ENSG00000240386	ENST00000334371	T	0.04119	3.7	4.56	4.56	0.56223	.	.	.	.	.	T	0.02848	0.0085	L	0.39326	1.205	0.24725	N	0.993127	B	0.28760	0.221	B	0.34138	0.176	T	0.30736	-0.9968	9	0.87932	D	0	.	13.0238	0.58804	0.0:1.0:0.0:0.0	.	39	Q5T754	LCE1F_HUMAN	S	39	ENSP00000334187:P39S	ENSP00000334187:P39S	P	+	1	0	LCE1F	151015586	0.776000	0.28616	0.936000	0.37596	0.529000	0.34654	2.029000	0.41098	2.516000	0.84829	0.557000	0.71058	CCT	C|0.998;T|0.002	0.002	strong		0.677	LCE1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034523.2	NM_178354	
MATN2	4147	hgsc.bcm.edu	37	8	99019799	99019799	+	Missense_Mutation	SNP	G	G	A	rs372608950		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:99019799G>A	ENST00000520016.1	+	9	1667	c.1543G>A	c.(1543-1545)Gtg>Atg	p.V515M	MATN2_ENST00000522025.2_Missense_Mutation_p.V231M|MATN2_ENST00000524308.1_Missense_Mutation_p.V474M|MATN2_ENST00000521689.1_Missense_Mutation_p.V515M|MATN2_ENST00000254898.5_Missense_Mutation_p.V515M			O00339	MATN2_HUMAN	matrilin 2	515	EGF-like 7. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			TGAGGGACACGTGCTCCGCAG	0.567																																					p.V515M		Atlas-SNP	.											.	MATN2	165	.	0			c.G1543A						PASS	.						143.0	140.0	141.0					8																	99019799		2145	4249	6394	SO:0001583	missense	4147	exon10			GGACACGTGCTCC	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1543G>A	8.37:g.99019799G>A	ENSP00000430487:p.Val515Met	75.0	0.0	0		95.0	51.0	0.536842	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Missense_Mutation	SNP	ENST00000520016.1	37	CCDS55264.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	6.569|6.569	0.473360|0.473360	0.12461|0.12461	.|.	.|.	ENSG00000132561|ENSG00000132561	ENST00000518154|ENST00000521689;ENST00000254898;ENST00000378716;ENST00000524308;ENST00000522025;ENST00000520016	.|D;D;D;T;D	.|0.87887	.|-2.3;-2.3;-2.31;1.5;-2.3	5.65|5.65	2.57|2.57	0.30868|0.30868	.|Epidermal growth factor-like (1);	.|0.695407	.|0.13029	.|N	.|0.419495	T|T	0.80259|0.80259	0.4590|0.4590	L|L	0.41961|0.41961	1.31|1.31	0.21355|0.21355	N|N	0.999711|0.999711	.|B;B;B;B	.|0.21606	.|0.058;0.026;0.02;0.014	.|B;B;B;B	.|0.11329	.|0.006;0.003;0.005;0.003	T|T	0.68157|0.68157	-0.5483|-0.5483	5|10	.|0.45353	.|T	.|0.12	-6.9692|-6.9692	6.4777|6.4777	0.22045|0.22045	0.4096:0.0:0.5904:0.0|0.4096:0.0:0.5904:0.0	.|.	.|474;515;515;515	.|C9JH87;E9PF03;O00339-2;O00339	.|.;.;.;MATN2_HUMAN	H|M	297|515;515;474;474;231;515	.|ENSP00000429977:V515M;ENSP00000254898:V515M;ENSP00000430221:V474M;ENSP00000429010:V231M;ENSP00000430487:V515M	.|ENSP00000254898:V515M	R|V	+|+	2|1	0|0	MATN2|MATN2	99088975|99088975	0.000000|0.000000	0.05858|0.05858	0.315000|0.315000	0.25238|0.25238	0.144000|0.144000	0.21451|0.21451	-0.333000|-0.333000	0.07894|0.07894	0.577000|0.577000	0.29470|0.29470	-0.126000|-0.126000	0.14955|0.14955	CGT|GTG	.	.	weak		0.567	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
STK31	56164	hgsc.bcm.edu	37	7	23811822	23811822	+	Silent	SNP	A	A	G	rs147172261		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:23811822A>G	ENST00000355870.3	+	15	2009	c.1890A>G	c.(1888-1890)ctA>ctG	p.L630L	STK31_ENST00000354639.3_Silent_p.L607L|STK31_ENST00000433467.2_Silent_p.L630L|STK31_ENST00000405627.3_3'UTR|STK31_ENST00000428484.1_Silent_p.L607L	NM_031414.4	NP_113602.2	Q9BXU1	STK31_HUMAN	serine/threonine kinase 31	630						acrosomal vesicle (GO:0001669)	ATP binding (GO:0005524)|hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(31)|ovary(2)|prostate(1)|skin(7)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	67						ATCACTTGCTATCCATTAAGA	0.313																																					p.L630L		Atlas-SNP	.											STK31,NS,carcinoma,+2,1	STK31	175	1	0			c.A1890G						PASS	.	A	,,	0,4406		0,0,2203	59.0	61.0	60.0		1821,1890,1821	-8.1	0.9	7	dbSNP_134	60	4,8582	3.7+/-12.6	0,4,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	STK31	NM_001122833.1,NM_031414.3,NM_032944.2	,,	0,4,6492	GG,GA,AA		0.0466,0.0,0.0308	,,	607/997,630/1020,607/997	23811822	4,12988	2203	4293	6496	SO:0001819	synonymous_variant	56164	exon15			CTTGCTATCCATT	AF285599	CCDS5386.1, CCDS43556.1, CCDS59049.1	7p15.3	2014-04-23			ENSG00000196335	ENSG00000196335		"""Tudor domain containing"""	11407	protein-coding gene	gene with protein product		605790				11279525	Standard	NM_031414		Approved	TDRD8, SgK396	uc003sws.5	Q9BXU1	OTTHUMG00000023053	ENST00000355870.3:c.1890A>G	7.37:g.23811822A>G		166.0	0.0	0		186.0	93.0	0.5	NM_031414	B4DZ06|B7WPP5|C9J4F9|Q6PCD3|Q9BXH8	Silent	SNP	ENST00000355870.3	37	CCDS5386.1																																																																																			A|1.000;G|0.000	0.000	weak		0.313	STK31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214036.2	NM_031414	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149212590	149212590	+	Silent	SNP	C	C	T	rs144195384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:149212590C>T	ENST00000309241.5	+	5	986	c.954C>T	c.(952-954)aaC>aaT	p.N318N	PPARGC1B_ENST00000394320.3_Silent_p.N318N|PPARGC1B_ENST00000403750.1_Silent_p.N254N|PPARGC1B_ENST00000360453.4_Silent_p.N279N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	318					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCTGCAGCAACCCCTCCCAGC	0.627													C|||	12	0.00239617	0.0068	0.0014	5008	,	,		16493	0.0		0.0	False		,,,				2504	0.002				p.N318N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.C954T						PASS	.	C	,,	25,4381	31.7+/-61.6	0,25,2178	46.0	52.0	50.0		837,762,954	5.6	1.0	5	dbSNP_134	50	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	,,	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	,,	279/985,254/960,318/1024	149212590	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	133522	exon5			CAGCAACCCCTCC	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.954C>T	5.37:g.149212590C>T		180.0	0.0	0		188.0	95.0	0.505319	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Silent	SNP	ENST00000309241.5	37	CCDS4298.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	0.907	-0.720352	0.03182	0.005674	0.0	ENSG00000155846	ENST00000434684	.	.	.	5.61	5.61	0.85477	.	.	.	.	.	T	0.69967	0.3170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71879	-0.4459	4	.	.	.	-7.6835	19.6373	0.95740	0.0:1.0:0.0:0.0	.	.	.	.	S	5	.	.	P	+	1	0	PPARGC1B	149192783	1.000000	0.71417	1.000000	0.80357	0.234000	0.25298	2.309000	0.43699	2.636000	0.89361	0.655000	0.94253	CCC	C|0.998;T|0.002	0.002	strong		0.627	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
CLK1	1195	hgsc.bcm.edu	37	2	201728858	201728858	+	Intron	SNP	C	C	T	rs140874256	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:201728858C>T	ENST00000321356.4	-	1	136				Y_RNA_ENST00000516950.1_RNA|CLK1_ENST00000434813.2_Missense_Mutation_p.R31H|CLK1_ENST00000492793.1_Intron	NM_004071.3	NP_004062.2	P49759	CLK1_HUMAN	CDC-like kinase 1						cell proliferation (GO:0008283)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|regulation of RNA splicing (GO:0043484)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(12)|ovary(1)|pancreas(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33						GCTTGGCTCACGCACATTCTG	0.587													C|||	6	0.00119808	0.0	0.0029	5008	,	,		15982	0.001		0.002	False		,,,				2504	0.001				p.R31H		Atlas-SNP	.											.	CLK1	103	.	0			c.G92A						PASS	.	C	HIS/ARG,	0,1384		0,0,692	100.0	89.0	92.0		92,	-2.6	0.0	2	dbSNP_134	92	3,3179		0,3,1588	yes	missense,intron	CLK1	NM_001162407.1,NM_004071.3	29,	0,3,2280	TT,TC,CC		0.0943,0.0,0.0657	,	31/527,	201728858	3,4563	692	1591	2283	SO:0001627	intron_variant	1195	exon1			GGCTCACGCACAT	L29219	CCDS2331.1, CCDS54427.1	2q33	2008-05-02			ENSG00000013441	ENSG00000013441		"""CDC-like kinases"""	2068	protein-coding gene	gene with protein product		601951				9856501	Standard	NM_004071		Approved		uc002uwe.2	P49759	OTTHUMG00000132784	ENST00000321356.4:c.0+428G>A	2.37:g.201728858C>T		71.0	0.0	0		74.0	44.0	0.594595	NM_001162407	B4DFW7|Q0P694|Q8N5V8	Missense_Mutation	SNP	ENST00000321356.4	37	CCDS2331.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	C	6.751	0.507366	0.12883	0.0	9.43E-4	ENSG00000013441	ENST00000434813	T	0.70631	-0.5	2.28	-2.64	0.06114	.	.	.	.	.	T	0.43077	0.1231	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11916	-1.0568	9	0.46703	T	0.11	.	2.9621	0.05896	0.1488:0.4118:0.3218:0.1176	.	31	B4DFW7	.	H	31	ENSP00000394734:R31H	ENSP00000394734:R31H	R	-	2	0	CLK1	201437103	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.543000	0.00436	-1.305000	0.02327	-2.739000	0.00128	CGT	C|0.998;T|0.002	0.002	strong		0.587	CLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256192.2		
LRRC14B	389257	hgsc.bcm.edu	37	5	192467	192467	+	Missense_Mutation	SNP	G	G	A	rs78454293	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:192467G>A	ENST00000328278.3	+	1	842	c.814G>A	c.(814-816)Gcc>Acc	p.A272T		NM_001080478.1	NP_001073947.1	A6NHZ5	LR14B_HUMAN	leucine rich repeat containing 14B	272										endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)|upper_aerodigestive_tract(2)	10						CGCCTCCATCGCCCGGGAGCT	0.682													G|||	10	0.00199681	0.0008	0.0029	5008	,	,		17788	0.0		0.007	False		,,,				2504	0.0				p.A272T		Atlas-SNP	.											.	LRRC14B	30	.	0			c.G814A						PASS	.	G	THR/ALA	13,4271		0,13,2129	9.0	12.0	11.0		814	4.4	1.0	5	dbSNP_131	11	61,8449		0,61,4194	yes	missense	LRRC14B	NM_001080478.1	58	0,74,6323	AA,AG,GG		0.7168,0.3035,0.5784	possibly-damaging	272/515	192467	74,12720	2142	4255	6397	SO:0001583	missense	389257	exon1			TCCATCGCCCGGG		CCDS47184.1	5p15.33	2010-02-17			ENSG00000185028	ENSG00000185028			37268	protein-coding gene	gene with protein product							Standard	NM_001080478		Approved		uc003jal.1	A6NHZ5	OTTHUMG00000161578	ENST00000328278.3:c.814G>A	5.37:g.192467G>A	ENSP00000327675:p.Ala272Thr	132.0	0.0	0		189.0	102.0	0.539683	NM_001080478		Missense_Mutation	SNP	ENST00000328278.3	37	CCDS47184.1	9	0.004120879120879121	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	17.09	3.300830	0.60195	0.003035	0.007168	ENSG00000185028	ENST00000328278	T	0.55052	0.54	5.33	4.43	0.53597	.	0.149049	0.64402	D	0.000010	T	0.42314	0.1197	L	0.38838	1.175	0.36111	D	0.844832	D	0.62365	0.991	P	0.52109	0.69	T	0.51779	-0.8662	10	0.18276	T	0.48	.	12.8535	0.57871	0.0:0.0:0.8357:0.1643	.	272	A6NHZ5	LR14B_HUMAN	T	272	ENSP00000327675:A272T	ENSP00000327675:A272T	A	+	1	0	LRRC14B	245467	1.000000	0.71417	0.987000	0.45799	0.131000	0.20780	7.463000	0.80869	1.185000	0.42971	0.462000	0.41574	GCC	G|0.996;A|0.004	0.004	strong		0.682	LRRC14B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000365393.2	NM_001080478	
POTEE	445582	hgsc.bcm.edu	37	2	132021908	132021908	+	Silent	SNP	G	G	A	rs201238743	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:132021908G>A	ENST00000356920.5	+	15	2974	c.2880G>A	c.(2878-2880)gcG>gcA	p.A960A	PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR|PLEKHB2_ENST00000303908.3_Intron	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	960	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCCCCGAGGCGCTCTTCCAGC	0.592																																					p.A960A		Atlas-SNP	.											.	.	.	.	0			c.G2880A						PASS	.						2.0	1.0	1.0					2																	132021908		762	1288	2050	SO:0001819	synonymous_variant	445582	exon15			CGAGGCGCTCTTC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2880G>A	2.37:g.132021908G>A		165.0	0.0	0		184.0	41.0	0.222826	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Silent	SNP	ENST00000356920.5	37	CCDS46414.1																																																																																			A|1.000;|0.000	1.000	weak		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
MT-CYB	4519	hgsc.bcm.edu	37	M	14996	14996	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14996G>A	ENST00000361789.2	+	1	250	c.250G>A	c.(250-252)Gcc>Acc	p.A84T	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-ND6_ENST00000361681.2_5'Flank			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	84					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						GCTACCTTCACGCCAATGGCG	0.483																																					p.A84T		Atlas-SNP	.											.	.	.	.	0			c.G250A						PASS	.																																			SO:0001583	missense	0	exon1			CTTCACGCCAATG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.250G>A	M.37:g.14996G>A	ENSP00000354554:p.Ala84Thr	7.0	0.0	0		28.0	27.0	0.964286	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Missense_Mutation	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.483	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
SNAPC3	6619	hgsc.bcm.edu	37	9	15453156	15453156	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:15453156C>T	ENST00000380821.3	+	7	1109	c.933C>T	c.(931-933)taC>taT	p.Y311Y	SNAPC3_ENST00000380799.1_Silent_p.Y108Y	NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	311					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		CTTACTTATACTGTCATCAGG	0.368																																					p.Y311Y		Atlas-SNP	.											.	SNAPC3	28	.	0			c.C933T						PASS	.						180.0	175.0	177.0					9																	15453156		2203	4300	6503	SO:0001819	synonymous_variant	6619	exon7			CTTATACTGTCAT	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.933C>T	9.37:g.15453156C>T		222.0	0.0	0		215.0	91.0	0.423256	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Silent	SNP	ENST00000380821.3	37	CCDS6478.1																																																																																			.	.	none		0.368	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
PCDHGA10	56106	hgsc.bcm.edu	37	5	140794750	140794750	+	Missense_Mutation	SNP	G	G	A	rs201831693		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140794750G>A	ENST00000398610.2	+	1	2008	c.2008G>A	c.(2008-2010)Gac>Aac	p.D670N	PCDHGB7_ENST00000398594.2_5'Flank|PCDHGB4_ENST00000519479.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron	NM_018913.2|NM_032090.1	NP_061736.1|NP_114479.1	Q9Y5H3	PCDGA_HUMAN	protocadherin gamma subfamily A, 10	670	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCCGTGGCCGACAGCATCCC	0.652													g|||	1	0.000199681	0.0	0.0014	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.D670N		Atlas-SNP	.											.	PCDHGA10	114	.	0			c.G2008A						PASS	.	G	,,ASN/ASP,,,,,,,,,,,,,,ASN/ASP	0,4400		0,0,2200	48.0	58.0	54.0		,,2008,,,,,,,,,,,,,,2008	5.6	1.0	5		54	5,8583		0,5,4289	no	intron,intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018913.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032090.1	,,23,,,,,,,,,,,,,,23	0,5,6489	AA,AG,GG		0.0582,0.0,0.0385	,,,,,,,,,,,,,,,,	,,670/937,,,,,,,,,,,,,,670/851	140794750	5,12983	2200	4294	6494	SO:0001583	missense	56106	exon1			GTGGCCGACAGCA		CCDS47292.1, CCDS75343.1	5q31	2010-01-26			ENSG00000253846	ENSG00000253846		"""Cadherins / Protocadherins : Clustered"""	8697	other	protocadherin		606297				10380929	Standard	NM_018913		Approved	PCDH-GAMMA-A10		Q9Y5H3	OTTHUMG00000163688	ENST00000398610.2:c.2008G>A	5.37:g.140794750G>A	ENSP00000381611:p.Asp670Asn	145.0	0.0	0		140.0	69.0	0.492857	NM_032090	Q9Y5E0	Missense_Mutation	SNP	ENST00000398610.2	37	CCDS47292.1	.	.	.	.	.	.	.	.	.	.	g	12.26	1.885612	0.33255	0.0	5.82E-4	ENSG00000253846	ENST00000398610	D	0.84298	-1.83	5.57	5.57	0.84162	Cadherin (3);Cadherin-like (1);	.	.	.	.	D	0.87916	0.6298	M	0.82630	2.6	0.32335	N	0.560538	P;P	0.39717	0.684;0.557	B;B	0.39119	0.291;0.152	D	0.90719	0.4633	9	0.51188	T	0.08	.	19.1633	0.93543	0.0:0.0:1.0:0.0	.	670;670	Q9Y5H3-2;Q9Y5H3	.;PCDGA_HUMAN	N	670	ENSP00000381611:D670N	ENSP00000381611:D670N	D	+	1	0	PCDHGA10	140774934	1.000000	0.71417	0.972000	0.41901	0.015000	0.08874	7.703000	0.84585	2.621000	0.88768	0.655000	0.94253	GAC	G|0.999;A|0.001	0.001	weak		0.652	PCDHGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374747.1	NM_018913	
OR11H6	122748	hgsc.bcm.edu	37	14	20692353	20692353	+	Missense_Mutation	SNP	T	T	C	rs146076639	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:20692353T>C	ENST00000315519.2	+	1	563	c.485T>C	c.(484-486)cTg>cCg	p.L162P		NM_001004480.1	NP_001004480.1	Q8NGC7	O11H6_HUMAN	olfactory receptor, family 11, subfamily H, member 6	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(13)|ovary(2)|prostate(1)|skin(2)	29	all_cancers(95;0.00108)		Epithelial(56;1.75e-06)|all cancers(55;1.22e-05)	GBM - Glioblastoma multiforme(265;0.0143)		TGTATAATTCTGGTCTGTGTA	0.463													t|||	9	0.00179712	0.0015	0.0029	5008	,	,		21313	0.0		0.004	False		,,,				2504	0.001				p.L162P		Atlas-SNP	.											.	OR11H6	60	.	0			c.T485C						PASS	.	T	PRO/LEU	4,4402	8.1+/-20.4	0,4,2199	101.0	99.0	100.0		485	5.0	1.0	14	dbSNP_134	100	34,8566	23.4+/-69.3	0,34,4266	yes	missense	OR11H6	NM_001004480.1	98	0,38,6465	CC,CT,TT		0.3953,0.0908,0.2922	probably-damaging	162/331	20692353	38,12968	2203	4300	6503	SO:0001583	missense	122748	exon1			TAATTCTGGTCTG		CCDS32033.1	14q11.2	2013-09-24			ENSG00000176219	ENSG00000176219		"""GPCR / Class A : Olfactory receptors"""	15349	protein-coding gene	gene with protein product							Standard	NM_001004480		Approved		uc010tlc.2	Q8NGC7	OTTHUMG00000170850	ENST00000315519.2:c.485T>C	14.37:g.20692353T>C	ENSP00000319071:p.Leu162Pro	150.0	0.0	0		104.0	56.0	0.538462	NM_001004480	Q6IF08	Missense_Mutation	SNP	ENST00000315519.2	37	CCDS32033.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	T	9.989	1.230400	0.22542	9.08E-4	0.003953	ENSG00000176219	ENST00000315519	T	0.45276	0.9	4.97	4.97	0.65823	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40818	N	0.001011	T	0.69142	0.3078	H	0.97240	3.965	0.23809	N	0.996783	D	0.89917	1.0	D	0.87578	0.998	T	0.72121	-0.4386	10	0.87932	D	0	.	12.6331	0.56669	0.0:0.0:0.0:1.0	.	162	Q8NGC7	O11H6_HUMAN	P	162	ENSP00000319071:L162P	ENSP00000319071:L162P	L	+	2	0	OR11H6	19762193	0.774000	0.28592	0.996000	0.52242	0.144000	0.21451	4.003000	0.57061	2.077000	0.62373	0.363000	0.22086	CTG	T|0.998;C|0.002	0.002	strong		0.463	OR11H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410676.1		
PIP5K1C	23396	hgsc.bcm.edu	37	19	3644220	3644220	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3644220G>A	ENST00000335312.3	-	12	1463	c.1375C>T	c.(1375-1377)Cgc>Tgc	p.R459C	PIP5K1C_ENST00000539785.1_Missense_Mutation_p.R459C|PIP5K1C_ENST00000537021.1_Missense_Mutation_p.R459C|PIP5K1C_ENST00000589578.1_Missense_Mutation_p.R459C	NM_001195733.1|NM_012398.2	NP_001182662.1|NP_036530.1	O60331	PI51C_HUMAN	phosphatidylinositol-4-phosphate 5-kinase, type I, gamma	459					actin cytoskeleton organization (GO:0030036)|adherens junction assembly (GO:0034333)|axon guidance (GO:0007411)|clathrin-mediated endocytosis (GO:0072583)|cytoskeletal anchoring at plasma membrane (GO:0007016)|neutrophil chemotaxis (GO:0030593)|phagocytosis (GO:0006909)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet aggregation (GO:0070527)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle exocytosis (GO:0016079)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|uropod (GO:0001931)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)			large_intestine(3)|ovary(1)|skin(3)|stomach(2)	9		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.95e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0026)|STAD - Stomach adenocarcinoma(1328;0.183)		GCTCCGCCGCGCCCCTTCTTG	0.687																																					p.R459C	Esophageal Squamous(135;99 1744 12852 27186 39851)	Atlas-SNP	.											.	PIP5K1C	63	.	0			c.C1375T						PASS	.						28.0	34.0	32.0					19																	3644220		2201	4293	6494	SO:0001583	missense	23396	exon12			CGCCGCGCCCCTT	AB011161	CCDS32872.1, CCDS56074.1, CCDS74257.1	19p13.3	2012-10-02			ENSG00000186111	ENSG00000186111			8996	protein-coding gene	gene with protein product		606102				9535851	Standard	NM_001195733		Approved	PIP5Kgamma, KIAA0589, LCCS3	uc002lyj.2	O60331	OTTHUMG00000180870	ENST00000335312.3:c.1375C>T	19.37:g.3644220G>A	ENSP00000335333:p.Arg459Cys	69.0	0.0	0		69.0	42.0	0.608696	NM_001195733	B7Z9E7|C6GIJ7|C6GIJ8|Q7LE07	Missense_Mutation	SNP	ENST00000335312.3	37	CCDS32872.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990963	0.35131	.	.	ENSG00000186111	ENST00000335312;ENST00000539785;ENST00000537021	T;T;T	0.34275	1.42;1.42;1.37	4.66	3.52	0.40303	.	0.000000	0.85682	D	0.000000	T	0.32882	0.0844	L	0.48642	1.525	0.54753	D	0.999987	B;B	0.32382	0.368;0.252	B;B	0.31614	0.133;0.063	T	0.41378	-0.9512	10	0.87932	D	0	-11.2654	14.5132	0.67802	0.0:0.0:0.843:0.157	.	459;459	O60331-3;O60331	.;PI51C_HUMAN	C	459	ENSP00000335333:R459C;ENSP00000445992:R459C;ENSP00000444779:R459C	ENSP00000335333:R459C	R	-	1	0	PIP5K1C	3595220	1.000000	0.71417	0.785000	0.31869	0.212000	0.24457	6.155000	0.71833	2.146000	0.66826	0.491000	0.48974	CGC	.	.	none		0.687	PIP5K1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453432.2	NM_012398	
KLK13	26085	hgsc.bcm.edu	37	19	51563265	51563265	+	Missense_Mutation	SNP	G	G	A	rs34089525	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:51563265G>A	ENST00000595793.1	-	3	367	c.325C>T	c.(325-327)Cac>Tac	p.H109Y	KLK13_ENST00000335422.3_Intron|KLK13_ENST00000595547.1_Intron|KLK13_ENST00000596955.1_Missense_Mutation_p.H109Y	NM_015596.1	NP_056411.1	Q9UKR3	KLK13_HUMAN	kallikrein-related peptidase 13	109	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		H -> Y (in dbSNP:rs34089525).		protein processing (GO:0016485)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|secretory granule (GO:0030141)	hydrolase activity (GO:0016787)|serine-type endopeptidase activity (GO:0004252)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)|skin(1)	16		all_neural(266;0.026)		OV - Ovarian serous cystadenocarcinoma(262;0.00224)|GBM - Glioblastoma multiforme(134;0.00432)		TATTCAGGGTGGGGGATAGAG	0.582													G|||	56	0.0111821	0.0015	0.0058	5008	,	,		11828	0.0		0.0298	False		,,,				2504	0.0204				p.H109Y		Atlas-SNP	.											.	KLK13	40	.	0			c.C325T						PASS	.	G	TYR/HIS	27,4379	34.3+/-65.2	0,27,2176	88.0	87.0	87.0		325	2.9	1.0	19	dbSNP_126	87	288,8312	106.0+/-166.9	9,270,4021	yes	missense	KLK13	NM_015596.1	83	9,297,6197	AA,AG,GG		3.3488,0.6128,2.422	probably-damaging	109/278	51563265	315,12691	2203	4300	6503	SO:0001583	missense	26085	exon3			CAGGGTGGGGGAT		CCDS12822.1	19q13.33	2008-02-05	2006-10-27			ENSG00000167759		"""Kallikreins"""	6361	protein-coding gene	gene with protein product		605505	"""kallikrein 13"""			16800724, 16800723	Standard	NM_015596		Approved	KLK-L4	uc002pvn.3	Q9UKR3		ENST00000595793.1:c.325C>T	19.37:g.51563265G>A	ENSP00000470555:p.His109Tyr	64.0	0.0	0		83.0	46.0	0.554217	NM_015596	A7UNK6|Q86VI8|Q9Y433	Missense_Mutation	SNP	ENST00000595793.1	37	CCDS12822.1	31	0.014194139194139194	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	11.51	1.659191	0.29515	0.006128	0.033488	ENSG00000167759	ENST00000156476	.	.	.	3.91	2.86	0.33363	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.132025	0.34700	N	0.003750	T	0.48607	0.1509	M	0.78049	2.395	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.984	T	0.64820	-0.6317	9	0.87932	D	0	.	7.6127	0.28139	0.1196:0.0:0.8804:0.0	rs34089525	109;109	B5BUM9;Q9UKR3	.;KLK13_HUMAN	Y	109	.	ENSP00000156476:H109Y	H	-	1	0	KLK13	56255077	1.000000	0.71417	0.987000	0.45799	0.002000	0.02628	4.613000	0.61176	1.001000	0.39076	-0.145000	0.13849	CAC	G|0.977;A|0.023	0.023	strong		0.582	KLK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464298.2	NM_015596	
LYST	1130	hgsc.bcm.edu	37	1	235907279	235907279	+	Splice_Site	SNP	A	A	G	rs201045270		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:235907279A>G	ENST00000389794.3	-	30	8325	c.8151T>C	c.(8149-8151)atT>atC	p.I2717I	LYST_ENST00000389793.2_Splice_Site_p.I2717I			Q99698	LYST_HUMAN	lysosomal trafficking regulator	2717					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ATTTACTTACAATAGATACTT	0.279																																					p.I2717I		Atlas-SNP	.											.	LYST	370	.	0			c.T8151C						PASS	.	A		0,4382		0,0,2191	31.0	36.0	34.0		8151	5.5	1.0	1		34	1,8567		0,1,4283	no	coding-synonymous-near-splice	LYST	NM_000081.2		0,1,6474	GG,GA,AA		0.0117,0.0,0.0077		2717/3802	235907279	1,12949	2191	4284	6475	SO:0001630	splice_region_variant	1130	exon30			ACTTACAATAGAT	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.8151+1T>C	1.37:g.235907279A>G		182.0	0.0	0		196.0	78.0	0.397959	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	weak		0.279	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		Silent
IFIH1	64135	hgsc.bcm.edu	37	2	163124637	163124637	+	Missense_Mutation	SNP	T	T	C	rs35667974	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:163124637T>C	ENST00000263642.2	-	14	3162	c.2767A>G	c.(2767-2769)Att>Gtt	p.I923V		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	923					cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						ATTTTCTCAATTACATGGATA	0.398													T|||	12	0.00239617	0.0008	0.0	5008	,	,		18807	0.0		0.0099	False		,,,				2504	0.001				p.I923V		Atlas-SNP	.											.	IFIH1	102	.	0			c.A2767G						PASS	.	T	VAL/ILE	11,4395	17.9+/-39.9	0,11,2192	128.0	128.0	128.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2767	5.1	0.9	2	dbSNP_126	128	140,8460	70.7+/-133.2	4,132,4164	yes	missense	IFIH1	NM_022168.2	29	4,143,6356	CC,CT,TT		1.6279,0.2497,1.161	benign	923/1026	163124637	151,12855	2203	4300	6503	SO:0001583	missense	64135	exon14			TCTCAATTACATG	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2767A>G	2.37:g.163124637T>C	ENSP00000263642:p.Ile923Val	183.0	0.0	0		226.0	103.0	0.455752	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Missense_Mutation	SNP	ENST00000263642.2	37	CCDS2217.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	17.27	3.347761	0.61183	0.002497	0.016279	ENSG00000115267	ENST00000263642;ENST00000543192	T	0.29917	1.55	5.13	5.13	0.70059	C-terminal domain of RIG-I (1);	0.048848	0.85682	D	0.000000	T	0.29684	0.0741	L	0.50919	1.6	0.50313	D	0.999862	D	0.53151	0.958	P	0.61397	0.888	T	0.09015	-1.0694	10	0.33141	T	0.24	-8.4883	14.9508	0.71071	0.0:0.0:0.0:1.0	rs35667974	923	Q9BYX4	IFIH1_HUMAN	V	923	ENSP00000263642:I923V	ENSP00000263642:I923V	I	-	1	0	IFIH1	162832883	1.000000	0.71417	0.917000	0.36280	0.768000	0.43524	7.427000	0.80284	1.932000	0.55993	0.528000	0.53228	ATT	T|0.991;C|0.009	0.009	strong		0.398	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
CRYM	1428	hgsc.bcm.edu	37	16	21272648	21272648	+	Silent	SNP	A	A	G	rs144588424	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:21272648A>G	ENST00000219599.3	-	9	1072	c.807T>C	c.(805-807)ttT>ttC	p.F269F	CRYM_ENST00000543948.1_Silent_p.F269F|CRYM_ENST00000415987.2_Silent_p.F227F|CRYM_ENST00000396023.2_Silent_p.F269F	NM_001888.3	NP_001879.1	Q14894	CRYM_HUMAN	crystallin, mu	269					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|sensory perception of sound (GO:0007605)|thyroid hormone metabolic process (GO:0042403)|thyroid hormone transport (GO:0070327)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|thiomorpholine-carboxylate dehydrogenase activity (GO:0047127)|thyroid hormone binding (GO:0070324)|transcription corepressor activity (GO:0003714)			large_intestine(1)|lung(3)	4				GBM - Glioblastoma multiforme(48;0.0573)		CCAGCTCAGCAAAGATCTCGG	0.507													A|||	9	0.00179712	0.0	0.0043	5008	,	,		17799	0.0		0.004	False		,,,				2504	0.002				p.F269F		Atlas-SNP	.											.	CRYM	13	.	0			c.T807C						PASS	.	A	,	3,4395	4.2+/-10.8	0,3,2196	114.0	94.0	101.0		681,807	-10.2	0.7	16	dbSNP_134	101	51,8549	33.3+/-86.6	1,49,4250	no	coding-synonymous,coding-synonymous	CRYM	NM_001014444.2,NM_001888.3	,	1,52,6446	GG,GA,AA		0.593,0.0682,0.4154	,	227/273,269/315	21272648	54,12944	2199	4300	6499	SO:0001819	synonymous_variant	1428	exon9			CTCAGCAAAGATC		CCDS10597.1	16p12.2	2013-02-14			ENSG00000103316	ENSG00000103316	1.5.1.25		2418	protein-coding gene	gene with protein product	"""thiomorpholine-carboxylate dehydrogenase"""	123740				1478656, 21332720	Standard	NM_001014444		Approved	DFNA40	uc002dim.3	Q14894	OTTHUMG00000090707	ENST00000219599.3:c.807T>C	16.37:g.21272648A>G		144.0	0.0	0		165.0	81.0	0.490909	NM_001888	D5MNX0|Q5HYB7	Silent	SNP	ENST00000219599.3	37	CCDS10597.1																																																																																			A|0.996;G|0.004	0.004	strong		0.507	CRYM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207398.1		
THBS4	7060	hgsc.bcm.edu	37	5	79374957	79374957	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:79374957C>T	ENST00000350881.2	+	19	2577	c.2387C>T	c.(2386-2388)gCa>gTa	p.A796V	THBS4_ENST00000504720.1_3'UTR|THBS4_ENST00000511733.1_Missense_Mutation_p.A705V|CTD-2201I18.1_ENST00000514042.1_RNA|CTD-2201I18.1_ENST00000503007.1_RNA	NM_003248.4	NP_003239.2	P35443	TSP4_HUMAN	thrombospondin 4	796	TSP C-terminal. {ECO:0000255|PROSITE- ProRule:PRU00635}.				behavioral response to pain (GO:0048266)|endothelial cell-cell adhesion (GO:0071603)|myoblast migration (GO:0051451)|negative regulation of angiogenesis (GO:0016525)|positive regulation of cell division (GO:0051781)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of tissue remodeling (GO:0034103)|response to endoplasmic reticulum stress (GO:0034976)|response to unfolded protein (GO:0006986)|tissue remodeling (GO:0048771)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|stomach(3)	34		Lung NSC(167;0.00328)|all_lung(232;0.00355)|Ovarian(174;0.0261)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-45)|Epithelial(54;1.77e-39)|all cancers(79;3.2e-34)		GATGACTATGCAGGCTTTATC	0.473																																					p.A796V		Atlas-SNP	.											.	THBS4	82	.	0			c.C2387T						PASS	.						138.0	128.0	131.0					5																	79374957		2203	4300	6503	SO:0001583	missense	7060	exon19			ACTATGCAGGCTT		CCDS4049.1	5q13	2008-05-15			ENSG00000113296	ENSG00000113296			11788	protein-coding gene	gene with protein product		600715				7852353	Standard	NM_003248		Approved		uc021yaw.1	P35443	OTTHUMG00000108173	ENST00000350881.2:c.2387C>T	5.37:g.79374957C>T	ENSP00000339730:p.Ala796Val	207.0	0.0	0		229.0	125.0	0.545852	NM_003248	B2R909|Q86TG2	Missense_Mutation	SNP	ENST00000350881.2	37	CCDS4049.1	.	.	.	.	.	.	.	.	.	.	C	29.2	4.987130	0.93106	.	.	ENSG00000113296	ENST00000350881;ENST00000511733	D;D	0.94280	-3.39;-3.39	5.06	5.06	0.68205	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Thrombospondin, C-terminal (2);	0.000000	0.85682	D	0.000000	D	0.91181	0.7222	N	0.16478	0.41	0.80722	D	1	D	0.71674	0.998	P	0.53266	0.722	D	0.89639	0.3861	10	0.25751	T	0.34	-23.1552	18.977	0.92742	0.0:1.0:0.0:0.0	.	796	P35443	TSP4_HUMAN	V	796;705	ENSP00000339730:A796V;ENSP00000422298:A705V	ENSP00000339730:A796V	A	+	2	0	THBS4	79410713	1.000000	0.71417	0.858000	0.33744	0.991000	0.79684	7.609000	0.82925	2.782000	0.95742	0.655000	0.94253	GCA	.	.	none		0.473	THBS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226977.1		
CACNA2D4	93589	hgsc.bcm.edu	37	12	1965211	1965211	+	Missense_Mutation	SNP	G	G	A	rs369720566		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:1965211G>A	ENST00000382722.5	-	22	2481	c.2119C>T	c.(2119-2121)Cgc>Tgc	p.R707C	CACNA2D4_ENST00000539048.2_5'UTR|CACNA2D4_ENST00000586184.1_Missense_Mutation_p.R707C|CACNA2D4_ENST00000585732.1_Missense_Mutation_p.R568C|CACNA2D4_ENST00000588077.1_Missense_Mutation_p.R643C|CACNA2D4_ENST00000585708.1_Missense_Mutation_p.R643C|CACNA2D4_ENST00000587995.1_Missense_Mutation_p.R682C	NM_172364.4	NP_758952.4	Q7Z3S7	CA2D4_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 4	707					calcium ion transmembrane transport (GO:0070588)|detection of light stimulus involved in visual perception (GO:0050908)	voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			endometrium(3)|kidney(2)|large_intestine(1)|liver(1)|lung(27)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	39	Ovarian(42;0.107)	Myeloproliferative disorder(1001;0.206)	OV - Ovarian serous cystadenocarcinoma(31;0.00113)	Kidney(2;0.0205)|KIRC - Kidney renal clear cell carcinoma(2;0.0451)		GTGAGGAAGCGGATCATGGCC	0.547																																					p.R707C	Colon(2;101 179 21030 23310 28141)	Atlas-SNP	.											.	CACNA2D4	220	.	0			c.C2119T						PASS	.	G	CYS/ARG	0,4086		0,0,2043	66.0	74.0	71.0		2119	3.3	0.8	12		71	1,8377		0,1,4188	no	missense	CACNA2D4	NM_172364.4	180	0,1,6231	AA,AG,GG		0.0119,0.0,0.0080	probably-damaging	707/1138	1965211	1,12463	2043	4189	6232	SO:0001583	missense	93589	exon22			GGAAGCGGATCAT	AF516695	CCDS44785.1	12p13.33	2003-03-05			ENSG00000151062	ENSG00000151062		"""Calcium channel subunits"""	20202	protein-coding gene	gene with protein product		608171				12181424	Standard	NM_172364		Approved		uc021qsx.1	Q7Z3S7	OTTHUMG00000168111	ENST00000382722.5:c.2119C>T	12.37:g.1965211G>A	ENSP00000372169:p.Arg707Cys	84.0	0.0	0		104.0	52.0	0.5	NM_172364	Q7Z3S8|Q86XZ5|Q8IZS9	Missense_Mutation	SNP	ENST00000382722.5	37	CCDS44785.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.188538	0.38609	0.0	1.19E-4	ENSG00000151062	ENST00000456077;ENST00000280663;ENST00000382722	T	0.31510	1.49	4.2	3.29	0.37713	.	0.257496	0.39909	N	0.001236	T	0.48995	0.1531	M	0.76002	2.32	0.31211	N	0.698629	D;D	0.76494	0.997;0.999	P;P	0.61397	0.888;0.8	T	0.57963	-0.7720	10	0.66056	D	0.02	.	10.5365	0.45007	0.0:0.0:0.6495:0.3505	.	707;707	Q7Z3S7-2;Q7Z3S7	.;CA2D4_HUMAN	C	643;707;707	ENSP00000372169:R707C	ENSP00000280663:R707C	R	-	1	0	CACNA2D4	1835472	0.445000	0.25657	0.765000	0.31456	0.218000	0.24690	3.494000	0.53273	0.867000	0.35654	0.462000	0.41574	CGC	.	.	weak		0.547	CACNA2D4-001	KNOWN	non_canonical_U12|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000398230.2		
MED13L	23389	hgsc.bcm.edu	37	12	116446355	116446355	+	Silent	SNP	A	A	G	rs61748071	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:116446355A>G	ENST00000281928.3	-	10	2069	c.1863T>C	c.(1861-1863)atT>atC	p.I621I		NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like	621						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		TCGAGGGCCTAATCCCACAAT	0.532													A|||	15	0.00299521	0.0	0.0043	5008	,	,		20935	0.0		0.0099	False		,,,				2504	0.002				p.I621I		Atlas-SNP	.											.	MED13L	193	.	0			c.T1863C						PASS	.	A		7,4399	12.9+/-30.5	0,7,2196	62.0	55.0	57.0		1863	-0.3	1.0	12	dbSNP_129	57	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	MED13L	NM_015335.4		0,53,6450	GG,GA,AA		0.5349,0.1589,0.4075		621/2211	116446355	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	23389	exon10			GGGCCTAATCCCA	AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.1863T>C	12.37:g.116446355A>G		226.0	0.0	0		242.0	127.0	0.524793	NM_015335	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	Silent	SNP	ENST00000281928.3	37	CCDS9177.1																																																																																			A|0.996;G|0.004	0.004	strong		0.532	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403879.3		
LILRA6	79168	hgsc.bcm.edu	37	19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	rs200657736		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54745659G>C	ENST00000396365.2	-	4	490	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Missense_Mutation_p.H151D|LILRA6_ENST00000245621.5_Missense_Mutation_p.H151D|LILRA6_ENST00000440558.2_Missense_Mutation_p.H151D|LILRA6_ENST00000270464.5_Missense_Mutation_p.H151D	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	151					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAAAATGGTGATATCCCTTC	0.592																																					p.H151D		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.C451G						scavenged	.						23.0	37.0	32.0					19																	54745659		2100	4266	6366	SO:0001583	missense	79168	exon4			AATGGTGATATCC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.451C>G	19.37:g.54745659G>C	ENSP00000379651:p.His151Asp	675.0	1.0	0.00148148		652.0	89.0	0.136503	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.647560	0.00111	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;4.04;2.82;2.82	2.64	-5.28	0.02755	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01870	0.0059	N	0.00237	-1.79	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.003;0.0;0.003;0.001;0.002;0.001	T	0.25537	-1.0129	10	0.02654	T	1	.	3.0381	0.06129	0.2388:0.2899:0.373:0.0983	.	151;151;151;151;151;151	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	D	151	ENSP00000390120:H151D;ENSP00000270464:H151D;ENSP00000411227:H151D;ENSP00000375615:H151D;ENSP00000379651:H151D;ENSP00000245621:H151D	ENSP00000245621:H151D	H	-	1	0	LILRA6	59437471	.	.	0.000000	0.03702	0.020000	0.10135	.	.	-3.099000	0.00245	-1.962000	0.00476	CAC	G|0.999;C|0.001	0.001	weak		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
TERT	7015	hgsc.bcm.edu	37	5	1253918	1253918	+	Silent	SNP	C	C	T	rs35033501	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1253918C>T	ENST00000310581.5	-	16	3381	c.3324G>A	c.(3322-3324)ccG>ccA	p.P1108P	TERT_ENST00000334602.6_Silent_p.P1045P|TERT_ENST00000296820.5_3'UTR	NM_001193376.1|NM_198253.2	NP_001180305.1|NP_937983.2	O14746	TERT_HUMAN	telomerase reverse transcriptase	1108	CTE.				DNA strand elongation (GO:0022616)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|replicative senescence (GO:0090399)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|telomerase holoenzyme complex (GO:0005697)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|telomerase activity (GO:0003720)|telomeric DNA binding (GO:0042162)|telomeric RNA binding (GO:0070034)|telomeric template RNA reverse transcriptase activity (GO:0003721)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(3)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	41	all_cancers(3;3.17e-16)|Lung NSC(6;8.55e-15)|all_lung(6;7.2e-14)|all_epithelial(6;1.87e-10)		Epithelial(17;0.00105)|all cancers(22;0.00178)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|Lung(60;0.185)		Zidovudine(DB00495)	GCGTCGTCCCCGGGAGCTTCC	0.657									TERT Mutation-Associated Haematological Disorders;Pulmonary Fibrosis, Idiopathic;Congenital Dyskeratosis				c|||	36	0.0071885	0.0	0.0101	5008	,	,		16253	0.0		0.0288	False		,,,				2504	0.0				p.P1108P		Atlas-SNP	.											.	TERT	2594	.	0			c.G3324A						PASS	.	C	,	23,4331		0,23,2154	22.0	31.0	28.0		3135,3324	-6.8	0.0	5	dbSNP_126	28	208,8314		1,206,4054	no	coding-synonymous,coding-synonymous	TERT	NM_001193376.1,NM_198253.2	,	1,229,6208	TT,TC,CC		2.4407,0.5282,1.794	,	1045/1070,1108/1133	1253918	231,12645	2177	4261	6438	SO:0001819	synonymous_variant	7015	exon16	Familial Cancer Database	;Hamman-Rich syndrome, Fibrocystic Pulmonary Dysplasia;Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita	CGTCCCCGGGAGC	AF015950	CCDS3861.2, CCDS54831.1	5p15.33	2014-09-17			ENSG00000164362	ENSG00000164362			11730	protein-coding gene	gene with protein product		187270				9252327	Standard	NM_198253		Approved	TRT, TP2, TCS1, hEST2, EST2	uc003jcb.1	O14746	OTTHUMG00000090357	ENST00000310581.5:c.3324G>A	5.37:g.1253918C>T		116.0	0.0	0		126.0	64.0	0.507937	NM_198253	O14783|Q2XS35|Q8N6C3|Q8NG38|Q8NG46	Silent	SNP	ENST00000310581.5	37	CCDS3861.2																																																																																			C|0.985;T|0.015	0.015	strong		0.657	TERT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206729.2		
ASIP	434	hgsc.bcm.edu	37	20	32856838	32856838	+	Silent	SNP	C	C	A	rs36093428	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32856838C>A	ENST00000568305.1	+	4	466	c.264C>A	c.(262-264)ccC>ccA	p.P88P	ASIP_ENST00000374954.3_Silent_p.P88P|RP4-785G19.5_ENST00000512005.1_RNA			P42127	ASIP_HUMAN	agouti signaling protein	88					adult feeding behavior (GO:0008343)|cell-cell signaling (GO:0007267)|generation of precursor metabolites and energy (GO:0006091)|genetic imprinting (GO:0071514)|hormone-mediated signaling pathway (GO:0009755)|melanin biosynthetic process (GO:0042438)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|regulation of molecular function, epigenetic (GO:0040030)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	receptor binding (GO:0005102)			central_nervous_system(1)|lung(2)	3						CCCGGACCCCCCTATCTGCGC	0.706													C|||	31	0.0061901	0.0008	0.0144	5008	,	,		11685	0.0		0.0199	False		,,,				2504	0.0				p.P88P		Atlas-SNP	.											.	ASIP	6	.	0			c.C264A						PASS	.	C		3,4325		0,3,2161	9.0	11.0	11.0		264	-1.8	0.0	20	dbSNP_126	11	48,8490		0,48,4221	no	coding-synonymous	ASIP	NM_001672.2		0,51,6382	AA,AC,CC		0.5622,0.0693,0.3964		88/133	32856838	51,12815	2164	4269	6433	SO:0001819	synonymous_variant	434	exon3			GACCCCCCTATCT		CCDS13232.1	20q11.2-q12	2010-06-24	2010-06-24		ENSG00000101440	ENSG00000101440			745	protein-coding gene	gene with protein product	"""nonagouti homolog (mouse)"""	600201	"""agouti (mouse)-signaling protein"", ""agouti signaling protein, nonagouti homolog (mouse)"""	AGTIL		7937887, 7757071	Standard	NM_001672		Approved	ASP	uc002xah.1	P42127	OTTHUMG00000032289	ENST00000568305.1:c.264C>A	20.37:g.32856838C>A		53.0	0.0	0		68.0	48.0	0.705882	NM_001672	Q3SXL2	Silent	SNP	ENST00000568305.1	37	CCDS13232.1																																																																																			C|0.994;A|0.006	0.006	strong		0.706	ASIP-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430541.1		
ADGB	79747	hgsc.bcm.edu	37	6	146977963	146977963	+	Silent	SNP	A	A	C	rs79354452	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:146977963A>C	ENST00000397944.3	+	5	535	c.459A>C	c.(457-459)ggA>ggC	p.G153G	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	153	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						TCAATGGAGGAATTTTGAGCA	0.418													A|||	37	0.00738818	0.0	0.0115	5008	,	,		16532	0.0		0.0109	False		,,,				2504	0.0184				p.G153G		Atlas-SNP	.											.	ADGB	93	.	0			c.A459C						PASS	.	A		2,1382		0,2,690	88.0	80.0	82.0		459	-4.7	0.0	6	dbSNP_132	82	73,3109		0,73,1518	no	coding-synonymous	C6orf103	NM_024694.3		0,75,2208	CC,CA,AA		2.2942,0.1445,1.6426		153/1668	146977963	75,4491	692	1591	2283	SO:0001819	synonymous_variant	79747	exon5			TGGAGGAATTTTG	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.459A>C	6.37:g.146977963A>C		182.0	0.0	0		183.0	95.0	0.519126	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.992;C|0.008	0.008	strong		0.418	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
FAM179A	165186	hgsc.bcm.edu	37	2	29259543	29259543	+	Missense_Mutation	SNP	T	T	C	rs72788155	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:29259543T>C	ENST00000379558.4	+	18	2906	c.2555T>C	c.(2554-2556)gTt>gCt	p.V852A	FAM179A_ENST00000465300.1_3'UTR|FAM179A_ENST00000403861.2_Missense_Mutation_p.V797A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	852										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						ATCATCACTGTTGCAGACAAC	0.562													T|||	18	0.00359425	0.0008	0.0014	5008	,	,		19875	0.0		0.0129	False		,,,				2504	0.0031				p.V852A		Atlas-SNP	.											.	FAM179A	106	.	0			c.T2555C						PASS	.	T	ALA/VAL	21,4385	29.0+/-57.7	0,21,2182	125.0	94.0	104.0		2555	3.7	0.4	2	dbSNP_130	104	191,8409	84.2+/-146.7	2,187,4111	yes	missense	FAM179A	NM_199280.2	64	2,208,6293	CC,CT,TT		2.2209,0.4766,1.63	benign	852/1020	29259543	212,12794	2203	4300	6503	SO:0001583	missense	165186	exon18			TCACTGTTGCAGA	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.2555T>C	2.37:g.29259543T>C	ENSP00000368876:p.Val852Ala	159.0	0.0	0		151.0	76.0	0.503311	NM_199280	Q6ZUF5	Missense_Mutation	SNP	ENST00000379558.4	37	CCDS1769.2	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	15.18	2.757343	0.49468	0.004766	0.022209	ENSG00000189350	ENST00000379558;ENST00000403861	T;T	0.69040	-0.37;-0.37	6.04	3.68	0.42216	Armadillo-like helical (1);Armadillo-type fold (1);	0.350805	0.24774	N	0.035714	T	0.37839	0.1018	L	0.38531	1.155	0.24198	N	0.995528	B;B;B	0.25390	0.096;0.125;0.082	B;B;B	0.25140	0.039;0.041;0.058	T	0.31024	-0.9958	10	0.34782	T	0.22	.	9.9505	0.41636	0.0:0.128:0.0:0.872	.	797;852;150	F8W8E4;Q6ZUX3;Q6ZUX3-3	.;F179A_HUMAN;.	A	852;797	ENSP00000368876:V852A;ENSP00000384699:V797A	ENSP00000368876:V852A	V	+	2	0	FAM179A	29113047	0.951000	0.32395	0.374000	0.26016	0.893000	0.52053	3.920000	0.56446	0.540000	0.28808	0.459000	0.35465	GTT	T|0.988;C|0.012	0.012	strong		0.562	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
LIMA1	51474	hgsc.bcm.edu	37	12	50571069	50571069	+	Silent	SNP	G	G	A	rs35414607	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:50571069G>A	ENST00000341247.4	-	11	2207	c.2058C>T	c.(2056-2058)tcC>tcT	p.S686S	LIMA1_ENST00000552783.1_Silent_p.S527S|LIMA1_ENST00000552823.1_Silent_p.S526S|LIMA1_ENST00000552909.1_Silent_p.S525S|LIMA1_ENST00000547825.1_Silent_p.S384S|LIMA1_ENST00000552491.1_Silent_p.S383S|LIMA1_ENST00000394943.3_Silent_p.S687S	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	686					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						CATCTTCATCGGAGTCTGCAC	0.408													G|||	57	0.0113818	0.0401	0.0058	5008	,	,		21645	0.0		0.0	False		,,,				2504	0.0				p.S687S		Atlas-SNP	.											.	LIMA1	67	.	0			c.C2061T						PASS	.	G	,,	121,4285	89.7+/-128.4	2,117,2084	283.0	278.0	279.0		2061,1581,2058	0.0	0.2	12	dbSNP_126	279	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	LIMA1	NM_001113546.1,NM_001113547.1,NM_016357.4	,,	2,118,6383	AA,AG,GG		0.0116,2.7463,0.938	,,	687/761,527/601,686/760	50571069	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	51474	exon11			TTCATCGGAGTCT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.2058C>T	12.37:g.50571069G>A		590.0	0.0	0		620.0	304.0	0.490323	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Silent	SNP	ENST00000341247.4	37	CCDS8802.1																																																																																			G|0.986;A|0.014	0.014	strong		0.408	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
PRMT2	3275	hgsc.bcm.edu	37	21	48068518	48068518	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:48068518C>T	ENST00000397637.1	+	5	1430	c.476C>T	c.(475-477)gCg>gTg	p.A159V	PRMT2_ENST00000291705.6_Missense_Mutation_p.A159V|PRMT2_ENST00000355680.3_Missense_Mutation_p.A159V|PRMT2_ENST00000451211.2_Missense_Mutation_p.A159V|PRMT2_ENST00000458387.2_Missense_Mutation_p.A159V|PRMT2_ENST00000397628.1_Missense_Mutation_p.A159V|PRMT2_ENST00000440086.1_Missense_Mutation_p.A159V|PRMT2_ENST00000334494.4_Missense_Mutation_p.A159V|PRMT2_ENST00000397638.2_Missense_Mutation_p.A159V|PRMT2_ENST00000491389.1_3'UTR			P55345	ANM2_HUMAN	protein arginine methyltransferase 2	159	Interaction with ESR1.|Interaction with RB1. {ECO:0000250}.|SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.A159V(1)		NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		GCACACTATGCGCGGCCTAGA	0.582																																					p.A159V		Atlas-SNP	.											PRMT2,NS,NS,0,1	PRMT2	48	1	1	Substitution - Missense(1)	NS(1)	c.C476T						PASS	.						148.0	133.0	138.0					21																	48068518		2203	4300	6503	SO:0001583	missense	3275	exon5			ACTATGCGCGGCC	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"""Protein arginine methyltransferases"""	5186	protein-coding gene	gene with protein product		601961	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1"", ""HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"""	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.476C>T	21.37:g.48068518C>T	ENSP00000380759:p.Ala159Val	131.0	0.0	0		139.0	62.0	0.446043	NM_001242864	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	31|31	5.064734|5.064734	0.93898|0.93898	.|.	.|.	ENSG00000160310|ENSG00000160310	ENST00000355680;ENST00000397638;ENST00000458387;ENST00000451211;ENST00000291705;ENST00000397637;ENST00000334494;ENST00000397628;ENST00000440086|ENST00000379844;ENST00000455177	T;T;T;T;T;T;T;T;T|.	0.73152|.	0.82;0.82;-0.54;-0.36;-0.6;0.82;-0.72;-0.71;-0.08|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.79747|0.79747	0.4499|0.4499	M|M	0.84846|0.84846	2.72|2.72	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.89917|.	1.0;1.0;0.999;1.0;1.0;1.0|.	D;D;P;D;D;D|.	0.81914|.	0.975;0.994;0.904;0.993;0.987;0.995|.	D|D	0.83443|0.83443	0.0044|0.0044	10|6	0.87932|0.87932	D|D	0|0	-9.6393|-9.6393	16.2791|16.2791	0.82664|0.82664	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	159;159;159;159;45;159|.	B7U632;B7U630;B7U631;Q498Y5;Q49AF9;P55345|.	.;.;.;.;.;ANM2_HUMAN|.	V|C	159|45;99	ENSP00000347906:A159V;ENSP00000380760:A159V;ENSP00000407463:A159V;ENSP00000411984:A159V;ENSP00000291705:A159V;ENSP00000380759:A159V;ENSP00000335490:A159V;ENSP00000380752:A159V;ENSP00000397266:A159V|.	ENSP00000291705:A159V|ENSP00000369173:R45C	A|R	+|+	2|1	0|0	PRMT2|PRMT2	46892946|46892946	0.999000|0.999000	0.42202|0.42202	0.035000|0.035000	0.18076|0.18076	0.008000|0.008000	0.06430|0.06430	5.491000|5.491000	0.66887|0.66887	2.531000|2.531000	0.85337|0.85337	0.655000|0.655000	0.94253|0.94253	GCG|CGC	.	.	none		0.582	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	
LALBA	3906	hgsc.bcm.edu	37	12	48961801	48961801	+	Splice_Site	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:48961801C>A	ENST00000301046.2	-	4	394		c.e4-1		LALBA_ENST00000549817.1_3'UTR	NM_002289.2	NP_002280.1	P00709	LALBA_HUMAN	lactalbumin, alpha-						apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|lactose biosynthetic process (GO:0005989)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|lactose synthase activity (GO:0004461)			large_intestine(1)|stomach(2)	3						ATGGGCCAACCTGATAATGGA	0.512																																					.		Atlas-SNP	.											.	LALBA	9	.	0			c.369-1G>T						PASS	.						112.0	85.0	94.0					12																	48961801		2203	4300	6503	SO:0001630	splice_region_variant	3906	exon5			GCCAACCTGATAA		CCDS8765.1	12q13	2012-10-02				ENSG00000167531			6480	protein-coding gene	gene with protein product		149750					Standard	XM_006719395		Approved	LYZL7	uc001rrt.3	P00709	OTTHUMG00000170391	ENST00000301046.2:c.369-1G>T	12.37:g.48961801C>A		88.0	0.0	0		109.0	53.0	0.486239	NM_002289	Q6FGX0|Q9UDK4	Splice_Site	SNP	ENST00000301046.2	37	CCDS8765.1	.	.	.	.	.	.	.	.	.	.	c	15.72	2.916330	0.52546	.	.	ENSG00000167531	ENST00000301046	.	.	.	4.88	4.88	0.63580	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.4099	0.60935	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LALBA	47248068	0.960000	0.32886	0.996000	0.52242	0.794000	0.44872	2.823000	0.48081	2.539000	0.85634	0.461000	0.40582	.	.	.	none		0.512	LALBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408836.1	NM_002289	Intron
OR10G4	390264	hgsc.bcm.edu	37	11	123886902	123886902	+	Silent	SNP	A	A	G	rs144455396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123886902A>G	ENST00000320891.4	+	1	621	c.621A>G	c.(619-621)tcA>tcG	p.S207S		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	207						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TAGTGGCCTCAGGCTGCTTTG	0.557													a|||	4	0.000798722	0.0	0.0014	5008	,	,		22457	0.0		0.003	False		,,,				2504	0.0				p.S207S		Atlas-SNP	.											.	OR10G4	77	.	0			c.A621G						PASS	.	G		4,4398	8.1+/-20.4	0,4,2197	293.0	244.0	261.0		621	-6.4	0.0	11	dbSNP_134	261	18,8580	13.3+/-46.6	0,18,4281	no	coding-synonymous	OR10G4	NM_001004462.1		0,22,6478	GG,GA,AA		0.2094,0.0909,0.1692		207/312	123886902	22,12978	2201	4299	6500	SO:0001819	synonymous_variant	390264	exon1			GGCCTCAGGCTGC	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.621A>G	11.37:g.123886902A>G		403.0	1.0	0.00248139		510.0	243.0	0.476471	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			A|0.998;G|0.002	0.002	strong		0.557	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
TNFRSF10D	8793	hgsc.bcm.edu	37	8	23002086	23002086	+	Silent	SNP	G	G	A	rs117862321	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:23002086G>A	ENST00000312584.3	-	7	925	c.831C>T	c.(829-831)aaC>aaT	p.N277N		NM_003840.4	NP_003831.2	Q9UBN6	TR10D_HUMAN	tumor necrosis factor receptor superfamily, member 10d, decoy with truncated death domain	277					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		TCAGGGTCTCGTTGCGGGCAT	0.572													.|||	21	0.00419329	0.0015	0.0014	5008	,	,		21181	0.0		0.0119	False		,,,				2504	0.0061				p.N277N		Atlas-SNP	.											.	TNFRSF10D	21	.	0			c.C831T						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	92.0	87.0	89.0		831	-0.3	0.0	8	dbSNP_132	89	63,8537	38.3+/-94.2	0,63,4237	no	coding-synonymous	TNFRSF10D	NM_003840.3		0,75,6428	AA,AG,GG		0.7326,0.2724,0.5767		277/387	23002086	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	8793	exon7			GGTCTCGTTGCGG	AF029761	CCDS6038.1	8p21	2006-02-22			ENSG00000173530	ENSG00000173530		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11907	protein-coding gene	gene with protein product		603614				9382840, 9537512	Standard	NM_003840		Approved	DcR2, TRUNDD, TRAILR4, CD264	uc003xcz.2	Q9UBN6	OTTHUMG00000097845	ENST00000312584.3:c.831C>T	8.37:g.23002086G>A		148.0	0.0	0		174.0	83.0	0.477012	NM_003840	B2R8W0|Q9Y6Q4	Silent	SNP	ENST00000312584.3	37	CCDS6038.1																																																																																			G|0.995;A|0.005	0.005	strong		0.572	TNFRSF10D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215135.1		
CEP192	55125	hgsc.bcm.edu	37	18	13015389	13015389	+	5'UTR	SNP	C	C	G	rs117292623	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:13015389C>G	ENST00000325971.8	+	0	662				CEP192_ENST00000506447.1_Missense_Mutation_p.H194Q			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa						centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACCTAAGCCACACTAGCTTAT	0.398													C|||	12	0.00239617	0.0008	0.0	5008	,	,		21062	0.0		0.006	False		,,,				2504	0.0051				p.H194Q		Atlas-SNP	.											CEP192_ENST00000506447,colon,carcinoma,+2,1	CEP192	340	1	0			c.C582G						PASS	.	C	GLN/HIS	1,1383		0,1,691	179.0	134.0	147.0		582	0.2	0.2	18	dbSNP_132	147	28,3154		0,28,1563	yes	missense	CEP192	NM_032142.3	24	0,29,2254	GG,GC,CC		0.8799,0.0723,0.6351	possibly-damaging	194/2538	13015389	29,4537	692	1591	2283	SO:0001623	5_prime_UTR_variant	55125	exon6			AAGCCACACTAGC	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.-932C>G	18.37:g.13015389C>G		79.0	0.0	0		110.0	59.0	0.536364	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	9.667	1.145783	0.21288	7.23E-4	0.008799	ENSG00000101639	ENST00000506447	T	0.05855	3.38	4.04	0.238	0.15480	.	.	.	.	.	T	0.02649	0.0080	N	0.24115	0.695	0.21878	N	0.999499	B	0.17268	0.021	B	0.18561	0.022	T	0.43065	-0.9414	9	0.40728	T	0.16	.	3.0221	0.06079	0.0:0.313:0.2373:0.4497	.	194	E9PF99	.	Q	194	ENSP00000427550:H194Q	ENSP00000427550:H194Q	H	+	3	2	CEP192	13005389	0.000000	0.05858	0.151000	0.22473	0.948000	0.59901	0.222000	0.17699	0.037000	0.15575	0.563000	0.77884	CAC	C|0.997;G|0.003	0.003	strong		0.398	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
WDR11	55717	hgsc.bcm.edu	37	10	122610983	122610983	+	Silent	SNP	G	G	T	rs35692153	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:122610983G>T	ENST00000263461.6	+	1	297	c.51G>T	c.(49-51)ggG>ggT	p.G17G	WDR11-AS1_ENST00000598981.1_RNA	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						CCCTCACGGGGGCCCTCAACG	0.682													G|||	290	0.0579073	0.208	0.0202	5008	,	,		14726	0.0		0.001	False		,,,				2504	0.0				p.G17G		Atlas-SNP	.											.	WDR11	95	.	0			c.G51T						PASS	.	G		707,3685		54,599,1543	18.0	20.0	19.0		51	0.9	1.0	10	dbSNP_126	19	4,8590		0,4,4293	no	coding-synonymous	WDR11	NM_018117.11		54,603,5836	TT,TG,GG		0.0465,16.0974,5.4751		17/1225	122610983	711,12275	2196	4297	6493	SO:0001819	synonymous_variant	55717	exon1			CACGGGGGCCCTC	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.51G>T	10.37:g.122610983G>T		101.0	0.0	0		114.0	44.0	0.385965	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000263461.6	37	CCDS7619.1																																																																																			G|0.952;T|0.048	0.048	strong		0.682	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
IL10RA	3587	hgsc.bcm.edu	37	11	117864062	117864062	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:117864062A>G	ENST00000227752.3	+	4	594	c.474A>G	c.(472-474)gaA>gaG	p.E158E	IL10RA_ENST00000545409.1_Silent_p.E9E|IL10RA_ENST00000541785.1_Silent_p.E138E|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	158					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		ACACATATGAAAGCATCTTCA	0.542																																					p.E158E		Atlas-SNP	.											.	IL10RA	46	.	0			c.A474G						PASS	.						97.0	86.0	90.0					11																	117864062		2200	4296	6496	SO:0001819	synonymous_variant	3587	exon4			ATATGAAAGCATC	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.474A>G	11.37:g.117864062A>G		121.0	0.0	0		102.0	52.0	0.509804	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			.	.	none		0.542	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
CDHR3	222256	hgsc.bcm.edu	37	7	105621474	105621474	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:105621474C>T	ENST00000317716.9	+	3	390	c.310C>T	c.(310-312)Cag>Tag	p.Q104*	CDHR3_ENST00000470188.1_3'UTR|CDHR3_ENST00000541203.1_Nonsense_Mutation_p.Q104*|CDHR3_ENST00000343407.5_5'UTR|CDHR3_ENST00000542731.1_Nonsense_Mutation_p.Q104*|CDHR3_ENST00000478080.1_Nonsense_Mutation_p.Q16*	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	104	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						ATTTGATTTGCAGATTTATGT	0.418																																					p.Q104X		Atlas-SNP	.											.	CDHR3	153	.	0			c.C310T						PASS	.						88.0	82.0	84.0					7																	105621474		1929	4140	6069	SO:0001587	stop_gained	222256	exon3			GATTTGCAGATTT	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.310C>T	7.37:g.105621474C>T	ENSP00000325954:p.Gln104*	160.0	0.0	0		179.0	72.0	0.402235	NM_152750	Q8TCI7	Nonsense_Mutation	SNP	ENST00000317716.9	37	CCDS47684.1	.	.	.	.	.	.	.	.	.	.	C	36	5.837584	0.97009	.	.	ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080;ENST00000541203	.	.	.	5.02	5.02	0.67125	.	0.000000	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.34782	T	0.22	-3.9079	17.6187	0.88075	0.0:1.0:0.0:0.0	.	.	.	.	X	104;104;16;104	.	ENSP00000325954:Q104X	Q	+	1	0	CDHR3	105408710	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	5.065000	0.64344	2.774000	0.95407	0.561000	0.74099	CAG	.	.	none		0.418	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
LRP2	4036	hgsc.bcm.edu	37	2	170002322	170002322	+	Missense_Mutation	SNP	G	G	A	rs543890594		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:170002322G>A	ENST00000263816.3	-	70	13208	c.12923C>T	c.(12922-12924)aCg>aTg	p.T4308M		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4308					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CACTACCAGCGTTTTCTCTTT	0.388																																					p.T4308M		Atlas-SNP	.											LRP2,right_lower_lobe,carcinoma,+1,1	LRP2	751	1	0			c.C12923T						PASS	.						108.0	100.0	103.0					2																	170002322		2203	4300	6503	SO:0001583	missense	4036	exon70			ACCAGCGTTTTCT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.12923C>T	2.37:g.170002322G>A	ENSP00000263816:p.Thr4308Met	64.0	0.0	0		69.0	40.0	0.57971	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	4.856	0.159199	0.09236	.	.	ENSG00000081479	ENST00000263816	D	0.91894	-2.93	5.38	3.0	0.34707	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.626869	0.17107	N	0.186765	D	0.85084	0.5616	L	0.37507	1.11	0.80722	D	1	B	0.18741	0.03	B	0.06405	0.002	T	0.75399	-0.3331	10	0.31617	T	0.26	.	5.8816	0.18858	0.7744:0.0:0.0793:0.1463	.	4308	P98164	LRP2_HUMAN	M	4308	ENSP00000263816:T4308M	ENSP00000263816:T4308M	T	-	2	0	LRP2	169710568	0.992000	0.36948	0.281000	0.24762	0.093000	0.18481	7.437000	0.80417	0.434000	0.26340	-1.087000	0.02190	ACG	.	.	none		0.388	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CFAP70	118491	hgsc.bcm.edu	37	10	75053071	75053071	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:75053071C>T	ENST00000310715.3	-	17	2050	c.1930G>A	c.(1930-1932)Gaa>Aaa	p.E644K	TTC18_ENST00000394865.1_Missense_Mutation_p.E644K|TTC18_ENST00000340329.3_Intron|TTC18_ENST00000493787.1_5'UTR|TTC18_ENST00000355577.3_Missense_Mutation_p.E113K|TTC18_ENST00000401621.2_Missense_Mutation_p.E644K	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		644						extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					ACTTCTGCTTCAAATGCAAAG	0.378																																					p.E644K		Atlas-SNP	.											.	TTC18	106	.	0			c.G1930A						PASS	.						121.0	106.0	111.0					10																	75053071		2203	4300	6503	SO:0001583	missense	118491	exon17			CTGCTTCAAATGC																												ENST00000310715.3:c.1930G>A	10.37:g.75053071C>T	ENSP00000310829:p.Glu644Lys	104.0	0.0	0		113.0	5.0	0.0442478	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	.	.	.	.	.	.	.	.	.	.	C	33	5.207975	0.95033	.	.	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	D;D;D;D	0.93488	-3.23;-3.23;-3.23;-3.23	5.63	5.63	0.86233	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.96191	0.8758	M	0.65498	2.005	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96140	0.9099	10	0.59425	D	0.04	-0.2715	17.1754	0.86840	0.0:1.0:0.0:0.0	.	644	Q5T0N1	TTC18_HUMAN	K	644;644;644;51;644	ENSP00000310829:E644K;ENSP00000384479:E644K;ENSP00000409527:E51K;ENSP00000378334:E644K	ENSP00000310829:E644K	E	-	1	0	TTC18	74723077	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.093000	0.71422	2.632000	0.89209	0.557000	0.71058	GAA	.	.	none		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
MICALCL	84953	hgsc.bcm.edu	37	11	12379949	12379949	+	Missense_Mutation	SNP	C	C	T	rs34898047	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:12379949C>T	ENST00000256186.2	+	9	2302	c.2011C>T	c.(2011-2013)Cgc>Tgc	p.R671C		NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like	671					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		AGAGGAACAACGCATCAGAGA	0.493													C|||	29	0.00579073	0.0008	0.0101	5008	,	,		17452	0.001		0.0189	False		,,,				2504	0.001				p.R671C		Atlas-SNP	.											.	MICALCL	59	.	0			c.C2011T						PASS	.	C	CYS/ARG	7,3929		0,7,1961	225.0	225.0	225.0		2011	4.3	0.7	11	dbSNP_126	225	132,8158		0,132,4013	yes	missense	MICALCL	NM_032867.2	180	0,139,5974	TT,TC,CC		1.5923,0.1778,1.1369	probably-damaging	671/696	12379949	139,12087	1968	4145	6113	SO:0001583	missense	84953	exon9			GAACAACGCATCA	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.2011C>T	11.37:g.12379949C>T	ENSP00000256186:p.Arg671Cys	78.0	0.0	0		76.0	31.0	0.407895	NM_032867	Q7RTP7|Q96JU6	Missense_Mutation	SNP	ENST00000256186.2	37	CCDS41620.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	10	0.013192612137203167	C	17.09	3.301535	0.60195	0.001778	0.015923	ENSG00000133808	ENST00000256186	T	0.53640	0.61	5.33	4.35	0.52113	Domain of unknown function DUF3585 (1);	0.000000	0.26248	U	0.025469	T	0.58722	0.2142	M	0.92604	3.325	0.40653	D	0.982057	D	0.89917	1.0	D	0.83275	0.996	T	0.74870	-0.3517	10	0.87932	D	0	.	10.2888	0.43584	0.3728:0.6272:0.0:0.0	rs34898047	671	Q6ZW33	MICLK_HUMAN	C	671	ENSP00000256186:R671C	ENSP00000256186:R671C	R	+	1	0	MICALCL	12336525	1.000000	0.71417	0.735000	0.30896	0.623000	0.37688	3.076000	0.50081	2.479000	0.83701	0.655000	0.94253	CGC	C|0.986;T|0.014	0.014	strong		0.493	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	
UBP1	7342	hgsc.bcm.edu	37	3	33467112	33467112	+	Missense_Mutation	SNP	G	G	A	rs61751640	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33467112G>A	ENST00000283629.3	-	2	764	c.235C>T	c.(235-237)Cat>Tat	p.H79Y	UBP1_ENST00000283628.5_Missense_Mutation_p.H79Y|UBP1_ENST00000447368.2_Missense_Mutation_p.H79Y	NM_001128161.1|NM_014517.4	NP_001121633.1|NP_055332.3	Q9NZI7	UBIP1_HUMAN	upstream binding protein 1 (LBP-1a)	79					angiogenesis (GO:0001525)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(4)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|urinary_tract(2)	23						GTTTCATCATGCAGTTTTACT	0.388													G|||	8	0.00159744	0.0	0.0014	5008	,	,		16266	0.0		0.006	False		,,,				2504	0.001				p.H79Y		Atlas-SNP	.											.	UBP1	42	.	0			c.C235T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	11,4395	19.1+/-41.9	0,11,2192	87.0	72.0	77.0		235,235,235	5.9	1.0	3	dbSNP_129	77	89,8511	50.6+/-110.7	0,89,4211	yes	missense,missense,missense	UBP1	NM_001128160.1,NM_001128161.1,NM_014517.4	83,83,83	0,100,6403	AA,AG,GG		1.0349,0.2497,0.7689	benign,benign,benign	79/505,79/541,79/541	33467112	100,12906	2203	4300	6503	SO:0001583	missense	7342	exon2			CATCATGCAGTTT	AF198487	CCDS2659.1, CCDS46788.1	3p22.3	2004-03-02			ENSG00000153560	ENSG00000153560			12507	protein-coding gene	gene with protein product		609784				8114710	Standard	NM_014517		Approved	LBP-1a	uc010hga.3	Q9NZI7	OTTHUMG00000130749	ENST00000283629.3:c.235C>T	3.37:g.33467112G>A	ENSP00000283629:p.His79Tyr	80.0	0.0	0		86.0	35.0	0.406977	NM_001128160	Q68CT0|Q86Y57|Q9H8V0|Q9UD76|Q9UD78	Missense_Mutation	SNP	ENST00000283629.3	37	CCDS2659.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	16.88	3.243954	0.58995	0.002497	0.010349	ENSG00000153560	ENST00000283629;ENST00000447368;ENST00000283628;ENST00000456378	T;T;T;T	0.18016	2.24;2.24;2.24;2.24	5.92	5.92	0.95590	CP2 transcription factor (1);	0.048704	0.85682	D	0.000000	T	0.12646	0.0307	L	0.41573	1.285	0.58432	D	0.999994	B;B	0.13145	0.006;0.007	B;B	0.23852	0.005;0.049	T	0.01587	-1.1318	10	0.56958	D	0.05	-21.3838	13.9369	0.64029	0.0778:0.0:0.9222:0.0	rs61751640	79;79	Q9NZI7-4;Q9NZI7	.;UBIP1_HUMAN	Y	79	ENSP00000283629:H79Y;ENSP00000395558:H79Y;ENSP00000283628:H79Y;ENSP00000401614:H79Y	ENSP00000283628:H79Y	H	-	1	0	UBP1	33442116	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.723000	0.74742	2.810000	0.96702	0.585000	0.79938	CAT	G|0.994;A|0.006	0.006	strong		0.388	UBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253249.2	NM_014517	
ADAM28	10863	hgsc.bcm.edu	37	8	24167750	24167750	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:24167750T>G	ENST00000265769.4	+	4	412	c.302T>G	c.(301-303)aTt>aGt	p.I101S	RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA|RP11-624C23.1_ENST00000518988.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000397649.3_De_novo_Start_OutOfFrame|ADAM28_ENST00000437154.2_Missense_Mutation_p.I101S|ADAM28_ENST00000540823.1_De_novo_Start_OutOfFrame	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	101					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		AGCCCACAAATTATGGTATAA	0.403																																					p.I101S	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.T302G						PASS	.						84.0	79.0	81.0					8																	24167750		2203	4300	6503	SO:0001583	missense	10863	exon4			CACAAATTATGGT	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.302T>G	8.37:g.24167750T>G	ENSP00000265769:p.Ile101Ser	128.0	0.0	0		123.0	62.0	0.504065	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Missense_Mutation	SNP	ENST00000265769.4	37	CCDS34865.1	.	.	.	.	.	.	.	.	.	.	T	17.10	3.302338	0.60195	.	.	ENSG00000042980	ENST00000265769;ENST00000437154	T;T	0.05786	3.39;3.39	4.97	3.84	0.44239	Peptidase M12B, propeptide (1);	.	.	.	.	T	0.12860	0.0312	L	0.55990	1.75	0.80722	D	1	D;P	0.62365	0.991;0.837	P;P	0.62089	0.898;0.457	T	0.13019	-1.0525	9	0.16420	T	0.52	.	6.8564	0.24042	0.0:0.101:0.0:0.899	.	101;101	Q9UKQ2;Q9UKQ2-2	ADA28_HUMAN;.	S	101	ENSP00000265769:I101S;ENSP00000393699:I101S	ENSP00000265769:I101S	I	+	2	0	ADAM28	24223695	1.000000	0.71417	1.000000	0.80357	0.538000	0.34931	2.018000	0.40991	2.222000	0.72286	0.477000	0.44152	ATT	.	.	none		0.403	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
TSPAN14	81619	hgsc.bcm.edu	37	10	82269158	82269158	+	Silent	SNP	C	C	T	rs145582053		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:82269158C>T	ENST00000429989.3	+	5	604	c.381C>T	c.(379-381)ttC>ttT	p.F127F	TSPAN14_ENST00000372158.1_Silent_p.F127F|TSPAN14_ENST00000372156.1_Silent_p.F127F|TSPAN14_ENST00000341863.6_Intron|TSPAN14_ENST00000372164.3_Silent_p.F110F|TSPAN14_ENST00000481124.1_Intron	NM_030927.2	NP_112189.2	Q8NG11	TSN14_HUMAN	tetraspanin 14	127					establishment of protein localization to plasma membrane (GO:0090002)|positive regulation of Notch signaling pathway (GO:0045747)|protein maturation (GO:0051604)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	enzyme binding (GO:0019899)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7			Colorectal(32;0.229)			GGGAGTTCTTCGAGAGCAACA	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		19378	0.0		0.001	False		,,,				2504	0.0				p.F127F		Atlas-SNP	.											.	TSPAN14	29	.	0			c.C381T						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	109.0	93.0	99.0		,381	-2.1	1.0	10	dbSNP_134	99	7,8593	5.7+/-21.5	0,7,4293	no	intron,coding-synonymous	TSPAN14	NM_001128309.1,NM_030927.2	,	0,10,6493	TT,TC,CC		0.0814,0.0681,0.0769	,	,127/271	82269158	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	81619	exon5			GTTCTTCGAGAGC	AF311903	CCDS7369.1, CCDS44448.1	10q23.1	2013-02-14	2005-03-21	2005-03-21	ENSG00000108219	ENSG00000108219		"""Tetraspanins"""	23303	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 14"""	TM4SF14		11230166	Standard	NM_030927		Approved	DC-TM4F2, MGC11352	uc001kcj.4	Q8NG11	OTTHUMG00000018615	ENST00000429989.3:c.381C>T	10.37:g.82269158C>T		145.0	0.0	0		133.0	70.0	0.526316	NM_030927	A6NHE1|B4DHY6|D3DWD7|D3DWD8|Q567U7|Q9BU34|Q9H0U1	Silent	SNP	ENST00000429989.3	37	CCDS7369.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	TSPAN14-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049081.2	NM_030927	
WNT9A	7483	hgsc.bcm.edu	37	1	228113073	228113073	+	Silent	SNP	C	C	G	rs8192628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:228113073C>G	ENST00000272164.5	-	2	253	c.243G>C	c.(241-243)acG>acC	p.T81T		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	81					canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal joint development (GO:0072498)|embryonic skeletal system morphogenesis (GO:0048704)|iris morphogenesis (GO:0061072)|mitotic cell cycle checkpoint (GO:0007093)|multicellular organismal development (GO:0007275)|negative regulation of cartilage development (GO:0061037)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of smoothened signaling pathway (GO:0045880)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Prostate(94;0.0405)				CCTCCACCAGCGTCTCTGCCA	0.701													C|||	10	0.00199681	0.0	0.0	5008	,	,		16240	0.0		0.008	False		,,,				2504	0.002				p.T81T		Atlas-SNP	.											.	WNT9A	39	.	0			c.G243C						PASS	.	C		8,4394		0,8,2193	17.0	18.0	17.0		243	-6.8	0.9	1	dbSNP_117	17	82,8506		0,82,4212	no	coding-synonymous	WNT9A	NM_003395.2		0,90,6405	GG,GC,CC		0.9548,0.1817,0.6928		81/366	228113073	90,12900	2201	4294	6495	SO:0001819	synonymous_variant	7483	exon2			CACCAGCGTCTCT	AB060283	CCDS31045.1	1q42	2008-02-05	2003-03-11	2003-03-14	ENSG00000143816	ENSG00000143816		"""Wingless-type MMTV integration sites"""	12778	protein-coding gene	gene with protein product		602863	"""wingless-type MMTV integration site family, member 14"""	WNT14		9441749	Standard	NM_003395		Approved		uc001hri.2	O14904	OTTHUMG00000037592	ENST00000272164.5:c.243G>C	1.37:g.228113073C>G		82.0	0.0	0		56.0	26.0	0.464286	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			G|0.005;C|0.995	0.005	strong		0.701	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
GPER1	2852	hgsc.bcm.edu	37	7	1132260	1132260	+	Missense_Mutation	SNP	G	G	A	rs150960969	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:1132260G>A	ENST00000297469.3	+	2	1587	c.896G>A	c.(895-897)cGc>cAc	p.R299H	GPER1_ENST00000397092.1_Missense_Mutation_p.R299H|GPER1_ENST00000401670.1_Missense_Mutation_p.R299H|GPER1_ENST00000397088.3_Missense_Mutation_p.R299H|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397098.3_Intron	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	299					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										CAGTCTTTCCGCCATGCCCAC	0.627																																					p.R299H		Atlas-SNP	.											.	GPER	25	.	0			c.G896A						PASS	.		HIS/ARG,HIS/ARG,,,HIS/ARG,	1,4405	2.1+/-5.4	0,1,2202	86.0	68.0	74.0		896,896,,,896,	5.7	1.0	7	dbSNP_134	74	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,intron,intron,missense,intron	GPER,C7orf50	NM_001039966.1,NM_001098201.1,NM_001134395.1,NM_001134396.1,NM_001505.2,NM_032350.5	29,29,,,29,	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	probably-damaging,probably-damaging,,,probably-damaging,	299/376,299/376,,,299/376,	1132260	9,12997	2203	4300	6503	SO:0001583	missense	2852	exon2			CTTTCCGCCATGC	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.896G>A	7.37:g.1132260G>A	ENSP00000297469:p.Arg299His	75.0	0.0	0		71.0	34.0	0.478873	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Missense_Mutation	SNP	ENST00000297469.3	37	CCDS5322.1	.	.	.	.	.	.	.	.	.	.	G	17.40	3.381327	0.61845	2.27E-4	9.3E-4	ENSG00000164850	ENST00000401670;ENST00000397092;ENST00000297469;ENST00000397088;ENST00000508834	T;T;T;T	0.37411	1.2;1.2;1.2;1.2	5.65	5.65	0.86999	GPCR, rhodopsin-like superfamily (1);	0.057131	0.64402	D	0.000001	T	0.51193	0.1660	L	0.37630	1.12	0.54753	D	0.999989	D	0.89917	1.0	D	0.71414	0.973	T	0.39663	-0.9603	10	0.39692	T	0.17	-32.5649	18.7284	0.91724	0.0:0.0:1.0:0.0	.	299	Q99527	GPER_HUMAN	H	299	ENSP00000385151:R299H;ENSP00000380281:R299H;ENSP00000297469:R299H;ENSP00000380277:R299H	ENSP00000297469:R299H	R	+	2	0	GPER	1098786	1.000000	0.71417	1.000000	0.80357	0.371000	0.29859	6.012000	0.70767	2.670000	0.90874	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.627	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
TBC1D17	79735	hgsc.bcm.edu	37	19	50381802	50381802	+	Silent	SNP	T	T	C	rs373760628		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:50381802T>C	ENST00000221543.5	+	3	467	c.168T>C	c.(166-168)gaT>gaC	p.D56D	AKT1S1_ENST00000391832.3_5'Flank|TBC1D17_ENST00000598789.1_3'UTR|AKT1S1_ENST00000391834.2_5'Flank|AKT1S1_ENST00000482622.1_5'Flank|AKT1S1_ENST00000391831.1_5'Flank|AKT1S1_ENST00000391835.1_5'Flank|AKT1S1_ENST00000344175.5_5'Flank|TBC1D17_ENST00000535102.2_Silent_p.D23D	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	56					autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		AGGCTGGAGATTCCACCCAAA	0.552													T|||	1	0.000199681	0.0	0.0	5008	,	,		18217	0.0		0.001	False		,,,				2504	0.0				p.D56D		Atlas-SNP	.											TBC1D17,NS,carcinoma,+2,1	TBC1D17	39	1	0			c.T168C						PASS	.	T	,	0,4406		0,0,2203	105.0	99.0	101.0		69,168	2.2	1.0	19		101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	,	23/616,56/649	50381802	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79735	exon3			TGGAGATTCCACC	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.168T>C	19.37:g.50381802T>C		88.0	0.0	0		101.0	48.0	0.475248	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			.	.	weak		0.552	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
ARVCF	421	hgsc.bcm.edu	37	22	19969587	19969587	+	Silent	SNP	G	G	A	rs372955497		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:19969587G>A	ENST00000263207.3	-	4	529	c.238C>T	c.(238-240)Ctg>Ttg	p.L80L	ARVCF_ENST00000406522.1_Silent_p.L17L|ARVCF_ENST00000487793.1_5'UTR|ARVCF_ENST00000401994.1_Silent_p.L17L|ARVCF_ENST00000344269.3_Silent_p.L17L|ARVCF_ENST00000406259.1_Silent_p.L80L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	80					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					ATCGTGGCCAGTGAGGCCTGG	0.642																																					p.L80L		Atlas-SNP	.											.	ARVCF	54	.	0			c.C238T						PASS	.	G		0,4404		0,0,2202	71.0	62.0	65.0		238	2.4	0.9	22		65	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ARVCF	NM_001670.2		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		80/963	19969587	3,13001	2202	4300	6502	SO:0001819	synonymous_variant	421	exon4			TGGCCAGTGAGGC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.238C>T	22.37:g.19969587G>A		88.0	0.0	0		118.0	55.0	0.466102	NM_001670	B7WNV2	Silent	SNP	ENST00000263207.3	37	CCDS13771.1																																																																																			.	.	weak		0.642	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
SGSM1	129049	hgsc.bcm.edu	37	22	25264353	25264353	+	Silent	SNP	C	C	T	rs61744681	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:25264353C>T	ENST00000400359.4	+	11	1012	c.1005C>T	c.(1003-1005)ggC>ggT	p.G335G	SGSM1_ENST00000400358.4_Silent_p.G335G	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	335	Required for interaction with RAP family members.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TTGACAGCGGCGGGACAGTGG	0.642													C|||	16	0.00319489	0.0	0.0101	5008	,	,		16926	0.002		0.007	False		,,,				2504	0.0				p.G335G		Atlas-SNP	.											.	SGSM1	150	.	0			c.C1005T						PASS	.	C	,,,	9,4055		0,9,2023	32.0	37.0	35.0		1005,1005,1005,1005	-9.8	0.5	22	dbSNP_129	35	93,8267		2,89,4089	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	2,98,6112	TT,TC,CC		1.1124,0.2215,0.821	,,,	335/1149,335/1094,335/1033,335/1088	25264353	102,12322	2032	4180	6212	SO:0001819	synonymous_variant	129049	exon11			CAGCGGCGGGACA	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.1005C>T	22.37:g.25264353C>T		114.0	0.0	0		138.0	64.0	0.463768	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			C|0.993;T|0.007	0.007	strong		0.642	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
ABHD17A	81926	hgsc.bcm.edu	37	19	1881348	1881348	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1881348C>T	ENST00000292577.7	-	2	651	c.218G>A	c.(217-219)cGt>cAt	p.R73H	ABHD17A_ENST00000250974.9_Missense_Mutation_p.R73H|ABHD17A_ENST00000590661.1_Missense_Mutation_p.R73H	NM_001130111.1	NP_001123583.1	Q96GS6	AB17A_HUMAN	abhydrolase domain containing 17A	73						extracellular region (GO:0005576)|membrane (GO:0016020)	hydrolase activity (GO:0016787)										GAAGTCGGCACGCTCCGTCAG	0.716																																					p.R73H		Atlas-SNP	.											FAM108A1,NS,carcinoma,+1,1	FAM108A1	29	1	0			c.G218A						scavenged	.						19.0	21.0	20.0					19																	1881348		2186	4259	6445	SO:0001583	missense	81926	exon2			TCGGCACGCTCCG	BC020512	CCDS32867.1, CCDS45902.1	19p13.3	2013-03-15	2013-03-15	2013-03-15	ENSG00000129968	ENSG00000129968		"""Abhydrolase domain containing"""	28756	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 27"", ""family with sequence similarity 108, member A1"""	C19orf27, FAM108A1		14702039	Standard	NM_031213		Approved	MGC5244	uc002lug.3	Q96GS6	OTTHUMG00000171872	ENST00000292577.7:c.218G>A	19.37:g.1881348C>T	ENSP00000292577:p.Arg73His	81.0	0.0	0		62.0	9.0	0.145161	NM_031213	A8K0G8|D6W5Z9|Q6PJU2|Q8WUH9|Q9BWL0|Q9H7Q9	Missense_Mutation	SNP	ENST00000292577.7	37	CCDS45902.1	.	.	.	.	.	.	.	.	.	.	c	17.49	3.402578	0.62288	.	.	ENSG00000129968	ENST00000250974;ENST00000292577	T;T	0.48201	0.82;0.95	3.76	3.76	0.43208	.	0.000000	0.85682	D	0.000000	T	0.53883	0.1824	M	0.78344	2.41	0.58432	D	0.999999	B;B;P;D	0.61080	0.014;0.325;0.857;0.989	B;B;B;P	0.45310	0.013;0.139;0.273;0.476	T	0.67031	-0.5773	10	0.87932	D	0	-24.7831	15.1068	0.72326	0.0:1.0:0.0:0.0	.	73;73;73;73	Q96GS6;Q96GS6-2;Q96GS6-3;Q96GS6-4	F18A1_HUMAN;.;.;.	H	73	ENSP00000250974:R73H;ENSP00000292577:R73H	ENSP00000250974:R73H	R	-	2	0	FAM108A1	1832348	1.000000	0.71417	0.927000	0.36925	0.901000	0.52897	7.466000	0.80914	2.108000	0.64289	0.561000	0.74099	CGT	.	.	none		0.716	ABHD17A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415556.2	NM_031213	
C16orf70	80262	hgsc.bcm.edu	37	16	67183867	67183867	+	IGR	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:67183867C>T	ENST00000219139.3	+	0	2865				B3GNT9_ENST00000449549.3_Silent_p.A174A	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70											cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		AGTGGGTTCGCGCGCCCTCCC	0.701																																					p.A174A		Atlas-SNP	.											B3GNT9,NS,carcinoma,-1,1	B3GNT9	25	1	0			c.G522A						scavenged	.						14.0	15.0	14.0					16																	67183867		1889	4052	5941	SO:0001628	intergenic_variant	84752	exon2			GGTTCGCGCGCCC	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 6"""	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510		16.37:g.67183867C>T		25.0	0.0	0		25.0	16.0	0.64	NM_033309	Q9HA86	Silent	SNP	ENST00000219139.3	37	CCDS10828.1																																																																																			.	.	none		0.701	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187	
DPP8	54878	hgsc.bcm.edu	37	15	65790319	65790319	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:65790319T>C	ENST00000341861.5	-	5	2226	c.646A>G	c.(646-648)Atg>Gtg	p.M216V	DPP8_ENST00000300141.6_Missense_Mutation_p.M200V|DPP8_ENST00000321118.7_Missense_Mutation_p.M216V|DPP8_ENST00000559233.1_Missense_Mutation_p.M216V|DPP8_ENST00000321147.6_Missense_Mutation_p.M216V|DPP8_ENST00000358939.4_Missense_Mutation_p.M200V|DPP8_ENST00000339244.5_Missense_Mutation_p.M216V	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	216					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						TTTGGATCCATCCGTATGTTG	0.383																																					p.M216V		Atlas-SNP	.											.	DPP8	78	.	0			c.A646G						PASS	.						158.0	128.0	138.0					15																	65790319		2201	4299	6500	SO:0001583	missense	54878	exon6			GATCCATCCGTAT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.646A>G	15.37:g.65790319T>C	ENSP00000339208:p.Met216Val	140.0	0.0	0		136.0	59.0	0.433824	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	T	22.1	4.240676	0.79912	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.39	5.39	0.77823	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51329	0.1668	L	0.61036	1.89	0.25881	N	0.983587	B;P;B;B	0.43578	0.178;0.811;0.178;0.213	B;P;B;B	0.60789	0.108;0.879;0.07;0.173	T	0.45338	-0.9268	10	0.44086	T	0.13	-21.8947	15.4176	0.74983	0.0:0.0:0.0:1.0	.	200;200;216;216	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	V	216;200;200;216;216;216;216	ENSP00000339208:M216V;ENSP00000351817:M200V;ENSP00000300141:M200V;ENSP00000318111:M216V;ENSP00000316373:M216V;ENSP00000341230:M216V;ENSP00000379013:M216V	ENSP00000300141:M200V	M	-	1	0	DPP8	63577372	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	7.119000	0.77145	2.027000	0.59764	0.533000	0.62120	ATG	.	.	none		0.383	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
MINK1	50488	hgsc.bcm.edu	37	17	4794407	4794407	+	Missense_Mutation	SNP	G	G	C	rs200592676	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:4794407G>C	ENST00000355280.6	+	15	1924	c.1728G>C	c.(1726-1728)gaG>gaC	p.E576D	MINK1_ENST00000453408.3_Missense_Mutation_p.E576D|MINK1_ENST00000347992.7_Missense_Mutation_p.E576D	NM_001024937.3|NM_015716.4|NM_153827.4	NP_001020108.1|NP_056531.1|NP_722549.2			misshapen-like kinase 1											central_nervous_system(2)|large_intestine(1)|lung(1)|skin(1)|stomach(1)	6						AGCCCCAGGAGGGACCGCACA	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		13597	0.0		0.002	False		,,,				2504	0.001				p.E576D		Atlas-SNP	.											.	MINK1	110	.	0			c.G1728C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	5,3705		0,5,1850	6.0	7.0	6.0		1728,1728,1728,1728	2.5	1.0	17		6	22,7980		0,22,3979	yes	missense,missense,missense,missense	MINK1	NM_001024937.3,NM_015716.4,NM_153827.4,NM_170663.4	45,45,45,45	0,27,5829	CC,CG,GG		0.2749,0.1348,0.2305	benign,benign,benign,benign	576/1313,576/1296,576/1333,576/1304	4794407	27,11685	1855	4001	5856	SO:0001583	missense	50488	exon15			CCAGGAGGGACCG	AY775058	CCDS45588.1, CCDS45589.1, CCDS45590.1	17p13.2	2011-04-14	2010-06-24		ENSG00000141503	ENSG00000141503			17565	protein-coding gene	gene with protein product	"""misshapen/NIK-related kinase"""	609426	"""misshapen-like kinase 1 (zebrafish)"""			10708748, 12087176	Standard	NM_015716		Approved	B55, MINK, ZC3, MAP4K6, YSK2	uc010vsl.2	Q8N4C8		ENST00000355280.6:c.1728G>C	17.37:g.4794407G>C	ENSP00000347427:p.Glu576Asp	106.0	0.0	0		145.0	55.0	0.37931	NM_170663		Missense_Mutation	SNP	ENST00000355280.6	37	CCDS45588.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.437336	0.25900	0.001348	0.002749	ENSG00000141503	ENST00000355280;ENST00000453408;ENST00000347992	T;T;T	0.73897	-0.79;0.99;-0.79	4.53	2.51	0.30379	.	0.072669	0.53938	D	0.000046	T	0.64918	0.2642	L	0.36672	1.1	0.38630	D	0.951355	P;P;P;P	0.51933	0.949;0.949;0.915;0.949	B;P;B;P	0.49953	0.444;0.627;0.424;0.627	T	0.61342	-0.7082	10	0.16896	T	0.51	.	5.7787	0.18294	0.2429:0.0:0.7571:0.0	.	576;576;576;576	Q8N4C8-2;Q8N4C8-4;Q8N4C8;Q8N4C8-3	.;.;MINK1_HUMAN;.	D	576	ENSP00000347427:E576D;ENSP00000406487:E576D;ENSP00000269296:E576D	ENSP00000269296:E576D	E	+	3	2	MINK1	4735189	0.997000	0.39634	1.000000	0.80357	0.993000	0.82548	0.254000	0.18314	1.229000	0.43630	0.561000	0.74099	GAG	G|0.995;C|0.005	0.005	weak		0.647	MINK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439801.1	NM_015716	
NACA	4666	hgsc.bcm.edu	37	12	57114435	57114435	+	Silent	SNP	C	C	T	rs376706368		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:57114435C>T	ENST00000454682.1	-	3	1160	c.879G>A	c.(877-879)gcG>gcA	p.A293A	NACA_ENST00000546392.1_Intron|NACA_ENST00000552540.1_Intron|NACA_ENST00000551793.1_Intron|NACA_ENST00000393891.4_Intron|NACA_ENST00000550952.1_Silent_p.A293A|NACA_ENST00000548563.1_Intron|NACA_ENST00000356769.3_Intron	NM_001113203.2	NP_001106674.2	E9PAV3	NACAM_HUMAN	nascent polypeptide-associated complex alpha subunit	293	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	10						TGTTGGGACCCGCAGTCTTTT	0.502			T	BCL6	NHL																																p.A293A		Atlas-SNP	.		Dom	yes		12	12q23-q24.1	4666	nascent-polypeptide-associated complex alpha polypeptide		L	.	NACA	131	.	0			c.G879A						PASS	.		,,,	0,3136		0,0,1568	61.0	61.0	61.0		,,879,	2.6	0.0	12		61	1,7163		0,1,3581	no	intron,intron,coding-synonymous,intron	NACA	NM_001113201.1,NM_001113202.1,NM_001113203.2,NM_005594.4	,,,	0,1,5149	TT,TC,CC		0.014,0.0,0.0097	,,,	,,293/926,	57114435	1,10299	1568	3582	5150	SO:0001819	synonymous_variant	4666	exon3			GGGACCCGCAGTC	X80909	CCDS31837.1, CCDS44925.1, CCDS44925.2	12q23-q24.1	2008-09-05	2007-04-20		ENSG00000196531	ENSG00000196531			7629	protein-coding gene	gene with protein product		601234	"""nascent-polypeptide-associated complex alpha polypeptide"""			8047162	Standard	NM_001113202		Approved	NACA1	uc001sma.2	E9PAV3		ENST00000454682.1:c.879G>A	12.37:g.57114435C>T		38.0	0.0	0		46.0	23.0	0.5	NM_001113203		Silent	SNP	ENST00000454682.1	37																																																																																				.	.	weak		0.502	NACA-201	KNOWN	basic	protein_coding	protein_coding		NM_005594	
CBFA2T2	9139	hgsc.bcm.edu	37	20	32210968	32210968	+	Silent	SNP	G	G	A	rs368919989		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32210968G>A	ENST00000346541.3	+	6	1122	c.585G>A	c.(583-585)gcG>gcA	p.A195A	CBFA2T2_ENST00000491618.1_3'UTR|CBFA2T2_ENST00000342704.6_Silent_p.A186A|CBFA2T2_ENST00000397800.1_Silent_p.A166A|CBFA2T2_ENST00000344201.3_Silent_p.A166A|CBFA2T2_ENST00000359606.3_Silent_p.A205A|CBFA2T2_ENST00000492345.1_Silent_p.A166A|CBFA2T2_ENST00000375279.2_Silent_p.A195A|CBFA2T2_ENST00000397798.2_Silent_p.A166A	NM_005093.3	NP_005084.1	O43439	MTG8R_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 2	195	TAFH. {ECO:0000255|PROSITE- ProRule:PRU00440}.				epithelial cell differentiation (GO:0030855)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|prostate(2)|skin(2)	20						GCGCTCGGGCGGCCAAGCAGA	0.582													G|||	1	0.000199681	0.0008	0.0	5008	,	,		5728	0.0		0.0	False		,,,				2504	0.0				p.A195A	Esophageal Squamous(174;142 1955 14837 21276 28041)	Atlas-SNP	.											.	CBFA2T2	93	.	0			c.G585A						PASS	.						83.0	70.0	75.0					20																	32210968		2203	4300	6503	SO:0001819	synonymous_variant	9139	exon6			TCGGGCGGCCAAG	AF052210	CCDS13221.1, CCDS46590.1	20q11	2007-01-29			ENSG00000078699	ENSG00000078699		"""Zinc fingers, MYND-type"""	1536	protein-coding gene	gene with protein product		603672				9790752	Standard	XM_006723886		Approved	MTGR1, ZMYND3	uc002wze.1	O43439	OTTHUMG00000032261	ENST00000346541.3:c.585G>A	20.37:g.32210968G>A		111.0	0.0	0		139.0	67.0	0.482014	NM_005093	B2RAE6|F8W6D7|Q5TGE4|Q5TGE5|Q5TGE6|Q5TGE7|Q8IWF3|Q96B06|Q96L00|Q9H436|Q9UJP8|Q9UJP9|Q9UP24	Silent	SNP	ENST00000346541.3	37	CCDS13221.1																																																																																			.	.	weak		0.582	CBFA2T2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078708.2	NM_001032999	
ESRRA	2101	hgsc.bcm.edu	37	11	64083273	64083273	+	Silent	SNP	C	C	T	rs41294422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64083273C>T	ENST00000405666.1	+	7	1341	c.1107C>T	c.(1105-1107)ccC>ccT	p.P369P	PRDX5_ENST00000352435.4_5'Flank|PRDX5_ENST00000347941.4_5'Flank|ESRRA_ENST00000406310.1_Silent_p.P368P|ESRRA_ENST00000000442.6_Silent_p.P369P|PRDX5_ENST00000265462.4_5'Flank	NM_001282450.1	NP_001269379.1	P11474	ERR1_HUMAN	estrogen-related receptor alpha	369	Ligand binding domain.				cartilage development (GO:0051216)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(4)|lung(8)	14						GGGCTGGCCCCGGAGGGGGTG	0.672													C|||	18	0.00359425	0.0008	0.0086	5008	,	,		17322	0.0		0.0109	False		,,,				2504	0.0				p.P369P		Atlas-SNP	.											.	ESRRA	56	.	0			c.C1107T						PASS	.	C		12,3752		0,12,1870	25.0	29.0	28.0		1107	-1.3	1.0	11	dbSNP_127	28	98,8094		1,96,3999	no	coding-synonymous	ESRRA	NM_004451.3		1,108,5869	TT,TC,CC		1.1963,0.3188,0.92		369/424	64083273	110,11846	1882	4096	5978	SO:0001819	synonymous_variant	2101	exon7			TGGCCCCGGAGGG	X51416, L38487	CCDS41667.1, CCDS60830.1	11q12	2013-01-16			ENSG00000173153	ENSG00000173153		"""Nuclear hormone receptors"""	3471	protein-coding gene	gene with protein product		601998		ESRL1		3267207	Standard	NM_004451		Approved	ERR1, ERRalpha, NR3B1, ERRa	uc001nzq.1	P11474	OTTHUMG00000150641	ENST00000405666.1:c.1107C>T	11.37:g.64083273C>T		56.0	0.0	0		67.0	23.0	0.343284	NM_004451	Q14514	Silent	SNP	ENST00000405666.1	37	CCDS41667.1	15	0.006868131868131868	0	0.0	6	0.016574585635359115	0	0.0	9	0.011873350923482849	C	6.975	0.549876	0.13374	0.003188	0.011963	ENSG00000173153	ENST00000545035	D	0.96396	-4.0	4.36	-1.26	0.09376	.	0.174873	0.28047	N	0.016807	T	0.80221	0.4583	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74523	-0.3637	7	0.05959	T	0.93	.	5.6486	0.17604	0.0:0.4931:0.1729:0.3339	rs41294422;rs61736654	.	.	.	L	150	ENSP00000444710:P150L	ENSP00000444710:P150L	P	+	2	0	ESRRA	63839849	0.165000	0.22948	0.993000	0.49108	0.953000	0.61014	-1.152000	0.03172	-0.298000	0.08921	-0.291000	0.09656	CCG	C|0.991;T|0.009	0.009	strong		0.672	ESRRA-003	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319304.1	NM_004451	
RYR3	6263	hgsc.bcm.edu	37	15	33842400	33842400	+	Silent	SNP	A	A	T	rs41279202	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:33842400A>T	ENST00000389232.4	+	10	925	c.855A>T	c.(853-855)cgA>cgT	p.R285R	RYR3_ENST00000415757.3_Silent_p.R285R	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	285	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AGGCTTTCCGACTCCGGCATC	0.483													A|||	68	0.0135783	0.0	0.0187	5008	,	,		17879	0.001		0.0447	False		,,,				2504	0.0092				p.R285R		Atlas-SNP	.											.	RYR3	760	.	0			c.A855T						PASS	.	A		34,4350	34.3+/-65.2	0,34,2158	40.0	42.0	41.0		855	-1.1	1.0	15	dbSNP_127	41	369,8219	120.2+/-179.5	8,353,3933	no	coding-synonymous	RYR3	NM_001036.3		8,387,6091	TT,TA,AA		4.2967,0.7755,3.1067		285/4871	33842400	403,12569	2192	4294	6486	SO:0001819	synonymous_variant	6263	exon10			TTTCCGACTCCGG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.855A>T	15.37:g.33842400A>T		94.0	0.0	0		95.0	48.0	0.505263	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.970;T|0.030	0.030	strong		0.483	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
MUC21	394263	hgsc.bcm.edu	37	6	30954309	30954309	+	Silent	SNP	A	A	T	rs150035336		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954309A>T	ENST00000376296.3	+	2	598	c.357A>T	c.(355-357)acA>acT	p.T119T	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	119	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						GGGCCAGCACAGCCACCAACT	0.597																																					p.T119T		Atlas-SNP	.											.	MUC21	98	.	0			c.A357T						PASS	.						180.0	166.0	171.0					6																	30954309		2203	4298	6501	SO:0001819	synonymous_variant	394263	exon2			CAGCACAGCCACC	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.357A>T	6.37:g.30954309A>T		107.0	0.0	0		166.0	15.0	0.0903614	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			.	.	weak		0.597	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
LYRM2	57226	hgsc.bcm.edu	37	6	90347516	90347516	+	Missense_Mutation	SNP	T	T	A	rs151021837	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90347516T>A	ENST00000523377.1	-	2	167	c.131A>T	c.(130-132)tAc>tTc	p.Y44F	LYRM2_ENST00000517396.1_5'UTR|LYRM2_ENST00000520441.1_Missense_Mutation_p.Y44F|LYRM2_ENST00000520318.1_Missense_Mutation_p.Y44F	NM_020466.4	NP_065199.1	Q9NU23	LYRM2_HUMAN	LYR motif containing 2	44						mitochondrion (GO:0005739)				kidney(1)|large_intestine(1)|lung(1)	3		all_cancers(76;2.76e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;3.72e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0131)		ATCTTTCAGGTATTTGCGATC	0.403													T|||	15	0.00299521	0.0008	0.0014	5008	,	,		16864	0.0		0.0129	False		,,,				2504	0.0				p.Y44F		Atlas-SNP	.											.	LYRM2	6	.	0			c.A131T						PASS	.	T	PHE/TYR	8,4398	14.3+/-33.2	0,8,2195	176.0	171.0	173.0		131	4.9	1.0	6	dbSNP_134	173	91,8509	51.5+/-111.7	1,89,4210	no	missense	LYRM2	NM_020466.4	22	1,97,6405	AA,AT,TT		1.0581,0.1816,0.7612	probably-damaging	44/89	90347516	99,12907	2203	4300	6503	SO:0001583	missense	57226	exon2			TTCAGGTATTTGC	BC009782	CCDS5023.1	6q15	2006-09-19			ENSG00000083099	ENSG00000083099		"""LYR motif containing"""	25229	protein-coding gene	gene with protein product						12477932	Standard	NM_020466		Approved	DJ122O8.2	uc003pnm.3	Q9NU23	OTTHUMG00000015203	ENST00000523377.1:c.131A>T	6.37:g.90347516T>A	ENSP00000430025:p.Tyr44Phe	257.0	0.0	0		318.0	161.0	0.506289	NM_020466	B2R4U2|E1P517	Missense_Mutation	SNP	ENST00000523377.1	37	CCDS5023.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	T	22.3	4.274655	0.80580	0.001816	0.010581	ENSG00000083099	ENST00000520441;ENST00000523377;ENST00000520318	T;T;T	0.72282	-0.64;-0.64;-0.64	6.03	4.86	0.63082	.	0.188192	0.47455	D	0.000240	T	0.49795	0.1578	.	.	.	0.41428	D	0.987849	B	0.14438	0.01	B	0.20767	0.031	T	0.54002	-0.8358	9	0.59425	D	0.04	.	11.4509	0.50151	0.1342:0.0:0.0:0.8658	.	44	Q9NU23	LYRM2_HUMAN	F	44	ENSP00000427859:Y44F;ENSP00000430025:Y44F;ENSP00000428207:Y44F	ENSP00000430316:Y44F	Y	-	2	0	LYRM2	90404237	1.000000	0.71417	0.999000	0.59377	0.787000	0.44495	4.337000	0.59310	1.083000	0.41159	0.455000	0.32223	TAC	T|0.994;A|0.006	0.006	strong		0.403	LYRM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041498.2	NM_020466	
LILRB3	11025	hgsc.bcm.edu	37	19	54725907	54725907	+	Missense_Mutation	SNP	G	G	C	rs55662384	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:54725907G>C	ENST00000391750.1	-	5	587	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRB3_ENST00000245620.9_Missense_Mutation_p.H151D|CTB-83J4.1_ENST00000601161.1_lincRNA|LILRB3_ENST00000407860.2_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Intron|LILRB3_ENST00000424807.1_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Intron|LILRB3_ENST00000469273.1_5'Flank|LILRA6_ENST00000440558.2_Intron|LILRB3_ENST00000346401.6_Missense_Mutation_p.H151D|LILRA6_ENST00000270464.5_Intron			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	151	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)	integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|kidney(13)|large_intestine(1)|lung(6)|ovary(2)|prostate(5)|skin(2)|stomach(1)|urinary_tract(1)	34	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAAAATGGTGATATCCCTTC	0.607													.|||	412	0.0822684	0.2844	0.0346	5008	,	,		11604	0.0		0.005	False		,,,				2504	0.0072				p.H151D		Atlas-SNP	.											.	LILRB3	67	.	0			c.C451G						PASS	.						21.0	14.0	17.0					19																	54725907		2080	3877	5957	SO:0001583	missense	11025	exon4			AATGGTGATATCC	U91928	CCDS33105.1, CCDS46175.1	19q13.4	2013-01-11			ENSG00000204577	ENSG00000204577		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6607	protein-coding gene	gene with protein product		604820				9278324, 9382880	Standard	NM_006864		Approved	LIR-3, HL9, ILT5, LIR3, CD85a	uc002qee.1	O75022	OTTHUMG00000066626	ENST00000391750.1:c.451C>G	19.37:g.54725907G>C	ENSP00000375630:p.His151Asp	130.0	0.0	0		224.0	81.0	0.361607	NM_006864	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	.	.	.	.	.	.	.	.	.	.	g	0.003	-2.570640	0.00133	.	.	ENSG00000204577	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000445347	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;2.82;2.82;5.85	2.87	-4.31	0.03698	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01905	0.0060	N	0.00128	-2.045	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.09377	0.004;0.0;0.003;0.0;0.001	T	0.48570	-0.9024	10	0.02654	T	1	.	8.7737	0.34749	0.1378:0.4079:0.4543:0.0	rs55662384	151;151;151;151;151	B5MCX0;F8WD89;O75022-2;O75022;O75022-3	.;.;.;LIRB3_HUMAN;.	D	151	ENSP00000375630:H151D;ENSP00000412771:H151D;ENSP00000345184:H151D;ENSP00000245620:H151D;ENSP00000384274:H151D;ENSP00000388199:H151D	ENSP00000245620:H151D	H	-	1	0	LILRB3	59417719	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.740000	0.00378	-0.678000	0.05224	-2.793000	0.00115	CAC	G|0.994;C|0.006	0.006	strong		0.607	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
CNTN3	5067	hgsc.bcm.edu	37	3	74334458	74334458	+	Missense_Mutation	SNP	G	G	A	rs141921900	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:74334458G>A	ENST00000263665.6	-	19	2729	c.2702C>T	c.(2701-2703)aCg>aTg	p.T901M		NM_020872.1	NP_065923.1	Q9P232	CNTN3_HUMAN	contactin 3 (plasmacytoma associated)	901	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|nervous system development (GO:0007399)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(39)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	83		Lung NSC(201;0.138)|Lung SC(41;0.21)		Epithelial(33;0.00212)|BRCA - Breast invasive adenocarcinoma(55;0.00258)|LUSC - Lung squamous cell carcinoma(21;0.00461)|Lung(16;0.01)		ATACTTACGCGTTTTCTTGGT	0.438													G|||	18	0.00359425	0.0	0.0043	5008	,	,		17726	0.0		0.0139	False		,,,				2504	0.001				p.T901M		Atlas-SNP	.											CNTN3,NS,lymphoid_neoplasm,+1,1	CNTN3	174	1	0			c.C2702T						PASS	.	G	MET/THR	7,4399	12.9+/-30.5	0,7,2196	116.0	124.0	121.0		2702	2.2	0.5	3	dbSNP_134	121	97,8503	54.4+/-115.2	1,95,4204	yes	missense	CNTN3	NM_020872.1	81	1,102,6400	AA,AG,GG		1.1279,0.1589,0.7996	benign	901/1029	74334458	104,12902	2203	4300	6503	SO:0001583	missense	5067	exon19			TTACGCGTTTTCT	AB040929	CCDS33790.1	3p12.3	2013-02-11			ENSG00000113805	ENSG00000113805		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2173	protein-coding gene	gene with protein product		601325		PANG		8661054, 8586965	Standard	XM_005264757		Approved	BIG-1	uc003dpm.1	Q9P232	OTTHUMG00000158813	ENST00000263665.6:c.2702C>T	3.37:g.74334458G>A	ENSP00000263665:p.Thr901Met	96.0	0.0	0		113.0	61.0	0.539823	NM_020872	B9EK50|Q9H039	Missense_Mutation	SNP	ENST00000263665.6	37	CCDS33790.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	11.68	1.709735	0.30322	0.001589	0.011279	ENSG00000113805	ENST00000263665	T	0.54675	0.56	5.4	2.15	0.27550	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.290390	0.38720	N	0.001587	T	0.27098	0.0664	N	0.16656	0.425	0.34827	D	0.73933	B	0.11235	0.004	B	0.16289	0.015	T	0.38866	-0.9641	10	0.62326	D	0.03	.	10.8289	0.46649	0.2572:0.0:0.7428:0.0	.	901	Q9P232	CNTN3_HUMAN	M	901	ENSP00000263665:T901M	ENSP00000263665:T901M	T	-	2	0	CNTN3	74417148	1.000000	0.71417	0.483000	0.27378	0.537000	0.34900	4.561000	0.60809	0.762000	0.33152	-0.126000	0.14955	ACG	G|0.995;A|0.005	0.005	strong		0.438	CNTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352306.1	NM_020872	
EHBP1L1	254102	hgsc.bcm.edu	37	11	65349037	65349037	+	Silent	SNP	G	G	A	rs74684453	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65349037G>A	ENST00000309295.4	+	9	1159	c.894G>A	c.(892-894)acG>acA	p.T298T		NM_001099409.1	NP_001092879.1	Q8N3D4	EH1L1_HUMAN	EH domain binding protein 1-like 1	298						membrane (GO:0016020)				central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23						CCCAGGACACGGCCCCCACCC	0.677													G|||	34	0.00678914	0.0008	0.0086	5008	,	,		13897	0.0		0.0239	False		,,,				2504	0.0031				p.T298T		Atlas-SNP	.											.	EHBP1L1	64	.	0			c.G894A						PASS	.	G		13,3719		0,13,1853	8.0	9.0	9.0		894	3.0	0.8	11	dbSNP_134	9	194,7914		2,190,3862	no	coding-synonymous	EHBP1L1	NM_001099409.1		2,203,5715	AA,AG,GG		2.3927,0.3483,1.7483		298/1524	65349037	207,11633	1866	4054	5920	SO:0001819	synonymous_variant	254102	exon9			GGACACGGCCCCC	AL834433	CCDS44649.1	11q13.1	2008-02-05			ENSG00000173442	ENSG00000173442			30682	protein-coding gene	gene with protein product							Standard	NM_001099409		Approved	DKFZp762C186, TANGERIN	uc001oeo.4	Q8N3D4	OTTHUMG00000166520	ENST00000309295.4:c.894G>A	11.37:g.65349037G>A		186.0	0.0	0		185.0	89.0	0.481081	NM_001099409	Q8TB89|Q9H7M7	Silent	SNP	ENST00000309295.4	37	CCDS44649.1																																																																																			G|0.989;A|0.011	0.011	strong		0.677	EHBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390145.1	XM_170658	
PKP4	8502	hgsc.bcm.edu	37	2	159517926	159517926	+	Silent	SNP	C	C	T	rs112890651	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:159517926C>T	ENST00000389759.3	+	13	2287	c.2175C>T	c.(2173-2175)atC>atT	p.I725I	PKP4_ENST00000389757.3_Silent_p.I725I|AC005042.4_ENST00000342892.4_RNA	NM_003628.3	NP_003619.2	Q99569	PKP4_HUMAN	plakophilin 4	725					cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|positive regulation of cytokinesis (GO:0032467)|positive regulation of gene expression (GO:0010628)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell adhesion (GO:0030155)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|desmosome (GO:0030057)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)				breast(2)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(21)|ovary(6)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	61						TGTATGTGATCCACACGTGTG	0.587										HNSCC(62;0.18)			C|||	18	0.00359425	0.0	0.0058	5008	,	,		20670	0.0		0.0129	False		,,,				2504	0.001				p.I725I		Atlas-SNP	.											.	PKP4	133	.	0			c.C2175T						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	127.0	113.0	118.0		2175,2175	5.7	1.0	2	dbSNP_132	118	103,8497	56.4+/-117.6	2,99,4199	no	coding-synonymous,coding-synonymous	PKP4	NM_001005476.1,NM_003628.3	,	2,104,6397	TT,TC,CC		1.1977,0.1135,0.8304	,	725/1150,725/1193	159517926	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	8502	exon13			TGTGATCCACACG	X81889	CCDS33305.1, CCDS33306.1	2q24.1	2013-02-14			ENSG00000144283	ENSG00000144283		"""Armadillo repeat containing"""	9026	protein-coding gene	gene with protein product		604276				9342840, 8937994	Standard	NM_003628		Approved	p0071	uc002tzv.3	Q99569	OTTHUMG00000153969	ENST00000389759.3:c.2175C>T	2.37:g.159517926C>T		37.0	0.0	0		55.0	28.0	0.509091	NM_001005476	Q86W91	Silent	SNP	ENST00000389759.3	37	CCDS33305.1																																																																																			C|0.990;T|0.010	0.010	strong		0.587	PKP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333250.1		
ZFHX3	463	hgsc.bcm.edu	37	16	72992630	72992630	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992630G>T	ENST00000268489.5	-	2	2087	c.1415C>A	c.(1414-1416)gCg>gAg	p.A472E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	472	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				ctcctcctccgcctcttcctc	0.577																																					p.A472E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.C1415A						PASS	.						38.0	42.0	41.0					16																	72992630		2198	4300	6498	SO:0001583	missense	463	exon2			TCCTCCGCCTCTT	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1415C>A	16.37:g.72992630G>T	ENSP00000268489:p.Ala472Glu	36.0	0.0	0		53.0	8.0	0.150943	NM_006885	D3DWS8|O15101|Q13719	Missense_Mutation	SNP	ENST00000268489.5	37	CCDS10908.1	.	.	.	.	.	.	.	.	.	.	G	0.252	-1.005988	0.02112	.	.	ENSG00000140836	ENST00000268489	T	0.73258	-0.73	4.63	-9.25	0.00666	.	1.213240	0.06591	N	0.751946	T	0.34048	0.0884	N	0.08118	0	0.54753	D	0.999985	B	0.23490	0.086	B	0.14023	0.01	T	0.29912	-0.9996	10	0.02654	T	1	.	3.1253	0.06405	0.2364:0.0793:0.1273:0.5569	.	472	Q15911	ZFHX3_HUMAN	E	472	ENSP00000268489:A472E	ENSP00000268489:A472E	A	-	2	0	ZFHX3	71550131	0.000000	0.05858	0.020000	0.16555	0.258000	0.26162	-0.323000	0.07997	-1.925000	0.01063	-0.759000	0.03464	GCG	.	.	none		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
PTPN3	5774	hgsc.bcm.edu	37	9	112145799	112145799	+	Silent	SNP	G	G	A	rs2304742	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:112145799G>A	ENST00000374541.2	-	23	2390	c.2286C>T	c.(2284-2286)ccC>ccT	p.P762P	PTPN3_ENST00000412145.1_Silent_p.P631P|PTPN3_ENST00000262539.3_Silent_p.P608P|PTPN3_ENST00000446349.1_Silent_p.P586P|PTPN3_ENST00000394827.3_Silent_p.P230P	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	762	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						TCATGACGTCGGGGGGATCTG	0.557													G|||	258	0.0515176	0.0008	0.1052	5008	,	,		17925	0.1399		0.0268	False		,,,				2504	0.0164				p.P762P		Atlas-SNP	.											.	PTPN3	106	.	0			c.C2286T						PASS	.	G	,,,,,	30,4376	36.0+/-67.5	0,30,2173	127.0	119.0	122.0		2151,1893,1758,1425,1290,2286	-7.5	0.0	9	dbSNP_100	122	277,8323	104.8+/-165.8	6,265,4029	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN3	NM_001145368.1,NM_001145369.1,NM_001145370.1,NM_001145371.1,NM_001145372.1,NM_002829.3	,,,,,	6,295,6202	AA,AG,GG		3.2209,0.6809,2.3604	,,,,,	717/869,631/783,586/738,475/627,430/582,762/914	112145799	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	5774	exon23			GACGTCGGGGGGA		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.2286C>T	9.37:g.112145799G>A		105.0	0.0	0		153.0	85.0	0.555556	NM_002829	A0AUW9|E7EN99|E9PGU7	Silent	SNP	ENST00000374541.2	37	CCDS6776.1																																																																																			G|0.959;A|0.041	0.041	strong		0.557	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
PPP2R1B	5519	hgsc.bcm.edu	37	11	111608216	111608216	+	IGR	SNP	T	T	A	rs61756429	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:111608216T>A	ENST00000527614.1	-	0	5587				PPP2R1B_ENST00000311129.5_Missense_Mutation_p.N623Y|PPP2R1B_ENST00000426998.2_Missense_Mutation_p.N559Y|PPP2R1B_ENST00000530787.1_5'Flank	NM_001177562.1|NM_002716.4	NP_001171033.1|NP_002707.3	P30154	2AAB_HUMAN	protein phosphatase 2, regulatory subunit A, beta						apoptotic process involved in morphogenesis (GO:0060561)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)	extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|liver(1)|lung(10)|prostate(1)|urinary_tract(2)	22		all_cancers(61;2.34e-15)|all_epithelial(67;1.72e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|Epithelial(105;2.36e-06)|all cancers(92;3.78e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0761)		GGGAAGTGGTTCTTGTCAGCC	0.597													T|||	10	0.00199681	0.0	0.0043	5008	,	,		20031	0.0		0.007	False		,,,				2504	0.0				p.N623Y		Atlas-SNP	.											.	PPP2R1B	44	.	0			c.A1867T						PASS	.	T	TYR/ASN,TYR/ASN	13,4389	21.2+/-45.6	0,13,2188	155.0	128.0	137.0		1867,1675	4.1	1.0	11	dbSNP_129	137	86,8508	48.9+/-108.6	0,86,4211	yes	missense,missense	PPP2R1B	NM_181699.2,NM_181700.1	143,143	0,99,6399	AA,AT,TT		1.0007,0.2953,0.7618	possibly-damaging,possibly-damaging	623/668,559/604	111608216	99,12897	2201	4297	6498	SO:0001628	intergenic_variant	5519	exon15			AGTGGTTCTTGTC	AF087438	CCDS8348.1, CCDS8349.1, CCDS53706.1, CCDS53707.1, CCDS53708.1	11q23.1	2010-06-18	2010-04-14		ENSG00000137713	ENSG00000137713	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9303	protein-coding gene	gene with protein product	"""PP2A-A-beta"", ""protein phosphatase 2A, regulatory subunit A, beta isoform"""	603113	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoform"""			2159327, 9795170	Standard	NM_181699		Approved	PR65B, PP2A-Abeta	uc001plw.1	P30154	OTTHUMG00000166741		11.37:g.111608216T>A		101.0	0.0	0		126.0	55.0	0.436508	NM_181699	A8MY67|B0YJ69|B4DGQ6|B4DK91|B4DWW5|F8W8G1|O75620|Q8NHV8	Missense_Mutation	SNP	ENST00000527614.1	37	CCDS8349.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	10.82	1.458179	0.26161	0.002953	0.010007	ENSG00000137713	ENST00000311129;ENST00000426998	.	.	.	5.25	4.13	0.48395	.	0.617749	0.15812	N	0.243438	T	0.27933	0.0688	N	0.08118	0	0.80722	D	1	P;D	0.54207	0.94;0.965	P;P	0.51135	0.459;0.66	T	0.18493	-1.0335	9	0.87932	D	0	-10.7806	7.9175	0.29827	0.0:0.0914:0.0:0.9086	rs61756429	559;623	B4DWW5;P30154-2	.;.	Y	623;559	.	ENSP00000311344:N623Y	N	-	1	0	PPP2R1B	111113426	1.000000	0.71417	0.991000	0.47740	0.214000	0.24535	1.866000	0.39489	1.132000	0.42129	0.496000	0.49642	AAC	T|0.992;A|0.008	0.008	strong		0.597	PPP2R1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391298.1	NM_002716	
SYNE1	23345	hgsc.bcm.edu	37	6	152457795	152457795	+	Silent	SNP	C	C	T	rs118187988	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:152457795C>T	ENST00000367255.5	-	141	26218	c.25617G>A	c.(25615-25617)gaG>gaA	p.E8539E	SYNE1_ENST00000356820.4_Silent_p.E3063E|SYNE1_ENST00000539504.1_Silent_p.E694E|SYNE1_ENST00000341594.5_Silent_p.E8151E|SYNE1_ENST00000423061.1_Silent_p.E8491E|SYNE1_ENST00000448038.1_Silent_p.E8491E|SYNE1_ENST00000354674.4_Silent_p.E717E|SYNE1_ENST00000347037.5_5'UTR|SYNE1_ENST00000265368.4_Silent_p.E8539E	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	8539					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCCGCCACTCCTCCAGCAGAG	0.602										HNSCC(10;0.0054)			C|||	7	0.00139776	0.0	0.0014	5008	,	,		18729	0.001		0.005	False		,,,				2504	0.0				p.E8539E		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G25617A						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	53.0	49.0	50.0		25473,25617	1.8	1.0	6	dbSNP_133	50	16,8584	12.6+/-44.7	0,16,4284	no	coding-synonymous,coding-synonymous	SYNE1	NM_033071.3,NM_182961.3	,	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	,	8491/8750,8539/8798	152457795	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	23345	exon141			CCACTCCTCCAGC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.25617G>A	6.37:g.152457795C>T		65.0	0.0	0		100.0	51.0	0.51	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Silent	SNP	ENST00000367255.5	37	CCDS5236.2																																																																																			C|0.998;T|0.002	0.002	strong		0.602	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
CLEC9A	283420	hgsc.bcm.edu	37	12	10217412	10217412	+	Missense_Mutation	SNP	C	C	T	rs147713876	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:10217412C>T	ENST00000355819.1	+	8	1166	c.553C>T	c.(553-555)Cgc>Tgc	p.R185C		NM_207345.2	NP_997228.1	Q6UXN8	CLC9A_HUMAN	C-type lectin domain family 9, member A	185	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				positive regulation of cytokine secretion (GO:0050715)|receptor-mediated endocytosis (GO:0006898)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|urinary_tract(1)	22						ACACAGCGGACGCTGGCTTTG	0.438																																					p.R185C		Atlas-SNP	.											.	CLEC9A	41	.	0			c.C553T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	125.0	116.0	119.0		553	-3.0	0.0	12	dbSNP_134	119	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLEC9A	NM_207345.2	180	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	probably-damaging	185/242	10217412	3,13003	2203	4300	6503	SO:0001583	missense	283420	exon8			AGCGGACGCTGGC		CCDS8611.1	12p13.31	2010-04-27				ENSG00000197992		"""C-type lectin domain containing"""	26705	protein-coding gene	gene with protein product		612252					Standard	NM_207345		Approved	UNQ9341, HEEE9341	uc001qxa.3	Q6UXN8		ENST00000355819.1:c.553C>T	12.37:g.10217412C>T	ENSP00000348074:p.Arg185Cys	119.0	0.0	0		139.0	71.0	0.510791	NM_207345	B0ZBM2	Missense_Mutation	SNP	ENST00000355819.1	37	CCDS8611.1	.	.	.	.	.	.	.	.	.	.	C	16.08	3.021102	0.54576	2.27E-4	2.33E-4	ENSG00000197992	ENST00000355819	T	0.19394	2.15	5.24	-3.0	0.05480	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.955151	0.08603	N	0.921157	T	0.22551	0.0544	M	0.64997	1.995	0.09310	N	1	D	0.53312	0.959	P	0.48901	0.594	T	0.18903	-1.0322	10	0.59425	D	0.04	.	1.5356	0.02544	0.1565:0.2573:0.1343:0.4519	.	185	Q6UXN8	CLC9A_HUMAN	C	185	ENSP00000348074:R185C	ENSP00000348074:R185C	R	+	1	0	CLEC9A	10108679	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-1.238000	0.02919	-0.348000	0.08286	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.438	CLEC9A-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000399564.1	NM_207345	
ITGA9	3680	hgsc.bcm.edu	37	3	37550109	37550109	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:37550109A>G	ENST00000264741.5	+	8	1144	c.888A>G	c.(886-888)tcA>tcG	p.S296S	ITGA9_ENST00000422441.1_Silent_p.S296S	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	296					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		TTCAAGCATCAGGTAAAAAGG	0.338																																					p.S296S		Atlas-SNP	.											.	ITGA9	98	.	0			c.A888G						PASS	.						100.0	105.0	103.0					3																	37550109		2203	4300	6503	SO:0001819	synonymous_variant	3680	exon8			AGCATCAGGTAAA	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.888A>G	3.37:g.37550109A>G		144.0	0.0	0		160.0	80.0	0.5	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			.	.	none		0.338	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
IGSF22	283284	hgsc.bcm.edu	37	11	18735570	18735570	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:18735570A>G	ENST00000513874.1	-	14	2063	c.1924T>C	c.(1924-1926)Tac>Cac	p.Y642H	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	642	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CCATCCTTGTACCATGTCACT	0.597																																					p.Y642H		Atlas-SNP	.											.	IGSF22	211	.	0			c.T1924C						PASS	.						118.0	122.0	121.0					11																	18735570		2176	4259	6435	SO:0001583	missense	283284	exon14			CCTTGTACCATGT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.1924T>C	11.37:g.18735570A>G	ENSP00000421191:p.Tyr642His	227.0	0.0	0		250.0	16.0	0.064	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	.	.	.	.	.	.	.	.	.	.	A	13.08	2.131488	0.37630	.	.	ENSG00000179057	ENST00000513874	T	0.47528	0.84	4.11	2.99	0.34606	.	0.000000	0.31519	U	0.007518	T	0.54334	0.1852	L	0.58354	1.805	0.22541	N	0.999007	D	0.65815	0.995	D	0.63283	0.913	T	0.42916	-0.9423	10	0.18710	T	0.47	.	7.6466	0.28323	0.9009:0.0:0.0991:0.0	.	642	D6RGV7	.	H	642	ENSP00000421191:Y642H	ENSP00000322422:Y642H	Y	-	1	0	IGSF22	18692146	1.000000	0.71417	0.964000	0.40570	0.991000	0.79684	2.903000	0.48711	0.655000	0.30866	0.450000	0.29827	TAC	.	.	none		0.597	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110492352	110492352	+	Missense_Mutation	SNP	C	C	T	rs117952538	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110492352C>T	ENST00000378402.5	+	55	9415	c.9311C>T	c.(9310-9312)aCc>aTc	p.T3104I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3104	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTGAATGCTACCTACATATCA	0.333										HNSCC(38;0.096)			C|||	31	0.0061901	0.0008	0.0086	5008	,	,		17368	0.0		0.0179	False		,,,				2504	0.0061				p.T3104I		Atlas-SNP	.											PKHD1L1,NS,carcinoma,-1,1	PKHD1L1	522	1	0			c.C9311T						PASS	.	C	ILE/THR	8,3650		0,8,1821	50.0	49.0	49.0		9311	5.2	1.0	8	dbSNP_132	49	106,8056		0,106,3975	yes	missense	PKHD1L1	NM_177531.4	89	0,114,5796	TT,TC,CC		1.2987,0.2187,0.9645	probably-damaging	3104/4244	110492352	114,11706	1829	4081	5910	SO:0001583	missense	93035	exon55			ATGCTACCTACAT	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9311C>T	8.37:g.110492352C>T	ENSP00000367655:p.Thr3104Ile	141.0	0.0	0		122.0	56.0	0.459016	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	17	0.007783882783882784	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	13	0.017150395778364115	C	17.97	3.519012	0.64634	0.002187	0.012987	ENSG00000205038	ENST00000378402	D	0.89415	-2.51	5.25	5.25	0.73442	G8 domain (2);	0.139370	0.49305	D	0.000142	D	0.84683	0.5526	M	0.82056	2.57	0.30997	N	0.720711	B	0.29766	0.256	B	0.37989	0.262	D	0.86191	0.1612	10	0.34782	T	0.22	.	16.7128	0.85389	0.0:1.0:0.0:0.0	.	3104	Q86WI1	PKHL1_HUMAN	I	3104	ENSP00000367655:T3104I	ENSP00000367655:T3104I	T	+	2	0	PKHD1L1	110561528	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	3.752000	0.55172	2.604000	0.88044	0.650000	0.86243	ACC	C|0.992;T|0.008	0.008	strong		0.333	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
GAL3ST3	89792	hgsc.bcm.edu	37	11	65810612	65810612	+	Missense_Mutation	SNP	G	G	T	rs35285455	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:65810612G>T	ENST00000312006.4	-	3	943	c.662C>A	c.(661-663)gCc>gAc	p.A221D	GAL3ST3_ENST00000527878.1_Missense_Mutation_p.A221D	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	221			A -> D (in dbSNP:rs35285455).		monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						CAGGTAGGCGGCGTCGTCGCG	0.657													G|||	66	0.0131789	0.0242	0.0101	5008	,	,		9967	0.0		0.0189	False		,,,				2504	0.0082				p.A221D		Atlas-SNP	.											GAL3ST3,rectum,carcinoma,0,3	GAL3ST3	40	3	0			c.C662A						PASS	.	G	ASP/ALA	81,4313		1,79,2117	31.0	37.0	35.0		662	2.6	1.0	11	dbSNP_126	35	157,8411		1,155,4128	yes	missense	GAL3ST3	NM_033036.2	126	2,234,6245	TT,TG,GG		1.8324,1.8434,1.8361	benign	221/432	65810612	238,12724	2197	4284	6481	SO:0001583	missense	89792	exon3			TAGGCGGCGTCGT	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"""Sulfotransferases, membrane-bound"""	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.662C>A	11.37:g.65810612G>T	ENSP00000308591:p.Ala221Asp	32.0	0.0	0		50.0	38.0	0.76	NM_033036	Q14D05	Missense_Mutation	SNP	ENST00000312006.4	37	CCDS8128.1	21	0.009615384615384616	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	G	7.938	0.742112	0.15642	0.018434	0.018324	ENSG00000175229	ENST00000312006;ENST00000527878	T;T	0.14391	2.51;2.51	4.51	2.57	0.30868	.	0.445001	0.22406	N	0.060466	T	0.02012	0.0063	N	0.02158	-0.66	0.32668	N	0.517241	B	0.02656	0.0	B	0.01281	0.0	T	0.32375	-0.9909	10	0.14656	T	0.56	-4.5024	9.826	0.40912	0.0:0.0:0.6262:0.3738	rs35285455	221	Q96A11	G3ST3_HUMAN	D	221	ENSP00000308591:A221D;ENSP00000434829:A221D	ENSP00000308591:A221D	A	-	2	0	GAL3ST3	65567188	0.040000	0.19996	0.968000	0.41197	0.996000	0.88848	0.659000	0.24994	0.417000	0.25871	0.561000	0.74099	GCC	G|0.983;T|0.017	0.017	strong		0.657	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036	
CHST13	166012	hgsc.bcm.edu	37	3	126260791	126260791	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:126260791C>T	ENST00000319340.2	+	3	446	c.396C>T	c.(394-396)cgC>cgT	p.R132R		NM_152889.2	NP_690849.1	Q8NET6	CHSTD_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 13	132					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin 4-sulfotransferase activity (GO:0047756)|N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			central_nervous_system(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(114;0.151)		GCCAAGCCCGCGGCGACCCGC	0.726																																					p.R132R		Atlas-SNP	.											.	CHST13	21	.	0			c.C396T						PASS	.						16.0	13.0	14.0					3																	126260791		2183	4262	6445	SO:0001819	synonymous_variant	166012	exon3			AGCCCGCGGCGAC	AY120869	CCDS3039.1	3q21.3	2008-02-05			ENSG00000180767	ENSG00000180767	2.8.2.5	"""Sulfotransferases, membrane-bound"""	21755	protein-coding gene	gene with protein product		610124				12080076	Standard	NM_152889		Approved	C4ST3	uc003eja.3	Q8NET6	OTTHUMG00000162721	ENST00000319340.2:c.396C>T	3.37:g.126260791C>T		4.0	0.0	0		5.0	5.0	1	NM_152889	Q3SYA3|Q3SYA5	Silent	SNP	ENST00000319340.2	37	CCDS3039.1																																																																																			.	.	none		0.726	CHST13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370201.2	NM_152889	
SV2B	9899	hgsc.bcm.edu	37	15	91827271	91827271	+	Missense_Mutation	SNP	A	A	G	rs117361551	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91827271A>G	ENST00000394232.1	+	11	1998	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	SV2B_ENST00000545111.2_Missense_Mutation_p.I359V|SV2B_ENST00000330276.4_Missense_Mutation_p.I510V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	510					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GCACAAGTTCATCAACTGTCG	0.507													A|||	56	0.0111821	0.0008	0.013	5008	,	,		19869	0.0		0.0169	False		,,,				2504	0.0297				p.I510V		Atlas-SNP	.											.	SV2B	98	.	0			c.A1528G						PASS	.	A	VAL/ILE,VAL/ILE	12,4384	19.1+/-41.9	0,12,2186	192.0	184.0	187.0		1075,1528	5.6	1.0	15	dbSNP_132	187	127,8469	64.9+/-127.2	2,123,4173	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	2,135,6359	GG,GA,AA		1.4774,0.273,1.0699	benign,benign	359/533,510/684	91827271	139,12853	2198	4298	6496	SO:0001583	missense	9899	exon12			AAGTTCATCAACT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1528A>G	15.37:g.91827271A>G	ENSP00000377779:p.Ile510Val	141.0	0.0	0		178.0	96.0	0.539326	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	10.16	1.274723	0.23307	0.00273	0.014774	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.41400	1.0;1.0;1.0	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099589	0.64402	D	0.000004	T	0.21145	0.0509	L	0.39245	1.2	0.47584	D	0.999462	B	0.23937	0.094	B	0.31016	0.123	T	0.08911	-1.0699	10	0.12766	T	0.61	-31.4023	14.6867	0.69055	1.0:0.0:0.0:0.0	.	510	Q7L1I2	SV2B_HUMAN	V	359;510;510	ENSP00000443243:I359V;ENSP00000377779:I510V;ENSP00000332818:I510V	ENSP00000332818:I510V	I	+	1	0	SV2B	89628275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.317000	0.43770	2.152000	0.67230	0.477000	0.44152	ATC	A|0.990;G|0.010	0.010	strong		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
PDGFRA	5156	hgsc.bcm.edu	37	4	55143577	55143577	+	Silent	SNP	G	G	A	rs10028020	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55143577G>A	ENST00000257290.5	+	13	2140	c.1809G>A	c.(1807-1809)gcG>gcA	p.A603A	FIP1L1_ENST00000507166.1_Silent_p.A363A	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	603	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	GGTCTGGAGCGTTTGGGAAGG	0.532			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			G|||	1142	0.228035	0.3366	0.2666	5008	,	,		16391	0.1726		0.1064	False		,,,				2504	0.2362				p.A603A	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	PDGFRA	1583	.	0			c.G1809A						PASS	.	G		1306,3100	441.2+/-346.3	179,948,1076	141.0	145.0	144.0		1809	-11.3	0.1	4	dbSNP_119	144	855,7745	193.8+/-239.4	54,747,3499	no	coding-synonymous	PDGFRA	NM_006206.4		233,1695,4575	AA,AG,GG		9.9419,29.6414,16.6154		603/1090	55143577	2161,10845	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon13	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	TGGAGCGTTTGGG	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.1809G>A	4.37:g.55143577G>A		252.0	0.0	0		267.0	117.0	0.438202	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			A|0.170;C|0.000;G|0.830	0.170	strong		0.532	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
COL6A6	131873	hgsc.bcm.edu	37	3	130380710	130380710	+	Silent	SNP	C	C	T	rs201325545	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:130380710C>T	ENST00000358511.6	+	34	6091	c.6060C>T	c.(6058-6060)ttC>ttT	p.F2020F	COL6A6_ENST00000453409.2_Silent_p.F2020F	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	2020	Nonhelical region.|VWFA 9. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						CCCCCGACTTCCTACCCAACA	0.512													C|||	2	0.000399361	0.0	0.0	5008	,	,		18044	0.0		0.0	False		,,,				2504	0.002				p.F2020F		Atlas-SNP	.											.	COL6A6	497	.	0			c.C6060T						PASS	.	C		1,3759		0,1,1879	56.0	54.0	55.0		6060	4.1	1.0	3		55	10,8210		0,10,4100	no	coding-synonymous	COL6A6	NM_001102608.1		0,11,5979	TT,TC,CC		0.1217,0.0266,0.0918		2020/2264	130380710	11,11969	1880	4110	5990	SO:0001819	synonymous_variant	131873	exon34			CGACTTCCTACCC	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.6060C>T	3.37:g.130380710C>T		113.0	0.0	0		141.0	58.0	0.411348	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.996;T|0.004	0.004	strong		0.512	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
DGKE	8526	hgsc.bcm.edu	37	17	54940127	54940127	+	Missense_Mutation	SNP	A	A	G	rs61751972	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:54940127A>G	ENST00000284061.3	+	12	1859	c.1679A>G	c.(1678-1680)cAa>cGa	p.Q560R		NM_003647.2	NP_003638.1	P52429	DGKE_HUMAN	diacylglycerol kinase, epsilon 64kDa	560					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|phospholipid biosynthetic process (GO:0008654)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25	Breast(9;3.59e-07)					ACTTCGGATCAAGAAGATATA	0.393													A|||	4	0.000798722	0.0	0.0	5008	,	,		18984	0.0		0.004	False		,,,				2504	0.0				p.Q560R		Atlas-SNP	.											.	DGKE	47	.	0			c.A1679G						PASS	.	A	ARG/GLN	2,4404	4.2+/-10.8	0,2,2201	77.0	70.0	72.0		1679	0.8	1.0	17	dbSNP_129	72	21,8579	16.0+/-53.3	0,21,4279	yes	missense	DGKE	NM_003647.2	43	0,23,6480	GG,GA,AA		0.2442,0.0454,0.1768	benign	560/568	54940127	23,12983	2203	4300	6503	SO:0001583	missense	8526	exon12			CGGATCAAGAAGA	U49379	CCDS11590.1	17q22	2008-07-18	2002-08-29			ENSG00000153933	2.7.1.107		2852	protein-coding gene	gene with protein product		601440	"""diacylglycerol kinase, epsilon (64kD)"""			8626589, 10051413	Standard	NM_003647		Approved	DAGK6, DGK	uc002iur.3	P52429		ENST00000284061.3:c.1679A>G	17.37:g.54940127A>G	ENSP00000284061:p.Gln560Arg	57.0	0.0	0		44.0	24.0	0.545455	NM_003647	Q8TBM4|Q9UKQ3	Missense_Mutation	SNP	ENST00000284061.3	37	CCDS11590.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	15.11	2.734675	0.48939	4.54E-4	0.002442	ENSG00000153933	ENST00000284061	T	0.16897	2.31	5.92	0.807	0.18714	.	0.762462	0.13392	N	0.391343	T	0.13114	0.0318	L	0.36672	1.1	0.80722	D	1	B	0.19583	0.037	B	0.19391	0.025	T	0.10753	-1.0616	10	0.27082	T	0.32	.	10.1281	0.42663	0.5593:0.3798:0.061:0.0	rs61751972	560	P52429	DGKE_HUMAN	R	560	ENSP00000284061:Q560R	ENSP00000284061:Q560R	Q	+	2	0	DGKE	52295126	0.990000	0.36364	0.996000	0.52242	0.993000	0.82548	1.290000	0.33319	0.120000	0.18254	0.524000	0.50904	CAA	A|0.998;G|0.002	0.002	strong		0.393	DGKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440601.1	NM_003647	
RALGAPB	57148	hgsc.bcm.edu	37	20	37203571	37203571	+	Silent	SNP	A	A	G	rs143567036	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:37203571A>G	ENST00000262879.6	+	30	4730	c.4446A>G	c.(4444-4446)tcA>tcG	p.S1482S	RALGAPB_ENST00000490114.1_3'UTR|RALGAPB_ENST00000397040.1_Silent_p.S1482S|RALGAPB_ENST00000397042.3_Silent_p.S1479S|RALGAPB_ENST00000397038.1_Silent_p.S1261S			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1482					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TTTATACTTCACTTTTCCAGG	0.463																																					p.S1482S		Atlas-SNP	.											.	RALGAPB	134	.	0			c.A4446G						PASS	.	A		0,4406		0,0,2203	84.0	89.0	87.0		4446	2.4	1.0	20	dbSNP_134	87	3,8597	4.3+/-15.6	0,3,4297	no	coding-synonymous	RALGAPB	NM_020336.2		0,3,6500	GG,GA,AA		0.0349,0.0,0.0231		1482/1495	37203571	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon30			TACTTCACTTTTC	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4446A>G	20.37:g.37203571A>G		155.0	0.0	0		144.0	57.0	0.395833	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			A|0.999;G|0.001	0.001	strong		0.463	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
POLQ	10721	hgsc.bcm.edu	37	3	121252048	121252048	+	Missense_Mutation	SNP	T	T	G	rs73179915	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:121252048T>G	ENST00000264233.5	-	6	877	c.749A>C	c.(748-750)gAt>gCt	p.D250A	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	250	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ACTGGCTAGATCTGCCTGACT	0.368								DNA polymerases (catalytic subunits)					T|||	3	0.000599042	0.0	0.0	5008	,	,		18003	0.0		0.003	False		,,,				2504	0.0				p.D250A	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.A749C						PASS	.	T	ALA/ASP	1,4405	2.1+/-5.4	0,1,2202	78.0	77.0	77.0		749	1.6	0.9	3	dbSNP_130	77	19,8581	14.0+/-48.4	0,19,4281	yes	missense	POLQ	NM_199420.3	126	0,20,6483	GG,GT,TT		0.2209,0.0227,0.1538	benign	250/2591	121252048	20,12986	2203	4300	6503	SO:0001583	missense	10721	exon6			GCTAGATCTGCCT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.749A>C	3.37:g.121252048T>G	ENSP00000264233:p.Asp250Ala	149.0	0.0	0		139.0	65.0	0.467626	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	5.065	0.197617	0.09652	2.27E-4	0.002209	ENSG00000051341	ENST00000264233;ENST00000393672	T	0.49139	0.79	5.3	1.56	0.23342	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	1.695750	0.02414	N	0.081944	T	0.29749	0.0743	N	0.11364	0.135	0.09310	N	1	B	0.21452	0.056	B	0.24394	0.053	T	0.20505	-1.0273	10	0.12103	T	0.63	.	8.008	0.30336	0.0:0.3139:0.0:0.6861	.	250	O75417	DPOLQ_HUMAN	A	250;385	ENSP00000264233:D250A	ENSP00000264233:D250A	D	-	2	0	POLQ	122734738	0.029000	0.19370	0.855000	0.33649	0.438000	0.31896	0.913000	0.28611	0.393000	0.25203	0.383000	0.25322	GAT	T|0.999;G|0.001	0.001	strong		0.368	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
BMP3	651	hgsc.bcm.edu	37	4	81967240	81967240	+	Missense_Mutation	SNP	C	C	T	rs34505126	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:81967240C>T	ENST00000282701.2	+	2	985	c.665C>T	c.(664-666)aCg>aTg	p.T222M		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	222			T -> M (in dbSNP:rs34505126).		cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						TTTAACATTACGTCCAAGGGA	0.433													C|||	125	0.0249601	0.0847	0.0115	5008	,	,		20614	0.0		0.001	False		,,,				2504	0.0041				p.T222M		Atlas-SNP	.											.	BMP3	59	.	0			c.C665T						PASS	.	C	MET/THR	273,4133	154.4+/-187.8	5,263,1935	115.0	123.0	120.0		665	5.1	0.3	4	dbSNP_126	120	6,8594	4.3+/-15.6	0,6,4294	yes	missense	BMP3	NM_001201.2	81	5,269,6229	TT,TC,CC		0.0698,6.1961,2.1452	probably-damaging	222/473	81967240	279,12727	2203	4300	6503	SO:0001583	missense	651	exon2			ACATTACGTCCAA	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.665C>T	4.37:g.81967240C>T	ENSP00000282701:p.Thr222Met	51.0	0.0	0		88.0	40.0	0.454545	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	43	0.019688644688644688	38	0.07723577235772358	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.519	1.107725	0.20714	0.061961	6.98E-4	ENSG00000152785	ENST00000282701	T	0.74632	-0.86	5.08	5.08	0.68730	.	0.361129	0.33610	N	0.004726	T	0.27349	0.0671	M	0.68952	2.095	0.09310	N	1	D	0.89917	1.0	D	0.69307	0.963	T	0.54866	-0.8229	10	0.56958	D	0.05	.	14.6465	0.68764	0.1459:0.8541:0.0:0.0	rs34505126;rs61679463	222	P12645	BMP3_HUMAN	M	222	ENSP00000282701:T222M	ENSP00000282701:T222M	T	+	2	0	BMP3	82186264	0.293000	0.24371	0.254000	0.24359	0.004000	0.04260	2.015000	0.40961	2.806000	0.96561	0.655000	0.94253	ACG	C|0.975;T|0.025	0.025	strong		0.433	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
HECW1	23072	hgsc.bcm.edu	37	7	43547692	43547692	+	Silent	SNP	G	G	A	rs17172219	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:43547692G>A	ENST00000395891.2	+	23	4433	c.3828G>A	c.(3826-3828)caG>caA	p.Q1276Q	AC011738.4_ENST00000436105.1_RNA|HECW1_ENST00000453890.1_Silent_p.Q1242Q	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	1276	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						AAGAGCTCCAGCGAAACAAGC	0.547													G|||	20	0.00399361	0.0151	0.0	5008	,	,		20717	0.0		0.0	False		,,,				2504	0.0				p.Q1276Q		Atlas-SNP	.											.	HECW1	540	.	0			c.G3828A						PASS	.	G		74,3858		1,72,1893	76.0	78.0	77.0		3828	5.8	1.0	7	dbSNP_123	77	1,8287		0,1,4143	no	coding-synonymous	HECW1	NM_015052.3		1,73,6036	AA,AG,GG		0.0121,1.882,0.6137		1276/1607	43547692	75,12145	1966	4144	6110	SO:0001819	synonymous_variant	23072	exon23			GCTCCAGCGAAAC	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.3828G>A	7.37:g.43547692G>A		108.0	0.0	0		116.0	66.0	0.568965	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			G|0.995;A|0.005	0.005	strong		0.547	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
BLM	641	hgsc.bcm.edu	37	15	91341535	91341535	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:91341535T>A	ENST00000355112.3	+	17	3444	c.3326T>A	c.(3325-3327)tTt>tAt	p.F1109Y	BLM_ENST00000560509.1_Missense_Mutation_p.F1109Y|BLM_ENST00000560136.1_3'UTR	NM_000057.2	NP_000048.1	P54132	BLM_HUMAN	Bloom syndrome, RecQ helicase-like	1109					alpha-beta T cell differentiation (GO:0046632)|ATP catabolic process (GO:0006200)|cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA strand renaturation (GO:0000733)|double-strand break repair via homologous recombination (GO:0000724)|mitotic G2 DNA damage checkpoint (GO:0007095)|negative regulation of cell division (GO:0051782)|negative regulation of DNA recombination (GO:0045910)|negative regulation of mitotic recombination (GO:0045950)|negative regulation of thymocyte apoptotic process (GO:0070244)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of transcription, DNA-templated (GO:0045893)|protein oligomerization (GO:0051259)|regulation of binding (GO:0051098)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to X-ray (GO:0010165)|telomere maintenance (GO:0000723)	cytoplasm (GO:0005737)|lateral element (GO:0000800)|male germ cell nucleus (GO:0001673)|nuclear chromosome (GO:0000228)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|PML body (GO:0016605)|pronucleus (GO:0045120)|replication fork (GO:0005657)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent helicase activity (GO:0008026)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|p53 binding (GO:0002039)|single-stranded DNA binding (GO:0003697)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(11)|liver(4)|lung(9)|ovary(6)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	Lung NSC(78;0.0875)|all_lung(78;0.109)		Lung(145;0.189)			TCTGGAAGATTTACTATGAAT	0.313			"""Mis, N, F"""			"""leukemia, lymphoma, skin squamous cell , other cancers"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Bloom syndrome																												p.F1109Y		Atlas-SNP	.	yes	Rec		Bloom Syndrome	15	15q26.1	641	Bloom Syndrome		"""L, E"""	.	BLM	122	.	0			c.T3326A						PASS	.						131.0	131.0	131.0					15																	91341535		2198	4296	6494	SO:0001583	missense	641	exon17	Familial Cancer Database		GAAGATTTACTAT	U39817	CCDS10363.1, CCDS73782.1	15q26.1	2014-09-17	2009-03-19		ENSG00000197299	ENSG00000197299			1058	protein-coding gene	gene with protein product		604610	"""Bloom syndrome"""			9388193	Standard	NM_000057		Approved	BS, RECQL3, RECQ2	uc002bpr.3	P54132	OTTHUMG00000149834	ENST00000355112.3:c.3326T>A	15.37:g.91341535T>A	ENSP00000347232:p.Phe1109Tyr	152.0	0.0	0		137.0	48.0	0.350365	NM_000057	Q52M96	Missense_Mutation	SNP	ENST00000355112.3	37	CCDS10363.1	.	.	.	.	.	.	.	.	.	.	T	14.42	2.529829	0.45073	.	.	ENSG00000197299	ENST00000355112;ENST00000536925;ENST00000543977	T	0.51325	0.71	5.36	5.36	0.76844	RQC domain (2);	0.134612	0.52532	D	0.000066	T	0.37758	0.1015	N	0.25380	0.74	0.31109	N	0.710145	B;B	0.24882	0.113;0.113	B;B	0.30401	0.115;0.115	T	0.42464	-0.9450	10	0.33141	T	0.24	-20.8792	13.2993	0.60315	0.0:0.0:0.0:1.0	.	1109;1109	B2RAN0;P54132	.;BLM_HUMAN	Y	1109;739;296	ENSP00000347232:F1109Y	ENSP00000347232:F1109Y	F	+	2	0	BLM	89142539	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.846000	0.62860	2.037000	0.60232	0.477000	0.44152	TTT	.	.	none		0.313	BLM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313495.1		
PTPRQ	374462	hgsc.bcm.edu	37	12	80878310	80878310	+	Missense_Mutation	SNP	C	C	G	rs61729287	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:80878310C>G	ENST00000266688.5	+	14	1273	c.1273C>G	c.(1273-1275)Caa>Gaa	p.Q425E				Q9UMZ3	PTPRQ_HUMAN	protein tyrosine phosphatase, receptor type, Q	471	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fat cell differentiation (GO:0045598)	integral component of membrane (GO:0016021)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(7)|kidney(9)|lung(2)|prostate(1)|skin(2)|stomach(2)	24						AATTATTAACCAATACCGAGT	0.368													C|||	48	0.00958466	0.0	0.013	5008	,	,		15111	0.0		0.0249	False		,,,				2504	0.0143				p.Q257E		Atlas-SNP	.											.	PTPRQ	119	.	0			c.C769G						PASS	.	C	GLU/GLN	8,1376		0,8,684	114.0	103.0	106.0		831	6.1	1.0	12	dbSNP_129	106	89,3093		0,89,1502	yes	missense	PTPRQ	NM_001145026.1	29	0,97,2186	GG,GC,CC		2.797,0.578,2.1244	possibly-damaging	429/2300	80878310	97,4469	692	1591	2283	SO:0001583	missense	374462	exon6			ATTAACCAATACC	AF169351	CCDS73501.1	12q21.31	2013-02-11	2001-12-04		ENSG00000139304	ENSG00000139304		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9679	protein-coding gene	gene with protein product		603317	"""deafness, autosomal recessive 84"""	DFNB84		20346435	Standard	NM_001145026		Approved		uc001sze.2	Q9UMZ3	OTTHUMG00000170171	ENST00000266688.5:c.1273C>G	12.37:g.80878310C>G	ENSP00000266688:p.Gln425Glu	71.0	0.0	0		80.0	30.0	0.375	NM_001145026		Missense_Mutation	SNP	ENST00000266688.5	37		28	0.01282051282051282	0	0.0	7	0.019337016574585635	0	0.0	21	0.027704485488126648	C	18.99	3.740500	0.69304	0.00578	0.02797	ENSG00000139304	ENST00000266688	T	0.52526	0.66	6.06	6.06	0.98353	Fibronectin, type III (3);Immunoglobulin-like fold (1);	.	.	.	.	T	0.15349	0.0370	.	.	.	0.36172	D	0.848855	P	0.50369	0.934	P	0.44422	0.449	T	0.15954	-1.0419	8	0.02654	T	1	.	20.6397	0.99537	0.0:1.0:0.0:0.0	rs61729287	471	Q9UMZ3	PTPRQ_HUMAN	E	425	ENSP00000266688:Q425E	ENSP00000266688:Q425E	Q	+	1	0	PTPRQ	79402441	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	5.276000	0.65580	2.880000	0.98712	0.650000	0.86243	CAA	C|0.987;G|0.013	0.013	strong		0.368	PTPRQ-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145026	
CCDC132	55610	hgsc.bcm.edu	37	7	92900576	92900576	+	Splice_Site	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:92900576T>G	ENST00000305866.5	+	10	830		c.e10+2		CCDC132_ENST00000541136.1_Splice_Site|CCDC132_ENST00000544910.1_Splice_Site|CCDC132_ENST00000535481.1_Intron|CCDC132_ENST00000317751.6_Splice_Site|CCDC132_ENST00000251739.5_Splice_Site	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132							extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGATTGAGGTAAGAAGTATT	0.294																																					.		Atlas-SNP	.											.	CCDC132	136	.	0			c.702+2T>G						PASS	.						121.0	129.0	126.0					7																	92900576		2203	4298	6501	SO:0001630	splice_region_variant	55610	exon10			TTGAGGTAAGAAG	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.702+2T>G	7.37:g.92900576T>G		101.0	0.0	0		111.0	43.0	0.387387	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Splice_Site	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.030563	0.75504	.	.	ENSG00000004766	ENST00000251739;ENST00000305866;ENST00000544910;ENST00000541136;ENST00000458707	.	.	.	5.44	5.44	0.79542	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3837	0.74681	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCDC132	92738512	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.413000	0.80104	2.367000	0.80283	0.528000	0.53228	.	.	.	none		0.294	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	Intron
TTC38	55020	hgsc.bcm.edu	37	22	46669924	46669924	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:46669924G>A	ENST00000381031.3	+	4	399	c.323G>A	c.(322-324)cGg>cAg	p.R108Q	TTC38_ENST00000445282.2_Missense_Mutation_p.R108Q	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	108						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						CTGACAAGGCGGGAGCAGCTG	0.602																																					p.R108Q		Atlas-SNP	.											.	TTC38	40	.	0			c.G323A						PASS	.						46.0	52.0	50.0					22																	46669924		2080	4217	6297	SO:0001583	missense	55020	exon4			CAAGGCGGGAGCA		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.323G>A	22.37:g.46669924G>A	ENSP00000370419:p.Arg108Gln	86.0	0.0	0		116.0	56.0	0.482759	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	37	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249754	0.80024	.	.	ENSG00000075234	ENST00000381031;ENST00000445282;ENST00000421359	T;T;T	0.67865	0.97;0.24;-0.29	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.84188	0.5417	M	0.85710	2.77	0.24599	N	0.993783	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.995	T	0.78427	-0.2208	10	0.62326	D	0.03	-0.2222	18.5029	0.90888	0.0:0.0:1.0:0.0	.	108;108	E7ES35;Q5R3I4	.;TTC38_HUMAN	Q	108	ENSP00000370419:R108Q;ENSP00000393960:R108Q;ENSP00000410095:R108Q	ENSP00000370419:R108Q	R	+	2	0	TTC38	45048588	1.000000	0.71417	0.595000	0.28798	0.086000	0.17979	9.017000	0.93651	2.596000	0.87737	0.650000	0.86243	CGG	.	.	none		0.602	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
LMO7	4008	hgsc.bcm.edu	37	13	76370783	76370783	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:76370783A>G	ENST00000341547.4	+	7	1776	c.516A>G	c.(514-516)acA>acG	p.T172T	LMO7_ENST00000321797.8_5'UTR|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000526202.1_Silent_p.T81T|LMO7_ENST00000377534.3_Silent_p.T172T|LMO7_ENST00000357063.3_Silent_p.T172T|LMO7_ENST00000465261.2_5'UTR	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	172					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T172T(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		TTTTGATAACATTGTACTGGC	0.363																																					p.T172T		Atlas-SNP	.											LMO7_ENST00000357063,NS,carcinoma,0,2	LMO7	334	2	2	Substitution - coding silent(2)	breast(2)	c.A516G						PASS	.						80.0	75.0	77.0					13																	76370783		2203	4300	6503	SO:0001819	synonymous_variant	4008	exon7			GATAACATTGTAC	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.516A>G	13.37:g.76370783A>G		61.0	0.0	0		78.0	35.0	0.448718	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Silent	SNP	ENST00000341547.4	37	CCDS9454.1																																																																																			.	.	none		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
MT-ND5	4540	hgsc.bcm.edu	37	M	14037	14037	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14037A>G	ENST00000361567.2	+	1	1701	c.1701A>G	c.(1699-1701)tcA>tcG	p.S567S	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	567					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AAAACAATTTCACAGCACCAA	0.448																																					p.S567S		Atlas-SNP	.											.	.	.	.	0			c.A1701G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AATTTCACAGCAC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1701A>G	M.37:g.14037A>G		11.0	0.0	0		28.0	27.0	0.964286	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
GAA	2548	hgsc.bcm.edu	37	17	78078656	78078656	+	Missense_Mutation	SNP	G	G	A	rs1800299	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78078656G>A	ENST00000302262.3	+	2	490	c.271G>A	c.(271-273)Gat>Aat	p.D91N	GAA_ENST00000390015.3_Missense_Mutation_p.D91N	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	91	P-type. {ECO:0000255|PROSITE- ProRule:PRU00779}.		D -> N (in allele GAA*2; lower affinity for glycogen and starch but not for lower-molecular weight substrates; dbSNP:rs1800299). {ECO:0000269|PubMed:21109266, ECO:0000269|PubMed:2203258, ECO:0000269|PubMed:9521422}.		cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	CAGCCGCTTCGATTGCGCCCC	0.692													G|||	58	0.0115815	0.0053	0.0173	5008	,	,		15176	0.001		0.0278	False		,,,				2504	0.0102				p.D91N		Atlas-SNP	.											.	GAA	66	.	0			c.G271A	GRCh37	CD983801	GAA	D	rs1800299	PASS	.	G	ASN/ASP,ASN/ASP,ASN/ASP	29,4377	34.3+/-65.2	0,29,2174	35.0	33.0	34.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	271,271,271	4.9	1.0	17	dbSNP_89	34	271,8329	100.8+/-162.1	6,259,4035	yes	missense,missense,missense	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	23,23,23	6,288,6209	AA,AG,GG		3.1512,0.6582,2.3066	probably-damaging,probably-damaging,probably-damaging	91/953,91/953,91/953	78078656	300,12706	2203	4300	6503	SO:0001583	missense	2548	exon3			CGCTTCGATTGCG		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.271G>A	17.37:g.78078656G>A	ENSP00000305692:p.Asp91Asn	132.0	0.0	0		122.0	72.0	0.590164	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Missense_Mutation	SNP	ENST00000302262.3	37	CCDS32760.1	34	0.015567765567765568	4	0.008130081300813009	8	0.022099447513812154	0	0.0	22	0.029023746701846966	G	16.20	3.054964	0.55325	0.006582	0.031512	ENSG00000171298	ENST00000302262;ENST00000390015	T;T	0.58210	0.35;0.35	4.94	4.94	0.65067	P-type trefoil, conserved site (1);P-type trefoil (4);	0.000000	0.85682	D	0.000000	T	0.41811	0.1175	L	0.45051	1.395	0.53688	D	0.99997	D	0.89917	1.0	D	0.91635	0.999	T	0.56836	-0.7913	10	0.41790	T	0.15	-47.1701	16.922	0.86166	0.0:0.0:1.0:0.0	rs1800299;rs52818006	91	P10253	LYAG_HUMAN	N	91	ENSP00000305692:D91N;ENSP00000374665:D91N	ENSP00000305692:D91N	D	+	1	0	GAA	75693251	1.000000	0.71417	0.992000	0.48379	0.213000	0.24496	9.466000	0.97665	2.279000	0.76181	0.655000	0.94253	GAT	G|0.979;A|0.021	0.021	strong		0.692	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
SCARA3	51435	hgsc.bcm.edu	37	8	27516323	27516323	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:27516323G>A	ENST00000301904.3	+	5	656	c.636G>A	c.(634-636)gaG>gaA	p.E212E	SCARA3_ENST00000337221.4_Silent_p.E212E	NM_016240.2	NP_057324.2	Q6AZY7	SCAR3_HUMAN	scavenger receptor class A, member 3	212					receptor-mediated endocytosis (GO:0006898)|response to oxidative stress (GO:0006979)|UV protection (GO:0009650)	collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)			breast(1)|large_intestine(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	9		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0219)|Colorectal(74;0.148)		TCACCCAGGAGTGCTACGATG	0.612																																					p.E212E		Atlas-SNP	.											.	SCARA3	93	.	0			c.G636A						PASS	.						38.0	39.0	39.0					8																	27516323		2203	4300	6503	SO:0001819	synonymous_variant	51435	exon5			CCAGGAGTGCTAC	AB007829	CCDS34870.1, CCDS34871.1	8p21	2010-03-24			ENSG00000168077	ENSG00000168077			19000	protein-coding gene	gene with protein product	"""macrophage scavenger receptor-like 1"""	602728				9747040, 9580669	Standard	NM_182826		Approved	CSR1, CSR, MSLR1, APC7, MSRL1	uc003xga.1	Q6AZY7	OTTHUMG00000163898	ENST00000301904.3:c.636G>A	8.37:g.27516323G>A		86.0	0.0	0		118.0	54.0	0.457627	NM_182826	Q9UM15|Q9UM16	Silent	SNP	ENST00000301904.3	37	CCDS34871.1																																																																																			.	.	none		0.612	SCARA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376258.2	NM_016240	
MTRR	4552	hgsc.bcm.edu	37	5	7892933	7892933	+	Silent	SNP	A	A	G	rs35890938	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7892933A>G	ENST00000264668.2	+	11	1575	c.1545A>G	c.(1543-1545)gtA>gtG	p.V515V	MTRR_ENST00000440940.2_Silent_p.V488V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	515	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	GGAAGGGAGTATGTACAGGCT	0.473													G|||	40	0.00798722	0.0015	0.0245	5008	,	,		18051	0.0		0.0189	False		,,,				2504	0.002				p.V515V		Atlas-SNP	.											.	MTRR	74	.	0			c.A1545G						PASS	.	G	,	46,4360	822.1+/-416.4	0,46,2157	150.0	129.0	136.0		1464,1545	0.7	0.5	5	dbSNP_126	136	207,8393	810.1+/-407.1	2,203,4095	no	coding-synonymous,coding-synonymous	MTRR	NM_002454.2,NM_024010.2	,	2,249,6252	GG,GA,AA		2.407,1.044,1.9453	,	488/699,515/726	7892933	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	4552	exon11			GGGAGTATGTACA	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1545A>G	5.37:g.7892933A>G		158.0	0.0	0		186.0	93.0	0.5	NM_024010	O60471|Q32MA9|Q7Z4M8	Silent	SNP	ENST00000264668.2	37	CCDS3874.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
MT-CO3	4514	hgsc.bcm.edu	37	M	9716	9716	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:9716T>C	ENST00000362079.2	+	1	510	c.510T>C	c.(508-510)ggT>ggC	p.G170G	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	170					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						ATTTTACTGGGTCTCTATTTT	0.428																																					p.G170G		Atlas-SNP	.											.	.	.	.	0			c.T510C						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			ACTGGGTCTCTAT			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.510T>C	M.37:g.9716T>C		7.0	0.0	0		19.0	19.0	1	ENST00000362079	Q14Y83	Silent	SNP	ENST00000362079.2	37																																																																																				.	.	none		0.428	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
DOLPP1	57171	hgsc.bcm.edu	37	9	131848488	131848488	+	Missense_Mutation	SNP	G	G	A	rs149976737	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:131848488G>A	ENST00000372546.4	+	6	564	c.532G>A	c.(532-534)Gcc>Acc	p.A178T	DOLPP1_ENST00000540102.1_Intron|DOLPP1_ENST00000406974.3_Intron	NM_020438.4	NP_065171.2	Q86YN1	DOPP1_HUMAN	dolichyldiphosphatase 1	178					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|lipid biosynthetic process (GO:0008610)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichyldiphosphatase activity (GO:0047874)			endometrium(3)|kidney(2)|lung(7)|skin(1)	13						CATGGCCATCGCCTGGTTCAT	0.622													G|||	5	0.000998403	0.0	0.0	5008	,	,		20902	0.0		0.005	False		,,,				2504	0.0				p.A178T		Atlas-SNP	.											.	DOLPP1	17	.	0			c.G532A						PASS	.	G	,THR/ALA	0,4406		0,0,2203	103.0	80.0	87.0		,532	5.5	1.0	9	dbSNP_134	87	5,8595	4.3+/-15.6	0,5,4295	yes	intron,missense	DOLPP1	NM_001135917.1,NM_020438.4	,58	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,benign	,178/239	131848488	5,13001	2203	4300	6503	SO:0001583	missense	57171	exon6			GCCATCGCCTGGT	BC009493	CCDS6918.1, CCDS48039.1	9q34.1	2013-05-21	2013-05-21		ENSG00000167130	ENSG00000167130	3.6.1.43		29565	protein-coding gene	gene with protein product	"""linked to Surfeit genes in Fugu rubripes 2"""	614516	"""dolichyl pyrophosphate phosphatase 1"""			10369878, 12198133	Standard	NM_020438		Approved	LSFR2	uc004bxc.3	Q86YN1	OTTHUMG00000020771	ENST00000372546.4:c.532G>A	9.37:g.131848488G>A	ENSP00000361625:p.Ala178Thr	88.0	0.0	0		85.0	34.0	0.4	NM_020438	A8K3U8|B0QZG4|Q96GF8|Q9Y3G1	Missense_Mutation	SNP	ENST00000372546.4	37	CCDS6918.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	17.16	3.317356	0.60524	0.0	5.81E-4	ENSG00000167130	ENST00000372546	T	0.75589	-0.95	5.51	5.51	0.81932	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.107308	0.64402	D	0.000004	T	0.70316	0.3210	L	0.49256	1.55	0.80722	D	1	P	0.50710	0.938	B	0.41571	0.36	T	0.68969	-0.5269	10	0.24483	T	0.36	-10.1792	18.4662	0.90755	0.0:0.0:1.0:0.0	.	178	Q86YN1	DOPP1_HUMAN	T	178	ENSP00000361625:A178T	ENSP00000361625:A178T	A	+	1	0	DOLPP1	130888309	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	7.230000	0.78097	2.604000	0.88044	0.456000	0.33151	GCC	G|0.999;A|0.001	0.001	strong		0.622	DOLPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054548.4	NM_020438	
RB1	5925	hgsc.bcm.edu	37	13	49039405	49039405	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:49039405T>A	ENST00000267163.4	+	23	2528	c.2390T>A	c.(2389-2391)tTa>tAa	p.L797*		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	797	Domain C; mediates interaction with E4F1.|Interaction with LIMD1.				androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(11)|p.L797fs*1(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	AGTTCACCCTTACGGATTCCT	0.403		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																											p.L797X		Atlas-SNP	.	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	retinoblastoma gene		"""L, E, M, O"""	.	RB1	1068	.	27	Whole gene deletion(15)|Unknown(11)|Deletion - Frameshift(1)	bone(11)|haematopoietic_and_lymphoid_tissue(4)|breast(4)|adrenal_gland(1)|eye(1)|soft_tissue(1)|endometrium(1)|urinary_tract(1)|lung(1)|ovary(1)|liver(1)	c.T2390A	GRCh37	CM023820	RB1	M		PASS	.						131.0	133.0	133.0					13																	49039405		2203	4300	6503	SO:0001587	stop_gained	5925	exon23	Familial Cancer Database		CACCCTTACGGAT	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.2390T>A	13.37:g.49039405T>A	ENSP00000267163:p.Leu797*	131.0	0.0	0		80.0	7.0	0.0875	NM_000321	A8K5E3|P78499|Q5VW46|Q8IZL4	Nonsense_Mutation	SNP	ENST00000267163.4	37	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	T	39	7.903488	0.98554	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	.	.	.	5.87	5.87	0.94306	.	0.091849	0.44902	D	0.000409	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7061	0.51597	0.0:0.0:0.158:0.842	.	.	.	.	X	776;797	.	ENSP00000267163:L797X	L	+	2	0	RB1	47937406	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	5.593000	0.67550	2.242000	0.73789	0.482000	0.46254	TTA	.	.	none		0.403	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		
CAPN5	726	hgsc.bcm.edu	37	11	76826545	76826545	+	Silent	SNP	A	A	G	rs143460583	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:76826545A>G	ENST00000278559.3	+	6	993	c.804A>G	c.(802-804)ctA>ctG	p.L268L	CAPN5_ENST00000531028.1_Intron|CAPN5_ENST00000529629.1_Silent_p.L268L|CAPN5_ENST00000456580.2_Silent_p.L308L	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	268	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						GCCACGGCCTACTGGCCTTCT	0.657													a|||	7	0.00139776	0.0008	0.0043	5008	,	,		20264	0.0		0.003	False		,,,				2504	0.0				p.L268L		Atlas-SNP	.											CAPN5,NS,carcinoma,0,1	CAPN5	67	1	0			c.A804G						PASS	.			0,4400		0,0,2200	43.0	41.0	42.0		804	2.0	1.0	11	dbSNP_134	42	29,8555	21.0+/-64.5	0,29,4263	no	coding-synonymous	CAPN5	NM_004055.4		0,29,6463	GG,GA,AA		0.3378,0.0,0.2234		268/641	76826545	29,12955	2200	4292	6492	SO:0001819	synonymous_variant	726	exon6			CGGCCTACTGGCC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.804A>G	11.37:g.76826545A>G		145.0	0.0	0		168.0	72.0	0.428571	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			A|0.997;G|0.003	0.003	strong		0.657	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
PCNT	5116	hgsc.bcm.edu	37	21	47847700	47847700	+	Silent	SNP	C	C	T	rs61735817	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47847700C>T	ENST00000359568.5	+	34	7592	c.7485C>T	c.(7483-7485)atC>atT	p.I2495I	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2495					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGAAGATCATCCGTGAGCAGG	0.582													c|||	92	0.0183706	0.0008	0.0259	5008	,	,		19242	0.001		0.0676	False		,,,				2504	0.0041				p.I2495I		Atlas-SNP	.											.	PCNT	283	.	0			c.C7485T						PASS	.	T		60,4346	56.8+/-93.2	1,58,2144	57.0	57.0	57.0		7485	0.3	0.0	21	dbSNP_129	57	523,8077	146.3+/-201.9	10,503,3787	no	coding-synonymous	PCNT	NM_006031.5		11,561,5931	TT,TC,CC		6.0814,1.3618,4.4825		2495/3337	47847700	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	5116	exon34			GATCATCCGTGAG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7485C>T	21.37:g.47847700C>T		55.0	0.0	0		43.0	17.0	0.395349	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.958;T|0.042	0.042	strong		0.582	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MMS22L	253714	hgsc.bcm.edu	37	6	97599674	97599674	+	Missense_Mutation	SNP	G	G	A	rs138146580	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:97599674G>A	ENST00000275053.4	-	23	3720	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P1112L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1152					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CTGGGAGGAAGGTTCTTCTTC	0.433													G|||	37	0.00738818	0.0023	0.0058	5008	,	,		15425	0.0		0.0239	False		,,,				2504	0.0061				p.P1152L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3455T						PASS	.	G	LEU/PRO	17,4389	24.3+/-50.5	0,17,2186	204.0	203.0	203.0		3455	3.6	1.0	6	dbSNP_134	203	155,8445	73.5+/-136.2	2,151,4147	yes	missense	MMS22L	NM_198468.2	98	2,168,6333	AA,AG,GG		1.8023,0.3858,1.3225	benign	1152/1244	97599674	172,12834	2203	4300	6503	SO:0001583	missense	253714	exon23			GAGGAAGGTTCTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3455C>T	6.37:g.97599674G>A	ENSP00000275053:p.Pro1152Leu	214.0	1.0	0.0046729		187.0	100.0	0.534759	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	9.389	1.074903	0.20227	0.003858	0.018023	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29655	3.93;1.56	5.44	3.59	0.41128	.	0.290094	0.38492	N	0.001666	T	0.09202	0.0227	L	0.56769	1.78	0.44966	D	0.997984	B;B	0.31548	0.328;0.082	B;B	0.27380	0.079;0.036	T	0.13255	-1.0516	10	0.14252	T	0.57	.	3.4047	0.07336	0.1576:0.1261:0.5698:0.1465	.	1112;1152	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1152;1112	ENSP00000275053:P1152L;ENSP00000358254:P1112L	ENSP00000275053:P1152L	P	-	2	0	MMS22L	97706395	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.175000	0.31944	0.606000	0.29965	0.650000	0.86243	CCT	G|0.987;A|0.013	0.013	strong		0.433	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
KIAA0020	9933	hgsc.bcm.edu	37	9	2812282	2812282	+	Missense_Mutation	SNP	A	A	T	rs142216382	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:2812282A>T	ENST00000397885.2	-	14	1556	c.1350T>A	c.(1348-1350)gaT>gaA	p.D450E		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	450	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		TATGTGCAGGATCTCTGGGGC	0.358																																					p.D450E		Atlas-SNP	.											.	KIAA0020	56	.	0			c.T1350A						PASS	.	A	GLU/ASP	1,4405	2.1+/-5.4	0,1,2202	215.0	193.0	200.0		1350	0.9	1.0	9	dbSNP_134	200	6,8594	5.0+/-18.6	0,6,4294	yes	missense	KIAA0020	NM_014878.4	45	0,7,6496	TT,TA,AA		0.0698,0.0227,0.0538	possibly-damaging	450/649	2812282	7,12999	2203	4300	6503	SO:0001583	missense	9933	exon14			TGCAGGATCTCTG	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1350T>A	9.37:g.2812282A>T	ENSP00000380982:p.Asp450Glu	214.0	0.0	0		229.0	115.0	0.502183	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	.	.	.	.	.	.	.	.	.	.	A	21.3	4.134740	0.77662	2.27E-4	6.98E-4	ENSG00000080608	ENST00000397885	T	0.52754	0.65	5.5	0.953	0.19590	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.134559	0.64402	D	0.000003	T	0.62208	0.2409	M	0.80746	2.51	0.54753	D	0.999989	D;D	0.54397	0.966;0.966	P;P	0.61874	0.861;0.895	T	0.59894	-0.7368	10	0.35671	T	0.21	-21.8403	10.3652	0.44019	0.613:0.0:0.387:0.0	.	310;450	B2RDG4;Q15397	.;K0020_HUMAN	E	450	ENSP00000380982:D450E	ENSP00000380982:D450E	D	-	3	2	KIAA0020	2802282	0.947000	0.32204	1.000000	0.80357	0.997000	0.91878	0.103000	0.15292	0.093000	0.17368	0.482000	0.46254	GAT	A|0.999;T|0.001	0.001	strong		0.358	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
KREMEN1	83999	hgsc.bcm.edu	37	22	29521353	29521353	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:29521353G>A	ENST00000407188.1	+	5	574	c.574G>A	c.(574-576)Ggg>Agg	p.G192R	KREMEN1_ENST00000327813.5_Missense_Mutation_p.G194R|KREMEN1_ENST00000400335.4_Missense_Mutation_p.G194R|KREMEN1_ENST00000400338.2_Missense_Mutation_p.G194R			Q96MU8	KREM1_HUMAN	kringle containing transmembrane protein 1	192	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558}.				cell communication (GO:0007154)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	20						CGTCTGCTTCGGGGATCACAC	0.552																																					p.G194R		Atlas-SNP	.											.	KREMEN1	46	.	0			c.G580A						PASS	.						165.0	170.0	168.0					22																	29521353		2146	4261	6407	SO:0001583	missense	83999	exon5			TGCTTCGGGGATC	AB059618	CCDS43000.1, CCDS13849.1, CCDS43000.2	22q12.1	2008-03-27	2002-11-13	2002-11-15	ENSG00000183762	ENSG00000183762			17550	protein-coding gene	gene with protein product		609898	"""kringle containing transmembrane protein"""	KREMEN		11267660	Standard	NM_001039570		Approved	KRM1	uc011akm.1	Q96MU8	OTTHUMG00000030987	ENST00000407188.1:c.574G>A	22.37:g.29521353G>A	ENSP00000385431:p.Gly192Arg	116.0	0.0	0		146.0	67.0	0.458904	NM_001039570	B0QY46|B0QY47|B1AJR5|Q5TIB9|Q6P3X6|Q9BY70|Q9UGS5|Q9UGU1	Missense_Mutation	SNP	ENST00000407188.1	37	CCDS43000.2	.	.	.	.	.	.	.	.	.	.	G	23.7	4.442407	0.83993	.	.	ENSG00000183762	ENST00000400335;ENST00000400338;ENST00000327813;ENST00000407188	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.74	4.73	0.59995	Carbohydrate-binding WSC (2);	0.000000	0.64402	D	0.000006	D	0.84906	0.5576	M	0.92970	3.365	0.58432	D	0.999999	D;D;B	0.89917	1.0;1.0;0.357	D;D;B	0.97110	1.0;1.0;0.072	D	0.88314	0.2958	10	0.87932	D	0	.	12.87	0.57960	0.079:0.0:0.921:0.0	.	192;194;194	Q96MU8;Q96MU8-2;Q96MU8-3	KREM1_HUMAN;.;.	R	194;194;194;192	ENSP00000383189:G194R;ENSP00000383192:G194R;ENSP00000331242:G194R;ENSP00000385431:G192R	ENSP00000331242:G194R	G	+	1	0	KREMEN1	27851353	1.000000	0.71417	0.997000	0.53966	0.790000	0.44656	9.146000	0.94640	1.579000	0.49836	0.650000	0.86243	GGG	.	.	none		0.552	KREMEN1-004	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320947.1		
SPRR3	6707	hgsc.bcm.edu	37	1	152975810	152975810	+	Missense_Mutation	SNP	G	G	A	rs72704847|rs527966074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152975810G>A	ENST00000295367.4	+	2	356	c.314G>A	c.(313-315)gGc>gAc	p.G105D	SPRR3_ENST00000331860.3_Missense_Mutation_p.G105D|SPRR3_ENST00000542696.1_Missense_Mutation_p.G97D	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	105	14 X 8 AA approximate tandem repeats.		Missing.		epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTGAGCCAGGCTACACCAAG	0.572													-|||	33	0.00658946	0.0008	0.0159	5008	,	,		20523	0.0		0.0209	False		,,,				2504	0.0				p.G105D		Atlas-SNP	.											.	SPRR3	45	.	0			c.G314A						PASS	.	G	ASP/GLY,ASP/GLY	27,4379	32.6+/-62.9	0,27,2176	99.0	80.0	87.0		314,314	1.0	0.0	1	dbSNP_131	87	142,8458	71.0+/-133.6	1,140,4159	yes	missense,missense	SPRR3	NM_001097589.1,NM_005416.2	94,94	1,167,6335	AA,AG,GG		1.6512,0.6128,1.2994	probably-damaging,probably-damaging	105/170,105/170	152975810	169,12837	2203	4300	6503	SO:0001583	missense	6707	exon2			AGCCAGGCTACAC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.314G>A	1.37:g.152975810G>A	ENSP00000295367:p.Gly105Asp	109.0	0.0	0		154.0	65.0	0.422078	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Missense_Mutation	SNP	ENST00000295367.4	37	CCDS1033.1	21	0.009615384615384616	0	0.0	8	0.022099447513812154	0	0.0	13	0.017150395778364115	G	10.84	1.465063	0.26335	0.006128	0.016512	ENSG00000163209	ENST00000331860;ENST00000443178;ENST00000295367;ENST00000542696	T;T;T;T	0.11385	2.78;2.78;2.78;2.78	5.31	0.967	0.19674	.	.	.	.	.	T	0.05823	0.0152	L	0.31664	0.95	0.09310	N	1	D;P	0.62365	0.991;0.606	D;B	0.65233	0.933;0.177	T	0.29912	-0.9996	9	0.12766	T	0.61	.	8.245	0.31682	0.0767:0.0:0.5068:0.4165	.	97;105	F5GZ12;Q9UBC9	.;SPRR3_HUMAN	D	105;105;105;97	ENSP00000330391:G105D;ENSP00000402016:G105D;ENSP00000295367:G105D;ENSP00000441477:G97D	ENSP00000295367:G105D	G	+	2	0	SPRR3	151242434	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.009000	0.12765	0.242000	0.21303	-0.321000	0.08615	GGC	G|0.988;A|0.012	0.012	strong		0.572	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
PCNX	22990	hgsc.bcm.edu	37	14	71500217	71500217	+	Silent	SNP	C	C	T	rs71425297	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:71500217C>T	ENST00000304743.2	+	17	4076	c.3630C>T	c.(3628-3630)taC>taT	p.Y1210Y	PCNX_ENST00000238570.5_Silent_p.Y1210Y|PCNX_ENST00000439984.3_Silent_p.Y1099Y	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1210						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CAGTGTCTTACCATCTCAGCC	0.338													C|||	18	0.00359425	0.0	0.0	5008	,	,		15944	0.0		0.0179	False		,,,				2504	0.0				p.Y1210Y		Atlas-SNP	.											.	PCNX	198	.	0			c.C3630T						PASS	.	C		10,4396	16.8+/-37.8	1,8,2194	153.0	138.0	143.0		3630	0.5	1.0	14	dbSNP_130	143	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	PCNX	NM_014982.2		1,95,6407	TT,TC,CC		1.0116,0.227,0.7458		1210/2342	71500217	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	22990	exon17			GTCTTACCATCTC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.3630C>T	14.37:g.71500217C>T		145.0	0.0	0		187.0	82.0	0.438503	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Silent	SNP	ENST00000304743.2	37	CCDS9806.1	14	0.00641025641025641	0	0.0	0	0.0	0	0.0	14	0.018469656992084433	C	8.208	0.799745	0.16397	0.00227	0.010116	ENSG00000100731	ENST00000554691	.	.	.	5.72	0.525	0.17072	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38286	-0.9668	4	.	.	.	.	9.1872	0.37178	0.0:0.3569:0.0:0.6431	.	.	.	.	I	269	.	.	T	+	2	0	PCNX	70569970	1.000000	0.71417	0.997000	0.53966	0.954000	0.61252	1.090000	0.30902	0.105000	0.17753	-0.300000	0.09419	ACC	C|0.992;T|0.008	0.008	strong		0.338	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319185	21319185	+	Silent	SNP	T	T	A	rs149832249	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:21319185T>A	ENST00000583088.1	+	3	1426	c.531T>A	c.(529-531)atT>atA	p.I177I	KCNJ12_ENST00000331718.5_Silent_p.I177I	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	177					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CCTTCATGATTGGTGCCATCA	0.637										Prostate(3;0.18)																											p.I177I		Atlas-SNP	.											.	.	.	.	0			c.T531A						PASS	.	T		2,4404		0,2,2201	87.0	81.0	83.0		531	-4.0	0.9	17	dbSNP_134	83	18,8582	5.7+/-21.5	0,18,4282	no	coding-synonymous	KCNJ12	NM_021012.4		0,20,6483	AA,AT,TT		0.2093,0.0454,0.1538		177/434	21319185	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	100134444	exon3			CATGATTGGTGCC	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.531T>A	17.37:g.21319185T>A		180.0	0.0	0		212.0	23.0	0.108491	NM_001194958	O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																			T|0.999;A|0.001	0.001	strong		0.637	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
PHF12	57649	hgsc.bcm.edu	37	17	27277200	27277200	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:27277200T>A	ENST00000332830.4	-	2	941	c.131A>T	c.(130-132)gAg>gTg	p.E44V	PHF12_ENST00000577226.1_Missense_Mutation_p.E44V|PHF12_ENST00000268756.3_Missense_Mutation_p.E44V	NM_001033561.1	NP_001028733.1			PHD finger protein 12											breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_cancers(5;1.95e-14)|all_epithelial(6;5e-18)|Lung NSC(42;0.01)		Epithelial(11;1.64e-05)|all cancers(11;7.47e-05)|BRCA - Breast invasive adenocarcinoma(11;9.79e-05)			GGGCTCCTTCTCAGGCTTCCG	0.622																																					p.E44V		Atlas-SNP	.											.	PHF12	69	.	0			c.A131T						PASS	.						69.0	66.0	67.0					17																	27277200		2203	4300	6503	SO:0001583	missense	57649	exon2			TCCTTCTCAGGCT	AB040956	CCDS11247.1, CCDS32598.1	17q11.2	2013-01-28			ENSG00000109118	ENSG00000109118		"""Zinc fingers, PHD-type"""	20816	protein-coding gene	gene with protein product						11390640	Standard	XM_005258015		Approved	PF1, KIAA1523	uc002hdg.1	Q96QT6	OTTHUMG00000132676	ENST00000332830.4:c.131A>T	17.37:g.27277200T>A	ENSP00000329933:p.Glu44Val	76.0	0.0	0		102.0	46.0	0.45098	NM_020889		Missense_Mutation	SNP	ENST00000332830.4	37	CCDS32598.1	.	.	.	.	.	.	.	.	.	.	T	11.87	1.766609	0.31228	.	.	ENSG00000109118	ENST00000332830;ENST00000378879;ENST00000268756	D;D;D	0.94576	-3.45;-3.46;-3.46	4.43	4.43	0.53597	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE/PHD-type (1);	0.187807	0.45867	D	0.000333	D	0.90383	0.6990	L	0.44542	1.39	0.58432	D	0.999998	B;B;B;B;B	0.31611	0.128;0.331;0.202;0.03;0.01	B;B;B;B;B	0.25884	0.026;0.064;0.058;0.012;0.012	D	0.89168	0.3535	10	0.40728	T	0.16	-1.4833	12.955	0.58421	0.0:0.0:0.0:1.0	.	26;44;44;44;44	B4DFE2;A8K5V5;Q96QT6-2;Q2TAK2;Q96QT6	.;.;.;.;PHF12_HUMAN	V	44	ENSP00000329933:E44V;ENSP00000368157:E44V;ENSP00000268756:E44V	ENSP00000268756:E44V	E	-	2	0	PHF12	24301326	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.609000	0.61148	1.978000	0.57642	0.533000	0.62120	GAG	.	.	none		0.622	PHF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255941.1	NM_020889	
BAG3	9531	hgsc.bcm.edu	37	10	121429394	121429394	+	Missense_Mutation	SNP	G	G	T	rs35434411	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:121429394G>T	ENST00000369085.3	+	2	518	c.212G>T	c.(211-213)cGg>cTg	p.R71L		NM_004281.3	NP_004272.2	O95817	BAG3_HUMAN	BCL2-associated athanogene 3	71			R -> Q (in dbSNP:rs35434411). {ECO:0000269|PubMed:21459883}.|R -> W (in CMD1HH). {ECO:0000269|PubMed:21353195}.		brain development (GO:0007420)|cellular response to mechanical stimulus (GO:0071260)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|negative regulation of apoptotic process (GO:0043066)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|spinal cord development (GO:0021510)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|Z disc (GO:0030018)				endometrium(3)|kidney(1)|large_intestine(3)|liver(2)|lung(5)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	20		Lung NSC(174;0.109)|all_lung(145;0.142)		all cancers(201;0.00187)|BRCA - Breast invasive adenocarcinoma(275;0.148)		GGCCCTTCCCGGGAGGGCTCT	0.577																																					p.R71L		Atlas-SNP	.											.	BAG3	42	.	0			c.G212T						PASS	.						83.0	87.0	85.0					10																	121429394		2203	4300	6503	SO:0001583	missense	9531	exon2			CTTCCCGGGAGGG	AF095193	CCDS7615.1	10q25.2-q26.2	2014-09-17			ENSG00000151929	ENSG00000151929			939	protein-coding gene	gene with protein product		603883				9873016, 18094623	Standard	XM_005270287		Approved		uc001lem.3	O95817	OTTHUMG00000019155	ENST00000369085.3:c.212G>T	10.37:g.121429394G>T	ENSP00000358081:p.Arg71Leu	80.0	0.0	0		115.0	66.0	0.573913	NM_004281	A8K5L8|Q3B763|Q9NT20|Q9P120	Missense_Mutation	SNP	ENST00000369085.3	37	CCDS7615.1	.	.	.	.	.	.	.	.	.	.	G	15.89	2.967365	0.53507	.	.	ENSG00000151929	ENST00000369085;ENST00000450186	T;T	0.75367	-0.93;-0.91	5.4	3.12	0.35913	.	0.417057	0.28219	N	0.016148	T	0.65101	0.2659	L	0.57536	1.79	0.09310	N	1	P;P	0.37276	0.589;0.589	B;B	0.29524	0.103;0.103	T	0.61657	-0.7018	10	0.59425	D	0.04	-12.1508	10.3289	0.43809	0.3064:0.0:0.6936:0.0	.	71;71	O95817;Q53GY1	BAG3_HUMAN;.	L	71;13	ENSP00000358081:R71L;ENSP00000410036:R13L	ENSP00000358081:R71L	R	+	2	0	BAG3	121419384	0.073000	0.21202	0.995000	0.50966	0.981000	0.71138	1.137000	0.31479	1.217000	0.43442	0.561000	0.74099	CGG	G|0.979;A|0.021	.	alt		0.577	BAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050662.1	NM_004281	
HELB	92797	hgsc.bcm.edu	37	12	66704098	66704098	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:66704098A>G	ENST00000247815.4	+	4	1449	c.1390A>G	c.(1390-1392)Atg>Gtg	p.M464V		NM_033647.3	NP_387467.2	Q8NG08	HELB_HUMAN	helicase (DNA) B	464					DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication, synthesis of RNA primer (GO:0006269)		ATP binding (GO:0005524)|ATP-dependent 5'-3' DNA helicase activity (GO:0043141)|single-stranded DNA-dependent ATP-dependent DNA helicase activity (GO:0017116)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)	40			GBM - Glioblastoma multiforme(2;0.000142)	GBM - Glioblastoma multiforme(28;0.0265)		TGCTTTGGAAATGATTTGCTC	0.428																																					p.M464V		Atlas-SNP	.											HELB,NS,carcinoma,-2,1	HELB	90	1	0			c.A1390G						PASS	.						90.0	90.0	90.0					12																	66704098		2203	4300	6503	SO:0001583	missense	92797	exon4			TTGGAAATGATTT	AF319995	CCDS8976.1	12q14.2	2009-01-15			ENSG00000127311	ENSG00000127311			17196	protein-coding gene	gene with protein product		614539				12181327	Standard	NM_033647		Approved		uc001sti.3	Q8NG08	OTTHUMG00000169006	ENST00000247815.4:c.1390A>G	12.37:g.66704098A>G	ENSP00000247815:p.Met464Val	70.0	0.0	0		93.0	45.0	0.483871	NM_033647	A8K4C9|Q4G0T2|Q9H7L5	Missense_Mutation	SNP	ENST00000247815.4	37	CCDS8976.1	.	.	.	.	.	.	.	.	.	.	A	14.62	2.589061	0.46110	.	.	ENSG00000127311	ENST00000247815	T	0.40476	1.03	6.04	6.04	0.98038	.	0.083556	0.85682	D	0.000000	T	0.34629	0.0904	L	0.28344	0.845	0.28916	N	0.892402	P	0.40144	0.704	B	0.42462	0.388	T	0.28964	-1.0027	9	.	.	.	-27.9413	13.0143	0.58749	0.8657:0.1343:0.0:0.0	.	464	Q8NG08	HELB_HUMAN	V	464	ENSP00000247815:M464V	.	M	+	1	0	HELB	64990365	1.000000	0.71417	0.993000	0.49108	0.790000	0.44656	5.571000	0.67404	2.317000	0.78254	0.459000	0.35465	ATG	.	.	none		0.428	HELB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401919.1		
TRAPPC10	7109	hgsc.bcm.edu	37	21	45502758	45502758	+	Missense_Mutation	SNP	G	G	A	rs367993178		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:45502758G>A	ENST00000291574.4	+	14	1988	c.1813G>A	c.(1813-1815)Gtt>Att	p.V605I		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	605					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)	p.V605F(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						CGTGGGCGGCGTTTTGTGCGT	0.483																																					p.V605I		Atlas-SNP	.											TRAPPC10,colon,carcinoma,0,1	TRAPPC10	109	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1813A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	194.0	163.0	173.0		1813	-3.0	0.0	21		173	1,8599	1.2+/-3.3	0,1,4299	no	missense	TRAPPC10	NM_003274.4	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	605/1260	45502758	1,13005	2203	4300	6503	SO:0001583	missense	7109	exon14			GGCGGCGTTTTGT	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.1813G>A	21.37:g.45502758G>A	ENSP00000291574:p.Val605Ile	184.0	0.0	0		177.0	72.0	0.40678	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Missense_Mutation	SNP	ENST00000291574.4	37	CCDS13704.1	.	.	.	.	.	.	.	.	.	.	G	6.340	0.430748	0.12045	0.0	1.16E-4	ENSG00000160218	ENST00000291574	T	0.40756	1.02	5.58	-2.99	0.05497	.	0.845087	0.10694	N	0.644857	T	0.22666	0.0547	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.04013	0.001	T	0.21965	-1.0230	10	0.23891	T	0.37	.	8.3648	0.32380	0.6995:0.0:0.1746:0.1259	.	605	P48553	TPC10_HUMAN	I	605	ENSP00000291574:V605I	ENSP00000291574:V605I	V	+	1	0	TRAPPC10	44327186	0.001000	0.12720	0.000000	0.03702	0.031000	0.12232	1.285000	0.33261	-0.457000	0.07033	-0.768000	0.03414	GTT	.	.	weak		0.483	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000544413.1_Silent_p.T515T|HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						scavenged	.	G		175,4231	113.3+/-151.4	4,167,2032	68.0	70.0	70.0		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1545G>A	12.37:g.121437114G>A		184.0	1.0	0.00543478		175.0	80.0	0.457143	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
OR5M3	219482	hgsc.bcm.edu	37	11	56237609	56237609	+	Missense_Mutation	SNP	A	A	G	rs200070203	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:56237609A>G	ENST00000312240.2	-	1	405	c.365T>C	c.(364-366)aTg>aCg	p.M122T		NM_001004742.2	NP_001004742.2	Q8NGP4	OR5M3_HUMAN	olfactory receptor, family 5, subfamily M, member 3	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(2)|endometrium(2)|large_intestine(7)|lung(15)|ovary(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	37	Esophageal squamous(21;0.00448)					CCCAATTGCCATGTATCTATC	0.383													a|||	26	0.00519169	0.0	0.0058	5008	,	,		20815	0.0		0.0169	False		,,,				2504	0.0051				p.M122T		Atlas-SNP	.											.	OR5M3	103	.	0			c.T365C						PASS	.						92.0	86.0	88.0					11																	56237609		2201	4280	6481	SO:0001583	missense	219482	exon1			ATTGCCATGTATC	AB065746	CCDS31532.1	11q11	2012-08-09			ENSG00000174937	ENSG00000174937		"""GPCR / Class A : Olfactory receptors"""	14806	protein-coding gene	gene with protein product							Standard	NM_001004742		Approved		uc010rjk.2	Q8NGP4	OTTHUMG00000166875	ENST00000312240.2:c.365T>C	11.37:g.56237609A>G	ENSP00000312208:p.Met122Thr	146.0	0.0	0		85.0	9.0	0.105882	NM_001004742	B2RNM7|Q6IEW4|Q96RC0	Missense_Mutation	SNP	ENST00000312240.2	37	CCDS31532.1	.	.	.	.	.	.	.	.	.	.	A	7.717	0.696444	0.15106	.	.	ENSG00000174937	ENST00000312240	T	0.01323	5.01	5.13	4.0	0.46444	GPCR, rhodopsin-like superfamily (1);	0.215738	0.32852	N	0.005578	T	0.01870	0.0059	L	0.43646	1.37	0.28098	N	0.931539	B	0.06786	0.001	B	0.10450	0.005	T	0.30995	-0.9959	10	0.56958	D	0.05	-7.874	9.9755	0.41781	0.9186:0.0:0.0814:0.0	.	122	Q8NGP4	OR5M3_HUMAN	T	122	ENSP00000312208:M122T	ENSP00000312208:M122T	M	-	2	0	OR5M3	55994185	0.001000	0.12720	0.975000	0.42487	0.077000	0.17291	1.595000	0.36708	0.794000	0.33899	-0.536000	0.04276	ATG	.	.	weak		0.383	OR5M3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391639.1	NM_001004742	
CATSPER3	347732	hgsc.bcm.edu	37	5	134332143	134332143	+	Missense_Mutation	SNP	G	G	A	rs114447625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:134332143G>A	ENST00000282611.6	+	3	519	c.433G>A	c.(433-435)Gct>Act	p.A145T		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	145					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCTGTATATCGCTGATGGCAT	0.547													G|||	43	0.00858626	0.0008	0.0101	5008	,	,		20081	0.0		0.0258	False		,,,				2504	0.0092				p.A145T		Atlas-SNP	.											.	CATSPER3	38	.	0			c.G433A						PASS	.	G	THR/ALA	20,4386	27.2+/-55.0	0,20,2183	135.0	117.0	123.0		433	4.1	0.0	5	dbSNP_132	123	264,8336	102.9+/-164.1	6,252,4042	yes	missense	CATSPER3	NM_178019.2	58	6,272,6225	AA,AG,GG		3.0698,0.4539,2.1836	probably-damaging	145/399	134332143	284,12722	2203	4300	6503	SO:0001583	missense	347732	exon3			TATATCGCTGATG	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.433G>A	5.37:g.134332143G>A	ENSP00000282611:p.Ala145Thr	107.0	0.0	0		113.0	54.0	0.477876	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	G	13.19	2.164341	0.38217	0.004539	0.030698	ENSG00000152705	ENST00000282611	D	0.98550	-4.99	4.14	4.14	0.48551	Ion transport (1);	0.256502	0.27886	N	0.017445	D	0.91676	0.7369	M	0.63843	1.955	0.09310	N	1	P	0.51537	0.946	B	0.41174	0.349	D	0.88435	0.3038	10	0.66056	D	0.02	-7.0009	12.2204	0.54431	0.0:0.0:1.0:0.0	.	145	Q86XQ3	CTSR3_HUMAN	T	145	ENSP00000282611:A145T	ENSP00000282611:A145T	A	+	1	0	CATSPER3	134360042	0.001000	0.12720	0.008000	0.14137	0.158000	0.22134	1.002000	0.29796	2.587000	0.87381	0.561000	0.74099	GCT	G|0.981;A|0.019	0.019	strong		0.547	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
USP7	7874	hgsc.bcm.edu	37	16	9057083	9057083	+	Silent	SNP	G	G	A	rs374020920	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:9057083G>A	ENST00000344836.4	-	1	258	c.60C>T	c.(58-60)ccC>ccT	p.P20P	RP11-77H9.8_ENST00000564485.1_lincRNA	NM_003470.2	NP_003461.2	Q93009	UBP7_HUMAN	ubiquitin specific peptidase 7 (herpes virus-associated)	20	Interaction with TSPYL5.				maintenance of DNA methylation (GO:0010216)|multicellular organismal development (GO:0007275)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|protein deubiquitination (GO:0016579)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|transcription-coupled nucleotide-excision repair (GO:0006283)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(13)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	48						CCATGTCCTCGGGCTCGCTCA	0.756													G|||	12	0.00239617	0.0	0.0014	5008	,	,		3991	0.0		0.004	False		,,,				2504	0.0072				p.P20P		Atlas-SNP	.											.	USP7	116	.	0			c.C60T						PASS	.	G		7,2427		0,7,1210	5.0	6.0	6.0		60	1.3	1.0	16		6	26,4274		0,26,2124	no	coding-synonymous	USP7	NM_003470.2		0,33,3334	AA,AG,GG		0.6047,0.2876,0.4901		20/1103	9057083	33,6701	1217	2150	3367	SO:0001819	synonymous_variant	7874	exon1			GTCCTCGGGCTCG	Z72499	CCDS32385.1, CCDS66941.1	16p13.3	2008-04-11	2005-08-08			ENSG00000187555		"""Ubiquitin-specific peptidases"""	12630	protein-coding gene	gene with protein product		602519	"""ubiquitin specific protease 7 (herpes virus-associated)"""	HAUSP		12838346, 9925944	Standard	NM_003470		Approved		uc002czl.2	Q93009		ENST00000344836.4:c.60C>T	16.37:g.9057083G>A		12.0	0.0	0		15.0	11.0	0.733333	NM_003470	A6NMY8|B7Z815|H0Y3G8	Silent	SNP	ENST00000344836.4	37	CCDS32385.1																																																																																			.	.	weak		0.756	USP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434268.2		
KIAA0922	23240	hgsc.bcm.edu	37	4	154388363	154388363	+	Splice_Site	SNP	C	C	T	rs78441178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:154388363C>T	ENST00000409663.3	+	2	177	c.125C>T	c.(124-126)gCg>gTg	p.A42V	KIAA0922_ENST00000440693.1_Splice_Site_p.A42V|KIAA0922_ENST00000409959.3_Splice_Site_p.A42V	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	42						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				GTTCCTGCAGCGATTGAGCCG	0.577													c|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.A42V		Atlas-SNP	.											.	KIAA0922	214	.	0			c.C125T						PASS	.		VAL/ALA,VAL/ALA	1,1383		0,1,691	198.0	177.0	183.0		125,125	4.2	1.0	4	dbSNP_131	183	15,3167		0,15,1576	yes	missense-near-splice,missense-near-splice	KIAA0922	NM_001131007.1,NM_015196.3	64,64	0,16,2267	TT,TC,CC		0.4714,0.0723,0.3504	benign,benign	42/1611,42/1610	154388363	16,4550	692	1591	2283	SO:0001630	splice_region_variant	23240	exon2			CTGCAGCGATTGA	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.125-1C>T	4.37:g.154388363C>T		210.0	0.0	0		218.0	104.0	0.477064	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Missense_Mutation	SNP	ENST00000409663.3	37	CCDS3783.2	.	.	.	.	.	.	.	.	.	.	c	15.31	2.796674	0.50208	7.23E-4	0.004714	ENSG00000121210	ENST00000409663;ENST00000440693;ENST00000409959	T;T;T	0.28255	1.89;1.62;1.9	5.23	4.19	0.49359	.	.	.	.	.	T	0.27798	0.0684	L	0.55481	1.735	0.27301	N	0.957589	B;B	0.32526	0.374;0.257	B;B	0.29942	0.109;0.051	T	0.08827	-1.0703	8	.	.	.	.	10.079	0.42377	0.0:0.8247:0.0:0.1753	.	42;42	A2VDJ0-5;A2VDJ0	.;T131L_HUMAN	V	42	ENSP00000386574:A42V;ENSP00000409663:A42V;ENSP00000386787:A42V	.	A	+	2	0	KIAA0922	154607813	0.991000	0.36638	1.000000	0.80357	0.988000	0.76386	1.197000	0.32211	2.442000	0.82660	0.550000	0.68814	GCG	.	.	weak		0.577	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	Missense_Mutation
EPS15	2060	hgsc.bcm.edu	37	1	51829575	51829575	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:51829575C>T	ENST00000371733.3	-	23	2418	c.2322G>A	c.(2320-2322)aaG>aaA	p.K774K	EPS15_ENST00000396122.4_Silent_p.K451K|EPS15_ENST00000371730.2_Silent_p.K640K	NM_001981.2	NP_001972.1	P42566	EPS15_HUMAN	epidermal growth factor receptor pathway substrate 15	774	15 X 3 AA repeats of D-P-F.|Pro-rich.				cell proliferation (GO:0008283)|clathrin coat assembly (GO:0048268)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|Golgi to endosome transport (GO:0006895)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|protein transport (GO:0015031)|vesicle organization (GO:0016050)	AP-2 adaptor complex (GO:0030122)|ciliary membrane (GO:0060170)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|polyubiquitin binding (GO:0031593)	p.0?(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(13)|prostate(2)|skin(1)|stomach(1)|urinary_tract(2)	35						GAGTTCCGATCTTTGGTGGCA	0.448			T	MLL	ALL																																p.K774K		Atlas-SNP	.		Dom	yes		1	1p32	2060	epidermal growth factor receptor pathway substrate 15 (AF1p)		L	EPS15,right_upper_lobe,carcinoma,0,1	EPS15	72	1	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.G2322A						PASS	.						215.0	194.0	201.0					1																	51829575		2203	4300	6503	SO:0001819	synonymous_variant	2060	exon23			TCCGATCTTTGGT	BC054006	CCDS557.1	1p32	2013-01-10			ENSG00000085832	ENSG00000085832		"""EF-hand domain containing"""	3419	protein-coding gene	gene with protein product		600051				8183552	Standard	NM_001159969		Approved	AF-1P, MLLT5	uc001csq.1	P42566	OTTHUMG00000008192	ENST00000371733.3:c.2322G>A	1.37:g.51829575C>T		255.0	1.0	0.00392157		236.0	106.0	0.449153	NM_001981	B2R8J7|D3DPJ2|Q5SRH4	Silent	SNP	ENST00000371733.3	37	CCDS557.1																																																																																			.	.	none		0.448	EPS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022422.1	NM_001981	
CSMD3	114788	hgsc.bcm.edu	37	8	113841971	113841971	+	Silent	SNP	A	A	G	rs142880481	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:113841971A>G	ENST00000297405.5	-	12	2047	c.1803T>C	c.(1801-1803)gaT>gaC	p.D601D	CSMD3_ENST00000455883.2_Silent_p.D497D|CSMD3_ENST00000343508.3_Silent_p.D561D|CSMD3_ENST00000352409.3_Silent_p.D601D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	601	CUB 3. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TTGTCAAGGTATCATAGCCAA	0.403										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	6	0.00119808	0.0	0.0014	5008	,	,		15247	0.0		0.005	False		,,,				2504	0.0				p.D601D		Atlas-SNP	.											.	CSMD3	2325	.	0			c.T1803C						PASS	.	A	,,	1,4405	2.1+/-5.4	0,1,2202	108.0	97.0	100.0		1491,1803,1683	-3.2	0.9	8	dbSNP_134	100	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	0,19,6484	GG,GA,AA		0.2093,0.0227,0.1461	,,	497/3539,601/3708,561/3668	113841971	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon12			CAAGGTATCATAG	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.1803T>C	8.37:g.113841971A>G		66.0	0.0	0		76.0	35.0	0.460526	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.999;G|0.001	0.001	strong		0.403	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
GPR75	10936	hgsc.bcm.edu	37	2	54081548	54081548	+	Missense_Mutation	SNP	C	C	T	rs34000641	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54081548C>T	ENST00000394705.2	-	2	616	c.346G>A	c.(346-348)Gct>Act	p.A116T	GPR75-ASB3_ENST00000352846.3_Intron|ASB3_ENST00000498475.2_Intron|ASB3_ENST00000406625.2_Intron	NM_006794.3	NP_006785.1	O95800	GPR75_HUMAN	G protein-coupled receptor 75	116	Phe-rich.		A -> T (in dbSNP:rs34000641). {ECO:0000269|PubMed:11466257}.		chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of neuron death (GO:1901214)	integral component of plasma membrane (GO:0005887)	C-C chemokine receptor activity (GO:0016493)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18			Lung(47;0.125)|LUSC - Lung squamous cell carcinoma(58;0.181)			AAGCAGAAAGCATCCGGGATA	0.517													C|||	82	0.0163738	0.0015	0.0331	5008	,	,		22590	0.0		0.0358	False		,,,				2504	0.0215				p.A116T		Atlas-SNP	.											.	GPR75	55	.	0			c.G346A						PASS	.	C	,THR/ALA	25,4381	30.8+/-60.4	0,25,2178	78.0	79.0	79.0		,346	1.9	0.0	2	dbSNP_126	79	288,8312	107.0+/-167.8	4,280,4016	yes	intron,missense	GPR75,GPR75-ASB3	NM_001164165.1,NM_006794.3	,58	4,305,6194	TT,TC,CC		3.3488,0.5674,2.4066	,benign	,116/541	54081548	313,12693	2203	4300	6503	SO:0001583	missense	10936	exon2			AGAAAGCATCCGG	AF101472	CCDS1849.1	2p16	2012-08-21			ENSG00000119737	ENSG00000119737		"""GPCR / Class A : Orphans"""	4526	protein-coding gene	gene with protein product		606704				10381362	Standard	NM_006794		Approved	WI-31133	uc002rxo.3	O95800	OTTHUMG00000129280	ENST00000394705.2:c.346G>A	2.37:g.54081548C>T	ENSP00000378195:p.Ala116Thr	110.0	0.0	0		154.0	77.0	0.5	NM_006794	B2RC02|Q6NWR2	Missense_Mutation	SNP	ENST00000394705.2	37	CCDS1849.1	41	0.018772893772893772	3	0.006097560975609756	13	0.03591160220994475	0	0.0	25	0.032981530343007916	C	11.13	1.546930	0.27652	0.005674	0.033488	ENSG00000119737	ENST00000394705	T	0.73789	-0.78	5.75	1.93	0.25924	GPCR, rhodopsin-like superfamily (1);	0.420647	0.28057	N	0.016775	T	0.23926	0.0579	.	.	.	0.26102	N	0.980802	B	0.02656	0.0	B	0.09377	0.004	T	0.10177	-1.0641	9	0.17369	T	0.5	0.8186	10.2743	0.43501	0.0:0.6632:0.0:0.3368	rs34000641	116	O95800	GPR75_HUMAN	T	116	ENSP00000378195:A116T	ENSP00000378195:A116T	A	-	1	0	GPR75	53935052	0.005000	0.15991	0.026000	0.17262	0.978000	0.69477	0.367000	0.20382	0.073000	0.16731	0.561000	0.74099	GCT	C|0.975;T|0.025	0.025	strong		0.517	GPR75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251403.2		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110447469	110447469	+	Missense_Mutation	SNP	G	G	A	rs376326343		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110447469G>A	ENST00000378402.5	+	29	3495	c.3391G>A	c.(3391-3393)Gtt>Att	p.V1131I		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	1131	IPT/TIG 4.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACATGCCCCCGTTGCTGTGTC	0.413										HNSCC(38;0.096)			G|||	1	0.000199681	0.0	0.0	5008	,	,		19159	0.0		0.001	False		,,,				2504	0.0				p.V1131I		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.G3391A						PASS	.	G	ILE/VAL	0,3716		0,0,1858	173.0	171.0	172.0		3391	4.3	0.0	8		172	3,8233		0,3,4115	no	missense	PKHD1L1	NM_177531.4	29	0,3,5973	AA,AG,GG		0.0364,0.0,0.0251	probably-damaging	1131/4244	110447469	3,11949	1858	4118	5976	SO:0001583	missense	93035	exon29			GCCCCCGTTGCTG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.3391G>A	8.37:g.110447469G>A	ENSP00000367655:p.Val1131Ile	142.0	0.0	0		173.0	80.0	0.462428	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	.	.	.	.	.	.	.	.	.	.	G	5.667	0.307710	0.10733	0.0	3.64E-4	ENSG00000205038	ENST00000378402	T	0.80033	-1.33	6.07	4.28	0.50868	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.146172	0.44902	N	0.000403	T	0.73133	0.3548	L	0.52759	1.655	0.22142	N	0.999333	B	0.12630	0.006	B	0.12156	0.007	T	0.59279	-0.7484	10	0.28530	T	0.3	.	9.7436	0.40433	0.1605:0.0:0.8395:0.0	.	1131	Q86WI1	PKHL1_HUMAN	I	1131	ENSP00000367655:V1131I	ENSP00000367655:V1131I	V	+	1	0	PKHD1L1	110516645	0.934000	0.31675	0.041000	0.18516	0.005000	0.04900	2.374000	0.44274	0.883000	0.36040	-0.150000	0.13652	GTT	.	.	weak		0.413	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
GNA13	10672	hgsc.bcm.edu	37	17	63010494	63010494	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:63010494G>A	ENST00000439174.2	-	4	1260	c.1015C>T	c.(1015-1017)Cag>Tag	p.Q339*	GNA13_ENST00000541118.1_Nonsense_Mutation_p.Q244*	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	339					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						AAGGGCTTCTGTTGCTGGTCC	0.473																																					p.Q339X		Atlas-SNP	.											.	GNA13	69	.	0			c.C1015T						PASS	.						133.0	107.0	116.0					17																	63010494		2203	4300	6503	SO:0001587	stop_gained	10672	exon4			GCTTCTGTTGCTG	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.1015C>T	17.37:g.63010494G>A	ENSP00000400717:p.Gln339*	309.0	0.0	0		147.0	127.0	0.863946	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Nonsense_Mutation	SNP	ENST00000439174.2	37	CCDS11661.1	.	.	.	.	.	.	.	.	.	.	G	36	5.876075	0.97055	.	.	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	.	.	.	5.93	5.93	0.95920	.	0.048927	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.41790	T	0.15	.	19.949	0.97192	0.0:0.0:1.0:0.0	.	.	.	.	X	339;244;314	.	ENSP00000239138:Q314X	Q	-	1	0	GNA13	60440956	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.664000	0.74437	2.826000	0.97356	0.655000	0.94253	CAG	.	.	none		0.473	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572	
MYO16	23026	hgsc.bcm.edu	37	13	109793246	109793246	+	Silent	SNP	G	G	C	rs80260507	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:109793246G>C	ENST00000357550.2	+	31	4661	c.4620G>C	c.(4618-4620)ccG>ccC	p.P1540P	MYO16_ENST00000356711.2_Silent_p.P1540P	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			CGCTGTCCCCGCAGTACTCCA	0.711													G|||	231	0.0461262	0.0272	0.0648	5008	,	,		5556	0.0		0.1083	False		,,,				2504	0.0419				p.P1562P		Atlas-SNP	.											MYO16,NS,carcinoma,0,2	MYO16	285	2	0			c.G4686C						PASS	.	G	,	129,4247		2,125,2061	16.0	20.0	18.0		4686,4620	-7.8	0.0	13	dbSNP_131	18	799,7773		42,715,3529	no	coding-synonymous,coding-synonymous	MYO16	NM_001198950.1,NM_015011.1	,	44,840,5590	CC,CG,GG		9.321,2.9479,7.1671	,	1562/1881,1540/1859	109793246	928,12020	2188	4286	6474	SO:0001819	synonymous_variant	23026	exon32			GTCCCCGCAGTAC		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.4620G>C	13.37:g.109793246G>C		40.0	0.0	0		33.0	18.0	0.545455	NM_001198950		Silent	SNP	ENST00000357550.2	37	CCDS32008.1																																																																																			G|0.933;C|0.067	0.067	strong		0.711	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
PNISR	25957	hgsc.bcm.edu	37	6	99848998	99848998	+	Silent	SNP	A	A	C	rs369239036		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:99848998A>C	ENST00000369239.5	-	12	2040	c.1836T>G	c.(1834-1836)ccT>ccG	p.P612P	PNISR_ENST00000438806.1_Silent_p.P612P	NM_032870.2	NP_116259.2	Q8TF01	PNISR_HUMAN	PNN-interacting serine/arginine-rich protein	612						cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24						TCTCTCGGGAAGGACTCCGAT	0.428																																					p.P612P		Atlas-SNP	.											.	PNISR	74	.	0			c.T1836G						PASS	.	A	,	0,4406		0,0,2203	110.0	98.0	102.0		1836,1836	4.2	1.0	6		102	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PNISR	NM_015491.1,NM_032870.2	,	0,2,6501	CC,CA,AA		0.0233,0.0,0.0154	,	612/806,612/806	99848998	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	25957	exon11			TCGGGAAGGACTC	AK027759	CCDS5043.1	6q16.3	2011-06-06	2011-06-06	2011-06-06	ENSG00000132424	ENSG00000132424			21222	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 111"", ""splicing factor, arginine/serine-rich 18"""	C6orf111, SFRS18		14578391	Standard	NM_032870		Approved	FLJ14752, bA98I9.2, DKFZp564B0769, SRrp130	uc021zdd.1	Q8TF01	OTTHUMG00000015262	ENST00000369239.5:c.1836T>G	6.37:g.99848998A>C		113.0	0.0	0		164.0	83.0	0.506098	NM_015491	A8K540|E1P5D2|Q5T064|Q5T065|Q6P2B4|Q6P2N4|Q6PJ93|Q6PK36|Q7Z640|Q8N2L1|Q8TF00|Q96K10|Q96SI3|Q96SM5|Q9P076|Q9P0C0|Q9Y4N3	Silent	SNP	ENST00000369239.5	37	CCDS5043.1																																																																																			.	.	weak		0.428	PNISR-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041598.1	NM_032870	
TMTC4	84899	hgsc.bcm.edu	37	13	101266580	101266580	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:101266580G>A	ENST00000376234.3	-	15	2073	c.1884C>T	c.(1882-1884)ctC>ctT	p.L628L	TMTC4_ENST00000328767.5_Silent_p.L517L|TMTC4_ENST00000342624.5_Silent_p.L647L	NM_001079669.1	NP_001073137.1	Q5T4D3	TMTC4_HUMAN	transmembrane and tetratricopeptide repeat containing 4	628						integral component of membrane (GO:0016021)				breast(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					CTGTATTGTCGAGGAGTATAA	0.463																																					p.L647L		Atlas-SNP	.											.	TMTC4	103	.	0			c.C1941T						PASS	.						166.0	143.0	151.0					13																	101266580		2203	4300	6503	SO:0001819	synonymous_variant	84899	exon16			ATTGTCGAGGAGT		CCDS9497.2, CCDS41904.1, CCDS66575.1	13q32.3	2013-01-10	2006-01-06		ENSG00000125247	ENSG00000125247		"""Tetratricopeptide (TTC) repeat domain containing"""	25904	protein-coding gene	gene with protein product							Standard	XM_005254082		Approved	FLJ14624, FLJ22153	uc001vot.3	Q5T4D3	OTTHUMG00000017289	ENST00000376234.3:c.1884C>T	13.37:g.101266580G>A		288.0	1.0	0.00347222		305.0	141.0	0.462295	NM_032813	A6NLI7|B7Z666|Q5T4D4|Q5T4D5|Q5T4D6|Q8WV63|Q96SU8	Silent	SNP	ENST00000376234.3	37	CCDS41904.1																																																																																			.	.	none		0.463	TMTC4-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045649.2	NM_032813	
N4BP2	55728	hgsc.bcm.edu	37	4	40122453	40122453	+	Missense_Mutation	SNP	C	C	T	rs78417585	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:40122453C>T	ENST00000261435.6	+	9	3138	c.2722C>T	c.(2722-2724)Ccc>Tcc	p.P908S		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	908					nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphorylation (GO:0016310)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ATP-dependent polydeoxyribonucleotide 5'-hydroxyl-kinase activity (GO:0046404)|endonuclease activity (GO:0004519)	p.P908S(1)		breast(4)|endometrium(3)|kidney(12)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)	60						TTTAAGTGAGCCCAACCTAGA	0.398													C|||	14	0.00279553	0.0	0.0058	5008	,	,		22081	0.0		0.0099	False		,,,				2504	0.0				p.P908S		Atlas-SNP	.											N4BP2,NS,carcinoma,0,1	N4BP2	166	1	1	Substitution - Missense(1)	pancreas(1)	c.C2722T						PASS	.	C	SER/PRO	13,4393	19.1+/-41.9	0,13,2190	50.0	48.0	49.0		2722	1.6	0.2	4	dbSNP_131	49	82,8518	46.3+/-105.2	1,80,4219	yes	missense	N4BP2	NM_018177.4	74	1,93,6409	TT,TC,CC		0.9535,0.2951,0.7304	benign	908/1771	40122453	95,12911	2203	4300	6503	SO:0001583	missense	55728	exon9			AGTGAGCCCAACC	AB037834	CCDS3457.1	4p14	2008-01-18			ENSG00000078177	ENSG00000078177			29851	protein-coding gene	gene with protein product	"""BCL-3 binding protein"""					10718198, 11717310	Standard	NM_018177		Approved	B3BP	uc003guy.4	Q86UW6	OTTHUMG00000128599	ENST00000261435.6:c.2722C>T	4.37:g.40122453C>T	ENSP00000261435:p.Pro908Ser	254.0	0.0	0		263.0	132.0	0.501901	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	C|C	0.446|0.446	-0.896370|-0.896370	0.02472|0.02472	0.002951|0.002951	0.009535|0.009535	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.14391	.|2.51	5.48|5.48	1.64|1.64	0.23874|0.23874	.|.	.|0.866997	.|0.10353	.|N	.|0.684921	T|T	0.06962|0.06962	0.0177|0.0177	L|L	0.45581|0.45581	1.43|1.43	0.09310|0.09310	N|N	1|1	.|B;B	.|0.14438	.|0.01;0.006	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.41928|0.41928	-0.9481|-0.9481	5|10	.|0.10636	.|T	.|0.68	-0.6285|-0.6285	4.8249|4.8249	0.13410|0.13410	0.0:0.4947:0.1599:0.3453|0.0:0.4947:0.1599:0.3453	.|.	.|908;908	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	V|S	554|908;828	.|ENSP00000261435:P908S	.|ENSP00000261435:P908S	A|P	+|+	2|1	0|0	N4BP2|N4BP2	39798848|39798848	0.000000|0.000000	0.05858|0.05858	0.230000|0.230000	0.23976|0.23976	0.286000|0.286000	0.27126|0.27126	0.125000|0.125000	0.15749|0.15749	0.803000|0.803000	0.34113|0.34113	0.655000|0.655000	0.94253|0.94253	GCC|CCC	C|0.992;T|0.008	0.008	strong		0.398	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
TBC1D2B	23102	hgsc.bcm.edu	37	15	78317679	78317679	+	Silent	SNP	C	C	T	rs148026593		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:78317679C>T	ENST00000300584.3	-	5	1007	c.1008G>A	c.(1006-1008)ccG>ccA	p.P336P	TBC1D2B_ENST00000409931.3_Silent_p.P336P	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	336							Rab GTPase activator activity (GO:0005097)	p.P336P(2)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						TTTCGGAGGCCGGCTTCCTGA	0.502													c|||	1	0.000199681	0.0	0.0	5008	,	,		13209	0.0		0.001	False		,,,				2504	0.0				p.P336P		Atlas-SNP	.											TBC1D2B_ENST00000300584,NS,carcinoma,0,2	TBC1D2B	104	2	2	Substitution - coding silent(2)	endometrium(2)	c.G1008A						PASS	.	T	,	0,4392		0,0,2196	110.0	99.0	103.0		1008,1008	-8.8	0.0	15	dbSNP_134	103	4,8582	3.7+/-12.6	0,4,4289	no	coding-synonymous,coding-synonymous	TBC1D2B	NM_015079.5,NM_144572.1	,	0,4,6485	TT,TC,CC		0.0466,0.0,0.0308	,	336/915,336/964	78317679	4,12974	2196	4293	6489	SO:0001819	synonymous_variant	23102	exon5			GGAGGCCGGCTTC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.1008G>A	15.37:g.78317679C>T		128.0	0.0	0		112.0	66.0	0.589286	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Silent	SNP	ENST00000300584.3	37	CCDS45314.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	5.989	0.366325	0.11352	0.0	4.66E-4	ENSG00000167202	ENST00000418039	.	.	.	5.61	-8.8	0.00817	.	.	.	.	.	T	0.15998	0.0385	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21177	-1.0253	4	.	.	.	.	3.3969	0.07310	0.0858:0.2262:0.2483:0.4397	.	.	.	.	Q	218	.	.	R	-	2	0	TBC1D2B	76104734	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.861000	0.00177	-1.282000	0.02396	-1.027000	0.02421	CGG	C|0.999;T|0.001	0.001	strong		0.502	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
ILF2	3608	hgsc.bcm.edu	37	1	153635022	153635022	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:153635022A>G	ENST00000361891.4	-	14	1148	c.1023T>C	c.(1021-1023)tcT>tcC	p.S341S	ILF2_ENST00000480213.1_5'UTR	NM_001267809.1|NM_004515.3	NP_001254738.1|NP_004506.2	Q12905	ILF2_HUMAN	interleukin enhancer binding factor 2	341	DZF. {ECO:0000255|PROSITE- ProRule:PRU01040}.				immune response (GO:0006955)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)|transferase activity (GO:0016740)			cervix(1)|kidney(1)|lung(4)|skin(1)	7	all_lung(78;1.84e-32)|Lung NSC(65;6.67e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TAGATATTTCAGAAGCAAGAT	0.393																																					p.S341S		Atlas-SNP	.											.	ILF2	25	.	0			c.T1023C						PASS	.						121.0	120.0	120.0					1																	153635022		2203	4300	6503	SO:0001819	synonymous_variant	3608	exon14			TATTTCAGAAGCA	U10323	CCDS1050.1, CCDS72919.1	1q21.3	2012-12-04	2012-12-04		ENSG00000143621	ENSG00000143621			6037	protein-coding gene	gene with protein product		603181	"""interleukin enhancer binding factor 2, 45kD"", ""interleukin enhancer binding factor 2, 45kDa"""			7519613	Standard	NM_004515		Approved	NF45	uc001fcr.4	Q12905	OTTHUMG00000037087	ENST00000361891.4:c.1023T>C	1.37:g.153635022A>G		87.0	0.0	0		152.0	71.0	0.467105	NM_004515	A6NDB0|B2R8G7|Q5SR10|Q5SR11|Q7L7R3|Q9BWD4|Q9P1N0	Silent	SNP	ENST00000361891.4	37	CCDS1050.1																																																																																			.	.	none		0.393	ILF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090040.1	NM_004515	
SLC43A2	124935	hgsc.bcm.edu	37	17	1479963	1479963	+	Silent	SNP	G	G	A	rs142934102		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1479963G>A	ENST00000301335.5	-	13	1564	c.1476C>T	c.(1474-1476)agC>agT	p.S492S	SLC43A2_ENST00000571650.1_Silent_p.S496S|SLC43A2_ENST00000382147.4_Silent_p.S496S|SLC43A2_ENST00000412517.3_Silent_p.S355S	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	492					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CGAAGAGCGCGCTGATCAGAG	0.637													G|||	1	0.000199681	0.0	0.0	5008	,	,		14140	0.0		0.001	False		,,,				2504	0.0				p.S492S		Atlas-SNP	.											.	SLC43A2	37	.	0			c.C1476T						PASS	.	G		0,4406		0,0,2203	46.0	44.0	45.0		1476	-10.0	0.1	17	dbSNP_134	45	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	SLC43A2	NM_152346.1		0,6,6497	AA,AG,GG		0.0698,0.0,0.0461		492/570	1479963	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon13			GAGCGCGCTGATC	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.1476C>T	17.37:g.1479963G>A		36.0	0.0	0		25.0	14.0	0.56	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			G|1.000;A|0.000	0.000	weak		0.637	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
MCM3AP	8888	hgsc.bcm.edu	37	21	47666744	47666744	+	Missense_Mutation	SNP	G	G	T	rs17183220	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47666744G>T	ENST00000397708.1	-	22	4601	c.4347C>A	c.(4345-4347)gaC>gaA	p.D1449E	MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP_ENST00000291688.1_Missense_Mutation_p.D1449E|MCM3AP-AS1_ENST00000590829.1_RNA|AP001469.7_ENST00000444966.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000414659.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1449			D -> E (in dbSNP:rs17183220). {ECO:0000269|Ref.2}.		DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					CTCCCAGGAGGTCCTTCTGTG	0.587													G|||	105	0.0209665	0.0045	0.0375	5008	,	,		19253	0.001		0.0666	False		,,,				2504	0.0051				p.D1449E		Atlas-SNP	.											.	MCM3AP	146	.	0			c.C4347A						PASS	.	G	GLU/ASP	72,4334	63.5+/-100.7	1,70,2132	109.0	105.0	107.0		4347	0.8	1.0	21	dbSNP_123	107	568,8032	152.7+/-207.2	13,542,3745	yes	missense	MCM3AP	NM_003906.3	45	14,612,5877	TT,TG,GG		6.6047,1.6341,4.9208	benign	1449/1981	47666744	640,12366	2203	4300	6503	SO:0001583	missense	8888	exon21			CAGGAGGTCCTTC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.4347C>A	21.37:g.47666744G>T	ENSP00000380820:p.Asp1449Glu	197.0	0.0	0		228.0	103.0	0.451754	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	81	0.03708791208791209	6	0.012195121951219513	19	0.052486187845303865	1	0.0017482517482517483	55	0.07255936675461741	G	9.045	0.990724	0.18966	0.016341	0.066047	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.03212	4.01;4.01	5.68	0.83	0.18854	.	0.187758	0.56097	N	0.000033	T	0.00178	0.0005	N	0.11927	0.2	0.37779	D	0.926956	B	0.09022	0.002	B	0.09377	0.004	T	0.55547	-0.8124	10	0.18710	T	0.47	-9.1595	0.8098	0.01091	0.217:0.2784:0.2857:0.2189	rs17183220;rs17183220	1449	O60318	MCM3A_HUMAN	E	1449	ENSP00000380820:D1449E;ENSP00000291688:D1449E	ENSP00000291688:D1449E	D	-	3	2	MCM3AP	46491172	0.997000	0.39634	0.998000	0.56505	0.655000	0.38815	0.417000	0.21214	0.080000	0.16959	0.650000	0.86243	GAC	G|0.957;T|0.043	0.043	strong		0.587	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
LMTK3	114783	hgsc.bcm.edu	37	19	49013809	49013809	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49013809G>T	ENST00000600059.1	-	2	344	c.117C>A	c.(115-117)taC>taA	p.Y39*	LMTK3_ENST00000270238.3_Nonsense_Mutation_p.Y68*|CTC-273B12.10_ENST00000598924.1_lincRNA			Q96Q04	LMTK3_HUMAN	lemur tyrosine kinase 3	39					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(9)|prostate(1)	16		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000114)|all cancers(93;0.000141)|Epithelial(262;0.00854)|GBM - Glioblastoma multiforme(486;0.0231)		GGACCACAGCGTAGGGAGGAG	0.627																																					p.Y68X		Atlas-SNP	.											LMTK3_ENST00000270238,caecum,carcinoma,-1,3	LMTK3	125	3	0			c.C204A						PASS	.						41.0	57.0	51.0					19																	49013809		2064	4205	6269	SO:0001587	stop_gained	114783	exon3			CACAGCGTAGGGA	AB067470	CCDS46136.1	19q13.33	2014-06-12				ENSG00000142235			19295	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 101"""						Standard	NM_001080434		Approved	KIAA1883, LMR3, TYKLM3, PPP1R101	uc002pjk.3	Q96Q04		ENST00000600059.1:c.117C>A	19.37:g.49013809G>T	ENSP00000472020:p.Tyr39*	123.0	0.0	0		152.0	67.0	0.440789	NM_001080434	Q4G0U1	Nonsense_Mutation	SNP	ENST00000600059.1	37		.	.	.	.	.	.	.	.	.	.	g	20.9	4.066456	0.76187	.	.	ENSG00000142235	ENST00000270238	.	.	.	3.95	-2.25	0.06888	.	0.000000	0.64402	U	0.000009	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05959	T	0.93	.	8.747	0.34591	0.6394:0.0:0.3606:0.0	.	.	.	.	X	68	.	ENSP00000270238:Y68X	Y	-	3	2	LMTK3	53705621	0.797000	0.28877	0.989000	0.46669	0.972000	0.66771	-0.150000	0.10189	-0.406000	0.07588	0.282000	0.19409	TAC	.	.	none		0.627	LMTK3-002	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000466137.1	NM_052895	
FAM66D	100132923	hgsc.bcm.edu	37	8	11990882	11990882	+	RNA	SNP	C	C	T	rs9720235	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:11990882C>T	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		GTGTCTGAAACGCCGTGGCAG	0.498													t|||	2043	0.407947	0.2897	0.5187	5008	,	,		24947	0.4077		0.4513	False		,,,				2504	0.4448				p.V213I		Atlas-SNP	.											.	.	.	.	0			c.G637A						PASS	.																																					392197	exon1			CTGAAACGCCGTG			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990882C>T		0.0	0.0	.		4.0	4.0	1	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				C|0.499;T|0.501	0.501	strong		0.498	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
OR10G7	390265	hgsc.bcm.edu	37	11	123908971	123908971	+	Silent	SNP	C	C	T	rs142080661	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:123908971C>T	ENST00000330487.5	-	1	746	c.738G>A	c.(736-738)gtG>gtA	p.V246V		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		AGCAAAGGACCACGATACAGT	0.567													C|||	12	0.00239617	0.0	0.0	5008	,	,		18724	0.0		0.0	False		,,,				2504	0.0123				p.V246V		Atlas-SNP	.											.	OR10G7	103	.	0			c.G738A						PASS	.	C		0,4400		0,0,2200	110.0	95.0	100.0		738	2.4	1.0	11	dbSNP_134	100	8,8590	6.4+/-24.3	0,8,4291	no	coding-synonymous	OR10G7	NM_001004463.1		0,8,6491	TT,TC,CC		0.093,0.0,0.0615		246/312	123908971	8,12990	2200	4299	6499	SO:0001819	synonymous_variant	390265	exon1			AAGGACCACGATA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.738G>A	11.37:g.123908971C>T		186.0	0.0	0		196.0	103.0	0.52551	NM_001004463	Q6IFE8	Silent	SNP	ENST00000330487.5	37	CCDS31705.1																																																																																			C|1.000;T|0.000	0.000	strong		0.567	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
CARD14	79092	hgsc.bcm.edu	37	17	78177680	78177680	+	Missense_Mutation	SNP	G	G	A	rs143600438		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:78177680G>A	ENST00000573882.1	+	18	2815	c.2279G>A	c.(2278-2280)cGc>cAc	p.R760H	CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.R760H|RP11-334C17.5_ENST00000576824.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	760					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ACCGTGACCCGCAAGGTGAGG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		16335	0.001		0.0	False		,,,				2504	0.0				p.R760H		Atlas-SNP	.											.	CARD14	98	.	0			c.G2279A						PASS	.	G	HIS/ARG	2,4390		0,2,2194	22.0	21.0	21.0		2279	4.1	1.0	17	dbSNP_134	21	0,8592		0,0,4296	no	missense	CARD14	NM_024110.3	29	0,2,6490	AA,AG,GG		0.0,0.0455,0.0154	probably-damaging	760/1005	78177680	2,12982	2196	4296	6492	SO:0001583	missense	79092	exon16			TGACCCGCAAGGT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2279G>A	17.37:g.78177680G>A	ENSP00000458715:p.Arg760His	298.0	0.0	0		319.0	148.0	0.46395	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	.	.	.	.	.	.	.	.	.	.	G	15.52	2.859093	0.51376	4.55E-4	0.0	ENSG00000141527	ENST00000344227	T	0.05855	3.38	4.12	4.12	0.48240	.	6.592470	0.00481	U	0.000120	T	0.18635	0.0447	M	0.76328	2.33	0.80722	D	1	P	0.42584	0.784	B	0.44224	0.444	T	0.16482	-1.0401	10	0.44086	T	0.13	-13.3243	15.1676	0.72840	0.0:0.0:1.0:0.0	.	760	Q9BXL6	CAR14_HUMAN	H	760	ENSP00000344549:R760H	ENSP00000344549:R760H	R	+	2	0	CARD14	75792275	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	3.682000	0.54656	1.865000	0.54081	0.485000	0.47835	CGC	G|1.000;A|0.000	0.000	weak		0.672	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
MUC21	394263	hgsc.bcm.edu	37	6	30954327	30954327	+	Silent	SNP	C	C	T	rs149194643	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:30954327C>T	ENST00000376296.3	+	2	616	c.375C>T	c.(373-375)tcC>tcT	p.S125S	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	125	28 X 15 AA approximate tandem repeats.|Ser-rich.				cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACTCTGAGTCCAGCACACCCT	0.592																																					p.S125S		Atlas-SNP	.											.	MUC21	98	.	0			c.C375T						PASS	.						174.0	162.0	166.0					6																	30954327		2203	4299	6502	SO:0001819	synonymous_variant	394263	exon2			TGAGTCCAGCACA	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.375C>T	6.37:g.30954327C>T		94.0	0.0	0		151.0	12.0	0.0794702	NM_001010909	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Silent	SNP	ENST00000376296.3	37	CCDS34388.1																																																																																			C|0.989;T|0.011	0.011	strong		0.592	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000128579.3	NM_001010909	
GLI2	2736	hgsc.bcm.edu	37	2	121742124	121742124	+	Silent	SNP	G	G	A	rs61732852	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:121742124G>A	ENST00000452319.1	+	12	1821	c.1761G>A	c.(1759-1761)acG>acA	p.T587T	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000361492.4_Silent_p.T587T|GLI2_ENST00000314490.11_Silent_p.T259T					GLI family zinc finger 2											NS(1)|breast(3)|central_nervous_system(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|lung(24)|ovary(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	64	Renal(3;0.0496)	Prostate(154;0.0623)				ATGTGAAAACGGTCCACGGCC	0.597													G|||	22	0.00439297	0.0	0.0043	5008	,	,		19759	0.0		0.0139	False		,,,				2504	0.0051				p.T587T		Atlas-SNP	.											.	GLI2	187	.	0			c.G1761A						PASS	.	G		13,4393	19.1+/-41.9	0,13,2190	154.0	147.0	149.0		1761	-9.0	0.3	2	dbSNP_129	149	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	GLI2	NM_005270.4		0,130,6373	AA,AG,GG		1.3605,0.2951,0.9995		587/1587	121742124	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	2736	exon11			GAAAACGGTCCAC		CCDS33283.1	2q14	2013-01-25	2009-03-05		ENSG00000074047	ENSG00000074047		"""Zinc fingers, C2H2-type"""	4318	protein-coding gene	gene with protein product	"""tax-responsive element-2 holding protein"", ""tax helper protein 1"", ""tax helper protein 2"""	165230	"""GLI-Kruppel family member GLI2"", ""glioma-associated oncogene family zinc finger 2"""			2850480, 9557682	Standard	NM_005270		Approved	THP2, HPE9, THP1	uc010flp.3	P10070	OTTHUMG00000153741	ENST00000452319.1:c.1761G>A	2.37:g.121742124G>A		179.0	0.0	0		199.0	82.0	0.41206	NM_005270		Silent	SNP	ENST00000452319.1	37	CCDS33283.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
PLCB1	23236	hgsc.bcm.edu	37	20	8703060	8703060	+	Missense_Mutation	SNP	A	A	T	rs138851178	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:8703060A>T	ENST00000338037.6	+	15	1600	c.1573A>T	c.(1573-1575)Atg>Ttg	p.M525L	PLCB1_ENST00000378641.3_Missense_Mutation_p.M525L|PLCB1_ENST00000494924.1_3'UTR|PLCB1_ENST00000378637.2_Missense_Mutation_p.M525L	NM_015192.2	NP_056007.1	Q9NQ66	PLCB1_HUMAN	phospholipase C, beta 1 (phosphoinositide-specific)	525					activation of meiosis involved in egg activation (GO:0060466)|cerebral cortex development (GO:0021987)|fat cell differentiation (GO:0045444)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G2/M transition of mitotic cell cycle (GO:0000086)|glutamate receptor signaling pathway (GO:0007215)|inositol phosphate metabolic process (GO:0043647)|insulin-like growth factor receptor signaling pathway (GO:0048009)|interleukin-1-mediated signaling pathway (GO:0070498)|interleukin-12-mediated signaling pathway (GO:0035722)|interleukin-15-mediated signaling pathway (GO:0035723)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|memory (GO:0007613)|negative regulation of monocyte extravasation (GO:2000438)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphatidylinositol metabolic process (GO:0046488)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of CD24 biosynthetic process (GO:2000560)|positive regulation of developmental growth (GO:0048639)|positive regulation of embryonic development (GO:0040019)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of GTPase activity (GO:0043547)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of JNK cascade (GO:0046330)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of fertilization (GO:0080154)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|phosphatidylinositol phospholipase C activity (GO:0004435)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein homodimerization activity (GO:0042803)|signal transducer activity (GO:0004871)			NS(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(11)|liver(2)|lung(41)|ovary(4)|prostate(3)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	95						AAAATCTTCAATGGATGAGGT	0.448																																					p.E525X		Atlas-SNP	.											.	PLCB1	394	.	0			c.G1573T						PASS	.						201.0	160.0	174.0					20																	8703060		2203	4300	6503	SO:0001583	missense	23236	exon15			TCTTCAATGGATG	AB011153	CCDS13102.1, CCDS13103.1	20p12	2008-03-18			ENSG00000182621	ENSG00000182621	3.1.4.11		15917	protein-coding gene	gene with protein product		607120				10760467, 11118617	Standard	NM_015192		Approved	KIAA0581, PLC-I, PLC154	uc002wnb.4	Q9NQ66	OTTHUMG00000031849	ENST00000338037.6:c.1573A>T	20.37:g.8703060A>T	ENSP00000338185:p.Met525Leu	97.0	0.0	0		76.0	33.0	0.434211	NM_015192	D3DW12|D3DW13|O60325|Q17RQ6|Q5TFF7|Q5TGC9|Q8IV93|Q9BQW2|Q9H4H2|Q9H8H5|Q9NQ65|Q9NQH9|Q9NTH4|Q9UJP6|Q9UM26	Nonsense_Mutation	SNP	ENST00000338037.6	37	CCDS13102.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.190382	0.58017	.	.	ENSG00000182621	ENST00000378641;ENST00000338037;ENST00000378637;ENST00000441163;ENST00000535719	T;T;T	0.49432	0.78;0.78;0.78	5.96	5.96	0.96718	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (1);	0.157283	0.37906	U	0.001882	T	0.42245	0.1194	L	0.44542	1.39	0.52501	D	0.999952	B;B	0.13145	0.0;0.007	B;B	0.16289	0.001;0.015	T	0.19516	-1.0303	10	0.28530	T	0.3	.	15.6296	0.76893	1.0:0.0:0.0:0.0	.	525;525	Q9NQ66;Q9NQ66-2	PLCB1_HUMAN;.	L	525;525;525;445;445	ENSP00000367908:M525L;ENSP00000338185:M525L;ENSP00000367904:M525L	ENSP00000338185:M525L	M	+	1	0	PLCB1	8651060	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.524000	0.81866	2.285000	0.76669	0.533000	0.62120	ATG	A|1.000;G|0.000	.	alt		0.448	PLCB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077938.3		
ERBB2	2064	hgsc.bcm.edu	37	17	37879588	37879588	+	Missense_Mutation	SNP	A	A	G	rs1136201	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:37879588A>G	ENST00000269571.5	+	17	2122	c.1963A>G	c.(1963-1965)Atc>Gtc	p.I655V	ERBB2_ENST00000541774.1_Missense_Mutation_p.I640V|ERBB2_ENST00000584601.1_Missense_Mutation_p.I625V|ERBB2_ENST00000540147.1_Missense_Mutation_p.I625V|ERBB2_ENST00000445658.2_Missense_Mutation_p.I379V|ERBB2_ENST00000406381.2_Missense_Mutation_p.I625V|ERBB2_ENST00000584450.1_Missense_Mutation_p.I655V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	655			I -> V (in allele B2 and allele B3; dbSNP:rs1136201). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8095488, ECO:0000269|Ref.3}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GACGTCCATCATCTCTGCGGT	0.612		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			A|||	608	0.121406	0.0098	0.1369	5008	,	,		13960	0.124		0.2455	False		,,,				2504	0.1309				p.I655V		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.A1963G	GRCh37	CM004332	ERBB2	M	rs1136201	PASS	.	A	VAL/ILE,VAL/ILE	212,4194	132.1+/-168.6	5,202,1996	113.0	103.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1873,1963	5.0	1.0	17	dbSNP_86	106	1980,6620	346.8+/-326.3	223,1534,2543	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	29,29	228,1736,4539	GG,GA,AA		23.0233,4.8116,16.8538	benign,benign	625/1226,655/1256	37879588	2192,10814	2203	4300	6503	SO:0001583	missense	2064	exon17			TCCATCATCTCTG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1963A>G	17.37:g.37879588A>G	ENSP00000269571:p.Ile655Val	181.0	0.0	0		204.0	106.0	0.519608	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	339	0.15521978021978022	5	0.01016260162601626	58	0.16022099447513813	83	0.1451048951048951	193	0.2546174142480211	A	13.67	2.306999	0.40795	0.048116	0.230233	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76316	-1.01;-1.01;-0.99;-1.01;-1.01	4.97	4.97	0.65823	Cytochrome c1, transmembrane anchor, C-terminal (1);	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.09310	P	1.0	B;P;B	0.39576	0.406;0.679;0.406	B;B;B	0.37650	0.108;0.255;0.108	T	0.05920	-1.0856	8	0.22706	T	0.39	.	8.987	0.35999	0.9164:0.0:0.0836:0.0	rs1136201;rs1801200;rs2006406;rs2230699;rs17606815;rs59955961;rs1801200	379;640;655	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	625;640;379;655;625	ENSP00000385185:I625V;ENSP00000446466:I640V;ENSP00000404047:I379V;ENSP00000269571:I655V;ENSP00000443562:I625V	ENSP00000269571:I655V	I	+	1	0	ERBB2	35133114	1.000000	0.71417	0.995000	0.50966	0.892000	0.51952	4.008000	0.57103	1.880000	0.54463	0.459000	0.35465	ATC	A|0.845;G|0.155;N|0.000;T|0.000	0.155	strong		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
OR10G3	26533	hgsc.bcm.edu	37	14	22038731	22038731	+	Missense_Mutation	SNP	C	C	G	rs12886819	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:22038731C>G	ENST00000303532.1	-	1	144	c.145G>C	c.(145-147)Gtc>Ctc	p.V49L		NM_001005465.1	NP_001005465.1	Q8NGC4	O10G3_HUMAN	olfactory receptor, family 10, subfamily G, member 3	49						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)	15	all_cancers(95;0.000987)			GBM - Glioblastoma multiforme(265;0.0139)		TCTGCCCAGACAGTGATTAAA	0.463													C|||	42	0.00838658	0.0023	0.0101	5008	,	,		21952	0.0		0.0298	False		,,,				2504	0.002				p.V49L		Atlas-SNP	.											.	OR10G3	40	.	0			c.G145C						PASS	.	C	LEU/VAL	28,4378	34.3+/-65.2	0,28,2175	75.0	73.0	74.0		145	3.4	1.0	14	dbSNP_121	74	231,8369	95.2+/-157.0	2,227,4071	yes	missense	OR10G3	NM_001005465.1	32	2,255,6246	GG,GC,CC		2.686,0.6355,1.9914	benign	49/314	22038731	259,12747	2203	4300	6503	SO:0001583	missense	26533	exon1			CCCAGACAGTGAT		CCDS32046.1	14q11.2	2013-09-24			ENSG00000169208	ENSG00000169208		"""GPCR / Class A : Olfactory receptors"""	8171	protein-coding gene	gene with protein product						8188290	Standard	NM_001005465		Approved		uc010tmb.2	Q8NGC4	OTTHUMG00000168886	ENST00000303532.1:c.145G>C	14.37:g.22038731C>G	ENSP00000302437:p.Val49Leu	69.0	0.0	0		83.0	43.0	0.518072	NM_001005465	Q6IET7|Q96R77	Missense_Mutation	SNP	ENST00000303532.1	37	CCDS32046.1	27	0.012362637362637362	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	21	0.027704485488126648	C	11.04	1.521943	0.27211	0.006355	0.02686	ENSG00000169208	ENST00000303532	T	0.03124	4.04	4.33	3.44	0.39384	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42053	D	0.000763	T	0.02342	0.0072	M	0.84846	2.72	0.23070	N	0.99835	B	0.22346	0.068	B	0.27380	0.079	T	0.16719	-1.0393	10	0.87932	D	0	-33.6789	7.2391	0.26086	0.0:0.7924:0.0:0.2076	rs12886819;rs12886819	49	Q8NGC4	O10G3_HUMAN	L	49	ENSP00000302437:V49L	ENSP00000302437:V49L	V	-	1	0	OR10G3	21108571	0.014000	0.17966	0.997000	0.53966	0.860000	0.49131	0.027000	0.13621	0.943000	0.37553	-0.224000	0.12420	GTC	C|0.975;G|0.025	0.025	strong		0.463	OR10G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401521.1		
MNS1	55329	hgsc.bcm.edu	37	15	56736681	56736681	+	Missense_Mutation	SNP	A	A	G	rs35775595	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:56736681A>G	ENST00000260453.3	-	5	811	c.647T>C	c.(646-648)aTt>aCt	p.I216T	TEX9_ENST00000352903.2_Intron|TEX9_ENST00000537232.1_Intron	NM_018365.2	NP_060835.1	Q8NEH6	MNS1_HUMAN	meiosis-specific nuclear structural 1	216	Glu-rich.		I -> T (in dbSNP:rs35775595).		cilium organization (GO:0044782)|left/right axis specification (GO:0070986)|meiotic nuclear division (GO:0007126)	axoneme (GO:0005930)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)|sperm flagellum (GO:0036126)	identical protein binding (GO:0042802)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(4)|ovary(2)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	20				all cancers(107;0.0196)|GBM - Glioblastoma multiforme(80;0.101)		AATTTCATCAATCATGAGTTT	0.328													A|||	30	0.00599042	0.0008	0.013	5008	,	,		18617	0.0		0.0169	False		,,,				2504	0.0031				p.I216T		Atlas-SNP	.											.	MNS1	39	.	0			c.T647C						PASS	.	A	THR/ILE,	23,4361	29.9+/-59.1	0,23,2169	114.0	107.0	110.0		647,	5.4	1.0	15	dbSNP_126	110	234,8348	95.6+/-157.4	0,234,4057	yes	missense,intron	MNS1,TEX9	NM_018365.2,NM_198524.1	89,	0,257,6226	GG,GA,AA		2.7266,0.5246,1.9821	possibly-damaging,	216/496,	56736681	257,12709	2192	4291	6483	SO:0001583	missense	55329	exon5			TCATCAATCATGA	AK002084	CCDS10158.1	15q21.3	2013-01-16			ENSG00000138587	ENSG00000138587			29636	protein-coding gene	gene with protein product	"""spermatogenesis associated 40"""	610766				7625268, 8032679	Standard	NM_018365		Approved	FLJ11222, SPATA40	uc002adr.2	Q8NEH6	OTTHUMG00000132034	ENST00000260453.3:c.647T>C	15.37:g.56736681A>G	ENSP00000260453:p.Ile216Thr	134.0	0.0	0		168.0	74.0	0.440476	NM_018365	Q8IYT6|Q9NUP4	Missense_Mutation	SNP	ENST00000260453.3	37	CCDS10158.1	20	0.009157509157509158	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	15	0.01978891820580475	A	24.5	4.537928	0.85917	0.005246	0.027266	ENSG00000138587	ENST00000260453	T	0.11385	2.78	5.43	5.43	0.79202	.	0.154112	0.56097	D	0.000023	T	0.10594	0.0259	M	0.81497	2.545	0.50171	D	0.99985	D	0.52996	0.957	P	0.54431	0.752	T	0.00583	-1.1659	10	0.42905	T	0.14	-5.7208	14.6574	0.68844	1.0:0.0:0.0:0.0	rs35775595	216	Q8NEH6	MNS1_HUMAN	T	216	ENSP00000260453:I216T	ENSP00000260453:I216T	I	-	2	0	MNS1	54523973	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.070000	0.93974	2.053000	0.61076	0.523000	0.50628	ATT	A|0.984;G|0.016	0.016	strong		0.328	MNS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255047.2	NM_018365	
RBM43	375287	hgsc.bcm.edu	37	2	152112161	152112161	+	Missense_Mutation	SNP	C	C	G	rs147060862	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:152112161C>G	ENST00000331426.5	-	2	251	c.100G>C	c.(100-102)Gta>Cta	p.V34L		NM_198557.2	NP_940959.1	Q6ZSC3	RBM43_HUMAN	RNA binding motif protein 43	34	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.						nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(2)|large_intestine(3)|lung(2)|ovary(1)	8				BRCA - Breast invasive adenocarcinoma(221;0.131)		TTCACTAATACGGCCAATAAT	0.408													C|||	72	0.014377	0.0151	0.0245	5008	,	,		13812	0.001		0.0288	False		,,,				2504	0.0051				p.V34L		Atlas-SNP	.											RBM43,colon,carcinoma,0,1	RBM43	35	1	0			c.G100C						PASS	.	C	LEU/VAL	60,4346	56.8+/-93.2	0,60,2143	131.0	130.0	130.0		100	-1.3	0.0	2	dbSNP_134	130	251,8349	99.5+/-161.0	5,241,4054	yes	missense	RBM43	NM_198557.2	32	5,301,6197	GG,GC,CC		2.9186,1.3618,2.3912	benign	34/358	152112161	311,12695	2203	4300	6503	SO:0001583	missense	375287	exon2			CTAATACGGCCAA	AK127552	CCDS2191.1	2q23.3	2007-01-30	2007-01-30	2007-01-30	ENSG00000184898	ENSG00000184898		"""RNA binding motif (RRM) containing"""	24790	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 38"""	C2orf38			Standard	NM_198557		Approved	FLJ45645	uc002txh.3	Q6ZSC3	OTTHUMG00000131866	ENST00000331426.5:c.100G>C	2.37:g.152112161C>G	ENSP00000331211:p.Val34Leu	188.0	0.0	0		213.0	111.0	0.521127	NM_198557	B2RMT5	Missense_Mutation	SNP	ENST00000331426.5	37	CCDS2191.1	34	0.015567765567765568	6	0.012195121951219513	9	0.024861878453038673	1	0.0017482517482517483	18	0.023746701846965697	C	2.210	-0.380974	0.05000	0.013618	0.029186	ENSG00000184898	ENST00000331426	T	0.42131	0.98	4.25	-1.31	0.09230	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.899723	0.09370	N	0.811424	T	0.05593	0.0147	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23119	-1.0197	10	0.09843	T	0.71	-0.7126	4.1354	0.10169	0.0:0.414:0.209:0.377	.	34	Q6ZSC3	RBM43_HUMAN	L	34	ENSP00000331211:V34L	ENSP00000331211:V34L	V	-	1	0	RBM43	151820407	0.000000	0.05858	0.025000	0.17156	0.004000	0.04260	0.426000	0.21363	-0.071000	0.12886	-2.222000	0.00295	GTA	C|0.974;G|0.026	0.026	strong		0.408	RBM43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254816.2	NM_198557	
SLC27A5	10998	hgsc.bcm.edu	37	19	59012675	59012675	+	Missense_Mutation	SNP	C	C	T	rs142672241	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:59012675C>T	ENST00000263093.2	-	4	1269	c.1160G>A	c.(1159-1161)cGg>cAg	p.R387Q	SLC27A5_ENST00000594786.1_5'Flank|SLC27A5_ENST00000599700.1_5'Flank|SLC27A5_ENST00000601355.1_Missense_Mutation_p.R303Q	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	387					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		ACACAAGTACCGCAGGAGCTC	0.527													C|||	5	0.000998403	0.0	0.0029	5008	,	,		16011	0.0		0.003	False		,,,				2504	0.0				p.R387Q		Atlas-SNP	.											SLC27A5,NS,carcinoma,0,1	SLC27A5	58	1	0			c.G1160A						scavenged	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	128.0	131.0	130.0		1160	3.8	1.0	19	dbSNP_134	130	25,8575	18.5+/-59.3	0,25,4275	yes	missense	SLC27A5	NM_012254.2	43	0,27,6476	TT,TC,CC		0.2907,0.0454,0.2076	probably-damaging	387/691	59012675	27,12979	2203	4300	6503	SO:0001583	missense	10998	exon4			AAGTACCGCAGGA	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.1160G>A	19.37:g.59012675C>T	ENSP00000263093:p.Arg387Gln	37.0	0.0	0		31.0	2.0	0.0645161	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	25.5	4.648722	0.87958	4.54E-4	0.002907	ENSG00000083807	ENST00000263093	T	0.44482	0.92	4.9	3.85	0.44370	AMP-dependent synthetase/ligase (1);	0.135756	0.49305	N	0.000150	T	0.58119	0.2100	M	0.91038	3.17	0.35105	D	0.765588	D	0.76494	0.999	P	0.62184	0.899	T	0.76852	-0.2806	10	0.87932	D	0	-32.5211	9.865	0.41138	0.0:0.9026:0.0:0.0974	.	387	Q9Y2P5	S27A5_HUMAN	Q	387	ENSP00000263093:R387Q	ENSP00000263093:R387Q	R	-	2	0	SLC27A5	63704487	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	4.953000	0.63624	1.188000	0.43014	0.563000	0.77884	CGG	C|0.997;T|0.003	0.003	strong		0.527	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
CDHR2	54825	hgsc.bcm.edu	37	5	176011444	176011444	+	Missense_Mutation	SNP	C	C	T	rs115050587	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:176011444C>T	ENST00000510636.1	+	19	2436	c.2162C>T	c.(2161-2163)gCg>gTg	p.A721V	CDHR2_ENST00000261944.5_Missense_Mutation_p.A721V|CDHR2_ENST00000506348.1_Missense_Mutation_p.A721V	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	721	Cadherin 7. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GCCTGGGACGCGGACCAGACG	0.637													C|||	9	0.00179712	0.0015	0.0014	5008	,	,		18356	0.0		0.005	False		,,,				2504	0.001				p.A721V		Atlas-SNP	.											.	CDHR2	152	.	0			c.C2162T						PASS	.	C	VAL/ALA,VAL/ALA	14,4392	21.2+/-45.6	0,14,2189	93.0	96.0	95.0		2162,2162	4.2	0.1	5	dbSNP_132	95	119,8481	61.0+/-122.8	0,119,4181	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	64,64	0,133,6370	TT,TC,CC		1.3837,0.3177,1.0226	probably-damaging,probably-damaging	721/1311,721/1311	176011444	133,12873	2203	4300	6503	SO:0001583	missense	54825	exon19			GGGACGCGGACCA	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2162C>T	5.37:g.176011444C>T	ENSP00000424565:p.Ala721Val	115.0	0.0	0		136.0	76.0	0.558824	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	13.57	2.277159	0.40294	0.003177	0.013837	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.55413	0.52;0.52;0.52	5.12	4.24	0.50183	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66470	0.2792	M	0.91920	3.255	0.33621	D	0.604834	D	0.67145	0.996	P	0.59546	0.859	T	0.81061	-0.1103	9	0.36615	T	0.2	-11.2568	12.946	0.58373	0.2944:0.7056:0.0:0.0	.	721	Q9BYE9	CDHR2_HUMAN	V	721	ENSP00000424565:A721V;ENSP00000261944:A721V;ENSP00000421078:A721V	ENSP00000261944:A721V	A	+	2	0	CDHR2	175944050	0.874000	0.30092	0.079000	0.20413	0.097000	0.18754	1.646000	0.37249	1.248000	0.43934	0.549000	0.68633	GCG	C|0.991;T|0.009	0.009	strong		0.637	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
ZC3HAV1	56829	hgsc.bcm.edu	37	7	138764741	138764741	+	Missense_Mutation	SNP	T	T	G	rs142490389	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:138764741T>G	ENST00000242351.5	-	4	1262	c.946A>C	c.(946-948)Act>Cct	p.T316P	ZC3HAV1_ENST00000464606.1_Missense_Mutation_p.T316P|ZC3HAV1_ENST00000471652.1_Missense_Mutation_p.T316P	NM_020119.3	NP_064504.2	Q7Z2W4	ZCCHV_HUMAN	zinc finger CCCH-type, antiviral 1	316					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of viral genome replication (GO:0045071)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of mRNA catabolic process (GO:0061014)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|NAD+ ADP-ribosyltransferase activity (GO:0003950)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(4)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|prostate(4)|skin(1)	37						CCAAGATCAGTAGCCTTGGAC	0.582													T|||	2	0.000399361	0.0	0.0	5008	,	,		19261	0.0		0.002	False		,,,				2504	0.0				p.T316P		Atlas-SNP	.											.	ZC3HAV1	75	.	0			c.A946C						PASS	.	T	PRO/THR,PRO/THR	4,4402	8.1+/-20.4	0,4,2199	51.0	51.0	51.0		946,946	-8.9	0.0	7	dbSNP_134	51	22,8578	16.0+/-53.3	0,22,4278	yes	missense,missense	ZC3HAV1	NM_020119.3,NM_024625.3	38,38	0,26,6477	GG,GT,TT		0.2558,0.0908,0.1999	benign,benign	316/903,316/700	138764741	26,12980	2203	4300	6503	SO:0001583	missense	56829	exon4			GATCAGTAGCCTT	BX571742	CCDS5851.1, CCDS55171.1	7q34	2012-07-05			ENSG00000105939	ENSG00000105939		"""Zinc fingers, CCCH-type domain containing"", ""Poly (ADP-ribose) polymerases"""	23721	protein-coding gene	gene with protein product	"""zinc finger antiviral protein"", "" CCCH-type zinc finger antiviral protein"""	607312				12215647, 12851707	Standard	NM_024625		Approved	ZAP, FLB6421, FLJ13288, MGC48898, ZC3HDC2, ZC3H2, PARP13	uc003vun.3	Q7Z2W4	OTTHUMG00000157471	ENST00000242351.5:c.946A>C	7.37:g.138764741T>G	ENSP00000242351:p.Thr316Pro	78.0	0.0	0		63.0	38.0	0.603175	NM_024625	A4D1R2|A4D1S4|Q8IW57|Q8TAJ3|Q96N79|Q9H8R9|Q9P0Y7	Missense_Mutation	SNP	ENST00000242351.5	37	CCDS5851.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	11.79	1.745165	0.30955	9.08E-4	0.002558	ENSG00000105939	ENST00000242351;ENST00000464606;ENST00000471652;ENST00000540247	T;T;T	0.30448	1.53;1.53;1.53	4.47	-8.94	0.00768	.	1.426730	0.04367	N	0.358508	T	0.16896	0.0406	L	0.36672	1.1	0.09310	N	1	B;B	0.21225	0.053;0.001	B;B	0.15484	0.013;0.002	T	0.17592	-1.0364	10	0.48119	T	0.1	.	0.8161	0.01103	0.3267:0.2947:0.2199:0.1588	.	316;316	Q7Z2W4-2;Q7Z2W4	.;ZCCHV_HUMAN	P	316;316;316;76	ENSP00000242351:T316P;ENSP00000418385:T316P;ENSP00000419855:T316P	ENSP00000242351:T316P	T	-	1	0	ZC3HAV1	138415281	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-4.989000	0.00162	-1.691000	0.01430	0.528000	0.53228	ACT	T|0.999;G|0.001	0.001	strong		0.582	ZC3HAV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348915.1	NM_020119	
JAK2	3717	hgsc.bcm.edu	37	9	5081828	5081828	+	Missense_Mutation	SNP	G	G	C	rs150221602	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:5081828G>C	ENST00000381652.3	+	19	3032	c.2538G>C	c.(2536-2538)gaG>gaC	p.E846D	JAK2_ENST00000544510.1_Missense_Mutation_p.E697D|AL161450.1_ENST00000601793.1_Intron|JAK2_ENST00000539801.1_Missense_Mutation_p.E846D	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	846					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	AGTTTGAAGAGAGACATTTGA	0.358		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																												p.E846D		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.G2538C						PASS	.	G	ASP/GLU	1,4405	2.1+/-5.4	0,1,2202	104.0	104.0	104.0		2538	0.0	1.0	9	dbSNP_134	104	5,8595	4.3+/-15.6	0,5,4295	yes	missense	JAK2	NM_004972.3	45	0,6,6497	CC,CG,GG		0.0581,0.0227,0.0461	benign	846/1133	5081828	6,13000	2203	4300	6503	SO:0001583	missense	3717	exon19	Familial Cancer Database		TGAAGAGAGACAT		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.2538G>C	9.37:g.5081828G>C	ENSP00000371067:p.Glu846Asp	83.0	0.0	0		120.0	54.0	0.45	NM_004972	O14636|O75297	Missense_Mutation	SNP	ENST00000381652.3	37	CCDS6457.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.648097	0.47258	2.27E-4	5.81E-4	ENSG00000096968	ENST00000539801;ENST00000381652;ENST00000544510	D;D;D	0.89123	-2.47;-2.47;-2.47	5.42	0.0118	0.14089	Protein kinase-like domain (1);	0.000000	0.85682	D	0.000000	D	0.85948	0.5816	M	0.73962	2.25	0.47245	D	0.999367	B	0.31100	0.308	B	0.27076	0.076	T	0.79249	-0.1881	10	0.62326	D	0.03	-17.9695	10.7256	0.46066	0.6272:0.0:0.3728:0.0	.	846	O60674	JAK2_HUMAN	D	846;846;697	ENSP00000440387:E846D;ENSP00000371067:E846D;ENSP00000443103:E697D	ENSP00000371067:E846D	E	+	3	2	JAK2	5071828	1.000000	0.71417	0.992000	0.48379	0.995000	0.86356	0.585000	0.23879	-0.298000	0.08921	0.655000	0.94253	GAG	G|0.999;C|0.001	0.001	strong		0.358	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
DSG3	1830	hgsc.bcm.edu	37	18	29054294	29054294	+	Missense_Mutation	SNP	C	C	T	rs111986709	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:29054294C>T	ENST00000257189.4	+	15	2395	c.2312C>T	c.(2311-2313)tCc>tTc	p.S771F		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	771					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			ACAAGGCATTCCACTGGAGGA	0.493													C|||	58	0.0115815	0.0015	0.013	5008	,	,		18033	0.0		0.0249	False		,,,				2504	0.0225				p.S771F		Atlas-SNP	.											.	DSG3	172	.	0			c.C2312T						PASS	.	C	PHE/SER	40,4366	43.1+/-76.7	0,40,2163	130.0	127.0	128.0		2312	6.1	1.0	18	dbSNP_132	128	309,8291	111.4+/-171.7	4,301,3995	yes	missense	DSG3	NM_001944.2	155	4,341,6158	TT,TC,CC		3.593,0.9079,2.6834	probably-damaging	771/1000	29054294	349,12657	2203	4300	6503	SO:0001583	missense	1830	exon15			GGCATTCCACTGG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.2312C>T	18.37:g.29054294C>T	ENSP00000257189:p.Ser771Phe	146.0	0.0	0		170.0	94.0	0.552941	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	27	0.012362637362637362	0	0.0	4	0.011049723756906077	0	0.0	23	0.030343007915567283	C	16.16	3.045378	0.55110	0.009079	0.03593	ENSG00000134757	ENST00000257189	T	0.63255	-0.03	6.06	6.06	0.98353	.	0.000000	0.50627	D	0.000110	T	0.37732	0.1014	M	0.71581	2.175	0.41681	D	0.989299	P	0.35700	0.516	B	0.41174	0.349	T	0.60712	-0.7209	10	0.59425	D	0.04	.	18.8049	0.92032	0.0:1.0:0.0:0.0	.	771	P32926	DSG3_HUMAN	F	771	ENSP00000257189:S771F	ENSP00000257189:S771F	S	+	2	0	DSG3	27308292	0.993000	0.37304	1.000000	0.80357	0.130000	0.20726	3.179000	0.50887	2.879000	0.98667	0.650000	0.86243	TCC	C|0.975;T|0.025	0.025	strong		0.493	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
THAP6	152815	hgsc.bcm.edu	37	4	76452302	76452302	+	Missense_Mutation	SNP	T	T	A	rs150566447		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:76452302T>A	ENST00000311638.3	+	5	615	c.547T>A	c.(547-549)Ttg>Atg	p.L183M	THAP6_ENST00000504190.1_Intron|THAP6_ENST00000514480.1_Missense_Mutation_p.L183M|THAP6_ENST00000507556.1_Intron|THAP6_ENST00000507885.1_Intron|THAP6_ENST00000380837.3_Missense_Mutation_p.L141M|THAP6_ENST00000502620.1_Intron|THAP6_ENST00000507557.1_Intron	NM_144721.4	NP_653322.1	Q8TBB0	THAP6_HUMAN	THAP domain containing 6	183						microtubule cytoskeleton (GO:0015630)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(5)	5			Lung(101;0.0973)|LUSC - Lung squamous cell carcinoma(112;0.122)			TCAGAAATCATTGAGGAAGAC	0.398													T|||	1	0.000199681	0.0	0.0	5008	,	,		19622	0.0		0.001	False		,,,				2504	0.0				p.L183M		Atlas-SNP	.											.	THAP6	14	.	0			c.T547A						PASS	.	T	MET/LEU	1,4405	2.1+/-5.4	0,1,2202	114.0	118.0	117.0		547	-3.8	0.7	4	dbSNP_134	117	27,8573	18.5+/-59.3	0,27,4273	yes	missense	THAP6	NM_144721.4	15	0,28,6475	AA,AT,TT		0.314,0.0227,0.2153	probably-damaging	183/223	76452302	28,12978	2203	4300	6503	SO:0001583	missense	152815	exon5			AAATCATTGAGGA	BC022989	CCDS3568.1	4q21.21	2013-01-25			ENSG00000174796	ENSG00000174796		"""THAP (C2CH-type zinc finger) domain containing"""	23189	protein-coding gene	gene with protein product		612535				12575992	Standard	NM_144721		Approved	MGC30052	uc003him.3	Q8TBB0	OTTHUMG00000130108	ENST00000311638.3:c.547T>A	4.37:g.76452302T>A	ENSP00000309007:p.Leu183Met	213.0	1.0	0.00469484		250.0	129.0	0.516	NM_144721	B4E146|Q5HYJ7|Q5JPC6	Missense_Mutation	SNP	ENST00000311638.3	37	CCDS3568.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	17.57	3.422570	0.62622	2.27E-4	0.00314	ENSG00000174796	ENST00000311638;ENST00000380837;ENST00000514480	D;D;D	0.98666	-5.06;-2.37;-5.06	4.67	-3.82	0.04281	.	0.149661	0.28828	N	0.014010	D	0.97102	0.9053	N	0.19112	0.55	0.21445	N	0.999684	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.963	D	0.93524	0.6864	10	0.33141	T	0.24	-10.7559	11.1423	0.48411	0.0:0.5762:0.0:0.4238	.	141;183	Q8TBB0-2;Q8TBB0	.;THAP6_HUMAN	M	183;141;183	ENSP00000309007:L183M;ENSP00000370217:L141M;ENSP00000423720:L183M	ENSP00000309007:L183M	L	+	1	2	THAP6	76671326	0.071000	0.21146	0.716000	0.30569	0.983000	0.72400	-1.212000	0.02994	-0.636000	0.05524	0.533000	0.62120	TTG	T|0.998;A|0.002	0.002	strong		0.398	THAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252414.1	NM_144721	
SLC16A8	23539	hgsc.bcm.edu	37	22	38478666	38478666	+	Splice_Site	SNP	C	C	G	rs77968014	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:38478666C>G	ENST00000320521.5	-	2	323		c.e2+1		SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8						blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	GGGACACTGACCCGTGCCGTA	0.701													C|||	17	0.00339457	0.0	0.0058	5008	,	,		12685	0.0		0.0119	False		,,,				2504	0.001				.		Atlas-SNP	.											.	SLC16A8	13	.	0			c.214+1G>C						PASS	.	C		5,4307		0,5,2151	7.0	9.0	8.0			4.2	1.0	22	dbSNP_132	8	51,8433		0,51,4191	yes	splice-5	SLC16A8	NM_013356.2		0,56,6342	GG,GC,CC		0.6011,0.116,0.4376			38478666	56,12740	2156	4242	6398	SO:0001630	splice_region_variant	23539	exon3			CACTGACCCGTGC	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"""Solute carriers"""	16270	protein-coding gene	gene with protein product	"""monocarboxylate transporter 3"""	610409	"""solute carrier 16 (monocarboxylic acid transporters), member 8"""			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.214+1G>C	22.37:g.38478666C>G		38.0	0.0	0		57.0	32.0	0.561404	NM_013356	Q9UBE2	Splice_Site	SNP	ENST00000320521.5	37	CCDS13966.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	21.4	4.146560	0.77888	0.00116	0.006011	ENSG00000100156	ENST00000320521;ENST00000427592	.	.	.	4.23	4.23	0.50019	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.0149	0.86415	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC16A8	36808612	1.000000	0.71417	0.975000	0.42487	0.835000	0.47333	7.622000	0.83099	2.094000	0.63399	0.485000	0.47835	.	C|0.997;G|0.003	0.003	strong		0.701	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	Intron
DCHS2	54798	hgsc.bcm.edu	37	4	155298432	155298432	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:155298432A>G	ENST00000357232.4	-	3	398	c.399T>C	c.(397-399)taT>taC	p.Y133Y	DCHS2_ENST00000339452.1_Silent_p.Y739Y	NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	133	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CCAGGAGATCATAGGTAGCTG	0.443																																					p.Y739Y		Atlas-SNP	.											.	DCHS2	594	.	0			c.T2217C						PASS	.						134.0	121.0	126.0					4																	155298432		2203	4300	6503	SO:0001819	synonymous_variant	54798	exon2			GAGATCATAGGTA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.399T>C	4.37:g.155298432A>G		92.0	0.0	0		88.0	38.0	0.431818	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			.	.	none		0.443	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
TUT1	64852	hgsc.bcm.edu	37	11	62343667	62343667	+	Silent	SNP	A	A	T	rs118073625	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:62343667A>T	ENST00000476907.1	-	9	2215	c.1524T>A	c.(1522-1524)cgT>cgA	p.R508R	MIR3654_ENST00000496634.2_Intron|EEF1G_ENST00000329251.4_5'Flank|EEF1G_ENST00000378019.3_5'Flank|EEF1G_ENST00000532986.1_5'Flank|TUT1_ENST00000308436.7_Silent_p.R546R			Q9H6E5	STPAP_HUMAN	terminal uridylyl transferase 1, U6 snRNA-specific	508	PAP-associated.				mRNA cleavage (GO:0006379)|mRNA polyadenylation (GO:0006378)|snRNA processing (GO:0016180)	intercellular bridge (GO:0045171)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|mRNA 3'-UTR binding (GO:0003730)|polynucleotide adenylyltransferase activity (GO:0004652)|RNA binding (GO:0003723)|RNA uridylyltransferase activity (GO:0050265)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						GCAGGGAGCCACGAAGATCCC	0.612													A|||	9	0.00179712	0.0	0.0014	5008	,	,		18897	0.0		0.007	False		,,,				2504	0.001				p.R546R		Atlas-SNP	.											.	TUT1	122	.	0			c.T1638A						PASS	.	A		4,4374		0,4,2185	18.0	20.0	19.0		1638	-0.2	1.0	11	dbSNP_133	19	81,8511		0,81,4215	no	coding-synonymous	TUT1	NM_022830.2		0,85,6400	TT,TA,AA		0.9427,0.0914,0.6554		546/913	62343667	85,12885	2189	4296	6485	SO:0001819	synonymous_variant	64852	exon9			GGAGCCACGAAGA	BC005013	CCDS8021.1, CCDS8021.2	11q12.2	2014-03-05	2006-10-06	2006-10-06	ENSG00000149016	ENSG00000149016	2.7.7.52	"""RNA binding motif (RRM) containing"""	26184	protein-coding gene	gene with protein product	"""RNA uridylyltransferase"", ""U6 TUTase"", ""TUTase 6"""	610641	"""RNA binding motif protein 21"""	RBM21		16790842	Standard	NM_022830		Approved	FLJ22347, FLJ22267, FLJ21850, PAPD2, TUTase	uc001nto.2	Q9H6E5	OTTHUMG00000158564	ENST00000476907.1:c.1524T>A	11.37:g.62343667A>T		48.0	0.0	0		52.0	17.0	0.326923	NM_022830	A1A527|A8K995|Q2NL65|Q7L583|Q9H6H7	Silent	SNP	ENST00000476907.1	37																																																																																				A|0.995;T|0.005	0.005	strong		0.612	TUT1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000351319.2	NM_022830	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32552000	32552000	+	Missense_Mutation	SNP	C	C	T	rs17880292	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32552000C>T	ENST00000360004.5	-	2	361	c.256G>A	c.(256-258)Gac>Aac	p.D86N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	86	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TACTCAGCGTCAGGCCGCCCC	0.632										Multiple Myeloma(14;0.17)			C|||	334	0.0666933	0.0938	0.0591	5008	,	,		7793	0.1002		0.0487	False		,,,				2504	0.0194				p.D86N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G256A						PASS	.																																			SO:0001583	missense	3123	exon2			CAGCGTCAGGCCG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.256G>A	6.37:g.32552000C>T	ENSP00000353099:p.Asp86Asn	33.0	0.0	0		50.0	16.0	0.32	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	13.25	2.179960	0.38511	.	.	ENSG00000196126	ENST00000360004	T	0.00224	8.51	3.52	-1.57	0.08506	MHC class II, alpha/beta chain, N-terminal (1);MHC class II, beta chain, N-terminal (3);MHC classes I/II-like antigen recognition protein (1);	11.458300	0.00979	N	0.003354	T	0.00073	0.0002	M	0.63428	1.95	0.09310	N	1	B	0.21606	0.058	B	0.28385	0.089	T	0.33777	-0.9855	10	0.72032	D	0.01	.	3.0064	0.06030	0.3359:0.2318:0.0:0.4323	rs17880292	86	P01911	2B1F_HUMAN	N	86	ENSP00000353099:D86N	ENSP00000353099:D86N	D	-	1	0	HLA-DRB1	32659978	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.770000	0.00188	-0.268000	0.09312	0.453000	0.30009	GAC	C|0.989;T|0.011	0.011	strong		0.632	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PRSS53	339105	hgsc.bcm.edu	37	16	31097689	31097689	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:31097689C>T	ENST00000280606.6	-	5	785	c.632G>A	c.(631-633)gGc>gAc	p.G211D		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	211	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						AGGCTGGGGGCCCCCACATAG	0.642																																					p.G211D		Atlas-SNP	.											.	PRSS53	29	.	0			c.G632A						PASS	.						42.0	48.0	46.0					16																	31097689		1877	4102	5979	SO:0001583	missense	339105	exon5			TGGGGGCCCCCAC		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.632G>A	16.37:g.31097689C>T	ENSP00000280606:p.Gly211Asp	63.0	0.0	0		100.0	39.0	0.39	NM_001039503		Missense_Mutation	SNP	ENST00000280606.6	37	CCDS42153.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.109734	0.77096	.	.	ENSG00000151006	ENST00000280606	D	0.90133	-2.62	5.77	5.77	0.91146	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.36778	U	0.002401	D	0.95385	0.8502	M	0.84773	2.715	0.53688	D	0.999979	D	0.89917	1.0	D	0.97110	1.0	D	0.95533	0.8605	10	0.87932	D	0	.	13.1188	0.59314	0.0:0.8394:0.1606:0.0	.	211	Q2L4Q9	PRS53_HUMAN	D	211	ENSP00000280606:G211D	ENSP00000280606:G211D	G	-	2	0	PRSS53	31005190	0.992000	0.36948	1.000000	0.80357	0.946000	0.59487	3.137000	0.50562	2.723000	0.93209	0.655000	0.94253	GGC	.	.	none		0.642	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
REEP6	92840	hgsc.bcm.edu	37	19	1489817	1489817	+	5'Flank	SNP	C	C	T	rs12972390	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:1489817C>T	ENST00000233596.3	+	0	0				PCSK4_ENST00000300954.5_Missense_Mutation_p.R90H|PCSK4_ENST00000587784.1_Intron	NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6						regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)		CAGGTGCAGGCGGTGGCCCCA	0.677													C|||	60	0.0119808	0.0015	0.0231	5008	,	,		14349	0.0		0.0268	False		,,,				2504	0.0153				p.R90H		Atlas-SNP	.											.	PCSK4	44	.	0			c.G269A						PASS	.	C	HIS/ARG	21,4373		0,21,2176	21.0	24.0	23.0		269	2.0	1.0	19	dbSNP_121	23	316,8284		6,304,3990	yes	missense	PCSK4	NM_017573.3	29	6,325,6166	TT,TC,CC		3.6744,0.4779,2.5935	benign	90/756	1489817	337,12657	2197	4300	6497	SO:0001631	upstream_gene_variant	54760	exon2			TGCAGGCGGTGGC	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"""Receptor accessory proteins"""	30078	protein-coding gene	gene with protein product	"""polyposis locus protein 1-like 1"", ""deleted in polyposis 1-like 1"""	609346	"""chromosome 19 open reading frame 32"""	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072		19.37:g.1489817C>T	Exception_encountered	160.0	0.0	0		172.0	96.0	0.55814	NM_017573	B2RE01|D6W5Z0|Q96LM0	Missense_Mutation	SNP	ENST00000233596.3	37	CCDS12070.1	32	0.014652014652014652	0	0.0	10	0.027624309392265192	0	0.0	22	0.029023746701846966	C	2.756	-0.259014	0.05791	0.004779	0.036744	ENSG00000115257	ENST00000300954	T	0.27720	1.65	3.13	2.03	0.26663	Proteinase inhibitor, propeptide (1);	0.604415	0.14044	N	0.345214	T	0.01976	0.0062	N	0.04203	-0.255	0.28129	N	0.930294	B	0.21688	0.059	B	0.09377	0.004	T	0.32052	-0.9921	10	0.02654	T	1	.	5.578	0.17235	0.0:0.7484:0.0:0.2516	rs12972390;rs12972390	90	Q6UW60	PCSK4_HUMAN	H	90	ENSP00000300954:R90H	ENSP00000300954:R90H	R	-	2	0	PCSK4	1440817	0.000000	0.05858	1.000000	0.80357	0.837000	0.47467	0.348000	0.20031	1.606000	0.50161	0.561000	0.74099	CGC	C|0.980;T|0.020	0.020	strong		0.677	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393	
PKP2	5318	hgsc.bcm.edu	37	12	33021917	33021917	+	Missense_Mutation	SNP	C	C	G	rs200586695		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:33021917C>G	ENST00000070846.6	-	4	1138	c.1114G>C	c.(1114-1116)Gct>Cct	p.A372P	PKP2_ENST00000340811.4_Missense_Mutation_p.A372P	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	372			A -> P. {ECO:0000269|PubMed:20031617, ECO:0000269|PubMed:21062920}.		adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					GTAGCTGCAGCAGAAATCCTG	0.498																																					p.A372P		Atlas-SNP	.											.	PKP2	110	.	0			c.G1114C						PASS	.	C	PRO/ALA,PRO/ALA	0,4406		0,0,2203	118.0	106.0	110.0		1114,1114	4.2	0.0	12		110	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	27,27	0,6,6497	GG,GC,CC		0.0698,0.0,0.0461	benign,benign	372/838,372/882	33021917	6,13000	2203	4300	6503	SO:0001583	missense	5318	exon4			CTGCAGCAGAAAT	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.1114G>C	12.37:g.33021917C>G	ENSP00000070846:p.Ala372Pro	74.0	0.0	0		81.0	42.0	0.518519	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	C	11.66	1.703879	0.30232	0.0	6.98E-4	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.52754	0.65;0.65	5.09	4.2	0.49525	Armadillo-like helical (1);Armadillo-type fold (1);	2.116220	0.01794	N	0.032478	T	0.55940	0.1952	L	0.55481	1.735	0.31883	N	0.618224	P;P;P	0.43662	0.676;0.548;0.814	P;B;P	0.47015	0.506;0.309;0.534	T	0.41556	-0.9502	10	0.30854	T	0.27	-1.899	11.5273	0.50586	0.0:0.9155:0.0:0.0845	.	372;372;372	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	P	372	ENSP00000342800:A372P;ENSP00000070846:A372P	ENSP00000070846:A372P	A	-	1	0	PKP2	32913184	0.805000	0.28982	0.017000	0.16124	0.333000	0.28666	2.159000	0.42339	1.136000	0.42199	0.650000	0.86243	GCT	C|0.999;G|0.001	0.001	weak		0.498	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3425749	3425749	+	Missense_Mutation	SNP	C	C	T	rs145733257		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:3425749C>T	ENST00000324266.5	+	4	1457	c.1262C>T	c.(1261-1263)aCg>aTg	p.T421M	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.T421M	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	421					vesicle-mediated transport (GO:0016192)												ACCAGCCACACGACAGATTCA	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		20473	0.0		0.001	False		,,,				2504	0.0				p.T421M		Atlas-SNP	.											.	.	.	.	0			c.C1262T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	28.0	27.0	28.0		1262	4.7	0.8	2	dbSNP_134	28	19,8581	12.6+/-44.7	0,19,4281	yes	missense	TTC15	NM_016030.5	81	0,20,6483	TT,TC,CC		0.2209,0.0227,0.1538	probably-damaging	421/736	3425749	20,12986	2203	4300	6503	SO:0001583	missense	51112	exon4			GCCACACGACAGA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1262C>T	2.37:g.3425749C>T	ENSP00000324318:p.Thr421Met	108.0	0.0	0		161.0	74.0	0.459627	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	24.4|24.4	4.524474|4.524474	0.85600|0.85600	2.27E-4|2.27E-4	0.002209|0.002209	ENSG00000171853|ENSG00000171853	ENST00000441983|ENST00000382110;ENST00000304601;ENST00000324266	.|T;T	.|0.54866	.|0.55;0.55	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	.|T	.|0.72906	.|0.3519	M|M	0.78637|0.78637	2.42|2.42	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.73380	.|0.964;0.98	.|T	.|0.76942	.|-0.2772	.|10	.|0.66056	.|D	.|0.02	.|.	16.8604|16.8604	0.86016|0.86016	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|404;421	.|E7ENL7;Q8WVT3	.|.;TPC12_HUMAN	X|M	101|421;404;421	.|ENSP00000371544:T421M;ENSP00000324318:T421M	.|ENSP00000303612:T404M	R|T	+|+	1|2	2|0	TTC15|TTC15	3404756|3404756	1.000000|1.000000	0.71417|0.71417	0.841000|0.841000	0.33234|0.33234	0.976000|0.976000	0.68499|0.68499	7.133000|7.133000	0.77259|0.77259	2.439000|2.439000	0.82584|0.82584	0.563000|0.563000	0.77884|0.77884	CGA|ACG	C|0.999;T|0.001	0.001	strong		0.587	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
MRC2	9902	hgsc.bcm.edu	37	17	60767594	60767594	+	Silent	SNP	C	C	A	rs147759673		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:60767594C>A	ENST00000303375.5	+	26	4222	c.3820C>A	c.(3820-3822)Cgg>Agg	p.R1274R	MRC2_ENST00000446119.2_Silent_p.R140R	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1274	C-type lectin 8. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GATTCCCTTCCGGGAGCACTG	0.617																																					p.R1274R		Atlas-SNP	.											.	MRC2	126	.	0			c.C3820A						PASS	.	C		0,4406		0,0,2203	36.0	44.0	42.0		3820	3.8	1.0	17	dbSNP_134	42	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	MRC2	NM_006039.3		0,6,6497	AA,AC,CC		0.0698,0.0,0.0461		1274/1480	60767594	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	9902	exon26			CCCTTCCGGGAGC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3820C>A	17.37:g.60767594C>A		192.0	0.0	0		227.0	116.0	0.511013	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Silent	SNP	ENST00000303375.5	37	CCDS11634.1																																																																																			C|1.000;A|0.000	0.000	weak		0.617	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32925226	32925226	+	Silent	SNP	T	T	G	rs77143444	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:32925226T>G	ENST00000361627.3	+	9	1874	c.1152T>G	c.(1150-1152)tcT>tcG	p.S384S	ARHGAP11A_ENST00000563864.1_Intron|ARHGAP11A_ENST00000567348.1_Silent_p.S384S|ARHGAP11A_ENST00000543522.1_Silent_p.S195S|ARHGAP11A_ENST00000565905.1_Silent_p.S195S	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	384					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)		GTTCACTCTCTCCTGTACTCA	0.393													T|||	15	0.00299521	0.0	0.0014	5008	,	,		16649	0.0		0.0129	False		,,,				2504	0.001				p.S384S	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T1152G						PASS	.	T	,	5,4397		0,5,2196	159.0	154.0	156.0		1152,1152	2.1	1.0	15	dbSNP_131	156	63,8537		1,61,4238	no	coding-synonymous,coding-synonymous	ARHGAP11A	NM_014783.3,NM_199357.1	,	1,66,6434	GG,GT,TT		0.7326,0.1136,0.523	,	384/1024,384/502	32925226	68,12934	2201	4300	6501	SO:0001819	synonymous_variant	9824	exon9			ACTCTCTCCTGTA	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.1152T>G	15.37:g.32925226T>G		154.0	0.0	0		165.0	81.0	0.490909	NM_199357	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	37	CCDS10028.1																																																																																			T|0.995;G|0.005	0.005	strong		0.393	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110510964	110510964	+	Missense_Mutation	SNP	A	A	C	rs191412861	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:110510964A>C	ENST00000378402.5	+	67	10896	c.10792A>C	c.(10792-10794)Agt>Cgt	p.S3598R		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3598					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			AGGAATCATGAGTTACAATGC	0.408										HNSCC(38;0.096)			A|||	28	0.00559105	0.0008	0.0072	5008	,	,		16193	0.0		0.005	False		,,,				2504	0.0174				p.S3598R		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A10792C						PASS	.	A	ARG/SER	2,3744		0,2,1871	81.0	77.0	78.0		10792	6.0	1.0	8		78	48,8134		1,46,4044	yes	missense	PKHD1L1	NM_177531.4	110	1,48,5915	CC,CA,AA		0.5867,0.0534,0.4192	probably-damaging	3598/4244	110510964	50,11878	1873	4091	5964	SO:0001583	missense	93035	exon67			ATCATGAGTTACA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.10792A>C	8.37:g.110510964A>C	ENSP00000367655:p.Ser3598Arg	138.0	0.0	0		158.0	59.0	0.373418	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	A	26.4	4.731514	0.89390	5.34E-4	0.005867	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.86865	-2.18;-1.99	6.02	6.02	0.97574	.	0.109105	0.64402	D	0.000010	D	0.83723	0.5316	M	0.78637	2.42	0.40619	D	0.981744	B	0.25719	0.132	B	0.22601	0.04	D	0.84175	0.0436	10	0.59425	D	0.04	.	14.5014	0.67724	1.0:0.0:0.0:0.0	.	3598	Q86WI1	PKHL1_HUMAN	R	3598;526	ENSP00000367655:S3598R;ENSP00000437376:S526R	ENSP00000367655:S3598R	S	+	1	0	PKHD1L1	110580140	1.000000	0.71417	1.000000	0.80357	0.907000	0.53573	7.683000	0.84093	2.299000	0.77371	0.528000	0.53228	AGT	A|0.997;C|0.003	0.003	strong		0.408	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
DBF4	10926	hgsc.bcm.edu	37	7	87537183	87537183	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:87537183A>G	ENST00000265728.1	+	12	2234	c.1730A>G	c.(1729-1731)aAa>aGa	p.K577R		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	577					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				ATACATCGAAAAGTGAAAATA	0.333																																					p.K577R		Atlas-SNP	.											.	DBF4	67	.	0			c.A1730G						PASS	.						48.0	55.0	52.0					7																	87537183		2201	4266	6467	SO:0001583	missense	10926	exon12			ATCGAAAAGTGAA	AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"""Zinc fingers, DBF-type"""	17364	protein-coding gene	gene with protein product	"""activator of S phase kinase"", ""chiffon homolog (Drosophila)"", ""zinc finger, DBF-type containing 1"", ""DBF4 zinc finger A"""	604281	"""DBF4 homolog (S. cerevisiae)"""			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1730A>G	7.37:g.87537183A>G	ENSP00000265728:p.Lys577Arg	234.0	0.0	0		297.0	158.0	0.531987	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	.	.	.	.	.	.	.	.	.	.	A	16.90	3.250022	0.59212	.	.	ENSG00000006634	ENST00000265728	T	0.52295	0.67	5.13	5.13	0.70059	.	0.000000	0.64402	D	0.000002	T	0.46718	0.1407	M	0.63843	1.955	0.47905	D	0.999544	P;P	0.52463	0.953;0.802	B;B	0.41036	0.346;0.277	T	0.55798	-0.8084	10	0.87932	D	0	-13.7887	13.5232	0.61580	1.0:0.0:0.0:0.0	.	353;577	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	R	577	ENSP00000265728:K577R	ENSP00000265728:K577R	K	+	2	0	DBF4	87375119	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.326000	0.59241	1.934000	0.56057	0.528000	0.53228	AAA	.	.	none		0.333	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716	
ZNF490	57474	hgsc.bcm.edu	37	19	12691497	12691497	+	Silent	SNP	G	G	A	rs140620156	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:12691497G>A	ENST00000311437.6	-	5	1514	c.1392C>T	c.(1390-1392)caC>caT	p.H464H	ZNF490_ENST00000465656.1_5'Flank|CTD-2192J16.20_ENST00000593682.1_Missense_Mutation_p.T98M	NM_020714.2	NP_065765.1	Q9ULM2	ZN490_HUMAN	zinc finger protein 490	464					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	18						GACTTCTTTCGTGCCTTCGAA	0.418													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		20275	0.0		0.003	False		,,,				2504	0.0				p.H464H		Atlas-SNP	.											.	ZNF490	42	.	0			c.C1392T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	129.0	128.0	128.0		1392	-1.5	0.0	19	dbSNP_134	128	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	ZNF490	NM_020714.2		0,40,6463	AA,AG,GG		0.407,0.1135,0.3076		464/530	12691497	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	57474	exon5			TCTTTCGTGCCTT	AB033024	CCDS12272.1	19p13.2	2013-01-08			ENSG00000188033	ENSG00000188033		"""Zinc fingers, C2H2-type"", ""-"""	23705	protein-coding gene	gene with protein product							Standard	NM_020714		Approved	KIAA1198	uc002mtz.2	Q9ULM2	OTTHUMG00000156398	ENST00000311437.6:c.1392C>T	19.37:g.12691497G>A		94.0	0.0	0		102.0	42.0	0.411765	NM_020714		Silent	SNP	ENST00000311437.6	37	CCDS12272.1																																																																																			G|0.997;A|0.003	0.003	strong		0.418	ZNF490-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344073.1	NM_020714	
CLASP2	23122	hgsc.bcm.edu	37	3	33543195	33543195	+	Silent	SNP	C	C	T	rs111990025	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:33543195C>T	ENST00000468888.2	-	38	4453	c.4407G>A	c.(4405-4407)gcG>gcA	p.A1469A	CLASP2_ENST00000399362.4_Silent_p.A1468A|CLASP2_ENST00000480013.1_Silent_p.A1248A|CLASP2_ENST00000539981.1_3'UTR|CLASP2_ENST00000359576.5_Silent_p.A1460A|CLASP2_ENST00000461133.3_Silent_p.A1228A|CLASP2_ENST00000307312.7_Silent_p.A950A			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	1249					axon guidance (GO:0007411)|establishment or maintenance of cell polarity (GO:0007163)|fucosylation (GO:0036065)|microtubule anchoring (GO:0034453)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of microtubule depolymerization (GO:0007026)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of microtubule-based process (GO:0032886)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|trans-Golgi network (GO:0005802)	galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)|microtubule plus-end binding (GO:0051010)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	48						CACCAATTACCGCATGAACAG	0.443													C|||	57	0.0113818	0.0008	0.0072	5008	,	,		19135	0.001		0.0219	False		,,,				2504	0.0286				p.A1470A		Atlas-SNP	.											.	CLASP2	138	.	0			c.G4410A						PASS	.	C	,	24,3892		0,24,1934	141.0	135.0	137.0		3747,4410	-6.2	0.4	3	dbSNP_132	137	206,8106		3,200,3953	no	coding-synonymous,coding-synonymous	CLASP2	NM_001207044.1,NM_015097.2	,	3,224,5887	TT,TC,CC		2.4783,0.6129,1.8809	,	1249/1295,1470/1516	33543195	230,11998	1958	4156	6114	SO:0001819	synonymous_variant	23122	exon38			AATTACCGCATGA	AB014527		3p24.3	2013-01-18			ENSG00000163539	ENSG00000163539			17078	protein-coding gene	gene with protein product		605853				9734811, 10899121	Standard	NM_015097		Approved	KIAA0627	uc021wvc.1	O75122	OTTHUMG00000156489	ENST00000468888.2:c.4407G>A	3.37:g.33543195C>T		61.0	0.0	0		71.0	32.0	0.450704	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37		22	0.010073260073260074	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	20	0.026385224274406333	C	6.469	0.454728	0.12283	0.006129	0.024783	ENSG00000163539	ENST00000487553	.	.	.	5.7	-6.15	0.02105	.	.	.	.	.	T	0.29126	0.0724	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52953	-0.8506	4	.	.	.	-6.566	11.4283	0.50025	0.085:0.3006:0.0:0.6144	.	.	.	.	S	175	.	.	G	-	1	0	CLASP2	33518199	0.000000	0.05858	0.395000	0.26283	0.793000	0.44817	-2.319000	0.01120	-1.720000	0.01380	-2.945000	0.00085	GGT	C|0.987;T|0.013	0.013	strong		0.443	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
SLFN5	162394	hgsc.bcm.edu	37	17	33586111	33586111	+	Silent	SNP	G	G	A	rs141928271	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:33586111G>A	ENST00000299977.4	+	2	550	c.402G>A	c.(400-402)ctG>ctA	p.L134L	SLFN5_ENST00000542451.1_Silent_p.L134L|SLFN5_ENST00000592325.1_Silent_p.L134L	NM_144975.3	NP_659412.3	Q08AF3	SLFN5_HUMAN	schlafen family member 5	134					cell differentiation (GO:0030154)	nucleus (GO:0005634)	ATP binding (GO:0005524)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(8)|liver(2)|lung(6)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	34		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0191)		AGGAAGCTCTGGCATTCCTCA	0.458													G|||	12	0.00239617	0.0008	0.0	5008	,	,		21328	0.0		0.0089	False		,,,				2504	0.002				p.L134L		Atlas-SNP	.											.	SLFN5	92	.	0			c.G402A						PASS	.	G		8,4398	15.5+/-35.6	0,8,2195	115.0	113.0	114.0		402	2.7	0.0	17	dbSNP_134	114	68,8532	41.2+/-98.3	0,68,4232	no	coding-synonymous	SLFN5	NM_144975.3		0,76,6427	AA,AG,GG		0.7907,0.1816,0.5843		134/892	33586111	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	162394	exon2			AGCTCTGGCATTC	BX647942	CCDS32619.1	17q12	2006-04-05				ENSG00000166750			28286	protein-coding gene	gene with protein product		614952				9846487	Standard	NM_144975		Approved	MGC19764	uc002hjf.4	Q08AF3		ENST00000299977.4:c.402G>A	17.37:g.33586111G>A		201.0	0.0	0		198.0	96.0	0.484848	NM_144975	Q08AF2|Q8WU54|Q96A82	Silent	SNP	ENST00000299977.4	37	CCDS32619.1																																																																																			G|0.994;A|0.006	0.006	strong		0.458	SLFN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448649.2	NM_144975	
TRIM29	23650	hgsc.bcm.edu	37	11	119998151	119998151	+	Missense_Mutation	SNP	C	C	G	rs146343820	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:119998151C>G	ENST00000341846.5	-	3	1448	c.1027G>C	c.(1027-1029)Gtg>Ctg	p.V343L	TRIM29_ENST00000528870.1_5'Flank|TRIM29_ENST00000529044.1_Missense_Mutation_p.V82L|TRIM29_ENST00000541857.1_Missense_Mutation_p.V76L	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	343					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		ATCACCTTCACTTGGTCCACA	0.587																																					p.V343L		Atlas-SNP	.											.	TRIM29	78	.	0			c.G1027C						PASS	.	C	LEU/VAL	4,4394	8.1+/-20.4	0,4,2195	181.0	148.0	159.0		1027	4.2	0.9	11	dbSNP_134	159	9,8581	7.1+/-27.0	0,9,4286	yes	missense	TRIM29	NM_012101.3	32	0,13,6481	GG,GC,CC		0.1048,0.091,0.1001	benign	343/589	119998151	13,12975	2199	4295	6494	SO:0001583	missense	23650	exon3			CCTTCACTTGGTC	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1027G>C	11.37:g.119998151C>G	ENSP00000343129:p.Val343Leu	174.0	0.0	0		197.0	90.0	0.456853	NM_012101	Q96AA9|Q9BZY7	Missense_Mutation	SNP	ENST00000341846.5	37	CCDS8428.1	.	.	.	.	.	.	.	.	.	.	C	15.46	2.840150	0.51057	9.1E-4	0.001048	ENSG00000137699	ENST00000341846;ENST00000541857;ENST00000529044	T	0.35605	1.3	5.14	4.23	0.50019	.	0.220732	0.32147	N	0.006505	T	0.20659	0.0497	N	0.19112	0.55	0.36728	D	0.881557	B;B;B	0.21452	0.003;0.011;0.056	B;B;B	0.17433	0.009;0.017;0.018	T	0.14035	-1.0487	9	.	.	.	.	8.188	0.31350	0.0:0.7621:0.0:0.2379	.	76;82;343	B7Z8U9;E9PRL4;Q14134	.;.;TRI29_HUMAN	L	343;76;82	ENSP00000343129:V343L	.	V	-	1	0	TRIM29	119503361	0.533000	0.26354	0.908000	0.35775	0.971000	0.66376	0.465000	0.22004	1.183000	0.42943	0.655000	0.94253	GTG	C|0.999;G|0.001	0.001	strong		0.587	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
ZNF211	10520	hgsc.bcm.edu	37	19	58153465	58153465	+	Nonsense_Mutation	SNP	T	T	A	rs146505315	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58153465T>A	ENST00000347302.3	+	3	1790	c.1611T>A	c.(1609-1611)taT>taA	p.Y537*	ZNF211_ENST00000420680.1_Nonsense_Mutation_p.Y541*|ZNF211_ENST00000254182.7_Nonsense_Mutation_p.Y528*|ZNF211_ENST00000391703.3_Nonsense_Mutation_p.Y476*|ZNF211_ENST00000544273.1_Nonsense_Mutation_p.Y549*|ZNF211_ENST00000299871.5_Nonsense_Mutation_p.Y602*|ZNF211_ENST00000240731.4_Nonsense_Mutation_p.Y550*|ZNF211_ENST00000541801.1_Nonsense_Mutation_p.Y528*	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	537					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(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		AAAGGCCTTATCAGTGCAGTC	0.453													T|||	6	0.00119808	0.0008	0.0014	5008	,	,		21540	0.0		0.004	False		,,,				2504	0.0				p.Y602X		Atlas-SNP	.											.	ZNF211	78	.	0			c.T1806A						PASS	.	T	stop/TYR,stop/TYR	10,4396	16.8+/-37.8	0,10,2193	105.0	102.0	103.0		1650,1611	-4.0	0.0	19	dbSNP_134	103	49,8551	31.2+/-83.2	0,49,4251	yes	stop-gained,stop-gained	ZNF211	NM_006385.3,NM_198855.2	,	0,59,6444	AA,AT,TT		0.5698,0.227,0.4536	,	550/578,537/565	58153465	59,12947	2203	4300	6503	SO:0001587	stop_gained	10520	exon5			GCCTTATCAGTGC	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.1611T>A	19.37:g.58153465T>A	ENSP00000339562:p.Tyr537*	43.0	0.0	0		53.0	20.0	0.377358	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Nonsense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	t|t	37|37	5.990100|5.990100	0.97179|0.97179	0.00227|0.00227	0.005698|0.005698	ENSG00000121417|ENSG00000121417	ENST00000407202|ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731	.|.	.|.	.|.	2.37|2.37	-4.02|-4.02	0.04034|0.04034	.|.	.|.	.|.	.|.	.|.	T|.	0.10809|.	0.0264|.	.|.	.|.	.|.	0.41247|0.41247	D|D	0.986684|0.986684	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.41484|.	-0.9506|.	4|.	.|0.02654	.|T	.|1	.|.	1.7708|1.7708	0.03011|0.03011	0.1459:0.3803:0.1482:0.3256|0.1459:0.3803:0.1482:0.3256	.|.	.|.	.|.	.|.	T|X	541|541;537;528;476;528;602;549;550	.|.	.|ENSP00000240731:Y550X	S|Y	+|+	1|3	0|2	ZNF211|ZNF211	62845277|62845277	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.940000|0.940000	0.58332|0.58332	-0.503000|-0.503000	0.06383|0.06383	-1.154000|-1.154000	0.02825|0.02825	0.477000|0.477000	0.44152|0.44152	TCA|TAT	T|0.996;A|0.004	0.004	strong		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
MT-ND5	4540	hgsc.bcm.edu	37	M	14053	14053	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:14053A>G	ENST00000361567.2	+	1	1717	c.1717A>G	c.(1717-1719)Acc>Gcc	p.T573A	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	573					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACCAAATCTCCACCTCCATCA	0.423																																					p.T573A		Atlas-SNP	.											.	.	.	.	0			c.A1717G						PASS	.																																			SO:0001583	missense	0	exon1			ATCTCCACCTCCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1717A>G	M.37:g.14053A>G	ENSP00000354813:p.Thr573Ala	13.0	0.0	0		30.0	29.0	0.966667	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.423	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
OR4C15	81309	hgsc.bcm.edu	37	11	55322099	55322099	+	Missense_Mutation	SNP	C	C	G	rs17496724	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:55322099C>G	ENST00000314644.2	+	1	317	c.317C>G	c.(316-318)gCt>gGt	p.A106G		NM_001001920.1	NP_001001920.1	Q8NGM1	OR4CF_HUMAN	olfactory receptor, family 4, subfamily C, member 15	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(31)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(5)	56						AGCAGCCCTGCTCTTCTGGTG	0.443										HNSCC(20;0.049)																											p.A106G		Atlas-SNP	.											.	OR4C15	145	.	0			c.C317G						PASS	.						172.0	137.0	149.0					11																	55322099		2201	4296	6497	SO:0001583	missense	81309	exon1			GCCCTGCTCTTCT	BK004319	CCDS31501.1	11q11	2012-08-09			ENSG00000181939	ENSG00000181939		"""GPCR / Class A : Olfactory receptors"""	15171	protein-coding gene	gene with protein product							Standard	NM_001001920		Approved		uc010rig.2	Q8NGM1	OTTHUMG00000166714	ENST00000314644.2:c.317C>G	11.37:g.55322099C>G	ENSP00000324958:p.Ala106Gly	66.0	0.0	0		77.0	36.0	0.467532	NM_001001920	Q6IFE2	Missense_Mutation	SNP	ENST00000314644.2	37	CCDS31501.1	.	.	.	.	.	.	.	.	.	.	C	10.68	1.417099	0.25552	.	.	ENSG00000181939	ENST00000314644	T	0.01092	5.35	4.79	4.79	0.61399	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.01523	0.0049	N	0.20881	0.62	0.09310	N	1	B	0.34264	0.446	B	0.35813	0.211	T	0.54344	-0.8308	9	0.62326	D	0.03	.	15.7279	0.77777	0.0:1.0:0.0:0.0	.	52	Q8NGM1	OR4CF_HUMAN	G	106	ENSP00000324958:A106G	ENSP00000324958:A106G	A	+	2	0	OR4C15	55078675	0.000000	0.05858	0.765000	0.31456	0.191000	0.23601	-0.885000	0.04161	2.665000	0.90641	0.385000	0.25706	GCT	C|0.966;A|0.034	.	alt		0.443	OR4C15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391164.1	NM_001001920	
ECI1	1632	hgsc.bcm.edu	37	16	2294549	2294549	+	Missense_Mutation	SNP	C	C	T	rs145543160		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:2294549C>T	ENST00000301729.4	-	4	346	c.299G>A	c.(298-300)cGc>cAc	p.R100H	RP11-304L19.11_ENST00000565709.1_RNA|ECI1_ENST00000562238.1_Missense_Mutation_p.R100H|ECI1_ENST00000570258.1_Missense_Mutation_p.R41H	NM_001919.3	NP_001910.2	P42126	ECI1_HUMAN	enoyl-CoA delta isomerase 1	100					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|intramolecular oxidoreductase activity (GO:0016860)			endometrium(1)|large_intestine(2)|lung(6)	9						GACACCCGGGCGGTCCTGCAG	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		16248	0.0		0.001	False		,,,				2504	0.0				p.R100H		Atlas-SNP	.											ECI1,NS,carcinoma,-1,1	ECI1	20	1	0			c.G299A						PASS	.	C	HIS/ARG,HIS/ARG	3,4349		0,3,2173	20.0	19.0	19.0		299,299	3.1	0.0	16	dbSNP_134	19	14,8564		0,14,4275	yes	missense,missense	ECI1	NM_001178029.1,NM_001919.3	29,29	0,17,6448	TT,TC,CC		0.1632,0.0689,0.1315	possibly-damaging,possibly-damaging	100/286,100/303	2294549	17,12913	2176	4289	6465	SO:0001583	missense	1632	exon4			CCCGGGCGGTCCT		CCDS10464.1, CCDS58410.1	16p13.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000167969	ENSG00000167969	5.3.3.8		2703	protein-coding gene	gene with protein product	"""3,2 trans-enoyl-CoA isomerase"""	600305	"""dodecenoyl-Coenzyme A delta isomerase (3,2 trans-enoyl-Coenzyme A isomerase)"", ""dodecenoyl-CoA isomerase"""	DCI		7829074	Standard	NM_001178029		Approved		uc002cpr.3	P42126	OTTHUMG00000128830	ENST00000301729.4:c.299G>A	16.37:g.2294549C>T	ENSP00000301729:p.Arg100His	108.0	0.0	0		109.0	42.0	0.385321	NM_001178029	A8K512|Q13290|Q7Z2L6|Q7Z2L7|Q9BUB8|Q9BW05|Q9UDG6	Missense_Mutation	SNP	ENST00000301729.4	37	CCDS10464.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.396	1.076878	0.20227	6.89E-4	0.001632	ENSG00000167969	ENST00000301729	D	0.85702	-2.02	5.1	3.08	0.35506	Crotonase, core (1);	1.086010	0.06745	N	0.778936	T	0.78502	0.4293	L	0.52573	1.65	0.09310	N	1	P;B	0.40476	0.718;0.084	B;B	0.30105	0.111;0.024	T	0.63892	-0.6534	10	0.35671	T	0.21	-4.2812	8.5437	0.33408	0.1653:0.5146:0.3201:0.0	.	100;100	P42126-2;P42126	.;ECI1_HUMAN	H	100	ENSP00000301729:R100H	ENSP00000301729:R100H	R	-	2	0	ECI1	2234550	0.000000	0.05858	0.047000	0.18901	0.030000	0.12068	-0.936000	0.03946	0.697000	0.31718	0.650000	0.86243	CGC	C|0.998;T|0.002	0.002	strong		0.692	ECI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250768.1		
SKP2	6502	hgsc.bcm.edu	37	5	36163858	36163858	+	Splice_Site	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:36163858C>T	ENST00000274255.6	+	3	588	c.392C>T	c.(391-393)gCg>gTg	p.A131V	SKP2_ENST00000274254.5_Splice_Site_p.A131V|SKP2_ENST00000508514.1_Intron|SKP2_ENST00000546211.1_Intron	NM_005983.3	NP_005974.2	Q13309	SKP2_HUMAN	S-phase kinase-associated protein 2, E3 ubiquitin protein ligase	131	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|cellular response to cell-matrix adhesion (GO:0071460)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein polyubiquitination (GO:0000209)|regulation of cell cycle (GO:0051726)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SCF ubiquitin ligase complex (GO:0019005)	identical protein binding (GO:0042802)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(2)|ovary(1)	4	all_lung(31;5.63e-05)		Epithelial(62;0.0396)|Lung(74;0.111)|all cancers(62;0.115)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TATCGCCTAGCGTAAGTATTT	0.458																																					p.A131V		Atlas-SNP	.											.	SKP2	70	.	0			c.C392T						PASS	.						118.0	101.0	107.0					5																	36163858		2203	4300	6503	SO:0001630	splice_region_variant	6502	exon3			GCCTAGCGTAAGT	U33761	CCDS3915.1, CCDS3916.1, CCDS58944.1	5p13	2012-02-23	2012-02-23		ENSG00000145604	ENSG00000145604		"""F-boxes / Leucine-rich repeats"""	10901	protein-coding gene	gene with protein product		601436	"""S-phase kinase-associated protein 2 (p45)"""			8646875	Standard	NM_005983		Approved	FBXL1, FBL1, p45	uc003jkc.2	Q13309	OTTHUMG00000131106	ENST00000274255.6:c.392+1C>T	5.37:g.36163858C>T		173.0	0.0	0		185.0	95.0	0.513514	NM_032637	A8K5E0|B4DJT4|Q8TDZ0|Q8TDZ1|Q9BV69	Missense_Mutation	SNP	ENST00000274255.6	37	CCDS3916.1	.	.	.	.	.	.	.	.	.	.	C	14.54	2.565020	0.45694	.	.	ENSG00000145604	ENST00000274254;ENST00000274255;ENST00000308927;ENST00000513151	T;T;T	0.55930	0.49;0.49;0.49	4.92	4.05	0.47172	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.382188	0.30723	N	0.009015	T	0.37376	0.1001	N	0.24115	0.695	0.80722	D	1	B;B	0.23806	0.059;0.091	B;B	0.09377	0.003;0.004	T	0.31223	-0.9951	10	0.72032	D	0.01	-7.66	11.5359	0.50636	0.0:0.9161:0.0:0.0839	.	131;131	Q13309-2;Q13309	.;SKP2_HUMAN	V	131;131;97;131	ENSP00000274254:A131V;ENSP00000274255:A131V;ENSP00000423188:A131V	ENSP00000274254:A131V	A	+	2	0	SKP2	36199615	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.113000	0.57851	1.437000	0.47472	0.650000	0.86243	GCG	.	.	none		0.458	SKP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253769.2	NM_005983	Missense_Mutation
TBXAS1	6916	hgsc.bcm.edu	37	7	139715645	139715645	+	Missense_Mutation	SNP	C	C	A	rs5763	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:139715645C>A	ENST00000336425.5	+	15	1738	c.1349C>A	c.(1348-1350)aCc>aAc	p.T450N	TBXAS1_ENST00000414508.2_Missense_Mutation_p.T451N|TBXAS1_ENST00000411653.1_Missense_Mutation_p.T450N|TBXAS1_ENST00000448866.1_Missense_Mutation_p.T450N|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000436047.2_Missense_Mutation_p.T451N|TBXAS1_ENST00000263552.6_Missense_Mutation_p.T451N|TBXAS1_ENST00000425687.1_Missense_Mutation_p.T383N|TBXAS1_ENST00000458722.1_Missense_Mutation_p.T496N|TBXAS1_ENST00000416849.2_Missense_Mutation_p.T497N			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	450			T -> N (in allele CYP5A1*8; dbSNP:rs5763). {ECO:0000269|PubMed:11465543}.		arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	AGCCCGGAGACCTTCAACCCT	0.602													C|||	27	0.00539137	0.0015	0.0072	5008	,	,		16586	0.0		0.0149	False		,,,				2504	0.0051				p.T497N		Atlas-SNP	.											.	TBXAS1	121	.	0			c.C1490A	GRCh37	CM054133	TBXAS1	M	rs5763	PASS	.	C	ASN/THR,ASN/THR,ASN/THR,ASN/THR,ASN/THR	15,4391	22.3+/-47.3	0,15,2188	53.0	52.0	53.0		1352,1352,1490,1148,1352	0.3	0.1	7	dbSNP_52	53	178,8422	78.6+/-141.3	3,172,4125	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	65,65,65,65,65	3,187,6313	AA,AC,CC		2.0698,0.3404,1.4839	benign,benign,benign,benign,benign	451/535,451/535,497/581,383/467,451/461	139715645	193,12813	2203	4300	6503	SO:0001583	missense	6916	exon12			CGGAGACCTTCAA	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1349C>A	7.37:g.139715645C>A	ENSP00000338087:p.Thr450Asn	76.0	0.0	0		57.0	25.0	0.438596	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		14	0.00641025641025641	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	3.350	-0.132775	0.06711	0.003404	0.020698	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.69435	-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4;-0.4	4.52	0.297	0.15762	.	0.380726	0.27577	N	0.018760	T	0.37293	0.0998	L	0.47190	1.495	0.80722	D	1	B;B;B;B;B;B;B	0.14805	0.011;0.009;0.003;0.002;0.002;0.004;0.004	B;B;B;B;B;B;B	0.26517	0.025;0.01;0.014;0.007;0.07;0.014;0.009	T	0.33497	-0.9866	10	0.52906	T	0.07	.	4.2042	0.10481	0.459:0.3493:0.0:0.1916	rs5763;rs52807031;rs61074508;rs5763	431;497;402;383;451;451;450	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	N	383;451;450;497;451;451;450;496;450	ENSP00000388736:T383N;ENSP00000263552:T451N;ENSP00000338087:T450N;ENSP00000389414:T497N;ENSP00000392361:T451N;ENSP00000392702:T451N;ENSP00000402536:T450N;ENSP00000411274:T496N;ENSP00000411326:T450N	ENSP00000263552:T451N	T	+	2	0	TBXAS1	139362114	0.703000	0.27826	0.050000	0.19076	0.020000	0.10135	-0.032000	0.12266	0.039000	0.15632	-0.379000	0.06801	ACC	C|0.988;A|0.012	0.012	strong		0.602	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
PSMB8	5696	hgsc.bcm.edu	37	6	32809947	32809947	+	Silent	SNP	G	G	A	rs11540143	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:32809947G>A	ENST00000374882.3	-	4	551	c.501C>T	c.(499-501)ctC>ctT	p.L167L	PSMB8_ENST00000374881.2_Silent_p.L163L|TAPSAR1_ENST00000453426.1_lincRNA|PSMB9_ENST00000395330.1_5'Flank|PSMB8_ENST00000395339.3_Silent_p.L143L	NM_148919.3	NP_683720.2	P28062	PSB8_HUMAN	proteasome (prosome, macropain) subunit, beta type, 8	167					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|proteasome complex (GO:0000502)|proteasome core complex (GO:0005839)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)			NS(1)|cervix(1)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	11					Carfilzomib(DB08889)	TGCCCATAGAGAGGCCCATGC	0.532													G|||	6	0.00119808	0.0	0.0029	5008	,	,		20162	0.001		0.003	False		,,,				2504	0.0				p.L167L	NSCLC(48;53 1172 10859 13624 22883)	Atlas-SNP	.											.	PSMB8	42	.	0			c.C501T						PASS	.	G	,	0,3022		0,0,1511	133.0	117.0	122.0		489,501	4.2	1.0	6	dbSNP_120	122	35,5383		0,35,2674	no	coding-synonymous,coding-synonymous	PSMB8	NM_004159.4,NM_148919.3	,	0,35,4185	AA,AG,GG		0.646,0.0,0.4147	,	163/273,167/277	32809947	35,8405	1511	2709	4220	SO:0001819	synonymous_variant	5696	exon4			CATAGAGAGGCCC		CCDS4756.1, CCDS4757.1	6p21.3	2013-03-27	2013-03-27		ENSG00000204264	ENSG00000204264		"""Proteasome (prosome, macropain) subunits"""	9545	protein-coding gene	gene with protein product		177046	"""proteasome (prosome, macropain) subunit, beta type, 8 (large multifunctional protease 7)"", ""large multifunctional peptidase 7"""	LMP7		1529427, 10329130	Standard	XM_005275000		Approved	RING10, D6S216E, PSMB5i, beta5i	uc003oce.3	P28062	OTTHUMG00000031285	ENST00000374882.3:c.501C>T	6.37:g.32809947G>A		116.0	0.0	0		119.0	54.0	0.453782	NM_148919	B0UZC0|Q29824|Q5JNW6|Q5QNR8|Q96J48	Silent	SNP	ENST00000374882.3	37	CCDS4757.1																																																																																			G|0.996;A|0.004	0.004	strong		0.532	PSMB8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076617.3	NM_148919	
NRDE2	55051	hgsc.bcm.edu	37	14	90745442	90745442	+	Silent	SNP	T	T	C	rs141933992	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:90745442T>C	ENST00000354366.3	-	13	3565	c.3333A>G	c.(3331-3333)gtA>gtG	p.V1111V	NRDE2_ENST00000357904.3_Silent_p.V880V	NM_017970.3	NP_060440.2	Q9H7Z3	NRDE2_HUMAN	NRDE-2, necessary for RNA interference, domain containing	1111																	CTTTGTAGAATACACCTTTGC	0.458													T|||	8	0.00159744	0.0	0.0	5008	,	,		23470	0.0		0.006	False		,,,				2504	0.002				p.V1111V		Atlas-SNP	.											.	.	.	.	0			c.A3333G						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	230.0	214.0	220.0		3333,2640	-0.1	1.0	14	dbSNP_134	220	35,8565	22.8+/-68.1	0,35,4265	no	coding-synonymous,coding-synonymous	C14orf102	NM_017970.3,NM_199043.1	,	0,36,6467	CC,CT,TT		0.407,0.0227,0.2768	,	1111/1165,880/934	90745442	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	55051	exon13			GTAGAATACACCT	AK000870	CCDS9890.1	14q32.11	2012-12-14	2012-09-25	2012-09-25	ENSG00000119720	ENSG00000119720			20186	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 102"""	C14orf102			Standard	NM_017970		Approved	FLJ14051	uc001xyi.2	Q9H7Z3	OTTHUMG00000171020	ENST00000354366.3:c.3333A>G	14.37:g.90745442T>C		96.0	0.0	0		107.0	46.0	0.429907	NM_017970	B4DH71|Q4G0A7|Q9NWH6	Silent	SNP	ENST00000354366.3	37	CCDS9890.1																																																																																			T|0.998;C|0.002	0.002	strong		0.458	NRDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411264.1	NM_017970	
TRERF1	55809	hgsc.bcm.edu	37	6	42236589	42236589	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:42236589C>G	ENST00000372922.4	-	5	1302	c.740G>C	c.(739-741)gGa>gCa	p.G247A	TRERF1_ENST00000354325.2_Missense_Mutation_p.G247A|TRERF1_ENST00000541110.1_Missense_Mutation_p.G247A|TRERF1_ENST00000372917.4_Missense_Mutation_p.G247A|TRERF1_ENST00000340840.2_Missense_Mutation_p.G247A	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	247	Gln-rich.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			TGGCTGTCCTCCCTGCACTGG	0.602																																					p.G247A		Atlas-SNP	.											.	TRERF1	124	.	0			c.G740C						PASS	.						48.0	47.0	47.0					6																	42236589		2202	4299	6501	SO:0001583	missense	55809	exon5			TGTCCTCCCTGCA	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.740G>C	6.37:g.42236589C>G	ENSP00000362013:p.Gly247Ala	84.0	0.0	0		119.0	60.0	0.504202	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Missense_Mutation	SNP	ENST00000372922.4	37	CCDS4867.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648503	0.47258	.	.	ENSG00000124496	ENST00000541110;ENST00000372917;ENST00000372922;ENST00000340840;ENST00000354325	T;T;T;T;T	0.12465	2.84;2.68;2.84;2.68;2.68	5.54	3.63	0.41609	.	0.268702	0.25566	N	0.029784	T	0.07593	0.0191	N	0.24115	0.695	0.25742	N	0.985152	D;D;D;B;B	0.71674	0.998;0.997;0.997;0.008;0.008	D;D;D;B;B	0.70935	0.971;0.936;0.936;0.015;0.015	T	0.15206	-1.0445	10	0.25106	T	0.35	-6.3785	4.8502	0.13533	0.0:0.4353:0.3986:0.1661	.	247;247;247;86;86	Q96PN7-4;Q05GC8;Q96PN7;Q96PN7-2;Q96PN7-3	.;.;TREF1_HUMAN;.;.	A	247	ENSP00000439689:G247A;ENSP00000362008:G247A;ENSP00000362013:G247A;ENSP00000339438:G247A;ENSP00000346285:G247A	ENSP00000339438:G247A	G	-	2	0	TRERF1	42344567	0.891000	0.30450	0.993000	0.49108	0.992000	0.81027	0.852000	0.27764	1.319000	0.45190	0.462000	0.41574	GGA	.	.	none		0.602	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
C2orf42	54980	hgsc.bcm.edu	37	2	70387826	70387826	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:70387826C>A	ENST00000264434.2	-	9	1826	c.1447G>T	c.(1447-1449)Gaa>Taa	p.E483*	C2orf42_ENST00000420306.1_Nonsense_Mutation_p.E483*	NM_017880.1	NP_060350.1	Q9NWW7	CB042_HUMAN	chromosome 2 open reading frame 42	483										endometrium(2)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	12						CCGTAGGTTTCTGCTATGCTT	0.418																																					p.E483X		Atlas-SNP	.											.	C2orf42	30	.	0			c.G1447T						PASS	.						156.0	154.0	154.0					2																	70387826		2203	4300	6503	SO:0001587	stop_gained	54980	exon9			AGGTTTCTGCTAT	AK000565	CCDS1899.1	2p14	2011-03-08			ENSG00000115998	ENSG00000115998			26056	protein-coding gene	gene with protein product						12477932	Standard	XM_005264389		Approved	FLJ20558	uc002sgh.3	Q9NWW7	OTTHUMG00000129642	ENST00000264434.2:c.1447G>T	2.37:g.70387826C>A	ENSP00000264434:p.Glu483*	262.0	0.0	0		370.0	247.0	0.667568	NM_017880	D6W5G3|Q9H629	Nonsense_Mutation	SNP	ENST00000264434.2	37	CCDS1899.1	.	.	.	.	.	.	.	.	.	.	C	37	6.198271	0.97367	.	.	ENSG00000115998	ENST00000264434;ENST00000420306	.	.	.	5.24	5.24	0.73138	.	0.212745	0.47852	D	0.000210	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	-25.1419	17.5771	0.87953	0.0:1.0:0.0:0.0	.	.	.	.	X	483	.	ENSP00000264434:E483X	E	-	1	0	C2orf42	70241330	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.278000	0.65592	2.726000	0.93360	0.650000	0.86243	GAA	.	.	none		0.418	C2orf42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251840.1	NM_017880	
FRMD1	79981	hgsc.bcm.edu	37	6	168461516	168461516	+	Missense_Mutation	SNP	C	C	T	rs148097635	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:168461516C>T	ENST00000283309.6	-	9	1331	c.1267G>A	c.(1267-1269)Ggg>Agg	p.G423R	FRMD1_ENST00000432403.1_5'UTR|FRMD1_ENST00000440994.2_Missense_Mutation_p.G355R|FRMD1_ENST00000537786.1_Missense_Mutation_p.G194R	NM_024919.3	NP_079195.3	Q8N878	FRMD1_HUMAN	FERM domain containing 1	423						cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|urinary_tract(1)	19		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		TCATGGAGCCCGTGGACCTCC	0.657													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17850	0.002		0.0	False		,,,				2504	0.0				p.G423R	GBM(50;8 1094 9538 34399)|Ovarian(80;676 1857 8675 49015)	Atlas-SNP	.											.	FRMD1	52	.	0			c.G1267A						PASS	.	C	ARG/GLY,ARG/GLY	1,4405	2.1+/-5.4	0,1,2202	47.0	42.0	44.0		1063,1267	-2.6	0.0	6	dbSNP_134	44	17,8583	11.2+/-40.8	0,17,4283	yes	missense,missense	FRMD1	NM_001122841.1,NM_024919.3	125,125	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign,benign	355/482,423/550	168461516	18,12988	2203	4300	6503	SO:0001583	missense	79981	exon9			GGAGCCCGTGGAC		CCDS5306.1, CCDS47518.1	6q27	2008-10-23			ENSG00000153303	ENSG00000153303			21240	protein-coding gene	gene with protein product							Standard	NM_001122841		Approved	FLJ00181, DKFZp434O0117, FLJ40260, FLJ22615, bA164L23.1	uc003qwo.4	Q8N878	OTTHUMG00000016037	ENST00000283309.6:c.1267G>A	6.37:g.168461516C>T	ENSP00000283309:p.Gly423Arg	100.0	0.0	0		148.0	78.0	0.527027	NM_024919	B2RNV8|B3KUM6|Q5SZU7|Q9UFB0	Missense_Mutation	SNP	ENST00000283309.6	37	CCDS5306.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.675	-0.276625	0.05679	2.27E-4	0.001977	ENSG00000153303	ENST00000283309;ENST00000440994;ENST00000537786	T;T;T	0.50277	0.75;0.75;0.75	2.48	-2.6	0.06190	.	2.404160	0.02924	U	0.138326	T	0.09642	0.0237	L	0.36672	1.1	0.09310	N	1	B;P;B;B	0.36733	0.076;0.567;0.207;0.262	B;B;B;B	0.22152	0.012;0.038;0.027;0.021	T	0.04053	-1.0981	10	0.10636	T	0.68	.	4.8184	0.13378	0.1237:0.1851:0.5734:0.1178	.	358;423;355;318	B7Z8G9;Q8N878;Q8N878-2;Q5SZU5	.;FRMD1_HUMAN;.;.	R	423;355;194	ENSP00000283309:G423R;ENSP00000414115:G355R;ENSP00000440078:G194R	ENSP00000283309:G423R	G	-	1	0	FRMD1	168204365	0.001000	0.12720	0.000000	0.03702	0.053000	0.15095	0.872000	0.28037	-0.378000	0.07918	0.313000	0.20887	GGG	C|0.999;T|0.001	0.001	strong		0.657	FRMD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362513.2	NM_024919	
KIF27	55582	hgsc.bcm.edu	37	9	86474262	86474262	+	Missense_Mutation	SNP	T	T	C	rs79324787	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:86474262T>C	ENST00000297814.2	-	14	3102	c.2959A>G	c.(2959-2961)Ata>Gta	p.I987V	RP11-575L7.4_ENST00000590417.1_RNA|RP11-575L7.4_ENST00000591217.1_RNA|KIF27_ENST00000413982.1_Missense_Mutation_p.I921V|RP11-575L7.4_ENST00000592283.1_RNA|KIF27_ENST00000334204.2_Missense_Mutation_p.I890V|RP11-575L7.4_ENST00000589233.1_RNA|RP11-575L7.4_ENST00000589817.1_RNA|RP11-575L7.4_ENST00000586211.1_RNA|RP11-575L7.4_ENST00000608866.1_RNA|RP11-575L7.4_ENST00000590813.1_RNA|RP11-575L7.4_ENST00000590368.1_RNA|RP11-575L7.4_ENST00000421734.3_RNA|RP11-575L7.4_ENST00000586206.1_RNA	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	987					ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CGAGTTGATATTTTCAAACTA	0.378													T|||	54	0.0107827	0.0333	0.0043	5008	,	,		16078	0.001		0.003	False		,,,				2504	0.0031				p.I987V		Atlas-SNP	.											.	KIF27	103	.	0			c.A2959G						PASS	.	T	VAL/ILE	16,4390	9.9+/-24.2	0,16,2187	94.0	81.0	85.0		2959	4.5	1.0	9	dbSNP_131	85	1,8599		0,1,4299	yes	missense	KIF27	NM_017576.1	29	0,17,6486	CC,CT,TT		0.0116,0.3631,0.1307	benign	987/1402	86474262	17,12989	2203	4300	6503	SO:0001583	missense	55582	exon14			TTGATATTTTCAA	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.2959A>G	9.37:g.86474262T>C	ENSP00000297814:p.Ile987Val	121.0	0.0	0		136.0	11.0	0.0808824	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	T	1.953	-0.440642	0.04636	0.003631	1.16E-4	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.55930	0.49;0.49;0.49	4.49	4.49	0.54785	.	0.125199	0.34067	N	0.004296	T	0.28466	0.0704	N	0.20685	0.6	0.09310	N	0.999999	B;P;P	0.35656	0.049;0.514;0.506	B;B;B	0.36989	0.05;0.238;0.12	T	0.35599	-0.9782	10	0.02654	T	1	.	4.0383	0.09740	0.2382:0.0971:0.0:0.6647	.	890;921;987	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	V	987;921;890	ENSP00000297814:I987V;ENSP00000401688:I921V;ENSP00000333928:I890V	ENSP00000297814:I987V	I	-	1	0	KIF27	85664082	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	2.394000	0.44450	1.880000	0.54463	0.397000	0.26171	ATA	T|0.994;C|0.006	0.006	strong		0.378	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
DYX1C1	161582	hgsc.bcm.edu	37	15	55722956	55722956	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55722956G>A	ENST00000321149.3	-	10	1542	c.1175C>T	c.(1174-1176)gCa>gTa	p.A392V	DYX1C1_ENST00000457155.2_Missense_Mutation_p.H357Y|DYX1C1_ENST00000348518.3_Missense_Mutation_p.H357Y|DYX1C1_ENST00000380679.1_Intron|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000448430.2_Intron	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	392					cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		AATCTTAAGTGCCGCTTCATA	0.294																																					p.A392V		Atlas-SNP	.											DYX1C1,NS,carcinoma,-1,1	DYX1C1	54	1	0			c.C1175T						PASS	.						126.0	123.0	124.0					15																	55722956		2192	4290	6482	SO:0001583	missense	161582	exon10			TTAAGTGCCGCTT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.1175C>T	15.37:g.55722956G>A	ENSP00000323275:p.Ala392Val	130.0	0.0	0		125.0	60.0	0.48	NM_130810	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	32|32	5.120950|5.120950	0.94385|0.94385	.|.	.|.	ENSG00000256061|ENSG00000256061	ENST00000321149|ENST00000457155;ENST00000348518	D|T;T	0.82803|0.27557	-1.65|1.66;1.66	5.6|5.6	5.6|5.6	0.85130|0.85130	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.19846|0.19846	0.0477|0.0477	.|.	.|.	.|.	0.34596|0.34596	D|D	0.715963|0.715963	D|B	0.89917|0.29766	1.0|0.256	D|B	0.91635|0.34138	0.999|0.176	T|T	0.05632|0.05632	-1.0873|-1.0873	9|8	0.66056|0.02654	D|T	0.02|1	.|.	18.6754|18.6754	0.91526|0.91526	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	392|357	Q8WXU2|Q8WXU2-3	DYXC1_HUMAN|.	V|Y	392|357	ENSP00000323275:A392V|ENSP00000402640:H357Y;ENSP00000299561:H357Y	ENSP00000323275:A392V|ENSP00000299561:H357Y	A|H	-|-	2|1	0|0	DYX1C1|DYX1C1	53510248|53510248	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	7.977000|7.977000	0.88081|0.88081	2.650000|2.650000	0.89964|0.89964	0.558000|0.558000	0.71614|0.71614	GCA|CAC	.	.	none		0.294	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872869	51872869	+	Missense_Mutation	SNP	C	C	A	rs61760185	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:51872869C>A	ENST00000371497.5	+	2	3759	c.2872C>A	c.(2872-2874)Cgc>Agc	p.R958S	TSHZ2_ENST00000603338.2_Missense_Mutation_p.R955S|RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000329613.6_Missense_Mutation_p.R955S	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	958					multicellular organismal development (GO:0007275)|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(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			GGACATGACCCGCTTGTCAGT	0.507													C|||	2	0.000399361	0.0	0.0	5008	,	,		19232	0.0		0.002	False		,,,				2504	0.0				p.R958S		Atlas-SNP	.											.	TSHZ2	209	.	0			c.C2872A						PASS	.	C	SER/ARG,SER/ARG	2,4404	4.2+/-10.8	0,2,2201	77.0	77.0	77.0		2863,2872	4.7	1.0	20	dbSNP_129	77	25,8575	16.0+/-53.3	0,25,4275	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	110,110	0,27,6476	AA,AC,CC		0.2907,0.0454,0.2076	probably-damaging,probably-damaging	955/1032,958/1035	51872869	27,12979	2203	4300	6503	SO:0001583	missense	128553	exon2			ATGACCCGCTTGT	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2872C>A	20.37:g.51872869C>A	ENSP00000360552:p.Arg958Ser	84.0	0.0	0		121.0	75.0	0.619835	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	17.55	3.417888	0.62622	4.54E-4	0.002907	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.15603	2.42;2.41	5.7	4.7	0.59300	.	0.047245	0.85682	D	0.000000	T	0.14700	0.0355	N	0.22421	0.69	0.52501	D	0.999954	P	0.52842	0.956	P	0.45681	0.49	T	0.00844	-1.1543	10	0.62326	D	0.03	-11.6406	11.9946	0.53194	0.3361:0.6639:0.0:0.0	rs61760185	958	Q9NRE2	TSH2_HUMAN	S	958;955;484	ENSP00000360552:R958S;ENSP00000333114:R955S	ENSP00000333114:R955S	R	+	1	0	TSHZ2	51306276	1.000000	0.71417	1.000000	0.80357	0.756000	0.42949	6.371000	0.73119	2.685000	0.91497	0.643000	0.83706	CGC	C|0.999;A|0.001	0.001	strong		0.507	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
CCT5	22948	hgsc.bcm.edu	37	5	10261764	10261764	+	Missense_Mutation	SNP	C	C	G	rs141675330	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:10261764C>G	ENST00000280326.4	+	8	1506	c.1086C>G	c.(1084-1086)atC>atG	p.I362M	CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000515390.1_Missense_Mutation_p.I307M|CCT5_ENST00000515676.1_Missense_Mutation_p.I324M|CCT5_ENST00000506600.1_Missense_Mutation_p.I269M|CCT5_ENST00000503026.1_Missense_Mutation_p.I341M	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	362					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TACAGGAGATCTCATTTGGGA	0.478													C|||	15	0.00299521	0.0008	0.0144	5008	,	,		19303	0.0		0.004	False		,,,				2504	0.0				p.I362M		Atlas-SNP	.											.	CCT5	49	.	0			c.C1086G						PASS	.	C	MET/ILE	8,4398	14.3+/-33.2	0,8,2195	146.0	154.0	151.0		1086	3.6	1.0	5	dbSNP_134	151	57,8543	36.4+/-91.3	0,57,4243	yes	missense	CCT5	NM_012073.3	10	0,65,6438	GG,GC,CC		0.6628,0.1816,0.4998	benign	362/542	10261764	65,12941	2203	4300	6503	SO:0001583	missense	22948	exon8			GGAGATCTCATTT	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1086C>G	5.37:g.10261764C>G	ENSP00000280326:p.Ile362Met	374.0	1.0	0.0026738		376.0	196.0	0.521277	NM_012073	A8JZY8|A8K2X8|B4DYD8	Missense_Mutation	SNP	ENST00000280326.4	37	CCDS3877.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	13.57	2.278030	0.40294	0.001816	0.006628	ENSG00000150753	ENST00000280326;ENST00000503026;ENST00000515390;ENST00000440011;ENST00000515676;ENST00000506600	T;T;T;T;T	0.78481	-1.18;-1.18;-1.18;-1.18;-1.18	5.39	3.59	0.41128	.	0.045544	0.85682	D	0.000000	T	0.59959	0.2232	L	0.28014	0.82	0.58432	D	0.999999	B;B;B;B;B;B	0.25772	0.113;0.012;0.134;0.006;0.006;0.006	B;B;B;B;B;B	0.34722	0.188;0.079;0.049;0.049;0.049;0.049	T	0.62286	-0.6886	10	0.45353	T	0.12	-30.4305	9.1905	0.37195	0.0:0.7727:0.0:0.2273	.	269;307;211;360;362;362	B4DYD8;E7ENZ3;B4DZY9;Q9BU08;A8K2X8;P48643	.;.;.;.;.;TCPE_HUMAN	M	362;341;307;335;324;269	ENSP00000280326:I362M;ENSP00000423318:I341M;ENSP00000426923:I307M;ENSP00000427297:I324M;ENSP00000423052:I269M	ENSP00000280326:I362M	I	+	3	3	CCT5	10314764	1.000000	0.71417	0.997000	0.53966	0.985000	0.73830	1.786000	0.38694	1.266000	0.44231	0.558000	0.71614	ATC	C|0.996;G|0.004	0.004	strong		0.478	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
CSRNP1	64651	hgsc.bcm.edu	37	3	39185525	39185525	+	Missense_Mutation	SNP	G	G	A	rs375810664		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:39185525G>A	ENST00000273153.5	-	5	968	c.791C>T	c.(790-792)aCa>aTa	p.T264I	CSRNP1_ENST00000514182.1_Missense_Mutation_p.T264I	NM_033027.3	NP_149016.2	Q96S65	CSRN1_HUMAN	cysteine-serine-rich nuclear protein 1	264	Cys-rich.				apoptotic process (GO:0006915)|face morphogenesis (GO:0060325)|palate development (GO:0060021)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|skeletal system morphogenesis (GO:0048705)	nucleus (GO:0005634)	RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(5)|lung(3)|ovary(5)|skin(3)	24						GGGGAATGCTGTGTGGTCCAT	0.552																																					p.T264I		Atlas-SNP	.											.	CSRNP1	59	.	0			c.C791T						PASS	.	G	ILE/THR	0,4406		0,0,2203	39.0	39.0	39.0		791	4.5	0.9	3		39	1,8599	1.2+/-3.3	0,1,4299	no	missense	CSRNP1	NM_033027.3	89	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	264/590	39185525	1,13005	2203	4300	6503	SO:0001583	missense	64651	exon5			AATGCTGTGTGGT	AB053121	CCDS2682.1	3p22	2009-04-17	2009-04-17	2009-04-17	ENSG00000144655	ENSG00000144655			14300	protein-coding gene	gene with protein product		606458	"""AXIN1 up-regulated 1"""	AXUD1		11526492, 17726538	Standard	NM_033027		Approved	URAX1, DKFZp566F164, FAM130B, TAIP-3	uc003cjg.3	Q96S65	OTTHUMG00000131293	ENST00000273153.5:c.791C>T	3.37:g.39185525G>A	ENSP00000273153:p.Thr264Ile	36.0	0.0	0		52.0	21.0	0.403846	NM_033027	Q69YY5	Missense_Mutation	SNP	ENST00000273153.5	37	CCDS2682.1	.	.	.	.	.	.	.	.	.	.	G	16.31	3.087702	0.55968	0.0	1.16E-4	ENSG00000144655	ENST00000273153;ENST00000514182	T;T	0.14516	2.5;2.5	4.48	4.48	0.54585	.	0.061123	0.64402	D	0.000003	T	0.28599	0.0708	L	0.51422	1.61	0.36804	D	0.885495	D	0.67145	0.996	P	0.59889	0.865	T	0.10042	-1.0647	10	0.46703	T	0.11	-16.1823	17.7133	0.88328	0.0:0.0:1.0:0.0	.	264	Q96S65	CSRN1_HUMAN	I	264	ENSP00000273153:T264I;ENSP00000422532:T264I	ENSP00000273153:T264I	T	-	2	0	CSRNP1	39160529	0.997000	0.39634	0.946000	0.38457	0.905000	0.53344	2.532000	0.45659	2.475000	0.83589	0.561000	0.74099	ACA	.	.	weak		0.552	CSRNP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254061.1	NM_033027	
MYH9	4627	hgsc.bcm.edu	37	22	36685329	36685329	+	Silent	SNP	C	C	T	rs202127454		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36685329C>T	ENST00000216181.5	-	32	4589	c.4359G>A	c.(4357-4359)gaG>gaA	p.E1453E		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1453					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						AGATGGTCTTCTCCTCCGCCA	0.677			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				C|||	1	0.000199681	0.0	0.0	5008	,	,		19418	0.0		0.001	False		,,,				2504	0.0				p.E1453E		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.G4359A						PASS	.	C		0,4406		0,0,2203	22.0	20.0	21.0		4359	4.0	1.0	22		21	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MYH9	NM_002473.4		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		1453/1961	36685329	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	4627	exon32	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GGTCTTCTCCTCC		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.4359G>A	22.37:g.36685329C>T		55.0	0.0	0		57.0	22.0	0.385965	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	9.292	1.050864	0.19827	0.0	5.81E-4	ENSG00000100345	ENST00000397231	.	.	.	5.02	4.01	0.46588	.	.	.	.	.	T	0.31136	0.0787	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.12993	-1.0526	5	0.02654	T	1	.	9.9391	0.41570	0.0:0.8436:0.0:0.1564	.	.	.	.	K	56	.	ENSP00000380408:R56K	R	-	2	0	MYH9	35015275	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	3.320000	0.51991	1.253000	0.44018	0.491000	0.48974	AGA	C|1.000;T|0.000	0.000	strong		0.677	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
DECR2	26063	hgsc.bcm.edu	37	16	461554	461554	+	Missense_Mutation	SNP	C	C	G	rs370013477		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:461554C>G	ENST00000219481.5	+	8	993	c.855C>G	c.(853-855)ttC>ttG	p.F285L	DECR2_ENST00000461947.1_Intron|DECR2_ENST00000424398.2_Missense_Mutation_p.F273L	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	285					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				TGCCGGATTTCGCATCCTTCT	0.622																																					p.F285L		Atlas-SNP	.											.	DECR2	47	.	0			c.C855G						PASS	.	C	LEU/PHE	0,4404		0,0,2202	149.0	121.0	131.0		855	-10.7	0.0	16		131	1,8599	1.2+/-3.3	0,1,4299	no	missense	DECR2	NM_020664.3	22	0,1,6501	GG,GC,CC		0.0116,0.0,0.0077	benign	285/293	461554	1,13003	2202	4300	6502	SO:0001583	missense	26063	exon8			GGATTTCGCATCC	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.855C>G	16.37:g.461554C>G	ENSP00000219481:p.Phe285Leu	123.0	0.0	0		123.0	64.0	0.520325	NM_020664	Q6ZRS7|Q96ET0	Missense_Mutation	SNP	ENST00000219481.5	37	CCDS10409.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.995624	0.35226	0.0	1.16E-4	ENSG00000242612	ENST00000219481;ENST00000424398	T;T	0.80909	-1.43;-1.06	5.34	-10.7	0.00240	.	1.461700	0.03592	N	0.232010	T	0.59004	0.2162	N	0.04297	-0.235	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.55134	-0.8188	10	0.21014	T	0.42	.	15.9692	0.79998	0.0:0.6665:0.1013:0.2322	.	285	Q9NUI1	DECR2_HUMAN	L	285;273	ENSP00000219481:F285L;ENSP00000400374:F273L	ENSP00000219481:F285L	F	+	3	2	DECR2	401555	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.158000	0.03153	-2.920000	0.00305	-1.036000	0.02392	TTC	.	.	weak		0.622	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
TMEM125	128218	hgsc.bcm.edu	37	1	43738760	43738760	+	Missense_Mutation	SNP	G	G	A	rs143350378	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43738760G>A	ENST00000432792.2	+	4	937	c.367G>A	c.(367-369)Gtg>Atg	p.V123M	TMEM125_ENST00000439858.1_Missense_Mutation_p.V123M			Q96AQ2	TM125_HUMAN	transmembrane protein 125	123						integral component of membrane (GO:0016021)				breast(1)|large_intestine(1)|lung(1)	3	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CAGTGGCCTCGTGCTGCTGGT	0.721													G|||	5	0.000998403	0.0008	0.0014	5008	,	,		15058	0.0		0.003	False		,,,				2504	0.0				p.V123M		Atlas-SNP	.											.	TMEM125	18	.	0			c.G367A						PASS	.	G	MET/VAL	5,4391		0,5,2193	22.0	24.0	23.0		367	5.2	0.9	1	dbSNP_134	23	33,8553		1,31,4261	no	missense	TMEM125	NM_144626.2	21	1,36,6454	AA,AG,GG		0.3843,0.1137,0.2927	possibly-damaging	123/220	43738760	38,12944	2198	4293	6491	SO:0001583	missense	128218	exon4			GGCCTCGTGCTGC	BC016858	CCDS480.1	1p34.2	2006-02-16			ENSG00000179178	ENSG00000179178			28275	protein-coding gene	gene with protein product							Standard	NM_144626		Approved	MGC17299	uc021oml.1	Q96AQ2	OTTHUMG00000007288	ENST00000432792.2:c.367G>A	1.37:g.43738760G>A	ENSP00000429275:p.Val123Met	13.0	0.0	0		24.0	13.0	0.541667	NM_144626	D3DPX1	Missense_Mutation	SNP	ENST00000432792.2	37	CCDS480.1	.	.	.	.	.	.	.	.	.	.	G	17.47	3.397316	0.62177	0.001137	0.003843	ENSG00000179178	ENST00000439858;ENST00000432792	T;T	0.47177	0.85;0.85	5.24	5.24	0.73138	.	0.350030	0.29059	N	0.013275	T	0.46268	0.1384	L	0.27053	0.805	0.30773	N	0.742775	D	0.69078	0.997	P	0.53360	0.724	T	0.52946	-0.8507	10	0.62326	D	0.03	.	12.2066	0.54355	0.0783:0.0:0.9217:0.0	.	123	Q96AQ2	TM125_HUMAN	M	123	ENSP00000429775:V123M;ENSP00000429275:V123M	ENSP00000429275:V123M	V	+	1	0	TMEM125	43511347	0.980000	0.34600	0.929000	0.37066	0.676000	0.39594	2.566000	0.45948	2.446000	0.82766	0.455000	0.32223	GTG	G|0.997;A|0.003	0.003	strong		0.721	TMEM125-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019032.2	NM_144626	
FAM166A	401565	hgsc.bcm.edu	37	9	140139106	140139106	+	Silent	SNP	G	G	A	rs62584882	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:140139106G>A	ENST00000344774.4	-	5	789	c.735C>T	c.(733-735)ttC>ttT	p.F245F		NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	245						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						GGCTCTTGTCGAATTCGTCCA	0.582													G|||	11	0.00219649	0.0008	0.0	5008	,	,		19622	0.0		0.0089	False		,,,				2504	0.001				p.F245F		Atlas-SNP	.											.	FAM166A	44	.	0			c.C735T						PASS	.	G		6,4392	12.9+/-30.5	0,6,2193	139.0	119.0	126.0		735	-3.4	0.8	9	dbSNP_129	126	94,8504	51.9+/-112.3	1,92,4206	no	coding-synonymous	FAM166A	NM_001001710.1		1,98,6399	AA,AG,GG		1.0933,0.1364,0.7695		245/318	140139106	100,12896	2199	4299	6498	SO:0001819	synonymous_variant	401565	exon5			CTTGTCGAATTCG	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.735C>T	9.37:g.140139106G>A		184.0	0.0	0		223.0	98.0	0.439462	NM_001001710	A6NND9|Q8N830	Silent	SNP	ENST00000344774.4	37	CCDS35186.1																																																																																			G|0.994;A|0.006	0.006	strong		0.582	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710	
MYH9	4627	hgsc.bcm.edu	37	22	36708244	36708244	+	Silent	SNP	G	G	C	rs201827299		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:36708244G>C	ENST00000216181.5	-	14	1808	c.1578C>G	c.(1576-1578)gcC>gcG	p.A526A		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	526	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CGTCCAGCAGGGCCAGAATGC	0.647			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				G|||	1	0.000199681	0.0	0.0	5008	,	,		16777	0.0		0.001	False		,,,				2504	0.0				p.A526A		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.C1578G						PASS	.						67.0	60.0	62.0					22																	36708244		2203	4300	6503	SO:0001819	synonymous_variant	4627	exon14	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	CAGCAGGGCCAGA		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.1578C>G	22.37:g.36708244G>C		71.0	0.0	0		92.0	50.0	0.543478	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			G|1.000;C|0.000	0.000	strong		0.647	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
SLC4A8	9498	hgsc.bcm.edu	37	12	51856159	51856159	+	Silent	SNP	C	C	T	rs71449805	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:51856159C>T	ENST00000453097.2	+	10	1384	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC4A8_ENST00000358657.3_Silent_p.F416F|SLC4A8_ENST00000514353.3_Silent_p.F336F|SLC4A8_ENST00000535225.2_Silent_p.F336F|SLC4A8_ENST00000394856.1_Silent_p.F336F	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTGATGAGTTCCTAGACCAGG	0.473													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18122	0.0		0.0278	False		,,,				2504	0.0051				p.F389F		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C1167T						PASS	.	C	,	36,4370	41.6+/-74.8	0,36,2167	123.0	118.0	120.0		1167,1167	4.3	1.0	12	dbSNP_130	120	351,8249	118.5+/-177.9	5,341,3954	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	5,377,6121	TT,TC,CC		4.0814,0.8171,2.9755	,	389/1094,389/1045	51856159	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon10			TGAGTTCCTAGAC	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1167C>T	12.37:g.51856159C>T		101.0	0.0	0		109.0	58.0	0.53211	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
PXDNL	137902	hgsc.bcm.edu	37	8	52321728	52321728	+	Missense_Mutation	SNP	G	G	C	rs201184283		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:52321728G>C	ENST00000356297.4	-	17	2556	c.2456C>G	c.(2455-2457)cCt>cGt	p.P819R	PXDNL_ENST00000543296.1_Missense_Mutation_p.P819R	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	819					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				GCTCAGCGCAGGCACTGTGTG	0.677																																					p.P819R		Atlas-SNP	.											PXDNL_ENST00000356297,uveal_tract,malignant_melanoma,0,2	PXDNL	414	2	0			c.C2456G						PASS	.	G	ARG/PRO	0,4240		0,0,2120	15.0	19.0	18.0		2456	2.5	0.0	8		18	14,8462		0,14,4224	yes	missense	PXDNL	NM_144651.4	103	0,14,6344	CC,CG,GG		0.1652,0.0,0.1101	possibly-damaging	819/1464	52321728	14,12702	2120	4238	6358	SO:0001583	missense	137902	exon17			AGCGCAGGCACTG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2456C>G	8.37:g.52321728G>C	ENSP00000348645:p.Pro819Arg	39.0	0.0	0		28.0	15.0	0.535714	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.	.	.	.	.	.	.	.	.	.	G	7.942	0.742913	0.15642	0.0	0.001652	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.67698	-0.28;-0.28	3.4	2.49	0.30216	.	0.143845	0.31989	N	0.006753	T	0.75803	0.3899	M	0.80746	2.51	0.27711	N	0.945471	D	0.58620	0.983	D	0.63703	0.917	T	0.66705	-0.5856	10	0.62326	D	0.03	.	4.3235	0.11029	0.1247:0.0:0.6474:0.2279	.	819	A1KZ92	PXDNL_HUMAN	R	819	ENSP00000348645:P819R;ENSP00000444865:P819R	ENSP00000348645:P819R	P	-	2	0	PXDNL	52484281	0.809000	0.29036	0.007000	0.13788	0.001000	0.01503	2.425000	0.44723	0.516000	0.28340	-0.188000	0.12872	CCT	.	.	weak		0.677	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
TDRD6	221400	hgsc.bcm.edu	37	6	46658915	46658915	+	Missense_Mutation	SNP	G	G	A	rs140575009	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46658915G>A	ENST00000316081.6	+	1	3050	c.3050G>A	c.(3049-3051)tGt>tAt	p.C1017Y	TDRD6_ENST00000544460.1_Missense_Mutation_p.C1017Y	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	1017					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			CAGTTGTCATGTAGTATTACA	0.348																																					p.C1017Y		Atlas-SNP	.											.	TDRD6	205	.	0			c.G3050A						PASS	.	G	TYR/CYS,TYR/CYS	1,4405	2.1+/-5.4	0,1,2202	50.0	54.0	53.0		3050,3050	-1.1	0.0	6	dbSNP_134	53	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	TDRD6	NM_001010870.2,NM_001168359.1	194,194	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	benign,benign	1017/2097,1017/2067	46658915	6,13000	2203	4300	6503	SO:0001583	missense	221400	exon1			TGTCATGTAGTAT	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.3050G>A	6.37:g.46658915G>A	ENSP00000346065:p.Cys1017Tyr	80.0	0.0	0		65.0	28.0	0.430769	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	0.004	-2.250495	0.00268	2.27E-4	5.81E-4	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09073	3.02;3.02	5.36	-1.1	0.09872	Maternal tudor protein (1);	1.918670	0.01499	N	0.017422	T	0.02012	0.0063	N	0.20986	0.625	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.45731	-0.9241	10	0.51188	T	0.08	1.382	8.6227	0.33870	0.6481:0.1225:0.2294:0.0	.	1017;1017	F5H5M3;O60522	.;TDRD6_HUMAN	Y	1017	ENSP00000443299:C1017Y;ENSP00000346065:C1017Y	ENSP00000346065:C1017Y	C	+	2	0	TDRD6	46766874	0.000000	0.05858	0.000000	0.03702	0.985000	0.73830	0.088000	0.14979	-0.617000	0.05664	-0.136000	0.14681	TGT	G|0.999;A|0.001	0.001	strong		0.348	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
ENPP2	5168	hgsc.bcm.edu	37	8	120575249	120575249	+	Missense_Mutation	SNP	C	C	T	rs61758149	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:120575249C>T	ENST00000075322.6	-	24	2327	c.2269G>A	c.(2269-2271)Gtg>Atg	p.V757M	ENPP2_ENST00000259486.6_Missense_Mutation_p.V809M|ENPP2_ENST00000522826.1_Missense_Mutation_p.V782M|ENPP2_ENST00000427067.2_Missense_Mutation_p.V778M|ENPP2_ENST00000522167.1_Missense_Mutation_p.V392M	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	757					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			CTGCCTTCCACGTACCTGAAA	0.443													C|||	7	0.00139776	0.0	0.0014	5008	,	,		20547	0.0		0.002	False		,,,				2504	0.0041				p.V809M	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											.	ENPP2	254	.	0			c.G2425A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	120.0	101.0	108.0		2269,2344,2425	5.7	1.0	8	dbSNP_129	108	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense,missense	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	21,21,21	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	possibly-damaging,possibly-damaging,possibly-damaging	757/864,782/889,809/916	120575249	14,12992	2203	4300	6503	SO:0001583	missense	5168	exon25			CTTCCACGTACCT	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2269G>A	8.37:g.120575249C>T	ENSP00000075322:p.Val757Met	79.0	0.0	0		124.0	57.0	0.459677	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	CCDS34936.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	21.3	4.123821	0.77436	2.27E-4	0.001512	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522167;ENST00000522826;ENST00000075322	T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52	5.67	5.67	0.87782	DNA/RNA non-specific endonuclease (2);Extracellular Endonuclease, subunit A (2);	0.000000	0.46442	D	0.000285	T	0.51517	0.1679	L	0.49778	1.585	0.80722	D	1	D;D;D;D;D	0.89917	0.997;0.993;0.999;0.998;1.0	D;P;D;P;D	0.67548	0.952;0.894;0.919;0.896;0.919	T	0.46261	-0.9204	10	0.56958	D	0.05	.	19.7743	0.96385	0.0:1.0:0.0:0.0	rs61758149	295;782;757;809;392	B4DJD3;E9PHP7;Q13822;Q13822-2;E5RIA2	.;.;ENPP2_HUMAN;.;.	M	809;778;392;782;757	ENSP00000259486:V809M;ENSP00000403315:V778M;ENSP00000429476:V392M;ENSP00000428291:V782M;ENSP00000075322:V757M	ENSP00000075322:V757M	V	-	1	0	ENPP2	120644430	1.000000	0.71417	0.993000	0.49108	0.949000	0.60115	5.281000	0.65609	2.663000	0.90544	0.557000	0.71058	GTG	C|0.998;T|0.002	0.002	strong		0.443	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
OR13C5	138799	hgsc.bcm.edu	37	9	107361002	107361002	+	Silent	SNP	C	C	G	rs78992791	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:107361002C>G	ENST00000374779.2	-	1	786	c.693G>C	c.(691-693)tcG>tcC	p.S231S		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(2)|prostate(2)|skin(4)	28						TTCTCCCCTCCGAAGAGCTAA	0.428													G|||	5	0.000998403	0.0	0.0014	5008	,	,		22312	0.0		0.001	False		,,,				2504	0.0031				p.S231S		Atlas-SNP	.											OR13C5,right_upper_lobe,carcinoma,0,2	OR13C5	60	2	0			c.G693C						PASS	.						123.0	114.0	117.0					9																	107361002		2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			CCCCTCCGAAGAG		CCDS35091.1	9q31.1	2012-10-03			ENSG00000255800	ENSG00000277556		"""GPCR / Class A : Olfactory receptors"""	15100	protein-coding gene	gene with protein product							Standard	NM_001004482		Approved		uc011lvp.2	Q8NGS8	OTTHUMG00000020408	ENST00000374779.2:c.693G>C	9.37:g.107361002C>G		154.0	0.0	0		218.0	109.0	0.5	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			C|0.999;G|0.001	0.001	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
BRSK2	9024	hgsc.bcm.edu	37	11	1411572	1411572	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:1411572C>T	ENST00000528841.1	+	1	442	c.58C>T	c.(58-60)Cgg>Tgg	p.R20W	BRSK2_ENST00000308230.5_Missense_Mutation_p.R20W|BRSK2_ENST00000526678.1_Missense_Mutation_p.R20W|BRSK2_ENST00000531197.1_Missense_Mutation_p.R20W|BRSK2_ENST00000308219.9_Missense_Mutation_p.R20W			Q8IWQ3	BRSK2_HUMAN	BR serine/threonine kinase 2	20	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|axonogenesis (GO:0007409)|establishment of cell polarity (GO:0030010)|exocytosis (GO:0006887)|G2/M transition of mitotic cell cycle (GO:0000086)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|mitotic nuclear division (GO:0007067)|neuron differentiation (GO:0030182)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			endometrium(4)|large_intestine(1)|lung(5)	10		all_epithelial(84;4.17e-05)|Breast(177;0.000307)|Ovarian(85;0.0014)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00144)|Lung(200;0.0713)|LUSC - Lung squamous cell carcinoma(625;0.0842)		TGGGCCCTACCGGCTGGAGAA	0.796																																					p.R20W		Atlas-SNP	.											.	BRSK2	97	.	0			c.C58T						PASS	.						4.0	6.0	6.0					11																	1411572		1915	4006	5921	SO:0001583	missense	9024	exon1			CCCTACCGGCTGG	AF020089	CCDS41590.1, CCDS58106.1, CCDS58107.1, CCDS58108.1, CCDS60696.1	11p15.5	2008-02-05	2003-09-11	2005-01-27	ENSG00000174672	ENSG00000174672			11405	protein-coding gene	gene with protein product	"""serine/threonine kinase 29"""	609236	"""chromsosome 11 open reading frame 7"""	C11orf7, STK29		9852686, 9929968	Standard	NM_001256629		Approved	PEN11B	uc001ltm.4	Q8IWQ3	OTTHUMG00000167089	ENST00000528841.1:c.58C>T	11.37:g.1411572C>T	ENSP00000432000:p.Arg20Trp	23.0	0.0	0		23.0	13.0	0.565217	NM_001256629	B3KVE9|E9PLM7|O60843|O95099|Q5J5B4|Q6ZMQ4|Q8TB60	Missense_Mutation	SNP	ENST00000528841.1	37	CCDS58107.1	.	.	.	.	.	.	.	.	.	.	c	17.64	3.440051	0.63067	.	.	ENSG00000174672	ENST00000308219;ENST00000531197;ENST00000308230;ENST00000528841;ENST00000526678	T;T;T;T;T	0.67345	-0.26;-0.26;-0.26;-0.26;-0.26	1.54	1.54	0.23209	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.78868	0.4351	M	0.86573	2.825	0.80722	D	1	D;D;D;D	0.67145	0.996;0.994;0.988;0.985	P;P;P;P	0.61722	0.721;0.606;0.893;0.828	T	0.79960	-0.1583	9	0.87932	D	0	.	8.6612	0.34093	0.0:1.0:0.0:0.0	.	20;20;20;20	Q8IWQ3-4;Q8IWQ3-3;Q8IWQ3;Q8IWQ3-2	.;.;BRSK2_HUMAN;.	W	20	ENSP00000310697:R20W;ENSP00000431152:R20W;ENSP00000310805:R20W;ENSP00000432000:R20W;ENSP00000433370:R20W	ENSP00000310697:R20W	R	+	1	2	BRSK2	1368148	0.920000	0.31207	1.000000	0.80357	0.993000	0.82548	0.856000	0.27818	0.855000	0.35359	0.409000	0.27619	CGG	.	.	none		0.796	BRSK2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393033.1	NM_003957	
ZNF721	170960	hgsc.bcm.edu	37	4	436991	436991	+	Missense_Mutation	SNP	C	C	T	rs376220761		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:436991C>T	ENST00000338977.5	-	2	1277	c.1229G>A	c.(1228-1230)cGt>cAt	p.R410H	ZNF721_ENST00000506646.1_Intron|ABCA11P_ENST00000451020.2_RNA|ZNF721_ENST00000511833.2_Missense_Mutation_p.R422H|ZNF721_ENST00000507078.1_Intron			Q8TF20	ZN721_HUMAN	zinc finger protein 721	410				R -> C (in Ref. 1; CAH10687). {ECO:0000305}.	regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(15)|lung(6)|ovary(1)|skin(1)|stomach(5)|urinary_tract(1)	33						GGCTCTGCCACGATCTTCACA	0.378																																					p.P422H		Atlas-SNP	.											ZNF721_ENST00000511833,NS,carcinoma,-1,2	ZNF721	205	2	0			c.C1265A						scavenged	.	C	HIS/ARG	0,4098		0,0,2049	75.0	78.0	77.0		1265	1.0	0.0	4		77	1,8439		0,1,4219	no	missense	ZNF721	NM_133474.2	29	0,1,6268	TT,TC,CC		0.0118,0.0,0.0080	possibly-damaging	422/924	436991	1,12537	2049	4220	6269	SO:0001583	missense	170960	exon3			CTGCCACGATCTT	AK092362	CCDS46991.1	4p16.3	2013-01-08			ENSG00000182903	ENSG00000182903		"""Zinc fingers, C2H2-type"", ""-"""	29425	protein-coding gene	gene with protein product						11853319	Standard	NM_133474		Approved	KIAA1982	uc003gag.4	Q8TF20		ENST00000338977.5:c.1229G>A	4.37:g.436991C>T	ENSP00000340524:p.Arg410His	47.0	1.0	0.0212766		39.0	16.0	0.410256	NM_133474	Q69YG7	Missense_Mutation	SNP	ENST00000338977.5	37		.	.	.	.	.	.	.	.	.	.	C	12.31	1.900631	0.33535	0.0	1.18E-4	ENSG00000182903	ENST00000338977;ENST00000511833	T;T	0.17854	2.25;2.25	1.03	1.03	0.20045	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13798	0.0334	N	0.25647	0.755	0.09310	N	1	D;D;D	0.62365	0.991;0.975;0.985	B;B;P	0.45881	0.208;0.301;0.496	T	0.17961	-1.0352	9	0.87932	D	0	.	7.9579	0.30053	0.0:1.0:0.0:0.0	.	410;422;422	Q8TF20;D9N162;Q8TF20-2	ZN721_HUMAN;.;.	H	410;422	ENSP00000340524:R410H;ENSP00000428878:R422H	ENSP00000340524:R410H	R	-	2	0	ZNF721	426991	0.888000	0.30383	0.003000	0.11579	0.003000	0.03518	2.751000	0.47508	0.890000	0.36211	0.194000	0.17425	CGT	.	.	weak		0.378	ZNF721-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000357939.1	NM_133474	
TCERG1	10915	hgsc.bcm.edu	37	5	145838656	145838656	+	Silent	SNP	G	G	A	rs569890952		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:145838656G>A	ENST00000296702.5	+	4	686	c.648G>A	c.(646-648)caG>caA	p.Q216Q	TCERG1_ENST00000394421.2_Silent_p.Q216Q	NM_006706.3	NP_006697.2	O14776	TCRG1_HUMAN	transcription elongation regulator 1	216	Ala/Gln-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II repressing transcription factor binding (GO:0001103)|RNA polymerase II transcription corepressor activity (GO:0001106)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(18)|lung(9)|ovary(2)|prostate(3)|skin(1)	46		Lung NSC(249;0.00188)|all_lung(500;0.00307)|all_neural(839;0.0424)|Breast(839;0.0743)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			cccaggcccaggcccaggccc	0.731																																					p.Q216Q		Atlas-SNP	.											TCERG1,NS,carcinoma,0,2	TCERG1	148	2	0			c.G648A						scavenged	.						10.0	14.0	13.0					5																	145838656		2190	4261	6451	SO:0001819	synonymous_variant	10915	exon4			GGCCCAGGCCCAG	AF017789	CCDS4282.1, CCDS43379.1	5q31	2010-01-25	2002-01-24	2002-01-25	ENSG00000113649	ENSG00000113649			15630	protein-coding gene	gene with protein product	"""transcription factor CA150"", ""co-activator of 150 kDa"", ""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"", ""TATA box-binding protein-associated factor 2S"""	605409	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, S, 150kD"""	TAF2S		9315662, 11003711	Standard	XM_005268365		Approved	CA150, Urn1	uc003lob.3	O14776	OTTHUMG00000129683	ENST00000296702.5:c.648G>A	5.37:g.145838656G>A		22.0	0.0	0		26.0	3.0	0.115385	NM_006706	Q2NKN2|Q59EA1	Silent	SNP	ENST00000296702.5	37	CCDS4282.1																																																																																			.	.	none		0.731	TCERG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251886.1	NM_001040006	
PDE1C	5137	hgsc.bcm.edu	37	7	31855625	31855625	+	Missense_Mutation	SNP	C	C	G	rs61736729	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31855625C>G	ENST00000396191.1	-	15	2181	c.1726G>C	c.(1726-1728)Gtc>Ctc	p.V576L	PDE1C_ENST00000396184.3_Missense_Mutation_p.V576L|PDE1C_ENST00000321453.7_Missense_Mutation_p.V576L|PDE1C_ENST00000479980.1_5'UTR|PDE1C_ENST00000396182.2_Missense_Mutation_p.V576L|PDE1C_ENST00000396193.1_Missense_Mutation_p.V636L	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	576					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GTTCCATTGACTTGATTCTTA	0.473													C|||	13	0.00259585	0.0	0.0072	5008	,	,		20836	0.0		0.008	False		,,,				2504	0.0				p.V636L		Atlas-SNP	.											.	PDE1C	465	.	0			c.G1906C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	11,4395	17.9+/-39.9	0,11,2192	271.0	268.0	269.0		1726,1726,1906,1726,1726	5.3	1.0	7	dbSNP_129	269	108,8492	59.1+/-120.7	0,108,4192	yes	missense,missense,missense,missense,missense	PDE1C	NM_001191056.1,NM_001191057.1,NM_001191058.1,NM_001191059.1,NM_005020.2	32,32,32,32,32	0,119,6384	GG,GC,CC		1.2558,0.2497,0.915	benign,benign,benign,benign,benign	576/635,576/710,636/770,576/710,576/635	31855625	119,12887	2203	4300	6503	SO:0001583	missense	5137	exon16			CATTGACTTGATT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1726G>C	7.37:g.31855625C>G	ENSP00000379494:p.Val576Leu	254.0	1.0	0.00393701		333.0	168.0	0.504505	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	8.002	0.755676	0.15846	0.002497	0.012558	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	T;T;T;T;T	0.72835	-0.69;-0.69;-0.69;-0.65;-0.65	5.34	5.34	0.76211	.	2.382430	0.01786	N	0.032006	T	0.53578	0.1805	N	0.19112	0.55	0.19775	N	0.999959	B;B;B	0.12630	0.006;0.003;0.003	B;B;B	0.13407	0.009;0.004;0.004	T	0.40608	-0.9554	10	0.25751	T	0.34	.	12.0225	0.53352	0.0:0.9176:0.0:0.0824	rs61736729	576;636;576	Q14123-2;E9PE92;Q14123	.;.;PDE1C_HUMAN	L	636;576;576;576;576	ENSP00000379496:V636L;ENSP00000379494:V576L;ENSP00000318105:V576L;ENSP00000379487:V576L;ENSP00000379485:V576L	ENSP00000318105:V576L	V	-	1	0	PDE1C	31822150	0.060000	0.20803	0.993000	0.49108	0.186000	0.23388	1.274000	0.33132	2.779000	0.95612	0.655000	0.94253	GTC	C|0.983;G|0.017	0.017	strong		0.473	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
BCAT1	586	hgsc.bcm.edu	37	12	24970966	24970966	+	Silent	SNP	G	G	A	rs117200620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:24970966G>A	ENST00000261192.7	-	11	1663	c.1137C>T	c.(1135-1137)agC>agT	p.S379S	BCAT1_ENST00000538118.1_Silent_p.S378S|BCAT1_ENST00000539282.1_Silent_p.S391S|BCAT1_ENST00000342945.5_Silent_p.S318S|BCAT1_ENST00000539780.1_Silent_p.S342S	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	379					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			breast(1)|large_intestine(1)|lung(3)|prostate(2)	7	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)	TTGTCCAGTCGCTCTCTTCTC	0.398													G|||	71	0.0141773	0.003	0.0058	5008	,	,		21169	0.001		0.0099	False		,,,				2504	0.0532				p.S391S		Atlas-SNP	.											BCAT1,NS,carcinoma,0,1	BCAT1	44	1	0			c.C1173T						scavenged	.	G	,,,,	24,3794		0,24,1885	165.0	153.0	157.0		1026,954,1173,1134,1137	-5.2	0.8	12	dbSNP_132	157	101,8187		1,99,4044	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BCAT1	NM_001178091.1,NM_001178092.1,NM_001178093.1,NM_001178094.1,NM_005504.6	,,,,	1,123,5929	AA,AG,GG		1.2186,0.6286,1.0325	,,,,	342/350,318/326,391/399,378/386,379/387	24970966	125,11981	1909	4144	6053	SO:0001819	synonymous_variant	586	exon11			CCAGTCGCTCTCT		CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1	12p12.1	2012-10-02	2010-05-07		ENSG00000060982	ENSG00000060982	2.6.1.42		976	protein-coding gene	gene with protein product		113520	"""branched chain aminotransferase 1, cytosolic"""	BCT1		9165094	Standard	NM_005504		Approved		uc010six.2	P54687	OTTHUMG00000169053	ENST00000261192.7:c.1137C>T	12.37:g.24970966G>A		202.0	1.0	0.00495049		240.0	114.0	0.475	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Silent	SNP	ENST00000261192.7	37	CCDS44845.1																																																																																			G|0.992;A|0.008	0.008	strong		0.398	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						scavenged	.	A	,,,,,	11,4395		0,11,2192	70.0	75.0	73.0		,,,1584,,1584	1.3	1.0	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1584A>G	5.37:g.140188356A>G		107.0	0.0	0		60.0	15.0	0.25	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
C1orf210	149466	hgsc.bcm.edu	37	1	43748763	43748763	+	Missense_Mutation	SNP	G	G	A	rs35465732	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43748763G>A	ENST00000523677.1	-	3	268	c.35C>T	c.(34-36)tCg>tTg	p.S12L	C1orf210_ENST00000423420.1_Missense_Mutation_p.S12L	NM_001164829.1|NM_182517.2	NP_001158301.1|NP_872323.1	Q8IVY1	CA210_HUMAN	chromosome 1 open reading frame 210	12			S -> L (in dbSNP:rs35465732).			integral component of membrane (GO:0016021)				breast(1)	1	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				GGGGAGCTCCGAAGGCCCAAC	0.642													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		15217	0.0		0.0189	False		,,,				2504	0.0072				p.S12L		Atlas-SNP	.											C1orf210,NS,carcinoma,+1,1	C1orf210	9	1	0			c.C35T						PASS	.	G	LEU/SER,LEU/SER	16,4390	24.3+/-50.5	0,16,2187	25.0	27.0	26.0		35,35	2.0	0.0	1	dbSNP_126	26	158,8442	71.6+/-134.2	0,158,4142	yes	missense,missense	C1orf210	NM_001164829.1,NM_182517.2	145,145	0,174,6329	AA,AG,GG		1.8372,0.3631,1.3378	possibly-damaging,possibly-damaging	12/114,12/114	43748763	174,12832	2203	4300	6503	SO:0001583	missense	149466	exon3			AGCTCCGAAGGCC	BC041633	CCDS481.1	1p34.2	2006-03-22			ENSG00000253313	ENSG00000253313			28755	protein-coding gene	gene with protein product						12477932	Standard	NM_182517		Approved	MGC52423	uc001cit.4	Q8IVY1	OTTHUMG00000007289	ENST00000523677.1:c.35C>T	1.37:g.43748763G>A	ENSP00000430918:p.Ser12Leu	98.0	0.0	0		137.0	67.0	0.489051	NM_182517	D3DPX2	Missense_Mutation	SNP	ENST00000523677.1	37	CCDS481.1	18	0.008241758241758242	0	0.0	2	0.0055248618784530384	0	0.0	16	0.021108179419525065	G	17.71	3.457811	0.63401	0.003631	0.018372	ENSG00000253313	ENST00000523677;ENST00000423420	T;T	0.47869	0.83;0.83	4.96	2.04	0.26737	.	0.670270	0.13234	N	0.403431	T	0.18593	0.0446	L	0.36672	1.1	0.09310	N	1	B	0.17465	0.022	B	0.09377	0.004	T	0.23154	-1.0196	10	0.72032	D	0.01	.	3.4949	0.07651	0.2809:0.0:0.5414:0.1777	rs35465732	12	Q8IVY1	CA210_HUMAN	L	12	ENSP00000430918:S12L;ENSP00000429399:S12L	ENSP00000429399:S12L	S	-	2	0	C1orf210	43521350	0.129000	0.22400	0.008000	0.14137	0.346000	0.29079	0.752000	0.26362	0.277000	0.22141	0.561000	0.74099	TCG	G|0.989;A|0.011	0.011	strong		0.642	C1orf210-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019035.2	NM_182517	
RAB1B	81876	hgsc.bcm.edu	37	11	66043586	66043586	+	Silent	SNP	G	G	A	rs367843963		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66043586G>A	ENST00000311481.6	+	6	630	c.483G>A	c.(481-483)gcG>gcA	p.A161A	RP11-867G23.4_ENST00000526951.1_RNA|RAB1B_ENST00000527397.1_Silent_p.A129A|CNIH2_ENST00000311445.6_5'Flank|CNIH2_ENST00000528852.1_5'Flank|RP11-867G23.4_ENST00000528650.1_RNA|RP11-867G23.3_ENST00000501708.1_lincRNA	NM_030981.2	NP_112243.1	Q9H0U4	RAB1B_HUMAN	RAB1B, member RAS oncogene family	161					ER to Golgi vesicle-mediated transport (GO:0006888)|positive regulation of glycoprotein metabolic process (GO:1903020)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)|virion assembly (GO:0019068)	endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)			large_intestine(2)|lung(1)|ovary(1)|prostate(1)	5						TCGAGCAGGCGTTCATGACCA	0.582																																					p.A161A		Atlas-SNP	.											.	RAB1B	14	.	0			c.G483A						PASS	.	G		0,4400		0,0,2200	46.0	44.0	45.0		483	-7.8	1.0	11		45	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	RAB1B	NM_030981.2		0,1,6494	AA,AG,GG		0.0116,0.0,0.0077		161/202	66043586	1,12989	2200	4295	6495	SO:0001819	synonymous_variant	81876	exon6			GCAGGCGTTCATG	AJ245875	CCDS31613.1	11q13.1	2008-02-05			ENSG00000174903	ENSG00000174903		"""RAB, member RAS oncogene"""	18370	protein-coding gene	gene with protein product		612565				9030196	Standard	NM_030981		Approved		uc001ohf.3	Q9H0U4	OTTHUMG00000166916	ENST00000311481.6:c.483G>A	11.37:g.66043586G>A		88.0	0.0	0		109.0	45.0	0.412844	NM_030981	A8K7S1	Silent	SNP	ENST00000311481.6	37	CCDS31613.1	.	.	.	.	.	.	.	.	.	.	G	8.325	0.825167	0.16749	0.0	1.16E-4	ENSG00000174903	ENST00000314965	.	.	.	3.9	-7.77	0.01227	.	.	.	.	.	T	0.49712	0.1573	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61068	-0.7137	5	0.87932	D	0	.	2.2152	0.03958	0.3414:0.3799:0.1636:0.1151	.	.	.	.	H	161	.	ENSP00000313814:R161H	R	+	2	0	RAB1B	65800162	0.031000	0.19500	0.975000	0.42487	0.825000	0.46686	-0.719000	0.04974	-0.989000	0.03485	0.313000	0.20887	CGT	.	.	weak		0.582	RAB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391886.2	NM_030981	
LRTOMT	220074	hgsc.bcm.edu	37	11	71800166	71800166	+	Missense_Mutation	SNP	G	G	A	rs146942815	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:71800166G>A	ENST00000289488.2	+	3	415	c.37G>A	c.(37-39)Gag>Aag	p.E13K	LRTOMT_ENST00000539271.1_Intron|LRTOMT_ENST00000439209.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000536917.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000538478.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000539587.1_Intron|LAMTOR1_ENST00000545249.1_Intron|LRTOMT_ENST00000324866.7_Missense_Mutation_p.E13K|LRTOMT_ENST00000447974.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000419228.1_5'UTR|LRTOMT_ENST00000541614.1_Missense_Mutation_p.E13K|LRTOMT_ENST00000435085.1_5'UTR|LRTOMT_ENST00000307198.7_Intron|LRTOMT_ENST00000423494.2_Intron	NM_001271471.2|NM_145309.5	NP_001258400.1|NP_660352.1	Q96E66	LRC51_HUMAN	leucine rich transmembrane and O-methyltransferase domain containing	13						cytoplasm (GO:0005737)				large_intestine(2)|lung(1)|ovary(1)	4						TTCGGTACAGGAGCCCCCTCT	0.547													G|||	8	0.00159744	0.0008	0.0029	5008	,	,		17430	0.0		0.004	False		,,,				2504	0.001				p.E13K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.G37A						PASS	.	G	LYS/GLU,,,LYS/GLU	3,4397	6.2+/-15.9	0,3,2197	146.0	121.0	129.0		37,,,37	4.8	1.0	11	dbSNP_134	129	54,8532	34.8+/-89.0	1,52,4240	yes	missense,intron,intron,missense	LRTOMT	NM_001145307.2,NM_001145308.2,NM_001205138.1,NM_145309.3	56,,,56	1,55,6437	AA,AG,GG		0.6289,0.0682,0.4389	possibly-damaging,,,possibly-damaging	13/159,,,13/193	71800166	57,12929	2200	4293	6493	SO:0001583	missense	220074	exon3			GTACAGGAGCCCC		CCDS8208.1, CCDS44667.1, CCDS44668.1, CCDS55778.1, CCDS59227.1	11q13.4	2014-09-05	2013-08-19	2008-11-27	ENSG00000184154	ENSG00000184154			25033	protein-coding gene	gene with protein product		612414	"""leucine rich repeat containing 51"", ""deafness, autosomal recessive 63"""	LRRC51, DFNB63		18794526, 18953341	Standard	NM_145309		Approved	COMT2, CFAP111	uc010rqw.2	Q8WZ04	OTTHUMG00000154887	ENST00000289488.2:c.37G>A	11.37:g.71800166G>A	ENSP00000289488:p.Glu13Lys	82.0	0.0	0		80.0	34.0	0.425	NM_001271471	B2R7X1|B6CZ35|B6CZ36|B6CZ37|B6CZ38|B6CZ39|B7Z5I4	Missense_Mutation	SNP	ENST00000289488.2	37	CCDS8208.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.410355	0.83340	6.82E-4	0.006289	ENSG00000184154	ENST00000538413;ENST00000289488;ENST00000447974;ENST00000538478;ENST00000324866;ENST00000439209;ENST00000542846;ENST00000541614;ENST00000537483;ENST00000536917	T;T;T	0.30182	2.54;2.54;1.54	4.77	4.77	0.60923	.	0.057240	0.64402	D	0.000001	T	0.25306	0.0615	L	0.53249	1.67	0.80722	D	1	P;P	0.43352	0.628;0.804	B;B	0.40066	0.318;0.318	T	0.08889	-1.0700	10	0.46703	T	0.11	-25.2568	17.0634	0.86553	0.0:0.0:1.0:0.0	.	13;13	Q96E66-2;Q96E66	.;LRC51_HUMAN	K	13	ENSP00000289488:E13K;ENSP00000444583:E13K;ENSP00000395139:E13K	ENSP00000289488:E13K	E	+	1	0	LRTOMT	71477814	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	5.266000	0.65525	2.643000	0.89663	0.655000	0.94253	GAG	G|0.996;A|0.004	0.004	strong		0.547	LRTOMT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337504.1	NM_145309	
RAX2	84839	hgsc.bcm.edu	37	19	3771684	3771684	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:3771684G>A	ENST00000555633.1	-	2	397	c.57C>T	c.(55-57)ggC>ggT	p.G19G	RAX2_ENST00000555978.1_Silent_p.G19G			Q96IS3	RAX2_HUMAN	retina and anterior neural fold homeobox 2	19					regulation of transcription, DNA-templated (GO:0006355)|response to stimulus (GO:0050896)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)	1		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00463)|STAD - Stomach adenocarcinoma(1328;0.18)		GGGCCTCCTCGCCCGGCCCCA	0.701																																					p.G19G		Atlas-SNP	.											.	RAX2	4	.	0			c.C57T						PASS	.						45.0	40.0	42.0					19																	3771684		2200	4298	6498	SO:0001819	synonymous_variant	84839	exon2			CTCCTCGCCCGGC	AY211277	CCDS12112.1	19p13.3	2013-06-06	2007-08-28	2007-08-28				"""Homeoboxes / PRD class"""	18286	protein-coding gene	gene with protein product		610362	"""retina and anterior neural fold homeobox like 1"""	RAXL1			Standard	NM_032753		Approved	MGC15631, ARMD6, CORD11	uc002lys.3	Q96IS3		ENST00000555633.1:c.57C>T	19.37:g.3771684G>A		43.0	0.0	0		49.0	20.0	0.408163	NM_032753		Silent	SNP	ENST00000555633.1	37	CCDS12112.1	.	.	.	.	.	.	.	.	.	.	G	14.21	2.466341	0.43839	.	.	ENSG00000173976	ENST00000555978	.	.	.	2.98	-5.96	0.02234	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	3.1764	0.06570	0.3839:0.0:0.3174:0.2987	.	.	.	.	X	39	.	.	R	-	1	2	RAX2	3722684	0.000000	0.05858	0.160000	0.22671	0.866000	0.49608	-2.379000	0.01067	-1.095000	0.03050	0.491000	0.48974	CGA	.	.	none		0.701	RAX2-001	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411919.2	NM_032753	
PCNT	5116	hgsc.bcm.edu	37	21	47831621	47831621	+	Silent	SNP	C	C	T	rs61735811	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47831621C>T	ENST00000359568.5	+	28	5741	c.5634C>T	c.(5632-5634)gaC>gaT	p.D1878D	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	1878					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					TAGAAATCGACGCTCTGAACC	0.642													C|||	119	0.023762	0.0212	0.0303	5008	,	,		15874	0.001		0.0646	False		,,,				2504	0.0041				p.D1878D		Atlas-SNP	.											PCNT,colon,carcinoma,0,1	PCNT	283	1	0			c.C5634T						PASS	.	C		150,4246		2,146,2050	25.0	28.0	27.0		5634	-11.6	0.0	21	dbSNP_129	27	514,8068		9,496,3786	no	coding-synonymous	PCNT	NM_006031.5		11,642,5836	TT,TC,CC		5.9893,3.4122,5.1164		1878/3337	47831621	664,12314	2198	4291	6489	SO:0001819	synonymous_variant	5116	exon28			AATCGACGCTCTG	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.5634C>T	21.37:g.47831621C>T		64.0	0.0	0		58.0	29.0	0.5	NM_006031	O43152|Q7Z7C9	Silent	SNP	ENST00000359568.5	37	CCDS33592.1																																																																																			C|0.953;T|0.047	0.047	strong		0.642	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
TAF4	6874	hgsc.bcm.edu	37	20	60585139	60585139	+	Missense_Mutation	SNP	G	G	A	rs141880507		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60585139G>A	ENST00000252996.4	-	4	1723	c.1724C>T	c.(1723-1725)aCg>aTg	p.T575M	TAF4_ENST00000609045.1_5'UTR	NM_003185.3	NP_003176.2	O00268	TAF4_HUMAN	TAF4 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 135kDa	575					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|ovarian follicle development (GO:0001541)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	37	Breast(26;1e-08)		BRCA - Breast invasive adenocarcinoma(19;3.1e-07)			CCCTGGTACCGTGCGCTGAGG	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		16776	0.001		0.0	False		,,,				2504	0.0				p.T575M		Atlas-SNP	.											.	TAF4	84	.	0			c.C1724T						PASS	.						98.0	79.0	85.0					20																	60585139		2203	4300	6503	SO:0001583	missense	6874	exon4			GGTACCGTGCGCT	Y11354	CCDS33500.1	20q13.33	2010-02-26	2002-08-29	2002-01-18	ENSG00000130699	ENSG00000130699			11537	protein-coding gene	gene with protein product		601796	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, C1, 130kD"""	TAF4A, TAF2C1, TAF2C		8942982, 9192867	Standard	NM_003185		Approved	TAFII130, TAFII135	uc002ybs.3	O00268	OTTHUMG00000032893	ENST00000252996.4:c.1724C>T	20.37:g.60585139G>A	ENSP00000252996:p.Thr575Met	33.0	0.0	0		40.0	21.0	0.525	NM_003185	A6NGD9|Q5TBP6|Q99721|Q9BR40|Q9BX42	Missense_Mutation	SNP	ENST00000252996.4	37	CCDS33500.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	14.17	2.456706	0.43634	.	.	ENSG00000130699	ENST00000252996;ENST00000436129	T;T	0.26660	1.72;1.73	4.8	4.8	0.61643	.	0.550327	0.19671	N	0.108752	T	0.30479	0.0766	L	0.34521	1.04	0.22541	N	0.999006	D	0.69078	0.997	P	0.49332	0.607	T	0.13098	-1.0522	10	0.62326	D	0.03	-4.0056	17.8435	0.88722	0.0:0.0:1.0:0.0	.	575	O00268	TAF4_HUMAN	M	575;439	ENSP00000252996:T575M;ENSP00000399091:T439M	ENSP00000252996:T575M	T	-	2	0	TAF4	60018534	0.969000	0.33509	0.095000	0.20976	0.149000	0.21700	6.757000	0.74924	2.226000	0.72624	0.313000	0.20887	ACG	G|1.000;A|0.000	0.000	strong		0.612	TAF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079968.2	NM_003185	
GABBR2	9568	hgsc.bcm.edu	37	9	101151192	101151192	+	Silent	SNP	G	G	A	rs144313756		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101151192G>A	ENST00000259455.2	-	10	1932	c.1473C>T	c.(1471-1473)ctC>ctT	p.L491L		NM_005458.7	NP_005449.5	O75899	GABR2_HUMAN	gamma-aminobutyric acid (GABA) B receptor, 2	491					G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|G-protein coupled receptor heterodimeric complex (GO:0038039)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	G-protein coupled GABA receptor activity (GO:0004965)		NOTCH1_ENST00000277541/GABBR2(2)	breast(4)|endometrium(4)|large_intestine(12)|lung(21)|ovary(2)|skin(4)|stomach(1)|urinary_tract(1)	49		Acute lymphoblastic leukemia(62;0.0527)			Baclofen(DB00181)	TGATCATCCCGAGGATGGTGA	0.498													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21052	0.0		0.0	False		,,,				2504	0.0				p.L491L		Atlas-SNP	.											.	GABBR2	126	.	0			c.C1473T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	263.0	212.0	229.0		1473	-6.8	0.7	9	dbSNP_134	229	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	GABBR2	NM_005458.7		0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153		491/942	101151192	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	9568	exon10			CATCCCGAGGATG	AF069755	CCDS6736.1	9q22.1-q22.3	2012-08-29	2006-02-16	2006-02-16	ENSG00000136928	ENSG00000136928		"""GABA receptors"", ""GPCR / Class C : GABA(B) receptors"""	4507	protein-coding gene	gene with protein product		607340	"""G protein-coupled receptor 51"""	GPR51		10087195	Standard	NM_005458		Approved	HG20, GABABR2, GPRC3B	uc004ays.3	O75899	OTTHUMG00000020345	ENST00000259455.2:c.1473C>T	9.37:g.101151192G>A		309.0	0.0	0		393.0	203.0	0.516539	NM_005458	O75974|O75975|Q5VXZ2|Q8WX04|Q9P1R2|Q9UNR1|Q9UNS9	Silent	SNP	ENST00000259455.2	37	CCDS6736.1																																																																																			G|0.999;A|0.001	0.001	strong		0.498	GABBR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053373.1		
FAM47B	170062	hgsc.bcm.edu	37	X	34961479	34961479	+	Silent	SNP	C	C	T	rs149160457		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:34961479C>T	ENST00000329357.5	+	1	567	c.531C>T	c.(529-531)acC>acT	p.T177T		NM_152631.2	NP_689844.2	Q8NA70	FA47B_HUMAN	family with sequence similarity 47, member B	177										breast(3)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	71						AGGTACCCACCGAGTCTGGTA	0.612																																					p.T177T		Atlas-SNP	.											.	FAM47B	209	.	0			c.C531T						PASS	.	C		1,3832		0,1,1630,571	31.0	31.0	31.0		531	-1.7	0.0	X	dbSNP_134	31	0,6728		0,0,2428,1872	no	coding-synonymous	FAM47B	NM_152631.2		0,1,4058,2443	TT,TC,CC,C		0.0,0.0261,0.0095		177/646	34961479	1,10560	2202	4300	6502	SO:0001819	synonymous_variant	170062	exon1			ACCCACCGAGTCT	BC035026	CCDS14236.1	Xp21.1	2004-08-09			ENSG00000189132	ENSG00000189132			26659	protein-coding gene	gene with protein product						14702039	Standard	NM_152631		Approved	FLJ35782	uc004ddi.2	Q8NA70	OTTHUMG00000021345	ENST00000329357.5:c.531C>T	X.37:g.34961479C>T		85.0	0.0	0		124.0	107.0	0.862903	NM_152631	Q5JQN5|Q6PIG3	Silent	SNP	ENST00000329357.5	37	CCDS14236.1																																																																																			C|1.000;T|0.000	0.000	weak		0.612	FAM47B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056211.1	NM_152631	
ELF2	1998	hgsc.bcm.edu	37	4	140046466	140046466	+	Silent	SNP	A	A	C	rs115767880	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:140046466A>C	ENST00000394235.2	-	4	592	c.90T>G	c.(88-90)tcT>tcG	p.S30S	ELF2_ENST00000265495.4_Silent_p.S30S|ELF2_ENST00000379550.1_Silent_p.S30S	NM_001276458.1	NP_001263387.1			E74-like factor 2 (ets domain transcription factor)											endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	19	all_hematologic(180;0.162)					CTGGATATTCAGAAACCTTTT	0.373													a|||	6	0.00119808	0.0	0.0	5008	,	,		17185	0.0		0.006	False		,,,				2504	0.0				p.E30E		Atlas-SNP	.											.	ELF2	43	.	0			c.G90G						PASS	.	A		3,4403	8.1+/-20.4	0,3,2200	102.0	100.0	100.0		90	3.0	1.0	4	dbSNP_132	100	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	ELF2	NM_201999.1		0,54,6449	CC,CA,AA		0.593,0.0681,0.4152		30/582	140046466	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	1998	exon3			ATATTCAGAAACC	AF256222	CCDS3744.1, CCDS3745.1, CCDS64062.1, CCDS64063.1	4q28	2008-02-05			ENSG00000109381	ENSG00000109381			3317	protein-coding gene	gene with protein product						8756667	Standard	NM_201999		Approved	EU32, NERF, NERF-2, NERF-1A, NERF-1B	uc003ihm.2	Q15723	OTTHUMG00000133383	ENST00000394235.2:c.90T>G	4.37:g.140046466A>C		126.0	0.0	0		134.0	59.0	0.440298	NM_201999		Silent	SNP	ENST00000394235.2	37	CCDS3744.1																																																																																			A|0.997;C|0.003	0.003	strong		0.373	ELF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257233.2	NM_006874	
ST6GALNAC2	10610	hgsc.bcm.edu	37	17	74562308	74562308	+	Missense_Mutation	SNP	C	C	T	rs373585653		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:74562308C>T	ENST00000225276.5	-	9	1322	c.1003G>A	c.(1003-1005)Gac>Aac	p.D335N		NM_006456.2	NP_006447.2	Q9UJ37	SIA7B_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2	335					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	11						AAATAGTGGTCGGAAAATTTC	0.473																																					p.D335N		Atlas-SNP	.											.	ST6GALNAC2	29	.	0			c.G1003A						PASS	.	C	ASN/ASP	0,4406		0,0,2203	171.0	154.0	160.0		1003	3.5	0.7	17		160	1,8599	1.2+/-3.3	0,1,4299	no	missense	ST6GALNAC2	NM_006456.2	23	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	335/375	74562308	1,13005	2203	4300	6503	SO:0001583	missense	10610	exon9			AGTGGTCGGAAAA	U14550	CCDS11747.1	17q25.1	2013-03-01	2003-12-05	2005-02-07	ENSG00000070731	ENSG00000070731	2.4.99.7	"""Sialyltransferases"""	10867	protein-coding gene	gene with protein product		610137	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase)"", ""sialyltransferase-like 1"""	SIAT7, SIAT7B, SIATL1		11984005	Standard	NM_006456		Approved	ST6GalNAII, STHM	uc002jsg.4	Q9UJ37	OTTHUMG00000180301	ENST00000225276.5:c.1003G>A	17.37:g.74562308C>T	ENSP00000225276:p.Asp335Asn	76.0	0.0	0		82.0	36.0	0.439024	NM_006456	Q12971	Missense_Mutation	SNP	ENST00000225276.5	37	CCDS11747.1	.	.	.	.	.	.	.	.	.	.	C	18.54	3.646027	0.67358	0.0	1.16E-4	ENSG00000070731	ENST00000225276	T	0.29397	1.57	5.45	3.47	0.39725	.	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.54323	1.7	0.50171	D	0.999853	D	0.76494	0.999	P	0.62435	0.902	T	0.13629	-1.0502	10	0.31617	T	0.26	-26.2793	10.7107	0.45982	0.0:0.8435:0.0:0.1565	.	335	Q9UJ37	SIA7B_HUMAN	N	335	ENSP00000225276:D335N	ENSP00000225276:D335N	D	-	1	0	ST6GALNAC2	72073903	1.000000	0.71417	0.683000	0.30040	0.636000	0.38137	5.182000	0.65059	0.681000	0.31386	0.655000	0.94253	GAC	.	.	weak		0.473	ST6GALNAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450650.1	NM_006456	
ZNF362	149076	hgsc.bcm.edu	37	1	33764617	33764617	+	Silent	SNP	C	C	T	rs55887741	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:33764617C>T	ENST00000539719.1	+	9	1403	c.1233C>T	c.(1231-1233)ccC>ccT	p.P411P	ZNF362_ENST00000373428.5_Silent_p.P411P	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	411					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				CGGAGTCCCCCGGCATCCCGG	0.657											OREG0013343	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	7	0.00139776	0.0	0.0014	5008	,	,		16576	0.0		0.006	False		,,,				2504	0.0				p.P411P	Pancreas(162;1431 2676 35353 38425)	Atlas-SNP	.											.	ZNF362	31	.	0			c.C1233T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	70.0	68.0	69.0		1233	3.3	1.0	1	dbSNP_129	69	75,8525	43.1+/-100.9	0,75,4225	no	coding-synonymous	ZNF362	NM_152493.2		0,83,6420	TT,TC,CC		0.8721,0.1816,0.6382		411/421	33764617	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	149076	exon9			GTCCCCCGGCATC		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"""Zinc fingers, C2H2-type"""	18079	protein-coding gene	gene with protein product	"""rotund homolog (Drosophila)"""						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.1233C>T	1.37:g.33764617C>T		58.0	0.0	0	842	59.0	32.0	0.542373	NM_152493	Q8WYU4	Silent	SNP	ENST00000539719.1	37	CCDS377.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493	
OR4A5	81318	hgsc.bcm.edu	37	11	51412066	51412066	+	Silent	SNP	G	G	C	rs5002409	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:51412066G>C	ENST00000319760.6	-	1	382	c.330C>G	c.(328-330)gtC>gtG	p.V110V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	110						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CCAGAAGGAAGACCTCAGCCC	0.453													.|||	5	0.000998403	0.0	0.0029	5008	,	,		21048	0.0		0.003	False		,,,				2504	0.0				p.V110V		Atlas-SNP	.											.	OR4A5	116	.	0			c.C330G						PASS	.	A		2,4400		0,2,2199	72.0	71.0	71.0		330	-2.0	0.8	11	dbSNP_113	71	22,8570		0,22,4274	no	coding-synonymous	OR4A5	NM_001005272.3		0,24,6473	CC,CG,GG		0.2561,0.0454,0.1847		110/316	51412066	24,12970	2201	4296	6497	SO:0001819	synonymous_variant	81318	exon1			AAGGAAGACCTCA	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.330C>G	11.37:g.51412066G>C		112.0	0.0	0		142.0	74.0	0.521127	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			C|0.001;G|0.999	0.001	strong		0.453	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
NLRP3	114548	hgsc.bcm.edu	37	1	247588140	247588140	+	Silent	SNP	C	C	T	rs111400208	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:247588140C>T	ENST00000336119.3	+	3	2141	c.1395C>T	c.(1393-1395)caC>caT	p.H465H	NLRP3_ENST00000366497.2_Silent_p.H465H|NLRP3_ENST00000348069.2_Silent_p.H465H|NLRP3_ENST00000366496.2_Silent_p.H465H|NLRP3_ENST00000391828.3_Silent_p.H465H|NLRP3_ENST00000474792.1_3'UTR|NLRP3_ENST00000391827.2_Silent_p.H465H	NM_001127462.2|NM_001243133.1|NM_004895.4	NP_001120934.1|NP_001230062.1|NP_004886.3	Q96P20	NALP3_HUMAN	NLR family, pyrin domain containing 3	465	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|cellular response to lipopolysaccharide (GO:0071222)|defense response (GO:0006952)|defense response to virus (GO:0051607)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta production (GO:0032611)|interleukin-1 secretion (GO:0050701)|interleukin-18 production (GO:0032621)|negative regulation of acute inflammatory response (GO:0002674)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta secretion (GO:0050713)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|NLRP3 inflammasome complex assembly (GO:0044546)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|NLRP3 inflammasome complex (GO:0072559)	ATP binding (GO:0005524)|peptidoglycan binding (GO:0042834)			NS(1)|breast(3)|endometrium(6)|kidney(1)|large_intestine(19)|lung(85)|ovary(9)|pancreas(2)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	142	all_cancers(71;9.66e-05)|all_epithelial(71;1.85e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)	all_cancers(173;0.0172)	OV - Ovarian serous cystadenocarcinoma(106;0.0141)			TCTGCGCCCACCTCTGGGGGC	0.592													C|||	7	0.00139776	0.0	0.0014	5008	,	,		19340	0.0		0.006	False		,,,				2504	0.0				p.H465H		Atlas-SNP	.											.	NLRP3	286	.	0			c.C1395T						PASS	.	C	,,,,	4,4402	8.1+/-20.4	0,4,2199	28.0	28.0	28.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1395,1395,1395,1395,1395	3.2	0.0	1	dbSNP_132	28	47,8553	29.6+/-80.5	0,47,4253	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NLRP3	NM_001079821.2,NM_001127461.2,NM_001127462.2,NM_004895.4,NM_183395.2	,,,,	0,51,6452	TT,TC,CC		0.5465,0.0908,0.3921	,,,,	465/1037,465/980,465/980,465/1037,465/923	247588140	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	114548	exon3			CGCCCACCTCTGG	AF054176	CCDS1632.1, CCDS1633.1, CCDS44346.1, CCDS44347.1	1q44	2014-09-17	2006-12-08	2006-12-08	ENSG00000162711	ENSG00000162711		"""Nucleotide-binding domain and leucine rich repeat containing"""	16400	protein-coding gene	gene with protein product	"""Cryopyrin"", ""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 3"""	606416	"""cold autoinflammatory syndrome 1"""	C1orf7, CIAS1		10741953	Standard	NM_183395		Approved	AGTAVPRL, AII, AVP, FCAS, FCU, NALP3, PYPAF1, MWS, CLR1.1	uc001icr.3	Q96P20	OTTHUMG00000040647	ENST00000336119.3:c.1395C>T	1.37:g.247588140C>T		29.0	0.0	0		41.0	18.0	0.439024	NM_183395	B2RC97|B7ZKS9|B7ZKT2|B7ZKT3|O75434|Q17RS2|Q59H68|Q5JQS8|Q5JQS9|Q6TG35|Q8TCW0|Q8TEU9|Q8WXH9	Silent	SNP	ENST00000336119.3	37	CCDS1632.1																																																																																			C|0.997;T|0.003	0.003	strong		0.592	NLRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097740.1	NM_004895	
TREML4	285852	hgsc.bcm.edu	37	6	41196733	41196733	+	Silent	SNP	C	C	T	rs147088240	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:41196733C>T	ENST00000341495.2	+	2	449	c.345C>T	c.(343-345)tcC>tcT	p.S115S	TREML4_ENST00000448827.2_Silent_p.S115S	NM_198153.2	NP_937796.1	Q6UXN2	TRML4_HUMAN	triggering receptor expressed on myeloid cells-like 4	115	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|large_intestine(1)|lung(4)|skin(1)	8	Ovarian(28;0.0327)|Colorectal(47;0.196)					ACAACGCTTCCGAAAACATCA	0.488													C|||	12	0.00239617	0.0	0.0086	5008	,	,		19933	0.0		0.006	False		,,,				2504	0.0				p.S115S		Atlas-SNP	.											.	TREML4	25	.	0			c.C345T						PASS	.	C		6,4400		0,6,2197	83.0	80.0	81.0		345	-1.0	0.0	6	dbSNP_134	81	41,8559		0,41,4259	no	coding-synonymous	TREML4	NM_198153.2		0,47,6456	TT,TC,CC		0.4767,0.1362,0.3614		115/201	41196733	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	285852	exon2			CGCTTCCGAAAAC	AF534826	CCDS34446.1	6p21.1	2013-01-11			ENSG00000188056	ENSG00000188056		"""Immunoglobulin superfamily / V-set domain containing"""	30807	protein-coding gene	gene with protein product	"""TREM like transcript 4"""	614664				12645956	Standard	NM_198153		Approved	TLT4	uc003oqc.3	Q6UXN2	OTTHUMG00000016408	ENST00000341495.2:c.345C>T	6.37:g.41196733C>T		192.0	0.0	0		168.0	88.0	0.52381	NM_198153	B7ZL92	Silent	SNP	ENST00000341495.2	37	CCDS34446.1																																																																																			C|0.996;T|0.004	0.004	strong		0.488	TREML4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043873.2		
TATDN2	9797	hgsc.bcm.edu	37	3	10312633	10312633	+	Silent	SNP	G	G	A	rs115984909	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:10312633G>A	ENST00000287652.4	+	4	2818	c.1767G>A	c.(1765-1767)gtG>gtA	p.V589V	TATDN2_ENST00000448281.2_Silent_p.V589V|RP11-438J1.1_ENST00000450534.1_3'UTR	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	589					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CTAAGGCTGTGGCATTTGGAG	0.473													G|||	5	0.000998403	0.0	0.0	5008	,	,		20193	0.0		0.004	False		,,,				2504	0.001				p.V589V		Atlas-SNP	.											.	TATDN2	59	.	0			c.G1767A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	107.0	114.0	112.0		1767	0.4	1.0	3	dbSNP_132	112	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	TATDN2	NM_014760.3		0,20,6483	AA,AG,GG		0.2209,0.0227,0.1538		589/762	10312633	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GGCTGTGGCATTT	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.1767G>A	3.37:g.10312633G>A		28.0	0.0	0		30.0	18.0	0.6	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			G|0.998;A|0.002	0.002	strong		0.473	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
THEMIS2	9473	hgsc.bcm.edu	37	1	28203156	28203156	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:28203156A>G	ENST00000373921.3	+	2	156	c.152A>G	c.(151-153)aAg>aGg	p.K51R	THEMIS2_ENST00000373925.1_Missense_Mutation_p.K51R|THEMIS2_ENST00000328928.7_Missense_Mutation_p.K51R|THEMIS2_ENST00000373927.3_Missense_Mutation_p.K51R	NM_001105556.1	NP_001099026.1	Q5TEJ8	THMS2_HUMAN	thymocyte selection associated family member 2	51	CABIT 1.				cell adhesion (GO:0007155)|inflammatory response (GO:0006954)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACCTGATCAAGGTCACCCAG	0.592																																					p.K51R		Atlas-SNP	.											.	.	.	.	0			c.A152G						PASS	.						88.0	86.0	87.0					1																	28203156		2203	4300	6503	SO:0001583	missense	9473	exon2			TGATCAAGGTCAC	AF044896	CCDS30653.1, CCDS30654.1, CCDS41290.1, CCDS65461.1	1p35.2	2012-07-10	2012-07-10	2012-07-10	ENSG00000130775	ENSG00000130775			16839	protein-coding gene	gene with protein product	"""induced by contact to basement membrane 1"""		"""chromosome 1 open reading frame 38"""	C1orf38		16219472	Standard	XM_005246041		Approved	ICB-1, Icb-1	uc001bpc.4	Q5TEJ8	OTTHUMG00000003735	ENST00000373921.3:c.152A>G	1.37:g.28203156A>G	ENSP00000363031:p.Lys51Arg	57.0	0.0	0		63.0	39.0	0.619048	NM_001039477	A2RTZ3|B4DZT9|B4DZY3|O60560|Q5TEJ1|Q5TEJ9|Q5TEK1|Q68DP4|Q9BYB6|Q9NS90	Missense_Mutation	SNP	ENST00000373921.3	37	CCDS41290.1	.	.	.	.	.	.	.	.	.	.	A	19.45	3.829475	0.71258	.	.	ENSG00000130775	ENST00000373925;ENST00000328928;ENST00000373927;ENST00000442118;ENST00000373921	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.45054	0.1323	M	0.81802	2.56	0.46564	D	0.999102	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;0.999;1.0;0.991;0.989	T	0.47623	-0.9103	10	0.72032	D	0.01	-42.0968	14.6767	0.68986	1.0:0.0:0.0:0.0	.	51;51;51;51;51	Q5TEJ8-5;Q5TEJ8-6;Q5TEJ8;Q5TEJ8-4;Q5TEJ8-2	.;.;THMS2_HUMAN;.;.	R	51	ENSP00000363035:K51R;ENSP00000329862:K51R;ENSP00000363037:K51R;ENSP00000413725:K51R;ENSP00000363031:K51R	ENSP00000329862:K51R	K	+	2	0	C1orf38	28075743	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.414000	0.73318	2.146000	0.66826	0.528000	0.53228	AAG	.	.	none		0.592	THEMIS2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011148.1	NM_004848	
LIMCH1	22998	hgsc.bcm.edu	37	4	41687843	41687843	+	Missense_Mutation	SNP	C	C	T	rs76461603	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:41687843C>T	ENST00000313860.7	+	23	2986	c.2932C>T	c.(2932-2934)Cgg>Tgg	p.R978W	LIMCH1_ENST00000509277.1_Missense_Mutation_p.R811W|LIMCH1_ENST00000396595.3_Missense_Mutation_p.R823W|LIMCH1_ENST00000503057.1_Missense_Mutation_p.R1362W|LIMCH1_ENST00000514096.1_Missense_Mutation_p.R818W|LIMCH1_ENST00000508501.1_Missense_Mutation_p.R977W|LIMCH1_ENST00000513024.1_Missense_Mutation_p.R831W|LIMCH1_ENST00000381753.4_Missense_Mutation_p.R811W|LIMCH1_ENST00000512632.1_Missense_Mutation_p.R901W|LIMCH1_ENST00000512820.1_Missense_Mutation_p.R990W|LIMCH1_ENST00000511496.1_Missense_Mutation_p.R818W|LIMCH1_ENST00000512946.1_Missense_Mutation_p.R978W	NM_014988.2	NP_055803.2	Q9UPQ0	LIMC1_HUMAN	LIM and calponin homology domains 1	978					actomyosin structure organization (GO:0031032)		zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(5)	41						CAGTGAAAGGCGGAAGTGAGT	0.433													C|||	11	0.00219649	0.0	0.0043	5008	,	,		20909	0.0069		0.001	False		,,,				2504	0.0				p.R978W		Atlas-SNP	.											.	LIMCH1	233	.	0			c.C2932T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	83.0	71.0	75.0		2932,2929,2467,2431,2932	4.6	1.0	4	dbSNP_131	75	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	LIMCH1	NM_001112717.1,NM_001112718.1,NM_001112719.1,NM_001112720.1,NM_014988.2	101,101,101,101,101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	978/1058,977/1057,823/903,811/891,978/1084	41687843	1,13005	2203	4300	6503	SO:0001583	missense	22998	exon23			GAAAGGCGGAAGT	AB029025	CCDS33977.1, CCDS47047.1, CCDS54763.1, CCDS54764.1, CCDS54765.1, CCDS75119.1, CCDS75121.1	4p13	2007-06-14		2008-01-09	ENSG00000064042	ENSG00000064042			29191	protein-coding gene	gene with protein product						10470851	Standard	XM_005248057		Approved	DKFZP686A01247, LIMCH1A, LMO7B	uc003gvz.4	Q9UPQ0	OTTHUMG00000160575	ENST00000313860.7:c.2932C>T	4.37:g.41687843C>T	ENSP00000316891:p.Arg978Trp	116.0	0.0	0		127.0	16.0	0.125984	NM_014988	A8MXC3|E9PHM7|Q503B5|Q5CZB1|Q5CZB6|Q5H9S8|Q68E07|Q6PJ44|Q7Z3G5|Q8N3S9|Q8N6M2	Missense_Mutation	SNP	ENST00000313860.7	37	CCDS33977.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	5	0.008741258741258742	1	0.0013192612137203166	C	14.03	2.414116	0.42817	0.0	1.16E-4	ENSG00000064042	ENST00000513024;ENST00000508501;ENST00000512946;ENST00000313860;ENST00000512632;ENST00000512820;ENST00000503057;ENST00000511496;ENST00000313875;ENST00000514096;ENST00000509277;ENST00000396595;ENST00000381753;ENST00000537405	T;T;T;T;T;T;T;T;T;T;T;T	0.49720	0.82;1.38;1.39;1.38;0.8;1.39;0.79;0.79;0.79;0.77;0.8;0.79	5.51	4.61	0.57282	.	0.066428	0.64402	D	0.000014	T	0.53642	0.1809	L	0.60455	1.87	0.34467	D	0.702395	D;D;D;D;D;D;D;D;D;D;D;D	0.89917	0.999;0.999;0.998;1.0;1.0;1.0;1.0;0.999;1.0;1.0;1.0;1.0	P;P;P;D;D;D;D;D;D;D;D;D	0.79108	0.642;0.88;0.719;0.99;0.949;0.949;0.992;0.947;0.981;0.958;0.981;0.958	T	0.68969	-0.5269	10	0.87932	D	0	-20.9146	10.6354	0.45563	0.2036:0.7964:0.0:0.0	.	818;728;811;901;811;823;1362;831;990;977;978;978	E7EPK0;B7Z3G0;E9PDJ9;D6RD46;Q9UPQ0-9;Q9UPQ0-6;G5EA03;Q9UPQ0-5;Q9UPQ0-4;E9PHM7;Q9UPQ0-2;Q9UPQ0	.;.;.;.;.;.;.;.;.;.;.;LIMC1_HUMAN	W	831;977;978;978;901;990;1362;818;1361;818;811;823;811;330	ENSP00000425222:R831W;ENSP00000424825:R977W;ENSP00000424645:R978W;ENSP00000316891:R978W;ENSP00000427045:R901W;ENSP00000424437:R990W;ENSP00000425631:R1362W;ENSP00000421242:R818W;ENSP00000426334:R818W;ENSP00000422864:R811W;ENSP00000379840:R823W;ENSP00000371172:R811W	ENSP00000316891:R978W	R	+	1	2	LIMCH1	41382600	1.000000	0.71417	1.000000	0.80357	0.660000	0.38997	1.469000	0.35343	2.873000	0.98535	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.433	LIMCH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000361249.2	NM_014988	
DDX49	54555	hgsc.bcm.edu	37	19	19037176	19037176	+	Silent	SNP	G	G	A	rs115860110	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:19037176G>A	ENST00000247003.4	+	10	1159	c.1092G>A	c.(1090-1092)gaG>gaA	p.E364E	DDX49_ENST00000599156.1_3'UTR|AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000438170.2_3'UTR	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	364	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			ACGCCATCGAGGAGCAGATCA	0.627													G|||	22	0.00439297	0.0015	0.0101	5008	,	,		11044	0.0		0.0129	False		,,,				2504	0.0				p.E364E		Atlas-SNP	.											.	DDX49	37	.	0			c.G1092A						PASS	.	G		6,4368		0,6,2181	60.0	40.0	47.0		1092	4.7	1.0	19	dbSNP_132	47	88,8458		0,88,4185	no	coding-synonymous	DDX49	NM_019070.4		0,94,6366	AA,AG,GG		1.0297,0.1372,0.7276		364/484	19037176	94,12826	2187	4273	6460	SO:0001819	synonymous_variant	54555	exon10			CATCGAGGAGCAG		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.1092G>A	19.37:g.19037176G>A		216.0	0.0	0		224.0	90.0	0.401786	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Silent	SNP	ENST00000247003.4	37	CCDS12390.1																																																																																			G|0.993;A|0.007	0.007	strong		0.627	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
SCRN2	90507	hgsc.bcm.edu	37	17	45917703	45917703	+	Silent	SNP	C	C	T	rs11652952	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:45917703C>T	ENST00000290216.9	-	3	335	c.210G>A	c.(208-210)acG>acA	p.T70T	SCRN2_ENST00000584123.1_Silent_p.T78T|SCRN2_ENST00000407215.3_Silent_p.T70T	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	70						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TCACAGCGTGCGTCTTCGACA	0.592													C|||	147	0.029353	0.0658	0.0231	5008	,	,		20332	0.0		0.0358	False		,,,				2504	0.0082				p.T70T		Atlas-SNP	.											.	SCRN2	35	.	0			c.G210A						PASS	.	C	,	237,4169	139.2+/-174.8	7,223,1973	103.0	77.0	86.0		210,210	-10.2	0.3	17	dbSNP_120	86	295,8305	108.8+/-169.4	6,283,4011	no	coding-synonymous,coding-synonymous	SCRN2	NM_001145023.1,NM_138355.3	,	13,506,5984	TT,TC,CC		3.4302,5.379,4.0904	,	70/379,70/426	45917703	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	90507	exon3			AGCGTGCGTCTTC	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.210G>A	17.37:g.45917703C>T		142.0	0.0	0		185.0	89.0	0.481081	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	37	CCDS11519.1																																																																																			C|0.963;T|0.037	0.037	strong		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355	
AGRN	375790	hgsc.bcm.edu	37	1	985377	985377	+	Silent	SNP	C	C	T	rs113020870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:985377C>T	ENST00000379370.2	+	27	4889	c.4839C>T	c.(4837-4839)tgC>tgT	p.C1613C		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	1613	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		GTGCTCAGTGCGAGTGCCCCC	0.716													C|||	6	0.00119808	0.0	0.0043	5008	,	,		7759	0.0		0.002	False		,,,				2504	0.001				p.C1613C		Atlas-SNP	.											.	AGRN	110	.	0			c.C4839T						PASS	.	C		6,4366		0,6,2180	16.0	17.0	16.0		4839	0.6	0.7	1	dbSNP_132	16	26,8532		0,26,4253	no	coding-synonymous	AGRN	NM_198576.3		0,32,6433	TT,TC,CC		0.3038,0.1372,0.2475		1613/2046	985377	32,12898	2186	4279	6465	SO:0001819	synonymous_variant	375790	exon27			TCAGTGCGAGTGC	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.4839C>T	1.37:g.985377C>T		67.0	0.0	0		65.0	41.0	0.630769	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			C|0.998;T|0.002	0.002	strong		0.716	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SRRM4	84530	hgsc.bcm.edu	37	12	119568596	119568596	+	Missense_Mutation	SNP	G	G	A	rs7297606	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:119568596G>A	ENST00000267260.4	+	8	1116	c.728G>A	c.(727-729)aGt>aAt	p.S243N	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	243	Ser-rich.		S -> N (in dbSNP:rs7297606).		cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CGCCCGCCCAGTCAACCCCTC	0.627													G|||	500	0.0998403	0.2042	0.1124	5008	,	,		15715	0.0268		0.0547	False		,,,				2504	0.0716				p.S243N		Atlas-SNP	.											.	SRRM4	131	.	0			c.G728A						PASS	.	G	ASN/SER	638,3266		55,528,1369	25.0	31.0	29.0		728	3.3	1.0	12	dbSNP_116	29	626,7648		17,592,3528	yes	missense	SRRM4	NM_194286.3	46	72,1120,4897	AA,AG,GG		7.5659,16.3422,10.3794	benign	243/612	119568596	1264,10914	1952	4137	6089	SO:0001583	missense	84530	exon8			CGCCCAGTCAACC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.728G>A	12.37:g.119568596G>A	ENSP00000267260:p.Ser243Asn	19.0	0.0	0		30.0	17.0	0.566667	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	191	0.08745421245421245	94	0.1910569105691057	36	0.09944751381215469	20	0.03496503496503497	41	0.05408970976253298	G	7.164	0.586356	0.13749	0.163422	0.075659	ENSG00000139767	ENST00000267260	T	0.24538	1.85	5.21	3.34	0.38264	.	0.747332	0.13340	N	0.395235	T	0.00039	0.0001	L	0.44542	1.39	0.41880	P	0.009688999999999948	B	0.30281	0.275	B	0.29942	0.109	T	0.23440	-1.0188	9	0.12430	T	0.62	-8.2941	11.354	0.49605	0.0752:0.1274:0.7974:0.0	rs7297606;rs52809663;rs58175205;rs7297606	243	A7MD48	SRRM4_HUMAN	N	243	ENSP00000267260:S243N	ENSP00000267260:S243N	S	+	2	0	SRRM4	118052979	1.000000	0.71417	0.992000	0.48379	0.053000	0.15095	1.326000	0.33735	0.207000	0.20607	-1.688000	0.00730	AGT	G|0.908;A|0.092	0.092	strong		0.627	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
SP4	6671	hgsc.bcm.edu	37	7	21468934	21468934	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:21468934C>T	ENST00000222584.3	+	3	369	c.151C>T	c.(151-153)Ctg>Ttg	p.L51L		NM_003112.3	NP_003103.2	Q02446	SP4_HUMAN	Sp4 transcription factor	51					regulation of heart contraction (GO:0008016)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	35						TCTGGCTTTACTGGCAGCTAC	0.478																																					p.L51L		Atlas-SNP	.											.	SP4	91	.	0			c.C151T						PASS	.						39.0	42.0	41.0					7																	21468934		2203	4300	6503	SO:0001819	synonymous_variant	6671	exon3			GCTTTACTGGCAG		CCDS5373.1	7p15	2013-01-08			ENSG00000105866	ENSG00000105866		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	11209	protein-coding gene	gene with protein product		600540				1454515	Standard	XM_005249828		Approved	SPR-1, HF1B, MGC130008, MGC130009	uc003sva.3	Q02446	OTTHUMG00000094801	ENST00000222584.3:c.151C>T	7.37:g.21468934C>T		53.0	0.0	0		73.0	31.0	0.424658	NM_003112	O60402|Q32M52	Silent	SNP	ENST00000222584.3	37	CCDS5373.1																																																																																			.	.	none		0.478	SP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211617.2	NM_003112	
CCDC13	152206	hgsc.bcm.edu	37	3	42787467	42787467	+	Missense_Mutation	SNP	G	G	A	rs141737119	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:42787467G>A	ENST00000310232.6	-	7	856	c.773C>T	c.(772-774)tCg>tTg	p.S258L	CCDC13-AS1_ENST00000446950.1_RNA|CCDC13-AS1_ENST00000418161.1_RNA	NM_144719.3	NP_653320.3	Q8IYE1	CCD13_HUMAN	coiled-coil domain containing 13	258										endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|prostate(3)|skin(1)|urinary_tract(1)	25						GGTCCCTGGCGAAGATAGGAG	0.512																																					p.S258L		Atlas-SNP	.											CCDC13,colon,carcinoma,+1,1	CCDC13	71	1	0			c.C773T						PASS	.	G	LEU/SER	1,4405	2.1+/-5.4	0,1,2202	92.0	89.0	90.0		773	3.3	0.4	3	dbSNP_134	90	2,8598	2.2+/-6.3	0,2,4298	no	missense	CCDC13	NM_144719.3	145	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	benign	258/716	42787467	3,13003	2203	4300	6503	SO:0001583	missense	152206	exon7			CCTGGCGAAGATA	AK058196	CCDS2705.1	3p22.1	2005-01-25			ENSG00000244607	ENSG00000244607			26358	protein-coding gene	gene with protein product						12477932	Standard	NM_144719		Approved	FLJ25467	uc003cly.4	Q8IYE1	OTTHUMG00000133046	ENST00000310232.6:c.773C>T	3.37:g.42787467G>A	ENSP00000309836:p.Ser258Leu	110.0	0.0	0		75.0	42.0	0.56	NM_144719		Missense_Mutation	SNP	ENST00000310232.6	37	CCDS2705.1	.	.	.	.	.	.	.	.	.	.	G	8.690	0.907306	0.17833	2.27E-4	2.33E-4	ENSG00000244607	ENST00000310232	T	0.25085	1.82	5.08	3.27	0.37495	.	0.461691	0.22580	N	0.058238	T	0.22399	0.0540	L	0.52905	1.665	0.18873	N	0.999983	B	0.16396	0.017	B	0.12156	0.007	T	0.18777	-1.0326	10	0.26408	T	0.33	.	9.0645	0.36455	0.0787:0.0:0.7746:0.1466	.	258	Q8IYE1	CCD13_HUMAN	L	258	ENSP00000309836:S258L	ENSP00000309836:S258L	S	-	2	0	CCDC13	42762471	0.405000	0.25336	0.434000	0.26772	0.186000	0.23388	0.648000	0.24828	0.539000	0.28788	-0.137000	0.14449	TCG	G|1.000;A|0.000	0.000	strong		0.512	CCDC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256652.1	NM_144719	
CXCR5	643	hgsc.bcm.edu	37	11	118765108	118765108	+	Silent	SNP	G	G	A	rs113967672	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:118765108G>A	ENST00000292174.4	+	2	1031	c.855G>A	c.(853-855)gcG>gcA	p.A285A	BCL9L_ENST00000334801.3_3'UTR	NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	285					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		ACACCCTGGCGAGGCTGAAGG	0.602													G|||	5	0.000998403	0.0	0.0014	5008	,	,		22112	0.0		0.004	False		,,,				2504	0.0				p.A285A		Atlas-SNP	.											CXCR5,NS,carcinoma,+1,1	CXCR5	34	1	0			c.G855A						PASS	.	G	,	3,4397	8.1+/-20.4	0,3,2197	142.0	108.0	119.0		855,720	-2.9	0.0	11	dbSNP_132	119	36,8554	24.0+/-70.4	0,36,4259	no	coding-synonymous,coding-synonymous	CXCR5	NM_001716.4,NM_032966.2	,	0,39,6456	AA,AG,GG		0.4191,0.0682,0.3002	,	285/373,240/328	118765108	39,12951	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGCGAGGCTG	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.855G>A	11.37:g.118765108G>A		140.0	0.0	0		135.0	62.0	0.459259	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.997;A|0.003	0.003	strong		0.602	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
DHX34	9704	hgsc.bcm.edu	37	19	47858489	47858489	+	Missense_Mutation	SNP	C	C	G	rs34802163	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:47858489C>G	ENST00000328771.4	+	3	1248	c.899C>G	c.(898-900)cCc>cGc	p.P300R		NM_014681.5	NP_055496.2	Q14147	DHX34_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 34	300	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	membrane (GO:0016020)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(5)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(25;1.65e-09)|all_epithelial(76;9.95e-08)|all_lung(116;7.27e-07)|Lung NSC(112;1.6e-06)|Ovarian(192;0.0139)|all_neural(266;0.026)|Breast(70;0.0503)		all cancers(93;7.16e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.000489)|GBM - Glioblastoma multiforme(486;0.00413)|Epithelial(262;0.0132)		CGCCTGTTGCCCACGCGGCCT	0.587													C|||	66	0.0131789	0.0008	0.0115	5008	,	,		16986	0.001		0.0318	False		,,,				2504	0.0245				p.P300R		Atlas-SNP	.											DHX34,lower_third,carcinoma,-1,1	DHX34	98	1	0			c.C899G						PASS	.	C	ARG/PRO	21,4385	29.9+/-59.1	1,19,2183	133.0	115.0	121.0		899	4.4	1.0	19	dbSNP_126	121	258,8342	101.4+/-162.7	3,252,4045	yes	missense	DHX34	NM_014681.5	103	4,271,6228	GG,GC,CC		3.0,0.4766,2.1452	benign	300/1144	47858489	279,12727	2203	4300	6503	SO:0001583	missense	9704	exon3			TGTTGCCCACGCG	D50924	CCDS12700.1	19q13.3	2003-06-13	2003-06-13	2003-06-13	ENSG00000134815	ENSG00000134815		"""DEAH-boxes"""	16719	protein-coding gene	gene with protein product		615475	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 34"""	DDX34		10708517, 8590280	Standard	NM_014681		Approved	KIAA0134	uc010xyn.2	Q14147	OTTHUMG00000149959	ENST00000328771.4:c.899C>G	19.37:g.47858489C>G	ENSP00000331907:p.Pro300Arg	137.0	0.0	0		143.0	68.0	0.475524	NM_014681	B4DMY8	Missense_Mutation	SNP	ENST00000328771.4	37	CCDS12700.1	35	0.016025641025641024	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	27	0.03562005277044855	C	10.91	1.484804	0.26598	0.004766	0.03	ENSG00000134815	ENST00000328771;ENST00000257252	T	0.26373	1.74	4.41	4.41	0.53225	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.359689	0.23656	N	0.045867	T	0.04861	0.0131	N	0.02697	-0.525	0.36709	D	0.880551	B;D	0.62365	0.238;0.991	B;P	0.61658	0.126;0.892	T	0.18398	-1.0338	10	0.35671	T	0.21	0.6401	9.6656	0.39983	0.0:0.9004:0.0:0.0996	rs34802163;rs61750959	300;300	Q14147;B4E3G3	DHX34_HUMAN;.	R	300	ENSP00000331907:P300R	ENSP00000257252:P300R	P	+	2	0	DHX34	52550329	0.920000	0.31207	0.984000	0.44739	0.859000	0.49053	2.414000	0.44627	2.010000	0.58986	0.456000	0.33151	CCC	C|0.979;G|0.021	0.021	strong		0.587	DHX34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314313.3	NM_014681	
PGR	5241	hgsc.bcm.edu	37	11	100999245	100999245	+	Missense_Mutation	SNP	G	G	A	rs11571145	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:100999245G>A	ENST00000325455.5	-	1	2010	c.557C>T	c.(556-558)cCc>cTc	p.P186L	PGR_ENST00000534013.1_Intron|PGR_ENST00000263463.5_Missense_Mutation_p.P186L	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	186	Modulating, Pro-Rich.		P -> L (in dbSNP:rs11571145). {ECO:0000269|Ref.8}.		cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CAGGCCCCGGGGCAGCACTTT	0.721													G|||	24	0.00479233	0.0008	0.0086	5008	,	,		13887	0.0		0.0119	False		,,,				2504	0.0051				p.P186L	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											PGR,NS,carcinoma,0,1	PGR	115	1	0			c.C557T						PASS	.	G	LEU/PRO,LEU/PRO	6,4072		0,6,2033	5.0	7.0	6.0		557,65	2.7	0.8	11	dbSNP_120	6	97,8103		0,97,4003	yes	missense,missense	PGR	NM_000926.4,NM_001202474.1	98,98	0,103,6036	AA,AG,GG		1.1829,0.1471,0.8389	possibly-damaging,possibly-damaging	186/934,22/770	100999245	103,12175	2039	4100	6139	SO:0001583	missense	5241	exon1			CCCCGGGGCAGCA	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.557C>T	11.37:g.100999245G>A	ENSP00000325120:p.Pro186Leu	42.0	0.0	0		14.0	6.0	0.428571	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Missense_Mutation	SNP	ENST00000325455.5	37	CCDS8310.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	14.65	2.598041	0.46318	0.001471	0.011829	ENSG00000082175	ENST00000325455;ENST00000263463;ENST00000537623	T;T	0.18657	2.2;2.2	3.62	2.65	0.31530	.	1.295630	0.05245	N	0.512963	T	0.25680	0.0625	M	0.70275	2.135	0.46078	D	0.998855	B;B	0.31413	0.322;0.322	B;B	0.39876	0.312;0.312	T	0.11542	-1.0583	10	0.87932	D	0	.	8.4855	0.33069	0.0:0.0:0.5311:0.4689	rs11571145;rs11571145	186;186	Q8TDS3;P06401	.;PRGR_HUMAN	L	186	ENSP00000325120:P186L;ENSP00000263463:P186L	ENSP00000263463:P186L	P	-	2	0	PGR	100504455	1.000000	0.71417	0.840000	0.33206	0.780000	0.44128	3.317000	0.51968	0.788000	0.33755	0.561000	0.74099	CCC	G|0.994;A|0.006	0.006	strong		0.721	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
NOTCH3	4854	hgsc.bcm.edu	37	19	15299112	15299112	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:15299112T>C	ENST00000263388.2	-	9	1501	c.1426A>G	c.(1426-1428)Agc>Ggc	p.S476G		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	476	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			ACACAGGGGCTACTCTGACAC	0.592																																					p.S476G		Atlas-SNP	.											.	NOTCH3	340	.	0			c.A1426G						PASS	.						55.0	46.0	49.0					19																	15299112		2203	4300	6503	SO:0001583	missense	4854	exon9			AGGGGCTACTCTG	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1426A>G	19.37:g.15299112T>C	ENSP00000263388:p.Ser476Gly	83.0	0.0	0		96.0	4.0	0.0416667	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	.	.	.	.	.	.	.	.	.	.	t	16.92	3.255393	0.59321	.	.	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.91686	-2.89	5.04	5.04	0.67666	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.38058	N	0.001835	D	0.90823	0.7118	L	0.58101	1.795	0.36208	D	0.851202	P;B	0.35401	0.499;0.256	B;B	0.39617	0.168;0.305	D	0.92578	0.6072	10	0.41790	T	0.15	.	13.7877	0.63119	0.0:0.0:0.0:1.0	.	479;476	Q59FL3;Q9UM47	.;NOTC3_HUMAN	G	476;478	ENSP00000263388:S476G	ENSP00000263388:S476G	S	-	1	0	NOTCH3	15160112	1.000000	0.71417	0.999000	0.59377	0.848000	0.48234	5.718000	0.68455	1.903000	0.55091	0.454000	0.30748	AGC	.	.	none		0.592	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
IDH3B	3420	hgsc.bcm.edu	37	20	2641471	2641471	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:2641471T>C	ENST00000380843.4	-	6	433	c.403A>G	c.(403-405)Aag>Gag	p.K135E	IDH3B_ENST00000488299.1_5'UTR|IDH3B_ENST00000380851.5_Missense_Mutation_p.K135E	NM_006899.3	NP_008830.2	O43837	IDH3B_HUMAN	isocitrate dehydrogenase 3 (NAD+) beta	135					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|isocitrate metabolic process (GO:0006102)|NADH metabolic process (GO:0006734)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	electron carrier activity (GO:0009055)|isocitrate dehydrogenase (NAD+) activity (GO:0004449)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)			breast(1)|endometrium(3)|kidney(2)|lung(7)|prostate(1)	14						AAGTCCAACTTACGCCTGAGG	0.537																																					p.K135E		Atlas-SNP	.											.	IDH3B	25	.	0			c.A403G						PASS	.						118.0	110.0	113.0					20																	2641471		2203	4300	6503	SO:0001583	missense	3420	exon6			CCAACTTACGCCT		CCDS13031.1, CCDS13032.1, CCDS74696.1	20p13	2013-02-14			ENSG00000101365	ENSG00000101365	1.1.1.41		5385	protein-coding gene	gene with protein product		604526				10575215	Standard	NM_006899		Approved	RP46	uc002wgp.4	O43837	OTTHUMG00000031699	ENST00000380843.4:c.403A>G	20.37:g.2641471T>C	ENSP00000370223:p.Lys135Glu	75.0	0.0	0		78.0	35.0	0.448718	NM_006899	B2RDR1|D3DVX2|D3DVX3|O95106|Q5JXS8|Q9NQ06|Q9NQ07|Q9NUZ0|Q9UEX0|Q9UG99	Missense_Mutation	SNP	ENST00000380843.4	37	CCDS13032.1	.	.	.	.	.	.	.	.	.	.	T	8.127	0.782172	0.16189	.	.	ENSG00000101365	ENST00000380851;ENST00000380843;ENST00000341825	T;T	0.66638	-0.22;-0.22	5.28	5.28	0.74379	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.35799	0.0944	N	0.01809	-0.71	0.80722	D	1	B;B	0.10296	0.002;0.003	B;B	0.15052	0.009;0.012	T	0.42050	-0.9474	10	0.02654	T	1	-21.4299	13.2215	0.59890	0.0:0.0:0.0:1.0	.	135;135	O43837-2;O43837	.;IDH3B_HUMAN	E	135	ENSP00000370232:K135E;ENSP00000370223:K135E	ENSP00000343215:K135E	K	-	1	0	IDH3B	2589471	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.457000	0.80775	2.217000	0.71921	0.533000	0.62120	AAG	.	.	none		0.537	IDH3B-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077613.1		
USP40	55230	hgsc.bcm.edu	37	2	234449358	234449358	+	Missense_Mutation	SNP	C	C	G	rs202235068		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:234449358C>G	ENST00000427112.2	-	9	1152	c.1117G>C	c.(1117-1119)Gga>Cga	p.G373R	USP40_ENST00000450966.1_Missense_Mutation_p.G385R|USP40_ENST00000251722.6_Missense_Mutation_p.G373R			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	373	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CAAGATATTCCTATCTTTTTC	0.388																																					p.G385R		Atlas-SNP	.											.	USP40	174	.	0			c.G1153C						PASS	.	C	ARG/GLY	1,3697		0,1,1848	180.0	168.0	172.0		1153	5.1	1.0	2		172	2,8216		0,2,4107	yes	missense	USP40	NM_018218.2	125	0,3,5955	GG,GC,CC		0.0243,0.027,0.0252	probably-damaging	385/1248	234449358	3,11913	1849	4109	5958	SO:0001583	missense	55230	exon9			ATATTCCTATCTT	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.1117G>C	2.37:g.234449358C>G	ENSP00000387898:p.Gly373Arg	226.0	0.0	0		221.0	109.0	0.493213	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.026869	0.75390	2.7E-4	2.43E-4	ENSG00000085982	ENST00000450966;ENST00000251722;ENST00000427112	T;T;T	0.07021	3.23;3.24;3.24	5.09	5.09	0.68999	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	13.261800	0.00166	N	0.000000	T	0.31796	0.0808	M	0.66939	2.045	0.53005	D	0.999963	D;D	0.69078	0.997;0.996	D;D	0.77557	0.99;0.982	T	0.00540	-1.1681	10	0.87932	D	0	.	10.533	0.44988	0.0:0.8747:0.0:0.1253	.	373;385	Q9NVE5;Q9NVE5-3	UBP40_HUMAN;.	R	385;373;373	ENSP00000415434:G385R;ENSP00000251722:G373R;ENSP00000387898:G373R	ENSP00000251722:G373R	G	-	1	0	USP40	234114097	1.000000	0.71417	0.993000	0.49108	0.877000	0.50540	4.295000	0.59049	2.526000	0.85167	0.561000	0.74099	GGA	.	.	weak		0.388	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
BSN	8927	hgsc.bcm.edu	37	3	49698115	49698115	+	Missense_Mutation	SNP	G	G	A	rs116113662	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:49698115G>A	ENST00000296452.4	+	6	8951	c.8837G>A	c.(8836-8838)cGg>cAg	p.R2946Q		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	2946					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		GAGCTGGACCGGGACCTGCGG	0.642													G|||	24	0.00479233	0.0	0.0029	5008	,	,		18137	0.0		0.0139	False		,,,				2504	0.0082				p.R2946Q		Atlas-SNP	.											BSN,NS,carcinoma,-1,1	BSN	272	1	0			c.G8837A						PASS	.	G	GLN/ARG	16,4376		0,16,2180	23.0	24.0	24.0		8837	4.5	1.0	3	dbSNP_132	24	113,8475		0,113,4181	yes	missense	BSN	NM_003458.3	43	0,129,6361	AA,AG,GG		1.3158,0.3643,0.9938	probably-damaging	2946/3927	49698115	129,12851	2196	4294	6490	SO:0001583	missense	8927	exon6			TGGACCGGGACCT	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.8837G>A	3.37:g.49698115G>A	ENSP00000296452:p.Arg2946Gln	92.0	0.0	0		120.0	54.0	0.45	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	G	14.70	2.614137	0.46631	0.003643	0.013158	ENSG00000164061	ENST00000296452	T	0.24151	1.87	4.5	4.5	0.54988	.	0.080992	0.49305	D	0.000146	T	0.38026	0.1025	M	0.64404	1.975	0.43338	D	0.995383	D	0.76494	0.999	P	0.61275	0.886	T	0.46317	-0.9200	10	0.66056	D	0.02	-17.5126	17.2151	0.86941	0.0:0.0:1.0:0.0	.	2946	Q9UPA5	BSN_HUMAN	Q	2946	ENSP00000296452:R2946Q	ENSP00000296452:R2946Q	R	+	2	0	BSN	49673119	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.338000	0.59316	2.043000	0.60533	0.561000	0.74099	CGG	G|0.990;A|0.010	0.010	strong		0.642	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
MDN1	23195	hgsc.bcm.edu	37	6	90384216	90384216	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:90384216T>G	ENST00000369393.3	-	79	12969	c.12854A>C	c.(12853-12855)cAg>cCg	p.Q4285P	RP1-122O8.7_ENST00000438877.1_RNA|MDN1_ENST00000428876.1_Missense_Mutation_p.Q4285P|MDN1_ENST00000468568.1_5'Flank			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4285					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CTCTGTCCACTGCTGCACGCC	0.642																																					p.Q4285P		Atlas-SNP	.											.	MDN1	478	.	0			c.A12854C						PASS	.						22.0	23.0	23.0					6																	90384216		2203	4299	6502	SO:0001583	missense	23195	exon79			GTCCACTGCTGCA	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12854A>C	6.37:g.90384216T>G	ENSP00000358400:p.Gln4285Pro	20.0	0.0	0		30.0	13.0	0.433333	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	.	.	.	.	.	.	.	.	.	.	T	13.08	2.129345	0.37630	.	.	ENSG00000112159	ENST00000369393;ENST00000428876	T;T	0.03301	3.98;3.98	5.87	5.87	0.94306	.	0.308307	0.33691	N	0.004644	T	0.03263	0.0095	M	0.63428	1.95	0.34397	D	0.694857	P	0.51653	0.947	P	0.44597	0.454	T	0.41179	-0.9523	10	0.48119	T	0.1	.	12.0858	0.53695	0.0:0.0685:0.0:0.9315	.	4285	Q9NU22	MDN1_HUMAN	P	4285	ENSP00000358400:Q4285P;ENSP00000413970:Q4285P	ENSP00000358400:Q4285P	Q	-	2	0	MDN1	90440937	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.651000	0.37302	2.248000	0.74166	0.533000	0.62120	CAG	.	.	none		0.642	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						scavenged	.						70.0	75.0	74.0					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	107.0	1.0	0.00934579		56.0	13.0	0.232143	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
TNIP1	10318	hgsc.bcm.edu	37	5	150441711	150441711	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:150441711G>C	ENST00000389378.2	-	4	922	c.334C>G	c.(334-336)Cca>Gca	p.P112A	TNIP1_ENST00000522226.1_Missense_Mutation_p.P112A|TNIP1_ENST00000523338.1_Missense_Mutation_p.P112A|TNIP1_ENST00000518977.1_Missense_Mutation_p.P112A|TNIP1_ENST00000520931.1_Missense_Mutation_p.P59A|TNIP1_ENST00000521591.1_Missense_Mutation_p.P112A|TNIP1_ENST00000315050.7_Missense_Mutation_p.P112A|TNIP1_ENST00000524280.1_Missense_Mutation_p.P112A|TNIP1_ENST00000523200.1_Missense_Mutation_p.P112A	NM_001252385.1|NM_001252393.1|NM_001258454.1|NM_006058.4	NP_001239314.1|NP_001239322.1|NP_001245383.1|NP_006049.3	Q15025	TNIP1_HUMAN	TNFAIP3 interacting protein 1	112	Interacts with Nef.				defense response (GO:0006952)|glycoprotein biosynthetic process (GO:0009101)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|modulation by symbiont of host I-kappaB kinase/NF-kappaB cascade (GO:0085032)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of viral genome replication (GO:0045071)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|translation (GO:0006412)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	mitogen-activated protein kinase binding (GO:0051019)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|liver(1)|lung(5)|ovary(2)|prostate(2)|skin(3)	23		Medulloblastoma(196;0.0911)|all_hematologic(541;0.207)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TTCTGGACTGGTGCTGGCTTG	0.498																																					p.P112A		Atlas-SNP	.											.	TNIP1	51	.	0			c.C334G						PASS	.						115.0	102.0	106.0					5																	150441711		2203	4300	6503	SO:0001583	missense	10318	exon4			GGACTGGTGCTGG	AJ011895	CCDS34280.1, CCDS58982.1, CCDS58983.1, CCDS58984.1, CCDS58985.1, CCDS75359.1	5q32-q33.1	2008-07-18							16903	protein-coding gene	gene with protein product	"""virion-associated nuclear-shuttling protein"", ""Nef-associated factor 1 SNP"""	607714				9923610, 11090181	Standard	NM_001252385		Approved	NAF1, KIAA0113, ABIN-1, VAN	uc003ltj.3	Q15025		ENST00000389378.2:c.334C>G	5.37:g.150441711G>C	ENSP00000374029:p.Pro112Ala	132.0	0.0	0		133.0	68.0	0.511278	NM_001252385	A4F1W8|A4F1W9|A4F1X2|A4F1X4|A4F1X5|A4F1X6|A4F1X7|A4F1X9|B7Z699|E7EPY1|E7ET96|O76008|Q05KP3|Q05KP4|Q6N077|Q96EL9|Q99833|Q9H1J3	Missense_Mutation	SNP	ENST00000389378.2	37	CCDS34280.1	.	.	.	.	.	.	.	.	.	.	G	12.55	1.971545	0.34754	.	.	ENSG00000145901	ENST00000520931;ENST00000389378;ENST00000315050;ENST00000523338;ENST00000544828;ENST00000417127;ENST00000539213;ENST00000522226;ENST00000521591;ENST00000518977;ENST00000524280;ENST00000523200;ENST00000545840;ENST00000522100;ENST00000520695;ENST00000521001	T;T;T;T;T;T;T;T;T;T;T;T	0.34472	1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36;1.36	4.96	-1.53	0.08611	.	0.304128	0.34484	N	0.003934	T	0.23649	0.0572	L	0.56769	1.78	0.09310	N	1	B;B;B;B;B;B;B	0.23377	0.081;0.052;0.084;0.052;0.052;0.028;0.015	B;B;B;B;B;B;B	0.20184	0.028;0.011;0.022;0.017;0.024;0.015;0.015	T	0.09143	-1.0688	10	0.30078	T	0.28	-0.1324	1.0768	0.01634	0.2623:0.2792:0.3156:0.1429	.	112;66;66;112;112;112;112	B7Z8K2;A4F1X9;A4F1X7;E7EPY1;E7ET96;A4F1W9;Q15025	.;.;.;.;.;.;TNIP1_HUMAN	A	59;112;112;112;69;69;74;112;112;112;112;112;69;59;112;112	ENSP00000429891:P59A;ENSP00000374029:P112A;ENSP00000317891:P112A;ENSP00000428243:P112A;ENSP00000428187:P112A;ENSP00000430760:P112A;ENSP00000430971:P112A;ENSP00000429912:P112A;ENSP00000431105:P112A;ENSP00000428487:P59A;ENSP00000430279:P112A;ENSP00000428404:P112A	ENSP00000317891:P112A	P	-	1	0	TNIP1	150421904	0.527000	0.26306	0.003000	0.11579	0.632000	0.37999	1.069000	0.30641	0.009000	0.14813	-0.142000	0.14014	CCA	.	.	none		0.498	TNIP1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374914.1	NM_006058	
ALG12	79087	hgsc.bcm.edu	37	22	50301430	50301430	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:50301430G>A	ENST00000330817.6	-	7	1204	c.931C>T	c.(931-933)Cgc>Tgc	p.R311C		NM_024105.3	NP_077010.1	Q9BV10	ALG12_HUMAN	ALG12, alpha-1,6-mannosyltransferase	311					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-1,6-mannosyltransferase activity (GO:0000009)|dol-P-Man:Man(7)GlcNAc(2)-PP-Dol alpha-1,6-mannosyltransferase activity (GO:0052917)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(3)	12		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		BRCA - Breast invasive adenocarcinoma(115;0.199)|LUAD - Lung adenocarcinoma(64;0.247)		ATGATGAAGCGTAGCTCCTTG	0.547																																					p.R311C		Atlas-SNP	.											.	ALG12	35	.	0			c.C931T	GRCh37	CM050360	ALG12	M		PASS	.						125.0	109.0	115.0					22																	50301430		2203	4300	6503	SO:0001583	missense	79087	exon7			TGAAGCGTAGCTC	AJ303120	CCDS14081.1	22q13.33	2013-02-26	2013-02-26		ENSG00000182858	ENSG00000182858	2.4.1.260	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19358	protein-coding gene	gene with protein product	"""dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichol alpha-1,6-mannosyltransferase"", ""dol-P-Man dependent alpha-1,6-mannosyltransferase"""	607144	"""asparagine-linked glycosylation 12 homolog (yeast, alpha-1,6-mannosyltransferase)"", ""asparagine-linked glycosylation 12, alpha-1,6-mannosyltransferase homolog (S. cerevisiae)"""			11983712	Standard	NM_024105		Approved	ECM39	uc003biy.3	Q9BV10	OTTHUMG00000150289	ENST00000330817.6:c.931C>T	22.37:g.50301430G>A	ENSP00000333813:p.Arg311Cys	145.0	0.0	0		167.0	85.0	0.508982	NM_024105	A6PWM1|Q4KMH4|Q8NG10|Q96AA4	Missense_Mutation	SNP	ENST00000330817.6	37	CCDS14081.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368561|3.368561	0.61624|0.61624	.|.	.|.	ENSG00000182858|ENSG00000182858	ENST00000330817|ENST00000486602	D|.	0.91351|.	-2.83|.	4.28|4.28	4.28|4.28	0.50868|0.50868	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	D|D	0.87111|0.87111	0.6096|0.6096	H|H	0.95470|0.95470	3.675|3.675	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.97110|.	1.0|.	D|D	0.91436|0.91436	0.5170|0.5170	10|5	0.87932|.	D|.	0|.	-9.9379|-9.9379	17.2733|17.2733	0.87109|0.87109	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	311|.	Q9BV10|.	ALG12_HUMAN|.	C|M	311|46	ENSP00000333813:R311C|.	ENSP00000333813:R311C|.	R|T	-|-	1|2	0|0	ALG12|ALG12	48687434|48687434	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.041000|0.041000	0.13682|0.13682	9.334000|9.334000	0.96470|0.96470	2.378000|2.378000	0.81104|0.81104	0.655000|0.655000	0.94253|0.94253	CGC|ACG	.	.	none		0.547	ALG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317405.2	NM_024105	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	rs561061447	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71.0	76.0	74.0					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1581G>A	5.37:g.140188353G>A		107.0	0.0	0		58.0	15.0	0.258621	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
DNAJC24	120526	hgsc.bcm.edu	37	11	31447864	31447864	+	Missense_Mutation	SNP	A	A	G	rs144649932	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:31447864A>G	ENST00000465995.1	+	4	387	c.281A>G	c.(280-282)gAt>gGt	p.D94G	DNAJC24_ENST00000536040.1_3'UTR	NM_181706.4	NP_859057.4	Q6P3W2	DJC24_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 24	93					chaperone-mediated protein folding (GO:0061077)|oxidation-reduction process (GO:0055114)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|positive regulation of ATPase activity (GO:0032781)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ATPase activator activity (GO:0001671)|ferrous iron binding (GO:0008198)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|skin(1)|upper_aerodigestive_tract(2)	11						GGACCAGTAGATGCTCAAGTA	0.269													A|||	7	0.00139776	0.0	0.0014	5008	,	,		16417	0.0		0.005	False		,,,				2504	0.001				p.D94G		Atlas-SNP	.											.	DNAJC24	23	.	0			c.A281G						PASS	.	A	GLY/ASP	5,3647		0,5,1821	115.0	111.0	112.0		281	4.4	1.0	11	dbSNP_134	112	28,8128		0,28,4050	yes	missense	DNAJC24	NM_181706.4	94	0,33,5871	GG,GA,AA		0.3433,0.1369,0.2795	benign	94/150	31447864	33,11775	1826	4078	5904	SO:0001583	missense	120526	exon4			CAGTAGATGCTCA	AL833128	CCDS7873.2	11p14.1	2011-09-02	2008-07-03	2008-07-03	ENSG00000170946	ENSG00000170946		"""Heat shock proteins / DNAJ (HSP40)"""	26979	protein-coding gene	gene with protein product		611072	"""zinc finger, CSL-type containing 3"", ""DPH4 homolog (JJJ3, S. cerevisiae)"", ""DPH4, JJJ3 homolog (S. cerevisiae)"""	ZCSL3, DPH4		15485916	Standard	NM_181706		Approved	JJJ3	uc001msx.3	Q6P3W2	OTTHUMG00000133712	ENST00000465995.1:c.281A>G	11.37:g.31447864A>G	ENSP00000417548:p.Asp94Gly	46.0	0.0	0		59.0	28.0	0.474576	NM_181706	A8K0V0|B1ALC1|I6L9B4	Missense_Mutation	SNP	ENST00000465995.1	37	CCDS7873.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	15.76	2.927163	0.52759	0.001369	0.003433	ENSG00000170946	ENST00000465995	T	0.31769	1.48	5.52	4.4	0.53042	Zinc finger, DPH-type (1);	0.143219	0.64402	N	0.000012	T	0.21881	0.0527	L	0.59436	1.845	0.80722	D	1	B	0.14438	0.01	B	0.20577	0.03	T	0.04307	-1.0961	10	0.27785	T	0.31	.	10.0993	0.42495	0.924:0.0:0.076:0.0	.	93	Q6P3W2	DJC24_HUMAN	G	94	ENSP00000417548:D94G	ENSP00000417548:D94G	D	+	2	0	DNAJC24	31404440	1.000000	0.71417	0.999000	0.59377	0.980000	0.70556	5.131000	0.64751	1.037000	0.40024	0.528000	0.53228	GAT	A|0.998;G|0.002	0.002	strong		0.269	DNAJC24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258011.3	NM_181706	
COQ10A	93058	hgsc.bcm.edu	37	12	56664041	56664041	+	Silent	SNP	G	G	A	rs11543260	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56664041G>A	ENST00000308197.5	+	5	945	c.684G>A	c.(682-684)aaG>aaA	p.K228K	COQ10A_ENST00000546544.1_Silent_p.K211K|COQ10A_ENST00000433805.2_Silent_p.K196K|RP11-977G19.14_ENST00000546464.1_RNA	NM_144576.3	NP_653177.3	Q96MF6	CQ10A_HUMAN	coenzyme Q10 homolog A (S. cerevisiae)	228						mitochondrial inner membrane (GO:0005743)				cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	8						CAGCCACCAAGTTTGGTCCAG	0.527													G|||	43	0.00858626	0.0038	0.0115	5008	,	,		20738	0.0		0.0278	False		,,,				2504	0.002				p.K228K		Atlas-SNP	.											.	COQ10A	20	.	0			c.G684A						PASS	.	G	,	36,3956		0,36,1960	127.0	126.0	126.0		588,684	4.8	1.0	12	dbSNP_120	126	172,8168		3,166,4001	no	coding-synonymous,coding-synonymous	COQ10A	NM_001099337.1,NM_144576.3	,	3,202,5961	AA,AG,GG		2.0624,0.9018,1.6867	,	196/216,228/248	56664041	208,12124	1996	4170	6166	SO:0001819	synonymous_variant	93058	exon5			CACCAAGTTTGGT	AK057003	CCDS41796.1, CCDS44921.1	12q13.3	2011-09-16	2006-04-04		ENSG00000135469	ENSG00000135469			26515	protein-coding gene	gene with protein product			"""coenzyme Q10 homolog A (yeast)"""				Standard	NM_144576		Approved	FLJ32452	uc001sko.4	Q96MF6	OTTHUMG00000170283	ENST00000308197.5:c.684G>A	12.37:g.56664041G>A		111.0	0.0	0		120.0	57.0	0.475	NM_144576	Q6GMR6|Q6UWB9|Q86X16|Q8TAL2|Q96MF1|Q9BUP4	Silent	SNP	ENST00000308197.5	37	CCDS41796.1	23	0.010531135531135532	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	1.929	-0.446438	0.04604	0.009018	0.020624	ENSG00000135469	ENST00000553234;ENST00000551814	.	.	.	4.85	4.85	0.62838	.	.	.	.	.	T	0.41190	0.1148	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53158	-0.8478	4	.	.	.	.	13.5848	0.61924	0.0:0.1571:0.8428:0.0	rs11543260;rs11543260	.	.	.	N	134;45	.	.	S	+	2	0	COQ10A	54950308	1.000000	0.71417	1.000000	0.80357	0.278000	0.26855	0.701000	0.25616	2.675000	0.91044	0.655000	0.94253	AGT	G|0.986;A|0.014	0.014	strong		0.527	COQ10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408332.1	NM_144576	
DNAH9	1770	hgsc.bcm.edu	37	17	11502188	11502188	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:11502188C>T	ENST00000262442.4	+	1	441	c.373C>T	c.(373-375)Ctg>Ttg	p.L125L	DNAH9_ENST00000454412.2_Silent_p.L125L|DNAH9_ENST00000579828.1_Silent_p.L125L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	125	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTGCGGGGACCTGCCCGCGGC	0.701																																					p.L125L		Atlas-SNP	.											.	DNAH9	695	.	0			c.C373T						PASS	.						3.0	4.0	4.0					17																	11502188		1807	3723	5530	SO:0001819	synonymous_variant	1770	exon1			GGGGACCTGCCCG	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.373C>T	17.37:g.11502188C>T		19.0	0.0	0		9.0	6.0	0.666667	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			.	.	none		0.701	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CFAP61	26074	hgsc.bcm.edu	37	20	20055848	20055848	+	Silent	SNP	A	A	G	rs367870948		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:20055848A>G	ENST00000245957.5	+	5	463	c.387A>G	c.(385-387)gcA>gcG	p.A129A	C20orf26_ENST00000451767.2_Silent_p.A129A|C20orf26_ENST00000389656.3_5'UTR|C20orf26_ENST00000377306.1_Silent_p.A129A|C20orf26_ENST00000377309.2_5'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		129										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TGTATAAGGCAGTGCCAGAGC	0.502																																					p.A129A		Atlas-SNP	.											.	C20orf26	188	.	0			c.A387G						PASS	.	A	,	0,4406		0,0,2203	173.0	147.0	156.0		387,387	-11.4	0.4	20		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C20orf26	NM_001167816.1,NM_015585.3	,	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,	129/471,129/1238	20055848	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	26074	exon5			TAAGGCAGTGCCA																												ENST00000245957.5:c.387A>G	20.37:g.20055848A>G		137.0	0.0	0		157.0	78.0	0.496815	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Silent	SNP	ENST00000245957.5	37	CCDS33447.1																																																																																			.	.	weak		0.502	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
CCDC88B	283234	hgsc.bcm.edu	37	11	64120703	64120703	+	Silent	SNP	G	G	A	rs61744422	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:64120703G>A	ENST00000356786.5	+	21	3722	c.3678G>A	c.(3676-3678)acG>acA	p.T1226T	CCDC88B_ENST00000359902.2_Silent_p.T378T|CCDC88B_ENST00000301897.4_5'UTR|CCDC88B_ENST00000463837.1_3'UTR	NM_032251.5	NP_115627.6	A6NC98	CC88B_HUMAN	coiled-coil domain containing 88B	1226						membrane (GO:0016020)				endometrium(1)|kidney(2)|large_intestine(1)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	27						GGCTGACCACGCAGTGTGAGG	0.692													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		13374	0.0		0.0149	False		,,,				2504	0.0051				p.T1226T		Atlas-SNP	.											.	CCDC88B	89	.	0			c.G3678A						PASS	.	G		20,4252		0,20,2116	5.0	7.0	6.0		3678	-8.1	0.9	11	dbSNP_129	6	104,8316		1,102,4107	no	coding-synonymous	CCDC88B	NM_032251.5		1,122,6223	AA,AG,GG		1.2352,0.4682,0.977		1226/1477	64120703	124,12568	2136	4210	6346	SO:0001819	synonymous_variant	283234	exon21			GACCACGCAGTGT	AK090436	CCDS8072.2	11q13.1	2013-03-13	2007-05-31	2007-05-31	ENSG00000168071	ENSG00000168071			26757	protein-coding gene	gene with protein product	"""brain leucine zipper protein"", ""GRP78-interacting protein induced by ER stress"""	611205	"""coiled-coil domain containing 88"""	CCDC88		15882442, 21289099	Standard	NM_032251		Approved	FLJ37970, BRLZ, HkRP3, FLJ00354, GIPIE	uc001nzy.3	A6NC98	OTTHUMG00000045419	ENST00000356786.5:c.3678G>A	11.37:g.64120703G>A		45.0	0.0	0		53.0	31.0	0.584906	NM_032251	A5D8Y5|B5MDM2|Q05BL2|Q6RUV3|Q8N1Q6|Q8NF44|Q9H0H1	Silent	SNP	ENST00000356786.5	37	CCDS8072.2																																																																																			G|0.990;A|0.010	0.010	strong		0.692	CCDC88B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104845.1	NM_032251	
NUP107	57122	hgsc.bcm.edu	37	12	69090624	69090624	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:69090624C>T	ENST00000229179.4	+	6	806	c.474C>T	c.(472-474)ttC>ttT	p.F158F	NUP107_ENST00000539906.1_Silent_p.F129F|NUP107_ENST00000378905.2_Silent_p.F7F	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	158					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			TTTCTGATTTCCTGCAGTCTT	0.363																																					p.F158F		Atlas-SNP	.											.	NUP107	88	.	0			c.C474T						PASS	.						129.0	113.0	118.0					12																	69090624		2203	4300	6503	SO:0001819	synonymous_variant	57122	exon6			TGATTTCCTGCAG	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.474C>T	12.37:g.69090624C>T		81.0	0.0	0		56.0	4.0	0.0714286	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			.	.	none		0.363	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
SDHA	6389	hgsc.bcm.edu	37	5	256508	256508	+	Silent	SNP	C	C	T	rs3211499		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:256508C>T	ENST00000264932.6	+	15	2083	c.1968C>T	c.(1966-1968)acC>acT	p.T656T	SDHA_ENST00000510361.1_Silent_p.T608T|SDHA_ENST00000507522.1_3'UTR|SDHA_ENST00000504309.1_Silent_p.T575T	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	656					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	ACTGTGCCACCGTCCCGCCAG	0.438									Familial Paragangliomas																												p.T656T		Atlas-SNP	.											SDHA,NS,carcinoma,+2,1	SDHA	80	1	0			c.C1968T						scavenged	.						70.0	78.0	75.0					5																	256508		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon15	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	TGCCACCGTCCCG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1968C>T	5.37:g.256508C>T		137.0	0.0	0		144.0	6.0	0.0416667	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			.	.	weak		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
ZFHX3	463	hgsc.bcm.edu	37	16	72992626	72992626	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:72992626C>T	ENST00000268489.5	-	2	2091	c.1419G>A	c.(1417-1419)gaG>gaA	p.E473E	ZFHX3_ENST00000397992.5_Intron	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	473	Poly-Glu.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				cctcctcctcctccgcctctt	0.577																																					p.E473E		Atlas-SNP	.											.	ZFHX3	404	.	0			c.G1419A						PASS	.						41.0	44.0	43.0					16																	72992626		2198	4300	6498	SO:0001819	synonymous_variant	463	exon2			CTCCTCCTCCGCC	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.1419G>A	16.37:g.72992626C>T		38.0	0.0	0		57.0	9.0	0.157895	NM_006885	D3DWS8|O15101|Q13719	Silent	SNP	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	none		0.577	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
NCKIPSD	51517	hgsc.bcm.edu	37	3	48716536	48716536	+	Missense_Mutation	SNP	G	G	A	rs75577765	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:48716536G>A	ENST00000294129.2	-	10	1770	c.1651C>T	c.(1651-1653)Ccg>Tcg	p.P551S	NCKIPSD_ENST00000341520.4_Missense_Mutation_p.P551S|NCKIPSD_ENST00000416649.2_Missense_Mutation_p.P544S	NM_016453.2	NP_057537.1	Q9NZQ3	SPN90_HUMAN	NCK interacting protein with SH3 domain	551	Leu-rich.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|NLS-bearing protein import into nucleus (GO:0006607)|signal transduction (GO:0007165)	cytosol (GO:0005829)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	cytoskeletal protein binding (GO:0008092)			endometrium(1)|large_intestine(3)|lung(6)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		CAGAGGTCCGGCAGCTGCTCT	0.652													G|||	26	0.00519169	0.0	0.0029	5008	,	,		16917	0.0		0.0139	False		,,,				2504	0.0102				p.P551S		Atlas-SNP	.											.	NCKIPSD	52	.	0			c.C1651T						PASS	.	G	SER/PRO,SER/PRO	16,4390	22.3+/-47.3	0,16,2187	53.0	54.0	54.0		1651,1630	5.4	1.0	3	dbSNP_131	54	112,8488	52.3+/-112.8	0,112,4188	yes	missense,missense	NCKIPSD	NM_016453.2,NM_184231.1	74,74	0,128,6375	AA,AG,GG		1.3023,0.3631,0.9842	probably-damaging,probably-damaging	551/723,544/716	48716536	128,12878	2203	4300	6503	SO:0001583	missense	51517	exon10			GGTCCGGCAGCTG	AF178432	CCDS2776.1, CCDS46827.1	3p21	2008-07-18			ENSG00000213672	ENSG00000213672			15486	protein-coding gene	gene with protein product	"""dia interacting protein"", ""diaphanous protein interacting protein"", ""SH3 protein interacting with Nck, 90 kDa"""	606671				10648423, 10619843	Standard	NM_016453		Approved	AF3P21, SPIN90, ORF1, WISH, WASLBP, DIP1	uc003cun.3	Q9NZQ3	OTTHUMG00000133542	ENST00000294129.2:c.1651C>T	3.37:g.48716536G>A	ENSP00000294129:p.Pro551Ser	121.0	0.0	0		148.0	71.0	0.47973	NM_016453	B4DFL5|Q6GU34|Q6SPF3|Q8TC10|Q9UGM8	Missense_Mutation	SNP	ENST00000294129.2	37	CCDS2776.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	G|G	26.1|26.1	4.700036|4.700036	0.88924|0.88924	0.003631|0.003631	0.013023|0.013023	ENSG00000213672|ENSG00000213672	ENST00000415281|ENST00000341520;ENST00000416649;ENST00000294129;ENST00000413374	.|T;T;T;T	.|0.64260	.|1.02;-0.09;-0.09;1.02	5.37|5.37	5.37|5.37	0.77165|0.77165	.|Domain of unknown function DUF2013 (1);	.|0.000000	.|0.85682	.|U	.|0.000000	T|T	0.71813|0.71813	0.3384|0.3384	M|M	0.76328|0.76328	2.33|2.33	0.80722|0.80722	D|D	1|1	.|D;D	.|0.62365	.|0.991;0.989	.|D;P	.|0.66497	.|0.944;0.906	T|T	0.72067|0.72067	-0.4402|-0.4402	5|10	.|0.25106	.|T	.|0.35	.|.	19.105|19.105	0.93291|0.93291	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|551;544	.|Q9NZQ3;Q9NZQ3-3	.|SPN90_HUMAN;.	V|S	259|551;544;551;7	.|ENSP00000342621:P551S;ENSP00000389059:P544S;ENSP00000294129:P551S;ENSP00000396683:P7S	.|ENSP00000294129:P551S	A|P	-|-	2|1	0|0	NCKIPSD|NCKIPSD	48691540|48691540	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.839000|0.839000	0.47603|0.47603	9.307000|9.307000	0.96226|0.96226	2.498000|2.498000	0.84270|0.84270	0.650000|0.650000	0.86243|0.86243	GCC|CCG	G|0.990;A|0.010	0.010	strong		0.652	NCKIPSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257520.1	NM_016453	
C3orf58	205428	hgsc.bcm.edu	37	3	143708645	143708645	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:143708645C>A	ENST00000315691.3	+	3	1790	c.1255C>A	c.(1255-1257)Cgt>Agt	p.R419S	C3orf58_ENST00000493396.1_Intron|C3orf58_ENST00000495414.1_Missense_Mutation_p.R210S|C3orf58_ENST00000441925.2_Missense_Mutation_p.R181S	NM_173552.3	NP_775823.1	Q8NDZ4	DIA1_HUMAN	chromosome 3 open reading frame 58	419					cardiac muscle cell proliferation (GO:0060038)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	COPI vesicle coat (GO:0030126)|extracellular space (GO:0005615)|Golgi membrane (GO:0000139)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						AAAAGAACTGCGTGAATACCT	0.448																																					p.R419S		Atlas-SNP	.											.	C3orf58	36	.	0			c.C1255A						PASS	.						69.0	73.0	72.0					3																	143708645		2203	4300	6503	SO:0001583	missense	205428	exon3			GAACTGCGTGAAT	AK095161	CCDS3130.1, CCDS46929.1	3q24	2013-12-06			ENSG00000181744	ENSG00000181744			28490	protein-coding gene	gene with protein product	"""deleted in autism 1"", ""hypoxia and Akt induced stem cell factor"""	612200				21283809, 23784961, 24269490	Standard	NM_173552		Approved	MGC33365, DIA1, HASF	uc003evo.3	Q8NDZ4	OTTHUMG00000159380	ENST00000315691.3:c.1255C>A	3.37:g.143708645C>A	ENSP00000320081:p.Arg419Ser	104.0	0.0	0		90.0	48.0	0.533333	NM_173552	B2RCF2|B7Z1W3	Missense_Mutation	SNP	ENST00000315691.3	37	CCDS3130.1	.	.	.	.	.	.	.	.	.	.	C	17.43	3.387226	0.61956	.	.	ENSG00000181744	ENST00000315691;ENST00000495414;ENST00000441925	T	0.32272	1.46	6.17	4.35	0.52113	.	0.000000	0.85682	D	0.000000	T	0.46718	0.1407	L	0.45581	1.43	0.58432	D	0.999997	B;D	0.63046	0.168;0.992	B;D	0.72982	0.077;0.979	T	0.22730	-1.0208	10	0.21540	T	0.41	.	15.7877	0.78319	0.2489:0.7511:0.0:0.0	.	210;419	B7Z1W3;Q8NDZ4	.;CC058_HUMAN	S	419;210;181	ENSP00000320081:R419S	ENSP00000320081:R419S	R	+	1	0	C3orf58	145191335	1.000000	0.71417	0.991000	0.47740	0.998000	0.95712	4.658000	0.61497	0.900000	0.36469	0.655000	0.94253	CGT	.	.	none		0.448	C3orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355038.1	NM_173552	
CFAP57	149465	hgsc.bcm.edu	37	1	43647424	43647424	+	Missense_Mutation	SNP	C	C	T	rs138300205	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:43647424C>T	ENST00000372492.4	+	3	701	c.377C>T	c.(376-378)aCg>aTg	p.T126M	WDR65_ENST00000528956.1_Missense_Mutation_p.T126M	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		126										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTGGCTCAGACGTCACCTCCA	0.423													C|||	28	0.00559105	0.0015	0.0	5008	,	,		17818	0.0		0.0159	False		,,,				2504	0.0102				p.T126M		Atlas-SNP	.											.	WDR65	76	.	0			c.C377T						PASS	.	C	MET/THR,MET/THR,MET/THR	12,4394	20.2+/-43.8	0,12,2191	81.0	86.0	84.0		377,377,377	5.6	1.0	1	dbSNP_134	84	150,8450	72.6+/-135.2	0,150,4150	yes	missense,missense,missense	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	81,81,81	0,162,6341	TT,TC,CC		1.7442,0.2724,1.2456	probably-damaging,probably-damaging,probably-damaging	126/699,126/699,126/699	43647424	162,12844	2203	4300	6503	SO:0001583	missense	149465	exon3			CTCAGACGTCACC																												ENST00000372492.4:c.377C>T	1.37:g.43647424C>T	ENSP00000361570:p.Thr126Met	151.0	0.0	0		163.0	75.0	0.460123	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Missense_Mutation	SNP	ENST00000372492.4	37		13	0.005952380952380952	1	0.0020325203252032522	0	0.0	0	0.0	12	0.0158311345646438	C	20.1	3.937291	0.73557	0.002724	0.017442	ENSG00000243710	ENST00000372492;ENST00000528956;ENST00000529956	T;T;T	0.38401	4.93;1.14;4.93	5.57	5.57	0.84162	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.153918	0.64402	D	0.000017	T	0.43100	0.1232	M	0.66939	2.045	0.47862	D	0.999536	D;D	0.76494	0.999;0.998	P;D	0.67900	0.899;0.954	T	0.50931	-0.8769	10	0.48119	T	0.1	.	19.1541	0.93503	0.0:1.0:0.0:0.0	.	126;126	Q96MR6;Q96MR6-2	WDR65_HUMAN;.	M	126	ENSP00000361570:T126M;ENSP00000435310:T126M;ENSP00000434133:T126M	ENSP00000361570:T126M	T	+	2	0	WDR65	43420011	1.000000	0.71417	0.999000	0.59377	0.588000	0.36517	5.291000	0.65667	2.626000	0.88956	0.557000	0.71058	ACG	C|0.990;T|0.010	0.010	strong		0.423	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
MSLN	10232	hgsc.bcm.edu	37	16	816414	816414	+	Missense_Mutation	SNP	G	G	A	rs150147307		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:816414G>A	ENST00000382862.3	+	12	1249	c.1154G>A	c.(1153-1155)cGc>cAc	p.R385H	MSLN_ENST00000545450.2_Missense_Mutation_p.R385H|MSLN_ENST00000566549.1_Missense_Mutation_p.R385H|MSLN_ENST00000563941.1_Missense_Mutation_p.R385H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	385					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				GAGGACATTCGCAAGTGGAAT	0.567																																					p.R385H		Atlas-SNP	.											.	MSLN	109	.	0			c.G1154A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	0,4380		0,0,2190	88.0	78.0	81.0		1154,1154,1154	-3.5	0.0	16	dbSNP_134	81	1,8573	1.2+/-3.3	0,1,4286	no	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	29,29,29	0,1,6476	AA,AG,GG		0.0117,0.0,0.0077	benign,benign,benign	385/623,385/623,385/631	816414	1,12953	2190	4287	6477	SO:0001583	missense	10232	exon13			ACATTCGCAAGTG	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.1154G>A	16.37:g.816414G>A	ENSP00000372313:p.Arg385His	122.0	0.0	0		153.0	65.0	0.424837	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	.	.	.	.	.	.	.	.	.	.	G	0.244	-1.011226	0.02095	0.0	1.17E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.13420	2.59;2.59	4.97	-3.46	0.04767	.	1.820510	0.02850	N	0.129024	T	0.07279	0.0184	N	0.12569	0.235	0.09310	N	1	B;B;B;B	0.28350	0.029;0.037;0.208;0.029	B;B;B;B	0.16289	0.005;0.014;0.015;0.005	T	0.30679	-0.9970	10	0.13470	T	0.59	-0.7879	11.3272	0.49456	0.3512:0.0:0.6488:0.0	.	384;385;385;385	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	385	ENSP00000442965:R385H;ENSP00000372313:R385H	ENSP00000372313:R385H	R	+	2	0	MSLN	756415	0.000000	0.05858	0.043000	0.18650	0.104000	0.19210	-1.290000	0.02777	-0.567000	0.06046	0.297000	0.19635	CGC	G|1.000;A|0.000	0.000	weak		0.567	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
MFHAS1	9258	hgsc.bcm.edu	37	8	8748058	8748058	+	Silent	SNP	C	C	T	rs146502253	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:8748058C>T	ENST00000276282.6	-	1	3097	c.2511G>A	c.(2509-2511)aaG>aaA	p.K837K		NM_004225.2	NP_004216.2	Q9Y4C4	MFHA1_HUMAN	malignant fibrous histiocytoma amplified sequence 1	837										endometrium(1)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|stomach(1)	21		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.124)		AAGGCTTGCCCTTGGGTTTAT	0.537													C|||	3	0.000599042	0.0	0.0	5008	,	,		18898	0.0		0.002	False		,,,				2504	0.001				p.K837K	Melanoma(103;1201 2045 17515 28966)	Atlas-SNP	.											.	MFHAS1	58	.	0			c.G2511A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	73.0	72.0	72.0		2511	4.1	1.0	8	dbSNP_134	72	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	MFHAS1	NM_004225.2		0,16,6487	TT,TC,CC		0.1628,0.0454,0.123		837/1053	8748058	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	9258	exon1			CTTGCCCTTGGGT	AB016816	CCDS34844.1	8p23.1	2014-03-07			ENSG00000147324	ENSG00000147324			16982	protein-coding gene	gene with protein product	"""leucine rich repeat containing 65"", ""malignant fibrous histiocytoma-amplified sequences with leucine-rich tandem repeats 1"""	605352				9973190	Standard	NM_004225		Approved	MASL1, LRRC65	uc003wsj.1	Q9Y4C4	OTTHUMG00000163676	ENST00000276282.6:c.2511G>A	8.37:g.8748058C>T		53.0	0.0	0		44.0	24.0	0.545455	NM_004225	Q96CI0	Silent	SNP	ENST00000276282.6	37	CCDS34844.1																																																																																			C|0.998;T|0.002	0.002	strong		0.537	MFHAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374724.2	NM_004225	
EXOC4	60412	hgsc.bcm.edu	37	7	133692514	133692514	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:133692514T>G	ENST00000253861.4	+	17	2642	c.2613T>G	c.(2611-2613)tgT>tgG	p.C871W	EXOC4_ENST00000545148.1_Missense_Mutation_p.C481W|EXOC4_ENST00000539845.1_Missense_Mutation_p.C770W|EXOC4_ENST00000541309.1_Missense_Mutation_p.C159W	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	871					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				AGAAAATGTGTAGGAACATTT	0.502																																					p.C871W		Atlas-SNP	.											.	EXOC4	118	.	0			c.T2613G						PASS	.						86.0	72.0	77.0					7																	133692514		2203	4300	6503	SO:0001583	missense	60412	exon17			AATGTGTAGGAAC	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2613T>G	7.37:g.133692514T>G	ENSP00000253861:p.Cys871Trp	93.0	0.0	0		111.0	50.0	0.45045	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Missense_Mutation	SNP	ENST00000253861.4	37	CCDS5829.1	.	.	.	.	.	.	.	.	.	.	T	18.38	3.610461	0.66558	.	.	ENSG00000131558	ENST00000253861;ENST00000546185;ENST00000539845;ENST00000545148;ENST00000541309	.	.	.	5.45	-4.48	0.03515	.	0.000000	0.85682	D	0.000000	T	0.79782	0.4505	M	0.82716	2.605	0.80722	D	1	D;D;D	0.89917	0.996;1.0;1.0	P;D;D	0.80764	0.855;0.994;0.987	T	0.81232	-0.1026	9	0.48119	T	0.1	.	17.5564	0.87890	0.0:0.6695:0.0:0.3305	.	403;481;871	B7Z689;F5GZT1;Q96A65	.;.;EXOC4_HUMAN	W	871;490;770;481;159	.	ENSP00000253861:C871W	C	+	3	2	EXOC4	133343054	0.920000	0.31207	0.962000	0.40283	0.983000	0.72400	0.028000	0.13644	-0.786000	0.04516	-0.353000	0.07706	TGT	.	.	none		0.502	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
CAPN3	825	hgsc.bcm.edu	37	15	42679977	42679977	+	Silent	SNP	C	C	T	rs144383442		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:42679977C>T	ENST00000397163.3	+	4	744	c.525C>T	c.(523-525)gaC>gaT	p.D175D	RP11-164J13.1_ENST00000495723.1_RNA|CAPN3_ENST00000349748.3_Silent_p.D175D|CAPN3_ENST00000318023.7_Silent_p.D175D|CAPN3_ENST00000357568.3_Silent_p.D175D|CAPN3_ENST00000356316.3_Silent_p.D88D	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	175	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGTGGGTGGACGTGGTTATAG	0.493													C|||	1	0.000199681	0.0	0.0	5008	,	,		21839	0.0		0.0	False		,,,				2504	0.001				p.D175D		Atlas-SNP	.											CAPN3_ENST00000356316,NS,carcinoma,0,2	CAPN3	172	2	0			c.C525T						PASS	.	C	,,	3,4403	6.2+/-15.9	0,3,2200	310.0	251.0	271.0		525,525,525	-5.8	0.9	15	dbSNP_134	271	15,8583	9.8+/-36.6	0,15,4284	yes	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	0,18,6484	TT,TC,CC		0.1745,0.0681,0.1384	,,	175/822,175/816,175/730	42679977	18,12986	2203	4299	6502	SO:0001819	synonymous_variant	825	exon4			GGTGGACGTGGTT	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.525C>T	15.37:g.42679977C>T		217.0	0.0	0		137.0	129.0	0.941606	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			C|0.999;T|0.001	0.001	strong		0.493	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
WSCD2	9671	hgsc.bcm.edu	37	12	108641799	108641799	+	Silent	SNP	G	G	A	rs144706841	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:108641799G>A	ENST00000332082.4	+	10	2195	c.1377G>A	c.(1375-1377)ccG>ccA	p.P459P	WSCD2_ENST00000261400.3_Silent_p.P479P|WSCD2_ENST00000547525.1_Silent_p.P459P|WSCD2_ENST00000549903.1_Silent_p.P479P			Q2TBF2	WSCD2_HUMAN	WSC domain containing 2	459						integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(1)|large_intestine(16)|liver(2)|lung(23)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	57						ACTATGCCCCGTGGTGGGCCA	0.567													G|||	4	0.000798722	0.0008	0.0	5008	,	,		19841	0.0		0.003	False		,,,				2504	0.0				p.P459P		Atlas-SNP	.											.	WSCD2	125	.	0			c.G1377A						PASS	.	G		2,4082		0,2,2040	62.0	65.0	64.0		1377	-3.8	1.0	12	dbSNP_134	64	20,8424		0,20,4202	no	coding-synonymous	WSCD2	NM_014653.2		0,22,6242	AA,AG,GG		0.2369,0.049,0.1756		459/566	108641799	22,12506	2042	4222	6264	SO:0001819	synonymous_variant	9671	exon9			TGCCCCGTGGTGG		CCDS41828.1	12q23.3	2008-02-05				ENSG00000075035			29117	protein-coding gene	gene with protein product							Standard	NM_014653		Approved	KIAA0789	uc001tms.3	Q2TBF2		ENST00000332082.4:c.1377G>A	12.37:g.108641799G>A		73.0	0.0	0		125.0	58.0	0.464	NM_014653	B2RN48|B4DES1|Q8IY35|Q9Y4B7	Silent	SNP	ENST00000332082.4	37	CCDS41828.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	WSCD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405554.1	NM_014653	
PLA2R1	22925	hgsc.bcm.edu	37	2	160885432	160885432	+	Missense_Mutation	SNP	T	T	C	rs139957604	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:160885432T>C	ENST00000283243.7	-	5	1090	c.884A>G	c.(883-885)aAt>aGt	p.N295S	PLA2R1_ENST00000392771.1_Missense_Mutation_p.N295S	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	295	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						ATCCAGCTGATTGAGGCCCAT	0.468																																					p.N295S		Atlas-SNP	.											.	PLA2R1	153	.	0			c.A884G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	119.0	94.0	103.0		884,884,884	5.8	1.0	2	dbSNP_134	103	11,8589	7.7+/-29.5	0,11,4289	yes	missense,missense,missense	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	46,46,46	0,11,6492	CC,CT,TT		0.1279,0.0,0.0846	probably-damaging,probably-damaging,probably-damaging	295/1325,295/1462,295/1464	160885432	11,12995	2203	4300	6503	SO:0001583	missense	22925	exon5			AGCTGATTGAGGC	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.884A>G	2.37:g.160885432T>C	ENSP00000283243:p.Asn295Ser	263.0	0.0	0		298.0	155.0	0.520134	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Missense_Mutation	SNP	ENST00000283243.7	37	CCDS33309.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.932188	0.52866	0.0	0.001279	ENSG00000153246	ENST00000283243;ENST00000392771	T;T	0.15718	2.4;2.4	5.83	5.83	0.93111	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.000000	0.85682	D	0.000000	T	0.35711	0.0941	L	0.48935	1.535	0.58432	D	0.999993	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.995;0.998;0.999	T	0.02498	-1.1150	10	0.48119	T	0.1	.	15.1831	0.72975	0.0:0.0:0.0:1.0	.	295;295;295	B7ZML4;Q13018-2;Q13018	.;.;PLA2R_HUMAN	S	295	ENSP00000283243:N295S;ENSP00000376524:N295S	ENSP00000283243:N295S	N	-	2	0	PLA2R1	160593678	1.000000	0.71417	0.998000	0.56505	0.093000	0.18481	4.310000	0.59141	2.227000	0.72691	0.528000	0.53228	AAT	T|0.999;C|0.001	0.001	strong		0.468	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
SON	6651	hgsc.bcm.edu	37	21	34922804	34922804	+	Missense_Mutation	SNP	C	C	T	rs201446136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:34922804C>T	ENST00000356577.4	+	3	1742	c.1267C>T	c.(1267-1269)Cca>Tca	p.P423S	SON_ENST00000381679.4_Missense_Mutation_p.P423S|SON_ENST00000290239.6_Missense_Mutation_p.P423S|SON_ENST00000300278.4_Missense_Mutation_p.P423S|SON_ENST00000381692.2_Intron	NM_138927.1	NP_620305	P18583	SON_HUMAN	SON DNA binding protein	423					cytokinesis (GO:0000910)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of cell cycle (GO:0051726)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|nucleic acid binding (GO:0003676)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|central_nervous_system(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(25)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	72						CCTTTCTACCCCAGTGCCTGA	0.652													C|||	2	0.000399361	0.0	0.0	5008	,	,		18430	0.0		0.002	False		,,,				2504	0.0				p.P423S		Atlas-SNP	.											SON_ENST00000300278,right_lower_lobe,carcinoma,0,2	SON	343	2	0			c.C1267T						PASS	.	C	SER/PRO,SER/PRO	0,4406		0,0,2203	40.0	44.0	43.0		1267,1267	3.6	1.0	21		43	3,8593		0,3,4295	yes	missense,missense	SON	NM_032195.1,NM_138927.1	74,74	0,3,6498	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	423/2304,423/2427	34922804	3,12999	2203	4298	6501	SO:0001583	missense	6651	exon3			TCTACCCCAGTGC	AF380181	CCDS13629.1, CCDS13631.1, CCDS74784.1	21q22.1-q22.2	2013-01-28			ENSG00000159140	ENSG00000159140		"""G patch domain containing"""	11183	protein-coding gene	gene with protein product	"""NRE-binding protein"", ""negative regulatory element-binding protein"", ""Bax antagonist selected in Saccharomyces 1"""	182465		C21orf50		8318737, 21551269	Standard	NM_032195		Approved	DBP-5, NREBP, KIAA1019, BASS1, FLJ21099, FLJ33914	uc002yse.1	P18583	OTTHUMG00000065806	ENST00000356577.4:c.1267C>T	21.37:g.34922804C>T	ENSP00000348984:p.Pro423Ser	71.0	0.0	0		86.0	41.0	0.476744	NM_032195	D3DSF5|D3DSF6|E7ETE8|E7EU67|E7EVW3|E9PFQ2|O14487|O95981|Q14120|Q6PKE0|Q9H7B1|Q9P070|Q9P072|Q9UKP9|Q9UPY0	Missense_Mutation	SNP	ENST00000356577.4	37	CCDS13629.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	12.68	2.010597	0.35511	0.0	3.49E-4	ENSG00000159140	ENST00000356577;ENST00000290239;ENST00000300278;ENST00000381679	T;T;T;T	0.12147	2.87;2.95;2.94;2.71	5.44	3.6	0.41247	.	0.239020	0.30219	N	0.010126	T	0.11024	0.0269	L	0.29908	0.895	0.27339	N	0.956563	B;P;B	0.34615	0.33;0.459;0.157	B;B;B	0.34824	0.093;0.19;0.069	T	0.13710	-1.0499	10	0.72032	D	0.01	.	10.8006	0.46487	0.0:0.8335:0.0:0.1665	.	423;423;423	P18583;P18583-3;P18583-6	SON_HUMAN;.;.	S	423	ENSP00000348984:P423S;ENSP00000290239:P423S;ENSP00000300278:P423S;ENSP00000371095:P423S	ENSP00000290239:P423S	P	+	1	0	SON	33844674	0.779000	0.28652	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	1.438000	0.47492	0.491000	0.48974	CCA	C|1.000;T|0.000	0.000	strong		0.652	SON-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140978.2	NM_138927	
PRCC	5546	hgsc.bcm.edu	37	1	156761540	156761540	+	Missense_Mutation	SNP	C	C	A	rs17850664	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:156761540C>A	ENST00000271526.4	+	4	1407	c.1135C>A	c.(1135-1137)Ccc>Acc	p.P379T	PRCC_ENST00000491853.1_3'UTR|PRCC_ENST00000353233.3_Intron	NM_005973.4	NP_005964.3	Q92733	PRCC_HUMAN	papillary renal cell carcinoma (translocation-associated)	379					mitotic cell cycle checkpoint (GO:0007093)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)			PRCC/TFE3(25)	breast(1)|central_nervous_system(3)|endometrium(1)|kidney(2)|large_intestine(1)|liver(1)|lung(5)|upper_aerodigestive_tract(1)	15	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					CCTGGTCCCCCCCCAGGAAAT	0.512			T	TFE3	papillary renal								C|||	21	0.00419329	0.0008	0.0043	5008	,	,		16912	0.0		0.0099	False		,,,				2504	0.0072				p.P379T		Atlas-SNP	.		Dom	yes		1	1q21.1	5546	papillary renal cell carcinoma (translocation-associated)		E	.	PRCC	39	.	0			c.C1135A						PASS	.	C	THR/PRO	12,4394	19.1+/-41.9	0,12,2191	74.0	74.0	74.0		1135	-1.0	0.2	1	dbSNP_123	74	84,8516	48.1+/-107.5	0,84,4216	yes	missense	PRCC	NM_005973.4	38	0,96,6407	AA,AC,CC		0.9767,0.2724,0.7381	benign	379/492	156761540	96,12910	2203	4300	6503	SO:0001583	missense	5546	exon4			GTCCCCCCCCAGG	X99720	CCDS1157.1	1q21.1	2008-02-05			ENSG00000143294	ENSG00000143294			9343	protein-coding gene	gene with protein product		179755				8872474	Standard	NM_005973		Approved	RCCP1	uc001fqa.3	Q92733	OTTHUMG00000041294	ENST00000271526.4:c.1135C>A	1.37:g.156761540C>A	ENSP00000271526:p.Pro379Thr	154.0	0.0	0		163.0	86.0	0.527607	NM_005973	A8K1F7|O00665|O00724|Q5SZ06	Missense_Mutation	SNP	ENST00000271526.4	37	CCDS1157.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	7.049	0.564048	0.13498	0.002724	0.009767	ENSG00000143294	ENST00000271526;ENST00000368201	T	0.44482	0.92	5.39	-1.04	0.10068	.	0.674960	0.15238	N	0.273053	T	0.07458	0.0188	N	0.14661	0.345	0.32356	N	0.557795	B	0.11235	0.004	B	0.08055	0.003	T	0.30090	-0.9990	10	0.20519	T	0.43	-0.1729	6.3416	0.21327	0.1139:0.5723:0.0:0.3138	rs17850664	379	Q92733	PRCC_HUMAN	T	379;355	ENSP00000271526:P379T	ENSP00000271526:P379T	P	+	1	0	PRCC	155028164	0.001000	0.12720	0.160000	0.22671	0.907000	0.53573	-0.090000	0.11163	-0.094000	0.12374	0.655000	0.94253	CCC	C|0.993;A|0.007	0.007	strong		0.512	PRCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098941.2	NM_005973	
NUFIP1	26747	hgsc.bcm.edu	37	13	45563215	45563215	+	Silent	SNP	A	A	G	rs116755008	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:45563215A>G	ENST00000379161.4	-	1	403	c.357T>C	c.(355-357)taT>taC	p.Y119Y	RP11-321C24.1_ENST00000437748.2_lincRNA|GPALPP1_ENST00000361121.2_5'Flank|GPALPP1_ENST00000379151.4_5'Flank	NM_012345.2	NP_036477.2	Q9UHK0	NUFP1_HUMAN	nuclear fragile X mental retardation protein interacting protein 1	119					box C/D snoRNP assembly (GO:0000492)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|RNA processing (GO:0006396)	cytosolic ribosome (GO:0022626)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|pre-snoRNP complex (GO:0070761)|presynaptic active zone (GO:0048786)|transcription elongation factor complex (GO:0008023)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)|RNA binding (GO:0003723)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(4)|skin(3)	18		Lung NSC(96;8.23e-05)|Breast(139;0.00378)|Prostate(109;0.0107)|all_hematologic(4;0.014)|Lung SC(185;0.0262)|Hepatocellular(98;0.0524)|Acute lymphoblastic leukemia(4;0.143)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000306)|BRCA - Breast invasive adenocarcinoma(63;0.125)		ACTGTCTCCAATACCACGATG	0.552													A|||	13	0.00259585	0.0008	0.0043	5008	,	,		19062	0.0		0.0089	False		,,,				2504	0.0				p.Y119Y		Atlas-SNP	.											.	NUFIP1	41	.	0			c.T357C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	47.0	45.0	46.0		357	2.2	1.0	13	dbSNP_132	46	45,8549	28.5+/-78.6	0,45,4252	yes	coding-synonymous	NUFIP1	NM_012345.2		0,48,6452	GG,GA,AA		0.5236,0.0681,0.3692		119/496	45563215	48,12952	2203	4297	6500	SO:0001819	synonymous_variant	26747	exon1			TCTCCAATACCAC	AF159548	CCDS9393.1	13q14	2008-02-05			ENSG00000083635	ENSG00000083635			8057	protein-coding gene	gene with protein product		604354				10556305, 10894927	Standard	NM_012345		Approved	NUFIP	uc001uzp.2	Q9UHK0	OTTHUMG00000016842	ENST00000379161.4:c.357T>C	13.37:g.45563215A>G		312.0	0.0	0		166.0	145.0	0.873494	NM_012345	Q8WVM5|Q96SG1	Silent	SNP	ENST00000379161.4	37	CCDS9393.1																																																																																			A|0.997;G|0.003	0.003	strong		0.552	NUFIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044755.2	NM_012345	
WWP1	11059	hgsc.bcm.edu	37	8	87473473	87473473	+	Silent	SNP	T	T	C	rs201436587		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:87473473T>C	ENST00000517970.1	+	23	2827	c.2520T>C	c.(2518-2520)aaT>aaC	p.N840N	WWP1_ENST00000341922.2_Silent_p.N710N|WWP1_ENST00000349423.2_Silent_p.N622N|WWP1_ENST00000265428.4_Silent_p.N840N	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	840	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						AGACAGACAATGAAGTAAGAA	0.343													T|||	1	0.000199681	0.0	0.0014	5008	,	,		19862	0.0		0.0	False		,,,				2504	0.0				p.N840N		Atlas-SNP	.											.	WWP1	97	.	0			c.T2520C						PASS	.	T		0,4406		0,0,2203	148.0	139.0	142.0		2520	2.9	1.0	8		142	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WWP1	NM_007013.3		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		840/923	87473473	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon23			AGACAATGAAGTA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.2520T>C	8.37:g.87473473T>C		88.0	0.0	0		123.0	63.0	0.512195	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			T|1.000;C|0.000	0.000	strong		0.343	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
SNTA1	6640	hgsc.bcm.edu	37	20	32026766	32026766	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:32026766G>A	ENST00000217381.2	-	2	648	c.377C>T	c.(376-378)aCa>aTa	p.T126I		NM_003098.2	NP_003089.1	Q13424	SNTA1_HUMAN	syntrophin, alpha 1	126	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				muscle contraction (GO:0006936)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|neuromuscular junction development (GO:0007528)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of vasoconstriction by circulating norepinephrine (GO:0003117)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|ventricular cardiac muscle cell action potential (GO:0086005)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular (GO:0005622)|neuromuscular junction (GO:0031594)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	ATPase binding (GO:0051117)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)			breast(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(1)	13						AAGGGCCTCTGTCTGGTCAGC	0.542																																					p.T126I		Atlas-SNP	.											.	SNTA1	35	.	0			c.C377T						PASS	.						127.0	124.0	125.0					20																	32026766		2203	4300	6503	SO:0001583	missense	6640	exon2			GCCTCTGTCTGGT	U40571	CCDS13220.1	20q11.2	2014-09-17	2012-06-15		ENSG00000101400	ENSG00000101400			11167	protein-coding gene	gene with protein product	"""pro-TGF-alpha cytoplasmic domain-interacting protein 1"", ""dystrophin-associated protein A1, 59kDa, acidic component"""	601017	"""syntrophin, alpha 1 (dystrophin-associated protein A1, 59kD, acidic component)"""	SNT1		8576247, 8612778	Standard	NM_003098		Approved	TACIP1, LQT12	uc002wzd.1	Q13424	OTTHUMG00000032259	ENST00000217381.2:c.377C>T	20.37:g.32026766G>A	ENSP00000217381:p.Thr126Ile	96.0	0.0	0		98.0	46.0	0.469388	NM_003098	A8K7H9|B4DX40|E1P5N1|Q16438	Missense_Mutation	SNP	ENST00000217381.2	37	CCDS13220.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.967218	0.74131	.	.	ENSG00000101400	ENST00000217381	T	0.27256	1.68	5.03	5.03	0.67393	PDZ/DHR/GLGF (4);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.55114	0.1900	M	0.80028	2.48	0.58432	D	0.999999	D;P	0.89917	1.0;0.918	D;D	0.81914	0.995;0.961	T	0.60757	-0.7200	10	0.87932	D	0	-14.1481	18.1836	0.89786	0.0:0.0:1.0:0.0	.	126;126	B4DX40;Q13424	.;SNTA1_HUMAN	I	126	ENSP00000217381:T126I	ENSP00000217381:T126I	T	-	2	0	SNTA1	31490427	1.000000	0.71417	0.987000	0.45799	0.833000	0.47200	6.092000	0.71414	2.614000	0.88457	0.561000	0.74099	ACA	.	.	none		0.542	SNTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078704.2	NM_003098	
PTGES2	80142	hgsc.bcm.edu	37	9	130886050	130886050	+	Missense_Mutation	SNP	C	C	G	rs149102151	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:130886050C>G	ENST00000338961.6	-	4	1361	c.617G>C	c.(616-618)gGc>gCc	p.G206A	PTGES2_ENST00000277462.5_Missense_Mutation_p.G15A|PTGES2_ENST00000483625.1_5'UTR	NM_001256335.1|NM_025072.6	NP_001243264.1|NP_079348.1	Q9H7Z7	PGES2_HUMAN	prostaglandin E synthase 2	206					cell redox homeostasis (GO:0045454)|positive regulation of transcription, DNA-templated (GO:0045893)|prostaglandin biosynthetic process (GO:0001516)|secretion (GO:0046903)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|electron carrier activity (GO:0009055)|glutathione binding (GO:0043295)|heme binding (GO:0020037)|lyase activity (GO:0016829)|prostaglandin-E synthase activity (GO:0050220)|protein disulfide oxidoreductase activity (GO:0015035)			endometrium(1)|large_intestine(1)|lung(2)	4						GTACTTATTGCCGAACTCGGT	0.592													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		14684	0.0		0.007	False		,,,				2504	0.0041				p.G206A		Atlas-SNP	.											.	PTGES2	14	.	0			c.G617C						PASS	.	C	ALA/GLY	4,4402	6.2+/-15.9	0,4,2199	175.0	125.0	142.0		617	4.9	0.9	9	dbSNP_134	142	62,8538	38.8+/-94.9	0,62,4238	yes	missense	PTGES2	NM_025072.5	60	0,66,6437	GG,GC,CC		0.7209,0.0908,0.5075	benign	206/378	130886050	66,12940	2203	4300	6503	SO:0001583	missense	80142	exon4			TTATTGCCGAACT	AK024100	CCDS6891.1	9q34.12	2008-05-06	2002-06-13	2002-06-14	ENSG00000148334	ENSG00000148334			17822	protein-coding gene	gene with protein product		608152	"""chromosome 9 open reading frame 15"""	C9orf15		11866447	Standard	NM_025072		Approved	FLJ14038	uc004bti.4	Q9H7Z7	OTTHUMG00000020730	ENST00000338961.6:c.617G>C	9.37:g.130886050C>G	ENSP00000345341:p.Gly206Ala	123.0	0.0	0		155.0	83.0	0.535484	NM_025072	Q53EW9|Q5SYV6|Q96GI0|Q96GL2	Missense_Mutation	SNP	ENST00000338961.6	37	CCDS6891.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	C	8.598	0.886079	0.17540	9.08E-4	0.007209	ENSG00000148334	ENST00000338961;ENST00000277462;ENST00000449878	T;T;T	0.39787	2.7;1.06;2.7	5.84	4.94	0.65067	Thioredoxin-like fold (1);	0.329789	0.40640	N	0.001045	T	0.19087	0.0458	L	0.28274	0.84	0.30778	N	0.742268	B	0.16603	0.018	B	0.10450	0.005	T	0.19321	-1.0309	10	0.09843	T	0.71	-0.0806	9.3167	0.37939	0.0:0.779:0.0:0.221	.	206	Q9H7Z7	PGES2_HUMAN	A	206;15;171	ENSP00000345341:G206A;ENSP00000277462:G15A;ENSP00000411378:G171A	ENSP00000277462:G15A	G	-	2	0	PTGES2	129925871	1.000000	0.71417	0.937000	0.37676	0.664000	0.39144	1.134000	0.31442	1.485000	0.48380	0.561000	0.74099	GGC	C|0.995;G|0.005	0.005	strong		0.592	PTGES2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054339.1		
FASTKD3	79072	hgsc.bcm.edu	37	5	7867027	7867027	+	Silent	SNP	A	A	G	rs77130393	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:7867027A>G	ENST00000264669.5	-	2	1306	c.1170T>C	c.(1168-1170)aaT>aaC	p.N390N	MTRR_ENST00000502509.1_Intron|MTRR_ENST00000341013.6_5'Flank|FASTKD3_ENST00000513658.1_Intron|MTRR_ENST00000264668.2_5'Flank|MTRR_ENST00000440940.2_5'Flank	NM_024091.3	NP_076996.2	Q14CZ7	FAKD3_HUMAN	FAST kinase domains 3	390					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(2)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CTGCCACTGCATTGAGGATGG	0.438													A|||	32	0.00638978	0.0	0.0173	5008	,	,		18240	0.0		0.0189	False		,,,				2504	0.001				p.N390N		Atlas-SNP	.											.	FASTKD3	88	.	0			c.T1170C						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	63.0	64.0	63.0		1170	-5.6	0.0	5	dbSNP_134	63	199,8401	87.1+/-149.5	1,197,4102	no	coding-synonymous	FASTKD3	NM_024091.3		1,221,6281	GG,GA,AA		2.314,0.5447,1.7146		390/663	7867027	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	79072	exon2			CACTGCATTGAGG	AK026927	CCDS3873.1	5p15.31	2008-02-05			ENSG00000124279	ENSG00000124279			28758	protein-coding gene	gene with protein product						12477932	Standard	NM_024091		Approved	MGC5297, FLJ23274	uc003jeb.3	Q14CZ7	OTTHUMG00000131029	ENST00000264669.5:c.1170T>C	5.37:g.7867027A>G		137.0	0.0	0		176.0	81.0	0.460227	NM_024091	Q9BVD3	Silent	SNP	ENST00000264669.5	37	CCDS3873.1																																																																																			A|0.984;G|0.016	0.016	strong		0.438	FASTKD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253673.1	NM_024091	
LAMA5	3911	hgsc.bcm.edu	37	20	60892545	60892545	+	Missense_Mutation	SNP	C	C	T	rs2427282	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:60892545C>T	ENST00000252999.3	-	55	7433	c.7367G>A	c.(7366-7368)cGc>cAc	p.R2456H		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	2456	Domain II and I.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GGCGGCGAGGCGCTCCAGCTC	0.662													.|||	37	0.00738818	0.0008	0.0115	5008	,	,		15961	0.0		0.0268	False		,,,				2504	0.001				p.R2456H		Atlas-SNP	.											.	LAMA5	268	.	0			c.G7367A						PASS	.		HIS/ARG	30,4310		0,30,2140	20.0	23.0	22.0		7367	-4.2	0.8	20	dbSNP_100	22	232,8314		3,226,4044	yes	missense	LAMA5	NM_005560.3	29	3,256,6184	TT,TC,CC		2.7147,0.6912,2.0332	benign	2456/3696	60892545	262,12624	2170	4273	6443	SO:0001583	missense	3911	exon55			GCGAGGCGCTCCA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.7367G>A	20.37:g.60892545C>T	ENSP00000252999:p.Arg2456His	107.0	0.0	0		103.0	54.0	0.524272	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	26	0.011904761904761904	0	0.0	5	0.013812154696132596	0	0.0	21	0.027704485488126648	c	7.206	0.594372	0.13875	0.006912	0.027147	ENSG00000130702	ENST00000252999	T	0.18960	2.18	3.54	-4.23	0.03789	.	0.473582	0.22319	N	0.061639	T	0.01592	0.0051	N	0.01048	-1.04	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39820	-0.9595	10	0.25106	T	0.35	.	10.7393	0.46143	0.0:0.3638:0.0:0.6362	rs2427282	2456	O15230	LAMA5_HUMAN	H	2456	ENSP00000252999:R2456H	ENSP00000252999:R2456H	R	-	2	0	LAMA5	60325940	0.672000	0.27530	0.804000	0.32291	0.108000	0.19459	-0.278000	0.08490	-0.734000	0.04843	0.436000	0.28706	CGC	C|0.984;T|0.016	0.016	strong		0.662	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
MAGEE1	57692	hgsc.bcm.edu	37	X	75649430	75649430	+	Silent	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:75649430G>A	ENST00000361470.2	+	1	1385	c.1107G>A	c.(1105-1107)ccG>ccA	p.P369P		NM_020932.2	NP_065983.1	Q9HCI5	MAGE1_HUMAN	melanoma antigen family E, 1	369	Pro-rich.					dendrite (GO:0030425)|dystrophin-associated glycoprotein complex (GO:0016010)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(12)|lung(20)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	51						CCTCTGTGCCGCCCACCGCCT	0.672																																					p.P369P		Atlas-SNP	.											.	MAGEE1	236	.	0			c.G1107A						PASS	.						33.0	26.0	28.0					X																	75649430		2203	4297	6500	SO:0001819	synonymous_variant	57692	exon1			TGTGCCGCCCACC	AF490507	CCDS14433.1	Xq13	2008-02-05			ENSG00000198934	ENSG00000198934			24934	protein-coding gene	gene with protein product		300759				14623885	Standard	NM_020932		Approved	KIAA1587, DAMAGE	uc004ecm.2	Q9HCI5	OTTHUMG00000021879	ENST00000361470.2:c.1107G>A	X.37:g.75649430G>A		48.0	0.0	0		70.0	64.0	0.914286	NM_020932	Q5JXC7|Q86TG0|Q8TD92|Q9H216	Silent	SNP	ENST00000361470.2	37	CCDS14433.1																																																																																			.	.	none		0.672	MAGEE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057298.1	NM_020932	
PDGFRA	5156	hgsc.bcm.edu	37	4	55130078	55130078	+	Silent	SNP	T	T	C	rs2229307	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:55130078T>C	ENST00000257290.5	+	4	943	c.612T>C	c.(610-612)aaT>aaC	p.N204N	PDGFRA_ENST00000508170.1_Silent_p.N204N|FIP1L1_ENST00000507166.1_Intron	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	204	Ig-like C2-type 3.				adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TCCCATTTAATGTTTATGCTT	0.393			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)			C|||	1183	0.236222	0.2776	0.3487	5008	,	,		19351	0.2034		0.1233	False		,,,				2504	0.2505				p.N204N	Pancreas(151;208 1913 7310 23853 37092)	Atlas-SNP	.		Dom	yes		4	4q11-q13	5156	"""platelet-derived growth factor, alpha-receptor"""		"""L, M, O"""	.	PDGFRA	1583	.	0			c.T612C						PASS	.	C		1102,3304	719.5+/-408.9	128,846,1229	73.0	73.0	73.0		612	-3.1	0.0	4	dbSNP_98	73	1044,7556	771.5+/-407.7	67,910,3323	no	coding-synonymous	PDGFRA	NM_006206.4		195,1756,4552	CC,CT,TT		12.1395,25.0113,16.5001		204/1090	55130078	2146,10860	2203	4300	6503	SO:0001819	synonymous_variant	5156	exon4	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	ATTTAATGTTTAT	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.612T>C	4.37:g.55130078T>C		37.0	0.0	0		48.0	27.0	0.5625	NM_006206	B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Silent	SNP	ENST00000257290.5	37	CCDS3495.1																																																																																			T|0.828;C|0.172	0.172	strong		0.393	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
CA11	770	hgsc.bcm.edu	37	19	49143533	49143533	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:49143533C>T	ENST00000084798.4	-	4	969	c.290G>A	c.(289-291)cGg>cAg	p.R97Q	SEC1P_ENST00000430145.2_RNA|DBP_ENST00000222122.5_5'Flank|DBP_ENST00000601104.1_5'Flank	NM_001217.3	NP_001208.2	O75493	CAH11_HUMAN	carbonic anhydrase XI	97						basolateral plasma membrane (GO:0016323)|extracellular region (GO:0005576)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)	14		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000103)|all cancers(93;0.000119)|GBM - Glioblastoma multiforme(486;0.00634)|Epithelial(262;0.016)	Zonisamide(DB00909)	CAAGGTTCCCCGGAGCTGTGG	0.552																																					p.R97Q		Atlas-SNP	.											.	CA11	29	.	0			c.G290A						PASS	.						47.0	47.0	47.0					19																	49143533		2203	4300	6503	SO:0001583	missense	770	exon4			GTTCCCCGGAGCT	AF067662	CCDS12729.1	19q13.3	2012-07-02			ENSG00000063180	ENSG00000063180		"""Carbonic anhydrases"""	1370	protein-coding gene	gene with protein product	"""CA-RP XI"", ""carbonic anhydrase-related protein XI"", ""carbonic anhydrase-related protein 2"""	604644				9878252	Standard	XR_243956		Approved	CARP2, CARPX1	uc002pjz.1	O75493		ENST00000084798.4:c.290G>A	19.37:g.49143533C>T	ENSP00000084798:p.Arg97Gln	74.0	0.0	0		98.0	41.0	0.418367	NM_001217	O60596|Q6FHI1|Q9UEC4	Missense_Mutation	SNP	ENST00000084798.4	37	CCDS12729.1	.	.	.	.	.	.	.	.	.	.	C	19.68	3.872278	0.72180	.	.	ENSG00000063180	ENST00000084798	T	0.67698	-0.28	3.46	3.46	0.39613	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.218732	0.39544	N	0.001325	T	0.48750	0.1517	N	0.10916	0.065	0.36952	D	0.892938	D	0.55385	0.971	P	0.45310	0.476	T	0.60910	-0.7169	10	0.54805	T	0.06	.	10.6521	0.45655	0.0:1.0:0.0:0.0	.	97	O75493	CAH11_HUMAN	Q	97	ENSP00000084798:R97Q	ENSP00000084798:R97Q	R	-	2	0	CA11	53835345	0.995000	0.38212	1.000000	0.80357	0.988000	0.76386	2.667000	0.46808	1.970000	0.57323	0.462000	0.41574	CGG	.	.	none		0.552	CA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466172.1	NM_001217	
MANBA	4126	hgsc.bcm.edu	37	4	103553372	103553372	+	Missense_Mutation	SNP	C	C	T	rs75826658	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:103553372C>T	ENST00000226578.4	-	17	2581	c.2482G>A	c.(2482-2484)Gtt>Att	p.V828I	MANBA_ENST00000505239.1_Missense_Mutation_p.V771I	NM_005908.3	NP_005899.3	O00462	MANBA_HUMAN	mannosidase, beta A, lysosomal	828					cellular protein modification process (GO:0006464)|glycoprotein catabolic process (GO:0006516)|mannan catabolic process (GO:0046355)	intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)	beta-mannosidase activity (GO:0004567)|mannose binding (GO:0005537)			cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;4.44e-08)		TCCAACCAAACAAAGGGAGCG	0.423													C|||	32	0.00638978	0.0008	0.0101	5008	,	,		20461	0.0		0.0239	False		,,,				2504	0.0				p.V828I		Atlas-SNP	.											.	MANBA	78	.	0			c.G2482A						PASS	.	C	ILE/VAL	17,4389	24.3+/-50.5	0,17,2186	102.0	106.0	105.0		2482	5.2	1.0	4	dbSNP_131	105	151,8449	74.5+/-137.1	1,149,4150	yes	missense	MANBA	NM_005908.3	29	1,166,6336	TT,TC,CC		1.7558,0.3858,1.2917	probably-damaging	828/880	103553372	168,12838	2203	4300	6503	SO:0001583	missense	4126	exon17			ACCAAACAAAGGG		CCDS3658.1	4q24	2013-09-20			ENSG00000109323	ENSG00000109323	3.2.1.25		6831	protein-coding gene	gene with protein product		609489				7876128	Standard	NM_005908		Approved		uc003hwg.3	O00462	OTTHUMG00000131123	ENST00000226578.4:c.2482G>A	4.37:g.103553372C>T	ENSP00000226578:p.Val828Ile	224.0	0.0	0		238.0	101.0	0.42437	NM_005908	Q96BC3|Q9NYX9	Missense_Mutation	SNP	ENST00000226578.4	37	CCDS3658.1	26	0.011904761904761904	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	20	0.026385224274406333	C	25.5	4.645483	0.87859	0.003858	0.017558	ENSG00000109323	ENST00000226578;ENST00000505239	T;T	0.77098	-1.06;-1.07	5.15	5.15	0.70609	.	0.000000	0.85682	D	0.000000	T	0.77644	0.4161	M	0.86740	2.835	0.58432	D	0.999992	D;D	0.76494	0.997;0.999	P;D	0.70016	0.907;0.967	D	0.85752	0.1344	10	0.72032	D	0.01	-22.6841	16.8489	0.85988	0.0:1.0:0.0:0.0	.	771;828	E9PFW2;O00462	.;MANBA_HUMAN	I	828;771	ENSP00000226578:V828I;ENSP00000427322:V771I	ENSP00000226578:V828I	V	-	1	0	MANBA	103772420	1.000000	0.71417	0.997000	0.53966	0.852000	0.48524	5.317000	0.65822	2.404000	0.81709	0.460000	0.39030	GTT	C|0.986;T|0.014	0.014	strong		0.423	MANBA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253803.2		
NPHP4	261734	hgsc.bcm.edu	37	1	5935096	5935096	+	Missense_Mutation	SNP	C	C	T	rs183885357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:5935096C>T	ENST00000378156.4	-	21	3147	c.2882G>A	c.(2881-2883)cGc>cAc	p.R961H	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	961			R -> H (in NPHP4; dbSNP:rs183885357). {ECO:0000269|PubMed:15776426}.		actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GGCCTTCGTGCGTTCCCGGTA	0.652													c|||	6	0.00119808	0.0	0.0029	5008	,	,		17500	0.0		0.004	False		,,,				2504	0.0				p.R961H		Atlas-SNP	.											.	NPHP4	119	.	0			c.G2882A	GRCh37	CM051580	NPHP4	M	rs183885357	PASS	.		HIS/ARG	6,4380	11.4+/-27.6	0,6,2187	63.0	78.0	73.0		2882	4.9	0.9	1		73	35,8527	23.4+/-69.3	0,35,4246	yes	missense	NPHP4	NM_015102.3	29	0,41,6433	TT,TC,CC		0.4088,0.1368,0.3167	possibly-damaging	961/1427	5935096	41,12907	2193	4281	6474	SO:0001583	missense	261734	exon21			TTCGTGCGTTCCC	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.2882G>A	1.37:g.5935096C>T	ENSP00000367398:p.Arg961His	61.0	0.0	0		72.0	33.0	0.458333	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	3	0.00395778364116095	c	12.12	1.841986	0.32513	0.001368	0.004088	ENSG00000131697	ENST00000378156	D	0.88431	-2.38	4.88	4.88	0.63580	.	0.074186	0.53938	D	0.000041	D	0.90188	0.6933	M	0.75264	2.295	0.48511	D	0.999666	D	0.56746	0.977	P	0.48840	0.592	D	0.90860	0.4738	10	0.56958	D	0.05	.	12.536	0.56142	0.0:0.9169:0.0:0.0831	.	961	O75161	NPHP4_HUMAN	H	961	ENSP00000367398:R961H	ENSP00000367398:R961H	R	-	2	0	NPHP4	5857683	1.000000	0.71417	0.923000	0.36655	0.015000	0.08874	3.579000	0.53900	2.272000	0.75746	0.550000	0.68814	CGC	C|0.996;T|0.004	0.004	strong		0.652	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
HSPG2	3339	hgsc.bcm.edu	37	1	22169926	22169926	+	Silent	SNP	G	G	A	rs62642513	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22169926G>A	ENST00000374695.3	-	66	8701	c.8622C>T	c.(8620-8622)caC>caT	p.H2874H		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	2874	Ig-like C2-type 14.				angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCAGTGGGCCGTGGACCTGGC	0.652													G|||	251	0.0501198	0.1589	0.0274	5008	,	,		16760	0.0		0.0189	False		,,,				2504	0.0031				p.H2874H		Atlas-SNP	.											.	HSPG2	311	.	0			c.C8622T						PASS	.	G		716,3690	288.1+/-279.7	60,596,1547	33.0	35.0	34.0		8622	-3.0	0.7	1	dbSNP_129	34	170,8430	75.4+/-138.0	2,166,4132	no	coding-synonymous	HSPG2	NM_005529.5		62,762,5679	AA,AG,GG		1.9767,16.2506,6.8122		2874/4392	22169926	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon66			TGGGCCGTGGACC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.8622C>T	1.37:g.22169926G>A		110.0	0.0	0		138.0	62.0	0.449275	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1																																																																																			G|0.935;A|0.065	0.065	strong		0.652	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
SLC47A1	55244	hgsc.bcm.edu	37	17	19474875	19474875	+	Missense_Mutation	SNP	C	C	T	rs111653425	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:19474875C>T	ENST00000270570.4	+	15	1480	c.1394C>T	c.(1393-1395)gCc>gTc	p.A465V	RP11-1113L8.1_ENST00000574267.1_RNA|SLC47A1_ENST00000457293.1_Missense_Mutation_p.A465V|SLC47A1_ENST00000436810.2_Intron|SLC47A1_ENST00000395585.1_Missense_Mutation_p.A465V|SLC47A1_ENST00000571335.1_Intron|SLC47A1_ENST00000575023.1_Intron	NM_018242.2	NP_060712.2	Q96FL8	S47A1_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 1	465					organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|monovalent cation:proton antiporter activity (GO:0005451)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(5)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	23	all_cancers(12;2.49e-05)|all_epithelial(12;0.00263)|Hepatocellular(7;0.00345)				Aciclovir(DB00787)|Bromodiphenhydramine(DB01237)|Cephalexin(DB00567)|Cimetidine(DB00501)|Metformin(DB00331)|Sirolimus(DB00877)	TGGAAAAAAGCCTGTCAGCAG	0.393													C|||	11	0.00219649	0.0	0.0043	5008	,	,		18046	0.0		0.007	False		,,,				2504	0.001				p.A465V		Atlas-SNP	.											.	SLC47A1	55	.	0			c.C1394T						PASS	.	C	VAL/ALA	17,4389	24.3+/-50.5	0,17,2186	117.0	110.0	112.0		1394	5.4	1.0	17	dbSNP_132	112	68,8532	41.2+/-98.3	0,68,4232	yes	missense	SLC47A1	NM_018242.2	64	0,85,6418	TT,TC,CC		0.7907,0.3858,0.6535	benign	465/571	19474875	85,12921	2203	4300	6503	SO:0001583	missense	55244	exon15			AAAAAGCCTGTCA		CCDS11209.1	17p11.2	2013-07-17	2013-07-17		ENSG00000142494	ENSG00000142494		"""Solute carriers"""	25588	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 1"""	609832				16330770, 16996621, 16928787	Standard	NM_018242		Approved	FLJ10847, MATE1	uc002gvy.1	Q96FL8	OTTHUMG00000059466	ENST00000270570.4:c.1394C>T	17.37:g.19474875C>T	ENSP00000270570:p.Ala465Val	170.0	0.0	0		174.0	92.0	0.528736	NM_018242	Q53HF5|Q6PD77|Q86VL4|Q9NVA3	Missense_Mutation	SNP	ENST00000270570.4	37	CCDS11209.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	C	14.34	2.506541	0.44558	0.003858	0.007907	ENSG00000142494	ENST00000270570;ENST00000457293;ENST00000395585;ENST00000424755	T;T;T	0.32023	1.48;1.47;1.47	5.4	5.4	0.78164	.	0.273024	0.41001	D	0.000979	T	0.20170	0.0485	L	0.42581	1.335	0.80722	D	1	B;P	0.40794	0.1;0.729	B;B	0.43251	0.109;0.413	T	0.01972	-1.1237	10	0.14656	T	0.56	-19.0703	10.1604	0.42849	0.0:0.9096:0.0:0.0904	.	465;465	Q96FL8;Q96FL8-3	S47A1_HUMAN;.	V	465;465;465;177	ENSP00000270570:A465V;ENSP00000415586:A465V;ENSP00000378951:A465V	ENSP00000270570:A465V	A	+	2	0	SLC47A1	19415467	1.000000	0.71417	0.964000	0.40570	0.629000	0.37895	2.731000	0.47343	2.539000	0.85634	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.393	SLC47A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132250.1	NM_018242	
CYP39A1	51302	hgsc.bcm.edu	37	6	46563779	46563779	+	Missense_Mutation	SNP	C	C	T	rs147961800	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:46563779C>T	ENST00000275016.2	-	8	1213	c.1010G>A	c.(1009-1011)cGt>cAt	p.R337H		NM_016593.3	NP_057677.2	Q9NYL5	CP39A_HUMAN	cytochrome P450, family 39, subfamily A, polypeptide 1	337					bile acid biosynthetic process (GO:0006699)|bile acid catabolic process (GO:0030573)|bile acid metabolic process (GO:0008206)|cholesterol catabolic process (GO:0006707)|digestion (GO:0007586)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	24-hydroxycholesterol 7alpha-hydroxylase activity (GO:0033782)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxysterol 7-alpha-hydroxylase activity (GO:0008396)|steroid 7-alpha-hydroxylase activity (GO:0008387)		EIF3K/CYP39A1(2)	NS(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(2)|skin(2)	21						AGCTTTTAAACGAATGGTTTC	0.338													C|||	7	0.00139776	0.0	0.0029	5008	,	,		15087	0.0		0.004	False		,,,				2504	0.001				p.R337H		Atlas-SNP	.											CYP39A1,caecum,carcinoma,-1,1	CYP39A1	41	1	0			c.G1010A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	92.0	98.0	96.0		1010	3.9	0.7	6	dbSNP_134	96	14,8586	10.5+/-38.8	0,14,4286	yes	missense	CYP39A1	NM_016593.3	29	0,14,6489	TT,TC,CC		0.1628,0.0,0.1076	probably-damaging	337/470	46563779	14,12992	2203	4300	6503	SO:0001583	missense	51302	exon8			TTTAAACGAATGG	AF237982	CCDS4916.1, CCDS75465.1	6p21.1-p11.2	2008-02-05	2003-01-14		ENSG00000146233	ENSG00000146233		"""Cytochrome P450s"""	17449	protein-coding gene	gene with protein product		605994	"""cytochrome P450, subfamily XXXIX (oxysterol 7 alpha-hydroxylase), polypeptide 1"""			10748047	Standard	NM_016593		Approved		uc003oyf.1	Q9NYL5	OTTHUMG00000014785	ENST00000275016.2:c.1010G>A	6.37:g.46563779C>T	ENSP00000275016:p.Arg337His	324.0	1.0	0.00308642		316.0	143.0	0.452532	NM_016593	Q5VTT0|Q96FW5	Missense_Mutation	SNP	ENST00000275016.2	37	CCDS4916.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	21.3	4.127159	0.77549	0.0	0.001628	ENSG00000146233	ENST00000275016	D	0.97505	-4.41	5.7	3.91	0.45181	.	0.141963	0.47455	D	0.000237	D	0.98099	0.9373	M	0.89601	3.045	0.51012	D	0.9999	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98321	1.0528	10	0.87932	D	0	-13.1901	9.8571	0.41092	0.0:0.7875:0.1394:0.0731	.	317;337	B7Z786;Q9NYL5	.;CP39A_HUMAN	H	337	ENSP00000275016:R337H	ENSP00000275016:R337H	R	-	2	0	CYP39A1	46671738	0.999000	0.42202	0.739000	0.30968	0.954000	0.61252	4.208000	0.58486	0.746000	0.32786	0.557000	0.71058	CGT	C|0.999;T|0.001	0.001	strong		0.338	CYP39A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040787.1		
POTEF	728378	hgsc.bcm.edu	37	2	130832545	130832545	+	Missense_Mutation	SNP	C	C	T	rs199777567	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:130832545C>T	ENST00000409914.2	-	17	2899	c.2500G>A	c.(2500-2502)Gtg>Atg	p.V834M	POTEF_ENST00000357462.5_Missense_Mutation_p.V834M	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	834	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						TGGATGGCCACGTACATGGCT	0.592													.|||	6	0.00119808	0.0	0.0014	5008	,	,		20796	0.0		0.005	False		,,,				2504	0.0				p.V834M		Atlas-SNP	.											.	POTEF	140	.	0			c.G2500A						PASS	.	C	MET/VAL	2,4392		0,2,2195	104.0	125.0	118.0		2500		0.3	2		118	26,8544		0,26,4259	no	missense	POTEF	NM_001099771.2	21	0,28,6454	TT,TC,CC		0.3034,0.0455,0.216	probably-damaging	834/1076	130832545	28,12936	2197	4285	6482	SO:0001583	missense	728378	exon17			TGGCCACGTACAT	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2500G>A	2.37:g.130832545C>T	ENSP00000386786:p.Val834Met	217.0	0.0	0		145.0	73.0	0.503448	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	15.44	2.834922	0.50951	4.55E-4	0.003034	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.94723	-3.5;-3.5	.	.	.	.	.	.	.	.	D	0.95695	0.8600	M	0.88570	2.965	0.80722	D	1	D	0.57257	0.979	P	0.55055	0.767	D	0.93384	0.6746	8	0.87932	D	0	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	834	A5A3E0	POTEF_HUMAN	M	834	ENSP00000350052:V834M;ENSP00000386786:V834M	ENSP00000350052:V834M	V	-	1	0	POTEF	130549015	1.000000	0.71417	0.299000	0.25016	0.302000	0.27658	3.653000	0.54446	0.119000	0.18210	0.121000	0.15741	GTG	C|0.993;T|0.007	0.007	strong		0.592	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
DMGDH	29958	hgsc.bcm.edu	37	5	78338202	78338202	+	Missense_Mutation	SNP	T	T	C	rs77116243	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:78338202T>C	ENST00000255189.3	-	7	1125	c.1097A>G	c.(1096-1098)aAt>aGt	p.N366S	DMGDH_ENST00000380311.4_Missense_Mutation_p.N165S|DMGDH_ENST00000540686.1_Intron	NM_013391.2	NP_037523.2	Q9UI17	M2GD_HUMAN	dimethylglycine dehydrogenase	366					amino-acid betaine catabolic process (GO:0006579)|choline metabolic process (GO:0019695)|glycine catabolic process (GO:0006546)|glycine metabolic process (GO:0006544)	mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|dimethylglycine dehydrogenase activity (GO:0047865)|electron carrier activity (GO:0009055)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|kidney(2)|large_intestine(10)|liver(1)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	34		all_lung(232;0.000638)|Lung NSC(167;0.00173)|Ovarian(174;0.0262)|Prostate(461;0.192)		OV - Ovarian serous cystadenocarcinoma(54;6.52e-45)|Epithelial(54;5.96e-40)|all cancers(79;3.56e-35)		ATTGACAACATTGATGATGTC	0.458													T|||	38	0.00758786	0.0	0.0072	5008	,	,		18599	0.0		0.0179	False		,,,				2504	0.0153				p.N366S		Atlas-SNP	.											.	DMGDH	88	.	0			c.A1097G						PASS	.	T	SER/ASN	8,4398	12.9+/-30.5	0,8,2195	128.0	117.0	120.0		1097	3.0	0.5	5	dbSNP_131	120	112,8488	61.0+/-122.8	1,110,4189	yes	missense	DMGDH	NM_013391.2	46	1,118,6384	CC,CT,TT		1.3023,0.1816,0.9227	benign	366/867	78338202	120,12886	2203	4300	6503	SO:0001583	missense	29958	exon7			ACAACATTGATGA	AF111858	CCDS4044.1	5q14.1	2008-02-05			ENSG00000132837	ENSG00000132837	1.5.99.2		24475	protein-coding gene	gene with protein product		605849				10767172, 11231903	Standard	NM_013391		Approved		uc003kfs.3	Q9UI17	OTTHUMG00000108159	ENST00000255189.3:c.1097A>G	5.37:g.78338202T>C	ENSP00000255189:p.Asn366Ser	177.0	0.0	0		204.0	96.0	0.470588	NM_013391	B2RBN0|B4E1J9	Missense_Mutation	SNP	ENST00000255189.3	37	CCDS4044.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	T	11.11	1.541978	0.27563	0.001816	0.013023	ENSG00000132837	ENST00000255189;ENST00000523732;ENST00000380311;ENST00000539598	T;T;T	0.80824	-1.42;-1.42;-1.42	5.44	3.01	0.34805	FAD dependent oxidoreductase (1);	0.194937	0.52532	D	0.000068	T	0.33644	0.0870	N	0.01649	-0.78	0.80722	D	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.002;0.002	T	0.15235	-1.0444	10	0.10377	T	0.69	.	8.0518	0.30583	0.0:0.0714:0.1365:0.7921	.	165;216;366	F8W6P8;F5H1C7;Q9UI17	.;.;M2GD_HUMAN	S	366;205;165;216	ENSP00000255189:N366S;ENSP00000430972:N205S;ENSP00000369667:N165S	ENSP00000255189:N366S	N	-	2	0	DMGDH	78373958	1.000000	0.71417	0.481000	0.27354	0.903000	0.53119	3.289000	0.51747	0.366000	0.24427	0.529000	0.55759	AAT	T|0.990;C|0.010	0.010	strong		0.458	DMGDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226963.3	NM_013391	
MSH3	4437	hgsc.bcm.edu	37	5	80109479	80109479	+	Missense_Mutation	SNP	T	T	G	rs41545019	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:80109479T>G	ENST00000265081.6	+	20	2812	c.2732T>G	c.(2731-2733)tTg>tGg	p.L911W		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	911					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|maintenance of DNA repeat elements (GO:0043570)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|heteroduplex DNA loop binding (GO:0000404)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	29		Lung NSC(167;0.00479)|all_lung(232;0.00507)|Ovarian(174;0.0261)|Breast(144;0.244)		OV - Ovarian serous cystadenocarcinoma(54;2.38e-45)|Epithelial(54;1.58e-38)|all cancers(79;4.93e-33)		CAAGTTGCATTGATTACCATC	0.413								Mismatch excision repair (MMR)					T|||	5	0.000998403	0.0	0.0014	5008	,	,		18784	0.0		0.004	False		,,,				2504	0.0				p.L911W	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.T2732G						PASS	.	T	TRP/LEU	2,4404	4.2+/-10.8	0,2,2201	192.0	187.0	188.0		2732	5.6	0.2	5	dbSNP_127	188	41,8559	27.4+/-76.7	0,41,4259	yes	missense	MSH3	NM_002439.3	61	0,43,6460	GG,GT,TT		0.4767,0.0454,0.3306	probably-damaging	911/1138	80109479	43,12963	2203	4300	6503	SO:0001583	missense	4437	exon20			TTGCATTGATTAC	U61981	CCDS34195.1	5q11-q12	2013-09-12	2013-09-12		ENSG00000113318	ENSG00000113318			7326	protein-coding gene	gene with protein product	"""Divergent upstream protein"", ""Mismatch repair protein 1"""	600887	"""mutS (E. coli) homolog 3"", ""mutS homolog 3 (E. coli)"""				Standard	NM_002439		Approved	DUP, MRP1	uc003kgz.4	P20585	OTTHUMG00000162540	ENST00000265081.6:c.2732T>G	5.37:g.80109479T>G	ENSP00000265081:p.Leu911Trp	196.0	1.0	0.00510204		229.0	120.0	0.524017	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	17.41	3.383061	0.61845	4.54E-4	0.004767	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.88896	-2.44	5.57	5.57	0.84162	DNA mismatch repair protein MutS, C-terminal (2);	0.000000	0.64402	D	0.000001	D	0.95968	0.8687	H	0.94698	3.57	0.47245	D	0.999368	D	0.89917	1.0	D	0.72625	0.978	D	0.97127	0.9815	9	.	.	.	-4.0755	15.7269	0.77766	0.0:0.0:0.0:1.0	rs41545019;rs61749610	911	P20585	MSH3_HUMAN	W	911;902	ENSP00000265081:L911W	.	L	+	2	0	MSH3	80145235	1.000000	0.71417	0.203000	0.23512	0.261000	0.26267	8.032000	0.88838	2.123000	0.65237	0.482000	0.46254	TTG	T|0.997;G|0.003	0.003	strong		0.413	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
DGCR6	8214	hgsc.bcm.edu	37	22	18898468	18898468	+	Missense_Mutation	SNP	G	G	A	rs139729355		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:18898468G>A	ENST00000331444.6	+	4	592	c.440G>A	c.(439-441)cGg>cAg	p.R147Q	DGCR6_ENST00000413981.1_Missense_Mutation_p.R11Q|DGCR6_ENST00000436645.1_3'UTR	NM_005675.4	NP_005666.2	Q14129	DGCR6_HUMAN	DiGeorge syndrome critical region gene 6	147					cell adhesion (GO:0007155)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|cervix(1)|upper_aerodigestive_tract(1)	3						GAGCTGGACCGGAAGGTGGCT	0.682													.|||	1	0.000199681	0.0	0.0	5008	,	,		14833	0.0		0.001	False		,,,				2504	0.0				p.R147Q		Atlas-SNP	.											.	DGCR6	12	.	0			c.G440A						PASS	.	G	GLN/ARG	1,4405	4.2+/-10.8	0,1,2202	96.0	79.0	84.0		440	3.3	1.0	22	dbSNP_134	84	40,8558	26.3+/-74.7	0,40,4259	no	missense	DGCR6	NM_005675.4	43	0,41,6461	AA,AG,GG		0.4652,0.0227,0.3153	benign	147/221	18898468	41,12963	2203	4299	6502	SO:0001583	missense	8214	exon4			TGGACCGGAAGGT	X96484	CCDS13753.1	22q11.21	2008-06-12			ENSG00000183628	ENSG00000183628			2846	protein-coding gene	gene with protein product		601279				8733130	Standard	NM_005675		Approved		uc002zoh.4	Q14129	OTTHUMG00000150162	ENST00000331444.6:c.440G>A	22.37:g.18898468G>A	ENSP00000331681:p.Arg147Gln	105.0	0.0	0		102.0	46.0	0.45098	NM_005675	B2RCH5|D3DX15|G5E9J8|Q9BY28	Missense_Mutation	SNP	ENST00000331444.6	37	CCDS13753.1	.	.	.	.	.	.	.	.	.	.	g	10.25	1.299748	0.23650	2.27E-4	0.004652	ENSG00000183628	ENST00000331444;ENST00000436645	T	0.24151	1.87	4.31	3.3	0.37823	.	0.058938	0.64402	D	0.000001	T	0.05044	0.0135	N	0.00569	-1.365	0.41386	D	0.987582	B	0.18741	0.03	B	0.12837	0.008	T	0.39035	-0.9633	10	0.02654	T	1	-40.3259	5.9322	0.19144	0.2095:0.0:0.7905:0.0	.	147	Q14129	DGCR6_HUMAN	Q	147;67	ENSP00000331681:R147Q	ENSP00000331681:R147Q	R	+	2	0	DGCR6	17278468	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	4.351000	0.59398	2.421000	0.82119	0.430000	0.28490	CGG	G|0.997;A|0.003	0.003	strong		0.682	DGCR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316631.2	NM_005675	
GALNT14	79623	hgsc.bcm.edu	37	2	31348076	31348076	+	Intron	SNP	G	G	A	rs41280621	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:31348076G>A	ENST00000349752.5	-	1	769				GALNT14_ENST00000356174.3_Intron|GALNT14_ENST00000420311.2_Intron|GALNT14_ENST00000324589.5_Missense_Mutation_p.A58V|GALNT14_ENST00000406653.1_5'UTR	NM_024572.3	NP_078848.2	Q96FL9	GLT14_HUMAN	polypeptide N-acetylgalactosaminyltransferase 14						cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(3)|large_intestine(10)|liver(1)|lung(21)|ovary(1)|skin(3)|upper_aerodigestive_tract(3)	43	Acute lymphoblastic leukemia(172;0.155)					CACCTGAGGCGCCCAAGGGCT	0.512													G|||	13	0.00259585	0.0008	0.0043	5008	,	,		20381	0.0		0.004	False		,,,				2504	0.0051				p.A58V		Atlas-SNP	.											.	GALNT14	103	.	0			c.C173T						PASS	.																																			SO:0001627	intron_variant	79623	exon2			TGAGGCGCCCAAG	AB078144	CCDS1773.2, CCDS58705.1, CCDS58706.1	2p23.2	2014-03-13	2014-03-13		ENSG00000158089	ENSG00000158089	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	22946	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 14"""	608225	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 14 (GalNAc-T14)"""			12507512	Standard	NM_024572		Approved	GalNac-T10, FLJ12691, GalNac-T14	uc002rns.3	Q96FL9	OTTHUMG00000074077	ENST00000349752.5:c.129+12747C>T	2.37:g.31348076G>A		57.0	0.0	0		57.0	29.0	0.508772	NM_001253826	B3KV89|Q4ZG75|Q53SU1|Q53TJ0|Q8IVI4|Q9BRH1|Q9H827|Q9H9J8	Missense_Mutation	SNP	ENST00000349752.5	37	CCDS1773.2	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	8.995	0.978610	0.18812	.	.	ENSG00000158089	ENST00000324589	T	0.58060	0.36	3.94	-7.88	0.01178	.	16.563700	0.00166	N	0.000002	T	0.23289	0.0563	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.08493	-1.0719	9	0.30078	T	0.28	.	3.8926	0.09125	0.3307:0.1169:0.4366:0.1157	rs41280621	58	Q96FL9-3	.	V	58	ENSP00000314500:A58V	ENSP00000314500:A58V	A	-	2	0	GALNT14	31201580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.055000	0.01397	-1.937000	0.01047	-4.460000	0.00005	GCG	G|0.994;A|0.006	0.006	strong		0.512	GALNT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157264.1	NM_024572	
PGAM2	5224	hgsc.bcm.edu	37	7	44104896	44104896	+	Nonsense_Mutation	SNP	C	C	T	rs10250779	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:44104896C>T	ENST00000297283.3	-	1	290	c.233G>A	c.(232-234)tGg>tAg	p.W78*	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	78					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CACAGGCAGCCACATCTGGTC	0.622													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		16885	0.0		0.0	False		,,,				2504	0.0				p.W78X		Atlas-SNP	.											.	PGAM2	20	.	0			c.G233A	GRCh37	CM930584	PGAM2	M	rs10250779	PASS	.	C	stop/TRP	40,4366	43.8+/-77.6	1,38,2164	85.0	74.0	78.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	233	5.9	1.0	7	dbSNP_119	78	0,8600		0,0,4300	yes	stop-gained	PGAM2	NM_000290.3		1,38,6464	TT,TC,CC		0.0,0.9079,0.3076		78/254	44104896	40,12966	2203	4300	6503	SO:0001587	stop_gained	5224	exon1			GGCAGCCACATCT		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.233G>A	7.37:g.44104896C>T	ENSP00000297283:p.Trp78*	103.0	0.0	0		129.0	66.0	0.511628	NM_000290		Nonsense_Mutation	SNP	ENST00000297283.3	37	CCDS34624.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	36	5.972079	0.97162	0.009079	0.0	ENSG00000164708	ENST00000297283	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-32.2844	17.8825	0.88844	0.0:1.0:0.0:0.0	rs10250779;rs10250779	.	.	.	X	78	.	ENSP00000297283:W78X	W	-	2	0	PGAM2	44071421	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	7.674000	0.83992	2.828000	0.97474	0.644000	0.83932	TGG	C|0.997;T|0.003	0.003	strong		0.622	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
PRTG	283659	hgsc.bcm.edu	37	15	55964778	55964778	+	Missense_Mutation	SNP	C	C	G	rs149494002	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr15:55964778C>G	ENST00000389286.4	-	11	1953	c.1906G>C	c.(1906-1908)Gtg>Ctg	p.V636L		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TGCCACCTCACAGAAATGGTG	0.458													C|||	12	0.00239617	0.0008	0.0029	5008	,	,		16822	0.0		0.008	False		,,,				2504	0.001				p.V636L		Atlas-SNP	.											.	PRTG	110	.	0			c.G1906C						PASS	.	C	LEU/VAL	8,3802		0,8,1897	78.0	74.0	75.0		1906	5.6	1.0	15	dbSNP_134	75	82,8162		0,82,4040	yes	missense	PRTG	NM_173814.4	32	0,90,5937	GG,GC,CC		0.9947,0.21,0.7466	benign	636/1151	55964778	90,11964	1905	4122	6027	SO:0001583	missense	283659	exon11			ACCTCACAGAAAT	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1906G>C	15.37:g.55964778C>G	ENSP00000373937:p.Val636Leu	128.0	0.0	0		152.0	66.0	0.434211	NM_173814		Missense_Mutation	SNP	ENST00000389286.4	37	CCDS42040.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	15.36	2.810509	0.50421	0.0021	0.009947	ENSG00000166450	ENST00000389286	T	0.22336	1.96	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.232951	0.37483	N	0.002061	T	0.16685	0.0401	L	0.43701	1.375	0.80722	D	1	B	0.22541	0.071	B	0.22152	0.038	T	0.01537	-1.1330	10	0.40728	T	0.16	-15.7028	18.6782	0.91537	0.0:1.0:0.0:0.0	.	636	Q2VWP7	PRTG_HUMAN	L	636	ENSP00000373937:V636L	ENSP00000373937:V636L	V	-	1	0	PRTG	53752070	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	4.585000	0.60977	2.648000	0.89879	0.650000	0.86243	GTG	C|0.994;G|0.006	0.006	strong		0.458	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
FAM86B1	85002	hgsc.bcm.edu	37	8	12044264	12044264	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr8:12044264C>T	ENST00000448228.2	-	4	368	c.319G>A	c.(319-321)Gcc>Acc	p.A107T	FAM86B1_ENST00000321602.8_Start_Codon_SNP_p.M1I|FAM86B1_ENST00000534520.1_Missense_Mutation_p.A107T|FAM86B1_ENST00000533852.2_Missense_Mutation_p.A141T|FAM86B1_ENST00000533513.1_Missense_Mutation_p.A141T	NM_001083537.1	NP_001077006.1	Q8N7N1	F86B1_HUMAN	family with sequence similarity 86, member B1	107										kidney(1)|prostate(1)|stomach(1)	3			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.0965)		TAGAGGGCGGCATCCCATGTG	0.612																																					p.A107T		Atlas-SNP	.											FAM86B1,NS,carcinoma,+2,1	FAM86B1	7	1	0			c.G319A						scavenged	.						1.0	1.0	1.0					8																	12044264		461	1070	1531	SO:0001583	missense	85002	exon4			GGGCGGCATCCCA	BC007983	CCDS59512.1	8p23.1	2014-02-12	2005-08-19		ENSG00000186523	ENSG00000186523			28268	protein-coding gene	gene with protein product						12477932	Standard	NM_001083537		Approved	MGC16279	uc010lse.3	Q8N7N1	OTTHUMG00000165298	ENST00000448228.2:c.319G>A	8.37:g.12044264C>T	ENSP00000407067:p.Ala107Thr	297.0	0.0	0		320.0	27.0	0.084375	NM_001083537		Missense_Mutation	SNP	ENST00000448228.2	37	CCDS59512.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	-|-	11.97|11.97	1.796969|1.796969	0.31777|0.31777	.|.	.|.	ENSG00000186523|ENSG00000186523	ENST00000431227;ENST00000340537;ENST00000448228;ENST00000534520;ENST00000526708;ENST00000524571;ENST00000533513|ENST00000321602;ENST00000526802	T;T;T;T;T|T	0.36340|0.24350	1.26;2.52;1.26;1.56;4.06|1.86	1.17|1.17	1.17|1.17	0.20885|0.20885	.|.	10.022600|.	0.01570|.	U|.	0.020538|.	T|T	0.33731|0.33731	0.0873|0.0873	M|M	0.90309|0.90309	3.105|3.105	0.80722|0.80722	D|D	1|1	P;P|B;B	0.46457|0.15719	0.878;0.749|0.014;0.003	D;P|B;B	0.64144|0.08055	0.922;0.624|0.003;0.002	T|T	0.42050|0.42050	-0.9474|-0.9474	10|9	0.72032|0.87932	D|D	0.01|0	.|.	8.2654|8.2654	0.31810|0.31810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	107;141|1;38	Q8N7N1;E9PN63|F6QN85;Q4KMP3	F86B1_HUMAN;.|.;.	T|I	141;107;107;107;141;79;141|1;102	ENSP00000342610:A107T;ENSP00000407067:A107T;ENSP00000431362:A107T;ENSP00000432790:A79T;ENSP00000435201:A141T|ENSP00000439686:M1I	ENSP00000342610:A107T|ENSP00000439686:M1I	A|M	-|-	1|3	0|0	FAM86B1|FAM86B1	12081673|12081673	1.000000|1.000000	0.71417|0.71417	0.088000|0.088000	0.20740|0.20740	0.049000|0.049000	0.14656|0.14656	6.283000|6.283000	0.72646|0.72646	0.950000|0.950000	0.37743|0.37743	0.173000|0.173000	0.16961|0.16961	GCC|ATG	.	.	none		0.612	FAM86B1-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000383317.1	NM_032916	
TULP4	56995	hgsc.bcm.edu	37	6	158910743	158910743	+	Missense_Mutation	SNP	G	G	A	rs61742077	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:158910743G>A	ENST00000367097.3	+	9	2967	c.1610G>A	c.(1609-1611)aGc>aAc	p.S537N	TULP4_ENST00000367094.2_Missense_Mutation_p.S537N	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	537					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TCCAGAGCTAGCAAATCACCC	0.473													G|||	9	0.00179712	0.0	0.0058	5008	,	,		19135	0.0		0.004	False		,,,				2504	0.001				p.S537N		Atlas-SNP	.											.	TULP4	137	.	0			c.G1610A						PASS	.	G	ASN/SER,ASN/SER	1,4405	2.1+/-5.4	0,1,2202	131.0	118.0	123.0		1610,1610	4.7	1.0	6	dbSNP_129	123	66,8534	40.3+/-97.0	0,66,4234	yes	missense,missense	TULP4	NM_001007466.1,NM_020245.3	46,46	0,67,6436	AA,AG,GG		0.7674,0.0227,0.5151	benign,benign	537/679,537/1544	158910743	67,12939	2203	4300	6503	SO:0001583	missense	56995	exon9			GAGCTAGCAAATC		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.1610G>A	6.37:g.158910743G>A	ENSP00000356064:p.Ser537Asn	132.0	0.0	0		152.0	74.0	0.486842	NM_020245	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Missense_Mutation	SNP	ENST00000367097.3	37	CCDS34561.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	G	17.26	3.344506	0.61073	2.27E-4	0.007674	ENSG00000130338	ENST00000367097;ENST00000367094	T;T	0.61627	0.09;0.89	5.57	4.68	0.58851	Tubby, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.22513	0.0543	N	0.10874	0.06	0.58432	D	0.999991	B;B	0.16166	0.002;0.016	B;B	0.14023	0.009;0.01	T	0.04678	-1.0934	10	0.24483	T	0.36	-30.6907	16.3085	0.82859	0.0:0.1325:0.8675:0.0	rs61742077	537;537	Q9NRJ4-2;Q9NRJ4	.;TULP4_HUMAN	N	537	ENSP00000356064:S537N;ENSP00000356061:S537N	ENSP00000356061:S537N	S	+	2	0	TULP4	158830731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.437000	0.80417	1.299000	0.44798	0.655000	0.94253	AGC	G|0.996;A|0.004	0.004	strong		0.473	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
PLA2G15	23659	hgsc.bcm.edu	37	16	68289739	68289739	+	Silent	SNP	C	C	T	rs76404867	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:68289739C>T	ENST00000219345.5	+	5	656	c.573C>T	c.(571-573)ccC>ccT	p.P191P	PLA2G15_ENST00000566188.1_Intron|RP11-96D1.7_ENST00000563175.1_RNA|PLA2G15_ENST00000444212.2_Intron|RP11-96D1.7_ENST00000569843.1_RNA|PLA2G15_ENST00000413021.2_Intron	NM_012320.3	NP_036452.1	Q8NCC3	PAG15_HUMAN	phospholipase A2, group XV	191					ceramide metabolic process (GO:0006672)|fatty acid catabolic process (GO:0009062)|phosphatidylcholine metabolic process (GO:0046470)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)|O-acyltransferase activity (GO:0008374)|phospholipid binding (GO:0005543)			kidney(2)|large_intestine(2)|lung(2)|ovary(2)|prostate(3)|skin(1)	12						ATGGGGGCCCCGTGGTGCTGG	0.607													C|||	22	0.00439297	0.0015	0.0043	5008	,	,		18228	0.0		0.0169	False		,,,				2504	0.0				p.P191P		Atlas-SNP	.											.	PLA2G15	30	.	0			c.C573T						PASS	.	C		18,4378	24.3+/-50.5	0,18,2180	49.0	53.0	52.0		573	-8.0	0.6	16	dbSNP_132	52	173,8427	79.8+/-142.4	2,169,4129	yes	coding-synonymous	PLA2G15	NM_012320.3		2,187,6309	TT,TC,CC		2.0116,0.4095,1.4697		191/413	68289739	191,12805	2198	4300	6498	SO:0001819	synonymous_variant	23659	exon5			GGGCCCCGTGGTG	AB017494	CCDS10864.1	16q22.1	2008-09-19	2008-09-19	2008-09-19	ENSG00000103066	ENSG00000103066			17163	protein-coding gene	gene with protein product		609362	"""lysophospholipase 3 (lysosomal phospholipase A2)"""	LYPLA3		10092508, 16973413	Standard	XM_005255886		Approved	LLPL, GXVPLA2	uc002evr.3	Q8NCC3	OTTHUMG00000137554	ENST00000219345.5:c.573C>T	16.37:g.68289739C>T		120.0	0.0	0		168.0	85.0	0.505952	NM_012320	B3KMF3|B4DUD1|Q53GZ1|Q9NPQ6|Q9UG04|Q9Y2B3	Silent	SNP	ENST00000219345.5	37	CCDS10864.1																																																																																			C|0.987;T|0.013	0.013	strong		0.607	PLA2G15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268888.2	NM_012320	
DSP	1832	hgsc.bcm.edu	37	6	7581032	7581032	+	Missense_Mutation	SNP	C	C	T	rs28763967	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr6:7581032C>T	ENST00000379802.3	+	23	4950	c.4609C>T	c.(4609-4611)Cgc>Tgc	p.R1537C	DSP_ENST00000418664.2_Intron	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	1537	Central fibrous rod domain.		R -> C (in dbSNP:rs28763967). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		AGAACTGACACGCCTGAGGAT	0.493													C|||	18	0.00359425	0.0008	0.0014	5008	,	,		21149	0.0		0.0159	False		,,,				2504	0.0				p.R1537C		Atlas-SNP	.											.	DSP	306	.	0			c.C4609T						PASS	.	C	,CYS/ARG	13,4393	20.2+/-43.8	0,13,2190	120.0	121.0	120.0		,4609	5.8	1.0	6	dbSNP_125	120	123,8477	62.8+/-124.8	3,117,4180	yes	intron,missense	DSP	NM_001008844.1,NM_004415.2	,180	3,130,6370	TT,TC,CC		1.4302,0.2951,1.0457	,probably-damaging	,1537/2872	7581032	136,12870	2203	4300	6503	SO:0001583	missense	1832	exon23			CTGACACGCCTGA	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.4609C>T	6.37:g.7581032C>T	ENSP00000369129:p.Arg1537Cys	72.0	0.0	0		81.0	28.0	0.345679	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	12	0.005494505494505495	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	16.80	3.224244	0.58668	0.002951	0.014302	ENSG00000096696	ENST00000379802	T	0.74737	-0.87	5.85	5.85	0.93711	.	0.000000	0.64402	D	0.000009	T	0.76047	0.3933	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.77800	-0.2452	10	0.59425	D	0.04	.	15.812	0.78571	0.1441:0.8559:0.0:0.0	rs28763967	1537	P15924	DESP_HUMAN	C	1537	ENSP00000369129:R1537C	ENSP00000369129:R1537C	R	+	1	0	DSP	7526031	0.859000	0.29813	0.966000	0.40874	0.971000	0.66376	2.051000	0.41307	2.772000	0.95346	0.655000	0.94253	CGC	C|0.992;T|0.008	0.008	strong		0.493	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
DGKB	1607	hgsc.bcm.edu	37	7	14620536	14620536	+	Silent	SNP	C	C	A	rs61753128		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:14620536C>A	ENST00000403951.2	-	19	1982	c.1563G>T	c.(1561-1563)ctG>ctT	p.L521L	DGKB_ENST00000402815.1_Silent_p.L520L|DGKB_ENST00000399322.3_Silent_p.L521L|DGKB_ENST00000403963.1_5'UTR|DGKB_ENST00000406247.3_Silent_p.L521L|DGKB_ENST00000258767.5_Silent_p.L521L|DGKB_ENST00000407950.1_Silent_p.L513L|DGKB_ENST00000444700.2_Silent_p.L502L			Q9Y6T7	DGKB_HUMAN	diacylglycerol kinase, beta 90kDa	521	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(34)|ovary(4)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72						TCCCAAGAGGCAGAATCGCAA	0.423																																					p.L521L		Atlas-SNP	.											.	DGKB	166	.	0			c.G1563T						PASS	.	C	,	1,3881		0,1,1940	94.0	84.0	87.0		1563,1563	3.9	1.0	7	dbSNP_129	87	9,8297		0,9,4144	no	coding-synonymous,coding-synonymous	DGKB	NM_004080.2,NM_145695.2	,	0,10,6084	AA,AC,CC		0.1084,0.0258,0.082	,	521/805,521/774	14620536	10,12178	1941	4153	6094	SO:0001819	synonymous_variant	1607	exon18			AAGAGGCAGAATC	AB018261	CCDS47547.1, CCDS47548.1	7p21.2	2013-01-10	2002-08-29		ENSG00000136267	ENSG00000136267	2.7.1.107	"""EF-hand domain containing"""	2850	protein-coding gene	gene with protein product		604070	"""diacylglycerol kinase, beta (90kD)"""	DAGK2		7689223	Standard	NM_004080		Approved	KIAA0718, DGK, DGK-BETA	uc003ssz.3	Q9Y6T7	OTTHUMG00000152477	ENST00000403951.2:c.1563G>T	7.37:g.14620536C>A		98.0	0.0	0		140.0	60.0	0.428571	NM_145695	A4D116|A4D117|A8MXU2|O75241|Q2M377|Q75MF9|Q75MU7|Q86UI5|Q86UM9|Q9UQ29	Silent	SNP	ENST00000403951.2	37	CCDS47547.1																																																																																			.	.	weak		0.423	DGKB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000326356.2	NM_004080	
ITGA2B	3674	hgsc.bcm.edu	37	17	42463054	42463054	+	Missense_Mutation	SNP	G	G	C	rs76066357	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:42463054G>C	ENST00000262407.5	-	4	470	c.439C>G	c.(439-441)Cta>Gta	p.L147V	ITGA2B_ENST00000377068.3_5'Flank|ITGA2B_ENST00000353281.4_Missense_Mutation_p.L147V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	147					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	GTCTTTTCTAGGACGTTCCAG	0.667													G|||	23	0.00459265	0.0008	0.0101	5008	,	,		11686	0.0		0.0139	False		,,,				2504	0.001				p.L147V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.C439G	GRCh37	CM073147	ITGA2B	M	rs76066357	PASS	.	G	VAL/LEU	14,4386	19.1+/-41.9	0,14,2186	29.0	36.0	34.0		439	3.5	0.0	17	dbSNP_134	34	113,8485	59.1+/-120.7	1,111,4187	yes	missense	ITGA2B	NM_000419.3	32	1,125,6373	CC,CG,GG		1.3143,0.3182,0.9771	benign	147/1040	42463054	127,12871	2200	4299	6499	SO:0001583	missense	3674	exon4			TTTCTAGGACGTT		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.439C>G	17.37:g.42463054G>C	ENSP00000262407:p.Leu147Val	56.0	0.0	0		43.0	25.0	0.581395	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Missense_Mutation	SNP	ENST00000262407.5	37	CCDS32665.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	11.09	1.537077	0.27475	0.003182	0.013143	ENSG00000005961	ENST00000262407;ENST00000353281	T;T	0.71698	-0.59;-0.59	5.55	3.52	0.40303	.	0.000000	0.28515	N	0.015074	T	0.51126	0.1656	L	0.52573	1.65	0.24187	N	0.995568	B	0.26363	0.147	B	0.20184	0.028	T	0.46884	-0.9159	10	0.37606	T	0.19	.	6.7565	0.23516	0.0824:0.0:0.6063:0.3113	.	147	P08514	ITA2B_HUMAN	V	147	ENSP00000262407:L147V;ENSP00000340536:L147V	ENSP00000262407:L147V	L	-	1	2	ITGA2B	39818580	0.018000	0.18449	0.011000	0.14972	0.617000	0.37484	0.063000	0.14410	0.666000	0.31087	-0.254000	0.11334	CTA	G|0.991;C|0.009	0.009	strong		0.667	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
ZSWIM4	65249	hgsc.bcm.edu	37	19	13941255	13941255	+	Silent	SNP	G	G	A	rs138305620	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:13941255G>A	ENST00000254323.2	+	13	2550	c.2361G>A	c.(2359-2361)gcG>gcA	p.A787A	ZSWIM4_ENST00000440752.2_Silent_p.A621A	NM_023072.2	NP_075560.2	Q9H7M6	ZSWM4_HUMAN	zinc finger, SWIM-type containing 4	787							zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27			OV - Ovarian serous cystadenocarcinoma(19;2.94e-23)|Epithelial(5;4.58e-19)			CCTTCGAGGCGGCCTACCAGA	0.706													G|||	2	0.000399361	0.0	0.0	5008	,	,		15823	0.0		0.002	False		,,,				2504	0.0				p.A787A		Atlas-SNP	.											.	ZSWIM4	69	.	0			c.G2361A						PASS	.	G		0,4406		0,0,2203	68.0	70.0	69.0		2361	-8.3	1.0	19	dbSNP_134	69	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	ZSWIM4	NM_023072.2		0,14,6489	AA,AG,GG		0.1628,0.0,0.1076		787/990	13941255	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	65249	exon13			CGAGGCGGCCTAC	AK022283	CCDS32924.1	19p13.13	2012-02-23			ENSG00000132003	ENSG00000132003		"""Zinc fingers, SWIM-type"""	25704	protein-coding gene	gene with protein product							Standard	NM_023072		Approved	FLJ12221	uc002mxh.1	Q9H7M6		ENST00000254323.2:c.2361G>A	19.37:g.13941255G>A		25.0	0.0	0		41.0	25.0	0.609756	NM_023072		Silent	SNP	ENST00000254323.2	37	CCDS32924.1																																																																																			G|0.999;A|0.001	0.001	strong		0.706	ZSWIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457457.1	XM_031342	
ZNF418	147686	hgsc.bcm.edu	37	19	58437623	58437623	+	Silent	SNP	A	A	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:58437623A>G	ENST00000396147.1	-	4	2217	c.1926T>C	c.(1924-1926)acT>acC	p.T642T	ZNF418_ENST00000595830.1_Silent_p.T642T|ZNF418_ENST00000599852.1_Silent_p.T557T|ZNF418_ENST00000425570.3_Silent_p.T663T|ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000599086.1_5'Flank	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	642					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		GCCTTTCTCCAGTGTGTACTC	0.443																																					p.T642T		Atlas-SNP	.											.	ZNF418	76	.	0			c.T1926C						PASS	.						119.0	121.0	120.0					19																	58437623		2202	4300	6502	SO:0001819	synonymous_variant	147686	exon4			TTCTCCAGTGTGT	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1926T>C	19.37:g.58437623A>G		109.0	0.0	0		89.0	16.0	0.179775	NM_133460	Q2M1S2|Q670L5|Q96N18	Silent	SNP	ENST00000396147.1	37	CCDS42642.1																																																																																			.	.	none		0.443	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
DNAH5	1767	hgsc.bcm.edu	37	5	13830749	13830749	+	Silent	SNP	A	A	G	rs368456533		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:13830749A>G	ENST00000265104.4	-	36	6122	c.6018T>C	c.(6016-6018)tgT>tgC	p.C2006C		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	2006	AAA 1. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCTGGTCTGAACAATTGAAAA	0.473									Kartagener syndrome																												p.C2006C		Atlas-SNP	.											.	DNAH5	868	.	0			c.T6018C						PASS	.	A		0,4406		0,0,2203	129.0	126.0	127.0		6018	1.7	1.0	5		127	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DNAH5	NM_001369.2		0,2,6501	GG,GA,AA		0.0233,0.0,0.0154		2006/4625	13830749	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon36	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	GTCTGAACAATTG	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.6018T>C	5.37:g.13830749A>G		107.0	0.0	0		110.0	59.0	0.536364	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			.	.	weak		0.473	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
EIF2B4	8890	hgsc.bcm.edu	37	2	27590415	27590415	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:27590415T>C	ENST00000347454.4	-	9	965	c.794A>G	c.(793-795)cAg>cGg	p.Q265R	SNX17_ENST00000233575.2_5'Flank|EIF2B4_ENST00000493344.2_Missense_Mutation_p.Q286R|EIF2B4_ENST00000451130.2_Missense_Mutation_p.Q285R|AC074117.10_ENST00000412749.1_RNA|EIF2B4_ENST00000445933.2_Missense_Mutation_p.Q264R	NM_001034116.1|NM_015636.3	NP_001029288.1|NP_056451.3	Q9UI10	EI2BD_HUMAN	eukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa	265					cellular protein metabolic process (GO:0044267)|cellular response to stimulus (GO:0051716)|gene expression (GO:0010467)|myelination (GO:0042552)|negative regulation of translational initiation (GO:0045947)|negative regulation of translational initiation in response to stress (GO:0032057)|oligodendrocyte development (GO:0014003)|ovarian follicle development (GO:0001541)|positive regulation of GTPase activity (GO:0043547)|regulation of translation (GO:0006417)|regulation of translational initiation (GO:0006446)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to peptide hormone (GO:0043434)|translation (GO:0006412)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation initiation factor 2B complex (GO:0005851)	translation initiation factor activity (GO:0003743)|translation initiation factor binding (GO:0031369)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|lung(5)|skin(1)	10	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGGACGGCACTGAGTCAGGAA	0.433																																					p.Q285R		Atlas-SNP	.											.	EIF2B4	48	.	0			c.A854G						PASS	.						108.0	104.0	105.0					2																	27590415		2203	4300	6503	SO:0001583	missense	8890	exon8			CGGCACTGAGTCA	AJ011306	CCDS33164.1, CCDS46244.1, CCDS46245.1	2p23.3	2008-02-05	2002-08-29		ENSG00000115211	ENSG00000115211			3260	protein-coding gene	gene with protein product		606687	"""eukaryotic translation initiation factor 2B, subunit 4 (delta, 67kD)"""			8929216, 7982969	Standard	NM_172195		Approved	EIF2Bdelta, EIF-2B, DKFZP586J0119, EIF2B	uc002rjz.3	Q9UI10	OTTHUMG00000151927	ENST00000347454.4:c.794A>G	2.37:g.27590415T>C	ENSP00000233552:p.Gln265Arg	64.0	0.0	0		62.0	28.0	0.451613	NM_172195	Q53RY7|Q5BJF4|Q9BUV9|Q9UBG4|Q9UIQ9|Q9UJ95	Missense_Mutation	SNP	ENST00000347454.4	37	CCDS33164.1	.	.	.	.	.	.	.	.	.	.	T	15.84	2.953247	0.53293	.	.	ENSG00000115211	ENST00000347454;ENST00000414437;ENST00000445933;ENST00000451130;ENST00000493344	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	5.97	5.97	0.96955	.	0.000000	0.85682	D	0.000000	D	0.90793	0.7109	L	0.60455	1.87	0.80722	D	1	B;B;B;B	0.31790	0.34;0.34;0.071;0.057	B;B;B;B	0.36922	0.108;0.236;0.055;0.032	D	0.88128	0.2836	10	0.21014	T	0.42	-20.7409	15.2744	0.73732	0.0:0.0:0.0:1.0	.	262;264;265;285	F5H6W1;Q9UI10-3;Q9UI10;Q9UI10-2	.;.;EI2BD_HUMAN;.	R	265;262;264;285;286	ENSP00000233552:Q265R;ENSP00000394397:Q264R;ENSP00000394869:Q285R;ENSP00000429323:Q286R	ENSP00000233552:Q265R	Q	-	2	0	EIF2B4	27443919	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.460000	0.80816	2.288000	0.76882	0.533000	0.62120	CAG	.	.	none		0.433	EIF2B4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324448.1		
HAS1	3036	hgsc.bcm.edu	37	19	52217128	52217128	+	Missense_Mutation	SNP	G	G	A	rs34682338	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:52217128G>A	ENST00000222115.1	-	5	1323	c.1289C>T	c.(1288-1290)gCg>gTg	p.A430V	HAS1_ENST00000601714.1_Missense_Mutation_p.A437V|HAS1_ENST00000540069.2_Missense_Mutation_p.A429V	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	430					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CCACAGCAGCGCCCAAGGGCG	0.697													g|||	10	0.00199681	0.0008	0.0014	5008	,	,		15365	0.0		0.005	False		,,,				2504	0.0031				p.A430V	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											HAS1,lower_third,carcinoma,0,1	HAS1	61	1	0			c.C1289T						scavenged	.		VAL/ALA	12,4360		0,12,2174	24.0	25.0	25.0		1289	3.2	1.0	19	dbSNP_126	25	93,8495		0,93,4201	yes	missense	HAS1	NM_001523.2	64	0,105,6375	AA,AG,GG		1.0829,0.2745,0.8102	possibly-damaging	430/579	52217128	105,12855	2186	4294	6480	SO:0001583	missense	3036	exon5			AGCAGCGCCCAAG	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.1289C>T	19.37:g.52217128G>A	ENSP00000222115:p.Ala430Val	5.0	0.0	0		5.0	3.0	0.6	NM_001523	Q14470|Q9NS49	Missense_Mutation	SNP	ENST00000222115.1	37	CCDS12838.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	g	13.44	2.236984	0.39498	0.002745	0.010829	ENSG00000105509	ENST00000540069;ENST00000222115	T;T	0.59083	0.29;0.29	3.19	3.19	0.36642	.	0.146701	0.44483	U	0.000446	T	0.27278	0.0669	N	0.22421	0.69	0.33217	D	0.554145	B;P;P	0.42757	0.334;0.789;0.789	B;B;B	0.32928	0.04;0.155;0.155	T	0.53085	-0.8488	10	0.66056	D	0.02	-18.9542	7.85	0.29448	0.0:0.0:0.7525:0.2475	rs34682338	429;430;429	G3V1S7;Q92839;Q8IYH3	.;HAS1_HUMAN;.	V	429;430	ENSP00000445021:A429V;ENSP00000222115:A430V	ENSP00000222115:A430V	A	-	2	0	HAS1	56908940	1.000000	0.71417	1.000000	0.80357	0.270000	0.26580	5.291000	0.65667	1.812000	0.52913	0.165000	0.16767	GCG	G|0.995;A|0.005	0.005	strong		0.697	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
FLG	2312	hgsc.bcm.edu	37	1	152283267	152283267	+	Silent	SNP	T	T	A	rs11581451	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:152283267T>A	ENST00000368799.1	-	3	4130	c.4095A>T	c.(4093-4095)gcA>gcT	p.A1365A	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1365	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGAGCTGTCTGCTGACTGCT	0.537									Ichthyosis				T|||	37	0.00738818	0.0	0.0072	5008	,	,		21371	0.001		0.0119	False		,,,				2504	0.0194				p.A1365A		Atlas-SNP	.											FLG,NS,carcinoma,-2,1	FLG	900	1	0			c.A4095T						scavenged	.	T		14,4392	21.2+/-45.6	0,14,2189	392.0	369.0	377.0		4095	-8.4	0.0	1	dbSNP_120	377	98,8498	55.2+/-116.2	1,96,4201	no	coding-synonymous	FLG	NM_002016.1		1,110,6390	AA,AT,TT		1.1401,0.3177,0.8614		1365/4062	152283267	112,12890	2203	4298	6501	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTGTCTGCTGAC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4095A>T	1.37:g.152283267T>A		147.0	1.0	0.00680272		176.0	91.0	0.517045	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.993;A|0.007	0.007	strong		0.537	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
AATK	9625	hgsc.bcm.edu	37	17	79093211	79093211	+	Silent	SNP	G	G	A	rs201255728	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:79093211G>A	ENST00000326724.4	-	13	4077	c.4053C>T	c.(4051-4053)caC>caT	p.H1351H	AATK_ENST00000417379.1_Silent_p.H1248H	NM_001080395.2	NP_001073864.2	Q6ZMQ8	LMTK1_HUMAN	apoptosis-associated tyrosine kinase	1351					brain development (GO:0007420)|negative regulation of axon extension (GO:0030517)|neuron apoptotic process (GO:0051402)|peptidyl-tyrosine autophosphorylation (GO:0038083)|Rab protein signal transduction (GO:0032482)	axonal growth cone (GO:0044295)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			endometrium(2)|kidney(2)|lung(8)|ovary(3)|prostate(1)|stomach(4)|upper_aerodigestive_tract(1)	21	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0228)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			AGTCAGACACGTGCGTGATGG	0.746													G|||	4	0.000798722	0.0	0.0	5008	,	,		12763	0.0		0.003	False		,,,				2504	0.001				p.H1351H		Atlas-SNP	.											.	AATK	102	.	0			c.C4053T						PASS	.	G	,	2,4040		0,2,2019	15.0	19.0	18.0		4053,3744	-2.3	0.7	17		18	15,8273		0,15,4129	no	coding-synonymous,coding-synonymous	AATK	NM_001080395.2,NM_004920.2	,	0,17,6148	AA,AG,GG		0.181,0.0495,0.1379	,	1351/1375,1248/1272	79093211	17,12313	2021	4144	6165	SO:0001819	synonymous_variant	9625	exon13			AGACACGTGCGTG	AB014541	CCDS45807.1, CCDS58607.1	17q25.3	2014-06-12			ENSG00000181409	ENSG00000181409			21	protein-coding gene	gene with protein product	"""lemur tyrosine kinase 1"", ""protein phosphatase 1, regulatory subunit 77"""	605276				9734811, 10083745	Standard	NM_001080395		Approved	AATYK, KIAA0641, LMTK1, LMR1, AATYK1, PPP1R77	uc010dia.3	Q6ZMQ8	OTTHUMG00000132717	ENST00000326724.4:c.4053C>T	17.37:g.79093211G>A		22.0	0.0	0		15.0	7.0	0.466667	NM_001080395	O75136|Q6ZN31|Q86X28	Silent	SNP	ENST00000326724.4	37	CCDS45807.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	5.059	0.196531	0.09599	4.95E-4	0.00181	ENSG00000181409	ENST00000417379	.	.	.	3.52	-2.34	0.06704	.	.	.	.	.	T	0.52289	0.1725	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48547	-0.9026	4	.	.	.	.	8.3273	0.32165	0.0794:0.0:0.3373:0.5832	.	.	.	.	M	1304	.	.	T	-	2	0	AATK	76707806	0.871000	0.30034	0.747000	0.31113	0.083000	0.17756	-0.123000	0.10611	-0.245000	0.09625	0.297000	0.19635	ACG	G|0.999;A|0.001	0.001	strong		0.746	AATK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256055.1	NM_004920	
IL3RA	3563	hgsc.bcm.edu	37	X	1471062	1471062	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrX:1471062G>C	ENST00000331035.4	+	5	717	c.368G>C	c.(367-369)aGc>aCc	p.S123T	IL3RA_ENST00000381469.2_Missense_Mutation_p.S45T	NM_001267713.1|NM_002183.3	NP_001254642.1|NP_002174.1	P26951	IL3RA_HUMAN	interleukin 3 receptor, alpha (low affinity)	123			S -> T (in dbSNP:rs17883572). {ECO:0000269|Ref.5}.		cellular response to interleukin-3 (GO:0036016)|interleukin-3-mediated signaling pathway (GO:0038156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-3 receptor activity (GO:0004912)			lung(1)|skin(2)	3		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)			Sargramostim(DB00020)	TTGAGCTGCAGCTGGGCGGTA	0.607													g|||	10	0.00199681	0.0008	0.0043	5008	,	,		15306	0.0		0.006	False		,,,				2504	0.0				p.S123T		Atlas-SNP	.											.	IL3RA	49	.	0			c.G368C						PASS	.	G	THR/SER	3,4399		0,3,2198	120.0	137.0	131.0		368	-1.7	0.0	X	dbSNP_134	131	34,8558		0,34,4262	no	missense	IL3RA	NM_002183.2	58	0,37,6460	CC,CG,GG		0.3957,0.0682,0.2847	benign	123/379	1471062	37,12957	2201	4296	6497	SO:0001583	missense	3563	exon5			GCTGCAGCTGGGC	M74782	CCDS14113.1, CCDS59158.1	Xp22.3 and Yp13.3	2008-07-21			ENSG00000185291	ENSG00000185291		"""Pseudoautosomal regions / PAR1"", ""Interleukins and interleukin receptors"", ""CD molecules"""	6012	protein-coding gene	gene with protein product		308385, 430000				1833064	Standard	NM_002183		Approved	CD123	uc004cps.3	P26951	OTTHUMG00000021059	ENST00000331035.4:c.368G>C	X.37:g.1471062G>C	ENSP00000327890:p.Ser123Thr	253.0	0.0	0		115.0	107.0	0.930435	NM_002183	A8K3F3|B9VI81|Q5HYQ7|Q5HYQ8|Q9UEH7	Missense_Mutation	SNP	ENST00000331035.4	37	CCDS14113.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	.	3.020	-0.202042	0.06219	6.82E-4	0.003957	ENSG00000185291	ENST00000331035;ENST00000432757;ENST00000381469	D;D;D	0.82803	-1.65;-1.65;-1.65	1.88	-1.72	0.08107	Interleukin-6 receptor alpha chain, binding (1);Fibronectin, type III (1);Short hematopoietin receptor, family 2, conserved site (1);Immunoglobulin-like fold (1);	12.972700	0.00397	U	0.000044	T	0.64853	0.2636	N	0.10707	0.03	0.09310	N	1	D;P	0.55172	0.97;0.62	P;B	0.53146	0.719;0.388	T	0.61739	-0.7001	10	0.11485	T	0.65	0.013	2.6035	0.04872	0.4136:0.2668:0.3195:0.0	.	44;123	P26951-2;P26951	.;IL3RA_HUMAN	T	123;45;45	ENSP00000327890:S123T;ENSP00000414867:S45T;ENSP00000370878:S45T	ENSP00000327890:S123T	S	+	2	0	IL3RA	1431062	0.115000	0.22152	0.001000	0.08648	0.020000	0.10135	-0.706000	0.05047	-0.389000	0.07786	0.365000	0.22127	AGC	.	.	weak		0.607	IL3RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055600.3		
KIAA0556	23247	hgsc.bcm.edu	37	16	27752099	27752099	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr16:27752099G>T	ENST00000261588.4	+	15	2500	c.2481G>T	c.(2479-2481)caG>caT	p.Q827H		NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	827						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AGAGACCCCAGAGGGCAACCA	0.607																																					p.Q827H		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G2481T						PASS	.						47.0	49.0	48.0					16																	27752099		2197	4300	6497	SO:0001583	missense	23247	exon15			ACCCCAGAGGGCA	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.2481G>T	16.37:g.27752099G>T	ENSP00000261588:p.Gln827His	59.0	0.0	0		79.0	38.0	0.481013	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	.	.	.	.	.	.	.	.	.	.	G	12.03	1.817035	0.32145	.	.	ENSG00000047578	ENST00000261588	T	0.10960	2.82	5.15	-1.1	0.09872	.	0.718739	0.13839	N	0.359178	T	0.12092	0.0294	L	0.50333	1.59	0.09310	N	1	P	0.42649	0.786	P	0.47251	0.542	T	0.15350	-1.0440	10	0.41790	T	0.15	-18.0325	5.0513	0.14511	0.3084:0.4201:0.2715:0.0	.	827	O60303	K0556_HUMAN	H	827	ENSP00000261588:Q827H	ENSP00000261588:Q827H	Q	+	3	2	KIAA0556	27659600	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.385000	0.20685	-0.176000	0.10707	-0.305000	0.09177	CAG	.	.	none		0.607	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
SPTBN1	6711	hgsc.bcm.edu	37	2	54858435	54858435	+	Missense_Mutation	SNP	C	C	T	rs377200533		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:54858435C>T	ENST00000356805.4	+	16	3532	c.3251C>T	c.(3250-3252)gCg>gTg	p.A1084V	SPTBN1_ENST00000333896.5_Missense_Mutation_p.A1071V	NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	1084					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			ACCCAGACAGCGATCGCCTCG	0.587																																					p.A1084V		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C3251T						PASS	.	C	VAL/ALA,VAL/ALA	0,4406		0,0,2203	91.0	87.0	88.0		3212,3251	5.6	1.0	2		88	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SPTBN1	NM_178313.2,NM_003128.2	64,64	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	1071/2156,1084/2365	54858435	1,13005	2203	4300	6503	SO:0001583	missense	6711	exon16			AGACAGCGATCGC		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.3251C>T	2.37:g.54858435C>T	ENSP00000349259:p.Ala1084Val	113.0	0.0	0		116.0	56.0	0.482759	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Missense_Mutation	SNP	ENST00000356805.4	37	CCDS33198.1	.	.	.	.	.	.	.	.	.	.	C	18.79	3.699502	0.68501	0.0	1.16E-4	ENSG00000115306	ENST00000356805;ENST00000333896	T;T	0.49432	0.78;0.78	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.49609	0.1567	L	0.49640	1.575	0.80722	D	1	B;B	0.22800	0.029;0.075	B;B	0.29598	0.046;0.104	T	0.45425	-0.9262	10	0.54805	T	0.06	.	19.5376	0.95260	0.0:1.0:0.0:0.0	.	1071;1084	Q01082-3;Q01082	.;SPTB2_HUMAN	V	1084;1071	ENSP00000349259:A1084V;ENSP00000334156:A1071V	ENSP00000334156:A1071V	A	+	2	0	SPTBN1	54711939	1.000000	0.71417	0.997000	0.53966	0.709000	0.40893	4.910000	0.63321	2.620000	0.88729	0.655000	0.94253	GCG	.	.	weak		0.587	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
ARHGAP32	9743	hgsc.bcm.edu	37	11	128839550	128839550	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:128839550G>T	ENST00000310343.9	-	22	5515	c.5516C>A	c.(5515-5517)gCc>gAc	p.A1839D	ARHGAP32_ENST00000524655.1_3'UTR|ARHGAP32_ENST00000527272.1_Missense_Mutation_p.A1490D|ARHGAP32_ENST00000392657.3_Missense_Mutation_p.A1490D	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	1839	Interaction with FYN.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GTGATGGTGGGCTCTGTCCAT	0.622																																					p.A1839D		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C5516A						PASS	.						72.0	65.0	67.0					11																	128839550		2201	4297	6498	SO:0001583	missense	9743	exon22			TGGTGGGCTCTGT	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.5516C>A	11.37:g.128839550G>T	ENSP00000310561:p.Ala1839Asp	65.0	0.0	0		59.0	26.0	0.440678	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Missense_Mutation	SNP	ENST00000310343.9	37	CCDS44769.1	.	.	.	.	.	.	.	.	.	.	G	9.632	1.136685	0.21123	.	.	ENSG00000134909	ENST00000310343;ENST00000392657;ENST00000527272	T;T;T	0.10099	2.93;2.91;2.91	5.95	4.11	0.48088	.	0.273133	0.35525	N	0.003151	T	0.14270	0.0345	M	0.62723	1.935	0.34234	D	0.676855	B	0.13594	0.008	B	0.10450	0.005	T	0.05989	-1.0852	10	0.87932	D	0	.	12.7738	0.57436	0.1319:0.0:0.8681:0.0	.	1839	A7KAX9	RHG32_HUMAN	D	1839;1490;1490	ENSP00000310561:A1839D;ENSP00000376425:A1490D;ENSP00000432862:A1490D	ENSP00000310561:A1839D	A	-	2	0	ARHGAP32	128344760	0.998000	0.40836	0.111000	0.21465	0.020000	0.10135	2.664000	0.46783	0.875000	0.35847	-0.126000	0.14955	GCC	.	.	none		0.622	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
HSPG2	3339	hgsc.bcm.edu	37	1	22182115	22182115	+	Missense_Mutation	SNP	G	G	A	rs2229474	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:22182115G>A	ENST00000374695.3	-	46	5834	c.5755C>T	c.(5755-5757)Cgc>Tgc	p.R1919C	HSPG2_ENST00000430507.1_5'Flank	NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	1919	Ig-like C2-type 4.		R -> C (in dbSNP:rs2229474).		angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)			breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	GCTGGCAGGCGCAGGATGCCG	0.687													G|||	10	0.00199681	0.0	0.0014	5008	,	,		13927	0.001		0.008	False		,,,				2504	0.0				p.R1919C		Atlas-SNP	.											.	HSPG2	311	.	0			c.C5755T						PASS	.	G	CYS/ARG	9,4359		0,9,2175	13.0	13.0	13.0		5755	5.1	1.0	1	dbSNP_98	13	74,8476		0,74,4201	no	missense	HSPG2	NM_005529.5	180	0,83,6376	AA,AG,GG		0.8655,0.206,0.6425	probably-damaging	1919/4392	22182115	83,12835	2184	4275	6459	SO:0001583	missense	3339	exon46			GCAGGCGCAGGAT	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.5755C>T	1.37:g.22182115G>A	ENSP00000363827:p.Arg1919Cys	82.0	0.0	0		52.0	28.0	0.538462	NM_005529	Q16287|Q5SZI3|Q9H3V5	Missense_Mutation	SNP	ENST00000374695.3	37	CCDS30625.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	1	0.0017482517482517483	5	0.006596306068601583	G	14.28	2.487173	0.44249	0.00206	0.008655	ENSG00000142798	ENST00000374695	T	0.69435	-0.4	5.12	5.12	0.69794	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.181406	0.26939	N	0.021731	T	0.80385	0.4613	M	0.89353	3.025	0.41354	D	0.987383	D	0.89917	1.0	D	0.91635	0.999	D	0.85946	0.1461	10	0.72032	D	0.01	.	16.0425	0.80695	0.0:0.0:1.0:0.0	rs2229474	1919	P98160	PGBM_HUMAN	C	1919	ENSP00000363827:R1919C	ENSP00000363827:R1919C	R	-	1	0	HSPG2	22054702	1.000000	0.71417	1.000000	0.80357	0.027000	0.11550	2.974000	0.49272	2.399000	0.81585	0.462000	0.41574	CGC	G|0.994;A|0.006	0.006	strong		0.687	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
MYO1G	64005	hgsc.bcm.edu	37	7	45005249	45005249	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:45005249C>T	ENST00000258787.7	-	17	2504	c.2368G>A	c.(2368-2370)Gca>Aca	p.A790T		NM_033054.2	NP_149043.2	B0I1T2	MYO1G_HUMAN	myosin IG	790						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|skin(4)	28						CAGAAGAGTGCGTGGCAGGTG	0.617																																					p.A790T		Atlas-SNP	.											.	MYO1G	86	.	0			c.G2368A						PASS	.						75.0	72.0	73.0					7																	45005249		2203	4300	6503	SO:0001583	missense	64005	exon17			AGAGTGCGTGGCA	AF380932	CCDS34629.1	7p13-p11.2	2011-09-27			ENSG00000136286	ENSG00000136286		"""Myosins / Myosin superfamily : Class I"""	13880	protein-coding gene	gene with protein product	"""minor histocompatibility antigen HA-2"""	600642					Standard	NM_033054		Approved	HA-2	uc003tmh.2	B0I1T2	OTTHUMG00000155821	ENST00000258787.7:c.2368G>A	7.37:g.45005249C>T	ENSP00000258787:p.Ala790Thr	61.0	0.0	0		97.0	40.0	0.412371	NM_033054	Q8TEI9|Q8TES2|Q96BE2|Q96RI5|Q96RI6	Missense_Mutation	SNP	ENST00000258787.7	37	CCDS34629.1	.	.	.	.	.	.	.	.	.	.	C	0.298	-0.975870	0.02215	.	.	ENSG00000136286	ENST00000258787	D	0.86956	-2.19	4.37	1.42	0.22433	.	0.867457	0.09344	U	0.815042	T	0.73156	0.3551	N	0.20986	0.625	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.54397	-0.8300	10	0.13470	T	0.59	.	2.1804	0.03873	0.1374:0.4415:0.2463:0.1748	.	790	B0I1T2	MYO1G_HUMAN	T	790	ENSP00000258787:A790T	ENSP00000258787:A790T	A	-	1	0	MYO1G	44971774	0.000000	0.05858	0.000000	0.03702	0.383000	0.30230	-0.095000	0.11077	0.042000	0.15717	0.462000	0.41574	GCA	.	.	none		0.617	MYO1G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341832.2		
WNT9B	7484	hgsc.bcm.edu	37	17	44949945	44949945	+	Missense_Mutation	SNP	A	A	G	rs118185468	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:44949945A>G	ENST00000290015.2	+	2	193	c.140A>G	c.(139-141)cAg>cGg	p.Q47R	WNT9B_ENST00000393461.2_Missense_Mutation_p.Q47R	NM_003396.1	NP_003387.1	O14905	WNT9B_HUMAN	wingless-type MMTV integration site family, member 9B	47					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to retinoic acid (GO:0071300)|cellular response to starvation (GO:0009267)|collecting duct development (GO:0072044)|cornea development in camera-type eye (GO:0061303)|embryonic cranial skeleton morphogenesis (GO:0048701)|establishment of planar polarity involved in nephron morphogenesis (GO:0072046)|in utero embryonic development (GO:0001701)|kidney rudiment formation (GO:0072003)|male genitalia development (GO:0030539)|mesenchymal stem cell maintenance involved in nephron morphogenesis (GO:0072038)|mesonephric duct formation (GO:0072181)|metanephric tubule formation (GO:0072174)|multicellular organismal development (GO:0007275)|neuron differentiation (GO:0030182)|palate development (GO:0060021)|positive regulation of catalytic activity (GO:0043085)|regulation of asymmetric cell division (GO:0009786)|regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003339)|regulation of protein phosphorylation (GO:0001932)|regulation of tube size (GO:0035150)|response to retinoic acid (GO:0032526)|uterus morphogenesis (GO:0061038)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			large_intestine(2)|lung(8)	10			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GCCCCGGCACAGGGCGGGGCC	0.687													A|||	17	0.00339457	0.0	0.0	5008	,	,		13354	0.0		0.006	False		,,,				2504	0.0112				p.Q47R		Atlas-SNP	.											.	WNT9B	37	.	0			c.A140G						PASS	.	A	ARG/GLN	5,4395		0,5,2195	37.0	43.0	41.0		140	4.5	0.1	17	dbSNP_133	41	52,8536		1,50,4243	no	missense	WNT9B	NM_003396.1	43	1,55,6438	GG,GA,AA		0.6055,0.1136,0.4389	benign	47/358	44949945	57,12931	2200	4294	6494	SO:0001583	missense	7484	exon2			CGGCACAGGGCGG	AF028703	CCDS11506.1	17q21	2008-01-07	2003-03-11	2003-03-14		ENSG00000158955		"""Wingless-type MMTV integration sites"""	12779	protein-coding gene	gene with protein product		602864	"""wingless-type MMTV integration site family, member 15"""	WNT15		9441749, 11713592	Standard	NM_003396		Approved	WNT14B	uc002ikw.1	O14905		ENST00000290015.2:c.140A>G	17.37:g.44949945A>G	ENSP00000290015:p.Gln47Arg	115.0	0.0	0		93.0	49.0	0.526882	NM_003396	Q6UXT4|Q96Q09	Missense_Mutation	SNP	ENST00000290015.2	37	CCDS11506.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	7.343	0.621314	0.14193	0.001136	0.006055	ENSG00000158955	ENST00000376843;ENST00000393461;ENST00000290015	T;T	0.78364	-1.17;-0.95	4.48	4.48	0.54585	.	0.507715	0.20964	N	0.082512	T	0.62974	0.2472	L	0.54323	1.7	0.29457	N	0.858057	B;B	0.22604	0.039;0.072	B;B	0.18871	0.011;0.023	T	0.58020	-0.7710	10	0.15952	T	0.53	.	11.5157	0.50520	0.8506:0.1494:0.0:0.0	.	47;47	E7EPC3;O14905	.;WNT9B_HUMAN	R	53;47;47	ENSP00000377105:Q47R;ENSP00000290015:Q47R	ENSP00000290015:Q47R	Q	+	2	0	WNT9B	42304944	.	.	0.080000	0.20451	0.128000	0.20619	.	.	2.013000	0.59113	0.374000	0.22700	CAG	A|0.997;G|0.003	0.003	strong		0.687	WNT9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440433.1	NM_003396	
NCOA6	23054	hgsc.bcm.edu	37	20	33342629	33342629	+	Missense_Mutation	SNP	G	G	C	rs148359628	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33342629G>C	ENST00000374796.2	-	9	4141	c.1571C>G	c.(1570-1572)gCc>gGc	p.A524G	NCOA6_ENST00000359003.2_Missense_Mutation_p.A524G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	524	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GTTCGGATTGGCCTGTCCTGC	0.478																																					p.A524G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1571G						PASS	.	G	GLY/ALA,GLY/ALA	0,4406		0,0,2203	115.0	106.0	109.0		1571,1571	6.0	1.0	20	dbSNP_134	109	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	NCOA6	NM_001242539.1,NM_014071.3	60,60	0,6,6497	CC,CG,GG		0.0698,0.0,0.0461	benign,benign	524/1071,524/2064	33342629	6,13000	2203	4300	6503	SO:0001583	missense	23054	exon8			GGATTGGCCTGTC	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1571C>G	20.37:g.33342629G>C	ENSP00000363929:p.Ala524Gly	152.0	0.0	0		144.0	76.0	0.527778	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.74	2.626084	0.46840	0.0	6.98E-4	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.25414	1.8;1.8	5.97	5.97	0.96955	.	0.081814	0.51477	D	0.000086	T	0.16685	0.0401	N	0.12182	0.205	0.48901	D	0.999723	B	0.09022	0.002	B	0.10450	0.005	T	0.08249	-1.0731	10	0.27082	T	0.32	-7.7298	15.8466	0.78899	0.0:0.1349:0.865:0.0	.	524	Q14686	NCOA6_HUMAN	G	524	ENSP00000363929:A524G;ENSP00000351894:A524G	ENSP00000351894:A524G	A	-	2	0	NCOA6	32806290	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	3.652000	0.54439	2.835000	0.97688	0.591000	0.81541	GCC	G|0.999;C|0.001	0.001	strong		0.478	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
Unknown	0	hgsc.bcm.edu	37	13	103410912	103410912	+	IGR	SNP	G	G	A	rs548678555		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:103410912G>A								LINC00283 (13338 upstream) : TEX30 (7427 downstream)																							TGCTTTTGGGGCAACTGTCTT	0.279																																					p.C82C		Atlas-SNP	.											.	.	.	.	0			c.C246T						PASS	.																																			SO:0001628	intergenic_variant	643677	exon2			TTTGGGGCAACTG																													13.37:g.103410912G>A		65.0	0.0	0		105.0	46.0	0.438095	NM_001146197		Silent	SNP		37																																																																																				.	.	none	0	0.279								
CCDC129	223075	hgsc.bcm.edu	37	7	31692409	31692409	+	Missense_Mutation	SNP	C	C	G	rs34177136	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:31692409C>G	ENST00000407970.3	+	14	3139	c.3101C>G	c.(3100-3102)cCt>cGt	p.P1034R	CCDC129_ENST00000409210.1_Missense_Mutation_p.P942R|CCDC129_ENST00000451887.2_Intron|CCDC129_ENST00000319386.3_Missense_Mutation_p.P886R	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	1034								p.P1034H(1)|p.P886H(1)		cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						TCAAATTGTCCTGTTGGAGAA	0.453													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		21006	0.0		0.003	False		,,,				2504	0.0				p.P1044R		Atlas-SNP	.											.	CCDC129	127	.	2	Substitution - Missense(2)	lung(2)	c.C3131G						PASS	.	C	ARG/PRO	1,4405	2.1+/-5.4	0,1,2202	107.0	98.0	101.0		3101	-0.3	0.0	7	dbSNP_126	101	41,8559	27.4+/-76.7	0,41,4259	yes	missense	CCDC129	NM_194300.2	103	0,42,6461	GG,GC,CC		0.4767,0.0227,0.3229	probably-damaging	1034/1045	31692409	42,12964	2203	4300	6503	SO:0001583	missense	223075	exon15			ATTGTCCTGTTGG	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.3101C>G	7.37:g.31692409C>G	ENSP00000384416:p.Pro1034Arg	216.0	0.0	0		275.0	140.0	0.509091	NM_001257967	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	9.917	1.211175	0.22289	2.27E-4	0.004767	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000538406;ENST00000409210	T;T;T	0.17691	2.26;2.53;2.27	3.96	-0.303	0.12792	.	1.098150	0.07119	N	0.843657	T	0.11836	0.0288	M	0.63428	1.95	0.09310	N	1	P;P;P	0.43701	0.815;0.815;0.815	B;B;B	0.39935	0.314;0.314;0.314	T	0.19549	-1.0302	10	0.42905	T	0.14	.	3.6334	0.08140	0.1791:0.504:0.0:0.3169	rs34177136	1044;1034;886	F5H2J8;Q6ZRS4;Q6ZRS4-2	.;CC129_HUMAN;.	R	886;1034;1044;942	ENSP00000313062:P886R;ENSP00000384416:P1034R;ENSP00000387214:P942R	ENSP00000313062:P886R	P	+	2	0	CCDC129	31658934	0.000000	0.05858	0.001000	0.08648	0.068000	0.16541	-0.005000	0.12855	-0.187000	0.10516	-0.793000	0.03317	CCT	C|0.997;G|0.003	0.003	strong		0.453	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
LBH	81606	hgsc.bcm.edu	37	2	30480466	30480466	+	Silent	SNP	G	G	A	rs372905950		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:30480466G>A	ENST00000395323.3	+	3	505	c.297G>A	c.(295-297)gcG>gcA	p.A99A	LBH_ENST00000407930.2_Silent_p.A82A|LBH_ENST00000401506.1_Silent_p.A105A|LBH_ENST00000406087.1_3'UTR|LBH_ENST00000467242.1_3'UTR|LBH_ENST00000404397.1_Intron	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	99					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					AAGAGACAGCGAAAGAAAATA	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.001				p.A99A		Atlas-SNP	.											.	LBH	14	.	0			c.G297A						PASS	.	G		0,4406		0,0,2203	43.0	45.0	44.0		297	2.0	0.1	2		44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	LBH	NM_030915.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		99/106	30480466	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	81606	exon3			GACAGCGAAAGAA	AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"""limb bud and heart development homolog (mouse)"""			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.297G>A	2.37:g.30480466G>A		68.0	0.0	0		69.0	34.0	0.492754	NM_030915	B2RBC2|Q9H0Q1	Silent	SNP	ENST00000395323.3	37	CCDS33173.1																																																																																			.	.	weak		0.542	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915	
DDC	1644	hgsc.bcm.edu	37	7	50611751	50611751	+	Silent	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:50611751C>T	ENST00000444124.2	-	2	233	c.33G>A	c.(31-33)aaG>aaA	p.K11K	DDC_ENST00000431062.1_Silent_p.K11K|DDC_ENST00000357936.5_Silent_p.K11K|DDC_ENST00000426377.1_Silent_p.K11K|AC018705.5_ENST00000454521.1_RNA|DDC_ENST00000380984.4_Silent_p.K11K	NM_001082971.1	NP_001076440	P20711	DDC_HUMAN	dopa decarboxylase (aromatic L-amino acid decarboxylase)	11					catecholamine biosynthetic process (GO:0042423)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to alkaloid (GO:0071312)|cellular response to drug (GO:0035690)|cellular response to growth factor stimulus (GO:0071363)|circadian rhythm (GO:0007623)|dopamine biosynthetic process (GO:0042416)|indolalkylamine biosynthetic process (GO:0046219)|isoquinoline alkaloid metabolic process (GO:0033076)|multicellular organismal aging (GO:0010259)|phytoalexin metabolic process (GO:0052314)|response to pyrethroid (GO:0046684)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)|synaptic vesicle amine transport (GO:0015842)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|neuronal cell body (GO:0043025)|synaptic vesicle (GO:0008021)	amino acid binding (GO:0016597)|aromatic-L-amino-acid decarboxylase activity (GO:0004058)|enzyme binding (GO:0019899)|L-dopa decarboxylase activity (GO:0036468)|pyridoxal phosphate binding (GO:0030170)			breast(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(23)|ovary(4)|skin(2)|stomach(1)	40	Glioma(55;0.08)|all_neural(89;0.245)				Amantadine(DB00915)|Carbidopa(DB00190)|Cycloserine(DB00260)|Droxidopa(DB06262)|Flupentixol(DB00875)|L-DOPA(DB01235)|L-Tryptophan(DB00150)|Methyldopa(DB00968)	CCACCATCTCCTTCCCTCTCC	0.537																																					p.K11K		Atlas-SNP	.											.	DDC	100	.	0			c.G33A						PASS	.						247.0	190.0	209.0					7																	50611751		2203	4300	6503	SO:0001819	synonymous_variant	1644	exon2			CATCTCCTTCCCT		CCDS5511.1, CCDS56485.1, CCDS56486.1, CCDS56487.1, CCDS75598.1, CCDS75599.1	7p12.1	2012-08-30			ENSG00000132437	ENSG00000132437	4.1.1.28		2719	protein-coding gene	gene with protein product		107930				1612608	Standard	NM_001082971		Approved	AADC	uc003tpf.4	P20711	OTTHUMG00000023353	ENST00000444124.2:c.33G>A	7.37:g.50611751C>T		179.0	0.0	0		192.0	95.0	0.494792	NM_001082971	C9IYA0|E7ER62|E7EU95|Q16723|Q5W5T9|Q75MJ6	Silent	SNP	ENST00000444124.2	37	CCDS5511.1																																																																																			.	.	none		0.537	DDC-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342593.1		
NCOA6	23054	hgsc.bcm.edu	37	20	33342623	33342623	+	Missense_Mutation	SNP	G	G	A	rs144477396	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:33342623G>A	ENST00000374796.2	-	9	4147	c.1577C>T	c.(1576-1578)cCg>cTg	p.P526L	NCOA6_ENST00000359003.2_Missense_Mutation_p.P526L			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	526	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						CATAAAGTTCGGATTGGCCTG	0.493																																					p.P526L		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1577T						PASS	.	G	LEU/PRO,LEU/PRO	0,4406		0,0,2203	117.0	107.0	110.0		1577,1577	3.8	1.0	20	dbSNP_134	110	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	NCOA6	NM_001242539.1,NM_014071.3	98,98	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	possibly-damaging,possibly-damaging	526/1071,526/2064	33342623	6,13000	2203	4300	6503	SO:0001583	missense	23054	exon8			AAGTTCGGATTGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1577C>T	20.37:g.33342623G>A	ENSP00000363929:p.Pro526Leu	162.0	0.0	0		152.0	80.0	0.526316	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Missense_Mutation	SNP	ENST00000374796.2	37	CCDS13241.1	.	.	.	.	.	.	.	.	.	.	G	14.37	2.514740	0.44763	0.0	6.98E-4	ENSG00000198646	ENST00000374796;ENST00000359003	T;T	0.23552	1.9;1.9	5.97	3.84	0.44239	.	0.486738	0.20890	N	0.083855	T	0.09598	0.0236	N	0.08118	0	0.46167	D	0.998908	P	0.45078	0.85	B	0.25614	0.062	T	0.20940	-1.0260	10	0.22706	T	0.39	-0.5866	13.5218	0.61572	0.0:0.0:0.6067:0.3933	.	526	Q14686	NCOA6_HUMAN	L	526	ENSP00000363929:P526L;ENSP00000351894:P526L	ENSP00000351894:P526L	P	-	2	0	NCOA6	32806284	1.000000	0.71417	1.000000	0.80357	0.922000	0.55478	1.538000	0.36094	1.470000	0.48102	0.591000	0.81541	CCG	G|0.999;A|0.001	0.001	strong		0.493	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
C1orf141	400757	hgsc.bcm.edu	37	1	67561087	67561087	+	Missense_Mutation	SNP	A	A	C	rs145227724		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:67561087A>C	ENST00000371007.2	-	7	543	c.434T>G	c.(433-435)aTg>aGg	p.M145R	C1orf141_ENST00000544837.1_Missense_Mutation_p.M145R|C1orf141_ENST00000371006.1_Missense_Mutation_p.M145R	NM_001276351.1	NP_001263280.1	Q5JVX7	CA141_HUMAN	chromosome 1 open reading frame 141	145										NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|skin(1)	18						AAAATCGTTCATCTGTGGAGA	0.368													A|||	1	0.000199681	0.0	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.001				p.M145R		Atlas-SNP	.											.	C1orf141	58	.	0			c.T434G						PASS	.	A	ARG/MET	0,4404		0,0,2202	47.0	44.0	45.0		434	-4.0	0.0	1	dbSNP_134	45	17,8579		0,17,4281	yes	missense	C1orf141	NM_001013674.1	91	0,17,6483	CC,CA,AA		0.1978,0.0,0.1308	possibly-damaging	145/401	67561087	17,12983	2202	4298	6500	SO:0001583	missense	400757	exon7			TCGTTCATCTGTG	BC090886	CCDS30745.1, CCDS72804.1	1p31.2	2012-07-23			ENSG00000203963	ENSG00000203963			32044	protein-coding gene	gene with protein product							Standard	NM_001276351		Approved		uc001ddm.2	Q5JVX7	OTTHUMG00000009406	ENST00000371007.2:c.434T>G	1.37:g.67561087A>C	ENSP00000360046:p.Met145Arg	75.0	0.0	0		93.0	41.0	0.44086	NM_001276351	Q0P5P5|Q5JVX5	Missense_Mutation	SNP	ENST00000371007.2	37	CCDS30745.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073770	0.36566	0.0	0.001978	ENSG00000203963	ENST00000371007;ENST00000371006;ENST00000544837;ENST00000371005;ENST00000448166	T;T;T	0.29397	1.57;1.57;1.57	5.76	-3.98	0.04082	.	0.801389	0.10895	N	0.622204	T	0.06962	0.0177	N	0.19112	0.55	0.09310	N	1	D	0.54601	0.967	P	0.52217	0.693	T	0.07829	-1.0752	10	0.10902	T	0.67	1.1288	2.2939	0.04145	0.3772:0.1336:0.3596:0.1296	.	145	Q5JVX7	CA141_HUMAN	R	145;145;145;216;216	ENSP00000360046:M145R;ENSP00000360045:M145R;ENSP00000444018:M145R	ENSP00000360044:M216R	M	-	2	0	C1orf141	67333675	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.277000	0.08502	-0.490000	0.06707	-0.263000	0.10527	ATG	A|0.999;C|0.001	0.001	strong		0.368	C1orf141-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026096.2	NM_001013674	
ZCCHC6	79670	hgsc.bcm.edu	37	9	88940359	88940359	+	Missense_Mutation	SNP	C	C	T	rs41310053	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:88940359C>T	ENST00000375963.3	-	12	1851	c.1679G>A	c.(1678-1680)cGg>cAg	p.R560Q	ZCCHC6_ENST00000375961.2_Missense_Mutation_p.R560Q|ZCCHC6_ENST00000375960.2_Missense_Mutation_p.R437Q|ZCCHC6_ENST00000277141.6_5'UTR|ZCCHC6_ENST00000469004.1_5'Flank	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	560	PAP-associated 1.				RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						AGCATAGAACCGCAGCAATTC	0.398													C|||	10	0.00199681	0.0	0.0014	5008	,	,		17480	0.0		0.0089	False		,,,				2504	0.0				p.R560Q		Atlas-SNP	.											.	ZCCHC6	105	.	0			c.G1679A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	84.0	82.0	83.0		1679,1310,1679	5.2	1.0	9	dbSNP_127	83	48,8552	30.7+/-82.3	0,48,4252	yes	missense,missense,missense	ZCCHC6	NM_001185059.1,NM_001185074.1,NM_024617.3	43,43,43	0,50,6453	TT,TC,CC		0.5581,0.0454,0.3844	probably-damaging,probably-damaging,probably-damaging	560/1496,437/1260,560/1496	88940359	50,12956	2203	4300	6503	SO:0001583	missense	79670	exon12			TAGAACCGCAGCA	AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.1679G>A	9.37:g.88940359C>T	ENSP00000365130:p.Arg560Gln	108.0	0.0	0		136.0	63.0	0.463235	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	Missense_Mutation	SNP	ENST00000375963.3	37	CCDS35057.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	28.5	4.923726	0.92319	4.54E-4	0.005581	ENSG00000083223	ENST00000375960;ENST00000375961;ENST00000375963	T;T;T	0.76709	-1.04;-1.04;-1.04	5.24	5.24	0.73138	PAP/25A-associated (1);	0.000000	0.85682	D	0.000000	D	0.84889	0.5572	M	0.75615	2.305	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.87244	0.2268	10	0.72032	D	0.01	-33.9822	19.0276	0.92939	0.0:1.0:0.0:0.0	rs41310053	437;560	Q5VYS8-4;Q5VYS8	.;TUT7_HUMAN	Q	437;560;560	ENSP00000365127:R437Q;ENSP00000365128:R560Q;ENSP00000365130:R560Q	ENSP00000365127:R437Q	R	-	2	0	ZCCHC6	88130179	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.420000	0.66441	2.745000	0.94114	0.650000	0.86243	CGG	C|0.997;T|0.003	0.003	strong		0.398	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
VDAC1	7416	hgsc.bcm.edu	37	5	133328003	133328003	+	Silent	SNP	A	A	G	rs142141751	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:133328003A>G	ENST00000265333.3	-	3	355	c.111T>C	c.(109-111)aaT>aaC	p.N37N	VDAC1_ENST00000395044.3_Silent_p.N37N|VDAC1_ENST00000466080.1_5'UTR|VDAC1_ENST00000395047.2_Silent_p.N37N	NM_003374.2	NP_003365.1	P21796	VDAC1_HUMAN	voltage-dependent anion channel 1	37					anion transport (GO:0006820)|apoptotic process (GO:0006915)|behavioral fear response (GO:0001662)|epithelial cell differentiation (GO:0030855)|learning (GO:0007612)|neuron-neuron synaptic transmission (GO:0007270)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|pore complex (GO:0046930)	porin activity (GO:0015288)|protein kinase binding (GO:0019901)|voltage-gated anion channel activity (GO:0008308)			endometrium(1)|large_intestine(1)|lung(1)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.00806)|Kidney(363;0.02)		Dihydroxyaluminium(DB01375)	TTACCAATCCATTCTCAGATT	0.308													A|||	2	0.000399361	0.0	0.0	5008	,	,		16993	0.0		0.002	False		,,,				2504	0.0				p.N37N	NSCLC(127;1776 1806 35523 41489 48154)	Atlas-SNP	.											.	VDAC1	17	.	0			c.T111C						PASS	.	A		5,4399	8.1+/-20.4	0,5,2197	48.0	48.0	48.0		111	4.4	1.0	5	dbSNP_134	48	25,8575	18.5+/-59.3	0,25,4275	no	coding-synonymous	VDAC1	NM_003374.2		0,30,6472	GG,GA,AA		0.2907,0.1135,0.2307		37/284	133328003	30,12974	2202	4300	6502	SO:0001819	synonymous_variant	7416	exon3			CAATCCATTCTCA		CCDS4168.1	5q31	2011-11-15			ENSG00000213585	ENSG00000213585		"""Voltage-dependent anion channels"""	12669	protein-coding gene	gene with protein product		604492				7517385	Standard	NM_003374		Approved	MGC111064, PORIN	uc003kyr.2	P21796	OTTHUMG00000129118	ENST00000265333.3:c.111T>C	5.37:g.133328003A>G		153.0	0.0	0		156.0	75.0	0.480769	NM_003374	B3KVK4|D3DQ93|Q5FVE7|Q9UIQ5|Q9UPL0	Silent	SNP	ENST00000265333.3	37	CCDS4168.1																																																																																			A|0.997;G|0.003	0.003	strong		0.308	VDAC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259208.1		
ZNF839	55778	hgsc.bcm.edu	37	14	102805556	102805556	+	Silent	SNP	C	C	T	rs199523800		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:102805556C>T	ENST00000558850.1	+	7	1925	c.1575C>T	c.(1573-1575)gcC>gcT	p.A525A	ZNF839_ENST00000442396.2_Silent_p.A641A|ZNF839_ENST00000262236.5_Silent_p.A525A|AL137229.1_ENST00000577622.1_RNA|ZNF839_ENST00000420933.2_3'UTR|ZNF839_ENST00000559185.1_Silent_p.A525A	NM_001267827.1	NP_001254756.1	A8K0R7	ZN839_HUMAN	zinc finger protein 839	525							metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	19						ATGCTTTGGCCGCTGGTGAGG	0.552													C|||	1	0.000199681	0.0	0.0	5008	,	,		19149	0.0		0.001	False		,,,				2504	0.0				p.A641A		Atlas-SNP	.											.	ZNF839	41	.	0			c.C1923T						PASS	.	C		0,3844		0,0,1922	52.0	54.0	53.0		1923	-5.2	0.0	14		53	5,8281		0,5,4138	no	coding-synonymous	ZNF839	NM_018335.3		0,5,6060	TT,TC,CC		0.0603,0.0,0.0412		641/928	102805556	5,12125	1922	4143	6065	SO:0001819	synonymous_variant	55778	exon7			TTTGGCCGCTGGT	AK093342	CCDS45164.1, CCDS58336.1	14q32.32	2010-05-06	2008-06-23	2008-06-23	ENSG00000022976	ENSG00000022976			20345	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 131"""	C14orf131			Standard	NM_018335		Approved		uc010awk.2	A8K0R7		ENST00000558850.1:c.1575C>T	14.37:g.102805556C>T		194.0	0.0	0		196.0	87.0	0.443878	NM_018335	B3KSD2|Q53FH5|Q6GPI5|Q86TU1|Q9BQ86|Q9NUU3	Silent	SNP	ENST00000558850.1	37	CCDS58336.1																																																																																			C|0.998;T|0.002	0.002	weak		0.552	ZNF839-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415492.2	NM_018335	
MDM1	56890	hgsc.bcm.edu	37	12	68708979	68708979	+	Silent	SNP	G	G	A	rs139553308	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:68708979G>A	ENST00000303145.7	-	9	1334	c.1248C>T	c.(1246-1248)atC>atT	p.I416I	MDM1_ENST00000540418.1_Silent_p.I136I|MDM1_ENST00000411698.2_Silent_p.I381I	NM_017440.4	NP_059136.2	Q8TC05	MDM1_HUMAN	Mdm1 nuclear protein homolog (mouse)	416					retina development in camera-type eye (GO:0060041)	nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(7)	33			Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.018)	GBM - Glioblastoma multiforme(7;0.000174)		GTTCTTCCACGATATTTCCTT	0.423													G|||	12	0.00239617	0.0008	0.0029	5008	,	,		18479	0.0		0.008	False		,,,				2504	0.001				p.I416I		Atlas-SNP	.											.	MDM1	74	.	0			c.C1248T						PASS	.	G	,	9,4397	15.5+/-35.6	0,9,2194	83.0	86.0	85.0		1143,1248	-2.7	0.0	12	dbSNP_134	85	99,8501	54.8+/-115.7	0,99,4201	no	coding-synonymous,coding-synonymous	MDM1	NM_001205028.1,NM_017440.4	,	0,108,6395	AA,AG,GG		1.1512,0.2043,0.8304	,	381/680,416/715	68708979	108,12898	2203	4300	6503	SO:0001819	synonymous_variant	56890	exon9			TTCCACGATATTT	AF007130	CCDS8983.1, CCDS44938.1, CCDS55841.1, CCDS55842.1	12q15	2008-04-14	2008-04-14			ENSG00000111554			29917	protein-coding gene	gene with protein product		613813	"""Mdm4, transformed 3T3 cell double minute 1, p53 binding protein (mouse)"""			8619474, 9110174	Standard	NM_017440		Approved		uc001stz.2	Q8TC05		ENST00000303145.7:c.1248C>T	12.37:g.68708979G>A		163.0	0.0	0		171.0	79.0	0.461988	NM_017440	B4DM65|E7EPQ3|O43406|Q8WTV9|Q9NR04	Silent	SNP	ENST00000303145.7	37	CCDS8983.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	MDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402402.1	NM_020128	
PTEN	5728	hgsc.bcm.edu	37	10	89690819	89690819	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:89690819T>G	ENST00000371953.3	+	4	1583	c.226T>G	c.(226-228)Tat>Gat	p.Y76D		NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	76	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.?(6)|p.R55fs*1(5)|p.Y76fs*1(4)|p.L70fs*7(4)|p.C71fs*6(2)|p.Y76del(2)|p.Y27fs*1(2)|p.H75_T78del(1)|p.F56fs*2(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TGAAAGACATTATGACACCGC	0.303		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																											p.Y76D		Atlas-SNP	.	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	phosphatase and tensin homolog gene		"""L, E, M, O"""	PTEN,NS,malignant_melanoma,-2,3	PTEN	3652	3	64	Whole gene deletion(37)|Deletion - Frameshift(18)|Unknown(6)|Deletion - In frame(3)	central_nervous_system(17)|prostate(17)|breast(6)|skin(6)|lung(5)|haematopoietic_and_lymphoid_tissue(4)|endometrium(3)|ovary(3)|stomach(1)|soft_tissue(1)|urinary_tract(1)	c.T226G						PASS	.						80.0	75.0	77.0					10																	89690819		2202	4295	6497	SO:0001583	missense	5728	exon4	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	AGACATTATGACA	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.226T>G	10.37:g.89690819T>G	ENSP00000361021:p.Tyr76Asp	162.0	0.0	0		72.0	60.0	0.833333	NM_000314	B2R904|F2YHV0|O00633|O02679|Q6ICT7	Missense_Mutation	SNP	ENST00000371953.3	37	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.697959	0.88830	.	.	ENSG00000171862	ENST00000371953	D	0.98585	-5.01	5.62	5.62	0.85841	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99102	0.9691	M	0.89904	3.07	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99556	1.0967	9	.	.	.	-12.1246	16.1135	0.81278	0.0:0.0:0.0:1.0	.	76	P60484	PTEN_HUMAN	D	76	ENSP00000361021:Y76D	.	Y	+	1	0	PTEN	89680799	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.586000	0.82596	2.267000	0.75376	0.383000	0.25322	TAT	.	.	none		0.303	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
SLC5A5	6528	hgsc.bcm.edu	37	19	17999239	17999239	+	Silent	SNP	C	C	T	rs45602038	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17999239C>T	ENST00000222248.3	+	13	1973	c.1626C>T	c.(1624-1626)tgC>tgT	p.C542C		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	542					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						CTGTGCTGTGCGGAGCCCTCA	0.587													C|||	66	0.0131789	0.0	0.0274	5008	,	,		15316	0.001		0.0239	False		,,,				2504	0.0225				p.C542C	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C1626T						PASS	.	C		23,4383	29.0+/-57.7	0,23,2180	117.0	102.0	107.0		1626	-4.6	0.7	19	dbSNP_127	107	252,8348	99.5+/-161.0	4,244,4052	no	coding-synonymous	SLC5A5	NM_000453.2		4,267,6232	TT,TC,CC		2.9302,0.522,2.1144		542/644	17999239	275,12731	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon13			GCTGTGCGGAGCC		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.1626C>T	19.37:g.17999239C>T		68.0	0.0	0		87.0	36.0	0.413793	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																			C|0.979;T|0.021	0.021	strong		0.587	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
SMYD4	114826	hgsc.bcm.edu	37	17	1704297	1704297	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:1704297T>C	ENST00000305513.7	-	5	558	c.391A>G	c.(391-393)Aga>Gga	p.R131G		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	131			R -> I (in dbSNP:rs7224496). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						GTCTGTGCTCTGTTAATGTCT	0.428																																					p.R131G		Atlas-SNP	.											.	SMYD4	50	.	0			c.A391G						PASS	.						131.0	132.0	132.0					17																	1704297		2203	4300	6503	SO:0001583	missense	114826	exon5			GTGCTCTGTTAAT	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.391A>G	17.37:g.1704297T>C	ENSP00000304360:p.Arg131Gly	97.0	0.0	0		109.0	48.0	0.440367	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	T	12.27	1.887796	0.33348	.	.	ENSG00000186532	ENST00000305513	T	0.19532	2.14	5.98	4.88	0.63580	Tetratricopeptide-like helical (1);	0.518027	0.24193	N	0.040700	T	0.45935	0.1367	M	0.90705	3.14	0.35409	D	0.792262	D	0.63880	0.993	P	0.62184	0.899	T	0.59762	-0.7393	10	0.34782	T	0.22	-5.7323	7.6552	0.28371	0.0:0.0712:0.1398:0.7889	.	131	Q8IYR2	SMYD4_HUMAN	G	131	ENSP00000304360:R131G	ENSP00000304360:R131G	R	-	1	2	SMYD4	1651047	0.997000	0.39634	0.826000	0.32828	0.064000	0.16182	3.040000	0.49799	1.038000	0.40049	0.528000	0.53228	AGA	.	.	none		0.428	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
STK10	6793	hgsc.bcm.edu	37	5	171523512	171523512	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:171523512G>A	ENST00000176763.5	-	8	1266	c.923C>T	c.(922-924)gCt>gTt	p.A308V	STK10_ENST00000517775.1_5'Flank	NM_005990.3	NP_005981.3	O94804	STK10_HUMAN	serine/threonine kinase 10	308					cell cycle (GO:0007049)|lymphocyte aggregation (GO:0071593)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of lymphocyte migration (GO:2000401)|signal transduction by phosphorylation (GO:0023014)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|polo kinase kinase activity (GO:0042801)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(6)|pancreas(1)|prostate(1)|testis(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	47	Renal(175;0.000159)|Lung NSC(126;0.0056)|all_lung(126;0.0094)	Medulloblastoma(196;0.00868)|all_neural(177;0.026)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CTTGGCCTCAGCCACCAGCTC	0.622																																					p.A308V		Atlas-SNP	.											.	STK10	100	.	0			c.C923T						PASS	.						109.0	104.0	106.0					5																	171523512		2203	4300	6503	SO:0001583	missense	6793	exon8			GCCTCAGCCACCA	AB015718	CCDS34290.1	5q35.1	2008-07-18			ENSG00000072786	ENSG00000072786			11388	protein-coding gene	gene with protein product		603919				10199912	Standard	NM_005990		Approved	LOK, PRO2729	uc003mbo.1	O94804	OTTHUMG00000163265	ENST00000176763.5:c.923C>T	5.37:g.171523512G>A	ENSP00000176763:p.Ala308Val	47.0	0.0	0		62.0	7.0	0.112903	NM_005990	A6ND35|B2R8F5|B3KMY1|Q6NSK0|Q9UIW4	Missense_Mutation	SNP	ENST00000176763.5	37	CCDS34290.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.433688	0.83776	.	.	ENSG00000072786	ENST00000176763;ENST00000545839	T	0.69435	-0.4	4.96	4.96	0.65561	Protein kinase-like domain (1);	0.061568	0.64402	D	0.000005	T	0.73636	0.3612	M	0.74647	2.275	0.80722	D	1	D	0.56746	0.977	P	0.49922	0.626	T	0.76424	-0.2964	10	0.45353	T	0.12	.	15.7705	0.78164	0.0:0.0:1.0:0.0	.	308	O94804	STK10_HUMAN	V	308	ENSP00000176763:A308V	ENSP00000176763:A308V	A	-	2	0	STK10	171456117	1.000000	0.71417	0.947000	0.38551	0.941000	0.58515	9.834000	0.99428	2.320000	0.78422	0.485000	0.47835	GCT	.	.	none		0.622	STK10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372374.2	NM_005990	
ST14	6768	hgsc.bcm.edu	37	11	130079574	130079574	+	Silent	SNP	C	C	T	rs116956726	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:130079574C>T	ENST00000278742.5	+	19	2842	c.2424C>T	c.(2422-2424)ccC>ccT	p.P808P		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	808	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CCGGGGGACCCCTGTCCAGCG	0.716													C|||	36	0.0071885	0.0	0.0101	5008	,	,		12333	0.0		0.0159	False		,,,				2504	0.0133				p.P808P		Atlas-SNP	.											.	ST14	82	.	0			c.C2424T						PASS	.	C		13,4389	17.9+/-39.9	0,13,2188	41.0	43.0	42.0		2424	-4.3	1.0	11	dbSNP_132	42	108,8486	56.4+/-117.6	0,108,4189	no	coding-synonymous	ST14	NM_021978.3		0,121,6377	TT,TC,CC		1.2567,0.2953,0.9311		808/856	130079574	121,12875	2201	4297	6498	SO:0001819	synonymous_variant	6768	exon19			GGGACCCCTGTCC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.2424C>T	11.37:g.130079574C>T		41.0	0.0	0		44.0	23.0	0.522727	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Silent	SNP	ENST00000278742.5	37	CCDS8487.1																																																																																			C|0.993;T|0.007	0.007	strong		0.716	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
EGFR	1956	hgsc.bcm.edu	37	7	55224507	55224507	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:55224507A>C	ENST00000275493.2	+	10	1366	c.1189A>C	c.(1189-1191)Acc>Ccc	p.T397P	EGFR_ENST00000344576.2_Missense_Mutation_p.T397P|EGFR_ENST00000442591.1_Missense_Mutation_p.T397P|EGFR_ENST00000420316.2_Missense_Mutation_p.T397P|EGFR_ENST00000454757.2_Missense_Mutation_p.T344P|EGFR_ENST00000455089.1_Missense_Mutation_p.T352P|EGFR_ENST00000342916.3_Missense_Mutation_p.T397P	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	397					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TATTCTGAAAACCGTAAAGGA	0.393		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																											p.T397P		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	EGFR_ENST00000344576,NS,malignant_melanoma,0,2	EGFR	20426	2	0			c.A1189C						PASS	.						94.0	90.0	92.0					7																	55224507		2203	4300	6503	SO:0001583	missense	1956	exon10	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	CTGAAAACCGTAA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1189A>C	7.37:g.55224507A>C	ENSP00000275493:p.Thr397Pro	174.0	0.0	0		177.0	78.0	0.440678	NM_201283	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	.	.	.	.	.	.	.	.	.	.	A	16.99	3.274643	0.59649	.	.	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000420316;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89	5.95	5.95	0.96441	EGF receptor, L domain (1);	0.045464	0.85682	D	0.000000	T	0.69611	0.3130	M	0.91300	3.195	0.58432	D	0.999999	D;D;D;D;D	0.89917	1.0;0.998;1.0;0.997;0.999	D;D;D;D;D	0.87578	0.992;0.982;0.989;0.97;0.998	T	0.76263	-0.3023	10	0.87932	D	0	.	10.478	0.44676	0.855:0.0:0.0:0.145	.	352;397;397;397;397	Q504U8;P00533;P00533-3;P00533-4;P00533-2	.;EGFR_HUMAN;.;.;.	P	352;397;267;397;397;397;397;344;191	ENSP00000415559:T352P;ENSP00000342376:T397P;ENSP00000345973:T397P;ENSP00000413843:T397P;ENSP00000275493:T397P;ENSP00000410031:T397P;ENSP00000395243:T344P	ENSP00000275493:T397P	T	+	1	0	EGFR	55192001	1.000000	0.71417	0.591000	0.28745	0.427000	0.31564	6.996000	0.76263	2.279000	0.76181	0.533000	0.62120	ACC	.	.	none		0.393	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
RPL32	6161	hgsc.bcm.edu	37	3	12877704	12877704	+	Silent	SNP	G	G	A	rs6497	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr3:12877704G>A	ENST00000429711.2	-	4	396	c.297C>T	c.(295-297)atC>atT	p.I99I	RPL32_ENST00000273223.6_Silent_p.I117I|RPL32_ENST00000435983.1_Silent_p.I99I|RPL32_ENST00000396953.2_Silent_p.I99I|RPL32_ENST00000396957.1_Silent_p.I99I	NM_000994.3	NP_000985.1	P62910	RL32_HUMAN	ribosomal protein L32	99					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)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						CATTGTGAGCGATCTCGGCAC	0.517													G|||	119	0.023762	0.0461	0.0072	5008	,	,		20645	0.0109		0.0249	False		,,,				2504	0.0174				p.I99I		Atlas-SNP	.											RPL32,NS,carcinoma,0,1	RPL32	11	1	0			c.C297T						scavenged	.	G	,,	183,4223	113.8+/-151.8	1,181,2021	67.0	58.0	61.0		297,297,297	-1.0	1.0	3	dbSNP_52	61	243,8357	93.8+/-155.7	5,233,4062	no	coding-synonymous,coding-synonymous,coding-synonymous	RPL32	NM_000994.3,NM_001007073.1,NM_001007074.1	,,	6,414,6083	AA,AG,GG		2.8256,4.1534,3.2754	,,	99/136,99/136,99/136	12877704	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	6161	exon4			GTGAGCGATCTCG	CA436299, CF124158, CR608027	CCDS2614.1	3q13.3-q21	2011-04-06			ENSG00000144713	ENSG00000144713		"""L ribosomal proteins"""	10336	protein-coding gene	gene with protein product						9284913	Standard	NM_001007073		Approved	L32	uc003bxl.3	P62910	OTTHUMG00000129804	ENST00000429711.2:c.297C>T	3.37:g.12877704G>A		8.0	0.0	0		12.0	3.0	0.25	NM_001007073	B2R4Q3|P02433	Silent	SNP	ENST00000429711.2	37	CCDS2614.1																																																																																			G|0.971;A|0.029	0.029	strong		0.517	RPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252032.2	NM_000994	
IL27RA	9466	hgsc.bcm.edu	37	19	14162740	14162740	+	Silent	SNP	A	A	G	rs148749814	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:14162740A>G	ENST00000263379.2	+	13	1796	c.1671A>G	c.(1669-1671)aaA>aaG	p.K557K		NM_004843.3	NP_004834.1	Q6UWB1	I27RA_HUMAN	interleukin 27 receptor, alpha	557					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of T-helper 1 type immune response (GO:0002827)|regulation of isotype switching to IgG isotypes (GO:0048302)	integral component of plasma membrane (GO:0005887)	interleukin-27 receptor activity (GO:0045509)|transmembrane signaling receptor activity (GO:0004888)			breast(3)|endometrium(3)|kidney(2)|large_intestine(8)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	26						TCTGGGAGAAAGTTCCTGATC	0.622													a|||	14	0.00279553	0.0	0.0	5008	,	,		13386	0.001		0.001	False		,,,				2504	0.0123				p.K557K	Colon(164;1849 1896 4443 37792 47834)	Atlas-SNP	.											.	IL27RA	56	.	0			c.A1671G						PASS	.	A		0,4402		0,0,2201	32.0	29.0	30.0		1671	-5.4	0.1	19	dbSNP_134	30	8,8582		0,8,4287	no	coding-synonymous	IL27RA	NM_004843.2		0,8,6488	GG,GA,AA		0.0931,0.0,0.0616		557/637	14162740	8,12984	2201	4295	6496	SO:0001819	synonymous_variant	9466	exon13			GGAGAAAGTTCCT	AF053004	CCDS12303.1	19p13.11	2013-02-11				ENSG00000104998		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	17290	protein-coding gene	gene with protein product	"""T-cell cytokine receptor type 1"""	605350				9600072, 11057672	Standard	NM_004843		Approved	WSX-1, TCCR, CRL1, WSX1, zcytor1, IL-27R	uc002mxx.4	Q6UWB1		ENST00000263379.2:c.1671A>G	19.37:g.14162740A>G		181.0	0.0	0		182.0	91.0	0.5	NM_004843	A0N0L1|O60624	Silent	SNP	ENST00000263379.2	37	CCDS12303.1																																																																																			A|0.999;G|0.001	0.001	strong		0.622	IL27RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458539.1	NM_004843	
AUTS2	26053	hgsc.bcm.edu	37	7	70239034	70239034	+	Silent	SNP	C	C	T	rs139965676		TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:70239034C>T	ENST00000342771.4	+	12	2172	c.1851C>T	c.(1849-1851)gtC>gtT	p.V617V	AUTS2_ENST00000406775.2_Intron	NM_015570.2	NP_056385.1	Q8WXX7	AUTS2_HUMAN	autism susceptibility candidate 2	617										breast(2)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|urinary_tract(1)	50		all_cancers(73;0.0264)|all_epithelial(88;0.0198)|Lung NSC(55;0.0599)|all_lung(88;0.093)		LUSC - Lung squamous cell carcinoma(90;0.082)|Lung(90;0.186)		CTATCGATGTCGCTGCTCGGC	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19785	0.0		0.0	False		,,,				2504	0.0				p.V617V		Atlas-SNP	.											AUTS2,NS,carcinoma,0,1	AUTS2	173	1	0			c.C1851T						PASS	.	C	,	0,4406		0,0,2203	132.0	104.0	113.0		,1851	-12.1	0.6	7	dbSNP_134	113	3,8597	3.0+/-9.4	0,3,4297	no	intron,coding-synonymous	AUTS2	NM_001127231.1,NM_015570.2	,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,	,617/1260	70239034	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	26053	exon12			CGATGTCGCTGCT	AF326917	CCDS5539.1, CCDS47601.1, CCDS47602.1	7q11.22	2014-01-06			ENSG00000158321	ENSG00000158321			14262	protein-coding gene	gene with protein product		607270				12160723	Standard	XM_005250257		Approved	KIAA0442, FBRSL2	uc003tvw.4	Q8WXX7	OTTHUMG00000023865	ENST00000342771.4:c.1851C>T	7.37:g.70239034C>T		69.0	0.0	0		96.0	45.0	0.46875	NM_015570	A4D1Y9|L7QET3|L7QF75|Q5D049|Q6PJU5|Q9Y4F2	Silent	SNP	ENST00000342771.4	37	CCDS5539.1	.	.	.	.	.	.	.	.	.	.	C	9.577	1.122506	0.20877	0.0	3.49E-4	ENSG00000158321	ENST00000443672	.	.	.	6.06	-12.1	0.00011	.	.	.	.	.	T	0.41166	0.1147	.	.	.	0.49915	D	0.999835	.	.	.	.	.	.	T	0.52268	-0.8598	4	.	.	.	-18.381	6.7154	0.23300	0.0845:0.4459:0.3111:0.1585	.	.	.	.	L	144	.	.	S	+	2	0	AUTS2	69876970	0.002000	0.14202	0.582000	0.28627	0.972000	0.66771	-1.549000	0.02182	-1.627000	0.01550	-0.768000	0.03414	TCG	C|1.000;T|0.000	0.000	weak		0.488	AUTS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251971.2		
NFKBIA	4792	hgsc.bcm.edu	37	14	35871232	35871232	+	Missense_Mutation	SNP	C	C	T	rs142970414	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr14:35871232C>T	ENST00000216797.5	-	6	1042	c.941G>A	c.(940-942)cGt>cAt	p.R314H	NFKBIA_ENST00000557140.1_Missense_Mutation_p.R271H|NFKBIA_ENST00000557389.1_Missense_Mutation_p.R224H|NFKBIA_ENST00000557100.1_5'Flank	NM_020529.2	NP_065390.1	P25963	IKBA_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, alpha	314					apoptotic process (GO:0006915)|cellular response to cold (GO:0070417)|cytoplasmic sequestering of NF-kappaB (GO:0007253)|cytoplasmic sequestering of transcription factor (GO:0042994)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|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 DNA binding (GO:0043392)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070427)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|protein import into nucleus, translocation (GO:0000060)|regulation of cell proliferation (GO:0042127)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to exogenous dsRNA (GO:0043330)|response to muramyl dipeptide (GO:0032495)|T cell receptor signaling pathway (GO:0050852)|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)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|nuclear localization sequence binding (GO:0008139)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(1)|large_intestine(2)|liver(1)	7	Breast(36;0.0484)|Hepatocellular(127;0.158)		Lung(238;9.25e-06)|LUAD - Lung adenocarcinoma(48;1.53e-05)|Epithelial(34;0.00314)|all cancers(34;0.00891)	GBM - Glioblastoma multiforme(112;0.0222)	Acetylsalicylic acid(DB00945)	TAACGTCAGACGCTGGCCTCC	0.413																																					p.R314H		Atlas-SNP	.											.	NFKBIA	28	.	0			c.G941A						PASS	.	C	HIS/ARG	1,4405		0,1,2202	90.0	96.0	94.0		941	5.9	1.0	14	dbSNP_134	94	0,8600		0,0,4300	no	missense	NFKBIA	NM_020529.2	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	314/318	35871232	1,13005	2203	4300	6503	SO:0001583	missense	4792	exon6			GTCAGACGCTGGC		CCDS9656.1	14q13	2014-09-17			ENSG00000100906	ENSG00000100906		"""Ankyrin repeat domain containing"""	7797	protein-coding gene	gene with protein product		164008		NFKBI		1829648	Standard	NM_020529		Approved	IKBA, MAD-3, IkappaBalpha	uc001wtf.4	P25963	OTTHUMG00000140220	ENST00000216797.5:c.941G>A	14.37:g.35871232C>T	ENSP00000216797:p.Arg314His	202.0	0.0	0		184.0	75.0	0.407609	NM_020529	B2R8L6	Missense_Mutation	SNP	ENST00000216797.5	37	CCDS9656.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.866682	0.51588	2.27E-4	0.0	ENSG00000100906	ENST00000216797;ENST00000557140;ENST00000557389	T;T;T	0.50001	0.76;0.82;0.97	5.91	5.91	0.95273	.	.	.	.	.	T	0.29749	0.0743	N	0.14661	0.345	0.42889	D	0.994191	B;B	0.17465	0.022;0.013	B;B	0.09377	0.004;0.002	T	0.10894	-1.0610	9	0.41790	T	0.15	-16.9643	9.1946	0.37220	0.0:0.8795:0.0:0.1205	.	271;314	G3V3I4;P25963	.;IKBA_HUMAN	H	314;271;224	ENSP00000216797:R314H;ENSP00000451257:R271H;ENSP00000450514:R224H	ENSP00000216797:R314H	R	-	2	0	NFKBIA	34940983	0.999000	0.42202	0.995000	0.50966	0.865000	0.49528	2.991000	0.49409	2.808000	0.96608	0.655000	0.94253	CGT	C|1.000;T|0.000	0.000	strong		0.413	NFKBIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276683.1	NM_020529	
DAGLA	747	hgsc.bcm.edu	37	11	61511794	61511794	+	Missense_Mutation	SNP	C	C	G	rs117050893	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:61511794C>G	ENST00000257215.5	+	20	3078	c.2962C>G	c.(2962-2964)Ctc>Gtc	p.L988V	RP11-467L20.10_ENST00000536405.1_lincRNA	NM_006133.2	NP_006124.1	Q9Y4D2	DGLA_HUMAN	diacylglycerol lipase, alpha	988					arachidonic acid metabolic process (GO:0019369)|blood coagulation (GO:0007596)|cell death (GO:0008219)|diacylglycerol catabolic process (GO:0046340)|endocannabinoid signaling pathway (GO:0071926)|neuroblast proliferation (GO:0007405)|neurotransmitter biosynthetic process (GO:0042136)|platelet activation (GO:0030168)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(2)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	43				READ - Rectum adenocarcinoma(4;0.219)		GGGCATCTCACTCTCGCCCTC	0.667													C|||	33	0.00658946	0.0	0.0331	5008	,	,		16155	0.002		0.006	False		,,,				2504	0.002				p.L988V		Atlas-SNP	.											.	DAGLA	109	.	0			c.C2962G						PASS	.	C	VAL/LEU	18,4386	24.3+/-50.5	0,18,2184	56.0	62.0	60.0		2962	2.0	0.0	11	dbSNP_132	60	38,8560	25.7+/-73.6	0,38,4261	yes	missense	DAGLA	NM_006133.2	32	0,56,6445	GG,GC,CC		0.442,0.4087,0.4307	benign	988/1043	61511794	56,12946	2202	4299	6501	SO:0001583	missense	747	exon20			ATCTCACTCTCGC	AB014559	CCDS31578.1	11q12.3	2008-03-18	2007-02-28	2007-02-28		ENSG00000134780	3.1.1.-		1165	protein-coding gene	gene with protein product	"""neural stem cell-derived dendrite regulator"""	614015	"""chromosome 11 open reading frame 11"""	C11orf11		9734811	Standard	NM_006133		Approved	KIAA0659, NSDDR, DAGLALPHA	uc001nsa.3	Q9Y4D2		ENST00000257215.5:c.2962C>G	11.37:g.61511794C>G	ENSP00000257215:p.Leu988Val	78.0	0.0	0		93.0	37.0	0.397849	NM_006133	A7E233|Q6WQJ0	Missense_Mutation	SNP	ENST00000257215.5	37	CCDS31578.1	21	0.009615384615384616	0	0.0	15	0.04143646408839779	1	0.0017482517482517483	5	0.006596306068601583	C	5.197	0.221827	0.09863	0.004087	0.00442	ENSG00000134780	ENST00000257215	T	0.25085	1.82	4.03	1.95	0.26073	.	0.158981	0.41097	D	0.000955	T	0.01905	0.0060	N	0.03608	-0.345	0.18873	N	0.999989	B	0.02656	0.0	B	0.04013	0.001	T	0.32268	-0.9913	10	0.17369	T	0.5	-26.7772	8.6434	0.33991	0.0:0.5927:0.3026:0.1048	.	988	Q9Y4D2	DGLA_HUMAN	V	988	ENSP00000257215:L988V	ENSP00000257215:L988V	L	+	1	0	DAGLA	61268370	0.954000	0.32549	0.008000	0.14137	0.636000	0.38137	1.749000	0.38319	0.815000	0.34398	0.462000	0.41574	CTC	C|0.994;G|0.006	0.006	strong		0.667	DAGLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398516.1	NM_006133	
GRIK3	2899	hgsc.bcm.edu	37	1	37356579	37356579	+	Silent	SNP	G	G	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:37356579G>T	ENST00000373091.3	-	2	250	c.234C>A	c.(232-234)acC>acA	p.T78T	GRIK3_ENST00000373093.4_Silent_p.T78T	NM_000831.3	NP_000822.2	Q13003	GRIK3_HUMAN	glutamate receptor, ionotropic, kainate 3	78					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|dendrite cytoplasm (GO:0032839)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	adenylate cyclase inhibiting G-protein coupled glutamate receptor activity (GO:0001640)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|kainate selective glutamate receptor activity (GO:0015277)			breast(4)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(27)|lung(35)|ovary(5)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	89		Myeloproliferative disorder(586;0.0258)|all_neural(195;0.169)				CATAGGTCAAGGTTGTGTTGG	0.547																																					p.T78T		Atlas-SNP	.											.	GRIK3	195	.	0			c.C234A						PASS	.						299.0	234.0	256.0					1																	37356579		2203	4300	6503	SO:0001819	synonymous_variant	2899	exon2			GGTCAAGGTTGTG	U16127	CCDS416.1	1p34.3	2012-08-29			ENSG00000163873	ENSG00000163873		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4581	protein-coding gene	gene with protein product		138243				8128318	Standard	NM_000831		Approved	GluK3, GLUR7	uc001caz.2	Q13003	OTTHUMG00000004189	ENST00000373091.3:c.234C>A	1.37:g.37356579G>T		168.0	0.0	0		222.0	105.0	0.472973	NM_000831	A9Z1Z8|B1AMS6|Q13004|Q16136	Silent	SNP	ENST00000373091.3	37	CCDS416.1																																																																																			.	.	none		0.547	GRIK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012053.1	NM_000831	
ALG2	85365	hgsc.bcm.edu	37	9	101980707	101980707	+	Silent	SNP	A	A	G	rs62562374	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr9:101980707A>G	ENST00000476832.1	-	2	821	c.760T>C	c.(760-762)Ttg>Ctg	p.L254L	ALG2_ENST00000319033.6_Silent_p.L161L	NM_033087.3	NP_149078.1	O75340	PDCD6_HUMAN	ALG2, alpha-1,3/1,6-mannosyltransferase	0					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|cellular response to heat (GO:0034605)|intracellular protein transport (GO:0006886)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|proteolysis (GO:0006508)|response to calcium ion (GO:0051592)|vascular endothelial growth factor receptor-2 signaling pathway (GO:0036324)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|calcium-dependent protein binding (GO:0048306)|protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(11)|ovary(2)|prostate(2)	22		Acute lymphoblastic leukemia(62;0.0559)				TGGGATGTCAATCTTCCACGC	0.463													A|||	8	0.00159744	0.0	0.0014	5008	,	,		22624	0.0		0.007	False		,,,				2504	0.0				p.L254L		Atlas-SNP	.											.	ALG2	37	.	0			c.T760C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	153.0	153.0	153.0		760	-2.3	0.0	9	dbSNP_129	153	48,8552	31.2+/-83.2	0,48,4252	no	coding-synonymous	ALG2	NM_033087.3		0,51,6452	GG,GA,AA		0.5581,0.0681,0.3921		254/417	101980707	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	85365	exon2			ATGTCAATCTTCC	AK027417	CCDS6739.1	9q31.1	2013-02-22	2013-02-22		ENSG00000119523	ENSG00000119523	2.4.1.132, 2.4.1.257	"""Glycosyltransferase group 1 domain containing"""	23159	protein-coding gene	gene with protein product		607905	"""asparagine-linked glycosylation 2 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 2, alpha-1,3-mannosyltransferase homolog (S. cerevisiae)"""			12684507	Standard	NR_024532		Approved	CDGIi, FLJ14511, hALPG2, NET38	uc004azf.3	Q9H553	OTTHUMG00000020355	ENST00000476832.1:c.760T>C	9.37:g.101980707A>G		185.0	0.0	0		188.0	95.0	0.505319	NM_033087	B2RD16|E7ESR3|Q2YDC2|Q5TZS0	Silent	SNP	ENST00000476832.1	37	CCDS6739.1																																																																																			A|0.998;C|0.000;G|0.002	0.002	strong		0.463	ALG2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215080.1	NM_033087	
KDM6B	23135	hgsc.bcm.edu	37	17	7750010	7750010	+	Missense_Mutation	SNP	G	G	C	rs79548905	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:7750010G>C	ENST00000448097.2	+	8	994	c.663G>C	c.(661-663)gaG>gaC	p.E221D	KDM6B_ENST00000254846.5_Missense_Mutation_p.E221D			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	221	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						CAGGGGAGGAGGGCCTCAGCC	0.647													G|||	34	0.00678914	0.0	0.0159	5008	,	,		10042	0.0		0.0199	False		,,,				2504	0.0031				p.E221D		Atlas-SNP	.											.	KDM6B	95	.	0			c.G663C						PASS	.	G	ASP/GLU	25,4381	29.9+/-59.1	0,25,2178	60.0	63.0	62.0		663	1.5	1.0	17	dbSNP_131	62	250,8350	96.6+/-158.3	3,244,4053	yes	missense	KDM6B	NM_001080424.1	45	3,269,6231	CC,CG,GG		2.907,0.5674,2.1144	benign	221/1683	7750010	275,12731	2203	4300	6503	SO:0001583	missense	23135	exon8			GGAGGAGGGCCTC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.663G>C	17.37:g.7750010G>C	ENSP00000412513:p.Glu221Asp	75.0	0.0	0		87.0	35.0	0.402299	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		23	0.010531135531135532	0	0.0	8	0.022099447513812154	0	0.0	15	0.01978891820580475	G	10.43	1.347466	0.24426	0.005674	0.02907	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.38077	1.27;1.16	4.62	1.48	0.22813	.	0.000000	0.53938	D	0.000046	T	0.09291	0.0229	N	0.08118	0	0.23293	N	0.997964	D	0.59767	0.986	P	0.57720	0.826	T	0.11665	-1.0578	10	0.14252	T	0.57	-17.4424	6.792	0.23705	0.3837:0.0:0.6162:0.0	.	221	O15054-1	.	D	221	ENSP00000254846:E221D;ENSP00000412513:E221D	ENSP00000254846:E221D	E	+	3	2	KDM6B	7690735	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.076000	0.41548	0.274000	0.22072	0.561000	0.74099	GAG	G|0.981;C|0.019	0.019	strong		0.647	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240692	39240692	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr17:39240692G>C	ENST00000391417.4	+	1	234	c.234G>C	c.(232-234)agG>agC	p.R78S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	78	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						gccaccctaggtgctgcatct	0.667																																					p.R78S		Atlas-SNP	.											KRTAP4-9_ENST00000377734,colon,carcinoma,0,2	KRTAP4-7	49	2	0			c.G234C						scavenged	.																																			SO:0001583	missense	100132476	exon1			CCCTAGGTGCTGC	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.234G>C	17.37:g.39240692G>C	ENSP00000375236:p.Arg78Ser	44.0	1.0	0.0227273		49.0	7.0	0.142857	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0	-2.666022	0.00105	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00547	6.66	2.45	-4.9	0.03094	.	1.381260	0.05066	N	0.480753	T	0.00210	0.0006	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41070	-0.9529	9	0.02654	T	1	.	3.5468	0.07831	0.1616:0.2372:0.4895:0.1118	.	78	Q9BYR0	KRA47_HUMAN	S	78;69	ENSP00000375236:R78S	ENSP00000375236:R78S	R	+	3	2	KRTAP4-9;KRTAP4-7	36494218	0.000000	0.05858	0.005000	0.12908	0.273000	0.26683	-0.900000	0.04097	-0.963000	0.03600	-2.430000	0.00215	AGG	.	.	none		0.667	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
STAT2	6773	hgsc.bcm.edu	37	12	56740738	56740738	+	Splice_Site	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr12:56740738G>A	ENST00000314128.4	-	20	1749	c.1726C>T	c.(1726-1728)Cgc>Tgc	p.R576C	STAT2_ENST00000556539.1_5'UTR|STAT2_ENST00000557235.1_Splice_Site_p.R572C			P52630	STAT2_HUMAN	signal transducer and activator of transcription 2, 113kDa	576	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|kidney(5)|large_intestine(7)|liver(2)|lung(10)|ovary(1)|skin(3)	31						CCCATGATGCGTCTGGAGCAC	0.607																																					p.R576C		Atlas-SNP	.											.	STAT2	70	.	0			c.C1726T						PASS	.						63.0	56.0	58.0					12																	56740738		2203	4300	6503	SO:0001630	splice_region_variant	6773	exon20			TGATGCGTCTGGA	BC051284	CCDS8917.1, CCDS55836.1	12q13.2	2013-02-14	2002-08-29			ENSG00000170581		"""SH2 domain containing"""	11363	protein-coding gene	gene with protein product		600556	"""signal transducer and activator of transcription 2, 113kD"""			7885841	Standard	NM_005419		Approved	STAT113	uc001slc.3	P52630		ENST00000314128.4:c.1725-1C>T	12.37:g.56740738G>A		77.0	0.0	0		100.0	48.0	0.48	NM_005419	B4DLC7|G3V2M6|Q16430|Q16431|Q9UDL4	Missense_Mutation	SNP	ENST00000314128.4	37	CCDS8917.1	.	.	.	.	.	.	.	.	.	.	G	10.90	1.480269	0.26598	.	.	ENSG00000170581	ENST00000314128;ENST00000557235	D;D	0.96459	-4.02;-4.02	5.76	1.27	0.21489	SH2 motif (2);EF-hand-like domain (1);	0.907952	0.09678	N	0.770112	D	0.89681	0.6785	N	0.08118	0	0.09310	N	0.999993	B;B	0.17465	0.0;0.022	B;B	0.15484	0.002;0.013	T	0.79610	-0.1732	10	0.36615	T	0.2	3.6003	9.3617	0.38199	0.3354:0.0:0.6646:0.0	.	572;576	G3V2M6;P52630	.;STAT2_HUMAN	C	576;572	ENSP00000315768:R576C;ENSP00000450751:R572C	ENSP00000315768:R576C	R	-	1	0	STAT2	55027005	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	0.091000	0.15046	0.031000	0.15407	-0.229000	0.12294	CGC	.	.	none		0.607	STAT2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410277.1	NM_005419	Missense_Mutation
OR8G5	219865	hgsc.bcm.edu	37	11	124135619	124135619	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:124135619T>C	ENST00000524943.2	+	1	897	c.897T>C	c.(895-897)tcT>tcC	p.S299S	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		AGCCATCATCTGTCAGCTCCA	0.507																																					p.S299S	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.T897C						PASS	.						106.0	104.0	105.0					11																	124135619		2109	4260	6369	SO:0001819	synonymous_variant	219865	exon1			ATCATCTGTCAGC	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.897T>C	11.37:g.124135619T>C		260.0	0.0	0		311.0	22.0	0.0707396	NM_001005198	B2RND3|Q6IEU6	Silent	SNP	ENST00000524943.2	37																																																																																				.	.	none		0.507	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
FLNC	2318	hgsc.bcm.edu	37	7	128481578	128481578	+	Missense_Mutation	SNP	A	A	C	rs34972246	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:128481578A>C	ENST00000325888.8	+	13	2339	c.2078A>C	c.(2077-2079)gAt>gCt	p.D693A	FLNC_ENST00000346177.6_Missense_Mutation_p.D693A	NM_001458.4	NP_001449.3	Q14315	FLNC_HUMAN	filamin C, gamma	693					cell junction assembly (GO:0034329)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|cytoskeletal protein binding (GO:0008092)			biliary_tract(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(19)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(59)|ovary(2)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	128						TTCACCATTGATGCTCGTGCA	0.607													A|||	10	0.00199681	0.0008	0.0014	5008	,	,		20237	0.0		0.005	False		,,,				2504	0.0031				p.D693A		Atlas-SNP	.											.	FLNC	339	.	0			c.A2078C						PASS	.	A	ALA/ASP,ALA/ASP	5,4075		0,5,2035	139.0	144.0	142.0		2078,2078	5.6	1.0	7	dbSNP_126	142	45,8355		0,45,4155	yes	missense,missense	FLNC	NM_001127487.1,NM_001458.4	126,126	0,50,6190	CC,CA,AA		0.5357,0.1225,0.4006	benign,benign	693/2693,693/2726	128481578	50,12430	2040	4200	6240	SO:0001583	missense	2318	exon13			CCATTGATGCTCG	AB208865	CCDS43644.1, CCDS47705.1	7q32-q35	2014-09-17	2009-07-23		ENSG00000128591	ENSG00000128591			3756	protein-coding gene	gene with protein product	"""actin binding protein 280"""	102565	"""filamin C, gamma (actin binding protein 280)"""	FLN2		7689010, 8088838	Standard	NM_001458		Approved	ABP-280, ABPL	uc003vnz.4	Q14315	OTTHUMG00000023627	ENST00000325888.8:c.2078A>C	7.37:g.128481578A>C	ENSP00000327145:p.Asp693Ala	109.0	0.0	0		167.0	72.0	0.431138	NM_001127487	B2ZZ88|O95303|Q07985|Q9NS12|Q9NYE5|Q9UMR8|Q9Y503	Missense_Mutation	SNP	ENST00000325888.8	37	CCDS43644.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	35	5.430186	0.96131	0.001225	0.005357	ENSG00000128591	ENST00000325888;ENST00000346177	D;D	0.85411	-1.98;-1.98	5.57	5.57	0.84162	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.93167	0.7824	H	0.95950	3.745	0.58432	D	0.999999	D;P	0.89917	1.0;0.923	D;P	0.91635	0.999;0.85	D	0.94673	0.7858	10	0.87932	D	0	.	15.7306	0.77800	1.0:0.0:0.0:0.0	rs34972246	693;693	Q14315-2;Q14315	.;FLNC_HUMAN	A	693	ENSP00000327145:D693A;ENSP00000344002:D693A	ENSP00000327145:D693A	D	+	2	0	FLNC	128268814	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	7.035000	0.76517	2.117000	0.64856	0.459000	0.35465	GAT	A|0.996;C|0.004	0.004	strong		0.607	FLNC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059948.3		
TAB1	10454	hgsc.bcm.edu	37	22	39813800	39813800	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr22:39813800G>A	ENST00000216160.6	+	5	558	c.496G>A	c.(496-498)Gcc>Acc	p.A166T	TAB1_ENST00000331454.3_Missense_Mutation_p.A166T	NM_006116.2	NP_006107.1	Q15750	TAB1_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 1	166	PP2C-like.				activation of MAPK activity (GO:0000187)|activation of MAPKKK activity (GO:0000185)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart morphogenesis (GO:0003007)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|lung development (GO:0030324)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|stress-activated MAPK cascade (GO:0051403)|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)|transforming growth factor beta receptor signaling pathway (GO:0007179)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|nucleus (GO:0005634)|protein complex (GO:0043234)	catalytic activity (GO:0003824)|enzyme activator activity (GO:0008047)|kinase activator activity (GO:0019209)			breast(1)|endometrium(2)|large_intestine(2)|lung(8)|urinary_tract(1)	14						TTCGGGAGGGGCCATGGCCGT	0.577																																					p.A166T		Atlas-SNP	.											.	TAB1	36	.	0			c.G496A						PASS	.						86.0	73.0	77.0					22																	39813800		2203	4300	6503	SO:0001583	missense	10454	exon5			GGAGGGGCCATGG	U49928	CCDS13992.1, CCDS13993.1	22q13.1	2010-02-05	2010-02-05	2010-02-05	ENSG00000100324	ENSG00000100324			18157	protein-coding gene	gene with protein product	"""TAK1-binding protein 1"", ""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	602615	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 1"""	MAP3K7IP1		8638164, 10187861	Standard	NM_153497		Approved		uc003axt.3	Q15750	OTTHUMG00000151102	ENST00000216160.6:c.496G>A	22.37:g.39813800G>A	ENSP00000216160:p.Ala166Thr	108.0	0.0	0		131.0	68.0	0.519084	NM_153497	Q2PP09|Q8IZW2	Missense_Mutation	SNP	ENST00000216160.6	37	CCDS13993.1	.	.	.	.	.	.	.	.	.	.	G	18.07	3.541345	0.65085	.	.	ENSG00000100324	ENST00000216160;ENST00000331454	T;T	0.05382	3.45;3.45	5.34	5.34	0.76211	Protein phosphatase 2C-like (4);	0.225313	0.44097	D	0.000492	T	0.11324	0.0276	N	0.16098	0.37	0.80722	D	1	B;B;D	0.71674	0.017;0.29;0.998	B;B;D	0.81914	0.015;0.173;0.995	T	0.31971	-0.9924	10	0.07030	T	0.85	.	19.0356	0.92976	0.0:0.0:1.0:0.0	.	166;166;310	Q15750-2;Q15750;Q59FT7	.;TAB1_HUMAN;.	T	166	ENSP00000216160:A166T;ENSP00000333049:A166T	ENSP00000216160:A166T	A	+	1	0	TAB1	38143746	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	8.488000	0.90458	2.496000	0.84212	0.655000	0.94253	GCC	.	.	none		0.577	TAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321313.1	NM_153497	
MCM3AP	8888	hgsc.bcm.edu	37	21	47692531	47692531	+	Silent	SNP	T	T	C	rs17182739	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr21:47692531T>C	ENST00000397708.1	-	9	2663	c.2409A>G	c.(2407-2409)gaA>gaG	p.E803E	MCM3AP_ENST00000291688.1_Silent_p.E803E			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	803	SAC3 homology.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GGAACTCCGCTTCGCTGGCAC	0.478													T|||	97	0.019369	0.0015	0.0346	5008	,	,		21993	0.001		0.0646	False		,,,				2504	0.0051				p.E803E		Atlas-SNP	.											MCM3AP,colon,carcinoma,-2,1	MCM3AP	146	1	0			c.A2409G						PASS	.	T		62,4344	57.4+/-93.9	1,60,2142	170.0	148.0	155.0		2409	-7.0	0.0	21	dbSNP_123	155	560,8040	153.3+/-207.7	13,534,3753	no	coding-synonymous	MCM3AP	NM_003906.3		14,594,5895	CC,CT,TT		6.5116,1.4072,4.7824		803/1981	47692531	622,12384	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon8			CTCCGCTTCGCTG	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.2409A>G	21.37:g.47692531T>C		196.0	0.0	0		200.0	95.0	0.475	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			T|0.959;C|0.041	0.041	strong		0.478	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
IGSF21	84966	hgsc.bcm.edu	37	1	18692089	18692089	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:18692089C>T	ENST00000251296.1	+	6	1296	c.913C>T	c.(913-915)Ctc>Ttc	p.L305F		NM_032880.4	NP_116269.3	Q96ID5	IGS21_HUMAN	immunoglobin superfamily, member 21	305						extracellular region (GO:0005576)				endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	40		Colorectal(325;0.000147)|Renal(390;0.00145)|all_lung(284;0.00366)|Lung NSC(340;0.00376)|Breast(348;0.00387)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0121)|BRCA - Breast invasive adenocarcinoma(304;5.52e-05)|Kidney(64;0.00103)|KIRC - Kidney renal clear cell carcinoma(64;0.0102)|STAD - Stomach adenocarcinoma(196;0.0118)|READ - Rectum adenocarcinoma(331;0.157)		ACGTGCCCTGCTCACCTGGAC	0.647																																					p.L305F		Atlas-SNP	.											.	IGSF21	87	.	0			c.C913T						PASS	.						117.0	95.0	103.0					1																	18692089		2203	4300	6503	SO:0001583	missense	84966	exon6			GCCCTGCTCACCT	AK075316	CCDS184.1	1p36.13	2013-01-29			ENSG00000117154	ENSG00000117154		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28246	protein-coding gene	gene with protein product						12477932	Standard	NM_032880		Approved	MGC15730, RP11-121A23.1	uc001bau.2	Q96ID5	OTTHUMG00000002432	ENST00000251296.1:c.913C>T	1.37:g.18692089C>T	ENSP00000251296:p.Leu305Phe	150.0	0.0	0		194.0	97.0	0.5	NM_032880	Q8NBR8	Missense_Mutation	SNP	ENST00000251296.1	37	CCDS184.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.6|25.6	4.654766|4.654766	0.88056|0.88056	.|.	.|.	ENSG00000117154|ENSG00000117154	ENST00000412684|ENST00000251296	.|T	.|0.31510	.|1.49	4.28|4.28	4.28|4.28	0.50868|0.50868	.|Immunoglobulin-like fold (1);	.|0.120807	.|0.56097	.|D	.|0.000037	T|T	0.35451|0.35451	0.0932|0.0932	L|L	0.29908|0.29908	0.895|0.895	0.80722|0.80722	D|D	1|1	.|D	.|0.65815	.|0.995	.|P	.|0.56278	.|0.795	T|T	0.03231|0.03231	-1.1058|-1.1058	5|10	.|0.22109	.|T	.|0.4	-13.5806|-13.5806	15.7859|15.7859	0.78304|0.78304	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|305	.|Q96ID5	.|IGS21_HUMAN	V|F	257|305	.|ENSP00000251296:L305F	.|ENSP00000251296:L305F	A|L	+|+	2|1	0|0	IGSF21|IGSF21	18564676|18564676	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.976000|0.976000	0.68499|0.68499	4.004000|4.004000	0.57068|0.57068	2.383000|2.383000	0.81215|0.81215	0.561000|0.561000	0.74099|0.74099	GCT|CTC	.	.	none		0.647	IGSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006924.1	NM_032880	
PASK	23178	hgsc.bcm.edu	37	2	242080119	242080119	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:242080119A>C	ENST00000405260.1	-	3	944	c.246T>G	c.(244-246)atT>atG	p.I82M	PASK_ENST00000539818.1_Intron|PASK_ENST00000544142.1_Intron|PASK_ENST00000234040.4_Missense_Mutation_p.I82M|PASK_ENST00000403638.3_Missense_Mutation_p.I82M|PASK_ENST00000358649.4_Missense_Mutation_p.I82M	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	82					negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TACTTGTACAAATATTCTGGG	0.557																																					p.I82M		Atlas-SNP	.											.	PASK	230	.	0			c.T246G						PASS	.						70.0	70.0	70.0					2																	242080119		2203	4300	6503	SO:0001583	missense	23178	exon3			TGTACAAATATTC	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.246T>G	2.37:g.242080119A>C	ENSP00000384016:p.Ile82Met	426.0	0.0	0		483.0	211.0	0.436853	NM_001252122	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	.	.	.	.	.	.	.	.	.	.	A	12.70	2.015499	0.35511	.	.	ENSG00000115687	ENST00000234040;ENST00000405260;ENST00000358649;ENST00000403638;ENST00000452907	T;T;T;T	0.74842	-0.88;-0.88;-0.84;0.1	4.54	-2.86	0.05717	.	0.000000	0.52532	D	0.000076	T	0.78572	0.4304	M	0.61703	1.905	0.42674	D	0.993524	D;D;D;D	0.89917	1.0;1.0;0.999;1.0	D;D;D;D	0.87578	0.981;0.998;0.982;0.981	T	0.75470	-0.3306	10	0.87932	D	0	.	6.5076	0.22204	0.4255:0.1261:0.4485:0.0	.	82;82;82;82	B7Z7R6;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;PASK_HUMAN	M	82	ENSP00000234040:I82M;ENSP00000384016:I82M;ENSP00000351475:I82M;ENSP00000384438:I82M	ENSP00000234040:I82M	I	-	3	3	PASK	241728792	0.204000	0.23447	0.036000	0.18154	0.265000	0.26407	-0.645000	0.05409	-0.426000	0.07360	-0.464000	0.05259	ATT	.	.	none		0.557	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
LRCH4	4034	hgsc.bcm.edu	37	7	100175010	100175010	+	Missense_Mutation	SNP	C	C	T	rs140761835	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100175010C>T	ENST00000310300.6	-	11	1233	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	LRCH4_ENST00000497245.1_5'UTR	NM_002319.3	NP_002310.2	O75427	LRCH4_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 4	394					nervous system development (GO:0007399)	PML body (GO:0016605)				NS(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	23	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					CGGCTCCTCCCGCCTGAGGGA	0.741													C|||	25	0.00499201	0.0008	0.0115	5008	,	,		13720	0.0		0.0119	False		,,,				2504	0.0041				p.R394Q		Atlas-SNP	.											LRCH4,caecum,carcinoma,+1,1	LRCH4	53	1	0			c.G1181A						PASS	.	C	GLN/ARG	15,4287		0,15,2136	15.0	19.0	18.0		1181	3.2	1.0	7	dbSNP_134	18	139,8325		1,137,4094	yes	missense	LRCH4	NM_002319.3	43	1,152,6230	TT,TC,CC		1.6422,0.3487,1.2063	benign	394/684	100175010	154,12612	2151	4232	6383	SO:0001583	missense	4034	exon11			TCCTCCCGCCTGA	AF053356	CCDS34706.1	7q22	2008-05-20	2004-05-27	2004-05-28	ENSG00000077454	ENSG00000077454			6691	protein-coding gene	gene with protein product				LRN, LRRN1		9799793	Standard	XM_005250346		Approved		uc003uvj.3	O75427	OTTHUMG00000159544	ENST00000310300.6:c.1181G>A	7.37:g.100175010C>T	ENSP00000309689:p.Arg394Gln	34.0	0.0	0		28.0	20.0	0.714286	NM_002319	A4D2D5|Q8WV85|Q96ID0	Missense_Mutation	SNP	ENST00000310300.6	37	CCDS34706.1	16	0.007326007326007326	0	0.0	6	0.016574585635359115	0	0.0	10	0.013192612137203167	C	13.57	2.276222	0.40294	0.003487	0.016422	ENSG00000077454	ENST00000310300	T	0.34275	1.37	5.21	3.2	0.36748	.	0.501717	0.17581	N	0.169125	T	0.07863	0.0197	N	0.17312	0.475	0.80722	D	1	P	0.48998	0.918	B	0.34180	0.177	T	0.01492	-1.1341	10	0.29301	T	0.29	-22.7983	7.2591	0.26193	0.172:0.565:0.263:0.0	.	394	O75427	LRCH4_HUMAN	Q	394	ENSP00000309689:R394Q	ENSP00000309689:R394Q	R	-	2	0	LRCH4	100012946	1.000000	0.71417	1.000000	0.80357	0.435000	0.31806	0.771000	0.26633	2.460000	0.83146	0.536000	0.68110	CGG	C|0.991;T|0.009	0.009	strong		0.741	LRCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356110.1	NM_002319	
STIM2	57620	hgsc.bcm.edu	37	4	27024524	27024524	+	Missense_Mutation	SNP	G	G	A	rs147362228	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr4:27024524G>A	ENST00000467087.1	+	12	2675	c.2147G>A	c.(2146-2148)aGa>aAa	p.R716K	STIM2_ENST00000412829.2_3'UTR|STIM2_ENST00000382009.3_Missense_Mutation_p.R811K|STIM2_ENST00000237364.5_Missense_Mutation_p.R803K|STIM2_ENST00000467011.1_3'UTR|STIM2_ENST00000465503.1_Missense_Mutation_p.R724K			Q9P246	STIM2_HUMAN	stromal interaction molecule 2	716					activation of store-operated calcium channel activity (GO:0032237)|calcium ion transmembrane transport (GO:0070588)|cellular calcium ion homeostasis (GO:0006874)|positive regulation of calcium ion transport (GO:0051928)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|store-operated calcium channel activity (GO:0015279)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	25		Breast(46;0.0503)				AGTGTTGCCAGAATAAGCAGC	0.458													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20105	0.0		0.002	False		,,,				2504	0.0				p.R724K		Atlas-SNP	.											.	STIM2	77	.	0			c.G2171A						PASS	.	G	LYS/ARG,LYS/ARG,	0,4406		0,0,2203	99.0	100.0	99.0		2171,2147,	5.0	1.0	4	dbSNP_134	99	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,utr-3	STIM2	NM_001169118.1,NM_020860.3,NM_001169117.1	26,26,	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	possibly-damaging,possibly-damaging,	724/755,716/747,	27024524	3,13003	2203	4300	6503	SO:0001583	missense	57620	exon13			TTGCCAGAATAAG	AB040915	CCDS3440.1, CCDS3440.2, CCDS54751.1, CCDS54752.1	4p15.2	2013-01-10			ENSG00000109689	ENSG00000109689		"""Sterile alpha motif (SAM) domain containing"""	19205	protein-coding gene	gene with protein product		610841				11463338	Standard	NM_020860		Approved		uc003gsh.4	Q9P246	OTTHUMG00000097805	ENST00000467087.1:c.2147G>A	4.37:g.27024524G>A	ENSP00000419073:p.Arg716Lys	90.0	0.0	0		126.0	64.0	0.507937	NM_001169118	A6H8L7|B7ZVY0|Q96BF1|Q9BQH2|Q9H8R1	Missense_Mutation	SNP	ENST00000467087.1	37	CCDS3440.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	14.37	2.515082	0.44763	0.0	3.49E-4	ENSG00000109689	ENST00000467087;ENST00000382009;ENST00000237364;ENST00000465503	T;T;T;T	0.76968	-1.03;-1.06;-1.06;-1.04	5.87	5.02	0.67125	.	0.254762	0.44902	D	0.000414	T	0.67813	0.2933	N	0.24115	0.695	0.80722	D	1	P;P	0.48640	0.858;0.913	B;B	0.42593	0.22;0.392	T	0.71856	-0.4466	10	0.54805	T	0.06	.	14.2358	0.65925	0.0:0.0:0.7287:0.2713	.	811;803	E9PGD0;F5GXJ4	.;.	K	716;811;803;724	ENSP00000419073:R716K;ENSP00000371439:R811K;ENSP00000237364:R803K;ENSP00000417569:R724K	ENSP00000237364:R803K	R	+	2	0	STIM2	26633622	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.921000	0.48852	1.583000	0.49898	0.655000	0.94253	AGA	G|0.999;A|0.001	0.001	strong		0.458	STIM2-001	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215063.2	NM_020860	
METTL21C	196541	hgsc.bcm.edu	37	13	103339363	103339363	+	Missense_Mutation	SNP	C	C	G	rs148307139	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:103339363C>G	ENST00000267273.6	-	3	332	c.327G>C	c.(325-327)ttG>ttC	p.L109F		NM_001010977.1	NP_001010977.1	Q5VZV1	MT21C_HUMAN	methyltransferase like 21C	109					peptidyl-lysine methylation (GO:0018022)|protein methylation (GO:0006479)	nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)			breast(1)|large_intestine(3)|lung(2)|skin(1)	7						CTTGGAAATTCAATTCCTCGG	0.388																																					p.L109F		Atlas-SNP	.											METTL21C,NS,carcinoma,0,1	METTL21C	23	1	0			c.G327C						PASS	.	C	PHE/LEU	0,4406		0,0,2203	83.0	77.0	79.0		327	2.1	1.0	13	dbSNP_134	79	10,8590	7.7+/-29.5	0,10,4290	yes	missense	METTL21C	NM_001010977.1	22	0,10,6493	GG,GC,CC		0.1163,0.0,0.0769	benign	109/265	103339363	10,12996	2203	4300	6503	SO:0001583	missense	196541	exon3			GAAATTCAATTCC		CCDS32003.1	13q33.1	2011-03-03	2011-03-03	2011-03-03	ENSG00000139780	ENSG00000139780			33717	protein-coding gene	gene with protein product		615259	"""chromosome 13 open reading frame 39"""	C13orf39			Standard	NM_001010977		Approved	LOC196541	uc001vpj.4	Q5VZV1	OTTHUMG00000017304	ENST00000267273.6:c.327G>C	13.37:g.103339363C>G	ENSP00000267273:p.Leu109Phe	87.0	0.0	0		66.0	28.0	0.424242	NM_001010977		Missense_Mutation	SNP	ENST00000267273.6	37	CCDS32003.1	.	.	.	.	.	.	.	.	.	.	C	11.15	1.554827	0.27739	0.0	0.001163	ENSG00000139780	ENST00000267273	T	0.06528	3.29	5.96	2.13	0.27403	.	0.144833	0.48286	D	0.000182	T	0.04543	0.0124	N	0.20766	0.605	0.31573	N	0.656042	B	0.22541	0.071	B	0.22152	0.038	T	0.23833	-1.0177	10	0.20046	T	0.44	-0.0013	12.4417	0.55629	0.0:0.2593:0.6587:0.082	.	109	Q5VZV1	MT21C_HUMAN	F	109	ENSP00000267273:L109F	ENSP00000267273:L109F	L	-	3	2	METTL21C	102137364	0.993000	0.37304	0.974000	0.42286	0.493000	0.33554	0.487000	0.22356	0.381000	0.24851	0.650000	0.86243	TTG	C|0.999;G|0.001	0.001	strong		0.388	METTL21C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045682.2	NM_001010977	
CD248	57124	hgsc.bcm.edu	37	11	66083263	66083263	+	Silent	SNP	C	C	T	rs78560344	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr11:66083263C>T	ENST00000311330.3	-	1	1252	c.1236G>A	c.(1234-1236)ccG>ccA	p.P412P	RP11-867G23.13_ENST00000534065.1_RNA	NM_020404.2	NP_065137.1	Q9HCU0	CD248_HUMAN	CD248 molecule, endosialin	412	Pro-rich.				anatomical structure regression (GO:0060033)|cell migration (GO:0016477)|lymph node development (GO:0048535)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|extracellular matrix binding (GO:0050840)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	26						CTGGGAAGCTCGGTCTATAGG	0.647													C|||	27	0.00539137	0.0166	0.0029	5008	,	,		17487	0.0		0.003	False		,,,				2504	0.0				p.P412P		Atlas-SNP	.											CD248,NS,carcinoma,-1,1	CD248	69	1	0			c.G1236A						PASS	.	C		62,4338	57.4+/-93.9	0,62,2138	88.0	91.0	90.0		1236	-3.5	0.2	11	dbSNP_131	90	9,8581	7.1+/-27.0	0,9,4286	no	coding-synonymous	CD248	NM_020404.2		0,71,6424	TT,TC,CC		0.1048,1.4091,0.5466		412/758	66083263	71,12919	2200	4295	6495	SO:0001819	synonymous_variant	57124	exon1			GAAGCTCGGTCTA	AF279142	CCDS8134.1	11q13	2006-04-12	2006-03-28	2005-02-11	ENSG00000174807	ENSG00000174807		"""CD molecules"""	18219	protein-coding gene	gene with protein product	"""endosialin"", ""tumor endothelial marker 1"""	606064	"""CD164 sialomucin-like 1"", ""CD248 antigen, endosialin"""	CD164L1		10947988, 11084048	Standard	NM_020404		Approved	TEM1	uc001ohm.1	Q9HCU0	OTTHUMG00000167073	ENST00000311330.3:c.1236G>A	11.37:g.66083263C>T		49.0	0.0	0		74.0	43.0	0.581081	NM_020404	Q2M2V5|Q3SX55|Q96KB6	Silent	SNP	ENST00000311330.3	37	CCDS8134.1																																																																																			C|0.994;T|0.006	0.006	strong		0.647	CD248-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392922.2	NM_020404	
ZDHHC20	253832	hgsc.bcm.edu	37	13	21955582	21955582	+	Missense_Mutation	SNP	C	C	T	rs185661667	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr13:21955582C>T	ENST00000400590.3	-	11	1249	c.1051G>A	c.(1051-1053)Gtc>Atc	p.V351I	ZDHHC20_ENST00000415724.1_Missense_Mutation_p.V351I|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.V288I|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.V350I|ZDHHC20_ENST00000494731.1_5'UTR|ZDHHC20_ENST00000320220.9_3'UTR			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	351					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		CCTGATTTGACGATGCCTTCT	0.368													c|||	3	0.000599042	0.0008	0.0	5008	,	,		14111	0.001		0.001	False		,,,				2504	0.0				p.V350I		Atlas-SNP	.											.	ZDHHC20	36	.	0			c.G1048A						PASS	.	T	ILE/VAL	8,3764		0,8,1878	79.0	75.0	76.0		1048	-2.7	0.0	13		76	13,8195		0,13,4091	yes	missense	ZDHHC20	NM_153251.3	29	0,21,5969	TT,TC,CC		0.1584,0.2121,0.1753	benign	350/355	21955582	21,11959	1886	4104	5990	SO:0001583	missense	253832	exon11			ATTTGACGATGCC	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"""Zinc fingers, DHHC-type"""	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.1051G>A	13.37:g.21955582C>T	ENSP00000383433:p.Val351Ile	46.0	0.0	0		57.0	37.0	0.649123	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	1	0.0013192612137203166	c	0.034	-1.315557	0.01331	0.002121	0.001584	ENSG00000180776	ENST00000400590;ENST00000382466;ENST00000542645;ENST00000415724	T;T;T;T	0.52057	0.96;0.94;0.68;0.96	5.24	-2.7	0.06004	.	2.147630	0.01524	N	0.018465	T	0.41858	0.1177	L	0.47716	1.5	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.23511	-1.0186	10	0.22706	T	0.39	-10.2651	11.1755	0.48596	0.0:0.493:0.0:0.507	.	288;350	B4DRN8;Q5W0Z9-3	.;.	I	351;350;288;351	ENSP00000383433:V351I;ENSP00000371905:V350I;ENSP00000443236:V288I;ENSP00000401232:V351I	ENSP00000371905:V350I	V	-	1	0	ZDHHC20	20853582	0.000000	0.05858	0.000000	0.03702	0.486000	0.33341	0.041000	0.13927	-0.958000	0.03622	-0.735000	0.03563	GTC	C|0.998;T|0.002	0.002	strong		0.368	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
LAMB4	22798	hgsc.bcm.edu	37	7	107746265	107746265	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:107746265T>C	ENST00000388781.3	-	8	950	c.867A>G	c.(865-867)ggA>ggG	p.G289G	LAMB4_ENST00000418464.1_Silent_p.G289G|LAMB4_ENST00000414450.2_Silent_p.G289G|LAMB4_ENST00000205386.4_Silent_p.G289G|LAMB4_ENST00000388780.3_Silent_p.G289G	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	289	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AACTCACCATTCCAGGAGGGC	0.478																																					p.G289G		Atlas-SNP	.											.	LAMB4	253	.	0			c.A867G						PASS	.						80.0	72.0	75.0					7																	107746265		2203	4300	6503	SO:0001819	synonymous_variant	22798	exon8			CACCATTCCAGGA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.867A>G	7.37:g.107746265T>C		121.0	0.0	0		119.0	48.0	0.403361	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			.	.	none		0.478	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
UBE2E3	10477	hgsc.bcm.edu	37	2	181846844	181846844	+	Silent	SNP	A	A	T	rs146744789	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr2:181846844A>T	ENST00000410062.4	+	2	468	c.75A>T	c.(73-75)cgA>cgT	p.R25R	AC104076.3_ENST00000428080.1_RNA|UBE2E3_ENST00000602710.1_Silent_p.R25R|UBE2E3_ENST00000392415.2_Silent_p.R25R|UBE2E3_ENST00000602475.1_Silent_p.R25R|UBE2E3_ENST00000602632.1_Silent_p.R25R|UBE2E3_ENST00000602959.1_Silent_p.R25R	NM_006357.2	NP_006348.1	Q969T4	UB2E3_HUMAN	ubiquitin-conjugating enzyme E2E 3	25					protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked ubiquitination (GO:0070534)|regulation of growth (GO:0040008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(3)|lung(4)|ovary(1)|skin(1)	11						CGGACCAGCGAGACCCAGCCG	0.507													A|||	47	0.00938498	0.0008	0.0086	5008	,	,		15694	0.0		0.0169	False		,,,				2504	0.0235				p.R25R		Atlas-SNP	.											.	UBE2E3	26	.	0			c.A75T						PASS	.	A	,	11,4393	14.3+/-33.2	0,11,2191	37.0	45.0	42.0		75,75	0.9	1.0	2	dbSNP_134	42	146,8416	70.3+/-132.9	0,146,4135	no	coding-synonymous,coding-synonymous	UBE2E3	NM_006357.2,NM_182678.1	,	0,157,6326	TT,TA,AA		1.7052,0.2498,1.2109	,	25/208,25/208	181846844	157,12809	2202	4281	6483	SO:0001819	synonymous_variant	10477	exon2			CCAGCGAGACCCA	AB017644	CCDS2282.1	2q31.3	2011-05-19	2011-05-19		ENSG00000170035	ENSG00000170035		"""Ubiquitin-conjugating enzymes E2"""	12479	protein-coding gene	gene with protein product		604151	"""ubiquitin-conjugating enzyme E2E 3 (homologous to yeast UBC4/5)"", ""ubiquitin-conjugating enzyme E2E 3 (UBC4/5 homolog, yeast)"""			10343118	Standard	NM_006357		Approved	UbcH9	uc002unq.1	Q969T4	OTTHUMG00000132585	ENST00000410062.4:c.75A>T	2.37:g.181846844A>T		181.0	0.0	0		203.0	189.0	0.931035	NM_006357	B2RAD6|D3DPG3|Q5U0R7|Q7Z4W4	Silent	SNP	ENST00000410062.4	37	CCDS2282.1																																																																																			A|0.985;T|0.015	0.015	weak		0.507	UBE2E3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255795.6	NM_006357	
MET	4233	hgsc.bcm.edu	37	7	116436022	116436022	+	Silent	SNP	G	G	A	rs2023748	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:116436022G>A	ENST00000318493.6	+	21	4258	c.4071G>A	c.(4069-4071)gcG>gcA	p.A1357A	MET_ENST00000539704.1_Silent_p.A209A|MET_ENST00000397752.3_Silent_p.A1339A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)	p.A1357A(1)		NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGATATCAGCGATCTTCTCTA	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	1772	0.353834	0.034	0.4697	5008	,	,		21305	0.4673		0.4433	False		,,,				2504	0.4949				p.A1357A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4071A						PASS	.	G	,	405,3531		16,373,1579	140.0	130.0	133.0		4017,4071	-11.4	0.0	7	dbSNP_94	133	3536,4748		773,1990,1379	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	789,2363,2958	AA,AG,GG		42.6847,10.2896,32.2504	,	1339/1391,1357/1409	116436022	3941,8279	1968	4142	6110	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATCAGCGATCTTC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.4071G>A	7.37:g.116436022G>A		249.0	0.0	0		262.0	132.0	0.503817	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.618;A|0.382	0.382	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
SLC14A2	8170	hgsc.bcm.edu	37	18	43204744	43204744	+	Missense_Mutation	SNP	C	C	G	rs149251757	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr18:43204744C>G	ENST00000255226.6	+	2	931	c.115C>G	c.(115-117)Cca>Gca	p.P39A	SLC14A2_ENST00000586448.1_Missense_Mutation_p.P39A	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	39					transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GGATACTCACCCAGCTCTGCC	0.567													C|||	3	0.000599042	0.0	0.0	5008	,	,		20005	0.0		0.001	False		,,,				2504	0.002				p.P39A		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C115G						PASS	.	C	ALA/PRO,ALA/PRO	4,4402	8.1+/-20.4	0,4,2199	81.0	78.0	79.0		115,115	4.2	1.0	18	dbSNP_134	79	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	27,27	0,18,6485	GG,GC,CC		0.1628,0.0908,0.1384	benign,benign	39/921,39/921	43204744	18,12988	2203	4300	6503	SO:0001583	missense	8170	exon3			ACTCACCCAGCTC	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.115C>G	18.37:g.43204744C>G	ENSP00000255226:p.Pro39Ala	77.0	0.0	0		88.0	50.0	0.568182	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	10.95	1.496199	0.26861	9.08E-4	0.001628	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.54279	1.26;0.58	5.08	4.2	0.49525	.	0.077891	0.49305	D	0.000142	T	0.47820	0.1466	M	0.63428	1.95	0.35661	D	0.812527	P;P	0.40970	0.455;0.734	B;B	0.40165	0.142;0.321	T	0.56469	-0.7974	10	0.25751	T	0.34	-7.9968	9.6267	0.39754	0.0:0.9023:0.0:0.0977	.	39;39	Q15849;E7EPU1	UT2_HUMAN;.	A	39	ENSP00000255226:P39A;ENSP00000320689:P39A	ENSP00000255226:P39A	P	+	1	0	SLC14A2	41458742	0.100000	0.21855	0.995000	0.50966	0.555000	0.35460	0.953000	0.29162	1.269000	0.44280	0.462000	0.41574	CCA	C|0.999;G|0.001	0.001	strong		0.567	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
MUC17	140453	hgsc.bcm.edu	37	7	100679715	100679715	+	Missense_Mutation	SNP	C	C	T	rs143909059	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr7:100679715C>T	ENST00000306151.4	+	3	5082	c.5018C>T	c.(5017-5019)aCa>aTa	p.T1673I		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1673	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TCATCTCCTACACCTGCTGAA	0.498													C|||	3	0.000599042	0.0	0.0	5008	,	,		26255	0.0		0.003	False		,,,				2504	0.0				p.T1673I		Atlas-SNP	.											.	MUC17	804	.	0			c.C5018T						PASS	.	C	ILE/THR	0,4406		0,0,2203	210.0	221.0	217.0		5018	0.9	0.0	7	dbSNP_134	217	7,8593	4.3+/-15.6	0,7,4293	no	missense	MUC17	NM_001040105.1	89	0,7,6496	TT,TC,CC		0.0814,0.0,0.0538	possibly-damaging	1673/4494	100679715	7,12999	2203	4300	6503	SO:0001583	missense	140453	exon3			CTCCTACACCTGC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5018C>T	7.37:g.100679715C>T	ENSP00000302716:p.Thr1673Ile	78.0	0.0	0		54.0	34.0	0.62963	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	2.860	-0.236376	0.05944	0.0	8.14E-4	ENSG00000169876	ENST00000306151	T	0.03242	4.0	0.932	0.932	0.19466	.	.	.	.	.	T	0.01730	0.0055	N	0.17082	0.46	0.09310	N	1	P	0.42757	0.789	B	0.28849	0.095	T	0.48614	-0.9020	9	0.23891	T	0.37	.	5.3368	0.15961	0.0:1.0:0.0:0.0	.	1673	Q685J3	MUC17_HUMAN	I	1673	ENSP00000302716:T1673I	ENSP00000302716:T1673I	T	+	2	0	MUC17	100466435	0.004000	0.15560	0.001000	0.08648	0.004000	0.04260	1.442000	0.35046	0.857000	0.35407	0.134000	0.15878	ACA	C|1.000;T|0.000	0.000	weak		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ADAR	103	hgsc.bcm.edu	37	1	154573526	154573526	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr1:154573526T>C	ENST00000368474.4	-	2	1791	c.1592A>G	c.(1591-1593)cAt>cGt	p.H531R	ADAR_ENST00000368471.3_Missense_Mutation_p.H236R|ADAR_ENST00000292205.5_Missense_Mutation_p.H574R|ADAR_ENST00000471068.1_5'Flank	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	531	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		CCGAGGTTCATGGGGTGGTCC	0.527																																					p.H531R		Atlas-SNP	.											ADAR,NS,malignant_melanoma,-1,1	ADAR	113	1	0			c.A1592G						PASS	.						108.0	115.0	113.0					1																	154573526		2203	4300	6503	SO:0001583	missense	103	exon2			GGTTCATGGGGTG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.1592A>G	1.37:g.154573526T>C	ENSP00000357459:p.His531Arg	211.0	0.0	0		242.0	102.0	0.421488	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.978122	0.74360	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000368471;ENST00000529168	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.77	3.62	0.41486	Double-stranded RNA-binding (3);Double-stranded RNA-binding-like (1);	0.154749	0.56097	D	0.000026	D	0.88332	0.6408	M	0.91354	3.2	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.91635	0.999;0.999;0.994	D	0.89488	0.3755	10	0.66056	D	0.02	-17.755	10.7753	0.46346	0.1421:0.0:0.0:0.8579	.	531;531;531	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	R	574;531;236;526	ENSP00000292205:H574R;ENSP00000357459:H531R;ENSP00000357456:H236R;ENSP00000431794:H526R	ENSP00000292205:H574R	H	-	2	0	ADAR	152840150	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.312000	0.78968	0.815000	0.34398	0.459000	0.35465	CAT	.	.	none		0.527	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
MT-ND5	4540	hgsc.bcm.edu	37	M	13602	13602	+	Silent	SNP	T	T	C			TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chrM:13602T>C	ENST00000361567.2	+	1	1266	c.1266T>C	c.(1264-1266)taT>taC	p.Y422Y	MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TT_ENST00000387460.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	422					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACAAGCGCCTATAGCACTCGA	0.448																																					p.Y422Y		Atlas-SNP	.											.	.	.	.	0			c.T1266C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CGCCTATAGCACT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1266T>C	M.37:g.13602T>C		6.0	0.0	0		19.0	19.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.448	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
ZCCHC3	85364	hgsc.bcm.edu	37	20	279185	279185	+	Silent	SNP	C	C	T	rs45569040	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr20:279185C>T	ENST00000382352.3	+	1	1449	c.958C>T	c.(958-960)Ctg>Ttg	p.L320L		NM_033089.6	NP_149080	Q9NUD5	ZCHC3_HUMAN	zinc finger, CCHC domain containing 3	320							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(1)|lung(3)|prostate(2)	8		all_cancers(10;0.000209)|Lung NSC(37;0.0417)|all_lung(30;0.0713)|all_epithelial(17;0.0748)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			GGCCTTCTTCCTGGGGGCCGA	0.632													C|||	20	0.00399361	0.0	0.0029	5008	,	,		16576	0.0		0.0149	False		,,,				2504	0.0031				p.L320L		Atlas-SNP	.											.	ZCCHC3	20	.	0			c.C958T						PASS	.	C		13,3825		0,13,1906	40.0	47.0	45.0		958	2.2	1.0	20	dbSNP_127	45	144,8088		4,136,3976	no	coding-synonymous	ZCCHC3	NM_033089.6		4,149,5882	TT,TC,CC		1.7493,0.3387,1.3007		320/405	279185	157,11913	1919	4116	6035	SO:0001819	synonymous_variant	85364	exon1			TTCTTCCTGGGGG	AL034548	CCDS42844.1	20p13-p12.2	2014-04-10	2004-07-14	2004-07-14	ENSG00000177764	ENSG00000247315		"""Zinc fingers, CCHC domain containing"""	16230	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 99"""	C20orf99			Standard	NM_033089		Approved	dJ1103G7.7	uc002wdf.3	Q9NUD5	OTTHUMG00000188280	ENST00000382352.3:c.958C>T	20.37:g.279185C>T		133.0	0.0	0		163.0	163.0	1	NM_033089	Q3B7J3|Q6NT79	Silent	SNP	ENST00000382352.3	37	CCDS42844.1																																																																																			C|0.995;T|0.005	0.005	strong		0.632	ZCCHC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077447.1		
AKR1C2	1646	hgsc.bcm.edu	37	10	5042789	5042789	+	Silent	SNP	A	A	G	rs145355870	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr10:5042789A>G	ENST00000380753.4	-	3	509	c.322T>C	c.(322-324)Ttg>Ctg	p.L108L	AKR1C2_ENST00000407674.1_Silent_p.L108L|AKR1C2_ENST00000421196.3_Silent_p.L108L|AKR1C2_ENST00000455190.1_Silent_p.L108L	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	108					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	ACATAGTCCAATTGAAGATTT	0.398													A|||	15	0.00299521	0.0015	0.0115	5008	,	,		18331	0.003		0.002	False		,,,				2504	0.0				p.L108L		Atlas-SNP	.											.	AKR1C2	68	.	0			c.T322C						PASS	.	A	,,	7,4399	12.9+/-30.5	0,7,2196	128.0	118.0	122.0		322,322,322	-3.0	0.0	10	dbSNP_134	122	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	,,	0,37,6466	GG,GA,AA		0.3488,0.1589,0.2845	,,	108/140,108/324,108/324	5042789	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	1646	exon5			AGTCCAATTGAAG	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"""Aldo-keto reductases"""	385	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"""	600450	"""aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)"", ""testicular 17,20-desmolase deficiency"""	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.322T>C	10.37:g.5042789A>G		227.0	1.0	0.00440529		256.0	130.0	0.507812	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Silent	SNP	ENST00000380753.4	37	CCDS7062.1																																																																																			A|0.997;G|0.003	0.003	strong		0.398	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
MAP1S	55201	hgsc.bcm.edu	37	19	17835917	17835917	+	Silent	SNP	C	C	T	rs141175074	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr19:17835917C>T	ENST00000324096.4	+	4	514	c.363C>T	c.(361-363)tgC>tgT	p.C121C	CTD-3149D2.4_ENST00000595363.1_RNA|MAP1S_ENST00000544059.2_Silent_p.C95C|MAP1S_ENST00000597681.1_Intron	NM_018174.4	NP_060644.4	Q66K74	MAP1S_HUMAN	microtubule-associated protein 1S	121	Necessary for the microtubule-organizing center localization.				apoptotic DNA fragmentation (GO:0006309)|brain development (GO:0007420)|execution phase of apoptosis (GO:0097194)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|nervous system development (GO:0007399)|neuron projection morphogenesis (GO:0048812)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	actin filament binding (GO:0051015)|beta-tubulin binding (GO:0048487)|DNA binding (GO:0003677)|microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	25						CTGGGCCCTGCCTGGAGGAGA	0.612													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.001				p.C121C		Atlas-SNP	.											.	MAP1S	74	.	0			c.C363T						PASS	.	C		0,4406		0,0,2203	95.0	94.0	94.0		363	3.2	1.0	19	dbSNP_134	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP1S	NM_018174.4		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		121/1060	17835917	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55201	exon4			GCCCTGCCTGGAG	BC067115	CCDS32954.1	19p13.12	2008-02-05	2006-07-04	2006-07-04		ENSG00000130479			15715	protein-coding gene	gene with protein product		607573	"""chromosome 19 open reading frame 5"", ""VCY2 interacting protein 1"", ""BPY2 interacting protein 1"""	C19orf5, VCY2IP1, BPY2IP1		11827465, 15528209, 16297881, 14627543	Standard	NM_018174		Approved	FLJ10669, MAP8	uc002nhe.1	Q66K74		ENST00000324096.4:c.363C>T	19.37:g.17835917C>T		93.0	0.0	0		109.0	51.0	0.46789	NM_018174	B4DH53|Q27QB1|Q6NXF1|Q8N3L8|Q8N3W5|Q8NI88|Q96H94|Q96IT4|Q96SP8|Q9BRC6|Q9H928|Q9NVK7	Silent	SNP	ENST00000324096.4	37	CCDS32954.1																																																																																			C|1.000;T|0.000	0.000	strong		0.612	MAP1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466027.1	NM_018174	
SLC12A7	10723	hgsc.bcm.edu	37	5	1065514	1065514	+	Missense_Mutation	SNP	A	A	G	rs56350427	byFrequency	TCGA-G8-6907-01A-11D-2210-10	TCGA-G8-6907-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	c50abe38-50f3-4d17-b9dd-ec3adebe0a96	acab7c95-cc41-43da-a5fb-abe8c14cbcb7	g.chr5:1065514A>G	ENST00000264930.5	-	18	2364	c.2321T>C	c.(2320-2322)aTg>aCg	p.M774T	MIR4635_ENST00000583759.1_RNA	NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	774					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	CAGGTGGGACATGCCATCCCG	0.627													A|||	26	0.00519169	0.0	0.0014	5008	,	,		18614	0.0		0.0209	False		,,,				2504	0.0041				p.M774T		Atlas-SNP	.											.	SLC12A7	97	.	0			c.T2321C						PASS	.	A	THR/MET	14,4392	21.2+/-45.6	0,14,2189	67.0	69.0	68.0		2321	0.5	0.8	5	dbSNP_129	68	195,8405	85.6+/-148.0	4,187,4109	yes	missense	SLC12A7	NM_006598.2	81	4,201,6298	GG,GA,AA		2.2674,0.3177,1.607	benign	774/1084	1065514	209,12797	2203	4300	6503	SO:0001583	missense	10723	exon18			TGGGACATGCCAT	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.2321T>C	5.37:g.1065514A>G	ENSP00000264930:p.Met774Thr	118.0	0.0	0		145.0	66.0	0.455172	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Missense_Mutation	SNP	ENST00000264930.5	37	CCDS34129.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	a	8.557	0.876903	0.17395	0.003177	0.022674	ENSG00000113504	ENST00000264930	D	0.93426	-3.22	4.49	0.507	0.16967	.	0.552015	0.20357	N	0.093925	T	0.64349	0.2590	N	0.10645	0.015	0.24364	N	0.994864	B	0.02656	0.0	B	0.04013	0.001	T	0.64588	-0.6372	10	0.33141	T	0.24	.	7.1786	0.25760	0.5848:0.0:0.4152:0.0	rs56350427	774	Q9Y666	S12A7_HUMAN	T	774	ENSP00000264930:M774T	ENSP00000264930:M774T	M	-	2	0	SLC12A7	1118514	0.090000	0.21635	0.789000	0.31954	0.693000	0.40251	1.824000	0.39072	-0.143000	0.11334	0.383000	0.25322	ATG	A|0.987;G|0.013	0.013	strong		0.627	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
